I: pbuilder: network access will be disabled during build I: Current time: Fri May 17 09:05:41 +14 2024 I: pbuilder-time-stamp: 1715886341 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [unicycler_0.5.0+dfsg-1.dsc] I: copying [./unicycler_0.5.0+dfsg.orig.tar.xz] I: copying [./unicycler_0.5.0+dfsg-1.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Dec 6 15:30:28 2022 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./unicycler_0.5.0+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting unicycler in unicycler-0.5.0+dfsg dpkg-source: info: unpacking unicycler_0.5.0+dfsg.orig.tar.xz dpkg-source: info: unpacking unicycler_0.5.0+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying spades.patch dpkg-source: info: applying install_wo_extra_steps.patch dpkg-source: info: applying append_flags I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1967276/tmp/hooks/D01_modify_environment starting debug: Running on ionos1-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 16 19:06 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/1967276/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1967276/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=ab49d4c08ceb4aad83817416c02df04c LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=1967276 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.hcrlSHmG/pbuilderrc_Thqz --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.hcrlSHmG/b2 --logfile b2/build.log unicycler_0.5.0+dfsg-1.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 15 07:43 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1967276/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-all, python3-setuptools, default-jdk, bcftools, bowtie2, miniasm, ncbi-blast+, pilon, racon, samtools, spades (>= 3.14), libseqan2-dev, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19701 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-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on default-jdk; however: Package default-jdk is not installed. pbuilder-satisfydepends-dummy depends on bcftools; however: Package bcftools is not installed. pbuilder-satisfydepends-dummy depends on bowtie2; however: Package bowtie2 is not installed. pbuilder-satisfydepends-dummy depends on miniasm; however: Package miniasm is not installed. pbuilder-satisfydepends-dummy depends on ncbi-blast+; however: Package ncbi-blast+ is not installed. pbuilder-satisfydepends-dummy depends on pilon; however: Package pilon is not installed. pbuilder-satisfydepends-dummy depends on racon; however: Package racon is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on spades (>= 3.14); however: Package spades is not installed. pbuilder-satisfydepends-dummy depends on libseqan2-dev; however: Package libseqan2-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev 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: adwaita-icon-theme{a} at-spi2-common{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bamtools{a} bcftools{a} blt{a} bowtie2{a} bsdextrautils{a} bwa{a} ca-certificates{a} ca-certificates-java{a} debhelper{a} default-jdk{a} default-jdk-headless{a} default-jre{a} default-jre-headless{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-lyx{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} gtk-update-icon-cache{a} hicolor-icon-theme{a} intltool-debian{a} java-common{a} java-wrappers{a} libapache-pom-java{a} libarchive-zip-perl{a} libasound2-data{a} libasound2t64{a} libatk1.0-0t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libbamtools2.5.2{a} libblas3{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcom-err2{a} libcommons-compress-java{a} libcommons-jexl2-java{a} libcommons-lang-java{a} libcommons-logging-java{a} libcommons-parent-java{a} libcups2t64{a} libcurl3t64-gnutls{a} libdatrie1{a} libdbus-1-3{a} libdebhelper-perl{a} libdeflate0{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libedit2{a} libedlib1{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgdk-pixbuf-2.0-0{a} libgdk-pixbuf2.0-common{a} libgfortran5{a} libgif7{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0t64{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgtk2.0-0t64{a} libgtk2.0-common{a} libharfbuzz0b{a} libhts3t64{a} libhtscodecs2{a} libhtsjdk-java{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjsoncpp25{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} libllvm17t64{a} liblmdb0{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto7t64{a} libmbedtls14t64{a} libmbedx509-1t64{a} libmjson-java{a} libncbi-ngs3{a} libncbi-vdb3{a} libncurses6{a} libnghttp2-14{a} libngs-java{a} libngs-jni{a} libnlopt0{a} libnspr4{a} libnss3{a} libopenjp2-7{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpciaccess0{a} libpcsclite1{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libqhull-r8.0{a} libraqm0{a} libreadline8t64{a} librhino-java{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libseqan2-dev{a} libsharpyuv0{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libspoa7.0.0{a} libssh2-1t64{a} libssw0{a} libsub-override-perl{a} libtcl8.6{a} libthai-data{a} libthai0{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libvulkan1{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxau6{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-render0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcomposite1{a} libxcursor1{a} libxdamage1{a} libxdmcp6{a} libxext6{a} libxfixes3{a} libxft2{a} libxi6{a} libxinerama1{a} libxml2{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxslt1.1{a} libxss1{a} libxtst6{a} libxxf86vm1{a} libyaml-0-2{a} libz3-4{a} m4{a} man-db{a} media-types{a} miniasm{a} ncbi-blast+{a} ncbi-data{a} ncbi-vdb-data{a} netbase{a} openjdk-17-jdk{a} openjdk-17-jdk-headless{a} openjdk-17-jre{a} openjdk-17-jre-headless{a} openssl{a} pilon{a} po-debconf{a} procps{a} python-matplotlib-data{a} python3{a} python3-all{a} python3-appdirs{a} python3-argcomplete{a} python3-argh{a} python3-attr{a} python3-biopython{a} python3-brotli{a} python3-cairo{a} python3-chardet{a} python3-contourpy{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-distutils{a} python3-fonttools{a} python3-freetype{a} python3-fs{a} python3-gffutils{a} python3-importlib-metadata{a} python3-joblib{a} python3-kiwisolver{a} python3-lib2to3{a} python3-lxml{a} python3-lz4{a} python3-matplotlib{a} python3-minimal{a} python3-more-itertools{a} python3-mpmath{a} python3-numpy{a} python3-packaging{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-pyfaidx{a} python3-pyparsing{a} python3-reportlab{a} python3-rlpycairo{a} python3-scipy{a} python3-setuptools{a} python3-simplejson{a} python3-six{a} python3-sympy{a} python3-tk{a} python3-tz{a} python3-ufolib2{a} python3-yaml{a} python3-zipp{a} python3.11{a} python3.11-minimal{a} python3.12{a} python3.12-minimal{a} racon{a} readline-common{a} samtools{a} scala-library{a} sensible-utils{a} sgml-base{a} shared-mime-info{a} spades{a} tk8.6-blt2.5{a} tzdata{a} unicode-data{a} unzip{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf curl dbus fonts-dejavu-extra isympy-common javascript-common krb5-locales libarchive-cpio-perl libatk-wrapper-java-jni libgail-common libgdk-pixbuf2.0-bin libglib2.0-data libgpm2 libgtk2.0-bin libldap-common libltdl-dev libmail-sendmail-perl librsvg2-common libsasl2-modules libxt-dev lynx mesa-vulkan-drivers minimap psmisc publicsuffix python-biopython-doc python3-bs4 python3-cssselect python3-html5lib python3-olefile python3-psutil python3-pybedtools python3-pytest rampler wget xdg-user-dirs 0 packages upgraded, 295 newly installed, 0 to remove and 0 not upgraded. Need to get 344 MB of archives. After unpacking 1207 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.3-1 [809 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.3-1 [2139 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-4 [64.6 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-4 [880 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.2.1-3 [1360 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20240203 [158 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.1-1 [94.1 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-3 [307 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.80.2-1 [1485 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 shared-mime-info amd64 2.4-4 [759 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [113 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.4.0-0.1 [311 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.10+dfsg-3+b3 [138 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 gtk-update-icon-cache amd64 3.24.41-4 [46.6 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 hicolor-icon-theme all 0.17-2 [11.4 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 adwaita-icon-theme all 46.0-1 [614 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 at-spi2-common all 2.52.0-1 [166 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libbamtools2.5.2 amd64 2.5.2+dfsg-5 [159 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libjsoncpp25 amd64 1.9.5-6+b2 [81.9 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 bamtools amd64 2.5.2+dfsg-5 [206 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1~rc2-1 [22.6 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 62 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.7.1-5 [433 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.19+ds-1.1+b1 [448 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 python3-argcomplete all 3.3.0-1 [38.9 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 python3-argh all 0.31.2-1 [26.5 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.2.0-1 [59.9 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 1.0.0-6 [6696 B] Get: 78 http://deb.debian.org/debian unstable/main amd64 python3-importlib-metadata all 4.12.0-1 [24.9 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 python3-pyfaidx all 0.8.1.1-2 [29.0 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 python3-simplejson amd64 3.19.2-1+b1 [69.4 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.1.0-1 [836 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:1.26.4+ds-8 [5466 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1 [1034 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libfontenc1 amd64 1:1.1.8-1 [23.0 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 xfonts-utils amd64 1:7.7+6 [93.0 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 96 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-1 [144 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b1 [54.2 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1+b1 [17.0 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libtk8.6 amd64 8.6.14-1 [784 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7 [586 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 blt amd64 2.5.3+dfsg-7 [6024 B] Get: 111 http://deb.debian.org/debian unstable/main amd64 python3-tk amd64 3.12.3-1 [109 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 python3-pil.imagetk amd64 10.3.0-2 [79.5 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 2.18.0-1+b1 [35.3 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.0-2+b3 [190 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libraqm0 amd64 0.10.1-1+b1 [14.2 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [110 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.4.0-0.1 [123 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 python3-pil amd64 10.3.0-2 [564 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-1 [114 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-1 [105 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.0-3+b1 [531 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 python3-cairo amd64 1.26.0-1 [142 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 python3-freetype all 2.4.0-1 [80.3 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 130 http://deb.debian.org/debian unstable/main amd64 python3-reportlab all 4.2.0-2 [1149 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 python3-biopython amd64 1.83+dfsg1-2 [1634 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 python3-gffutils all 0.13-1 [1041 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 fonts-lyx all 2.4.0~RC4-1 [189 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 python-matplotlib-data all 3.6.3-2 [2744 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 python3-six all 1.16.0-6 [16.3 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 python3-dateutil all 2.9.0-2 [79.4 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 python3-contourpy amd64 1.0.7-3 [285 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 python3-cycler all 0.12.1-1 [9496 B] Get: 144 http://deb.debian.org/debian unstable/main amd64 python3-brotli amd64 1.1.0-2+b3 [312 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b1 [29.1 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 python3-scipy amd64 1.11.4-9 [19.5 MB] Get: 148 http://deb.debian.org/debian unstable/main amd64 python3-attr all 23.2.0-2 [65.5 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 python3-ufolib2 all 0.16.0+dfsg1-1 [32.9 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 python3-sympy all 1.12-7 [3869 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 python3-tz all 2024.1-2 [30.9 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 python3-appdirs all 1.4.4-4 [12.5 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 python3-fs all 2.4.16-4 [95.4 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 libxslt1.1 amd64 1.1.35-1+b1 [232 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 python3-lxml amd64 5.2.1-1 [1995 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 python3-lz4 amd64 4.0.2+dfsg-1+b3 [25.5 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 python3-distutils all 3.12.3-1 [131 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.3-1 [1951 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.3-1 [659 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.11.8-1 [1056 B] Get: 163 http://deb.debian.org/debian unstable/main amd64 unicode-data all 15.1.0-1 [8547 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 python3-fonttools amd64 4.46.0-1 [1623 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 python3-kiwisolver amd64 1.4.5-1 [80.7 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.0-1 [45.5 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 libqhull-r8.0 amd64 2020.2-6+b1 [245 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 python3-matplotlib amd64 3.6.3-2 [8167 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 bcftools amd64 1.20-1 [760 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 bowtie2 amd64 2.5.3-1 [1438 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 bwa amd64 0.7.17-7+b3 [212 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 179 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 180 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 182 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 183 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 185 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 java-common all 0.75 [6640 B] Get: 187 http://deb.debian.org/debian unstable/main amd64 libnspr4 amd64 2:4.35-1.1+b1 [109 kB] Get: 188 http://deb.debian.org/debian unstable/main amd64 libnss3 amd64 2:3.100-1 [1406 kB] Get: 189 http://deb.debian.org/debian unstable/main amd64 libpcsclite1 amd64 2.2.1-1 [54.8 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 openjdk-17-jre-headless amd64 17.0.11+9-1 [43.8 MB] Get: 191 http://deb.debian.org/debian unstable/main amd64 default-jre-headless amd64 2:1.17-75 [3068 B] Get: 192 http://deb.debian.org/debian unstable/main amd64 libgtk2.0-common all 2.24.33-4 [2661 kB] Get: 193 http://deb.debian.org/debian unstable/main amd64 libatk1.0-0t64 amd64 2.52.0-1 [50.8 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 libavahi-common-data amd64 0.8-13+b2 [112 kB] Get: 195 http://deb.debian.org/debian unstable/main amd64 libavahi-common3 amd64 0.8-13+b2 [43.3 kB] Get: 196 http://deb.debian.org/debian unstable/main amd64 libdbus-1-3 amd64 1.14.10-4+b1 [203 kB] Get: 197 http://deb.debian.org/debian unstable/main amd64 libavahi-client3 amd64 0.8-13+b2 [47.0 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 libcups2t64 amd64 2.4.7-1.2+b1 [247 kB] Get: 199 http://deb.debian.org/debian unstable/main amd64 fontconfig amd64 2.15.0-1.1 [463 kB] Get: 200 http://deb.debian.org/debian unstable/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 201 http://deb.debian.org/debian unstable/main amd64 libdatrie1 amd64 0.2.13-3 [37.7 kB] Get: 202 http://deb.debian.org/debian unstable/main amd64 libthai0 amd64 0.1.29-2 [49.1 kB] Get: 203 http://deb.debian.org/debian unstable/main amd64 libpango-1.0-0 amd64 1.52.2+ds-1 [218 kB] Get: 204 http://deb.debian.org/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.52.2+ds-1 [48.1 kB] Get: 205 http://deb.debian.org/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.52.2+ds-1 [35.0 kB] Get: 206 http://deb.debian.org/debian unstable/main amd64 libxcomposite1 amd64 1:0.4.5-1+b1 [14.9 kB] Get: 207 http://deb.debian.org/debian unstable/main amd64 libxfixes3 amd64 1:6.0.0-2+b1 [20.3 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 libxcursor1 amd64 1:1.2.1-1+b1 [36.2 kB] Get: 209 http://deb.debian.org/debian unstable/main amd64 libxdamage1 amd64 1:1.1.6-1+b1 [15.5 kB] Get: 210 http://deb.debian.org/debian unstable/main amd64 libxi6 amd64 2:1.8.1-1 [79.0 kB] Get: 211 http://deb.debian.org/debian unstable/main amd64 libxinerama1 amd64 2:1.1.4-3+b1 [16.0 kB] Get: 212 http://deb.debian.org/debian unstable/main amd64 libxrandr2 amd64 2:1.5.4-1 [36.1 kB] Get: 213 http://deb.debian.org/debian unstable/main amd64 libgtk2.0-0t64 amd64 2.24.33-4 [1816 kB] Get: 214 http://deb.debian.org/debian unstable/main amd64 libglvnd0 amd64 1.7.0-1+b1 [56.3 kB] Get: 215 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.120-2 [7688 B] Get: 216 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.120-2 [38.1 kB] Get: 217 http://deb.debian.org/debian unstable/main amd64 libglapi-mesa amd64 24.0.7-1 [36.4 kB] Get: 218 http://deb.debian.org/debian unstable/main amd64 libx11-xcb1 amd64 2:1.8.7-1+b1 [232 kB] Get: 219 http://deb.debian.org/debian unstable/main amd64 libxcb-dri2-0 amd64 1.17.0-1 [106 kB] Get: 220 http://deb.debian.org/debian unstable/main amd64 libxcb-dri3-0 amd64 1.17.0-1 [106 kB] Get: 221 http://deb.debian.org/debian unstable/main amd64 libxcb-glx0 amd64 1.17.0-1 [122 kB] Get: 222 http://deb.debian.org/debian unstable/main amd64 libxcb-present0 amd64 1.17.0-1 [105 kB] Get: 223 http://deb.debian.org/debian unstable/main amd64 libxcb-randr0 amd64 1.17.0-1 [116 kB] Get: 224 http://deb.debian.org/debian unstable/main amd64 libxcb-sync1 amd64 1.17.0-1 [108 kB] Get: 225 http://deb.debian.org/debian unstable/main amd64 libxcb-xfixes0 amd64 1.17.0-1 [109 kB] Get: 226 http://deb.debian.org/debian unstable/main amd64 libxshmfence1 amd64 1.3-1+b1 [8852 B] Get: 227 http://deb.debian.org/debian unstable/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get: 228 http://deb.debian.org/debian unstable/main amd64 libvulkan1 amd64 1.3.280.0-1 [123 kB] Get: 229 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.120-2 [21.4 kB] Get: 230 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b1 [51.9 kB] Get: 231 http://deb.debian.org/debian unstable/main amd64 libdrm-intel1 amd64 2.4.120-2 [62.7 kB] Get: 232 http://deb.debian.org/debian unstable/main amd64 libdrm-nouveau2 amd64 2.4.120-2 [19.3 kB] Get: 233 http://deb.debian.org/debian unstable/main amd64 libdrm-radeon1 amd64 2.4.120-2 [22.2 kB] Get: 234 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20230828-1+b1 [93.5 kB] Get: 235 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get: 236 http://deb.debian.org/debian unstable/main amd64 libllvm17t64 amd64 1:17.0.6-12 [23.7 MB] Get: 237 http://deb.debian.org/debian unstable/main amd64 libsensors-config all 1:3.6.0-9 [14.6 kB] Get: 238 http://deb.debian.org/debian unstable/main amd64 libsensors5 amd64 1:3.6.0-9 [34.6 kB] Get: 239 http://deb.debian.org/debian unstable/main amd64 libgl1-mesa-dri amd64 24.0.7-1 [8277 kB] Get: 240 http://deb.debian.org/debian unstable/main amd64 libglx-mesa0 amd64 24.0.7-1 [151 kB] Get: 241 http://deb.debian.org/debian unstable/main amd64 libglx0 amd64 1.7.0-1+b1 [35.0 kB] Get: 242 http://deb.debian.org/debian unstable/main amd64 libgl1 amd64 1.7.0-1+b1 [89.8 kB] Get: 243 http://deb.debian.org/debian unstable/main amd64 libasound2-data all 1.2.11-1 [20.9 kB] Get: 244 http://deb.debian.org/debian unstable/main amd64 libasound2t64 amd64 1.2.11-1+b1 [369 kB] Get: 245 http://deb.debian.org/debian unstable/main amd64 libgif7 amd64 5.2.2-1 [43.9 kB] Get: 246 http://deb.debian.org/debian unstable/main amd64 libxtst6 amd64 2:1.2.3-1.1+b1 [25.9 kB] Get: 247 http://deb.debian.org/debian unstable/main amd64 openjdk-17-jre amd64 17.0.11+9-1 [185 kB] Get: 248 http://deb.debian.org/debian unstable/main amd64 default-jre amd64 2:1.17-75 [1056 B] Get: 249 http://deb.debian.org/debian unstable/main amd64 openjdk-17-jdk-headless amd64 17.0.11+9-1 [71.4 MB] Get: 250 http://deb.debian.org/debian unstable/main amd64 default-jdk-headless amd64 2:1.17-75 [1108 B] Get: 251 http://deb.debian.org/debian unstable/main amd64 openjdk-17-jdk amd64 17.0.11+9-1 [10.4 kB] Get: 252 http://deb.debian.org/debian unstable/main amd64 default-jdk amd64 2:1.17-75 [1068 B] Get: 253 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 68.1.2-2 [468 kB] Get: 254 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20240422 [107 kB] Get: 255 http://deb.debian.org/debian unstable/main amd64 unzip amd64 6.0-28 [166 kB] Get: 256 http://deb.debian.org/debian unstable/main amd64 java-wrappers all 0.4 [8916 B] Get: 257 http://deb.debian.org/debian unstable/main amd64 libapache-pom-java all 29-2 [5276 B] Get: 258 http://deb.debian.org/debian unstable/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 259 http://deb.debian.org/debian unstable/main amd64 libcommons-compress-java all 1.25.0-1 [635 kB] Get: 260 http://deb.debian.org/debian unstable/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 261 http://deb.debian.org/debian unstable/main amd64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get: 262 http://deb.debian.org/debian unstable/main amd64 libcommons-lang-java all 2.6-10 [273 kB] Get: 263 http://deb.debian.org/debian unstable/main amd64 libedlib1 amd64 1.2.7-5 [17.7 kB] Get: 264 http://deb.debian.org/debian unstable/main amd64 libmjson-java all 1.4.0-3 [60.4 kB] Get: 265 http://deb.debian.org/debian unstable/main amd64 libmbedcrypto7t64 amd64 2.28.8-1 [284 kB] Get: 266 http://deb.debian.org/debian unstable/main amd64 libmbedx509-1t64 amd64 2.28.8-1 [131 kB] Get: 267 http://deb.debian.org/debian unstable/main amd64 libmbedtls14t64 amd64 2.28.8-1 [167 kB] Get: 268 http://deb.debian.org/debian unstable/main amd64 ncbi-vdb-data all 3.0.2+dfsg-2 [73.3 kB] Get: 269 http://deb.debian.org/debian unstable/main amd64 libncbi-vdb3 amd64 3.0.2+dfsg-2+b1 [1049 kB] Get: 270 http://deb.debian.org/debian unstable/main amd64 libncbi-ngs3 amd64 3.0.3+dfsg-7 [155 kB] Get: 271 http://deb.debian.org/debian unstable/main amd64 libngs-jni amd64 3.0.3+dfsg-7 [23.6 kB] Get: 272 http://deb.debian.org/debian unstable/main amd64 libngs-java amd64 3.0.3+dfsg-7 [110 kB] Get: 273 http://deb.debian.org/debian unstable/main amd64 librhino-java all 1.7.14-2.1 [1357 kB] Get: 274 http://deb.debian.org/debian unstable/main amd64 libsnappy1v5 amd64 1.2.0-2 [29.0 kB] Get: 275 http://deb.debian.org/debian unstable/main amd64 libsnappy-jni amd64 1.1.10.5-2 [6396 B] Get: 276 http://deb.debian.org/debian unstable/main amd64 libsnappy-java all 1.1.10.5-2 [87.5 kB] Get: 277 http://deb.debian.org/debian unstable/main amd64 libhtsjdk-java all 4.1.0+dfsg-2 [1833 kB] Get: 278 http://deb.debian.org/debian unstable/main amd64 liblmdb0 amd64 0.9.31-1+b1 [44.8 kB] Get: 279 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5-2 [104 kB] Get: 280 http://deb.debian.org/debian unstable/main amd64 libnlopt0 amd64 2.7.1-5+b3 [174 kB] Get: 281 http://deb.debian.org/debian unstable/main amd64 libseqan2-dev all 2.4.0+dfsg-16 [1216 kB] Get: 282 http://deb.debian.org/debian unstable/main amd64 libspoa7.0.0 amd64 4.1.4-1 [70.3 kB] Get: 283 http://deb.debian.org/debian unstable/main amd64 libssw0 amd64 1.1-14+b1 [21.2 kB] Get: 284 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-1+b1 [52.6 kB] Get: 285 http://deb.debian.org/debian unstable/main amd64 miniasm amd64 0.3+dfsg-4 [29.9 kB] Get: 286 http://deb.debian.org/debian unstable/main amd64 ncbi-data all 6.1.20170106+dfsg2-2 [3544 kB] Get: 287 http://deb.debian.org/debian unstable/main amd64 ncbi-blast+ amd64 2.12.0+ds-4+b1 [12.5 MB] Get: 288 http://deb.debian.org/debian unstable/main amd64 scala-library all 2.11.12-5 [9588 kB] Get: 289 http://deb.debian.org/debian unstable/main amd64 pilon all 1.24-3 [497 kB] Get: 290 http://deb.debian.org/debian unstable/main amd64 python3-joblib all 1.3.2-2 [218 kB] Get: 291 http://deb.debian.org/debian unstable/main amd64 python3-yaml amd64 6.0.1-2 [177 kB] Get: 292 http://deb.debian.org/debian unstable/main amd64 racon amd64 1.5.0-3 [3115 kB] Get: 293 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.19.2-1+b1 [645 kB] Get: 294 http://deb.debian.org/debian unstable/main amd64 spades amd64 3.15.5+dfsg-7 [9020 kB] Get: 295 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Fetched 344 MB in 16s (21.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19701 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.9-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_amd64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:amd64 (3.11.9-1) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20017 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_amd64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../5-libreadline8t64_8.2-4_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21009 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_amd64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package libpython3.12-minimal:amd64. Preparing to unpack .../001-libpython3.12-minimal_3.12.3-1_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../002-python3.12-minimal_3.12.3-1_amd64.deb ... Unpacking python3.12-minimal (3.12.3-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../003-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../004-libproc2-0_2%3a4.0.4-4_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-4) ... Selecting previously unselected package procps. Preparing to unpack .../005-procps_2%3a4.0.4-4_amd64.deb ... Unpacking procps (2:4.0.4-4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../006-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package openssl. 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Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../025-libdeflate0_1.20-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.20-1) ... Selecting previously unselected package libjbig0:amd64. Preparing to unpack .../026-libjbig0_2.1-6.1+b1_amd64.deb ... Unpacking libjbig0:amd64 (2.1-6.1+b1) ... Selecting previously unselected package liblerc4:amd64. Preparing to unpack .../027-liblerc4_4.0.0+ds-4+b1_amd64.deb ... Unpacking liblerc4:amd64 (4.0.0+ds-4+b1) ... Selecting previously unselected package libsharpyuv0:amd64. Preparing to unpack .../028-libsharpyuv0_1.4.0-0.1_amd64.deb ... Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ... Selecting previously unselected package libwebp7:amd64. Preparing to unpack .../029-libwebp7_1.4.0-0.1_amd64.deb ... Unpacking libwebp7:amd64 (1.4.0-0.1) ... Selecting previously unselected package libtiff6:amd64. Preparing to unpack .../030-libtiff6_4.5.1+git230720-4_amd64.deb ... Unpacking libtiff6:amd64 (4.5.1+git230720-4) ... Selecting previously unselected package libgdk-pixbuf-2.0-0:amd64. Preparing to unpack .../031-libgdk-pixbuf-2.0-0_2.42.10+dfsg-3+b3_amd64.deb ... Unpacking libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-3+b3) ... Selecting previously unselected package gtk-update-icon-cache. Preparing to unpack .../032-gtk-update-icon-cache_3.24.41-4_amd64.deb ... Unpacking gtk-update-icon-cache (3.24.41-4) ... Selecting previously unselected package hicolor-icon-theme. Preparing to unpack .../033-hicolor-icon-theme_0.17-2_all.deb ... Unpacking hicolor-icon-theme (0.17-2) ... Selecting previously unselected package adwaita-icon-theme. Preparing to unpack .../034-adwaita-icon-theme_46.0-1_all.deb ... Unpacking adwaita-icon-theme (46.0-1) ... Selecting previously unselected package at-spi2-common. Preparing to unpack .../035-at-spi2-common_2.52.0-1_all.deb ... Unpacking at-spi2-common (2.52.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../036-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../037-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../038-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../039-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../040-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libbamtools2.5.2:amd64. Preparing to unpack .../041-libbamtools2.5.2_2.5.2+dfsg-5_amd64.deb ... Unpacking libbamtools2.5.2:amd64 (2.5.2+dfsg-5) ... Selecting previously unselected package libjsoncpp25:amd64. Preparing to unpack .../042-libjsoncpp25_1.9.5-6+b2_amd64.deb ... Unpacking libjsoncpp25:amd64 (1.9.5-6+b2) ... 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Selecting previously unselected package spades. Preparing to unpack .../281-spades_3.15.5+dfsg-7_amd64.deb ... Unpacking spades (3.15.5+dfsg-7) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../282-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Setting up libhtscodecs2:amd64 (1.6.0-1+b1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:amd64 (1.5.7-2) ... Setting up liblmdb0:amd64 (0.9.31-1+b1) ... Setting up libgraphite2-3:amd64 (1.3.14-2) ... Setting up liblcms2-2:amd64 (2.14-2+b1) ... Setting up ncbi-data (6.1.20170106+dfsg2-2) ... Setting up libpixman-1-0:amd64 (0.42.2-1+b1) ... Setting up libsharpyuv0:amd64 (1.4.0-0.1) ... Setting up libpciaccess0:amd64 (0.17-3+b1) ... Setting up libxau6:amd64 (1:1.0.9-1+b1) ... Setting up libkeyutils1:amd64 (1.6.3-3) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up liblerc4:amd64 (4.0.0+ds-4+b1) ... Setting up bsdextrautils (2.40.1-1) ... Setting up hicolor-icon-theme (0.17-2) ... Setting up libmbedcrypto7t64:amd64 (2.28.8-1) ... Setting up java-common (0.75) ... Setting up libdatrie1:amd64 (0.2.13-3) ... Setting up miniasm (0.3+dfsg-4) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:amd64 (0.2.5-1+b1) ... Setting up bwa (0.7.17-7+b3) ... Setting up libglvnd0:amd64 (1.7.0-1+b1) ... Setting up libmjson-java (1.4.0-3) ... Setting up fonts-lyx (2.4.0~RC4-1) ... Setting up unzip (6.0-28) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:amd64 (1.1.0-2+b3) ... Setting up libgdk-pixbuf2.0-common (2.42.10+dfsg-3) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up libpython3.12-minimal:amd64 (3.12.3-1) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libsensors-config (1:3.6.0-9) ... Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.61.0-1+b1) ... Setting up libdeflate0:amd64 (1.20-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up scala-library (2.11.12-5) ... Setting up libqhull-r8.0:amd64 (2020.2-6+b1) ... Setting up libnlopt0:amd64 (2.7.1-5+b3) ... Setting up libcom-err2:amd64 (1.47.1~rc2-1) ... Setting up file (1:5.45-3) ... Setting up libjbig0:amd64 (2.1-6.1+b1) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up libsnappy1v5:amd64 (1.2.0-2) ... Setting up libkrb5support0:amd64 (1.20.1-6+b1) ... Setting up libseqan2-dev (2.4.0+dfsg-16) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Thu May 16 19:08:52 UTC 2024. Universal Time is now: Thu May 16 19:08:52 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (15.1.0-1) ... Setting up libasound2-data (1.2.11-1) ... Setting up libfontenc1:amd64 (1:1.1.8-1) ... Setting up librhino-java (1.7.14-2.1) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:amd64 (4.8.12-3.1+b2) ... Setting up libglib2.0-0t64:amd64 (2.80.2-1) ... No schema files found: doing nothing. Setting up libblas3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libasound2t64:amd64 (1.2.11-1+b1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libnspr4:amd64 (2:4.35-1.1+b1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libapache-pom-java (29-2) ... Setting up libavahi-common-data:amd64 (0.8-13+b2) ... Setting up libncurses6:amd64 (6.5-2) ... Setting up libdbus-1-3:amd64 (1.14.10-4+b1) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:amd64 (1.0.13-3+b1) ... Setting up libimagequant0:amd64 (2.18.0-1+b1) ... Setting up libproc2-0:amd64 (2:4.0.4-4) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libspoa7.0.0:amd64 (4.1.4-1) ... Setting up libpng16-16t64:amd64 (1.6.43-5) ... Setting up libtcl8.6:amd64 (8.6.14+dfsg-1) ... Setting up autopoint (0.21-14) ... Setting up libjsoncpp25:amd64 (1.9.5-6+b2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libpcsclite1:amd64 (2.2.1-1) ... Setting up libsensors5:amd64 (1:3.6.0-9) ... Setting up libk5crypto3:amd64 (1.20.1-6+b1) ... Setting up libbamtools2.5.2:amd64 (2.5.2+dfsg-5) ... Setting up libglapi-mesa:amd64 (24.0.7-1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Setting up libgfortran5:amd64 (14.1.0-1) ... Setting up libvulkan1:amd64 (1.3.280.0-1) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:amd64 (1.4.0-0.1) ... Setting up libgif7:amd64 (5.2.2-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Setting up libedlib1:amd64 (1.2.7-5) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libxshmfence1:amd64 (1.3-1+b1) ... Setting up at-spi2-common (2.52.0-1) ... Setting up libtiff6:amd64 (4.5.1+git230720-4) ... Setting up bamtools (2.5.2+dfsg-5) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up procps (2:4.0.4-4) ... Setting up libopenjp2-7:amd64 (2.5.0-2+b3) ... Setting up libsub-override-perl (0.10-1) ... Setting up ncbi-vdb-data (3.0.2+dfsg-2) ... Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up libgtk2.0-common (2.24.33-4) ... Setting up libkrb5-3:amd64 (1.20.1-6+b1) ... Setting up libssh2-1t64:amd64 (1.11.0-4.1+b2) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up python-matplotlib-data (3.6.3-2) ... Setting up openssl (3.2.1-3) ... Setting up libwebpmux3:amd64 (1.4.0-0.1) ... Setting up libbsd0:amd64 (0.12.2-1) ... Setting up libdrm-common (2.4.120-2) ... Setting up libsnappy-jni (1.1.10.5-2) ... Setting up libssw0:amd64 (1.1-14+b1) ... Setting up readline-common (8.2-4) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up python3.12-minimal (3.12.3-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3+b1) ... Setting up liblapack3:amd64 (3.12.0-3) ... 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 (1.17.0-1) ... Setting up gettext (0.21-14+b1) ... Setting up libmbedx509-1t64:amd64 (2.28.8-1) ... Setting up libxcb-xfixes0:amd64 (1.17.0-1) ... Setting up java-wrappers (0.4) ... Setting up libatk1.0-0t64:amd64 (2.52.0-1) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:amd64 (1.17.0-1) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libxcb-glx0:amd64 (1.17.0-1) ... Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... Setting up libedit2:amd64 (3.1-20230828-1+b1) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:amd64 (0.8-13+b2) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libnss3:amd64 (2:3.100-1) ... Setting up libxcb-shm0:amd64 (1.17.0-1) ... Setting up libcommons-lang-java (2.6-10) ... Setting up libldap-2.5-0:amd64 (2.5.17+dfsg-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libxcb-present0:amd64 (1.17.0-1) ... Setting up dh-autoreconf (20) ... Setting up libcommons-jexl2-java (2.1.1-6) ... Setting up libthai0:amd64 (0.1.29-2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libllvm17t64:amd64 (1:17.0.6-12) ... Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... Setting up libxcb-sync1:amd64 (1.17.0-1) ... Setting up shared-mime-info (2.4-4) ... Setting up racon (1.5.0-3) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up libxcb-dri2-0:amd64 (1.17.0-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libdrm2:amd64 (2.4.120-2) ... Setting up libmbedtls14t64:amd64 (2.28.8-1) ... Setting up groff-base (1.23.0-4) ... Setting up libxcb-randr0:amd64 (1.17.0-1) ... Setting up xml-core (0.19) ... Setting up libxslt1.1:amd64 (1.1.35-1+b1) ... Setting up libx11-6:amd64 (2:1.8.7-1+b1) ... Setting up libharfbuzz0b:amd64 (8.3.0-2+b1) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-3+b3) ... Setting up libsnappy-java (1.1.10.5-2) ... Setting up libfontconfig1:amd64 (2.15.0-1.1) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libxcomposite1:amd64 (1:0.4.5-1+b1) ... Setting up libavahi-client3:amd64 (0.8-13+b2) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1+b1) ... Setting up libdrm-amdgpu1:amd64 (2.4.120-2) ... Setting up libxcb-dri3-0:amd64 (1.17.0-1) ... Setting up gtk-update-icon-cache (3.24.41-4) ... Setting up libx11-xcb1:amd64 (2:1.8.7-1+b1) ... Setting up fontconfig (2.15.0-1.1) ... Regenerating fonts cache... done. Setting up libdrm-nouveau2:amd64 (2.4.120-2) ... Setting up libxdamage1:amd64 (1:1.1.6-1+b1) ... Setting up libpython3.12-stdlib:amd64 (3.12.3-1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b1) ... Setting up libcommons-compress-java (1.25.0-1) ... Setting up libdrm-radeon1:amd64 (2.4.120-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up python3.12 (3.12.3-1) ... Setting up libpango-1.0-0:amd64 (1.52.2+ds-1) ... Setting up libdrm-intel1:amd64 (2.4.120-2) ... Setting up libgl1-mesa-dri:amd64 (24.0.7-1) ... Setting up libncbi-vdb3:amd64 (3.0.2+dfsg-2+b1) ... Setting up libcurl3t64-gnutls:amd64 (8.7.1-5) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up xfonts-utils (1:7.7+6) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:amd64 (1.18.0-3+b1) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up adwaita-icon-theme (46.0-1) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up libxfixes3:amd64 (1:6.0.0-2+b1) ... Setting up libraqm0:amd64 (0.10.1-1+b1) ... Setting up libxinerama1:amd64 (2:1.1.4-3+b1) ... Setting up libxrandr2:amd64 (2:1.5.4-1) ... Setting up openjdk-17-jre-headless:amd64 (17.0.11+9-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libhts3t64:amd64 (1.19+ds-1.1+b1) ... Setting up libxss1:amd64 (1:1.2.3-1+b1) ... Setting up libpangoft2-1.0-0:amd64 (1.52.2+ds-1) ... Setting up libcups2t64:amd64 (2.4.7-1.2+b1) ... Setting up libpangocairo-1.0-0:amd64 (1.52.2+ds-1) ... Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up libncbi-ngs3:amd64 (3.0.3+dfsg-7) ... Setting up python3.11 (3.11.9-1) ... Setting up libngs-jni:amd64 (3.0.3+dfsg-7) ... Setting up libxft2:amd64 (2.3.6-1+b1) ... Setting up libglx-mesa0:amd64 (24.0.7-1) ... Setting up libxi6:amd64 (2:1.8.1-1) ... Setting up libglx0:amd64 (1.7.0-1+b1) ... Setting up libxtst6:amd64 (2:1.2.3-1.1+b1) ... Setting up libtk8.6:amd64 (8.6.14-1) ... Setting up libxcursor1:amd64 (1:1.2.1-1+b1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up python3-freetype (2.4.0-1) ... Setting up python3-tz (2024.1-2) ... Setting up samtools (1.19.2-1+b1) ... Setting up bowtie2 (2.5.3-1) ... Setting up ncbi-blast+ (2.12.0+ds-4+b1) ... Setting up python3-six (1.16.0-6) ... Setting up python3-simplejson (3.19.2-1+b1) ... Setting up python3-pil:amd64 (10.3.0-2) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (24.0-1) ... Setting up libgl1:amd64 (1.7.0-1+b1) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3-brotli (1.1.0-2+b3) ... Setting up python3-cycler (0.12.1-1) ... Setting up python3-kiwisolver (1.4.5-1) ... Setting up libgtk2.0-0t64:amd64 (2.24.33-4) ... Setting up python3-lxml:amd64 (5.2.1-1) ... Setting up python3-dateutil (2.9.0-2) ... Setting up libngs-java:amd64 (3.0.3+dfsg-7) ... Setting up python3-mpmath (1.3.0-1) ... Setting up python3-argcomplete (3.3.0-1) ... Setting up python3-lib2to3 (3.12.3-1) ... Setting up python3-appdirs (1.4.4-4) ... Setting up libhtsjdk-java (4.1.0+dfsg-2) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.3-1) ... python3.12: can't get files for byte-compilation Setting up python3-more-itertools (10.2.0-1) ... Setting up python3-sympy (1.12-7) ... Setting up python3-attr (23.2.0-2) ... Setting up python3-argh (0.31.2-1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... Setting up python3-cairo (1.26.0-1) ... Setting up python3-setuptools (68.1.2-2) ... Setting up python3-joblib (1.3.2-2) ... Setting up python3-lz4 (4.0.2+dfsg-1+b3) ... Setting up blt (2.5.3+dfsg-7) ... Setting up python3-all (3.11.8-1) ... Setting up python3-yaml (6.0.1-2) ... Setting up python3-tk:amd64 (3.12.3-1) ... Setting up python3-zipp (1.0.0-6) ... Setting up python3-fs (2.4.16-4) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-pil.imagetk:amd64 (10.3.0-2) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-numpy (1:1.26.4+ds-8) ... Setting up python3-reportlab (4.2.0-2) ... Setting up spades (3.15.5+dfsg-7) ... Setting up python3-contourpy (1.0.7-3) ... Setting up dh-python (6.20240422) ... Setting up python3-scipy (1.11.4-9) ... Setting up python3-importlib-metadata (4.12.0-1) ... Setting up python3-pyfaidx (0.8.1.1-2) ... Setting up python3-fonttools (4.46.0-1) ... Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... Setting up python3-matplotlib (3.6.3-2) ... Processing triggers for libc-bin (2.38-11) ... Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up openjdk-17-jdk-headless:amd64 (17.0.11+9-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up default-jre-headless (2:1.17-75) ... Setting up openjdk-17-jre:amd64 (17.0.11+9-1) ... Setting up default-jre (2:1.17-75) ... Setting up openjdk-17-jdk:amd64 (17.0.11+9-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode Setting up default-jdk-headless (2:1.17-75) ... Setting up pilon (1.24-3) ... Setting up default-jdk (2:1.17-75) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.83+dfsg1-2) ... Setting up python3-gffutils (0.13-1) ... Setting up bcftools (1.20-1) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20240118) ... 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 I: Building the package I: user script /srv/workspace/pbuilder/1967276/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/1967276/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/unicycler-0.5.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../unicycler_0.5.0+dfsg-1_source.changes dpkg-buildpackage: info: source package unicycler dpkg-buildpackage: info: source version 0.5.0+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/unicycler-0.5.0+dfsg' find . -name __pycache__ -type d | xargs rm -rf make distclean make[2]: Entering directory '/build/reproducible-path/unicycler-0.5.0+dfsg' Platform: Linux Compiler: g++ 13.2.0 rm -f unicycler/src/start_end_align.o unicycler/src/semi_global_align.o unicycler/src/semi_global_align_exhaustive.o unicycler/src/miniasm/paf.o unicycler/src/miniasm/hit.o unicycler/src/miniasm/sdict.o unicycler/src/miniasm/asg.o unicycler/src/miniasm/asm.o unicycler/src/miniasm/sys.o unicycler/src/miniasm/dotter.o unicycler/src/random_alignments.o unicycler/src/miniasm_assembly.o unicycler/src/path_align.o unicycler/src/scoredalignment.o unicycler/src/kmers.o unicycler/src/global_align.o unicycler/src/consensus_align.o unicycler/src/minimap_align.o unicycler/src/ref_seqs.o unicycler/src/string_functions.o unicycler/src/overlap_align.o unicycler/src/minimap/misc.o unicycler/src/minimap/bseq.o unicycler/src/minimap/kthread.o unicycler/src/minimap/map.o unicycler/src/minimap/sdust.o unicycler/src/minimap/sketch.o unicycler/src/minimap/index.o rm -f unicycler/cpp_functions.so make[2]: Leaving directory '/build/reproducible-path/unicycler-0.5.0+dfsg' make[1]: Leaving directory '/build/reproducible-path/unicycler-0.5.0+dfsg' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --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:311: python3.12 setup.py config /build/reproducible-path/unicycler-0.5.0+dfsg/unicycler/misc.py:641: SyntaxWarning: invalid escape sequence '\[' row_str = re.sub('\033\[4m', '', row_str) /build/reproducible-path/unicycler-0.5.0+dfsg/unicycler/misc.py:743: SyntaxWarning: invalid escape sequence '\ ' bold_red(" \ \___\n") + /build/reproducible-path/unicycler-0.5.0+dfsg/unicycler/misc.py:744: SyntaxWarning: invalid escape sequence '\ ' bold_red(" \ ___\\\n") + /build/reproducible-path/unicycler-0.5.0+dfsg/unicycler/misc.py:753: SyntaxWarning: invalid escape sequence '\ ' bold_yellow("| | | || '_ \ | | / __|| | | | / __|| | / _ \| '__|\n") + /build/reproducible-path/unicycler-0.5.0+dfsg/unicycler/misc.py:754: SyntaxWarning: invalid escape sequence '\_' bold_red("\\\\ \_ // ") + /build/reproducible-path/unicycler-0.5.0+dfsg/unicycler/misc.py:757: SyntaxWarning: invalid escape sequence '\_' bold_yellow("\____/ |_| |_||_| \___| \__, | \___||_| \___||_|\n") + /build/reproducible-path/unicycler-0.5.0+dfsg/unicycler/log.py:194: SyntaxWarning: invalid escape sequence '\[' return re.sub('\033\[2m', '', text) running config I: pybuild base:311: python3.11 setup.py config running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/unicycler-0.5.0+dfsg' make make[2]: Entering directory '/build/reproducible-path/unicycler-0.5.0+dfsg' Platform: Linux Compiler: g++ 13.2.0 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/start_end_align.o unicycler/src/start_end_align.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/semi_global_align.o unicycler/src/semi_global_align.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/semi_global_align_exhaustive.o unicycler/src/semi_global_align_exhaustive.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/miniasm/paf.o unicycler/src/miniasm/paf.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/miniasm/hit.o unicycler/src/miniasm/hit.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/miniasm/sdict.o unicycler/src/miniasm/sdict.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/miniasm/asg.o unicycler/src/miniasm/asg.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/miniasm/asm.o unicycler/src/miniasm/asm.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/miniasm/sys.o unicycler/src/miniasm/sys.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/miniasm/dotter.o unicycler/src/miniasm/dotter.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/random_alignments.o unicycler/src/random_alignments.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/miniasm_assembly.o unicycler/src/miniasm_assembly.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/path_align.o unicycler/src/path_align.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/scoredalignment.o unicycler/src/scoredalignment.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/kmers.o unicycler/src/kmers.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/global_align.o unicycler/src/global_align.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/consensus_align.o unicycler/src/consensus_align.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/minimap_align.o unicycler/src/minimap_align.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/ref_seqs.o unicycler/src/ref_seqs.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/string_functions.o unicycler/src/string_functions.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/overlap_align.o unicycler/src/overlap_align.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/minimap/misc.o unicycler/src/minimap/misc.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/minimap/bseq.o unicycler/src/minimap/bseq.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/minimap/kthread.o unicycler/src/minimap/kthread.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/minimap/map.o unicycler/src/minimap/map.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/minimap/sdust.o unicycler/src/minimap/sdust.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/minimap/sketch.o unicycler/src/minimap/sketch.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/minimap/index.o unicycler/src/minimap/index.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-soname,unicycler/cpp_functions.so -o unicycler/cpp_functions.so unicycler/src/start_end_align.o unicycler/src/semi_global_align.o unicycler/src/semi_global_align_exhaustive.o unicycler/src/miniasm/paf.o unicycler/src/miniasm/hit.o unicycler/src/miniasm/sdict.o unicycler/src/miniasm/asg.o unicycler/src/miniasm/asm.o unicycler/src/miniasm/sys.o unicycler/src/miniasm/dotter.o unicycler/src/random_alignments.o unicycler/src/miniasm_assembly.o unicycler/src/path_align.o unicycler/src/scoredalignment.o unicycler/src/kmers.o unicycler/src/global_align.o unicycler/src/consensus_align.o unicycler/src/minimap_align.o unicycler/src/ref_seqs.o unicycler/src/string_functions.o unicycler/src/overlap_align.o unicycler/src/minimap/misc.o unicycler/src/minimap/bseq.o unicycler/src/minimap/kthread.o unicycler/src/minimap/map.o unicycler/src/minimap/sdust.o unicycler/src/minimap/sketch.o unicycler/src/minimap/index.o -Wl,-z,relro -Wl,-z,now -shared -lz make[2]: Leaving directory '/build/reproducible-path/unicycler-0.5.0+dfsg' dh_auto_build I: pybuild base:311: /usr/bin/python3.12 setup.py build running build running build_py creating /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler copying unicycler/bridge_loop_unroll.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler copying unicycler/bridge_miniasm.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler copying unicycler/unicycler.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler copying unicycler/assembly_graph_segment.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler copying unicycler/alignment.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler copying unicycler/log.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler copying unicycler/bridge_common.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler copying unicycler/bridge_spades_contig.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler copying unicycler/string_graph.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler copying unicycler/miniasm_assembly.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler copying unicycler/unicycler_align.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler copying unicycler/assembly_graph_copy_depth.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler copying unicycler/bridge_long_read.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler copying unicycler/version.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler copying unicycler/blast_func.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler copying unicycler/__init__.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler copying unicycler/cpp_wrappers.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler copying unicycler/read_ref.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler copying unicycler/spades_func.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler copying unicycler/misc.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler copying unicycler/minimap_alignment.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler copying unicycler/bridge_long_read_simple.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler copying unicycler/assembly_graph.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler copying unicycler/settings.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler copying unicycler/path_finding.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler I: pybuild base:311: /usr/bin/python3 setup.py build running build running build_py creating /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler copying unicycler/bridge_loop_unroll.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler copying unicycler/bridge_miniasm.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler copying unicycler/unicycler.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler copying unicycler/assembly_graph_segment.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler copying unicycler/alignment.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler copying unicycler/log.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler copying unicycler/bridge_common.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler copying unicycler/bridge_spades_contig.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler copying unicycler/string_graph.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler copying unicycler/miniasm_assembly.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler copying unicycler/unicycler_align.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler copying unicycler/assembly_graph_copy_depth.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler copying unicycler/bridge_long_read.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler copying unicycler/version.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler copying unicycler/blast_func.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler copying unicycler/__init__.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler copying unicycler/cpp_wrappers.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler copying unicycler/read_ref.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler copying unicycler/spades_func.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler copying unicycler/misc.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler copying unicycler/minimap_alignment.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler copying unicycler/bridge_long_read_simple.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler copying unicycler/assembly_graph.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler copying unicycler/settings.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler copying unicycler/path_finding.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler make[1]: Leaving directory '/build/reproducible-path/unicycler-0.5.0+dfsg' dh_auto_test -O--buildsystem=pybuild I: pybuild pybuild:308: cp -a unicycler-runner.py /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build; cp -a unicycler/cpp_functions.so /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler; cp -a sample_data /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build I: pybuild base:311: cd /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build; python3.12 -m unittest discover -v /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/misc.py:641: SyntaxWarning: invalid escape sequence '\[' row_str = re.sub('\033\[4m', '', row_str) /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/misc.py:743: SyntaxWarning: invalid escape sequence '\ ' bold_red(" \ \___\n") + /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/misc.py:744: SyntaxWarning: invalid escape sequence '\ ' bold_red(" \ ___\\\n") + /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/misc.py:753: SyntaxWarning: invalid escape sequence '\ ' bold_yellow("| | | || '_ \ | | / __|| | | | / __|| | / _ \| '__|\n") + /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/misc.py:754: SyntaxWarning: invalid escape sequence '\_' bold_red("\\\\ \_ // ") + /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/misc.py:757: SyntaxWarning: invalid escape sequence '\_' bold_yellow("\____/ |_| |_||_| \___| \__, | \___||_| \___||_|\n") + /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/log.py:194: SyntaxWarning: invalid escape sequence '\[' return re.sub('\033\[2m', '', text) /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/bridge_long_read.py:619: SyntaxWarning: invalid escape sequence '\c' """ /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/bridge_common.py:43: SyntaxWarning: invalid escape sequence '\l' """ test_attributes (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_attributes) ... ok test_dead_end_count (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_dead_end_count) ... ok test_filter_by_read_depth (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_filter_by_read_depth) ... ok test_forward_links (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_forward_links) ... ok test_get_all_gfa_link_lines (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_get_all_gfa_link_lines) ... ok test_get_estimated_sequence_len (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_get_estimated_sequence_len) ... ok test_get_median_read_depth (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_get_median_read_depth) ... ok test_get_n_segment_length (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_get_n_segment_length) ... ok test_get_total_length (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_get_total_length) ... ok test_get_total_length_no_overlaps (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_get_total_length_no_overlaps) ... ok test_links_match (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_links_match) Tests that each segment's forward links match up with its reverse complement's reverse ... ok test_load_paths (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_load_paths) ... ok test_normalise_read_depths (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_normalise_read_depths) ... ok test_remove_all_overlaps (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_remove_all_overlaps) ... ok test_remove_segments (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_remove_segments) ... ok test_remove_small_components (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_remove_small_components) ... ok test_reverse_links (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_reverse_links) ... ok test_save_specific_segments_to_fasta (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_save_specific_segments_to_fasta) ... ok test_save_to_fasta (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_save_to_fasta) ... ok test_save_to_fasta_length (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_save_to_fasta_length) ... ok test_save_to_gfa (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_save_to_gfa) This test saves the graph to GFA, loads the GFA graph and then compares the two graphs to ... ok test_segments (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_segments) ... ok test_sequence (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_sequence) ... ok test_total_dead_end_count (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_total_dead_end_count) ... ok test_add_link_1 (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_add_link_1) ... ok test_add_link_2 (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_add_link_2) ... ok test_all_segments_below_depth (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_all_segments_below_depth) ... ok test_attributes (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_attributes) ... ok test_bad_overlaps (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_bad_overlaps) ... ok test_dead_end_change_if_deleted (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_dead_end_change_if_deleted) ... ok test_dead_end_change_if_path_deleted (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_dead_end_change_if_path_deleted) ... ok test_dead_end_count (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_dead_end_count) ... ok test_filter_homopolymer_loops (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_filter_homopolymer_loops) ... ok test_forward_links (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_forward_links) ... ok test_get_connected_components_and_remove_link (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_get_connected_components_and_remove_link) ... ok test_get_connected_segments (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_get_connected_segments) ... ok test_get_exclusive_inputs (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_get_exclusive_inputs) ... ok test_get_exclusive_outputs (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_get_exclusive_outputs) ... ok test_get_mean_path_depth (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_get_mean_path_depth) ... ok test_get_median_read_depth (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_get_median_read_depth) ... ok test_get_next_available_seg_number (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_get_next_available_seg_number) ... ok test_get_path_sequence (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_get_path_sequence) ... ok test_get_simple_path (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_get_simple_path) ... ok test_get_total_length (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_get_total_length) ... ok test_get_total_length_no_overlaps (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_get_total_length_no_overlaps) ... ok test_lead_exclusively_from (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_lead_exclusively_from) ... ok test_lead_exclusively_to (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_lead_exclusively_to) ... ok test_links_match (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_links_match) Tests that each segment's forward links match up with its reverse complement's reverse ... ok test_merge_all_possible (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_merge_all_possible) ... ok test_merge_simple_path_1 (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_merge_simple_path_1) ... ok test_merge_simple_path_2 (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_merge_simple_path_2) ... ok test_merge_simple_path_3 (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_merge_simple_path_3) ... ok test_normalise_read_depths (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_normalise_read_depths) ... ok test_remove_small_components (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_remove_small_components) ... ok test_remove_small_dead_ends (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_remove_small_dead_ends) ... ok test_reverse_links (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_reverse_links) ... ok test_segments (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_segments) ... ok test_seq_from_signed_seg_num (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_seq_from_signed_seg_num) ... ok test_sequence (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_sequence) ... ok test_total_dead_end_count (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_total_dead_end_count) ... ok test_expand_repeats_1 (test.test_assembly_graph.TestExpandRepeats.test_expand_repeats_1) Tests that the common sequence in segments 3 and 4 (just a C) is moved onto segment 2. ... ok test_expand_repeats_2 (test.test_assembly_graph.TestExpandRepeats.test_expand_repeats_2) Tests that the common sequence in segments 7 and 8 (GATTAGCG) is moved onto segment 6. ... ok test_expand_repeats_3 (test.test_assembly_graph.TestExpandRepeats.test_expand_repeats_3) Tests that the common sequence on both strands of segment 1 is moved onto segment 2. ... ok test_expand_repeats_4 (test.test_assembly_graph.TestExpandRepeats.test_expand_repeats_4) Tests that segment 5 isn't changed, because moving its common sequence (from each strand) ... ok test_expand_repeats_5 (test.test_assembly_graph.TestExpandRepeats.test_expand_repeats_5) Tests that paths through the graph are unchanged by the repeat expansion. ... ok test_graph (test.test_assembly_graph.TestRemoveZeroLengthSegments.test_graph) ... ok test_remove_zero_length_segs_1 (test.test_assembly_graph.TestRemoveZeroLengthSegments.test_remove_zero_length_segs_1) Tests that segment 9638 has been removed. ... ok test_remove_zero_length_segs_10 (test.test_assembly_graph.TestRemoveZeroLengthSegments.test_remove_zero_length_segs_10) Tests that segments 9125 and 9126 have been removed (results in a 3-way split). ... ok test_remove_zero_length_segs_11 (test.test_assembly_graph.TestRemoveZeroLengthSegments.test_remove_zero_length_segs_11) Tests that segments 8854 and 8855 have been removed (in a simple path). ... ok test_remove_zero_length_segs_2 (test.test_assembly_graph.TestRemoveZeroLengthSegments.test_remove_zero_length_segs_2) Tests that segment 5849 has been removed. ... ok test_remove_zero_length_segs_3 (test.test_assembly_graph.TestRemoveZeroLengthSegments.test_remove_zero_length_segs_3) Tests that segment 6513 has not been removed (it's a junction point). ... ok test_remove_zero_length_segs_4 (test.test_assembly_graph.TestRemoveZeroLengthSegments.test_remove_zero_length_segs_4) Tests that both segments 8851 and 8852 have been removed. ... ok test_remove_zero_length_segs_5 (test.test_assembly_graph.TestRemoveZeroLengthSegments.test_remove_zero_length_segs_5) Tests that segment 4907 has not been removed (it's a junction point and a dead end). ... ok test_remove_zero_length_segs_6 (test.test_assembly_graph.TestRemoveZeroLengthSegments.test_remove_zero_length_segs_6) Tests that segment 10029 has been removed (it's a dead end but not a junction). ... ok test_remove_zero_length_segs_7 (test.test_assembly_graph.TestRemoveZeroLengthSegments.test_remove_zero_length_segs_7) Tests that segment 9822 has been removed (it's on a simple path). ... ok test_remove_zero_length_segs_8 (test.test_assembly_graph.TestRemoveZeroLengthSegments.test_remove_zero_length_segs_8) Tests that segment 1 has been removed (it's isolated and unconnected). ... ok test_remove_zero_length_segs_9 (test.test_assembly_graph.TestRemoveZeroLengthSegments.test_remove_zero_length_segs_9) Tests that segment 8232 has been removed. ... ok test_graph (test.test_assembly_graph.TestRepairMultiwayJunction.test_graph) ... ok test_repair_multi_way_junctions_1 (test.test_assembly_graph.TestRepairMultiwayJunction.test_repair_multi_way_junctions_1) ... ok test_repair_multi_way_junctions_2 (test.test_assembly_graph.TestRepairMultiwayJunction.test_repair_multi_way_junctions_2) ... ok test_repair_multi_way_junctions_3 (test.test_assembly_graph.TestRepairMultiwayJunction.test_repair_multi_way_junctions_3) ... ok test_repair_multi_way_junctions_4 (test.test_assembly_graph.TestRepairMultiwayJunction.test_repair_multi_way_junctions_4) ... ok test_repair_multi_way_junctions_5 (test.test_assembly_graph.TestRepairMultiwayJunction.test_repair_multi_way_junctions_5) ... ok test_repair_multi_way_junctions_6 (test.test_assembly_graph.TestRepairMultiwayJunction.test_repair_multi_way_junctions_6) ... ok test_merge_1 (test.test_assembly_graph_copy_depth.TestCopyDepth.test_merge_1) Tests a particular part of the graph with merging and splitting. ... {141: 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[54.5586], 158: [36.4255], 197: [45.7528], 75: [42.669094948446855, 41.55861034939538, 40.88329470215778], 77: [48.184158446484815, 46.930141553515185], 76: [40.4899], 200: [40.8735], 202: [43.81269468512175, 37.473005314878264], 180: [40.098070229593354, 37.63872977040665], 70: [51.2727], 253: [52.2203165820695, 33.779683417930485], 255: [52.44146547832499, 36.85287936802854, 34.94991745736829, 33.92273769627816], 117: [53.36848431634724, 40.296048605124014, 37.504335483869625, 35.56773451443917, 34.52239708021996], 201: [43.8857], 295: [44.64628529730558, 36.35371470269442], 293: [45.136984861232165, 39.29074307462816, 36.75327206413967], 191: [45.20494064626781, 38.400059353732196], 170: [42.2174], 215: [44.568608410249986, 39.783891589750006], 131: [51.875], 251: [42.2421], 155: [52.133246866180784, 42.450053133819225], 156: [44.7083], 42: [43.42072613078557, 36.95418142216078, 35.82409244705365], 56: [39.67001090395544, 37.90888909604457], 222: [33.87840236876384, 32.374394886304074, 32.238702744932105], 137: [41.265475663334996, 39.43352433666499], 136: [44.6699], 10: [37.3954441907133, 31.053555809286703], 150: [38.01678937847866, 36.127537432670096, 30.00067318885124], 239: [32.38811697286138, 30.77858302713862], 274: [33.0294], 275: [49.5667], 323: [46.28], 102: [40.70164096791271, 32.89295903208729], 159: [39.82757357770982, 36.78784340290207, 32.186583019388124], 227: [45.685469096367044, 36.920630903632954], 161: [43.414], 8: [45.29157871424178, 32.71522128575823], 38: [44.9046], 37: [43.01317193262201, 30.39512806737799], 182: [42.5417], 145: [37.936194072240816, 35.06380592775917], 228: [41.1317], 303: [45.59716124134053, 42.30283875865948], 336: [47.393715299238856, 43.969594639145825, 33.08069006161533], 288: [47.35781340253773, 43.93628659746228], 290: [48.99999999999999], 257: [41.0987], 258: [42.66984874647549, 33.33015125352451], 64: [47.65603913067634, 43.40501072228278, 37.22495014704089], 62: [45.57996677245484, 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[47.346831968233474, 35.743408006317495, 33.90976002544903], 262: [67.7327415410003, 43.333634537745866, 31.933623921253847], 146: [43.6061], 318: [44.150138616023966, 34.88436138397604], 101: [47.80435417019734, 40.52897808705418, 37.77166774274848], 100: [42.68], 99: [38.56173643891318, 35.93826356108682], 263: [69.14876869275282, 32.60123130724718], 300: [63.9174], 301: [45.7895], 147: [66.19604264532316, 39.80395735467683], 93: [63.64623002344513, 41.036004402183956, 38.270744358736195, 36.58002121563471], 5: [59.49044208339057, 38.35655375538521, 35.77185168584166, 34.19152450563514, 24.10762796974743], 109: [46.56802142620704, 40.901469700682746, 37.91850887311021], 190: [41.27395382148669, 38.492659272946504, 36.79213238320927, 25.941254522357532], 307: [50.375], 305: [43.88547100955402, 33.44782899044598], 121: [45.13317269449633, 28.366827305503673], 69: [40.7136], 233: [41.2415], 298: [44.25920587798538, 41.74079412201461], 148: [45.287921586781096, 42.7109744440317, 42.05395614304147, 36.414147826145765], 16: [45.78125863318317, 43.176239910913345, 42.51206448156116, 37.000617198891604, 36.81081977545074], 224: [47.27957445345012, 32.72042554654988], 279: [43.0], 22: [45.05699485312401, 42.08187100460133, 38.86113414227466], 67: [43.1254], 108: [38.66849819978974, 37.33150180021026], 285: [42.5886], 32: [44.38481272104399, 42.52994056881594, 38.295457746659594, 35.45678896348048], 235: [45.29500646434315, 43.4020966833841, 36.18389685227275], 234: [42.417417028373606, 40.64476370864763, 35.719683520637155, 33.88513574234161], 169: [41.481854386135815, 39.7482988790481, 34.9318467348161], 143: [45.04], 165: [40.4661], 66: [42.202501825827646, 40.58129817417234], 65: [42.89002581860579, 41.972164731677985, 40.35980944971622], 167: [43.04265455744026, 37.95734544255975], 30: [46.10179446355208, 45.11520043923042, 43.382105846897986, 41.498899250319546], 221: [46.96361770115696, 41.41506323538286, 35.30531906346018], 31: [45.21455338225854, 44.246946617741465], 94: [43.34556007682222, 41.4639399231778], 95: [51.8]}ok test_merge_split_1 (test.test_assembly_graph_copy_depth.TestCopyDepth.test_merge_split_1) Tests a particular part of the graph with merging and splitting. ... ok test_merge_split_2 (test.test_assembly_graph_copy_depth.TestCopyDepth.test_merge_split_2) Tests a particular part of the graph with merging and splitting. ... ok test_single_copy_segments_1 (test.test_assembly_graph_copy_depth.TestCopyDepth.test_single_copy_segments_1) Tests large contigs from the largest replicon, all of which should have a copy depth of 1. ... ok test_single_copy_segments_2 (test.test_assembly_graph_copy_depth.TestCopyDepth.test_single_copy_segments_2) Tests single copy contigs from a smaller, higher depth replicon. They should have a copy ... ok test_random_seq_no_start_gene (test.test_blast_func.TestBlastFunc.test_random_seq_no_start_gene) ... ok test_random_seq_with_exact_gene_forward_strand (test.test_blast_func.TestBlastFunc.test_random_seq_with_exact_gene_forward_strand) ... ok test_random_seq_with_exact_gene_reverse_strand (test.test_blast_func.TestBlastFunc.test_random_seq_with_exact_gene_reverse_strand) ... ok test_1bp_deletion (test.test_cpp_wrappers.TestFullyGlobalAlignment.test_1bp_deletion) ... ok test_1bp_insertion (test.test_cpp_wrappers.TestFullyGlobalAlignment.test_1bp_insertion) ... ok test_2bp_deletion (test.test_cpp_wrappers.TestFullyGlobalAlignment.test_2bp_deletion) ... ok test_2bp_insertion (test.test_cpp_wrappers.TestFullyGlobalAlignment.test_2bp_insertion) ... ok test_2bp_insertion_and_2bp_deletion (test.test_cpp_wrappers.TestFullyGlobalAlignment.test_2bp_insertion_and_2bp_deletion) ... ok test_long_perfect_alignment (test.test_cpp_wrappers.TestFullyGlobalAlignment.test_long_perfect_alignment) ... ok test_one_mismatch (test.test_cpp_wrappers.TestFullyGlobalAlignment.test_one_mismatch) ... ok test_perfect_alignment (test.test_cpp_wrappers.TestFullyGlobalAlignment.test_perfect_alignment) ... ok test_random_seqs (test.test_cpp_wrappers.TestFullyGlobalAlignment.test_random_seqs) This test aligns two random sequences of different length, making sure that the scores are ... ok test_shift_big_band (test.test_cpp_wrappers.TestFullyGlobalAlignment.test_shift_big_band) This test has a 20 bp insertion near the start and a 20 bp deletion near the end, shifting ... ok test_shift_small_band (test.test_cpp_wrappers.TestFullyGlobalAlignment.test_shift_small_band) This test uses the same sequences as the previous test, but uses a smaller bandwidth than ... ok test_consensus_different_qualities (test.test_cpp_wrappers.TestMultipleSequenceAlignment.test_consensus_different_qualities) ... ok test_consensus_with_all (test.test_cpp_wrappers.TestMultipleSequenceAlignment.test_consensus_with_all) ... ok test_consensus_with_deletions (test.test_cpp_wrappers.TestMultipleSequenceAlignment.test_consensus_with_deletions) ... ok test_consensus_with_deletions_and_insertions (test.test_cpp_wrappers.TestMultipleSequenceAlignment.test_consensus_with_deletions_and_insertions) ... ok test_consensus_with_insertions (test.test_cpp_wrappers.TestMultipleSequenceAlignment.test_consensus_with_insertions) ... ok test_consensus_with_subs (test.test_cpp_wrappers.TestMultipleSequenceAlignment.test_consensus_with_subs) ... ok test_start_end_deletions (test.test_cpp_wrappers.TestMultipleSequenceAlignment.test_start_end_deletions) ... ok test_start_end_insertions (test.test_cpp_wrappers.TestMultipleSequenceAlignment.test_start_end_insertions) ... ok test_start_end_insertions_and_deletions (test.test_cpp_wrappers.TestMultipleSequenceAlignment.test_start_end_insertions_and_deletions) ... ok test_two_way_consensus (test.test_cpp_wrappers.TestMultipleSequenceAlignment.test_two_way_consensus) ... ok test_makeblastdb_not_found (test.test_dependencies.TestDependencies.test_makeblastdb_not_found) ... ok test_no_rotate (test.test_dependencies.TestDependencies.test_no_rotate) ... ok test_spades_not_found (test.test_dependencies.TestDependencies.test_spades_not_found) ... ok test_tblastn_not_found (test.test_dependencies.TestDependencies.test_tblastn_not_found) ... ok test_verbosity_1 (test.test_dependencies.TestDependencies.test_verbosity_1) ... ok test_verbosity_2 (test.test_dependencies.TestDependencies.test_verbosity_2) ... ok test_basic_options (test.test_help_text.TestBasicHelpText.test_basic_options) ... ok test_extended_options (test.test_help_text.TestBasicHelpText.test_extended_options) ... ok test_output (test.test_help_text.TestBasicHelpText.test_output) ... ok test_return_code (test.test_help_text.TestBasicHelpText.test_return_code) ... ok test_title (test.test_help_text.TestBasicHelpText.test_title) ... ok test_error_message (test.test_help_text.TestEmptyCommand.test_error_message) ... ok test_output (test.test_help_text.TestEmptyCommand.test_output) ... ok test_return_code (test.test_help_text.TestEmptyCommand.test_return_code) ... ok test_basic_options (test.test_help_text.TestExtendedHelpText.test_basic_options) ... ok test_extended_options (test.test_help_text.TestExtendedHelpText.test_extended_options) ... ok test_output (test.test_help_text.TestExtendedHelpText.test_output) ... ok test_return_code (test.test_help_text.TestExtendedHelpText.test_return_code) ... ok test_title (test.test_help_text.TestExtendedHelpText.test_title) ... ok test_contig_placement_1 (test.test_miniasm_assembly.TestContigPlacement.test_contig_placement_1) This covers the case where the contig sequences are in the middle of the unitig sequences. ... ok test_contig_placement_2 (test.test_miniasm_assembly.TestContigPlacement.test_contig_placement_2) This covers the case where a contig sequence spans the circular junction of the unitig ... ok test_contig_placement_3 (test.test_miniasm_assembly.TestContigPlacement.test_contig_placement_3) This covers the case where the a contig sequence starts right at the beginning of the ... ok test_contig_placement_4 (test.test_miniasm_assembly.TestContigPlacement.test_contig_placement_4) This covers the case where the a contig sequence ends right at the end of the unitig ... ok test_add_line_breaks_to_sequence (test.test_misc.TestMiscFunctions.test_add_line_breaks_to_sequence) ... ok test_colour (test.test_misc.TestMiscFunctions.test_colour) ... ok test_flip_number_order (test.test_misc.TestMiscFunctions.test_flip_number_order) ... ok test_float_to_str (test.test_misc.TestMiscFunctions.test_float_to_str) ... ok test_get_compression_type (test.test_misc.TestMiscFunctions.test_get_compression_type) ... ok test_get_nice_header (test.test_misc.TestMiscFunctions.test_get_nice_header) ... ok test_get_num_agreement (test.test_misc.TestMiscFunctions.test_get_num_agreement) ... ok test_get_percentile (test.test_misc.TestMiscFunctions.test_get_percentile) ... ok test_get_random_base (test.test_misc.TestMiscFunctions.test_get_random_base) ... ok test_get_random_sequence (test.test_misc.TestMiscFunctions.test_get_random_sequence) ... ok test_get_sequence_file_type (test.test_misc.TestMiscFunctions.test_get_sequence_file_type) ... ok test_int_to_str (test.test_misc.TestMiscFunctions.test_int_to_str) ... ok test_is_header_spades_format (test.test_misc.TestMiscFunctions.test_is_header_spades_format) ... ok test_len_without_format (test.test_misc.TestMiscFunctions.test_len_without_format) ... ok test_load_fasta (test.test_misc.TestMiscFunctions.test_load_fasta) ... ok test_load_fasta_with_full_header (test.test_misc.TestMiscFunctions.test_load_fasta_with_full_header) ... ok test_remove_formatting (test.test_misc.TestMiscFunctions.test_remove_formatting) ... ok test_reverse_complement (test.test_misc.TestMiscFunctions.test_reverse_complement) ... ok test_round_to_nearest_odd (test.test_misc.TestMiscFunctions.test_round_to_nearest_odd) ... ok test_score_function (test.test_misc.TestMiscFunctions.test_score_function) ... ok test_spades_version_parsing_1 (test.test_misc.TestMiscFunctions.test_spades_version_parsing_1) ... ok test_spades_version_parsing_2 (test.test_misc.TestMiscFunctions.test_spades_version_parsing_2) ... ok test_spades_version_parsing_3 (test.test_misc.TestMiscFunctions.test_spades_version_parsing_3) ... ok test_spades_version_parsing_4 (test.test_misc.TestMiscFunctions.test_spades_version_parsing_4) ... ok test_spades_version_status_1 (test.test_misc.TestMiscFunctions.test_spades_version_status_1) ... ok test_spades_version_status_10 (test.test_misc.TestMiscFunctions.test_spades_version_status_10) ... ok test_spades_version_status_11 (test.test_misc.TestMiscFunctions.test_spades_version_status_11) ... ok test_spades_version_status_12 (test.test_misc.TestMiscFunctions.test_spades_version_status_12) ... ok test_spades_version_status_13 (test.test_misc.TestMiscFunctions.test_spades_version_status_13) ... ok test_spades_version_status_2 (test.test_misc.TestMiscFunctions.test_spades_version_status_2) ... ok test_spades_version_status_3 (test.test_misc.TestMiscFunctions.test_spades_version_status_3) ... ok test_spades_version_status_4 (test.test_misc.TestMiscFunctions.test_spades_version_status_4) ... ok test_spades_version_status_5 (test.test_misc.TestMiscFunctions.test_spades_version_status_5) ... ok test_spades_version_status_6 (test.test_misc.TestMiscFunctions.test_spades_version_status_6) ... ok test_spades_version_status_7 (test.test_misc.TestMiscFunctions.test_spades_version_status_7) ... ok test_spades_version_status_8 (test.test_misc.TestMiscFunctions.test_spades_version_status_8) ... ok test_spades_version_status_9 (test.test_misc.TestMiscFunctions.test_spades_version_status_9) ... ok test_strip_read_extensions_capitals (test.test_misc.TestMiscFunctions.test_strip_read_extensions_capitals) ... ok test_strip_read_extensions_fa (test.test_misc.TestMiscFunctions.test_strip_read_extensions_fa) ... ok test_strip_read_extensions_fasta (test.test_misc.TestMiscFunctions.test_strip_read_extensions_fasta) ... ok test_strip_read_extensions_fastq (test.test_misc.TestMiscFunctions.test_strip_read_extensions_fastq) ... ok test_strip_read_extensions_fastq_extra_dots (test.test_misc.TestMiscFunctions.test_strip_read_extensions_fastq_extra_dots) ... ok test_strip_read_extensions_fna (test.test_misc.TestMiscFunctions.test_strip_read_extensions_fna) ... ok test_strip_read_extensions_fq (test.test_misc.TestMiscFunctions.test_strip_read_extensions_fq) ... ok test_strip_read_extensions_other_fasta (test.test_misc.TestMiscFunctions.test_strip_read_extensions_other_fasta) ... ok test_weighted_average (test.test_misc.TestMiscFunctions.test_weighted_average) ... ok test_weighted_average_list (test.test_misc.TestMiscFunctions.test_weighted_average_list) ... ok test_absolute_paths (test.test_options.TestUnicyclerOptions.test_absolute_paths) ... ok test_defaults (test.test_options.TestUnicyclerOptions.test_defaults) ... ok test_modes (test.test_options.TestUnicyclerOptions.test_modes) ... ok test_relative_paths (test.test_options.TestUnicyclerOptions.test_relative_paths) ... ok test_long_contained_read (test.test_semi_global_alignment.TestContainedReadAlignments.test_long_contained_read) ... ok test_medium_contained_read (test.test_semi_global_alignment.TestContainedReadAlignments.test_medium_contained_read) ... ok test_short_contained_read (test.test_semi_global_alignment.TestContainedReadAlignments.test_short_contained_read) ... ok test_end_to_end (test.test_semi_global_alignment.TestPerfectMatchAlignments.test_end_to_end) ... ok test_read_contained_1 (test.test_semi_global_alignment.TestPerfectMatchAlignments.test_read_contained_1) ... ok test_read_contained_2 (test.test_semi_global_alignment.TestPerfectMatchAlignments.test_read_contained_2) ... ok test_read_contained_3 (test.test_semi_global_alignment.TestPerfectMatchAlignments.test_read_contained_3) ... ok test_read_end_overlap (test.test_semi_global_alignment.TestPerfectMatchAlignments.test_read_end_overlap) ... ok test_read_start_overlap (test.test_semi_global_alignment.TestPerfectMatchAlignments.test_read_start_overlap) ... ok test_ref_contained_1 (test.test_semi_global_alignment.TestPerfectMatchAlignments.test_ref_contained_1) ... ok test_ref_contained_2 (test.test_semi_global_alignment.TestPerfectMatchAlignments.test_ref_contained_2) ... ok test_ref_contained_3 (test.test_semi_global_alignment.TestPerfectMatchAlignments.test_ref_contained_3) ... ok test_tough_alignment_0 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_0) The beginning of the reference in this case is repetitive, which was able to throw off ... ok test_tough_alignment_1 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_1) This read goes through a repetitive area, which means that the densest area of common ... ok test_tough_alignment_10 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_10) This is a very low quality read. ... ok test_tough_alignment_11 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_11) Repeats at one end of the read. ... ok test_tough_alignment_12 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_12) Repeats at one end of the read. ... ok test_tough_alignment_13 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_13) This read caused a crash before I added the getMaxSeedChainGapArea function in ... ok test_tough_alignment_14 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_14) This read caused a crash before I added made a few fixes to the line tracing code. It won't ... ok test_tough_alignment_15 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_15) This read should hit the same reference twice, even at low sensitivities. ... ok test_tough_alignment_2 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_2) This read goes through a repetitive area, which means that the densest area of common ... ok test_tough_alignment_3 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_3) The first line tracing of this alignment is bad but uses all the points. This previously ... ok test_tough_alignment_4 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_4) Like so many of these tough ones, this case has a read which enters a repetitive region ... ok test_tough_alignment_5 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_5) ... ok test_tough_alignment_6 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_6) This one misses the right alignment on lower sensitivities because the line tracing never ... ok test_tough_alignment_7 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_7) This one misses the right alignment on lower sensitivities because the line tracing never ... ok test_tough_alignment_8 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_8) This has a weird change in slope - the read has a good part and a bad part. Ideally the ... ok test_tough_alignment_9 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_9) This is a very low quality read. ... ok test_bad_fastq_1 (test.test_spades_func.TestSPAdesFunc.test_bad_fastq_1) ... ok test_bad_fastq_2 (test.test_spades_func.TestSPAdesFunc.test_bad_fastq_2) ... ok test_build_spades_command_1 (test.test_spades_func.TestSPAdesFunc.test_build_spades_command_1) ... ok test_build_spades_command_2 (test.test_spades_func.TestSPAdesFunc.test_build_spades_command_2) ... ok test_build_spades_command_3 (test.test_spades_func.TestSPAdesFunc.test_build_spades_command_3) ... ok test_build_spades_command_4 (test.test_spades_func.TestSPAdesFunc.test_build_spades_command_4) ... ok test_build_spades_command_5 (test.test_spades_func.TestSPAdesFunc.test_build_spades_command_5) ... ok test_build_spades_command_6 (test.test_spades_func.TestSPAdesFunc.test_build_spades_command_6) ... ok test_get_read_count_1 (test.test_spades_func.TestSPAdesFunc.test_get_read_count_1) ... ok test_get_read_count_2 (test.test_spades_func.TestSPAdesFunc.test_get_read_count_2) ... ok test_get_read_lengths_1 (test.test_spades_func.TestSPAdesFunc.test_get_read_lengths_1) ... ok test_get_read_lengths_2 (test.test_spades_func.TestSPAdesFunc.test_get_read_lengths_2) ... ok ---------------------------------------------------------------------- Ran 227 tests in 53.623s OK I: pybuild pybuild:334: rm /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler-runner.py; rm -r /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/sample_data; rm -r /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/__pycache__ I: pybuild pybuild:308: cp -a unicycler-runner.py /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build; cp -a unicycler/cpp_functions.so /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler; cp -a sample_data /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build I: pybuild base:311: cd /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build; python3.11 -m unittest discover -v test_attributes (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_attributes) ... ok test_dead_end_count (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_dead_end_count) ... ok test_filter_by_read_depth (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_filter_by_read_depth) ... ok test_forward_links (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_forward_links) ... ok test_get_all_gfa_link_lines (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_get_all_gfa_link_lines) ... ok test_get_estimated_sequence_len (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_get_estimated_sequence_len) ... ok test_get_median_read_depth (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_get_median_read_depth) ... ok test_get_n_segment_length (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_get_n_segment_length) ... ok test_get_total_length (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_get_total_length) ... ok test_get_total_length_no_overlaps (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_get_total_length_no_overlaps) ... ok test_links_match (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_links_match) Tests that each segment's forward links match up with its reverse complement's reverse ... ok test_load_paths (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_load_paths) ... ok test_normalise_read_depths (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_normalise_read_depths) ... ok test_remove_all_overlaps (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_remove_all_overlaps) ... ok test_remove_segments (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_remove_segments) ... ok test_remove_small_components (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_remove_small_components) ... ok test_reverse_links (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_reverse_links) ... ok test_save_specific_segments_to_fasta (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_save_specific_segments_to_fasta) ... ok test_save_to_fasta (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_save_to_fasta) ... ok test_save_to_fasta_length (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_save_to_fasta_length) ... ok test_save_to_gfa (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_save_to_gfa) This test saves the graph to GFA, loads the GFA graph and then compares the two graphs to ... ok test_segments (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_segments) ... ok test_sequence (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_sequence) ... ok test_total_dead_end_count (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_total_dead_end_count) ... ok test_add_link_1 (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_add_link_1) ... ok test_add_link_2 (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_add_link_2) ... ok test_all_segments_below_depth (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_all_segments_below_depth) ... ok test_attributes (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_attributes) ... ok test_bad_overlaps (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_bad_overlaps) ... ok test_dead_end_change_if_deleted (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_dead_end_change_if_deleted) ... ok test_dead_end_change_if_path_deleted (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_dead_end_change_if_path_deleted) ... ok test_dead_end_count (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_dead_end_count) ... ok test_filter_homopolymer_loops (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_filter_homopolymer_loops) ... ok test_forward_links (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_forward_links) ... ok test_get_connected_components_and_remove_link (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_get_connected_components_and_remove_link) ... ok test_get_connected_segments (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_get_connected_segments) ... ok test_get_exclusive_inputs (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_get_exclusive_inputs) ... ok test_get_exclusive_outputs (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_get_exclusive_outputs) ... ok test_get_mean_path_depth (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_get_mean_path_depth) ... ok test_get_median_read_depth (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_get_median_read_depth) ... ok test_get_next_available_seg_number (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_get_next_available_seg_number) ... ok test_get_path_sequence (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_get_path_sequence) ... ok test_get_simple_path (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_get_simple_path) ... ok test_get_total_length (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_get_total_length) ... ok test_get_total_length_no_overlaps (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_get_total_length_no_overlaps) ... ok test_lead_exclusively_from (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_lead_exclusively_from) ... ok test_lead_exclusively_to (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_lead_exclusively_to) ... ok test_links_match (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_links_match) Tests that each segment's forward links match up with its reverse complement's reverse ... ok test_merge_all_possible (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_merge_all_possible) ... ok test_merge_simple_path_1 (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_merge_simple_path_1) ... ok test_merge_simple_path_2 (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_merge_simple_path_2) ... ok test_merge_simple_path_3 (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_merge_simple_path_3) ... ok test_normalise_read_depths (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_normalise_read_depths) ... ok test_remove_small_components (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_remove_small_components) ... ok test_remove_small_dead_ends (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_remove_small_dead_ends) ... ok test_reverse_links (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_reverse_links) ... ok test_segments (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_segments) ... ok test_seq_from_signed_seg_num (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_seq_from_signed_seg_num) ... ok test_sequence (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_sequence) ... ok test_total_dead_end_count (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_total_dead_end_count) ... ok test_expand_repeats_1 (test.test_assembly_graph.TestExpandRepeats.test_expand_repeats_1) Tests that the common sequence in segments 3 and 4 (just a C) is moved onto segment 2. ... ok test_expand_repeats_2 (test.test_assembly_graph.TestExpandRepeats.test_expand_repeats_2) Tests that the common sequence in segments 7 and 8 (GATTAGCG) is moved onto segment 6. ... ok test_expand_repeats_3 (test.test_assembly_graph.TestExpandRepeats.test_expand_repeats_3) Tests that the common sequence on both strands of segment 1 is moved onto segment 2. ... ok test_expand_repeats_4 (test.test_assembly_graph.TestExpandRepeats.test_expand_repeats_4) Tests that segment 5 isn't changed, because moving its common sequence (from each strand) ... ok test_expand_repeats_5 (test.test_assembly_graph.TestExpandRepeats.test_expand_repeats_5) Tests that paths through the graph are unchanged by the repeat expansion. ... ok test_graph (test.test_assembly_graph.TestRemoveZeroLengthSegments.test_graph) ... ok test_remove_zero_length_segs_1 (test.test_assembly_graph.TestRemoveZeroLengthSegments.test_remove_zero_length_segs_1) Tests that segment 9638 has been removed. ... ok test_remove_zero_length_segs_10 (test.test_assembly_graph.TestRemoveZeroLengthSegments.test_remove_zero_length_segs_10) Tests that segments 9125 and 9126 have been removed (results in a 3-way split). ... ok test_remove_zero_length_segs_11 (test.test_assembly_graph.TestRemoveZeroLengthSegments.test_remove_zero_length_segs_11) Tests that segments 8854 and 8855 have been removed (in a simple path). ... ok test_remove_zero_length_segs_2 (test.test_assembly_graph.TestRemoveZeroLengthSegments.test_remove_zero_length_segs_2) Tests that segment 5849 has been removed. ... ok test_remove_zero_length_segs_3 (test.test_assembly_graph.TestRemoveZeroLengthSegments.test_remove_zero_length_segs_3) Tests that segment 6513 has not been removed (it's a junction point). ... ok test_remove_zero_length_segs_4 (test.test_assembly_graph.TestRemoveZeroLengthSegments.test_remove_zero_length_segs_4) Tests that both segments 8851 and 8852 have been removed. ... ok test_remove_zero_length_segs_5 (test.test_assembly_graph.TestRemoveZeroLengthSegments.test_remove_zero_length_segs_5) Tests that segment 4907 has not been removed (it's a junction point and a dead end). ... ok test_remove_zero_length_segs_6 (test.test_assembly_graph.TestRemoveZeroLengthSegments.test_remove_zero_length_segs_6) Tests that segment 10029 has been removed (it's a dead end but not a junction). ... ok test_remove_zero_length_segs_7 (test.test_assembly_graph.TestRemoveZeroLengthSegments.test_remove_zero_length_segs_7) Tests that segment 9822 has been removed (it's on a simple path). ... ok test_remove_zero_length_segs_8 (test.test_assembly_graph.TestRemoveZeroLengthSegments.test_remove_zero_length_segs_8) Tests that segment 1 has been removed (it's isolated and unconnected). ... ok test_remove_zero_length_segs_9 (test.test_assembly_graph.TestRemoveZeroLengthSegments.test_remove_zero_length_segs_9) Tests that segment 8232 has been removed. ... ok test_graph (test.test_assembly_graph.TestRepairMultiwayJunction.test_graph) ... ok test_repair_multi_way_junctions_1 (test.test_assembly_graph.TestRepairMultiwayJunction.test_repair_multi_way_junctions_1) ... ok test_repair_multi_way_junctions_2 (test.test_assembly_graph.TestRepairMultiwayJunction.test_repair_multi_way_junctions_2) ... ok test_repair_multi_way_junctions_3 (test.test_assembly_graph.TestRepairMultiwayJunction.test_repair_multi_way_junctions_3) ... ok test_repair_multi_way_junctions_4 (test.test_assembly_graph.TestRepairMultiwayJunction.test_repair_multi_way_junctions_4) ... ok test_repair_multi_way_junctions_5 (test.test_assembly_graph.TestRepairMultiwayJunction.test_repair_multi_way_junctions_5) ... ok test_repair_multi_way_junctions_6 (test.test_assembly_graph.TestRepairMultiwayJunction.test_repair_multi_way_junctions_6) ... ok test_merge_1 (test.test_assembly_graph_copy_depth.TestCopyDepth.test_merge_1) Tests a particular part of the graph with merging and splitting. ... {141: [40.2345], 41: [39.1254], 306: [38.3939], 299: [38.8948], 114: [37.197], 278: [40.1607], 125: [40.0341], 9: [39.702], 314: [38.5366], 54: [38.8453], 24: [38.4338], 133: [38.0085], 71: [38.3193], 27: [40.2781], 110: [39.7247], 242: [38.9116], 183: [39.3206], 328: [38.5908], 174: [38.6078], 271: [39.8314], 210: [36.9729], 181: [38.3666], 28: [33.7233], 264: [40.2367], 317: [38.4726], 135: [36.26], 120: [39.2552], 139: [37.4011], 287: [34.0933], 209: 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40.296048605124014, 37.504335483869625, 35.56773451443917, 34.52239708021996], 201: [43.8857], 295: [44.64628529730558, 36.35371470269442], 293: [45.136984861232165, 39.29074307462816, 36.75327206413967], 191: [45.20494064626781, 38.400059353732196], 170: [42.2174], 215: [44.568608410249986, 39.783891589750006], 131: [51.875], 251: [42.2421], 155: [52.133246866180784, 42.450053133819225], 156: [44.7083], 42: [43.42072613078557, 36.95418142216078, 35.82409244705365], 56: [39.67001090395544, 37.90888909604457], 222: [33.87840236876384, 32.374394886304074, 32.238702744932105], 137: [41.265475663334996, 39.43352433666499], 136: [44.6699], 10: [37.3954441907133, 31.053555809286703], 150: [38.01678937847866, 36.127537432670096, 30.00067318885124], 239: [32.38811697286138, 30.77858302713862], 274: [33.0294], 275: [49.5667], 323: [46.28], 102: [40.70164096791271, 32.89295903208729], 159: [39.82757357770982, 36.78784340290207, 32.186583019388124], 227: [45.685469096367044, 36.920630903632954], 161: [43.414], 8: [45.29157871424178, 32.71522128575823], 38: [44.9046], 37: [43.01317193262201, 30.39512806737799], 182: [42.5417], 145: [37.936194072240816, 35.06380592775917], 228: [41.1317], 303: [45.59716124134053, 42.30283875865948], 336: [47.39371529923885, 43.96959463914582, 33.08069006161532], 288: [47.35781340253772, 43.93628659746227], 290: [49.0], 257: [41.0987], 258: [42.66984874647549, 33.33015125352451], 64: [47.65603913067634, 43.40501072228278, 37.22495014704089], 62: [45.57996677245485, 41.51412879813157, 36.497610035687245, 35.603294393726344], 186: [42.1463], 276: [162.984], 272: [63.1288], 44: [54.56927239846077, 34.43072760153924], 43: [60.95306420561749, 41.0093260695084, 38.45860972487411], 326: [54.29060122649335, 34.25489877350666], 195: [40.55], 247: [45.93955982482657, 42.9023030449955, 39.09789124915622, 37.902245881021706], 249: [33.568831102107914, 32.54226889789207], 248: [47.24942885477717, 44.12557114522282], 207: [46.45549203961564, 43.38412481938687, 33.271383140997486], 324: [62.923100000000005], 203: [67.81166049698453, 36.176828191502906, 35.070511311512554], 204: [68.09178418893339, 46.647395376682816, 43.563340622794556, 36.326271319745636, 35.21538434713969, 33.40882414470386], 269: [68.29791131977223, 46.788606153939305, 43.695215363914805, 36.43623803849743, 35.321988194040244, 33.50995918100338, 32.2000817488325], 333: [69.68778117098257, 47.7407593284199, 44.5844177026526, 36.040794458053945, 34.1918904594418, 32.85535688044922], 144: [47.34683196823348, 35.7434080063175, 33.90976002544904], 262: [67.7327415410003, 43.333634537745866, 31.933623921253847], 146: [43.6061], 318: [44.150138616023966, 34.88436138397604], 101: [47.80435417019735, 40.528978087054185, 37.771667742748484], 100: [42.68], 99: [38.56173643891317, 35.93826356108681], 263: [69.14876869275282, 32.60123130724718], 300: [63.9174], 301: [45.7895], 147: [66.19604264532316, 39.80395735467683], 93: [63.64623002344513, 41.036004402183956, 38.270744358736195, 36.58002121563471], 5: [59.490442083390576, 38.356553755385214, 35.77185168584167, 34.191524505635144, 24.107627969747433], 109: [46.56802142620704, 40.901469700682746, 37.91850887311021], 190: [41.273953821486685, 38.492659272946504, 36.79213238320927, 25.941254522357532], 307: [50.375], 305: [43.88547100955402, 33.44782899044598], 121: [45.13317269449633, 28.36682730550368], 69: [40.7136], 233: [41.2415], 298: [44.25920587798538, 41.74079412201461], 148: [45.287921586781096, 42.7109744440317, 42.05395614304147, 36.414147826145765], 16: [45.78125863318317, 43.176239910913345, 42.51206448156116, 37.000617198891604, 36.81081977545074], 224: [47.27957445345012, 32.72042554654988], 279: [43.0], 22: [45.05699485312401, 42.08187100460133, 38.86113414227466], 67: [43.1254], 108: [38.66849819978974, 37.33150180021026], 285: [42.5886], 32: [44.38481272104399, 42.52994056881594, 38.295457746659594, 35.45678896348048], 235: [45.29500646434315, 43.4020966833841, 36.18389685227275], 234: [42.417417028373606, 40.64476370864763, 35.719683520637155, 33.88513574234161], 169: [41.481854386135815, 39.7482988790481, 34.9318467348161], 143: [45.04], 165: [40.4661], 66: [42.202501825827646, 40.58129817417234], 65: [42.8900258186058, 41.97216473167799, 40.359809449716224], 167: [43.04265455744026, 37.95734544255975], 30: [46.10179446355207, 45.11520043923041, 43.38210584689798, 41.498899250319525], 221: [46.963617701156956, 41.41506323538285, 35.305319063460175], 31: [45.214553382258536, 44.24694661774146], 94: [43.345560076822224, 41.46393992317779], 95: [51.8]}ok test_merge_split_1 (test.test_assembly_graph_copy_depth.TestCopyDepth.test_merge_split_1) Tests a particular part of the graph with merging and splitting. ... ok test_merge_split_2 (test.test_assembly_graph_copy_depth.TestCopyDepth.test_merge_split_2) Tests a particular part of the graph with merging and splitting. ... ok test_single_copy_segments_1 (test.test_assembly_graph_copy_depth.TestCopyDepth.test_single_copy_segments_1) Tests large contigs from the largest replicon, all of which should have a copy depth of 1. ... ok test_single_copy_segments_2 (test.test_assembly_graph_copy_depth.TestCopyDepth.test_single_copy_segments_2) Tests single copy contigs from a smaller, higher depth replicon. They should have a copy ... ok test_random_seq_no_start_gene (test.test_blast_func.TestBlastFunc.test_random_seq_no_start_gene) ... ok test_random_seq_with_exact_gene_forward_strand (test.test_blast_func.TestBlastFunc.test_random_seq_with_exact_gene_forward_strand) ... ok test_random_seq_with_exact_gene_reverse_strand (test.test_blast_func.TestBlastFunc.test_random_seq_with_exact_gene_reverse_strand) ... ok test_1bp_deletion (test.test_cpp_wrappers.TestFullyGlobalAlignment.test_1bp_deletion) ... ok test_1bp_insertion (test.test_cpp_wrappers.TestFullyGlobalAlignment.test_1bp_insertion) ... ok test_2bp_deletion (test.test_cpp_wrappers.TestFullyGlobalAlignment.test_2bp_deletion) ... ok test_2bp_insertion (test.test_cpp_wrappers.TestFullyGlobalAlignment.test_2bp_insertion) ... ok test_2bp_insertion_and_2bp_deletion (test.test_cpp_wrappers.TestFullyGlobalAlignment.test_2bp_insertion_and_2bp_deletion) ... ok test_long_perfect_alignment (test.test_cpp_wrappers.TestFullyGlobalAlignment.test_long_perfect_alignment) ... ok test_one_mismatch (test.test_cpp_wrappers.TestFullyGlobalAlignment.test_one_mismatch) ... ok test_perfect_alignment (test.test_cpp_wrappers.TestFullyGlobalAlignment.test_perfect_alignment) ... ok test_random_seqs (test.test_cpp_wrappers.TestFullyGlobalAlignment.test_random_seqs) This test aligns two random sequences of different length, making sure that the scores are ... ok test_shift_big_band (test.test_cpp_wrappers.TestFullyGlobalAlignment.test_shift_big_band) This test has a 20 bp insertion near the start and a 20 bp deletion near the end, shifting ... ok test_shift_small_band (test.test_cpp_wrappers.TestFullyGlobalAlignment.test_shift_small_band) This test uses the same sequences as the previous test, but uses a smaller bandwidth than ... ok test_consensus_different_qualities (test.test_cpp_wrappers.TestMultipleSequenceAlignment.test_consensus_different_qualities) ... ok test_consensus_with_all (test.test_cpp_wrappers.TestMultipleSequenceAlignment.test_consensus_with_all) ... ok test_consensus_with_deletions (test.test_cpp_wrappers.TestMultipleSequenceAlignment.test_consensus_with_deletions) ... ok test_consensus_with_deletions_and_insertions (test.test_cpp_wrappers.TestMultipleSequenceAlignment.test_consensus_with_deletions_and_insertions) ... ok test_consensus_with_insertions (test.test_cpp_wrappers.TestMultipleSequenceAlignment.test_consensus_with_insertions) ... ok test_consensus_with_subs (test.test_cpp_wrappers.TestMultipleSequenceAlignment.test_consensus_with_subs) ... ok test_start_end_deletions (test.test_cpp_wrappers.TestMultipleSequenceAlignment.test_start_end_deletions) ... ok test_start_end_insertions (test.test_cpp_wrappers.TestMultipleSequenceAlignment.test_start_end_insertions) ... ok test_start_end_insertions_and_deletions (test.test_cpp_wrappers.TestMultipleSequenceAlignment.test_start_end_insertions_and_deletions) ... ok test_two_way_consensus (test.test_cpp_wrappers.TestMultipleSequenceAlignment.test_two_way_consensus) ... ok test_makeblastdb_not_found (test.test_dependencies.TestDependencies.test_makeblastdb_not_found) ... ok test_no_rotate (test.test_dependencies.TestDependencies.test_no_rotate) ... ok test_spades_not_found (test.test_dependencies.TestDependencies.test_spades_not_found) ... ok test_tblastn_not_found (test.test_dependencies.TestDependencies.test_tblastn_not_found) ... ok test_verbosity_1 (test.test_dependencies.TestDependencies.test_verbosity_1) ... ok test_verbosity_2 (test.test_dependencies.TestDependencies.test_verbosity_2) ... ok test_basic_options (test.test_help_text.TestBasicHelpText.test_basic_options) ... ok test_extended_options (test.test_help_text.TestBasicHelpText.test_extended_options) ... ok test_output (test.test_help_text.TestBasicHelpText.test_output) ... ok test_return_code (test.test_help_text.TestBasicHelpText.test_return_code) ... ok test_title (test.test_help_text.TestBasicHelpText.test_title) ... ok test_error_message (test.test_help_text.TestEmptyCommand.test_error_message) ... ok test_output (test.test_help_text.TestEmptyCommand.test_output) ... ok test_return_code (test.test_help_text.TestEmptyCommand.test_return_code) ... ok test_basic_options (test.test_help_text.TestExtendedHelpText.test_basic_options) ... ok test_extended_options (test.test_help_text.TestExtendedHelpText.test_extended_options) ... ok test_output (test.test_help_text.TestExtendedHelpText.test_output) ... ok test_return_code (test.test_help_text.TestExtendedHelpText.test_return_code) ... ok test_title (test.test_help_text.TestExtendedHelpText.test_title) ... ok test_contig_placement_1 (test.test_miniasm_assembly.TestContigPlacement.test_contig_placement_1) This covers the case where the contig sequences are in the middle of the unitig sequences. ... ok test_contig_placement_2 (test.test_miniasm_assembly.TestContigPlacement.test_contig_placement_2) This covers the case where a contig sequence spans the circular junction of the unitig ... ok test_contig_placement_3 (test.test_miniasm_assembly.TestContigPlacement.test_contig_placement_3) This covers the case where the a contig sequence starts right at the beginning of the ... ok test_contig_placement_4 (test.test_miniasm_assembly.TestContigPlacement.test_contig_placement_4) This covers the case where the a contig sequence ends right at the end of the unitig ... ok test_add_line_breaks_to_sequence (test.test_misc.TestMiscFunctions.test_add_line_breaks_to_sequence) ... ok test_colour (test.test_misc.TestMiscFunctions.test_colour) ... ok test_flip_number_order (test.test_misc.TestMiscFunctions.test_flip_number_order) ... ok test_float_to_str (test.test_misc.TestMiscFunctions.test_float_to_str) ... ok test_get_compression_type (test.test_misc.TestMiscFunctions.test_get_compression_type) ... ok test_get_nice_header (test.test_misc.TestMiscFunctions.test_get_nice_header) ... ok test_get_num_agreement (test.test_misc.TestMiscFunctions.test_get_num_agreement) ... ok test_get_percentile (test.test_misc.TestMiscFunctions.test_get_percentile) ... ok test_get_random_base (test.test_misc.TestMiscFunctions.test_get_random_base) ... ok test_get_random_sequence (test.test_misc.TestMiscFunctions.test_get_random_sequence) ... ok test_get_sequence_file_type (test.test_misc.TestMiscFunctions.test_get_sequence_file_type) ... ok test_int_to_str (test.test_misc.TestMiscFunctions.test_int_to_str) ... ok test_is_header_spades_format (test.test_misc.TestMiscFunctions.test_is_header_spades_format) ... ok test_len_without_format (test.test_misc.TestMiscFunctions.test_len_without_format) ... ok test_load_fasta (test.test_misc.TestMiscFunctions.test_load_fasta) ... ok test_load_fasta_with_full_header (test.test_misc.TestMiscFunctions.test_load_fasta_with_full_header) ... ok test_remove_formatting (test.test_misc.TestMiscFunctions.test_remove_formatting) ... ok test_reverse_complement (test.test_misc.TestMiscFunctions.test_reverse_complement) ... ok test_round_to_nearest_odd (test.test_misc.TestMiscFunctions.test_round_to_nearest_odd) ... ok test_score_function (test.test_misc.TestMiscFunctions.test_score_function) ... ok test_spades_version_parsing_1 (test.test_misc.TestMiscFunctions.test_spades_version_parsing_1) ... ok test_spades_version_parsing_2 (test.test_misc.TestMiscFunctions.test_spades_version_parsing_2) ... ok test_spades_version_parsing_3 (test.test_misc.TestMiscFunctions.test_spades_version_parsing_3) ... ok test_spades_version_parsing_4 (test.test_misc.TestMiscFunctions.test_spades_version_parsing_4) ... ok test_spades_version_status_1 (test.test_misc.TestMiscFunctions.test_spades_version_status_1) ... ok test_spades_version_status_10 (test.test_misc.TestMiscFunctions.test_spades_version_status_10) ... ok test_spades_version_status_11 (test.test_misc.TestMiscFunctions.test_spades_version_status_11) ... ok test_spades_version_status_12 (test.test_misc.TestMiscFunctions.test_spades_version_status_12) ... ok test_spades_version_status_13 (test.test_misc.TestMiscFunctions.test_spades_version_status_13) ... ok test_spades_version_status_2 (test.test_misc.TestMiscFunctions.test_spades_version_status_2) ... ok test_spades_version_status_3 (test.test_misc.TestMiscFunctions.test_spades_version_status_3) ... ok test_spades_version_status_4 (test.test_misc.TestMiscFunctions.test_spades_version_status_4) ... ok test_spades_version_status_5 (test.test_misc.TestMiscFunctions.test_spades_version_status_5) ... ok test_spades_version_status_6 (test.test_misc.TestMiscFunctions.test_spades_version_status_6) ... ok test_spades_version_status_7 (test.test_misc.TestMiscFunctions.test_spades_version_status_7) ... ok test_spades_version_status_8 (test.test_misc.TestMiscFunctions.test_spades_version_status_8) ... ok test_spades_version_status_9 (test.test_misc.TestMiscFunctions.test_spades_version_status_9) ... ok test_strip_read_extensions_capitals (test.test_misc.TestMiscFunctions.test_strip_read_extensions_capitals) ... ok test_strip_read_extensions_fa (test.test_misc.TestMiscFunctions.test_strip_read_extensions_fa) ... ok test_strip_read_extensions_fasta (test.test_misc.TestMiscFunctions.test_strip_read_extensions_fasta) ... ok test_strip_read_extensions_fastq (test.test_misc.TestMiscFunctions.test_strip_read_extensions_fastq) ... ok test_strip_read_extensions_fastq_extra_dots (test.test_misc.TestMiscFunctions.test_strip_read_extensions_fastq_extra_dots) ... ok test_strip_read_extensions_fna (test.test_misc.TestMiscFunctions.test_strip_read_extensions_fna) ... ok test_strip_read_extensions_fq (test.test_misc.TestMiscFunctions.test_strip_read_extensions_fq) ... ok test_strip_read_extensions_other_fasta (test.test_misc.TestMiscFunctions.test_strip_read_extensions_other_fasta) ... ok test_weighted_average (test.test_misc.TestMiscFunctions.test_weighted_average) ... ok test_weighted_average_list (test.test_misc.TestMiscFunctions.test_weighted_average_list) ... ok test_absolute_paths (test.test_options.TestUnicyclerOptions.test_absolute_paths) ... ok test_defaults (test.test_options.TestUnicyclerOptions.test_defaults) ... ok test_modes (test.test_options.TestUnicyclerOptions.test_modes) ... ok test_relative_paths (test.test_options.TestUnicyclerOptions.test_relative_paths) ... ok test_long_contained_read (test.test_semi_global_alignment.TestContainedReadAlignments.test_long_contained_read) ... ok test_medium_contained_read (test.test_semi_global_alignment.TestContainedReadAlignments.test_medium_contained_read) ... ok test_short_contained_read (test.test_semi_global_alignment.TestContainedReadAlignments.test_short_contained_read) ... ok test_end_to_end (test.test_semi_global_alignment.TestPerfectMatchAlignments.test_end_to_end) ... ok test_read_contained_1 (test.test_semi_global_alignment.TestPerfectMatchAlignments.test_read_contained_1) ... ok test_read_contained_2 (test.test_semi_global_alignment.TestPerfectMatchAlignments.test_read_contained_2) ... ok test_read_contained_3 (test.test_semi_global_alignment.TestPerfectMatchAlignments.test_read_contained_3) ... ok test_read_end_overlap (test.test_semi_global_alignment.TestPerfectMatchAlignments.test_read_end_overlap) ... ok test_read_start_overlap (test.test_semi_global_alignment.TestPerfectMatchAlignments.test_read_start_overlap) ... ok test_ref_contained_1 (test.test_semi_global_alignment.TestPerfectMatchAlignments.test_ref_contained_1) ... ok test_ref_contained_2 (test.test_semi_global_alignment.TestPerfectMatchAlignments.test_ref_contained_2) ... ok test_ref_contained_3 (test.test_semi_global_alignment.TestPerfectMatchAlignments.test_ref_contained_3) ... ok test_tough_alignment_0 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_0) The beginning of the reference in this case is repetitive, which was able to throw off ... ok test_tough_alignment_1 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_1) This read goes through a repetitive area, which means that the densest area of common ... ok test_tough_alignment_10 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_10) This is a very low quality read. ... ok test_tough_alignment_11 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_11) Repeats at one end of the read. ... ok test_tough_alignment_12 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_12) Repeats at one end of the read. ... ok test_tough_alignment_13 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_13) This read caused a crash before I added the getMaxSeedChainGapArea function in ... ok test_tough_alignment_14 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_14) This read caused a crash before I added made a few fixes to the line tracing code. It won't ... ok test_tough_alignment_15 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_15) This read should hit the same reference twice, even at low sensitivities. ... ok test_tough_alignment_2 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_2) This read goes through a repetitive area, which means that the densest area of common ... ok test_tough_alignment_3 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_3) The first line tracing of this alignment is bad but uses all the points. This previously ... ok test_tough_alignment_4 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_4) Like so many of these tough ones, this case has a read which enters a repetitive region ... ok test_tough_alignment_5 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_5) ... ok test_tough_alignment_6 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_6) This one misses the right alignment on lower sensitivities because the line tracing never ... ok test_tough_alignment_7 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_7) This one misses the right alignment on lower sensitivities because the line tracing never ... ok test_tough_alignment_8 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_8) This has a weird change in slope - the read has a good part and a bad part. Ideally the ... ok test_tough_alignment_9 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_9) This is a very low quality read. ... ok test_bad_fastq_1 (test.test_spades_func.TestSPAdesFunc.test_bad_fastq_1) ... ok test_bad_fastq_2 (test.test_spades_func.TestSPAdesFunc.test_bad_fastq_2) ... ok test_build_spades_command_1 (test.test_spades_func.TestSPAdesFunc.test_build_spades_command_1) ... ok test_build_spades_command_2 (test.test_spades_func.TestSPAdesFunc.test_build_spades_command_2) ... ok test_build_spades_command_3 (test.test_spades_func.TestSPAdesFunc.test_build_spades_command_3) ... ok test_build_spades_command_4 (test.test_spades_func.TestSPAdesFunc.test_build_spades_command_4) ... ok test_build_spades_command_5 (test.test_spades_func.TestSPAdesFunc.test_build_spades_command_5) ... ok test_build_spades_command_6 (test.test_spades_func.TestSPAdesFunc.test_build_spades_command_6) ... ok test_get_read_count_1 (test.test_spades_func.TestSPAdesFunc.test_get_read_count_1) ... ok test_get_read_count_2 (test.test_spades_func.TestSPAdesFunc.test_get_read_count_2) ... ok test_get_read_lengths_1 (test.test_spades_func.TestSPAdesFunc.test_get_read_lengths_1) ... ok test_get_read_lengths_2 (test.test_spades_func.TestSPAdesFunc.test_get_read_lengths_2) ... ok ---------------------------------------------------------------------- Ran 227 tests in 55.560s OK I: pybuild pybuild:334: rm /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler-runner.py; rm -r /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/sample_data; rm -r /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler/__pycache__ create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/unicycler-0.5.0+dfsg' dh_auto_install --destdir=debian/unicycler I: pybuild base:311: /usr/bin/python3.12 setup.py install --root /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler running install /build/reproducible-path/unicycler-0.5.0+dfsg/setup.py:86: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! install.initialize_options(self) running build running build_py running install_lib creating /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr creating /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib creating /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12 creating /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages creating /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/bridge_loop_unroll.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/bridge_miniasm.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/unicycler.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/assembly_graph_segment.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/alignment.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/log.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/bridge_common.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/bridge_spades_contig.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/string_graph.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/miniasm_assembly.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/unicycler_align.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/assembly_graph_copy_depth.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/bridge_long_read.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/version.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/blast_func.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/__init__.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/cpp_functions.so -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/cpp_wrappers.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/read_ref.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/spades_func.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/misc.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/minimap_alignment.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/bridge_long_read_simple.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/assembly_graph.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/settings.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/path_finding.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/bridge_loop_unroll.py to bridge_loop_unroll.cpython-312.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/bridge_miniasm.py to bridge_miniasm.cpython-312.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/unicycler.py to unicycler.cpython-312.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/assembly_graph_segment.py to assembly_graph_segment.cpython-312.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/alignment.py to alignment.cpython-312.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/log.py to log.cpython-312.pyc /usr/lib/python3.12/dist-packages/unicycler/log.py:194: SyntaxWarning: invalid escape sequence '\[' byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/bridge_common.py to bridge_common.cpython-312.pyc /usr/lib/python3.12/dist-packages/unicycler/bridge_common.py:43: SyntaxWarning: invalid escape sequence '\l' byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/bridge_spades_contig.py to bridge_spades_contig.cpython-312.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/string_graph.py to string_graph.cpython-312.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/miniasm_assembly.py to miniasm_assembly.cpython-312.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/unicycler_align.py to unicycler_align.cpython-312.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/assembly_graph_copy_depth.py to assembly_graph_copy_depth.cpython-312.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/bridge_long_read.py to bridge_long_read.cpython-312.pyc /usr/lib/python3.12/dist-packages/unicycler/bridge_long_read.py:619: SyntaxWarning: invalid escape sequence '\c' byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/version.py to version.cpython-312.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/blast_func.py to blast_func.cpython-312.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/cpp_wrappers.py to cpp_wrappers.cpython-312.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/read_ref.py to read_ref.cpython-312.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/spades_func.py to spades_func.cpython-312.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/misc.py to misc.cpython-312.pyc /usr/lib/python3.12/dist-packages/unicycler/misc.py:641: SyntaxWarning: invalid escape sequence '\[' /usr/lib/python3.12/dist-packages/unicycler/misc.py:743: SyntaxWarning: invalid escape sequence '\ ' /usr/lib/python3.12/dist-packages/unicycler/misc.py:744: SyntaxWarning: invalid escape sequence '\ ' /usr/lib/python3.12/dist-packages/unicycler/misc.py:753: SyntaxWarning: invalid escape sequence '\ ' /usr/lib/python3.12/dist-packages/unicycler/misc.py:754: SyntaxWarning: invalid escape sequence '\_' /usr/lib/python3.12/dist-packages/unicycler/misc.py:757: SyntaxWarning: invalid escape sequence '\_' byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/minimap_alignment.py to minimap_alignment.cpython-312.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/bridge_long_read_simple.py to bridge_long_read_simple.cpython-312.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/assembly_graph.py to assembly_graph.cpython-312.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/settings.py to settings.cpython-312.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/path_finding.py to path_finding.cpython-312.pyc running install_egg_info running egg_info creating unicycler.egg-info writing unicycler.egg-info/PKG-INFO writing dependency_links to unicycler.egg-info/dependency_links.txt writing entry points to unicycler.egg-info/entry_points.txt writing top-level names to unicycler.egg-info/top_level.txt writing manifest file 'unicycler.egg-info/SOURCES.txt' reading manifest file 'unicycler.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'unicycler.egg-info/SOURCES.txt' Copying unicycler.egg-info to /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler-0.5.0.egg-info Skipping SOURCES.txt running install_scripts Installing unicycler script to /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/bin  __  \ \___  \ ___\  //  ____// _ _ _ _  //_ //\\ | | | | |_| | | // \// \\ | | | | _ __ _ ___ _ _ ___ | | ___ _ __ || (O) || | | | || '_ \ | | / __|| | | | / __|| | / _ \| '__| \\ \_ // | |__| || | | || || (__ | |_| || (__ | || __/| |  \\_____// \____/ |_| |_||_| \___| \__, | \___||_| \___||_|  __/ |  |___/ Unicycler is installed! Example commands: unicycler --help unicycler --help_all unicycler -1 short_reads_1.fastq.gz -2 short_reads_2.fastq.gz -o path/to/output_dir unicycler -1 short_reads_1.fastq.gz -2 short_reads_2.fastq.gz -l long_reads.fastq.gz -o path/to/output_dir All tools required by Unicycler were found. I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler running install /build/reproducible-path/unicycler-0.5.0+dfsg/setup.py:86: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! install.initialize_options(self) running build running build_py running install_lib creating /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11 creating /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages creating /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler/bridge_loop_unroll.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler/bridge_miniasm.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler/unicycler.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler/assembly_graph_segment.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler/alignment.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler/log.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler/bridge_common.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler/bridge_spades_contig.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler/string_graph.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler/miniasm_assembly.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler/unicycler_align.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler/assembly_graph_copy_depth.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler/bridge_long_read.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler/version.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler/blast_func.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler/__init__.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler/cpp_functions.so -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler/cpp_wrappers.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler/read_ref.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler/spades_func.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler/misc.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler/minimap_alignment.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler/bridge_long_read_simple.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler/assembly_graph.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler/settings.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler copying /build/reproducible-path/unicycler-0.5.0+dfsg/.pybuild/cpython3_3.11_unicycler/build/unicycler/path_finding.py -> /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler/bridge_loop_unroll.py to bridge_loop_unroll.cpython-311.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler/bridge_miniasm.py to bridge_miniasm.cpython-311.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler/unicycler.py to unicycler.cpython-311.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler/assembly_graph_segment.py to assembly_graph_segment.cpython-311.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler/alignment.py to alignment.cpython-311.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler/log.py to log.cpython-311.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler/bridge_common.py to bridge_common.cpython-311.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler/bridge_spades_contig.py to bridge_spades_contig.cpython-311.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler/string_graph.py to string_graph.cpython-311.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler/miniasm_assembly.py to miniasm_assembly.cpython-311.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler/unicycler_align.py to unicycler_align.cpython-311.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler/assembly_graph_copy_depth.py to assembly_graph_copy_depth.cpython-311.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler/bridge_long_read.py to bridge_long_read.cpython-311.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler/version.py to version.cpython-311.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler/blast_func.py to blast_func.cpython-311.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler/cpp_wrappers.py to cpp_wrappers.cpython-311.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler/read_ref.py to read_ref.cpython-311.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler/spades_func.py to spades_func.cpython-311.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler/misc.py to misc.cpython-311.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler/minimap_alignment.py to minimap_alignment.cpython-311.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler/bridge_long_read_simple.py to bridge_long_read_simple.cpython-311.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler/assembly_graph.py to assembly_graph.cpython-311.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler/settings.py to settings.cpython-311.pyc byte-compiling /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler/path_finding.py to path_finding.cpython-311.pyc running install_egg_info running egg_info writing unicycler.egg-info/PKG-INFO writing dependency_links to unicycler.egg-info/dependency_links.txt writing entry points to unicycler.egg-info/entry_points.txt writing top-level names to unicycler.egg-info/top_level.txt reading manifest file 'unicycler.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'unicycler.egg-info/SOURCES.txt' Copying unicycler.egg-info to /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/lib/python3.11/dist-packages/unicycler-0.5.0.egg-info Skipping SOURCES.txt running install_scripts Installing unicycler script to /build/reproducible-path/unicycler-0.5.0+dfsg/debian/unicycler/usr/bin  __  \ \___  \ ___\  //  ____// _ _ _ _  //_ //\\ | | | | |_| | | // \// \\ | | | | _ __ _ ___ _ _ ___ | | ___ _ __ || (O) || | | | || '_ \ | | / __|| | | | / __|| | / _ \| '__| \\ \_ // | |__| || | | || || (__ | |_| || (__ | || __/| |  \\_____// \____/ |_| |_||_| \___| \__, | \___||_| \___||_|  __/ |  |___/ Unicycler is installed! Example commands: unicycler --help unicycler --help_all unicycler -1 short_reads_1.fastq.gz -2 short_reads_2.fastq.gz -o path/to/output_dir unicycler -1 short_reads_1.fastq.gz -2 short_reads_2.fastq.gz -l long_reads.fastq.gz -o path/to/output_dir All tools required by Unicycler were found. make[1]: Leaving directory '/build/reproducible-path/unicycler-0.5.0+dfsg' dh_install -O--buildsystem=pybuild dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild debian/rules override_dh_python3 make[1]: Entering directory '/build/reproducible-path/unicycler-0.5.0+dfsg' dh_python3 --no-ext-rename make[1]: Leaving directory '/build/reproducible-path/unicycler-0.5.0+dfsg' 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 dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'unicycler' in '../unicycler_0.5.0+dfsg-1_amd64.deb'. dpkg-deb: building package 'unicycler-dbgsym' in '../unicycler-dbgsym_0.5.0+dfsg-1_amd64.deb'. dpkg-deb: building package 'unicycler-data' in '../unicycler-data_0.5.0+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../unicycler_0.5.0+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../unicycler_0.5.0+dfsg-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: user script /srv/workspace/pbuilder/1967276/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1967276/tmp/hooks/B01_cleanup finished 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/1967276 and its subdirectories I: Current time: Fri May 17 09:20:50 +14 2024 I: pbuilder-time-stamp: 1715887250