Fri Jan 6 01:16:31 UTC 2023 I: starting to build ariba/bullseye/amd64 on jenkins on '2023-01-06 01:16' Fri Jan 6 01:16:31 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_18/9633/console.log Fri Jan 6 01:16:32 UTC 2023 I: Downloading source for bullseye/ariba=2.14.6+ds-1 --2023-01-06 01:16:32-- http://cdn-fastly.deb.debian.org/debian/pool/main/a/ariba/ariba_2.14.6%2bds-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1958 (1.9K) [text/prs.lines.tag] Saving to: ‘ariba_2.14.6+ds-1.dsc’ 0K . 100% 156M=0s 2023-01-06 01:16:32 (156 MB/s) - ‘ariba_2.14.6+ds-1.dsc’ saved [1958/1958] Fri Jan 6 01:16:32 UTC 2023 I: ariba_2.14.6+ds-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: ariba Binary: ariba Architecture: any Version: 2.14.6+ds-1 Maintainer: Debian Med Packaging Team Uploaders: Sascha Steinbiss Homepage: https://github.com/sanger-pathogens/ariba Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/ariba Vcs-Git: https://salsa.debian.org/med-team/ariba.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), dh-python, python3-biopython, python3-all-dev, python3-dendropy, python3-setuptools, python3-pymummer (>= 0.10.2), python3-pysam (>= 0.9.1), python3-nose (>= 1.3), python3-bs4, python3-matplotlib, python3-tk, bowtie2 (>= 2.1.0), cd-hit, mash, libminimap-dev, libfml-dev (>= 0.1-4~), mummer, fastaq (>= 3.12.0), help2man, asciidoctor, spades [amd64] Package-List: ariba deb science optional arch=any Checksums-Sha1: 9e4b9ed6460de8733b121f1a1b9cfa9785c25cb9 1970492 ariba_2.14.6+ds.orig.tar.xz 94f30cfaac4181af30f84ff49bec93c15509bd24 9436 ariba_2.14.6+ds-1.debian.tar.xz Checksums-Sha256: b7329ba1983834d3d49a97f838b1fa7e3bdd4556fc45220c75fa7d59c271ec4c 1970492 ariba_2.14.6+ds.orig.tar.xz 5d4f44df229188cfa054de7762c8ec1507cf74a0114ca5dba9027cd307090202 9436 ariba_2.14.6+ds-1.debian.tar.xz Files: 908a550cb2c7683a271f16aee3f079ad 1970492 ariba_2.14.6+ds.orig.tar.xz b07395ee84575439878af220c1d8835f 9436 ariba_2.14.6+ds-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQEzBAEBCgAdFiEEhFH5F4Fy5+Lcc/eVUfhKj+zKfgkFAl9eUN8ACgkQUfhKj+zK fgnnlgf9FFtIHnhvBJmV5fx0/9rTyjv6gLLdl0qGhs/NkgF3UAV4LY5G6A3cFq3q zsL210g6gSQJY7ZIC9uOaN66eE0ncxJDdJ1oC7mjDBlhTQjtxfq7w2p7R648drvF 14/PReqs9EYmBKWvzhGrGLRG8HsJsoihzrE/BFVgjgHZShr868PscGVSBsBVYlaq dNqzZyq0bFppwCyw/zBszvu6Rn4ocTC9GotwGA3W/KWJZ2jG64AQ8dGapb1I0L6w +CYKT6PY7zmb7N/qQxnzV62rX4at2krqV0h3pDfC/eS6JT/DJrrdwuOqa0pEnbVJ Ei02awxnKVj86d4FIFF1pogoRdlQJA== =VRMb -----END PGP SIGNATURE----- Fri Jan 6 01:16:32 UTC 2023 I: Checking whether the package is not for us Fri Jan 6 01:16:32 UTC 2023 I: Starting 1st build on remote node ionos5-amd64.debian.net. Fri Jan 6 01:16:32 UTC 2023 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Fri Jan 6 01:20:06 UTC 2023 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Feb 7 19:39:35 -12 2024 I: pbuilder-time-stamp: 1707377975 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-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 [ariba_2.14.6+ds-1.dsc] I: copying [./ariba_2.14.6+ds.orig.tar.xz] I: copying [./ariba_2.14.6+ds-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.PHYSq33b/trustedkeys.kbx': General error gpgv: Signature made Sun Sep 13 05:03:27 2020 -12 gpgv: using RSA key 8451F9178172E7E2DC73F79551F84A8FECCA7E09 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./ariba_2.14.6+ds-1.dsc dpkg-source: info: extracting ariba in ariba-2.14.6+ds dpkg-source: info: unpacking ariba_2.14.6+ds.orig.tar.xz dpkg-source: info: unpacking ariba_2.14.6+ds-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_libs_for_extension.patch dpkg-source: info: applying use_bwa_compatible_fermi-lite.patch dpkg-source: info: applying add-testdata.patch dpkg-source: info: applying disable-tests-with-internet-access.patch dpkg-source: info: applying support-pymummer-0.11.patch dpkg-source: info: applying run-debian-spades-wrapper.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/22017/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=16' DISTRIBUTION='bullseye' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='767a22aece51445fb53a9f43b0d42f96' 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='22017' 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.u4MSBO5l/pbuilderrc_Yu8w --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.u4MSBO5l/b1 --logfile b1/build.log ariba_2.14.6+ds-1.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos5-amd64 6.0.0-0.deb11.6-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.0.12-1~bpo11+1 (2022-12-19) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Mar 27 2022 bash -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash -rwxr-xr-x 1 root root 113664 Sep 23 2020 date -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd -rwxr-xr-x 1 root root 93936 Sep 23 2020 df -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir -rwxr-xr-x 1 root root 84440 Jan 20 2022 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 39680 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 69032 Jan 20 2022 findmnt -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 203072 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98048 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln -rwxr-xr-x 1 root root 56952 Feb 7 2020 login -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls -rwxr-xr-x 1 root root 149736 Jan 20 2022 lsblk -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 59632 Jan 20 2022 more -rwsr-xr-x 1 root root 55528 Jan 20 2022 mount -rwxr-xr-x 1 root root 18664 Jan 20 2022 mountpoint -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jan 23 03:47 sh -> dash -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty -rwsr-xr-x 1 root root 71912 Jan 20 2022 su -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch -rwxr-xr-x 1 root root 39680 Sep 23 2020 true -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jan 20 2022 umount -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir -rwxr-xr-x 1 root root 63744 Jan 20 2022 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 5898 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8049 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/22017/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: amd64 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-python, python3-biopython, python3-all-dev, python3-dendropy, python3-setuptools, python3-pymummer (>= 0.10.2), python3-pysam (>= 0.9.1), python3-nose (>= 1.3), python3-bs4, python3-matplotlib, python3-tk, bowtie2 (>= 2.1.0), cd-hit, mash, libminimap-dev, libfml-dev (>= 0.1-4~), mummer, fastaq (>= 3.12.0), help2man, asciidoctor, spades dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19704 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-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-dendropy; however: Package python3-dendropy is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-pymummer (>= 0.10.2); however: Package python3-pymummer is not installed. pbuilder-satisfydepends-dummy depends on python3-pysam (>= 0.9.1); however: Package python3-pysam is not installed. pbuilder-satisfydepends-dummy depends on python3-nose (>= 1.3); however: Package python3-nose is not installed. pbuilder-satisfydepends-dummy depends on python3-bs4; however: Package python3-bs4 is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-tk; however: Package python3-tk is not installed. pbuilder-satisfydepends-dummy depends on bowtie2 (>= 2.1.0); however: Package bowtie2 is not installed. pbuilder-satisfydepends-dummy depends on cd-hit; however: Package cd-hit is not installed. pbuilder-satisfydepends-dummy depends on mash; however: Package mash is not installed. pbuilder-satisfydepends-dummy depends on libminimap-dev; however: Package libminimap-dev is not installed. pbuilder-satisfydepends-dummy depends on libfml-dev (>= 0.1-4~); however: Package libfml-dev is not installed. pbuilder-satisfydepends-dummy depends on mummer; however: Package mummer is not installed. pbuilder-satisfydepends-dummy depends on fastaq (>= 3.12.0); however: Package fastaq is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on asciidoctor; however: Package asciidoctor is not installed. pbuilder-satisfydepends-dummy depends on spades; however: Package spades 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: asciidoctor{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bamtools{a} blt{a} bowtie2{a} bsdextrautils{a} bwa{a} ca-certificates{a} cd-hit{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} fastaq{a} file{a} fontconfig-config{a} fonts-lyx{a} gawk{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libbamtools2.5.1{a} libblas3{a} libbrotli1{a} libbsd0{a} libcapnp-0.7.0{a} libcurl3-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libedit2{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfml-dev{a} libfml0{a} libfontconfig1{a} libfreetype6{a} libgfortran5{a} libgsl25{a} libgslcblas0{a} libhat-trie0{a} libhts3{a} libicu67{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} libjsoncpp24{a} liblapack3{a} liblcms2-2{a} libldap-2.4-2{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libmd0{a} libminimap-dev{a} libminimap0{a} libmpdec3{a} libmurmurhash2{a} libncurses6{a} libnghttp2-14{a} libnlopt0{a} libpipeline1{a} libpng16-16{a} libprocps8{a} libpsl5{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.9{a} libpython3.9-dev{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} librtmp1{a} libruby2.7{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libssw0{a} libsub-override-perl{a} libtbb2{a} libtcl8.6{a} libtiff5{a} libtk8.6{a} libtool{a} libuchardet0{a} libwebp6{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxss1{a} libyaml-0-2{a} m4{a} mailcap{a} man-db{a} mash{a} media-types{a} mime-support{a} mummer{a} openssl{a} po-debconf{a} procps{a} python-matplotlib-data{a} python3{a} python3-all{a} python3-all-dev{a} python3-biopython{a} python3-bs4{a} python3-cycler{a} python3-dateutil{a} python3-dendropy{a} python3-dev{a} python3-distutils{a} python3-joblib{a} python3-kiwisolver{a} python3-lib2to3{a} python3-matplotlib{a} python3-minimal{a} python3-nose{a} python3-numpy{a} python3-pil{a} python3-pkg-resources{a} python3-pymummer{a} python3-pyparsing{a} python3-pysam{a} python3-reportlab{a} python3-reportlab-accel{a} python3-setuptools{a} python3-six{a} python3-soupsieve{a} python3-tk{a} python3-yaml{a} python3.9{a} python3.9-dev{a} python3.9-minimal{a} rake{a} readline-common{a} ruby{a} ruby-asciidoctor{a} ruby-minitest{a} ruby-net-telnet{a} ruby-power-assert{a} ruby-rubygems{a} ruby-test-unit{a} ruby-xmlrpc{a} ruby2.7{a} rubygems-integration{a} samtools{a} sensible-utils{a} spades{a} tk8.6-blt2.5{a} ttf-bitstream-vera{a} ucf{a} x11-common{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-lato javascript-common libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx ncbi-blast+ psmisc publicsuffix python-biopython-doc python3-chardet python3-lxml python3-olefile python3-psutil python3-pytest python3-renderpm python3-simplejson wget zip 0 packages upgraded, 176 newly installed, 0 to remove and 0 not upgraded. Need to get 80.2 MB of archives. After unpacking 297 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8+deb11u1 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 gawk amd64 1:5.1.0-1 [605 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 liblocale-gettext-perl amd64 1.07-4+b1 [19.0 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2+deb11u5 [98.2 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 mailcap all 3.69 [31.7 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 mime-support all 3.66 [10.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 libncurses6 amd64 6.2+20201114-2 [102 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 libprocps8 amd64 2:3.3.17-5 [63.9 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 procps amd64 2:3.3.17-5 [502 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 openssl amd64 1.1.1n-0+deb11u3 [853 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 ca-certificates all 20210119 [158 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 ucf all 3.0043 [74.0 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 rubygems-integration all 1.18 [6704 B] Get: 35 http://deb.debian.org/debian bullseye/main amd64 rake all 13.0.3-1 [84.7 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 ruby-minitest all 5.13.0-1 [57.3 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 ruby-net-telnet all 0.1.1-2 [12.5 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 ruby-power-assert all 1.1.7-2 [11.5 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 ruby-test-unit all 3.3.9-1 [86.1 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 ruby-xmlrpc all 0.3.0-2 [23.7 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 libmd0 amd64 1.0.3-3 [28.0 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 libbsd0 amd64 0.11.3-1 [108 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 libedit2 amd64 3.1-20191231-2+b1 [96.7 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 libyaml-0-2 amd64 0.2.2-1 [49.6 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 libruby2.7 amd64 2.7.4-1+deb11u1 [4202 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 ruby2.7 amd64 2.7.4-1+deb11u1 [747 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 ruby-rubygems all 3.2.5-2 [281 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 ruby amd64 1:2.7+2 [11.7 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 ruby-asciidoctor all 2.0.12-2 [206 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 asciidoctor all 2.0.12-2 [83.9 kB] Get: 51 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 52 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 53 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 54 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 55 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 56 http://deb.debian.org/debian bullseye/main amd64 libbamtools2.5.1 amd64 2.5.1+dfsg-9 [158 kB] Get: 57 http://deb.debian.org/debian bullseye/main amd64 libjsoncpp24 amd64 1.9.4-4 [78.9 kB] Get: 58 http://deb.debian.org/debian bullseye/main amd64 bamtools amd64 2.5.1+dfsg-9 [183 kB] Get: 59 http://deb.debian.org/debian bullseye/main amd64 libtcl8.6 amd64 8.6.11+dfsg-1 [1018 kB] Get: 60 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get: 61 http://deb.debian.org/debian bullseye/main amd64 libpng16-16 amd64 1.6.37-3 [294 kB] Get: 62 http://deb.debian.org/debian bullseye/main amd64 libfreetype6 amd64 2.10.4+dfsg-1+deb11u1 [418 kB] Get: 63 http://deb.debian.org/debian bullseye/main amd64 ttf-bitstream-vera all 1.10-8.1 [223 kB] Get: 64 http://deb.debian.org/debian bullseye/main amd64 fontconfig-config all 2.13.1-4.2 [281 kB] Get: 65 http://deb.debian.org/debian bullseye/main amd64 libfontconfig1 amd64 2.13.1-4.2 [347 kB] Get: 66 http://deb.debian.org/debian bullseye/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 67 http://deb.debian.org/debian bullseye/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 68 http://deb.debian.org/debian bullseye/main amd64 libxcb1 amd64 1.14-3 [140 kB] Get: 69 http://deb.debian.org/debian bullseye/main amd64 libx11-data all 2:1.7.2-1 [311 kB] Get: 70 http://deb.debian.org/debian bullseye/main amd64 libx11-6 amd64 2:1.7.2-1 [772 kB] Get: 71 http://deb.debian.org/debian bullseye/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get: 72 http://deb.debian.org/debian bullseye/main amd64 libxft2 amd64 2.3.2-2 [57.2 kB] Get: 73 http://deb.debian.org/debian bullseye/main amd64 libxext6 amd64 2:1.3.3-1.1 [52.7 kB] Get: 74 http://deb.debian.org/debian bullseye/main amd64 x11-common all 1:7.7+22 [252 kB] Get: 75 http://deb.debian.org/debian bullseye/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get: 76 http://deb.debian.org/debian bullseye/main amd64 libtk8.6 amd64 8.6.11-2 [780 kB] Get: 77 http://deb.debian.org/debian bullseye/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-4.1 [593 kB] Get: 78 http://deb.debian.org/debian bullseye/main amd64 blt amd64 2.5.3+dfsg-4.1 [14.9 kB] Get: 79 http://deb.debian.org/debian bullseye/main amd64 libtbb2 amd64 2020.3-1 [161 kB] Get: 80 http://deb.debian.org/debian bullseye/main amd64 bowtie2 amd64 2.4.2-2+b3 [1342 kB] Get: 81 http://deb.debian.org/debian bullseye/main amd64 bwa amd64 0.7.17-6+b1 [212 kB] Get: 82 http://deb.debian.org/debian bullseye/main amd64 cd-hit amd64 4.8.1-3 [522 kB] Get: 83 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 84 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 85 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 86 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 87 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 88 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 89 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 90 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 91 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 92 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 93 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u3 [693 kB] Get: 94 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 95 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 96 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 97 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 98 http://deb.debian.org/debian bullseye/main amd64 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 99 http://deb.debian.org/debian bullseye/main amd64 python3-distutils all 3.9.2-1 [143 kB] Get: 100 http://deb.debian.org/debian bullseye/main amd64 dh-python all 4.20201102+nmu1 [99.4 kB] Get: 101 http://deb.debian.org/debian bullseye/main amd64 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 102 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1+deb11u1 [69.1 kB] Get: 103 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1+deb11u1 [106 kB] Get: 104 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3+deb11u1 [232 kB] Get: 105 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1 [77.1 kB] Get: 106 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get: 107 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 108 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2 [156 kB] Get: 109 http://deb.debian.org/debian bullseye/main amd64 libcurl3-gnutls amd64 7.74.0-1.3+deb11u3 [342 kB] Get: 110 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get: 111 http://deb.debian.org/debian bullseye/main amd64 libhts3 amd64 1.11-4 [378 kB] Get: 112 http://deb.debian.org/debian bullseye/main amd64 samtools amd64 1.11-1 [545 kB] Get: 113 http://deb.debian.org/debian bullseye/main amd64 fastaq all 3.17.0-3 [47.8 kB] Get: 114 http://deb.debian.org/debian bullseye/main amd64 fonts-lyx all 2.3.6-1 [205 kB] Get: 115 http://deb.debian.org/debian bullseye/main amd64 help2man amd64 1.48.1 [190 kB] Get: 116 http://deb.debian.org/debian bullseye/main amd64 libblas3 amd64 3.9.0-3 [153 kB] Get: 117 http://deb.debian.org/debian bullseye/main amd64 libcapnp-0.7.0 amd64 0.7.0-7 [1048 kB] Get: 118 http://deb.debian.org/debian bullseye/main amd64 libexpat1-dev amd64 2.2.10-2+deb11u5 [141 kB] Get: 119 http://deb.debian.org/debian bullseye/main amd64 libfml0 amd64 0.1+git20190320.b499514-1+b1 [71.4 kB] Get: 120 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2+deb11u2 [191 kB] Get: 121 http://deb.debian.org/debian bullseye/main amd64 libfml-dev amd64 0.1+git20190320.b499514-1+b1 [82.9 kB] Get: 122 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get: 123 http://deb.debian.org/debian bullseye/main amd64 libgslcblas0 amd64 2.6+dfsg-2 [102 kB] Get: 124 http://deb.debian.org/debian bullseye/main amd64 libgsl25 amd64 2.6+dfsg-2 [934 kB] Get: 125 http://deb.debian.org/debian bullseye/main amd64 libhat-trie0 amd64 0.1.2-2 [11.8 kB] Get: 126 http://deb.debian.org/debian bullseye/main amd64 libimagequant0 amd64 2.12.2-1.1 [32.5 kB] Get: 127 http://deb.debian.org/debian bullseye/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get: 128 http://deb.debian.org/debian bullseye/main amd64 libjpeg62-turbo amd64 1:2.0.6-4 [151 kB] Get: 129 http://deb.debian.org/debian bullseye/main amd64 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 130 http://deb.debian.org/debian bullseye/main amd64 libjs-jquery-ui all 1.12.1+dfsg-8+deb11u1 [232 kB] Get: 131 http://deb.debian.org/debian bullseye/main amd64 libjs-underscore all 1.9.1~dfsg-3 [100 kB] Get: 132 http://deb.debian.org/debian bullseye/main amd64 libjs-sphinxdoc all 3.4.3-2 [127 kB] Get: 133 http://deb.debian.org/debian bullseye/main amd64 liblapack3 amd64 3.9.0-3 [2166 kB] Get: 134 http://deb.debian.org/debian bullseye/main amd64 liblcms2-2 amd64 2.12~rc1-2 [150 kB] Get: 135 http://deb.debian.org/debian bullseye/main amd64 libminimap0 amd64 0.2-5 [22.9 kB] Get: 136 http://deb.debian.org/debian bullseye/main amd64 libminimap-dev amd64 0.2-5 [33.7 kB] Get: 137 http://deb.debian.org/debian bullseye/main amd64 libmurmurhash2 amd64 1.5-2 [5780 B] Get: 138 http://deb.debian.org/debian bullseye/main amd64 libnlopt0 amd64 2.7.0-4+b2 [172 kB] Get: 139 http://deb.debian.org/debian bullseye/main amd64 libpython3.9 amd64 3.9.2-1 [1691 kB] Get: 140 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-dev amd64 3.9.2-1 [4028 kB] Get: 141 http://deb.debian.org/debian bullseye/main amd64 libpython3-dev amd64 3.9.2-3 [21.7 kB] Get: 142 http://deb.debian.org/debian bullseye/main amd64 libpython3-all-dev amd64 3.9.2-3 [1068 B] Get: 143 http://deb.debian.org/debian bullseye/main amd64 libssw0 amd64 1.1-13 [19.7 kB] Get: 144 http://deb.debian.org/debian bullseye/main amd64 libwebp6 amd64 0.6.1-2.1 [258 kB] Get: 145 http://deb.debian.org/debian bullseye/main amd64 libtiff5 amd64 4.2.0-1+deb11u1 [289 kB] Get: 146 http://deb.debian.org/debian bullseye/main amd64 libwebpdemux2 amd64 0.6.1-2.1 [87.7 kB] Get: 147 http://deb.debian.org/debian bullseye/main amd64 libwebpmux3 amd64 0.6.1-2.1 [97.6 kB] Get: 148 http://deb.debian.org/debian bullseye/main amd64 mash amd64 2.2.2+dfsg-2 [153 kB] Get: 149 http://deb.debian.org/debian bullseye/main amd64 mummer amd64 3.23+dfsg-7 [664 kB] Get: 150 http://deb.debian.org/debian bullseye/main amd64 python-matplotlib-data all 3.3.4-1 [4153 kB] Get: 151 http://deb.debian.org/debian bullseye/main amd64 python3-all amd64 3.9.2-3 [1056 B] Get: 152 http://deb.debian.org/debian bullseye/main amd64 python3.9-dev amd64 3.9.2-1 [515 kB] Get: 153 http://deb.debian.org/debian bullseye/main amd64 python3-dev amd64 3.9.2-3 [24.8 kB] Get: 154 http://deb.debian.org/debian bullseye/main amd64 python3-all-dev amd64 3.9.2-3 [1064 B] Get: 155 http://deb.debian.org/debian bullseye/main amd64 python3-numpy amd64 1:1.19.5-1 [2693 kB] Get: 156 http://deb.debian.org/debian bullseye/main amd64 python3-reportlab-accel amd64 3.5.59-2 [39.1 kB] Get: 157 http://deb.debian.org/debian bullseye/main amd64 python3-pil amd64 8.1.2+dfsg-0.3+deb11u1 [445 kB] Get: 158 http://deb.debian.org/debian bullseye/main amd64 python3-reportlab all 3.5.59-2 [575 kB] Get: 159 http://deb.debian.org/debian bullseye/main amd64 python3-biopython amd64 1.78+dfsg-4 [1402 kB] Get: 160 http://deb.debian.org/debian bullseye/main amd64 python3-soupsieve all 2.2.1-1 [34.7 kB] Get: 161 http://deb.debian.org/debian bullseye/main amd64 python3-bs4 all 4.9.3-1 [112 kB] Get: 162 http://deb.debian.org/debian bullseye/main amd64 python3-six all 1.16.0-2 [17.5 kB] Get: 163 http://deb.debian.org/debian bullseye/main amd64 python3-cycler all 0.10.0-3 [8084 B] Get: 164 http://deb.debian.org/debian bullseye/main amd64 python3-dateutil all 2.8.1-6 [79.2 kB] Get: 165 http://deb.debian.org/debian bullseye/main amd64 python3-dendropy all 4.5.1-1 [273 kB] Get: 166 http://deb.debian.org/debian bullseye/main amd64 python3-joblib all 0.17.0-4 [213 kB] Get: 167 http://deb.debian.org/debian bullseye/main amd64 python3-kiwisolver amd64 1.3.1-1+b1 [55.7 kB] Get: 168 http://deb.debian.org/debian bullseye/main amd64 python3-pyparsing all 2.4.7-1 [109 kB] Get: 169 http://deb.debian.org/debian bullseye/main amd64 python3-matplotlib amd64 3.3.4-1 [4163 kB] Get: 170 http://deb.debian.org/debian bullseye/main amd64 python3-nose all 1.3.7-7 [133 kB] Get: 171 http://deb.debian.org/debian bullseye/main amd64 python3-pymummer all 0.11.0-2 [11.3 kB] Get: 172 http://deb.debian.org/debian bullseye/main amd64 python3-pysam amd64 0.15.4+ds-3+b2 [1536 kB] Get: 173 http://deb.debian.org/debian bullseye/main amd64 python3-setuptools all 52.0.0-4 [366 kB] Get: 174 http://deb.debian.org/debian bullseye/main amd64 python3-tk amd64 3.9.2-1 [101 kB] Get: 175 http://deb.debian.org/debian bullseye/main amd64 python3-yaml amd64 5.3.1-5 [138 kB] Get: 176 http://deb.debian.org/debian bullseye/main amd64 spades amd64 3.13.1+dfsg-2+b2 [4777 kB] Fetched 80.2 MB in 1s (76.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. 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Setting up libtiff5:amd64 (4.2.0-1+deb11u1) ... Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-7) ... Setting up python-matplotlib-data (3.3.4-1) ... Setting up openssl (1.1.1n-0+deb11u3) ... Setting up libwebpmux3:amd64 (0.6.1-2.1) ... Setting up libbsd0:amd64 (0.11.3-1) ... Setting up mailcap (3.69) ... Setting up libelf1:amd64 (0.183-1) ... Setting up libssw0:amd64 (1.1-13) ... Setting up ruby-xmlrpc (0.3.0-2) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7+deb11u3) ... Setting up liblocale-gettext-perl (1.07-4+b1) ... Setting up libprocps8:amd64 (2:3.3.17-5) ... Setting up libpython3.9-stdlib:amd64 (3.9.2-1) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up libjs-underscore (1.9.1~dfsg-3) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up liblapack3:amd64 (3.9.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb1:amd64 (1.14-3) ... Setting up gettext (0.21-4) ... Setting up libfml-dev:amd64 (0.1+git20190320.b499514-1+b1) ... Setting up mime-support (3.66) ... Setting up libtool (2.4.6-15) ... Setting up libwebpdemux2:amd64 (0.6.1-2.1) ... Setting up libedit2:amd64 (3.1-20191231-2+b1) ... Setting up libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Setting up libcurl3-gnutls:amd64 (7.74.0-1.3+deb11u3) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up help2man (1.48.1) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 129 added, 0 removed; done. Setting up libpython3.9:amd64 (3.9.2-1) ... Setting up libjs-jquery-ui (1.12.1+dfsg-8+deb11u1) ... Setting up libfreetype6:amd64 (2.10.4+dfsg-1+deb11u1) ... Setting up ucf (3.0043) ... Setting up libminimap-dev (0.2-5) ... Setting up libjs-sphinxdoc (3.4.3-2) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up procps (2:3.3.17-5) ... Setting up libx11-6:amd64 (2:1.7.2-1) ... Setting up python3.9 (3.9.2-1) ... Setting up libhts3:amd64 (1.11-4) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up fontconfig-config (2.13.1-4.2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:amd64 (2:1.3.3-1.1) ... Setting up libpython3.9-dev:amd64 (3.9.2-1) ... Setting up python3 (3.9.2-3) ... Setting up rubygems-integration (1.18) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up samtools (1.11-1) ... Setting up bowtie2 (2.4.2-2+b3) ... Setting up python3-six (1.16.0-2) ... Setting up python3-pil:amd64 (8.1.2+dfsg-0.3+deb11u1) ... Setting up python3-pyparsing (2.4.7-1) ... Setting up python3-cycler (0.10.0-3) ... Setting up python3-reportlab-accel:amd64 (3.5.59-2) ... Setting up python3-kiwisolver (1.3.1-1+b1) ... Setting up python3-reportlab (3.5.59-2) ... Setting up python3.9-dev (3.9.2-1) ... Setting up python3-dateutil (2.8.1-6) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up libfontconfig1:amd64 (2.13.1-4.2) ... Setting up python3-lib2to3 (3.9.2-1) ... Setting up python3-soupsieve (2.2.1-1) ... Setting up python3-pkg-resources (52.0.0-4) ... Setting up python3-distutils (3.9.2-1) ... Setting up dh-python (4.20201102+nmu1) ... Setting up libxft2:amd64 (2.3.2-2) ... Setting up python3-pysam (0.15.4+ds-3+b2) ... Setting up libpython3-dev:amd64 (3.9.2-3) ... Setting up python3-setuptools (52.0.0-4) ... Setting up python3-joblib (0.17.0-4) ... Setting up libtk8.6:amd64 (8.6.11-2) ... Setting up fastaq (3.17.0-3) ... Setting up python3-all (3.9.2-3) ... Setting up python3-yaml (5.3.1-5) ... Setting up debhelper (13.3.4) ... Setting up python3-nose (1.3.7-7) ... Setting up python3-bs4 (4.9.3-1) ... Setting up python3-pymummer (0.11.0-2) ... Setting up libpython3-all-dev:amd64 (3.9.2-3) ... Setting up python3-dev (3.9.2-3) ... Setting up python3-numpy (1:1.19.5-1) ... Setting up spades (3.13.1+dfsg-2+b2) ... Setting up python3-biopython (1.78+dfsg-4) ... Setting up python3-dendropy (4.5.1-1) ... Setting up python3-all-dev (3.9.2-3) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-4.1) ... Setting up python3-matplotlib (3.3.4-1) ... Setting up blt (2.5.3+dfsg-4.1) ... Setting up python3-tk:amd64 (3.9.2-1) ... Setting up rake (13.0.3-1) ... Setting up ruby-rubygems (3.2.5-2) ... Setting up libruby2.7:amd64 (2.7.4-1+deb11u1) ... Setting up ruby2.7 (2.7.4-1+deb11u1) ... Setting up ruby (1:2.7+2) ... Setting up ruby-asciidoctor (2.0.12-2) ... Setting up asciidoctor (2.0.12-2) ... Processing triggers for libc-bin (2.31-13+deb11u5) ... Processing triggers for ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 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 Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.25.3-1.1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/ariba-2.14.6+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 > ../ariba_2.14.6+ds-1_source.changes dpkg-buildpackage: info: source package ariba dpkg-buildpackage: info: source version 2.14.6+ds-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sascha Steinbiss dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/ariba-2.14.6+ds' rm -rf /build/ariba-2.14.6+ds/debian/man dh_auto_clean -- I: pybuild base:232: python3.9 setup.py clean running clean removing '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.9' does not exist -- can't clean it make[1]: Leaving directory '/build/ariba-2.14.6+ds' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules build dh build --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:232: python3.9 setup.py config running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:232: /usr/bin/python3 setup.py build running build running build_py creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/assembly.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/assembly_variants.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/reference_data.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/__init__.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/sequence_metadata.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/versions.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/clusters.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/ref_preparer.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/cluster.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/aln_to_metadata.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/mapping.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/ref_genes_getter.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/cdhit.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/common.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/faidx.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/mic_plotter.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/summary_sample.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/histogram.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/report.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/sequence_variant.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/pubmlst_getter.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/read_store.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/tb.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/report_filter.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/flag.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/external_progs.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/link.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/summary_cluster_variant.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/samtools_variants.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/mlst_reporter.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/megares_zip_parser.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/summary.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/megares_data_finder.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/bam_parse.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/read_filter.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/pubmlst_ref_preparer.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/mlst_profile.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/assembly_compare.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/scaffold_graph.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/report_flag_expander.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/vfdb_parser.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/summary_cluster.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/card_record.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/refdata_query.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/ref_seq_chooser.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks copying ariba/tasks/aln2meta.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks copying ariba/tasks/getref.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks copying ariba/tasks/__init__.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks copying ariba/tasks/pubmlstspecies.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks copying ariba/tasks/pubmlstget.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks copying ariba/tasks/test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks copying ariba/tasks/refquery.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks copying ariba/tasks/reportfilter.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks copying ariba/tasks/prepareref_tb.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks copying ariba/tasks/micplot.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks copying ariba/tasks/flag.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks copying ariba/tasks/summary.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks copying ariba/tasks/run.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks copying ariba/tasks/prepareref.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks copying ariba/tasks/version.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks copying ariba/tasks/expandflag.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/assembly_variants_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/ncbi_getter_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/mapping_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/common_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/__init__.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/scaffold_graph_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/megares_data_finder_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/cluster_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/cdhit_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/ref_seq_chooser_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/megares_zip_parser_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/versions_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/card_record_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/assembly_compare_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/test_refdata_query.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/summary_cluster_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/mlst_profile_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/summary_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/clusters_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/samtools_variants_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/ref_preparer_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/bam_parse_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/external_progs_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/ref_genes_getter_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/histogram_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/faidx_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/link_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/flag_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/tb_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/summary_cluster_variant_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/pubmlst_getter_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/sequence_metadata_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/sequence_variant_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/assembly_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/aln_to_metadata_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/read_filter_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/mlst_reporter_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/report_filter_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/summary_sample_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/mic_plotter_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/report_flag_expander_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/read_store_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/reference_data_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/vfdb_parser_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/pubmlst_ref_preparer_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/test_run_data copying ariba/test_run_data/ref_seqs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/test_run_data copying ariba/test_run_data/ref_fasta_to_make_reads_from.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/test_run_data copying ariba/test_run_data/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/test_run_data copying ariba/test_run_data/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/test_run_data copying ariba/test_run_data/metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/test_run_data creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tb_data copying ariba/tb_data/NC_000962.3.fa.gz -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20181115.json -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20181221.json -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20190102.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tb_data copying ariba/tb_data/NC_000962.3.gb -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20181115.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20181221.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20190102.json -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tb_data creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_test_get_variants_presence_absence.snps -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_test_get_variants_variants_only.snps -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_load_user_clusters_file.bad1 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_cluster_with_cdhit.expected.clusters.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_count_reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_variants_only.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/graph_test_update_from_sam.ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/megares_zip_parser_load_header_mappings.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/summary_gather_unfiltered_output_data.in.2.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_test_get_mummer_variants.none.snps -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_check_ok.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.all_refs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_load_user_clusters_file.bad3 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_parse.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_parse.reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_metadata_tsv.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_run_fermilite_fail.reads.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.clusterrefs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.new_st.report.out.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_whole_run.in.2.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run.in.ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_best_seq_reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_ok.rename.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.clusterrefs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.smi -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/megares_zip_parser_write_files.expect.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_coding.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_check_spades_log_file.log.good -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.expect.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_write_report.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/tb_write_prepareref_metadata_file.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_init.fofn -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_catted_assemblies_fasta.expected.out.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_sam_to_soft_clipped.reads.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.no_combinations.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_run.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.contigs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_fasta_file.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/graph_test_write_all_links_to_file.out -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_load_report_bad.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_scaffold_with_sspace_contigs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_load_vars_file_good.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_sequences_to_files.all.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads_subset.2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_remove_bad_noncoding.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.clusterrefs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_fake_run.non-unique.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.vcf -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_remove_bad_noncoding.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/vfdb_parser_test_run.out.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/report_flag_expander.run.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/vfdb_parser_test_run.out.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_make_cluster_file.out -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_total_depth_per_contig -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.2.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.all_present_perfect.report.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.profile.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_noncoding.out.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_init_good.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.clusters -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.2 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_files.properPairs -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_sam_pair_to_insert_reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/graph_test_update_from_sam.ref.fa.fai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/pubmlst_rename_seqs.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data_presence_absence.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_profile_test.init_multiple_extra_columns.profile.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run.in.read_store -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_best_seq_ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/test_common_cat_files.in.1 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite.reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.1 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_noncoding.out.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_check_spaces_in_name.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_parse_assembly_bam.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.het_snp.out.details.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_load_vars_file_bad.1.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_gene_fa.out.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_best_seq_reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_noncoding.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run.expected.reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/test_common_cat_files.in.2 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_cdhit_clstr_to_reads.in.clstr -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_sequence_type.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite.expected.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/test_common_cat_files.in.3 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite.expected.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_files.cluster2representative -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.het_snps.out.details.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_load_vars_file_bad.2.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_fails.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_cat_genes_match_ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.2 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_out_cluster_counts.in -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.make_link.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.contigs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.clstrs.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_rename_sequences.out -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.4.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_sequences_to_files.noncoding.varonly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run_cdhit_est_2d.ref.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.new_st.report.out.details.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_keep_seqs_from_dict.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_partial_asmbly.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/refdata_query_prepareref.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_read_depths.gz.tbi -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.het_snp.out.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/summary_sample_test_non_synon_variants.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_total_alignment_score_reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_sequences_to_files.gene.varonly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_load_user_clusters_file.bad2 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_test_flanking.contigs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_load_aln_file.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_fix_contig_orientation.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/summary_sample_test_column_summary_data.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.allrefs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads_1.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_fix_contig_orientation.out.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_compare_parse_nucmer_coords_file.coords -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_remove_bad_genes.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.ref_for_reads.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_ref.fa.fai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_metadata_tsv.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data.expected.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.pairs -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_coding.out.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ctg.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.allrefs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_parse.ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.out.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_variants_in_coords.vcf -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_make_reads_for_assembly.out1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_load_report_good.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_init_refdata.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_variant_positions_from_vcf.vcf -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/pubmlst_rename_seqs.expected.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run_cdhit_est_2d.reads.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.clusterrefs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa.fai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_fix_in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/graph_test_update_from_sam.reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_fasta_to_metadata.coding.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa.fai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_coding.out.cluster -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.in -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_load_mic_file.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_mlst_reports.out.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_noncoding.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_make_reads_for_assembly.out2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run.expected.reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_make_reads_for_assembly.in2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads_subset.1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_non_coding.metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.sma -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_gene_fa.db.fa.fai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_test_flanking.cluster_refs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_sort_file.in -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.2 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_partial_asmbly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_metadata_tsv.expected.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_variants_only.not_present.metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.no_combinations.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_non_coding.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_best_seq_ref.fa.fai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.1 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_rename_sequences_metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_all_non_wild_type_variants.ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_newick_from_dist_matrix.distances -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_dummy_reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_mlst_reports.ariba.report.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_sam_to_soft_clipped.ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.4.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.clstrs.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_delete_codon.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.for_reads.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_ok.params.json -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.all_refs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_coding.out.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.no_combinations.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_parse.reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_multiple_vars.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data.expected.metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_write_tb_resistance_calls_json.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_dummy_db.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.ref_for_reads.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_get_total_alignment_score.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/megares_zip_parser_load_annotations.csv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.sma -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.expect.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_fails.empty.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.3.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_test_get_variants_presence_absence.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_sequences_to_files.gene.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_report.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_ok.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_load_summary_file.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_fix_out.removed.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_cluster_with_cdhit.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_sequences_to_files.noncoding.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa.fai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.new_st.report.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_write_tb_resistance_calls_json.out.json -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.no_combinations.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.make_link_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_presence_absence.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.no_link_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_gene_fa.db.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/summary_sample_test_load_file.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.expect.clstrs.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_check_duplicate_name.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_varonly.not_present.always_report.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_sort_file.out -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_insert_codon.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_load_input_files.2.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/megares_zip_parse_extract_files_one_missing.zip -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.one_gene_missing.out.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.all_present_perfect.report.out.details.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.2.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.het_snps.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_whole_run.in.1.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.het_snp.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_all_fasta_files.in.1 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_total_alignment_score_reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_test_get_variants_variants_only.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_fasta_to_metadata.noncoding.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_sequence.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/graph_test_update_from_sam.reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.no_link_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data_variants_only.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_fix_out.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_write_distance_matrix.distances -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.reads.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.1 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/megares_zip_parser_write_files.expect.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.1.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_proper_pairs.in -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_fasta_to_metadata.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.hist -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa.fai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_sequence_type.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz.tbi -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_count_reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/test_common_cat_files.out -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_delete_codon.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_presence_absence.metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_sequence_is_in_fasta_file.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.contigs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/graph_test_update_from_sam.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/megares_zip_parse_extract_files_ok.zip -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_rename_sequences.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_run_get_clusters_from_dict_rename.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.ref.fa.fai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_read_depths.gz -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr2rep -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.het_snps.out.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_run_fermilite.expected.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.no_combinations.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite_fails.expected.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_run_fermilite.expected.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_coding.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_insert_codon.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_sequence.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/summary_gather_unfiltered_output_data.in.1.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data_non_coding.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads_2.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_test_get_mummer_variants.snp.snps -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_compress_and_index_file.in -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_assembly_fail.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_sorted.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_multiple_vars.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/pubmlst_getter.dbases.xml -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.cluster_refs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.no_combinations.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.make_link.bam.bai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/faidx_test_write_fa_subset.out.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_make_reads_for_assembly.in1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.contigs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_variants_only.present.metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_data_info_file -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/summary_sample_test_column_names_tuples_and_het_snps.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_run_fermilite_fails.expected.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/summary_to_matrix.2.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.1.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_fails.empty.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data.expected.all.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/faidx_test_write_fa_subset.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_parse_assembly_bam.assembly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_whole_run.out.csv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_fake_run.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_run_with_tb.reads_1.fq.gz -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_files.insertHistogram -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_write_cluster_allocation_file.expected -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_check_spades_log_file.log.bad -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.all_present_perfect.report.out.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/refdata_query_prepareref.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run.in.reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_load_fofn -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.make_link_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_cluster_with_cdhit.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_init_refdata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/tb_genbank_to_gene_coords.gb -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_all_metadata_tsvs.2.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_scaffold_with_sspace_reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr_count -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_dummy_db.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_mlst_reports.out.details.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.fai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_ok.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.cov -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_all_non_wild_type_variants.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/report_flag_expander.run.out.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_sam_pair_to_insert_reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_profile_test.init.profile.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_test_flanking.all_refs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.one_gene_missing.out.details.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.ref_for_reads.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_fix_out.rename -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_fix_out.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_remove_bad_genes.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.1 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_insert_histogram.in -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_sam_pair_to_insert.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.one_gene_missing.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_write_seqs_to_fasta.expected.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_rename_file.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_dummy_reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_keep_seqs_from_dict.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_remove_bad_noncoding.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_catted_assembled_genes_fasta.expected.out.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_run.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_sam_to_fastq.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_check_too_short.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_files.clusterCounts -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_mlst_reports.mlst_profile.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_run_fermilite.reads.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data_metadata.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_scaffold_with_sspace_reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_remove_bad_genes.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_load_user_clusters_file.good -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_run.expected.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run_cdhit_est_2d.expected.clstr -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_check_too_long.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_sam_to_soft_clipped.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.2 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/summary_sample_test_var_groups.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.coords -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.expect.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_test_flanking.expected_contigs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_load_input_files.1.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_clean.in -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.no_link.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.depths.gz -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/faidx_test_write_fa_subset.in.fa.fai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_noncoding.out.cluster -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_assembly_fail.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.allrefs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/dummy.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/tb_report_to_resistance_dict.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite.reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_all_metadata_tsvs.1.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_depths_at_position.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/summary_to_matrix.1.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_run_with_tb.reads_2.fq.gz -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_get_clusters_from_bak_file.in -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.contigs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_profile_test.profile.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.no_link.bam.bai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.meta.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/vfdb_parser_test_run.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_fix_contig_orientation.ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.allrefs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_all_fasta_files.in.2 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.smi -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_out_cluster2representative.in -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_check_not_gene.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run.in.reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_init_bad.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_variants.vcf -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_unsorted.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/00.info.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/01.filter.check_genes.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.varonly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.varonly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.pickle -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/00.rename_info -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/01.filter.check_noncoding.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/00.version_info.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.all.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding copying ariba/tests/data/cluster_test_full_run_ok_non_coding/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding copying ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding copying ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/00.info.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/01.filter.check_genes.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.varonly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.varonly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.pickle -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/01.filter.check_noncoding.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/00.version_info.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.all.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.info.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_genes.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.gene.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.noncoding.varonly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.clusters.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.gene.varonly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.clusters.pickle -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.rename_info -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_noncoding.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.version_info.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.noncoding.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_metadata.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.all.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/00.info.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_genes.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.varonly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/00.params.json -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.varonly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.pickle -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/00.version_info.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.all.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon copying ariba/tests/data/cluster_test_full_run_delete_codon/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon copying ariba/tests/data/cluster_test_full_run_delete_codon/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon copying ariba/tests/data/cluster_test_full_run_delete_codon/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon copying ariba/tests/data/cluster_test_full_run_delete_codon/for_reads.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail copying ariba/tests/data/cluster_test_full_run_assembly_fail/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail copying ariba/tests/data/cluster_test_full_run_assembly_fail/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail copying ariba/tests/data/cluster_test_full_run_assembly_fail/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence copying ariba/tests/data/cluster_test_full_run_ok_presence_absence/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence copying ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence copying ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars copying ariba/tests/data/cluster_test_full_run_multiple_vars/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars copying ariba/tests/data/cluster_test_full_run_multiple_vars/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars copying ariba/tests/data/cluster_test_full_run_multiple_vars/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars copying ariba/tests/data/cluster_test_full_run_multiple_vars/for_reads.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly copying ariba/tests/data/cluster_test_full_run_partial_asmbly/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly copying ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly copying ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in copying ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/gene2.tfa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in copying ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/gene1.tfa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in copying ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/profile.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa copying ariba/tests/data/cluster_test_init_no_refs_fa/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa copying ariba/tests/data/cluster_test_init_no_refs_fa/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2 copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2 copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2 copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2 creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail copying ariba/tests/data/cluster_test_full_run_choose_ref_fail/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail copying ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail copying ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.info.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_genes.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.varonly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.varonly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.pickle -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.auto_metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_noncoding.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.version_info.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.all.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/megares_zip_parser_write_files copying ariba/tests/data/megares_zip_parser_write_files/megares_database_v1.01.fasta -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/megares_zip_parser_write_files copying ariba/tests/data/megares_zip_parser_write_files/megares_annotations_v1.01.csv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/megares_zip_parser_write_files copying ariba/tests/data/megares_zip_parser_write_files/megares_to_external_header_mappings_v1.01.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/megares_zip_parser_write_files creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2 copying ariba/tests/data/cluster_test_init_no_reads_2/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2 copying ariba/tests/data/cluster_test_init_no_reads_2/genes.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2 creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir copying ariba/tests/data/clusters_load_ref_data_from_dir/01.filter.check_metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir copying ariba/tests/data/clusters_load_ref_data_from_dir/00.info.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir copying ariba/tests/data/clusters_load_ref_data_from_dir/00.params.json -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir copying ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.clusters.pickle -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir copying ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.all.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only copying ariba/tests/data/cluster_test_full_run_ok_variants_only/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only copying ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only copying ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon copying ariba/tests/data/cluster_test_full_run_insert_codon/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon copying ariba/tests/data/cluster_test_full_run_insert_codon/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon copying ariba/tests/data/cluster_test_full_run_insert_codon/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon copying ariba/tests/data/cluster_test_full_run_insert_codon/for_reads.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1 copying ariba/tests/data/cluster_test_init_no_reads_1/genes.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1 copying ariba/tests/data/cluster_test_init_no_reads_1/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1 creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene running build_ext building 'minimap_ariba' extension creating build creating build/temp.linux-x86_64-3.9 creating build/temp.linux-x86_64-3.9/ariba creating build/temp.linux-x86_64-3.9/ariba/ext x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/ariba-2.14.6+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/minimap -I/usr/include/python3.9 -c ariba/ext/minimap_ariba.cpp -o build/temp.linux-x86_64-3.9/ariba/ext/minimap_ariba.o ariba/ext/minimap_ariba.cpp: In function 'bool readMappingOk(const mm_reg1_t*, const mm_idx_t*, const kseq_t*, uint32_t)': ariba/ext/minimap_ariba.cpp:371:23: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 371 | if (r->qe - r->qs < std::min((unsigned) 50, (int) 0.5 * ks->seq.l)) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ariba/ext/minimap_ariba.cpp:381:26: warning: comparison of integer expressions of different signedness: 'const int32_t' {aka 'const int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 381 | startOk = (r->qs < endTolerance || refLength - r->re < endTolerance); | ~~~~~~^~~~~~~~~~~~~~ ariba/ext/minimap_ariba.cpp:382:60: warning: comparison of integer expressions of different signedness: 'const int32_t' {aka 'const int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 382 | endOk = (ks->seq.l - r->qe < endTolerance || r->rs < endTolerance); | ~~~~~~^~~~~~~~~~~~~~ ariba/ext/minimap_ariba.cpp:386:26: warning: comparison of integer expressions of different signedness: 'const int32_t' {aka 'const int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 386 | startOk = (r->qs < endTolerance || r->rs < endTolerance); | ~~~~~~^~~~~~~~~~~~~~ ariba/ext/minimap_ariba.cpp:386:50: warning: comparison of integer expressions of different signedness: 'const int32_t' {aka 'const int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 386 | startOk = (r->qs < endTolerance || r->rs < endTolerance); | ~~~~~~^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/ariba-2.14.6+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/ariba/ext/minimap_ariba.o -o /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/minimap_ariba.cpython-39-x86_64-linux-gnu.so -lz -lminimap building 'fermilite_ariba' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/ariba-2.14.6+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.9 -c ariba/ext/fml-asm_ariba.cpp -o build/temp.linux-x86_64-3.9/ariba/ext/fml-asm_ariba.o x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/ariba-2.14.6+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/ariba/ext/fml-asm_ariba.o -o /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/fermilite_ariba.cpython-39-x86_64-linux-gnu.so -lz -lfml building 'vcfcall_ariba' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/ariba-2.14.6+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.9 -c ariba/ext/vcfcall_ariba.cpp -o build/temp.linux-x86_64-3.9/ariba/ext/vcfcall_ariba.o x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/ariba-2.14.6+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/ariba/ext/vcfcall_ariba.o -o /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/vcfcall_ariba.cpython-39-x86_64-linux-gnu.so running build_scripts creating build/scripts-3.9 copying and adjusting scripts/ariba -> build/scripts-3.9 changing mode of build/scripts-3.9/ariba from 644 to 755 dh_auto_test -O--buildsystem=pybuild I: pybuild base:232: cd /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build; python3.9 -m nose -v WARNING: I tried to get the version of spades with: "/usr/bin/spades.py --version" and the output didn't match this regular expression: "SPAdes\s+v([0-9\.]+)" test _check_coding_seq ... ok test _check_insertion_coords ... ok test _check_seq_lengths_same ... ok test _check_sequences with coding seqs ... ok test _check_sequences with noncoding seqs ... ok test _check_variants_match_sequences ... ok test _insertion_coords ... ok test _load_aln_file ... ok test _load_vars_file bad input files ... ok test _load_vars_file good input file ... ok test _make_cluster_file ... ok test _make_unpadded_insertion_coords ... ok test _make_unpadded_seqs ... ok test _padded_to_unpadded_nt_position ... ok test run coding sequences ... Warning: position has a gap in sequence seq3 corresponding to variant A2D (id1) in sequence seq1 ... Ignoring for seq3 Warning: position has a gap in sequence seq1 corresponding to variant F2E (id2) in sequence seq5 ... Ignoring for seq1 Warning: position has a gap in sequence seq2 corresponding to variant F2E (id2) in sequence seq5 ... Ignoring for seq2 ok test run noncoding sequences ... Warning: position has a gap in sequence seq3 corresponding to variant C5T (id1) in sequence seq1 ... Ignoring for seq3 Warning: position has a gap in sequence seq1 corresponding to variant A5T (id2) in sequence seq5 ... Ignoring for seq1 Warning: position has a gap in sequence seq2 corresponding to variant A5T (id2) in sequence seq5 ... Ignoring for seq2 ok test _unpadded_to_padded_nt_position ... ok test variant_ids_are_unique ... ok test _variants_to_tsv_lines coding sequences ... Warning: position has a gap in sequence seq3 corresponding to variant A2D (id1) in sequence seq1 ... Ignoring for seq3 Warning: position has a gap in sequence seq1 corresponding to variant F2E (id2) in sequence seq5 ... Ignoring for seq1 Warning: position has a gap in sequence seq2 corresponding to variant F2E (id2) in sequence seq5 ... Ignoring for seq2 ok test _variants_to_tsv_lines noncoding sequences ... Warning: position has a gap in sequence seq3 corresponding to variant C5T (id1) in sequence seq1 ... Ignoring for seq3 Warning: position has a gap in sequence seq1 corresponding to variant A5T (id2) in sequence seq5 ... Ignoring for seq1 Warning: position has a gap in sequence seq2 corresponding to variant A5T (id2) in sequence seq5 ... Ignoring for seq2 ok test _find_next_stop_codon ... ok test _find_previous_start_codon ... ok test _gene_from_nucmer_match ... ok test _get_assembled_reference_sequences ... ok test _get_gene_matching_ref ... ok test _longest_nucmer_hit_in_ref ... ok test nucmer_hit_containing_reference_position ... ok test _nucmer_hits_to_assembly_coords ... ok test _nucmer_hits_to_percent_identity ... ok test _nucmer_hits_to_ref_and_qry_coords ... ok test nucmer_hits_to_ref_coords ... ok test _parse_nucmer_coords_file ... ok test ref_cov_per_contig ... ok test _ref_covered_by_at_least_one_full_length_contig ... ok test _ref_has_region_assembled_twice ... ok test _whole_gene_covered_by_nucmer_hits ... ok test _assemble_with_fermilite ... ok test _assemble_with_fermilite fails ... ok test _assemble_with_spades ... WARNING: I tried to get the version of spades with: "/usr/bin/spades.py --version" and the output didn't match this regular expression: "SPAdes\s+v([0-9\.]+)" ok test _assemble_with_spades handles spades fail ... WARNING: I tried to get the version of spades with: "/usr/bin/spades.py --version" and the output didn't match this regular expression: "SPAdes\s+v([0-9\.]+)" The following command failed with exit code 1 ['/usr/bin/spades.py', '-t', '1', '--pe1-1', '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_1.fq', '--pe1-2', '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_2.fq', '-o', '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/tmp.test_assemble_with_spades_fail/Assemble', '--only-assembler'] The output was: Command line: /usr/lib/spades/bin/spades.py -t 1 --pe1-1 /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_1.fq --pe1-2 /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_2.fq -o /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/tmp.test_assemble_with_spades_fail/Assemble --only-assembler System information: SPAdes version: 3.13.1 Python version: 3.9.2 OS: Linux-6.0.0-0.deb11.6-amd64-x86_64-with-glibc2.31 Output dir: /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/tmp.test_assemble_with_spades_fail/Assemble Mode: ONLY assembling (without read error correction) Debug mode is turned OFF Dataset parameters: Multi-cell mode (you should set '--sc' flag if input data was obtained with MDA (single-cell) technology or --meta flag if processing metagenomic dataset) Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_1.fq'] right reads: ['/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_2.fq'] interlaced reads: not specified single reads: not specified merged reads: not specified Assembly parameters: k: automatic selection based on read length Repeat resolution is enabled Mismatch careful mode is turned OFF MismatchCorrector will be SKIPPED Coverage cutoff is turned OFF Other parameters: Dir for temp files: /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/tmp.test_assemble_with_spades_fail/Assemble/tmp Threads: 1 Memory limit (in Gb): 47 ======= SPAdes pipeline started. Log can be found here: /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/tmp.test_assemble_with_spades_fail/Assemble/spades.log ===== Assembling started. == Running assembler: K21 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/tmp.test_assemble_with_spades_fail/Assemble/K21/configs/config.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 47 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 84) Starting SPAdes, built from N/A, git revision N/A 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/tmp.test_assemble_with_spades_fail/Assemble/dataset.info) with K=21 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 1 0:00:00.000 4M / 4M INFO General (launch.hpp : 52) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 59) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 66) Two-step RR enabled: 0 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.000 4M / 4M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #0 (takes a while) 0:00:00.000 4M / 4M INFO General (read_converter.hpp : 78) Converting paired reads 0:00:00.120 68M / 132M INFO General (binary_converter.hpp : 117) 1 reads written 0:00:00.120 4M / 132M INFO General (read_converter.hpp : 87) Converting single reads 0:00:00.369 132M / 260M INFO General (binary_converter.hpp : 117) 0 reads written 0:00:00.369 4M / 260M INFO General (read_converter.hpp : 95) Converting merged reads 0:00:00.611 132M / 260M INFO General (binary_converter.hpp : 117) 0 reads written 0:00:00.611 4M / 260M INFO General (construction.cpp : 111) Max read length 67 0:00:00.611 4M / 260M INFO General (construction.cpp : 117) Average read length 67 0:00:00.611 4M / 260M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.611 4M / 260M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1 files using 1 threads. This might take a while. 0:00:00.612 4M / 260M INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:00.612 4M / 260M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 15.6654 Gb 0:00:00.612 4M / 260M INFO General (kmer_splitters.hpp : 97) Using cell size of 67108864 0:00:00.612 568M / 1G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:00:00.612 4M / 1G INFO General (kmer_splitters.hpp : 308) Used 4 reads 0:00:00.612 4M / 1G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:00.613 4M / 1G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 46 kmers in total. 0:00:00.613 4M / 1G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:00.613 4M / 1G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:00:00.613 4M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:00.613 4M / 1G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 16 files using 1 threads. This might take a while. 0:00:00.613 4M / 1G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:00.613 4M / 1G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 15.6654 Gb 0:00:00.613 4M / 1G INFO General (kmer_splitters.hpp : 97) Using cell size of 4194304 0:00:00.622 580M / 1G INFO General (kmer_splitters.hpp : 385) Used 46 kmers. 0:00:00.622 4M / 1G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:00.629 4M / 1G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 47 kmers in total. 0:00:00.629 4M / 1G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:00.629 4M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:00.709 4M / 1G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:00.709 4M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9000 bytes occupied (1531.91 bits per kmer). 0:00:00.709 4M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:00:00.709 4M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:00:00.709 4M / 1G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping 0:00:00.709 4M / 1G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) 0:00:00.709 4M / 1G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping 0:00:00.710 4M / 1G INFO Early tip clipping (early_simplification.hpp : 184) 0 22-mers were removed by early tip clipper 0:00:00.710 4M / 1G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:00:00.710 4M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:00:00.710 4M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 1 sequences extracted 0:00:00.710 4M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:00:00.710 4M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected 0:00:00.710 4M / 1G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:00:00.710 4M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:00.710 4M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:00.717 4M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 608 bytes occupied (105.739 bits per kmer). 0:00:00.717 4M / 1G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:00:00.718 4M / 1G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:00:00.718 4M / 1G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding === Stack Trace === /usr/lib/spades/bin/spades-core(_ZN14coverage_model17KMerCoverageModel3FitEv+0xc2) [0x558c7d094622] /usr/lib/spades/bin/spades-core(_ZN14debruijn_graph17GenomicInfoFiller3runERNS_10graph_packINS_13DeBruijnGraphEEEPKc+0x687) [0x558c7d02e8e7] /usr/lib/spades/bin/spades-core(_ZN6spades12StageManager3runERN14debruijn_graph10graph_packINS1_13DeBruijnGraphEEEPKc+0x10d) [0x558c7d00212d] /usr/lib/spades/bin/spades-core(_ZN6spades15assemble_genomeEv+0xccf) [0x558c7ce9f80f] /usr/lib/spades/bin/spades-core(main+0x3ce) [0x558c7ce9716e] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xea) [0x7f35f11eed0a] /usr/lib/spades/bin/spades-core(_start+0x2a) [0x558c7ce9ce5a] Verification of expression 'cov_.size() > 10' failed in function 'void coverage_model::KMerCoverageModel::Fit()'. In file '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp' on line 187. Message 'Invalid kmer coverage histogram, make sure that the coverage is indeed uniform'. Verification of expression 'cov_.size() > 10' failed in function 'void coverage_model::KMerCoverageModel::Fit()'. In file '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp' on line 187. Message 'Invalid kmer coverage histogram, make sure that the coverage is indeed uniform'. spades-core: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp:187: void coverage_model::KMerCoverageModel::Fit(): Assertion `cov_.size() > 10' failed. == Error == system call for: "['/usr/lib/spades/bin/spades-core', '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/tmp.test_assemble_with_spades_fail/Assemble/K21/configs/config.info']" finished abnormally, err code: -6 In case you have troubles running SPAdes, you can write to spades.support@cab.spbu.ru or report an issue on our GitHub repository github.com/ablab/spades Please provide us with params.txt and spades.log files from the output directory. ok test _check_spades_log_file ... Error running SPAdes. Cannot continue. This is the error from the log file /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_check_spades_log_file.log.bad ... == Error == system call for: "['/foo/bar/SPAdes-3.6.0-Linux/bin/spades', '/spam/eggs/K21/configs/config.info']" finished abnormally, err code: -7 ok test _fix_contig_orientation ... ok test _parse_bam ... [E::idx_find_and_load] Could not retrieve index file for '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_parse_assembly_bam.bam' ok test _run_fermilite ... ok test _run_fermilite when it fails ... ok test filter_mummer_variants ... ok test _get_codon_start ... ok test _get_mummer_variants when there are variants ... ok test _get_mummer_variants when no variants ... ok test _get_remaining_known_ref_variants with amino acids ... ok test _get_remaining_known_ref_variants with nucleotides ... ok test _get_variant_effect ... ok test get_variants presence absence genes ... ok test get_variants variants only ... ok test _get_one_variant_for_one_contig_coding ... ok test _get_one_variant_for_one_contig_non_coding ... ok test parse ... [E::idx_find_and_load] Could not retrieve index file for '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_parse.bam' ok test _sam_to_soft_clipped ... [E::idx_find_and_load] Could not retrieve index file for '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.bam' [E::idx_find_and_load] Could not retrieve index file for '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.bam' ok test _update_soft_clipped_from_sam ... [E::idx_find_and_load] Could not retrieve index file for '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.bam' [E::idx_find_and_load] Could not retrieve index file for '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.bam' ok test _update_unmapped_mates_from_sam ... [E::idx_find_and_load] Could not retrieve index file for '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.bam' [E::idx_find_and_load] Could not retrieve index file for '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.bam' ok test _write_soft_clipped_to_file ... [E::idx_find_and_load] Could not retrieve index file for '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/dummy.bam' ok test _write_unmapped_mates_to_file ... [E::idx_find_and_load] Could not retrieve index file for '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/dummy.bam' ok test _ARO_accession ... ok test _ARO_description ... ok test _ARO_id ... ok test _ARO_name ... ok test _ARO_name_to_fasta_name ... ok test _dna_seqs_and_genbank_ids ... Missing data from foo Missing data from foo Missing data from foo Missing data from foo Missing data from foo Missing data from foo Missing data from foo ok test_get_data (ariba.tests.card_record_test.TestCardRecord) ... ok test snps ... ok test fake_run ... ok test fake_run min_cluster 42 ... ok test fake_run with non-unique names ... ok test _get_clusters_from_bak_file ... ok test_get_run_cmd_with_default_memory ... ok test_get_run_cmd_with_non_default_memory ... ok test_get_run_cmd_with_unlimited_memory ... ok test init_fail_infile_missing ... ok test_init_fail_invalid_memory ... ok test _load_user_clusters_file with bad input files ... ok test _load_user_clusters_file with good input file ... WARNING: ignoring sequence seq6 from clusters file because not in fasta file. This probably means it failed sanity checks - see the log files 01.filter.check_genes.log, 01.filter.check_metadata.log. ok test _load_user_clusters_file with good input file with some renamed ... ok test run ... ok test run_get_clusters_from_file ... ok test run_get_clusters_from_file with renaming ... ok test run with min_cluster_number 42 ... ok test complete run of cluster when assembly fails ... ok test complete run of cluster when choosing ref seq fails ... ok test complete run where samtools calls a snp at a known snp location in a presence/absence noncoding and sample has the var ... ok Test complete run where there is a deleted codon ... ok Test complete run where there is a inserted codon ... ok test complete run where samtools calls a snp at a known snp location in a presence/absence gene ... ok test complete run where samtools calls a snp at a known snp location in a presence/absence noncoding ... ok Test complete run where there is a codon with a SNP and an indel ... ok test complete run of cluster when filtering removes all reads ... ok test complete run where gene extended because too different at end for full nucmer match ... ok test complete run of cluster on a noncoding sequence ... ok test complete run of cluster on a presence absence gene ... ok test complete run of cluster on a variants only gene when variant is present ... ok test complete run of cluster on a variants only gene when variant not present ... ok test complete run of cluster on a variants only gene when variant not present but always report variant ... ok Test complete run where only part of the ref gene is present in the reads ... ok test complete run of cluster when nearest ref is outside cluster ... ok test complete run where samtools calls a snp in a presence/absence noncoding sequence at a known snp position ... ok test complete run where samtools calls a snp in a presence/absence gene ... ok test complete run where samtools calls a snp in a presence/absence noncoding sequence ... ok test complete run where samtools calls a snp at a known snp location in a variant only gene, gene does have variant ... ok test complete run where samtools calls a snp in a variant only gene ... ok test complete run where samtools calls a snp at a known snp location in a variant only gene, gene does not have variant ... ok test complete run where samtools calls a snp in a presence/absence noncoding sequence ... ok test complete run where samtools calls a snp at a known snp location in a presence/absence noncoding and sample does not have the var ... ok test init_fail_files_missing ... ok Test _make_reads_for_assembly when sampling from reads ... ok Test _make_reads_for_assembly when just makes symlinks ... ok Test _number_of_reads_for_assembly ... ok test _write_catted_genes_matching_refs_fasta ... ok test _load_minimap_files ... ok test _load_minimap_insert_histogram ... ok test _load_minimap_out_cluster2representative ... ok test _load_minimap_out_cluster_counts ... ok test _load_minimap_proper_pairs ... ok test _load_reference_data_from_dir ... ok test _load_reference_data_info_file ... ok test test_minimap_reads_to_all_ref_seqs ... ok test complete run with TB amr calling ... ok test _set_insert_size_data ... ok test _write_catted_assembled_seqs_fasta ... ok test _write_catted_assemblies_fasta ... ok test _write_mlst_reports ... ok test_write_report (ariba.tests.clusters_test.TestClusters) ... ok test _write_tb_resistance_calls_json ... ok test cat_files ... ok test rmtree ... ok Test that external programs are found ... ok test write_fa_subset ... ok Test add ... ok Test has ... ok Test __init__ and to_number ... ok Test set_flag ... ok Test __str__ ... ok Test to_comma_separated_string ... ok Test to_long_str ... ok Test add ... ok Test __len__ ... ok Test stats ... ok Test _to_bin ... ok test _distance_to_contig_end ... ok test _distance_to_contig_ends ... ok test link __init__ no links made ... ok test link __init__ link made ... ok test insert_size ... ok test __lt__ ... ok test merge ... ok test sort ... ok test _swap ... ok test bowtie2_index ... ok Test get_total_alignment_score ... [E::idx_find_and_load] Could not retrieve index file for '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mapping_test_get_total_alignment_score.bam' ok Test run_bowtie2 unsorted ... [E::idx_find_and_load] Could not retrieve index file for '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mapping_test_bowtie2_unsorted.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.out.bowtie2.bam' ok Test run_bowtie2 sorted ... [E::idx_find_and_load] Could not retrieve index file for '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mapping_test_bowtie2_sorted.bam' ok Test run_bowtie2 unsorted remove both unmapped ... [E::idx_find_and_load] Could not retrieve index file for '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.out.bowtie2_remove_both_unmapped.bam' ok test sam_pair_to_insert ... [E::idx_find_and_load] Could not retrieve index file for '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mapping_test_sam_pair_to_insert.bam' ok test sam_to_fastq ... [E::idx_find_and_load] Could not retrieve index file for '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mapping_test_sam_to_fastq.bam' ok test _get_url_for_version ... ok test _zips_from_index_page_string ... ok test _extract_files when all ok ... ok test _extract_files when one missing ... ok test _load_annotations_file ... ok test _load_header_mappings_file ... ok test _write_files ... WARNING: sequence "Only_in_fasta_file" has no record in annotations file WARNING: sequence "Only_in_fasta_file" has no record in header mappings file ok test _bottom_scatter_data ... ok test _filter_top_plot_data ... ok test _get_colours ... ok Test _get_top_plot_data ... ok Test _load_mic_file ... ok Test _load_summary_file ... ok Test _mic_string_to_float ... ok test _ordered_bottom_plot_rows ... ok test _ordered_colunns ... ok test _top_plot_scatter_counts ... ok test _top_plot_scatter_data ... ok test _top_plot_violin_data ... ok test _top_plot_y_ticks ... ok Test get_sequence_type ... ok Test has_gene ... ok test init ... WARNING: Same profile found twice in input file, but two different STs. Going to use the ST with the smaller number (2) ... STs are 2 3 and alleles are nusA:1, rpoB:26, eno:2, gltB:4, lepA:59, nuoL:2, nrdA:5 ok test init ... ok test when all alleles 100% there no variants ... ok test when one gene has a het snp ... ok test when one gene has two het snps ... ok test when allele combination is new ... ok test when one gene missing ... ok test _get_profile_and_fasta_urls ... ok test _get_species_list ... ok test _rename_seqs_in_fasta ... ok test _filter_seq_dict ... WARNING: Median sequence length is 5 but seq1 has length 1 which is too long or short. Removing. WARNING: Median sequence length is 5 but seq5 has length 14 which is too long or short. Removing. ok test _load_fasta_files_and_write_clusters_file ... WARNING: I tried to get the version of spades with: "/usr/bin/spades.py --version" and the output didn't match this regular expression: "SPAdes\s+v([0-9\.]+)" ok test _cdhit_clstr_to_reads ... ok Test clean ... ok Test _compress_and_index_file ... ok Test get_reads fasta pair ... ok Test get_reads fastq interleaved ... ok Test get_reads fastq pair ... ok Test get_reads subset ... ok test _sort_file ... ok test _fix_virulencefinder_fasta_file ... WARNING: found line with ">" not at the start! Fixing. Line:AC>seq3 in file /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.in.fa WARNING: found line with ">" at the end! Fixing. Line:AACGT> in file /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.in.fa ok test _fasta_to_metadata ... ok test _rename_clusters ... ok test run ... WARNING. 1 sequence(s) excluded. Please see the 01.filter.check_genes.log and 01.filter.check_noncoding.log for details. This will show them: grep REMOVE tmp.ref_preparer_test_run/01.filter.check_genes.log cat tmp.ref_preparer_test_run/01.filter.check_noncoding.log WARNING. Problem with at least one variant. Problem variants are removed. Please see the file tmp.ref_preparer_test_run/01.filter.check_metadata.log for details. ok test run with no metadata input, all sequences are noncoding ... ok test run with noncoding sequences that are outside of the allowed size range ... WARNING. 5 sequence(s) excluded. Please see the 01.filter.check_genes.log and 01.filter.check_noncoding.log for details. This will show them: grep REMOVE tmp.ref_preparer_test_run_noncoding_checks/01.filter.check_genes.log cat tmp.ref_preparer_test_run_noncoding_checks/01.filter.check_noncoding.log WARNING. Problem with at least one variant. Problem variants are removed. Please see the file tmp.ref_preparer_test_run_noncoding_checks/01.filter.check_metadata.log for details. ok test _make_matching_contig_pieces_fasta ... ok Test full run where the best match is in the cluster ... ok Test full run where there is a match in cluster, but better match to seq not in cluster ... ok Test full run where ref seq completely contains another seq outside cluster ... ok Test full run where amount of flanking seq varies ... ok Test full run when nearest match is not in the cluster ... ok Test full run when there is nearest match in cluster, but no nucmer matches ... ok Test all_non_wild_type_variants ... ok Test _check_noncoding_seq ... ok Test cluster_with_cd_hit clusters from file ... ok Test cluster_with_cd_hit do not run cdhit ... ok Test cluster_with_cd_hit ... ok Test _filter_bad_variant_data ... WARNING: sequence "non_coding_not_in_fasta" found in metadata, but not in fasta file. Ignoring it. WARNING: sequence "presence_absence_not_in_fasta" found in metadata, but not in fasta file. Ignoring it. WARNING: sequence "variants_only_not_in_fasta" found in metadata, but not in fasta file. Ignoring it. ok Test __init__ fails when it should ... ok Test init with good input ... ok Test _load_all_fasta_files ... ok Test _load_all_metadata_tsvs ... ok Test _load_fasta_file ... ok Test _load_input_files_and_check_seq_names with bad input ... ok Test _load_input_files_and_check_seq_names with good input ... WARNING: sequence "seq3" found in metadata, but not in fasta file. Ignoring it. ok Test _load_metadata_tsv ... ok Test _load_rename_file ... ok Test _new_seq_name ... ok Test _remove_bad_genes ... ok Test _remove_bad_noncoding_seqs ... ok Test _rename_metadata_set ... ok Test _rename_names_in_metadata ... ok Test _rename_names_in_seq_dict ... ok Test rename_sequences ... ok Test _seq_names_to_rename_dict ... ok Test sequence ... ok Test sequence_type ... ok Test _try_to_get_gene_seq ... ok Test write_cluster_allocation_file ... ok Test _write_metadata_tsv ... ok Test write_seqs_to_fasta ... ok Test _write_sequences_to_files ... ok Test _dict_to_report_line ... ok Test _filter_dicts ... ok Test _filter_list_of_dicts where all fail ... ok Test _filter_list_of_dicts with an essential line but all others fail ... ok Test _filter_list_of_dicts with a line that passes ... ok Test _flag_passes_filter ... ok test __init__ on bad input file ... ok test __init__ on good input file ... ok test_load_report (ariba.tests.report_filter_test.TestReportFilter) ... ok Test _remove_all_after_first_frameshift ... ok Test _remove_all_after_first_frameshift when gene is complete ... ok Test _report_dict_passes_essential_filters ... ok Test _report_dict_passes_non_essential_filters with known vars ... ok Test _report_dict_passes_non_essential_filters with synonymous AA changes ... ok test_report_line_to_dict (ariba.tests.report_filter_test.TestReportFilter) ... ok Test run ... ok Test write_report_tsv ... ok test run ... ok test get_depths_at_position ... ok test _get_read_depths ... ok test _get_variant_positions_from_vcf ... ok test _get_variants ... ok test _make_vcf_and_read_depths_files ... ok test total_depth_per_contig ... ok test variants_in_coords ... ok test _contig_graph_is_consistent ... ok test _make_graph ... ok test _remove_low_cov_links ... ok test update_from_sam ... [E::idx_find_and_load] Could not retrieve index file for '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/graph_test_update_from_sam.bam' ok test write_all_links_to_file ... ok test has_variant ... ok Test init fails on bad lines ... ok test init ok on good input ... ok test __str__ ... ok test to_string ... ok test has_variant ... ok Test init fails on bad variant strings ... ok Test init ok ... ok Test init ok and str ... ok test nucleotide_range ... ok test sanity_check_against_seq with translate False ... ok test sanity_check_against_seq with translate True ... ok Test add_data_dict ... ok Test column_summary_data ... ok test gather_data ... ok test _get_all_nonsynon_variants_set ... ok Test _get_known_noncoding_het_snp ... ok Test _get_nonsynonymous_var ... ok test_has_any_known_variant (ariba.tests.summary_cluster_test.TestSummaryCluster) ... ok Test _has_any_nonsynonymous ... ok Test _has_any_novel_nonsynonymous ... ok Test _has_any_part_of_ref_assembled ... ok Test _has_known_variant ... ok Test _has_match ... ok Test _has_nonsynonymous ... ok Test _has_novel_nonsynonymous ... ok Test has_var_groups ... ok test known_noncoding_het_snps ... ok Test _line2dict ... ok Test non_synon_variants ... ok Test _pc_id_and_read_depth_of_longest ... ok Test _to_cluster_summary_has_known_nonsynonymous ... ok Test _to_cluster_summary_has_nonsynonymous ... ok Test _to_cluster_summary_has_novel_nonsynonymous ... ok Test _to_cluster_summary_assembled ... ok test _filter_depths ... ok test _get_is_het_and_percent ... ok Test _has_nonsynonymous ... ok test __init__ ... ok Test _column_summary_data ... ok Test _load_file ... ok test _var_groups ... ok Test _variant_column_names_tuples_and_het_snps ... ok Test _add_phandango_colour_columns ... ok test_determine_cluster_cols (ariba.tests.summary_test.TestSummary) ... ok Test _distance_score_between_lists ... ok Test _distance_score_bewteen_values ... ok Test _filter_matrix_columns ... ok Test _filter_matrix_rows ... ok test gather_unfiltered_output_data ... ok Test init ... ok Test _load_fofn ... ok Test _load_input_files ... ok Test _matrix_to_csv ... ok Test _matrix_to_csv with remove_nas ... ok Test _newick_from_dist_matrix ... ok Test _to_matrix all columns ... ok Test _to_matrix with assembled column only ... ok Test _to_matrix with cluster columns only ... ok Test _to_matrix with groups ... ok Test _to_matrix with vars ... ok Test whole run to check csv ok (skip making tree) ... ok Test _write_distance_matrix ... ok test genbank_to_gene_coords ... ok test load_mutations ... ok test make_prepareref_dir ... ok test make_prepareref_files ... ok test report_to_resistance_dict ... ok test write_prepareref_fasta_file ... ok test write_prepareref_metadata_file ... ok test _cluster2seqs ... ok test _load_clusters ... ok test query with unknown query ... ok test _seq2cluster ... ok test _seqinfo ... ok Test get_all_versions ... WARNING: I tried to get the version of spades with: "/usr/bin/spades.py --version" and the output didn't match this regular expression: "SPAdes\s+v([0-9\.]+)" ok test _fa_header_to_name_and_metadata ... ok test _fa_header_to_name_pieces ... ok test run ... ok ---------------------------------------------------------------------- Ran 356 tests in 120.703s OK create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:232: /usr/bin/python3 setup.py install --root /build/ariba-2.14.6+ds/debian/ariba running install running build running build_py running build_ext running build_scripts running install_lib creating /build/ariba-2.14.6+ds/debian/ariba/usr creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9 creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/vcfcall_ariba.cpython-39-x86_64-linux-gnu.so -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/fermilite_ariba.cpython-39-x86_64-linux-gnu.so -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/minimap_ariba.cpython-39-x86_64-linux-gnu.so -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/summary.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/report_flag_expander.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/vfdb_parser.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/ref_genes_getter.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/refdata_query.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/read_filter.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/versions.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/pubmlst_ref_preparer.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/pubmlst_getter.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/mic_plotter.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/megares_zip_parser.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/megares_data_finder.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/faidx.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/ref_preparer.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/tb.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/sequence_metadata.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/reference_data.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/report_filter.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/read_store.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/summary_cluster_variant.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/summary_cluster.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/summary_sample.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/mlst_profile.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/mlst_reporter.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/histogram.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/clusters.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/samtools_variants.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/report.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/flag.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/cluster.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/cdhit.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/card_record.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/assembly_variants.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/assembly_compare.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/ref_seq_chooser.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/external_progs.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/link.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/scaffold_graph.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/bam_parse.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/mapping.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/common.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/assembly.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/sequence_variant.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/aln_to_metadata.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/__init__.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tb_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tb_data/panel.20190102.json -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tb_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tb_data/panel.20181221.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tb_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tb_data/panel.20181115.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tb_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tb_data/NC_000962.3.gb -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tb_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tb_data/panel.20190102.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tb_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tb_data/panel.20181221.json -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tb_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tb_data/panel.20181115.json -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tb_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tb_data/NC_000962.3.fa.gz -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tb_data creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/test_run_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/test_run_data/metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/test_run_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/test_run_data/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/test_run_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/test_run_data/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/test_run_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/test_run_data/ref_fasta_to_make_reads_from.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/test_run_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/test_run_data/ref_seqs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/test_run_data creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/vfdb_parser_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/versions_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/test_refdata_query.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/tb_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/summary_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/summary_sample_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/summary_cluster_variant_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/summary_cluster_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/sequence_variant_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/sequence_metadata_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/scaffold_graph_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/samtools_variants_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/report_flag_expander_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/report_filter_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/reference_data_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/ref_seq_chooser_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/ref_preparer_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/ref_genes_getter_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/read_store_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/read_filter_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/pubmlst_ref_preparer_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/pubmlst_getter_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/ncbi_getter_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/mlst_reporter_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/mlst_profile_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/mic_plotter_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/megares_zip_parser_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/megares_data_finder_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/mapping_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/link_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/histogram_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/flag_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/faidx_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/external_progs_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/common_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/clusters_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/cluster_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/cdhit_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/card_record_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/bam_parse_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/assembly_variants_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/assembly_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/assembly_compare_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/aln_to_metadata_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/__init__.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_init_no_reads_1 copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_init_no_reads_1 copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1/genes.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_init_no_reads_1 creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon/for_reads.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.all.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.clusters.pickle -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/00.params.json -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/00.info.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/01.filter.check_metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_init_no_reads_2 copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2/genes.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_init_no_reads_2 copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_init_no_reads_2 creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/megares_zip_parser_write_files copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/megares_zip_parser_write_files/megares_to_external_header_mappings_v1.01.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/megares_zip_parser_write_files copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/megares_zip_parser_write_files/megares_annotations_v1.01.csv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/megares_zip_parser_write_files copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/megares_zip_parser_write_files/megares_database_v1.01.fasta -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/megares_zip_parser_write_files creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.all.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.version_info.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_noncoding.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.auto_metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.pickle -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.varonly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.varonly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_genes.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.info.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2 copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2 copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2 copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2 creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_init_no_refs_fa copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_init_no_refs_fa copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_init_no_refs_fa creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/profile.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/gene1.tfa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/gene2.tfa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars/for_reads.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon/for_reads.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.all.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/00.version_info.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.pickle -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.varonly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/00.params.json -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.varonly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_genes.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/00.info.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_run_with_tb.ref creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.all.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_metadata.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.noncoding.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.version_info.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_noncoding.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.rename_info -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.clusters.pickle -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.gene.varonly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.clusters.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.noncoding.varonly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.gene.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_genes.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.info.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.all.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out/00.version_info.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_noncoding.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.pickle -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.varonly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.varonly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_genes.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out/00.info.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run.out creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.all.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref/00.version_info.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref/01.filter.check_noncoding.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref/00.rename_info -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.pickle -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.varonly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.varonly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref/01.filter.check_genes.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref/00.info.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mapping_test_bowtie2_unsorted.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_test_get_variants.vcf -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/report_filter_test_init_bad.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_filter_test_run.in.reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refcheck_test_check_not_gene.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_load_minimap_out_cluster2representative.in -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.smi -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_load_all_fasta_files.in.2 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.allrefs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_fix_contig_orientation.ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/vfdb_parser_test_run.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.meta.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/link_test_init.reads.no_link.bam.bai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_profile_test.profile.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.contigs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cdhit_test_get_clusters_from_bak_file.in -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.reads_2.fq.gz -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/summary_to_matrix.1.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_test_get_depths_at_position.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_load_all_metadata_tsvs.1.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite.reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/tb_report_to_resistance_dict.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/dummy.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.allrefs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.out.cluster -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/faidx_test_write_fa_subset.in.fa.fai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.depths.gz -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/link_test_init.reads.no_link.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_store_test_clean.in -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/link_test_init.reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/summary_test_load_input_files.1.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_test_flanking.expected_contigs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.expect.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.coords -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/summary_sample_test_var_groups.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.2 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refcheck_test_check_too_long.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_filter_test_run_cdhit_est_2d.expected.clstr -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/report_filter_test_run.expected.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cdhit_test_load_user_clusters_file.good -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_remove_bad_genes.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_scaffold_with_sspace_reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_filter_bad_data_metadata.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_run_fermilite.reads.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_write_mlst_reports.mlst_profile.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_load_minimap_files.clusterCounts -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refcheck_test_check_too_short.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mapping_test_sam_to_fastq.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mapping_test_bowtie2_reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cdhit_test_run.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_write_catted_assembled_genes_fasta.expected.out.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_remove_bad_noncoding.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_keep_seqs_from_dict.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_dummy_reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_load_rename_file.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_test_write_seqs_to_fasta.expected.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_reporter.one_gene_missing.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mapping_test_sam_pair_to_insert.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_load_minimap_insert_histogram.in -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.1 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_test_remove_bad_genes.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refcheck_test_fix_out.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refcheck_test_fix_out.rename -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.ref_for_reads.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_reporter.one_gene_missing.out.details.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_test_flanking.all_refs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_profile_test.init.profile.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/report_flag_expander.run.out.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_test_all_non_wild_type_variants.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.cov -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_init_ok.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.fai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_write_mlst_reports.out.details.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_dummy_db.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr_count -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_scaffold_with_sspace_reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_load_all_metadata_tsvs.2.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/tb_genbank_to_gene_coords.gb -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_init_refdata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_test_cluster_with_cdhit.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/link_test_init.reads.make_link_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/summary_test_load_fofn -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_filter_test_run.in.reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_reporter.all_present_perfect.report.out.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_check_spades_log_file.log.bad -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_test_write_cluster_allocation_file.expected -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_load_minimap_files.insertHistogram -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.reads_1.fq.gz -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cdhit_test_fake_run.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/summary_test_whole_run.out.csv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_parse_assembly_bam.assembly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/faidx_test_write_fa_subset.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.all.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_init_fails.empty.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.in.1.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/summary_to_matrix.2.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_run_fermilite_fails.expected.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/summary_sample_test_column_names_tuples_and_het_snps.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_load_data_info_file -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only.present.metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.contigs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_make_reads_for_assembly.in1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/faidx_test_write_fa_subset.out.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/link_test_init.reads.make_link.bam.bai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.no_combinations.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mapping_test_bowtie2_ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.cluster_refs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/pubmlst_getter.dbases.xml -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mapping_test_bowtie2_sorted.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_store_test_compress_and_index_file.in -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_variants_test_get_mummer_variants.snp.snps -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_2.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_filter_bad_data_non_coding.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/summary_gather_unfiltered_output_data.in.1.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_sequence.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_run_fermilite.expected.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite_fails.expected.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.no_combinations.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_run_fermilite.expected.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_reporter.het_snps.out.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr2rep -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_test_get_read_depths.gz -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/link_test_init.ref.fa.fai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cdhit_test_run_get_clusters_from_dict_rename.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_rename_sequences.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/megares_zip_parse_extract_files_ok.zip -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/graph_test_update_from_sam.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.contigs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_sequence_is_in_fasta_file.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence.metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/test_common_cat_files.out -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/link_test_init.reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_count_reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz.tbi -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_sequence_type.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa.fai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.hist -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_fasta_to_metadata.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_load_minimap_proper_pairs.in -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.in.1.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/megares_zip_parser_write_files.expect.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.1 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.reads.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/summary_test_write_distance_matrix.distances -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refcheck_test_fix_out.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_filter_bad_data_variants_only.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/link_test_init.reads.no_link_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/graph_test_update_from_sam.reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_sequence.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_fasta_to_metadata.noncoding.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_variants_test_get_variants_variants_only.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/best_seq_chooser_total_alignment_score_reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_load_all_fasta_files.in.1 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_reporter.het_snp.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/summary_test_whole_run.in.1.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_reporter.het_snps.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.in.2.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_reporter.all_present_perfect.report.out.details.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_reporter.one_gene_missing.out.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/megares_zip_parse_extract_files_one_missing.zip -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/summary_test_load_input_files.2.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_store_test_sort_file.out -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_varonly.not_present.always_report.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refcheck_test_check_duplicate_name.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.expect.clstrs.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/summary_sample_test_load_file.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_write_gene_fa.db.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/link_test_init.reads.no_link_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/link_test_init.reads.make_link_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.no_combinations.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_write_tb_resistance_calls_json.out.json -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_reporter.new_st.report.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa.fai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.noncoding.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_test_cluster_with_cdhit.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refcheck_test_fix_out.removed.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mic_plotter_load_summary_file.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_init_ok.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_write_report.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.gene.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_variants_test_get_variants_presence_absence.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.in.3.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_init_fails.empty.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.expect.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.sma -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/megares_zip_parser_load_annotations.csv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mapping_test_get_total_alignment_score.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.ref_for_reads.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_dummy_db.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_write_tb_resistance_calls_json.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_parse.reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.no_combinations.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.out.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.all_refs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_init_ok.params.json -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.for_reads.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.clstrs.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.in.4.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_write_mlst_reports.ariba.report.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_dummy_reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/summary_test_newick_from_dist_matrix.distances -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_test_all_non_wild_type_variants.ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_rename_sequences_metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.1 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/best_seq_chooser_best_seq_ref.fa.fai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mapping_test_bowtie2_reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.no_combinations.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only.not_present.metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_write_metadata_tsv.expected.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.2 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_store_test_sort_file.in -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_test_flanking.cluster_refs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_write_gene_fa.db.fa.fai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.sma -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding.metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_subset.1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_make_reads_for_assembly.in2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_filter_test_run.expected.reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_make_reads_for_assembly.out2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_write_mlst_reports.out.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mic_plotter_load_mic_file.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_store_test_get_reads.in -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.out.cluster -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa.fai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_fasta_to_metadata.coding.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/graph_test_update_from_sam.reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refcheck_test_fix_in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa.fai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.clusterrefs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_filter_test_run_cdhit_est_2d.reads.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/pubmlst_rename_seqs.expected.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_test_get_variant_positions_from_vcf.vcf -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_init_refdata.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/report_filter_test_load_report_good.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_make_reads_for_assembly.out1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_test_variants_in_coords.vcf -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.out.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_parse.ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.allrefs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ctg.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.out.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.pairs -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_write_metadata_tsv.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mapping_test_bowtie2_ref.fa.fai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.ref_for_reads.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_remove_bad_genes.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_compare_parse_nucmer_coords_file.coords -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_fix_contig_orientation.out.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_1.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.allrefs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/summary_sample_test_column_summary_data.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_fix_contig_orientation.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/aln_to_metadata_load_aln_file.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_test_flanking.contigs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cdhit_test_load_user_clusters_file.bad2 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.gene.varonly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/best_seq_chooser_total_alignment_score_reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/summary_sample_test_non_synon_variants.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_reporter.het_snp.out.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_test_get_read_depths.gz.tbi -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_keep_seqs_from_dict.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_reporter.new_st.report.out.details.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_filter_test_run_cdhit_est_2d.ref.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.noncoding.varonly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.in.4.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_test_rename_sequences.out -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.clstrs.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.contigs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/link_test_init.reads.make_link.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_load_minimap_out_cluster_counts.in -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.2 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_cat_genes_match_ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_init_fails.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/aln_to_metadata_load_vars_file_bad.2.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_reporter.het_snps.out.details.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_load_minimap_files.cluster2representative -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite.expected.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/test_common_cat_files.in.3 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite.expected.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_sequence_type.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_filter_cdhit_clstr_to_reads.in.clstr -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/test_common_cat_files.in.2 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_filter_test_run.expected.reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/best_seq_chooser_best_seq_reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_write_gene_fa.out.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/aln_to_metadata_load_vars_file_bad.1.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_reporter.het_snp.out.details.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_parse_assembly_bam.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/link_test_init.ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refcheck_test_check_spaces_in_name.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.out.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.1 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite.reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/test_common_cat_files.in.1 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/best_seq_chooser_best_seq_ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_filter_test_run.in.read_store -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_profile_test.init_multiple_extra_columns.profile.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_filter_bad_data_presence_absence.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/pubmlst_rename_seqs.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/graph_test_update_from_sam.ref.fa.fai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_load_minimap_files.properPairs -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.2 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.clusters -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/report_filter_test_init_good.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.out.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_reporter.profile.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_reporter.all_present_perfect.report.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.in.2.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_test_total_depth_per_contig -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/aln_to_metadata_make_cluster_file.out -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/vfdb_parser_test_run.out.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/report_flag_expander.run.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/vfdb_parser_test_run.out.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_remove_bad_noncoding.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.vcf -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cdhit_test_fake_run.non-unique.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.clusterrefs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_test_remove_bad_noncoding.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_subset.2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.all.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/aln_to_metadata_load_vars_file_good.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_scaffold_with_sspace_contigs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/report_filter_test_load_report_bad.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/graph_test_write_all_links_to_file.out -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_load_fasta_file.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.contigs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/report_filter_test_run.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.no_combinations.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.reads.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_write_catted_assemblies_fasta.expected.out.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/summary_test_init.fofn -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/tb_write_prepareref_metadata_file.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/report_filter_test_write_report.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.expect.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_check_spades_log_file.log.good -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/megares_zip_parser_write_files.expect.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.smi -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.clusterrefs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_init_ok.rename.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/best_seq_chooser_best_seq_reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_filter_test_run.in.ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/summary_test_whole_run.in.2.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_reporter.new_st.report.out.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.clusterrefs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_run_fermilite_fail.reads.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_load_metadata_tsv.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_parse.reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_parse.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cdhit_test_load_user_clusters_file.bad3 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.all_refs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_filter_bad_data.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refcheck_test_check_ok.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_variants_test_get_mummer_variants.none.snps -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/summary_gather_unfiltered_output_data.in.2.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/megares_zip_parser_load_header_mappings.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/graph_test_update_from_sam.ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_count_reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_test_cluster_with_cdhit.expected.clusters.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cdhit_test_load_user_clusters_file.bad1 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_variants_test_get_variants_variants_only.snps -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_variants_test_get_variants_presence_absence.snps -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/pubmlst_ref_preparer_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/vfdb_parser_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/reference_data_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/read_store_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/report_flag_expander_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/mic_plotter_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/summary_sample_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/report_filter_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/mlst_reporter_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/read_filter_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/aln_to_metadata_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/assembly_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/sequence_variant_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/sequence_metadata_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/pubmlst_getter_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/summary_cluster_variant_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/tb_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/flag_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/link_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/faidx_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/histogram_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/ref_genes_getter_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/external_progs_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/bam_parse_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/ref_preparer_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/samtools_variants_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/clusters_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/summary_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/mlst_profile_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/summary_cluster_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/test_refdata_query.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/assembly_compare_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/card_record_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/versions_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/megares_zip_parser_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/ref_seq_chooser_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/cdhit_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/cluster_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/megares_data_finder_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/scaffold_graph_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__init__.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/common_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/mapping_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/ncbi_getter_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/assembly_variants_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/__pycache__/version.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/__pycache__/test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/__pycache__/summary.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/__pycache__/run.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/__pycache__/reportfilter.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/__pycache__/refquery.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/__pycache__/pubmlstspecies.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/__pycache__/pubmlstget.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/__pycache__/prepareref_tb.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/__pycache__/prepareref.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/__pycache__/micplot.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/__pycache__/getref.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/__pycache__/flag.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/__pycache__/expandflag.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/__pycache__/aln2meta.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/__pycache__/__init__.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/expandflag.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/version.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/prepareref.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/run.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/summary.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/flag.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/micplot.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/prepareref_tb.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/reportfilter.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/refquery.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/pubmlstget.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/pubmlstspecies.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/__init__.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/getref.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/aln2meta.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/ref_seq_chooser.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/refdata_query.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/card_record.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/summary_cluster.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/vfdb_parser.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/report_flag_expander.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/scaffold_graph.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/assembly_compare.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/mlst_profile.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/pubmlst_ref_preparer.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/read_filter.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/bam_parse.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/megares_data_finder.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/summary.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/megares_zip_parser.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/mlst_reporter.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/samtools_variants.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/summary_cluster_variant.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/link.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/external_progs.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/flag.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/report_filter.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tb.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/read_store.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/pubmlst_getter.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/sequence_variant.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/report.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/histogram.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/summary_sample.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/mic_plotter.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/faidx.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/common.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/cdhit.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/ref_genes_getter.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/mapping.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/aln_to_metadata.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/cluster.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/ref_preparer.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/clusters.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/versions.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/sequence_metadata.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__init__.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/reference_data.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/assembly_variants.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/assembly.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/pubmlst_ref_preparer_test.py to pubmlst_ref_preparer_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/vfdb_parser_test.py to vfdb_parser_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/reference_data_test.py to reference_data_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/read_store_test.py to read_store_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/report_flag_expander_test.py to report_flag_expander_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/mic_plotter_test.py to mic_plotter_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/summary_sample_test.py to summary_sample_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/report_filter_test.py to report_filter_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/mlst_reporter_test.py to mlst_reporter_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/read_filter_test.py to read_filter_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/aln_to_metadata_test.py to aln_to_metadata_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/assembly_test.py to assembly_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/sequence_variant_test.py to sequence_variant_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/sequence_metadata_test.py to sequence_metadata_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/pubmlst_getter_test.py to pubmlst_getter_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/summary_cluster_variant_test.py to summary_cluster_variant_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/tb_test.py to tb_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/flag_test.py to flag_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/link_test.py to link_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/faidx_test.py to faidx_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/histogram_test.py to histogram_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/ref_genes_getter_test.py to ref_genes_getter_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/external_progs_test.py to external_progs_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/bam_parse_test.py to bam_parse_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/ref_preparer_test.py to ref_preparer_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/samtools_variants_test.py to samtools_variants_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/clusters_test.py to clusters_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/summary_test.py to summary_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/mlst_profile_test.py to mlst_profile_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/summary_cluster_test.py to summary_cluster_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/test_refdata_query.py to test_refdata_query.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/assembly_compare_test.py to assembly_compare_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/card_record_test.py to card_record_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/versions_test.py to versions_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/megares_zip_parser_test.py to megares_zip_parser_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/ref_seq_chooser_test.py to ref_seq_chooser_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/cdhit_test.py to cdhit_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/cluster_test.py to cluster_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/megares_data_finder_test.py to megares_data_finder_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/scaffold_graph_test.py to scaffold_graph_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__init__.py to __init__.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/common_test.py to common_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/mapping_test.py to mapping_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/ncbi_getter_test.py to ncbi_getter_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/assembly_variants_test.py to assembly_variants_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/expandflag.py to expandflag.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/version.py to version.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/prepareref.py to prepareref.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/run.py to run.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/summary.py to summary.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/flag.py to flag.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/micplot.py to micplot.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/prepareref_tb.py to prepareref_tb.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/reportfilter.py to reportfilter.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/refquery.py to refquery.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/test.py to test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/pubmlstget.py to pubmlstget.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/pubmlstspecies.py to pubmlstspecies.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/__init__.py to __init__.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/getref.py to getref.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/aln2meta.py to aln2meta.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/ref_seq_chooser.py to ref_seq_chooser.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/refdata_query.py to refdata_query.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/card_record.py to card_record.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/summary_cluster.py to summary_cluster.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/vfdb_parser.py to vfdb_parser.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/report_flag_expander.py to report_flag_expander.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/scaffold_graph.py to scaffold_graph.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/assembly_compare.py to assembly_compare.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/mlst_profile.py to mlst_profile.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/pubmlst_ref_preparer.py to pubmlst_ref_preparer.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/read_filter.py to read_filter.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/bam_parse.py to bam_parse.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/megares_data_finder.py to megares_data_finder.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/summary.py to summary.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/megares_zip_parser.py to megares_zip_parser.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/mlst_reporter.py to mlst_reporter.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/samtools_variants.py to samtools_variants.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/summary_cluster_variant.py to summary_cluster_variant.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/link.py to link.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/external_progs.py to external_progs.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/flag.py to flag.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/report_filter.py to report_filter.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tb.py to tb.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/read_store.py to read_store.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/pubmlst_getter.py to pubmlst_getter.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/sequence_variant.py to sequence_variant.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/report.py to report.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/histogram.py to histogram.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/summary_sample.py to summary_sample.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/mic_plotter.py to mic_plotter.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/faidx.py to faidx.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/common.py to common.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/cdhit.py to cdhit.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/ref_genes_getter.py to ref_genes_getter.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/mapping.py to mapping.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/aln_to_metadata.py to aln_to_metadata.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/cluster.py to cluster.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/ref_preparer.py to ref_preparer.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/clusters.py to clusters.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/versions.py to versions.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/sequence_metadata.py to sequence_metadata.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__init__.py to __init__.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/reference_data.py to reference_data.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/assembly_variants.py to assembly_variants.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/assembly.py to assembly.cpython-39.pyc running install_egg_info running egg_info creating ariba.egg-info writing ariba.egg-info/PKG-INFO writing dependency_links to ariba.egg-info/dependency_links.txt writing requirements to ariba.egg-info/requires.txt writing top-level names to ariba.egg-info/top_level.txt writing manifest file 'ariba.egg-info/SOURCES.txt' reading manifest file 'ariba.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*.h' under directory 'third_party' writing manifest file 'ariba.egg-info/SOURCES.txt' Copying ariba.egg-info to /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba-2.14.6.egg-info Skipping SOURCES.txt running install_scripts creating /build/ariba-2.14.6+ds/debian/ariba/usr/bin copying build/scripts-3.9/ariba -> /build/ariba-2.14.6+ds/debian/ariba/usr/bin changing mode of /build/ariba-2.14.6+ds/debian/ariba/usr/bin/ariba to 755 dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild debian/rules override_dh_installman make[1]: Entering directory '/build/ariba-2.14.6+ds' mkdir -p /build/ariba-2.14.6+ds/debian/man asciidoctor -a docdate='' -b manpage -o /build/ariba-2.14.6+ds/debian/man/ariba.1 /build/ariba-2.14.6+ds/debian/ariba.1.adoc dh_installman -- make[1]: Leaving directory '/build/ariba-2.14.6+ds' dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/ariba/usr/lib/python3/dist-packages/vcfcall_ariba.cpython-39-x86_64-linux-gnu.so was not linked against libpthread.so.0 (it uses none of the library's symbols) dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: package ariba: substitution variable ${python3:Versions} unused, but is defined dpkg-gencontrol: warning: package ariba: substitution variable ${python3:Versions} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'ariba-dbgsym' in '../ariba-dbgsym_2.14.6+ds-1_amd64.deb'. dpkg-deb: building package 'ariba' in '../ariba_2.14.6+ds-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../ariba_2.14.6+ds-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/22017 and its subdirectories I: Current time: Wed Feb 7 19:43:07 -12 2024 I: pbuilder-time-stamp: 1707378187 Fri Jan 6 01:20:06 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Fri Jan 6 01:20:06 UTC 2023 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Fri Jan 6 01:36:42 UTC 2023 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Fri Jan 6 01:36:42 UTC 2023 I: ariba_2.14.6+ds-1_amd64.changes: Format: 1.8 Date: Sun, 13 Sep 2020 18:34:46 +0200 Source: ariba Binary: ariba ariba-dbgsym Architecture: amd64 Version: 2.14.6+ds-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Sascha Steinbiss Description: ariba - Antibiotic Resistance Identification By Assembly Changes: ariba (2.14.6+ds-1) unstable; urgency=medium . * New upstream release. Checksums-Sha1: 687c119da07532f43c34218749eac08b446ff9f8 399592 ariba-dbgsym_2.14.6+ds-1_amd64.deb 21fa9ed270a37da97b65db5442b30a1849b2257d 9759 ariba_2.14.6+ds-1_amd64.buildinfo 736d731c5d6ea692f92e623f3dc869930bea7f82 1956512 ariba_2.14.6+ds-1_amd64.deb Checksums-Sha256: fd8db8ccafa4629a24ed7c6cf8a2aeadd45013c35d8c1f37f5a5653d9a03eb97 399592 ariba-dbgsym_2.14.6+ds-1_amd64.deb 27fa6a8078ee57b600b0118b21e9bece171285c6cc6e92cb4f6149af4fb1297a 9759 ariba_2.14.6+ds-1_amd64.buildinfo c2deea69ed933d3ed26cd9c5dedd0dd25e35b3cf42fd85edf405e68149991555 1956512 ariba_2.14.6+ds-1_amd64.deb Files: b0f2cd75813f7fd0facc12b1d1c17890 399592 debug optional ariba-dbgsym_2.14.6+ds-1_amd64.deb 6ed6a67f8f2cef4a7e7c84ddc5ccf84f 9759 science optional ariba_2.14.6+ds-1_amd64.buildinfo f99085e566c6e842e6ad1afe1d7be4b9 1956512 science optional ariba_2.14.6+ds-1_amd64.deb Fri Jan 6 01:36:45 UTC 2023 I: diffoscope 228 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.u4MSBO5l/ariba_2.14.6+ds-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.u4MSBO5l/ariba_2.14.6+ds-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.u4MSBO5l/ariba_2.14.6+ds-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.u4MSBO5l/b1/ariba_2.14.6+ds-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.u4MSBO5l/b2/ariba_2.14.6+ds-1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 2.620s) 2.620s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.220s) 0.219s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.001s) 0.001s 1 call specialize Fri Jan 6 01:36:50 UTC 2023 I: diffoscope 228 found no differences in the changes files, and a .buildinfo file also exists. Fri Jan 6 01:36:50 UTC 2023 I: ariba from bullseye built successfully and reproducibly on amd64. Fri Jan 6 01:36:53 UTC 2023 I: Submitting .buildinfo files to external archives: Fri Jan 6 01:36:53 UTC 2023 I: Submitting 12K b1/ariba_2.14.6+ds-1_amd64.buildinfo.asc Fri Jan 6 01:36:54 UTC 2023 I: Submitting 12K b2/ariba_2.14.6+ds-1_amd64.buildinfo.asc Fri Jan 6 01:36:55 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Jan 6 01:36:55 UTC 2023 I: Done submitting .buildinfo files. Fri Jan 6 01:36:55 UTC 2023 I: Removing signed ariba_2.14.6+ds-1_amd64.buildinfo.asc files: removed './b1/ariba_2.14.6+ds-1_amd64.buildinfo.asc' removed './b2/ariba_2.14.6+ds-1_amd64.buildinfo.asc'