0s autopkgtest [23:39:21]: starting date and time: 2024-11-14 23:39:21+0000 0s autopkgtest [23:39:21]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [23:39:21]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.xvvhq9ek/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python-biopython --apt-upgrade ariba --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python-biopython/1.84+dfsg-4build1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-ppc64el-2.secgroup --name adt-plucky-ppc64el-ariba-20241114-233126-juju-7f2275-prod-proposed-migration-environment-15-960a3276-6f42-4dbc-a8f6-e4e06cc9dc20 --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-ppc64el -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 95s autopkgtest [23:40:56]: testbed dpkg architecture: ppc64el 95s autopkgtest [23:40:56]: testbed apt version: 2.9.8 95s autopkgtest [23:40:56]: @@@@@@@@@@@@@@@@@@@@ test bed setup 96s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 96s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1015 kB] 97s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.5 kB] 97s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.1 kB] 97s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 97s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [121 kB] 97s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [759 kB] 97s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [8632 B] 97s Fetched 2100 kB in 1s (2356 kB/s) 97s Reading package lists... 99s Reading package lists... 99s Building dependency tree... 99s Reading state information... 100s Calculating upgrade... 100s The following packages will be upgraded: 100s bpfcc-tools bpftrace libbpfcc libcap-ng0 libgnutls30t64 libjson-glib-1.0-0 100s libjson-glib-1.0-common libnewt0.52 libutempter0 lxd-installer man-db 100s pastebinit python3-bpfcc python3-newt python3-systemd whiptail 100s 16 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 100s Need to get 6045 kB of archives. 100s After this operation, 453 kB of additional disk space will be used. 100s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcap-ng0 ppc64el 0.8.5-3build1 [16.3 kB] 100s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgnutls30t64 ppc64el 3.8.8-2ubuntu1 [1072 kB] 100s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-newt ppc64el 0.52.24-2ubuntu4 [21.8 kB] 100s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libnewt0.52 ppc64el 0.52.24-2ubuntu4 [62.1 kB] 100s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el whiptail ppc64el 0.52.24-2ubuntu4 [19.5 kB] 100s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el man-db ppc64el 2.13.0-1 [1361 kB] 100s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el libbpfcc ppc64el 0.30.0+ds-1ubuntu5 [696 kB] 100s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-bpfcc all 0.30.0+ds-1ubuntu5 [40.4 kB] 100s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpfcc-tools all 0.30.0+ds-1ubuntu5 [697 kB] 100s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpftrace ppc64el 0.21.2-2ubuntu2 [1898 kB] 101s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 101s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-0 ppc64el 1.10.0+ds-3 [76.0 kB] 101s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el libutempter0 ppc64el 1.2.1-4 [9850 B] 101s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el lxd-installer all 9 [5084 B] 101s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el pastebinit all 1.7.1-1 [14.9 kB] 101s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-systemd ppc64el 235-1build5 [48.7 kB] 101s Preconfiguring packages ... 101s Fetched 6045 kB in 1s (6718 kB/s) 101s (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 ... 73767 files and directories currently installed.) 101s Preparing to unpack .../libcap-ng0_0.8.5-3build1_ppc64el.deb ... 101s Unpacking libcap-ng0:ppc64el (0.8.5-3build1) over (0.8.5-1) ... 101s Setting up libcap-ng0:ppc64el (0.8.5-3build1) ... 101s (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 ... 73767 files and directories currently installed.) 101s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_ppc64el.deb ... 101s Unpacking libgnutls30t64:ppc64el (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 101s Setting up libgnutls30t64:ppc64el (3.8.8-2ubuntu1) ... 101s (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 ... 73767 files and directories currently installed.) 101s Preparing to unpack .../00-python3-newt_0.52.24-2ubuntu4_ppc64el.deb ... 101s Unpacking python3-newt:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 101s Preparing to unpack .../01-libnewt0.52_0.52.24-2ubuntu4_ppc64el.deb ... 101s Unpacking libnewt0.52:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 101s Preparing to unpack .../02-whiptail_0.52.24-2ubuntu4_ppc64el.deb ... 101s Unpacking whiptail (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 101s Preparing to unpack .../03-man-db_2.13.0-1_ppc64el.deb ... 101s Unpacking man-db (2.13.0-1) over (2.12.1-3) ... 102s Preparing to unpack .../04-libbpfcc_0.30.0+ds-1ubuntu5_ppc64el.deb ... 102s Unpacking libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 102s Preparing to unpack .../05-python3-bpfcc_0.30.0+ds-1ubuntu5_all.deb ... 102s Unpacking python3-bpfcc (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 102s Preparing to unpack .../06-bpfcc-tools_0.30.0+ds-1ubuntu5_all.deb ... 102s Unpacking bpfcc-tools (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 102s Preparing to unpack .../07-bpftrace_0.21.2-2ubuntu2_ppc64el.deb ... 102s Unpacking bpftrace (0.21.2-2ubuntu2) over (0.21.2-2) ... 102s Preparing to unpack .../08-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 102s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 102s Preparing to unpack .../09-libjson-glib-1.0-0_1.10.0+ds-3_ppc64el.deb ... 102s Unpacking libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) over (1.10.0+ds-2) ... 102s Preparing to unpack .../10-libutempter0_1.2.1-4_ppc64el.deb ... 102s Unpacking libutempter0:ppc64el (1.2.1-4) over (1.2.1-3build1) ... 102s Preparing to unpack .../11-lxd-installer_9_all.deb ... 102s Unpacking lxd-installer (9) over (8) ... 102s Preparing to unpack .../12-pastebinit_1.7.1-1_all.deb ... 102s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 102s Preparing to unpack .../13-python3-systemd_235-1build5_ppc64el.deb ... 102s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 102s Setting up libnewt0.52:ppc64el (0.52.24-2ubuntu4) ... 102s Setting up pastebinit (1.7.1-1) ... 102s Setting up python3-newt:ppc64el (0.52.24-2ubuntu4) ... 102s Setting up man-db (2.13.0-1) ... 102s Updating database of manual pages ... 105s man-db.service is a disabled or a static unit not running, not starting it. 105s Setting up lxd-installer (9) ... 105s Setting up libutempter0:ppc64el (1.2.1-4) ... 105s Setting up whiptail (0.52.24-2ubuntu4) ... 105s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 105s Setting up libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) ... 105s Setting up python3-bpfcc (0.30.0+ds-1ubuntu5) ... 105s Setting up python3-systemd (235-1build5) ... 106s Setting up bpftrace (0.21.2-2ubuntu2) ... 106s Setting up libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) ... 106s Setting up bpfcc-tools (0.30.0+ds-1ubuntu5) ... 106s Processing triggers for libc-bin (2.40-1ubuntu3) ... 106s Reading package lists... 106s Building dependency tree... 106s Reading state information... 106s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 106s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 106s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 107s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 107s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 108s Reading package lists... 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 108s Calculating upgrade... 108s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 108s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 109s autopkgtest [23:41:10]: rebooting testbed after setup commands that affected boot 112s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 140s autopkgtest [23:41:41]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 13:49:23 UTC 2024 142s autopkgtest [23:41:43]: @@@@@@@@@@@@@@@@@@@@ apt-source ariba 144s Get:1 http://ftpmaster.internal/ubuntu plucky/universe ariba 2.14.7+ds-4 (dsc) [2316 B] 144s Get:2 http://ftpmaster.internal/ubuntu plucky/universe ariba 2.14.7+ds-4 (tar) [1920 kB] 144s Get:3 http://ftpmaster.internal/ubuntu plucky/universe ariba 2.14.7+ds-4 (diff) [10.7 kB] 145s gpgv: Signature made Tue Nov 5 03:36:42 2024 UTC 145s gpgv: using RSA key 13796755BBC72BB8ABE2AEB5FA9DEC5DE11C63F1 145s gpgv: issuer "eamanu@debian.org" 145s gpgv: Can't check signature: No public key 145s dpkg-source: warning: cannot verify inline signature for ./ariba_2.14.7+ds-4.dsc: no acceptable signature found 145s autopkgtest [23:41:46]: testing package ariba version 2.14.7+ds-4 145s autopkgtest [23:41:46]: build not needed 149s autopkgtest [23:41:50]: test test-example: preparing testbed 150s Reading package lists... 151s Building dependency tree... 151s Reading state information... 151s Starting pkgProblemResolver with broken count: 0 151s Starting 2 pkgProblemResolver with broken count: 0 151s Done 151s The following additional packages will be installed: 151s ariba blt bowtie2 cd-hit fastaq fontconfig-config fonts-dejavu-core 151s fonts-dejavu-mono fonts-lyx fonts-urw-base35 libblas3 libcairo2 151s libcapnp-1.0.1 libdeflate0 libfml0 libfontconfig1 libfontenc1 libgfortran5 151s libgomp1 libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b libhts3t64 151s libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery 151s libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libminimap0 151s libmurmurhash2 libopenjp2-7 libpixman-1-0 libqhull-r8.0 libraqm0 151s libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 151s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 mash 151s mummer python-matplotlib-data python3-appdirs python3-biopython 151s python3-brotli python3-bs4 python3-cairo python3-contourpy python3-cycler 151s python3-dateutil python3-decorator python3-dendropy python3-fonttools 151s python3-freetype python3-fs python3-kiwisolver python3-lxml python3-lz4 151s python3-matplotlib python3-mpmath python3-numpy python3-packaging 151s python3-pil python3-pil.imagetk python3-pymummer python3-pysam 151s python3-reportlab python3-rlpycairo python3-scipy python3-six 151s python3-soupsieve python3-sympy python3-tk python3-tz python3-ufolib2 151s python3-unicodedata2 python3.12-tk samtools sgml-base tk8.6-blt2.5 151s unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 151s Suggested packages: 151s spades blt-demo bowtie2-examples fonts-freefont-otf | fonts-freefont-ttf 151s fonts-texgyre gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html 151s libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 bwa clustalo clustalw 151s dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons 151s python3-mysqldb python3-mmtf python3-rdflib python3-psycopg2 raxml t-coffee 151s wise python-cycler-doc python-lxml-doc cm-super-minimal dvipng ffmpeg 151s fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common 151s python-matplotlib-doc python3-cairocffi python3-gi-cairo python3-gobject 151s python3-pyqt5 python3-sip python3-tornado texlive-extra-utils 151s texlive-latex-extra python-mpmath-doc python3-gmpy2 gcc gfortran 151s python-numpy-doc python3-dev python3-pytest python-pil-doc pdf-viewer 151s python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm 151s python-scipy-doc texlive-fonts-extra python-sympy-doc tix python3-tk-dbg 151s python3.13-tk cwltool sgml-base-doc debhelper 151s Recommended packages: 151s javascript-common python-biopython-doc ncbi-blast+ python3-cssselect 151s python3-html5lib python3-olefile fonts-dejavu-extra g++ | c++-compiler 151s isympy-common 151s The following NEW packages will be installed: 151s ariba autopkgtest-satdep blt bowtie2 cd-hit fastaq fontconfig-config 151s fonts-dejavu-core fonts-dejavu-mono fonts-lyx fonts-urw-base35 libblas3 151s libcairo2 libcapnp-1.0.1 libdeflate0 libfml0 libfontconfig1 libfontenc1 151s libgfortran5 libgomp1 libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b 151s libhts3t64 libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 151s libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblerc4 151s libminimap0 libmurmurhash2 libopenjp2-7 libpixman-1-0 libqhull-r8.0 libraqm0 151s libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 151s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 mash 151s mummer python-matplotlib-data python3-appdirs python3-biopython 151s python3-brotli python3-bs4 python3-cairo python3-contourpy python3-cycler 151s python3-dateutil python3-decorator python3-dendropy python3-fonttools 151s python3-freetype python3-fs python3-kiwisolver python3-lxml python3-lz4 151s python3-matplotlib python3-mpmath python3-numpy python3-packaging 151s python3-pil python3-pil.imagetk python3-pymummer python3-pysam 151s python3-reportlab python3-rlpycairo python3-scipy python3-six 151s python3-soupsieve python3-sympy python3-tk python3-tz python3-ufolib2 151s python3-unicodedata2 python3.12-tk samtools sgml-base tk8.6-blt2.5 151s unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 151s 0 upgraded, 102 newly installed, 0 to remove and 0 not upgraded. 151s Need to get 90.9 MB/90.9 MB of archives. 151s After this operation, 394 MB of additional disk space will be used. 151s Get:1 /tmp/autopkgtest.W9i47c/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [704 B] 151s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el sgml-base all 1.31 [11.4 kB] 151s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdeflate0 ppc64el 1.22-1 [63.3 kB] 152s Get:4 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhtscodecs2 ppc64el 1.6.1-1 [113 kB] 152s Get:5 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhts3t64 ppc64el 1.20+ds-1 [567 kB] 152s Get:6 http://ftpmaster.internal/ubuntu plucky/universe ppc64el samtools ppc64el 1.20-3 [676 kB] 152s Get:7 http://ftpmaster.internal/ubuntu plucky/universe ppc64el fastaq all 3.17.0-8 [48.2 kB] 152s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el libblas3 ppc64el 3.12.0-3build2 [222 kB] 152s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 14.2.0-8ubuntu1 [571 kB] 152s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblapack3 ppc64el 3.12.0-3build2 [2806 kB] 152s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-11build1 [4434 kB] 152s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtcl8.6 ppc64el 8.6.15+dfsg-2 [1201 kB] 152s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB] 152s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB] 152s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfontenc1 ppc64el 1:1.1.8-1build1 [15.8 kB] 152s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el x11-common all 1:7.7+23ubuntu3 [21.7 kB] 152s Get:17 http://ftpmaster.internal/ubuntu plucky/main ppc64el xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 152s Get:18 http://ftpmaster.internal/ubuntu plucky/main ppc64el xfonts-utils ppc64el 1:7.7+7 [114 kB] 152s Get:19 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-urw-base35 all 20200910-8 [11.0 MB] 153s Get:20 http://ftpmaster.internal/ubuntu plucky/main ppc64el fontconfig-config ppc64el 2.15.0-1.1ubuntu2 [37.4 kB] 153s Get:21 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfontconfig1 ppc64el 2.15.0-1.1ubuntu2 [190 kB] 153s Get:22 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1build1 [23.1 kB] 153s Get:23 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxft2 ppc64el 2.3.6-1build1 [61.5 kB] 153s Get:24 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxss1 ppc64el 1:1.2.3-1build3 [7980 B] 153s Get:25 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtk8.6 ppc64el 8.6.15-1 [942 kB] 153s Get:26 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.12-tk ppc64el 3.12.7-3 [116 kB] 153s Get:27 http://ftpmaster.internal/ubuntu plucky/main ppc64el tk8.6-blt2.5 ppc64el 2.5.3+dfsg-7build1 [784 kB] 153s Get:28 http://ftpmaster.internal/ubuntu plucky/main ppc64el blt ppc64el 2.5.3+dfsg-7build1 [4840 B] 153s Get:29 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-tk ppc64el 3.12.6-1ubuntu1 [9806 B] 153s Get:30 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pil.imagetk ppc64el 10.4.0-1ubuntu1 [9810 B] 153s Get:31 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgomp1 ppc64el 14.2.0-8ubuntu1 [161 kB] 153s Get:32 http://ftpmaster.internal/ubuntu plucky/main ppc64el libimagequant0 ppc64el 2.18.0-1build1 [43.2 kB] 153s Get:33 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu2 [219 kB] 153s Get:34 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 153s Get:35 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblcms2-2 ppc64el 2.16-2 [243 kB] 153s Get:36 http://ftpmaster.internal/ubuntu plucky/main ppc64el libopenjp2-7 ppc64el 2.5.0-2ubuntu1 [246 kB] 153s Get:37 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgraphite2-3 ppc64el 1.3.14-2ubuntu1 [84.6 kB] 153s Get:38 http://ftpmaster.internal/ubuntu plucky/main ppc64el libharfbuzz0b ppc64el 10.0.1-1 [596 kB] 153s Get:39 http://ftpmaster.internal/ubuntu plucky/main ppc64el libraqm0 ppc64el 0.10.1-1build1 [19.4 kB] 153s Get:40 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu2 [35.9 kB] 153s Get:41 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblerc4 ppc64el 4.0.0+ds-4ubuntu2 [270 kB] 153s Get:42 http://ftpmaster.internal/ubuntu plucky/main ppc64el libsharpyuv0 ppc64el 1.4.0-0.1 [22.0 kB] 153s Get:43 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebp7 ppc64el 1.4.0-0.1 [309 kB] 153s Get:44 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtiff6 ppc64el 4.5.1+git230720-4ubuntu4 [272 kB] 153s Get:45 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebpdemux2 ppc64el 1.4.0-0.1 [14.1 kB] 153s Get:46 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebpmux3 ppc64el 1.4.0-0.1 [31.4 kB] 153s Get:47 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-pil ppc64el 10.4.0-1ubuntu1 [581 kB] 153s Get:48 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpixman-1-0 ppc64el 0.44.0-3 [334 kB] 153s Get:49 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcb-render0 ppc64el 1.17.0-2 [17.2 kB] 153s Get:50 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcb-shm0 ppc64el 1.17.0-2 [5980 B] 153s Get:51 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcairo2 ppc64el 1.18.2-2 [747 kB] 153s Get:52 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-cairo ppc64el 1.26.1-2 [129 kB] 153s Get:53 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-freetype all 2.5.1-1 [92.3 kB] 153s Get:54 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-rlpycairo all 0.3.0-3 [9130 B] 153s Get:55 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-reportlab all 4.2.5-1 [1107 kB] 153s Get:56 http://ftpmaster.internal/ubuntu plucky/main ppc64el xml-core all 0.19 [20.3 kB] 153s Get:57 http://ftpmaster.internal/ubuntu plucky/universe ppc64el w3c-sgml-lib all 1.3-3 [280 kB] 153s Get:58 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el python3-biopython ppc64el 1.84+dfsg-4build1 [1745 kB] 153s Get:59 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-soupsieve all 2.6-1 [33.0 kB] 153s Get:60 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-bs4 all 4.12.3-3 [109 kB] 153s Get:61 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-dendropy all 4.6.1-1 [278 kB] 153s Get:62 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 153s Get:63 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 153s Get:64 http://ftpmaster.internal/ubuntu plucky/universe ppc64el fonts-lyx all 2.4.2.1-1 [171 kB] 153s Get:65 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python-matplotlib-data all 3.8.3-3 [2928 kB] 153s Get:66 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-six all 1.16.0-7 [13.1 kB] 153s Get:67 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-dateutil all 2.9.0-2 [80.3 kB] 153s Get:68 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-contourpy ppc64el 1.3.0-2 [217 kB] 153s Get:69 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-cycler all 0.12.1-1 [9716 B] 153s Get:70 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-brotli ppc64el 1.1.0-2build2 [413 kB] 153s Get:71 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB] 153s Get:72 http://ftpmaster.internal/ubuntu plucky/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1build1 [33.0 kB] 153s Get:73 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-scipy ppc64el 1.13.1-5 [18.3 MB] 154s Get:74 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 154s Get:75 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-mpmath all 1.3.0-1 [425 kB] 154s Get:76 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-sympy all 1.13.3-1 [4228 kB] 154s Get:77 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-tz all 2024.1-2 [31.4 kB] 154s Get:78 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-appdirs all 1.4.4-4 [10.9 kB] 154s Get:79 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-fs all 2.4.16-4 [91.3 kB] 154s Get:80 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxslt1.1 ppc64el 1.1.39-0exp1ubuntu1 [191 kB] 154s Get:81 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-lxml ppc64el 5.3.0-1 [1354 kB] 154s Get:82 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-lz4 ppc64el 4.0.2+dfsg-1build4 [27.8 kB] 154s Get:83 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-unicodedata2 ppc64el 15.1.0+ds-1build2 [361 kB] 154s Get:84 http://ftpmaster.internal/ubuntu plucky/universe ppc64el unicode-data all 15.1.0-1 [8878 kB] 154s Get:85 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-fonttools ppc64el 4.46.0-1build2 [1473 kB] 154s Get:86 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-kiwisolver ppc64el 1.4.7-2build1 [72.9 kB] 154s Get:87 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-packaging all 24.1-1 [41.4 kB] 154s Get:88 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libqhull-r8.0 ppc64el 2020.2-6build1 [225 kB] 154s Get:89 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-matplotlib ppc64el 3.8.3-3 [4610 kB] 154s Get:90 http://ftpmaster.internal/ubuntu plucky/universe ppc64el mummer ppc64el 3.23+dfsg-8 [714 kB] 154s Get:91 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pymummer all 0.11.0-4 [17.1 kB] 154s Get:92 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pysam ppc64el 0.22.1+ds-2 [3818 kB] 154s Get:93 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libfml0 ppc64el 0.1+git20190320.b499514-1build1 [89.3 kB] 154s Get:94 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libminimap0 ppc64el 0.2-8 [26.3 kB] 154s Get:95 http://ftpmaster.internal/ubuntu plucky/universe ppc64el bowtie2 ppc64el 2.5.4-1 [1437 kB] 154s Get:96 http://ftpmaster.internal/ubuntu plucky/universe ppc64el cd-hit ppc64el 4.8.1-4 [547 kB] 154s Get:97 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libcapnp-1.0.1 ppc64el 1.0.1-4 [1561 kB] 154s Get:98 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libgslcblas0 ppc64el 2.8+dfsg-5 [276 kB] 154s Get:99 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libgsl28 ppc64el 2.8+dfsg-5 [1394 kB] 154s Get:100 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libmurmurhash2 ppc64el 1.6-1 [6626 B] 154s Get:101 http://ftpmaster.internal/ubuntu plucky/universe ppc64el mash ppc64el 2.3+dfsg-6build1 [162 kB] 154s Get:102 http://ftpmaster.internal/ubuntu plucky/universe ppc64el ariba ppc64el 2.14.7+ds-4 [2033 kB] 155s Fetched 90.9 MB in 3s (28.9 MB/s) 155s Selecting previously unselected package sgml-base. 155s (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 ... 73774 files and directories currently installed.) 155s Preparing to unpack .../000-sgml-base_1.31_all.deb ... 155s Unpacking sgml-base (1.31) ... 155s Selecting previously unselected package libdeflate0:ppc64el. 155s Preparing to unpack .../001-libdeflate0_1.22-1_ppc64el.deb ... 155s Unpacking libdeflate0:ppc64el (1.22-1) ... 155s Selecting previously unselected package libhtscodecs2:ppc64el. 155s Preparing to unpack .../002-libhtscodecs2_1.6.1-1_ppc64el.deb ... 155s Unpacking libhtscodecs2:ppc64el (1.6.1-1) ... 155s Selecting previously unselected package libhts3t64:ppc64el. 155s Preparing to unpack .../003-libhts3t64_1.20+ds-1_ppc64el.deb ... 155s Unpacking libhts3t64:ppc64el (1.20+ds-1) ... 155s Selecting previously unselected package samtools. 155s Preparing to unpack .../004-samtools_1.20-3_ppc64el.deb ... 155s Unpacking samtools (1.20-3) ... 155s Selecting previously unselected package fastaq. 155s Preparing to unpack .../005-fastaq_3.17.0-8_all.deb ... 155s Unpacking fastaq (3.17.0-8) ... 155s Selecting previously unselected package libblas3:ppc64el. 155s Preparing to unpack .../006-libblas3_3.12.0-3build2_ppc64el.deb ... 155s Unpacking libblas3:ppc64el (3.12.0-3build2) ... 155s Selecting previously unselected package libgfortran5:ppc64el. 155s Preparing to unpack .../007-libgfortran5_14.2.0-8ubuntu1_ppc64el.deb ... 155s Unpacking libgfortran5:ppc64el (14.2.0-8ubuntu1) ... 155s Selecting previously unselected package liblapack3:ppc64el. 155s Preparing to unpack .../008-liblapack3_3.12.0-3build2_ppc64el.deb ... 155s Unpacking liblapack3:ppc64el (3.12.0-3build2) ... 155s Selecting previously unselected package python3-numpy. 155s Preparing to unpack .../009-python3-numpy_1%3a1.26.4+ds-11build1_ppc64el.deb ... 155s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 156s Selecting previously unselected package libtcl8.6:ppc64el. 156s Preparing to unpack .../010-libtcl8.6_8.6.15+dfsg-2_ppc64el.deb ... 156s Unpacking libtcl8.6:ppc64el (8.6.15+dfsg-2) ... 156s Selecting previously unselected package fonts-dejavu-mono. 156s Preparing to unpack .../011-fonts-dejavu-mono_2.37-8_all.deb ... 156s Unpacking fonts-dejavu-mono (2.37-8) ... 156s Selecting previously unselected package fonts-dejavu-core. 156s Preparing to unpack .../012-fonts-dejavu-core_2.37-8_all.deb ... 156s Unpacking fonts-dejavu-core (2.37-8) ... 156s Selecting previously unselected package libfontenc1:ppc64el. 156s Preparing to unpack .../013-libfontenc1_1%3a1.1.8-1build1_ppc64el.deb ... 156s Unpacking libfontenc1:ppc64el (1:1.1.8-1build1) ... 156s Selecting previously unselected package x11-common. 156s Preparing to unpack .../014-x11-common_1%3a7.7+23ubuntu3_all.deb ... 156s Unpacking x11-common (1:7.7+23ubuntu3) ... 156s Selecting previously unselected package xfonts-encodings. 156s Preparing to unpack .../015-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 156s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 156s Selecting previously unselected package xfonts-utils. 156s Preparing to unpack .../016-xfonts-utils_1%3a7.7+7_ppc64el.deb ... 156s Unpacking xfonts-utils (1:7.7+7) ... 156s Selecting previously unselected package fonts-urw-base35. 156s Preparing to unpack .../017-fonts-urw-base35_20200910-8_all.deb ... 156s Unpacking fonts-urw-base35 (20200910-8) ... 156s Selecting previously unselected package fontconfig-config. 156s Preparing to unpack .../018-fontconfig-config_2.15.0-1.1ubuntu2_ppc64el.deb ... 156s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 156s Selecting previously unselected package libfontconfig1:ppc64el. 156s Preparing to unpack .../019-libfontconfig1_2.15.0-1.1ubuntu2_ppc64el.deb ... 156s Unpacking libfontconfig1:ppc64el (2.15.0-1.1ubuntu2) ... 156s Selecting previously unselected package libxrender1:ppc64el. 156s Preparing to unpack .../020-libxrender1_1%3a0.9.10-1.1build1_ppc64el.deb ... 156s Unpacking libxrender1:ppc64el (1:0.9.10-1.1build1) ... 156s Selecting previously unselected package libxft2:ppc64el. 156s Preparing to unpack .../021-libxft2_2.3.6-1build1_ppc64el.deb ... 156s Unpacking libxft2:ppc64el (2.3.6-1build1) ... 156s Selecting previously unselected package libxss1:ppc64el. 156s Preparing to unpack .../022-libxss1_1%3a1.2.3-1build3_ppc64el.deb ... 156s Unpacking libxss1:ppc64el (1:1.2.3-1build3) ... 156s Selecting previously unselected package libtk8.6:ppc64el. 156s Preparing to unpack .../023-libtk8.6_8.6.15-1_ppc64el.deb ... 156s Unpacking libtk8.6:ppc64el (8.6.15-1) ... 156s Selecting previously unselected package python3.12-tk. 156s Preparing to unpack .../024-python3.12-tk_3.12.7-3_ppc64el.deb ... 156s Unpacking python3.12-tk (3.12.7-3) ... 156s Selecting previously unselected package tk8.6-blt2.5. 156s Preparing to unpack .../025-tk8.6-blt2.5_2.5.3+dfsg-7build1_ppc64el.deb ... 156s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 156s Selecting previously unselected package blt. 156s Preparing to unpack .../026-blt_2.5.3+dfsg-7build1_ppc64el.deb ... 156s Unpacking blt (2.5.3+dfsg-7build1) ... 156s Selecting previously unselected package python3-tk:ppc64el. 156s Preparing to unpack .../027-python3-tk_3.12.6-1ubuntu1_ppc64el.deb ... 156s Unpacking python3-tk:ppc64el (3.12.6-1ubuntu1) ... 156s Selecting previously unselected package python3-pil.imagetk:ppc64el. 156s Preparing to unpack .../028-python3-pil.imagetk_10.4.0-1ubuntu1_ppc64el.deb ... 156s Unpacking python3-pil.imagetk:ppc64el (10.4.0-1ubuntu1) ... 156s Selecting previously unselected package libgomp1:ppc64el. 156s Preparing to unpack .../029-libgomp1_14.2.0-8ubuntu1_ppc64el.deb ... 156s Unpacking libgomp1:ppc64el (14.2.0-8ubuntu1) ... 156s Selecting previously unselected package libimagequant0:ppc64el. 156s Preparing to unpack .../030-libimagequant0_2.18.0-1build1_ppc64el.deb ... 156s Unpacking libimagequant0:ppc64el (2.18.0-1build1) ... 156s Selecting previously unselected package libjpeg-turbo8:ppc64el. 156s Preparing to unpack .../031-libjpeg-turbo8_2.1.5-2ubuntu2_ppc64el.deb ... 156s Unpacking libjpeg-turbo8:ppc64el (2.1.5-2ubuntu2) ... 156s Selecting previously unselected package libjpeg8:ppc64el. 156s Preparing to unpack .../032-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 156s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 156s Selecting previously unselected package liblcms2-2:ppc64el. 156s Preparing to unpack .../033-liblcms2-2_2.16-2_ppc64el.deb ... 156s Unpacking liblcms2-2:ppc64el (2.16-2) ... 156s Selecting previously unselected package libopenjp2-7:ppc64el. 156s Preparing to unpack .../034-libopenjp2-7_2.5.0-2ubuntu1_ppc64el.deb ... 156s Unpacking libopenjp2-7:ppc64el (2.5.0-2ubuntu1) ... 156s Selecting previously unselected package libgraphite2-3:ppc64el. 156s Preparing to unpack .../035-libgraphite2-3_1.3.14-2ubuntu1_ppc64el.deb ... 156s Unpacking libgraphite2-3:ppc64el (1.3.14-2ubuntu1) ... 156s Selecting previously unselected package libharfbuzz0b:ppc64el. 156s Preparing to unpack .../036-libharfbuzz0b_10.0.1-1_ppc64el.deb ... 156s Unpacking libharfbuzz0b:ppc64el (10.0.1-1) ... 156s Selecting previously unselected package libraqm0:ppc64el. 156s Preparing to unpack .../037-libraqm0_0.10.1-1build1_ppc64el.deb ... 156s Unpacking libraqm0:ppc64el (0.10.1-1build1) ... 156s Selecting previously unselected package libjbig0:ppc64el. 156s Preparing to unpack .../038-libjbig0_2.1-6.1ubuntu2_ppc64el.deb ... 156s Unpacking libjbig0:ppc64el (2.1-6.1ubuntu2) ... 156s Selecting previously unselected package liblerc4:ppc64el. 156s Preparing to unpack .../039-liblerc4_4.0.0+ds-4ubuntu2_ppc64el.deb ... 156s Unpacking liblerc4:ppc64el (4.0.0+ds-4ubuntu2) ... 156s Selecting previously unselected package libsharpyuv0:ppc64el. 156s Preparing to unpack .../040-libsharpyuv0_1.4.0-0.1_ppc64el.deb ... 156s Unpacking libsharpyuv0:ppc64el (1.4.0-0.1) ... 156s Selecting previously unselected package libwebp7:ppc64el. 156s Preparing to unpack .../041-libwebp7_1.4.0-0.1_ppc64el.deb ... 156s Unpacking libwebp7:ppc64el (1.4.0-0.1) ... 157s Selecting previously unselected package libtiff6:ppc64el. 157s Preparing to unpack .../042-libtiff6_4.5.1+git230720-4ubuntu4_ppc64el.deb ... 157s Unpacking libtiff6:ppc64el (4.5.1+git230720-4ubuntu4) ... 157s Selecting previously unselected package libwebpdemux2:ppc64el. 157s Preparing to unpack .../043-libwebpdemux2_1.4.0-0.1_ppc64el.deb ... 157s Unpacking libwebpdemux2:ppc64el (1.4.0-0.1) ... 157s Selecting previously unselected package libwebpmux3:ppc64el. 157s Preparing to unpack .../044-libwebpmux3_1.4.0-0.1_ppc64el.deb ... 157s Unpacking libwebpmux3:ppc64el (1.4.0-0.1) ... 157s Selecting previously unselected package python3-pil:ppc64el. 157s Preparing to unpack .../045-python3-pil_10.4.0-1ubuntu1_ppc64el.deb ... 157s Unpacking python3-pil:ppc64el (10.4.0-1ubuntu1) ... 157s Selecting previously unselected package libpixman-1-0:ppc64el. 157s Preparing to unpack .../046-libpixman-1-0_0.44.0-3_ppc64el.deb ... 157s Unpacking libpixman-1-0:ppc64el (0.44.0-3) ... 157s Selecting previously unselected package libxcb-render0:ppc64el. 157s Preparing to unpack .../047-libxcb-render0_1.17.0-2_ppc64el.deb ... 157s Unpacking libxcb-render0:ppc64el (1.17.0-2) ... 157s Selecting previously unselected package libxcb-shm0:ppc64el. 157s Preparing to unpack .../048-libxcb-shm0_1.17.0-2_ppc64el.deb ... 157s Unpacking libxcb-shm0:ppc64el (1.17.0-2) ... 157s Selecting previously unselected package libcairo2:ppc64el. 157s Preparing to unpack .../049-libcairo2_1.18.2-2_ppc64el.deb ... 157s Unpacking libcairo2:ppc64el (1.18.2-2) ... 157s Selecting previously unselected package python3-cairo. 157s Preparing to unpack .../050-python3-cairo_1.26.1-2_ppc64el.deb ... 157s Unpacking python3-cairo (1.26.1-2) ... 157s Selecting previously unselected package python3-freetype. 157s Preparing to unpack .../051-python3-freetype_2.5.1-1_all.deb ... 157s Unpacking python3-freetype (2.5.1-1) ... 157s Selecting previously unselected package python3-rlpycairo. 157s Preparing to unpack .../052-python3-rlpycairo_0.3.0-3_all.deb ... 157s Unpacking python3-rlpycairo (0.3.0-3) ... 157s Selecting previously unselected package python3-reportlab. 157s Preparing to unpack .../053-python3-reportlab_4.2.5-1_all.deb ... 157s Unpacking python3-reportlab (4.2.5-1) ... 157s Selecting previously unselected package xml-core. 157s Preparing to unpack .../054-xml-core_0.19_all.deb ... 157s Unpacking xml-core (0.19) ... 157s Selecting previously unselected package w3c-sgml-lib. 157s Preparing to unpack .../055-w3c-sgml-lib_1.3-3_all.deb ... 157s Unpacking w3c-sgml-lib (1.3-3) ... 157s Selecting previously unselected package python3-biopython. 157s Preparing to unpack .../056-python3-biopython_1.84+dfsg-4build1_ppc64el.deb ... 157s Unpacking python3-biopython (1.84+dfsg-4build1) ... 157s Selecting previously unselected package python3-soupsieve. 157s Preparing to unpack .../057-python3-soupsieve_2.6-1_all.deb ... 157s Unpacking python3-soupsieve (2.6-1) ... 157s Selecting previously unselected package python3-bs4. 157s Preparing to unpack .../058-python3-bs4_4.12.3-3_all.deb ... 157s Unpacking python3-bs4 (4.12.3-3) ... 157s Selecting previously unselected package python3-dendropy. 157s Preparing to unpack .../059-python3-dendropy_4.6.1-1_all.deb ... 157s Unpacking python3-dendropy (4.6.1-1) ... 157s Selecting previously unselected package libjs-jquery. 157s Preparing to unpack .../060-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 157s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 157s Selecting previously unselected package libjs-jquery-ui. 157s Preparing to unpack .../061-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 157s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 157s Selecting previously unselected package fonts-lyx. 157s Preparing to unpack .../062-fonts-lyx_2.4.2.1-1_all.deb ... 157s Unpacking fonts-lyx (2.4.2.1-1) ... 157s Selecting previously unselected package python-matplotlib-data. 157s Preparing to unpack .../063-python-matplotlib-data_3.8.3-3_all.deb ... 157s Unpacking python-matplotlib-data (3.8.3-3) ... 157s Selecting previously unselected package python3-six. 157s Preparing to unpack .../064-python3-six_1.16.0-7_all.deb ... 157s Unpacking python3-six (1.16.0-7) ... 157s Selecting previously unselected package python3-dateutil. 157s Preparing to unpack .../065-python3-dateutil_2.9.0-2_all.deb ... 157s Unpacking python3-dateutil (2.9.0-2) ... 157s Selecting previously unselected package python3-contourpy. 157s Preparing to unpack .../066-python3-contourpy_1.3.0-2_ppc64el.deb ... 157s Unpacking python3-contourpy (1.3.0-2) ... 157s Selecting previously unselected package python3-cycler. 157s Preparing to unpack .../067-python3-cycler_0.12.1-1_all.deb ... 157s Unpacking python3-cycler (0.12.1-1) ... 157s Selecting previously unselected package python3-brotli. 157s Preparing to unpack .../068-python3-brotli_1.1.0-2build2_ppc64el.deb ... 157s Unpacking python3-brotli (1.1.0-2build2) ... 157s Selecting previously unselected package python3-decorator. 157s Preparing to unpack .../069-python3-decorator_5.1.1-5_all.deb ... 157s Unpacking python3-decorator (5.1.1-5) ... 157s Selecting previously unselected package liblbfgsb0:ppc64el. 157s Preparing to unpack .../070-liblbfgsb0_3.0+dfsg.4-1build1_ppc64el.deb ... 157s Unpacking liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ... 157s Selecting previously unselected package python3-scipy. 157s Preparing to unpack .../071-python3-scipy_1.13.1-5_ppc64el.deb ... 157s Unpacking python3-scipy (1.13.1-5) ... 158s Selecting previously unselected package python3-ufolib2. 158s Preparing to unpack .../072-python3-ufolib2_0.16.1+dfsg1-1_all.deb ... 158s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ... 158s Selecting previously unselected package python3-mpmath. 158s Preparing to unpack .../073-python3-mpmath_1.3.0-1_all.deb ... 158s Unpacking python3-mpmath (1.3.0-1) ... 158s Selecting previously unselected package python3-sympy. 158s Preparing to unpack .../074-python3-sympy_1.13.3-1_all.deb ... 158s Unpacking python3-sympy (1.13.3-1) ... 158s Selecting previously unselected package python3-tz. 158s Preparing to unpack .../075-python3-tz_2024.1-2_all.deb ... 158s Unpacking python3-tz (2024.1-2) ... 158s Selecting previously unselected package python3-appdirs. 158s Preparing to unpack .../076-python3-appdirs_1.4.4-4_all.deb ... 158s Unpacking python3-appdirs (1.4.4-4) ... 158s Selecting previously unselected package python3-fs. 158s Preparing to unpack .../077-python3-fs_2.4.16-4_all.deb ... 158s Unpacking python3-fs (2.4.16-4) ... 158s Selecting previously unselected package libxslt1.1:ppc64el. 158s Preparing to unpack .../078-libxslt1.1_1.1.39-0exp1ubuntu1_ppc64el.deb ... 158s Unpacking libxslt1.1:ppc64el (1.1.39-0exp1ubuntu1) ... 158s Selecting previously unselected package python3-lxml:ppc64el. 158s Preparing to unpack .../079-python3-lxml_5.3.0-1_ppc64el.deb ... 158s Unpacking python3-lxml:ppc64el (5.3.0-1) ... 158s Selecting previously unselected package python3-lz4. 158s Preparing to unpack .../080-python3-lz4_4.0.2+dfsg-1build4_ppc64el.deb ... 158s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 158s Selecting previously unselected package python3-unicodedata2. 158s Preparing to unpack .../081-python3-unicodedata2_15.1.0+ds-1build2_ppc64el.deb ... 158s Unpacking python3-unicodedata2 (15.1.0+ds-1build2) ... 158s Selecting previously unselected package unicode-data. 158s Preparing to unpack .../082-unicode-data_15.1.0-1_all.deb ... 158s Unpacking unicode-data (15.1.0-1) ... 159s Selecting previously unselected package python3-fonttools. 159s Preparing to unpack .../083-python3-fonttools_4.46.0-1build2_ppc64el.deb ... 159s Unpacking python3-fonttools (4.46.0-1build2) ... 159s Selecting previously unselected package python3-kiwisolver. 159s Preparing to unpack .../084-python3-kiwisolver_1.4.7-2build1_ppc64el.deb ... 159s Unpacking python3-kiwisolver (1.4.7-2build1) ... 159s Selecting previously unselected package python3-packaging. 159s Preparing to unpack .../085-python3-packaging_24.1-1_all.deb ... 159s Unpacking python3-packaging (24.1-1) ... 159s Selecting previously unselected package libqhull-r8.0:ppc64el. 159s Preparing to unpack .../086-libqhull-r8.0_2020.2-6build1_ppc64el.deb ... 159s Unpacking libqhull-r8.0:ppc64el (2020.2-6build1) ... 159s Selecting previously unselected package python3-matplotlib. 159s Preparing to unpack .../087-python3-matplotlib_3.8.3-3_ppc64el.deb ... 159s Unpacking python3-matplotlib (3.8.3-3) ... 159s Selecting previously unselected package mummer. 159s Preparing to unpack .../088-mummer_3.23+dfsg-8_ppc64el.deb ... 159s Unpacking mummer (3.23+dfsg-8) ... 159s Selecting previously unselected package python3-pymummer. 159s Preparing to unpack .../089-python3-pymummer_0.11.0-4_all.deb ... 159s Unpacking python3-pymummer (0.11.0-4) ... 159s Selecting previously unselected package python3-pysam. 159s Preparing to unpack .../090-python3-pysam_0.22.1+ds-2_ppc64el.deb ... 159s Unpacking python3-pysam (0.22.1+ds-2) ... 159s Selecting previously unselected package libfml0:ppc64el. 159s Preparing to unpack .../091-libfml0_0.1+git20190320.b499514-1build1_ppc64el.deb ... 159s Unpacking libfml0:ppc64el (0.1+git20190320.b499514-1build1) ... 159s Selecting previously unselected package libminimap0:ppc64el. 159s Preparing to unpack .../092-libminimap0_0.2-8_ppc64el.deb ... 159s Unpacking libminimap0:ppc64el (0.2-8) ... 159s Selecting previously unselected package bowtie2. 159s Preparing to unpack .../093-bowtie2_2.5.4-1_ppc64el.deb ... 159s Unpacking bowtie2 (2.5.4-1) ... 159s Selecting previously unselected package cd-hit. 159s Preparing to unpack .../094-cd-hit_4.8.1-4_ppc64el.deb ... 159s Unpacking cd-hit (4.8.1-4) ... 159s Selecting previously unselected package libcapnp-1.0.1:ppc64el. 159s Preparing to unpack .../095-libcapnp-1.0.1_1.0.1-4_ppc64el.deb ... 159s Unpacking libcapnp-1.0.1:ppc64el (1.0.1-4) ... 159s Selecting previously unselected package libgslcblas0:ppc64el. 159s Preparing to unpack .../096-libgslcblas0_2.8+dfsg-5_ppc64el.deb ... 159s Unpacking libgslcblas0:ppc64el (2.8+dfsg-5) ... 159s Selecting previously unselected package libgsl28:ppc64el. 159s Preparing to unpack .../097-libgsl28_2.8+dfsg-5_ppc64el.deb ... 159s Unpacking libgsl28:ppc64el (2.8+dfsg-5) ... 159s Selecting previously unselected package libmurmurhash2:ppc64el. 159s Preparing to unpack .../098-libmurmurhash2_1.6-1_ppc64el.deb ... 159s Unpacking libmurmurhash2:ppc64el (1.6-1) ... 159s Selecting previously unselected package mash. 159s Preparing to unpack .../099-mash_2.3+dfsg-6build1_ppc64el.deb ... 159s Unpacking mash (2.3+dfsg-6build1) ... 159s Selecting previously unselected package ariba. 159s Preparing to unpack .../100-ariba_2.14.7+ds-4_ppc64el.deb ... 159s Unpacking ariba (2.14.7+ds-4) ... 160s Selecting previously unselected package autopkgtest-satdep. 160s Preparing to unpack .../101-1-autopkgtest-satdep.deb ... 160s Unpacking autopkgtest-satdep (0) ... 160s Setting up libhtscodecs2:ppc64el (1.6.1-1) ... 160s Setting up libgraphite2-3:ppc64el (1.3.14-2ubuntu1) ... 160s Setting up liblcms2-2:ppc64el (2.16-2) ... 160s Setting up libpixman-1-0:ppc64el (0.44.0-3) ... 160s Setting up libsharpyuv0:ppc64el (1.4.0-0.1) ... 160s Setting up liblerc4:ppc64el (4.0.0+ds-4ubuntu2) ... 160s Setting up libxrender1:ppc64el (1:0.9.10-1.1build1) ... 160s Setting up libgslcblas0:ppc64el (2.8+dfsg-5) ... 160s Setting up libmurmurhash2:ppc64el (1.6-1) ... 160s Setting up libcapnp-1.0.1:ppc64el (1.0.1-4) ... 160s Setting up python3-lz4 (4.0.2+dfsg-1build4) ... 160s Setting up libxcb-render0:ppc64el (1.17.0-2) ... 160s Setting up python3-unicodedata2 (15.1.0+ds-1build2) ... 160s Setting up fonts-lyx (2.4.2.1-1) ... 160s Setting up x11-common (1:7.7+23ubuntu3) ... 160s Setting up libdeflate0:ppc64el (1.22-1) ... 160s Setting up libqhull-r8.0:ppc64el (2020.2-6build1) ... 160s Setting up libxcb-shm0:ppc64el (1.17.0-2) ... 160s Setting up libgomp1:ppc64el (14.2.0-8ubuntu1) ... 160s Setting up python3-freetype (2.5.1-1) ... 160s Setting up libfml0:ppc64el (0.1+git20190320.b499514-1build1) ... 160s Setting up libjbig0:ppc64el (2.1-6.1ubuntu2) ... 160s Setting up python3-tz (2024.1-2) ... 160s Setting up bowtie2 (2.5.4-1) ... 160s Setting up unicode-data (15.1.0-1) ... 160s Setting up python3-six (1.16.0-7) ... 160s Setting up python3-decorator (5.1.1-5) ... 161s Setting up libminimap0:ppc64el (0.2-8) ... 161s Setting up libfontenc1:ppc64el (1:1.1.8-1build1) ... 161s Setting up libblas3:ppc64el (3.12.0-3build2) ... 161s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 161s Setting up python3-packaging (24.1-1) ... 161s Setting up python3-brotli (1.1.0-2build2) ... 161s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 161s Setting up python3-cycler (0.12.1-1) ... 161s Setting up libimagequant0:ppc64el (2.18.0-1build1) ... 161s Setting up fonts-dejavu-mono (2.37-8) ... 161s Setting up python3-kiwisolver (1.4.7-2build1) ... 161s Setting up libtcl8.6:ppc64el (8.6.15+dfsg-2) ... 161s Setting up fonts-dejavu-core (2.37-8) ... 161s Setting up libjpeg-turbo8:ppc64el (2.1.5-2ubuntu2) ... 161s Setting up libgfortran5:ppc64el (14.2.0-8ubuntu1) ... 161s Setting up libwebp7:ppc64el (1.4.0-0.1) ... 161s Setting up libxslt1.1:ppc64el (1.1.39-0exp1ubuntu1) ... 161s Setting up mummer (3.23+dfsg-8) ... 161s Setting up libhts3t64:ppc64el (1.20+ds-1) ... 161s Setting up libopenjp2-7:ppc64el (2.5.0-2ubuntu1) ... 161s Setting up libharfbuzz0b:ppc64el (10.0.1-1) ... 161s Setting up python3-dateutil (2.9.0-2) ... 161s Setting up sgml-base (1.31) ... 161s Setting up libxss1:ppc64el (1:1.2.3-1build3) ... 161s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 161s Setting up python3-mpmath (1.3.0-1) ... 162s Setting up libgsl28:ppc64el (2.8+dfsg-5) ... 162s Setting up python-matplotlib-data (3.8.3-3) ... 162s Setting up libwebpmux3:ppc64el (1.4.0-0.1) ... 162s Setting up python3-dendropy (4.6.1-1) ... 162s Setting up python3-appdirs (1.4.4-4) ... 162s Setting up python3-soupsieve (2.6-1) ... 163s Setting up cd-hit (4.8.1-4) ... 163s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 163s Setting up python3-sympy (1.13.3-1) ... 170s Setting up liblapack3:ppc64el (3.12.0-3build2) ... 170s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 170s Setting up python3-pysam (0.22.1+ds-2) ... 170s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 170s Setting up libwebpdemux2:ppc64el (1.4.0-0.1) ... 170s Setting up xfonts-utils (1:7.7+7) ... 170s Setting up python3-bs4 (4.12.3-3) ... 170s Setting up samtools (1.20-3) ... 170s Setting up python3-fs (2.4.16-4) ... 171s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 171s Setting up libraqm0:ppc64el (0.10.1-1build1) ... 171s Setting up mash (2.3+dfsg-6build1) ... 171s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 173s Setting up python3-lxml:ppc64el (5.3.0-1) ... 173s Setting up libtiff6:ppc64el (4.5.1+git230720-4ubuntu4) ... 173s Setting up xml-core (0.19) ... 173s Setting up python3-contourpy (1.3.0-2) ... 173s Setting up libfontconfig1:ppc64el (2.15.0-1.1ubuntu2) ... 173s Setting up liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ... 173s Setting up libxft2:ppc64el (2.3.6-1build1) ... 173s Setting up python3-scipy (1.13.1-5) ... 177s Setting up libtk8.6:ppc64el (8.6.15-1) ... 177s Setting up fastaq (3.17.0-8) ... 177s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:37: SyntaxWarning: invalid escape sequence '\s' 177s phylip_regex = re.compile('^\s*[0-9]+\s+[0-9]+$') 177s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:38: SyntaxWarning: invalid escape sequence '\s' 177s gbk_regex = re.compile('^LOCUS\s+\S') 177s Setting up python3.12-tk (3.12.7-3) ... 177s Setting up fonts-urw-base35 (20200910-8) ... 178s Setting up libcairo2:ppc64el (1.18.2-2) ... 178s Setting up python3-pymummer (0.11.0-4) ... 178s Setting up python3-pil:ppc64el (10.4.0-1ubuntu1) ... 178s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 178s Setting up python3-cairo (1.26.1-2) ... 178s Setting up blt (2.5.3+dfsg-7build1) ... 178s Setting up python3-tk:ppc64el (3.12.6-1ubuntu1) ... 178s Setting up python3-pil.imagetk:ppc64el (10.4.0-1ubuntu1) ... 178s Setting up python3-rlpycairo (0.3.0-3) ... 178s Setting up python3-reportlab (4.2.5-1) ... 179s Setting up python3-fonttools (4.46.0-1build2) ... 180s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... 180s Setting up python3-matplotlib (3.8.3-3) ... 182s Processing triggers for libc-bin (2.40-1ubuntu3) ... 182s Processing triggers for man-db (2.13.0-1) ... 184s Processing triggers for sgml-base (1.31) ... 184s Setting up w3c-sgml-lib (1.3-3) ... 215s Setting up python3-biopython (1.84+dfsg-4build1) ... 217s Setting up ariba (2.14.7+ds-4) ... 217s /usr/lib/python3/dist-packages/ariba/external_progs.py:34: SyntaxWarning: invalid escape sequence '\.' 217s 'cdhit': ('', re.compile('CD-HIT version ([0-9\.]+) \(')), 217s /usr/lib/python3/dist-packages/ariba/external_progs.py:35: SyntaxWarning: invalid escape sequence '\.' 217s 'nucmer': ('--version', re.compile('([0-9]+\.[0-9\.]+.*$)')), 217s /usr/lib/python3/dist-packages/ariba/external_progs.py:36: SyntaxWarning: invalid escape sequence '\.' 217s 'spades': ('--version', re.compile('SPAdes.*v([0-9\.]+)')) 217s Setting up autopkgtest-satdep (0) ... 221s (Reading database ... 84583 files and directories currently installed.) 221s Removing autopkgtest-satdep (0) ... 221s autopkgtest [23:43:02]: test test-example: [----------------------- 224s ARIBA version: 2.14.6 224s 224s External dependencies: 224s bowtie2 2.5.4 /usr/bin/bowtie2 224s cdhit 4.8.1 /usr/bin/cd-hit-est 224s nucmer 3.1 /usr/bin/nucmer 224s 224s External dependencies OK: True 224s 224s Python version: 224s 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 224s 224s Python packages: 224s ariba 2.14.6 /usr/lib/python3/dist-packages/ariba/__init__.py 224s bs4 4.12.3 /usr/lib/python3/dist-packages/bs4/__init__.py 224s dendropy 4.6.1 /usr/lib/python3/dist-packages/dendropy/__init__.py 224s pyfastaq 3.17.0 /usr/lib/python3/dist-packages/pyfastaq/__init__.py 224s pymummer 0.11.0 /usr/lib/python3/dist-packages/pymummer/__init__.py 224s pysam 0.22.1 /usr/lib/python3/dist-packages/pysam/__init__.py 224s 224s Python packages OK: True 224s 224s Everything looks OK: True 224s 224s Loading and checking input data 224s 224s Running cdhit 224s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.yl3K3bNiuP/foo/PREPAREREF/02.cdhit.noncoding.fa -o /tmp/tmp.yl3K3bNiuP/foo/tmp.run_cd-hit.6yjlpr80/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 224s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.yl3K3bNiuP/foo/PREPAREREF/02.cdhit.noncoding.varonly.fa -o /tmp/tmp.yl3K3bNiuP/foo/tmp.run_cd-hit.uydzp6pe/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 224s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.yl3K3bNiuP/foo/PREPAREREF/02.cdhit.gene.fa -o /tmp/tmp.yl3K3bNiuP/foo/tmp.run_cd-hit.meuc7ntz/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 225s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.yl3K3bNiuP/foo/PREPAREREF/02.cdhit.gene.varonly.fa -o /tmp/tmp.yl3K3bNiuP/foo/tmp.run_cd-hit.r448q27t/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 225s 225s Writing clusters to file. 10 in total 226s Found reads file: reads_1.fq 226s Found reads file: reads_2.fq 226s ARIBA version: 2.14.6 226s 226s External dependencies: 226s bowtie2 2.5.4 /usr/bin/bowtie2 226s cdhit 4.8.1 /usr/bin/cd-hit-est 226s nucmer 3.1 /usr/bin/nucmer 226s 226s External dependencies OK: True 226s 226s Python version: 226s 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 226s 226s Python packages: 226s ariba 2.14.6 /usr/lib/python3/dist-packages/ariba/__init__.py 226s bs4 4.12.3 /usr/lib/python3/dist-packages/bs4/__init__.py 226s dendropy 4.6.1 /usr/lib/python3/dist-packages/dendropy/__init__.py 226s pyfastaq 3.17.0 /usr/lib/python3/dist-packages/pyfastaq/__init__.py 226s pymummer 0.11.0 /usr/lib/python3/dist-packages/pymummer/__init__.py 226s pysam 0.22.1 /usr/lib/python3/dist-packages/pysam/__init__.py 226s 226s Python packages OK: True 226s 226s Everything looks OK: True 226s Temporary directory: /tmp/tmp.yl3K3bNiuP/foo/OUT/ariba.tmp.rlt542no 226s ______________________ Mapping reads to clustered genes _______________________ 226s Finished mapping 226s 226s _____________________________ Generating clusters _____________________________ 226s syscall: sort -k1,1 -k 2,2n /tmp/tmp.yl3K3bNiuP/foo/OUT/minimap.reads > /tmp/tmp.yl3K3bNiuP/foo/OUT/read_store 226s Compressing file /tmp/tmp.yl3K3bNiuP/foo/OUT/read_store 226s Found 51 proper read pairs from minimap 226s Total clusters to perform local assemblies: 9 226s 226s Insert size information from reads mapped to reference genes: 226s Insert size: 185.0 226s Insert sspace sd: 0.27 226s Max insert: 220.55 226s 226s ___________________________ Assembling each cluster ___________________________ 226s Will run 1 cluster(s) in parallel 226s Not constructing cluster cluster because it only has 2 reads (1 of 9) 226s Constructing cluster cluster_1 (2 of 9) 226s Constructing cluster cluster_2 (3 of 9) 226s Constructing cluster cluster_3 (4 of 9) 226s Constructing cluster cluster_4 (5 of 9) 226s Constructing cluster gene (6 of 9) 226s Constructing cluster gene_1 (7 of 9) 226s Constructing cluster noncoding (8 of 9) 226s Constructing cluster noncoding_1 (9 of 9) 226s Start running cluster cluster_1 in directory /tmp/tmp.yl3K3bNiuP/foo/OUT/ariba.tmp.rlt542no/cluster_1 228s cluster_1 detected 1 threads available to it 228s cluster_1 reported completion 228s Finished running cluster cluster_1 in directory /tmp/tmp.yl3K3bNiuP/foo/OUT/ariba.tmp.rlt542no/cluster_1 228s Deleting cluster dir /tmp/tmp.yl3K3bNiuP/foo/OUT/ariba.tmp.rlt542no/cluster_1 228s Start running cluster cluster_2 in directory /tmp/tmp.yl3K3bNiuP/foo/OUT/ariba.tmp.rlt542no/cluster_2 230s cluster_2 detected 1 threads available to it 230s cluster_2 reported completion 230s Finished running cluster cluster_2 in directory /tmp/tmp.yl3K3bNiuP/foo/OUT/ariba.tmp.rlt542no/cluster_2 230s Deleting cluster dir /tmp/tmp.yl3K3bNiuP/foo/OUT/ariba.tmp.rlt542no/cluster_2 230s Start running cluster cluster_3 in directory /tmp/tmp.yl3K3bNiuP/foo/OUT/ariba.tmp.rlt542no/cluster_3 233s cluster_3 detected 1 threads available to it 233s cluster_3 reported completion 233s Finished running cluster cluster_3 in directory /tmp/tmp.yl3K3bNiuP/foo/OUT/ariba.tmp.rlt542no/cluster_3 233s Deleting cluster dir /tmp/tmp.yl3K3bNiuP/foo/OUT/ariba.tmp.rlt542no/cluster_3 233s Start running cluster cluster_4 in directory /tmp/tmp.yl3K3bNiuP/foo/OUT/ariba.tmp.rlt542no/cluster_4 235s cluster_4 detected 1 threads available to it 235s cluster_4 reported completion 235s Finished running cluster cluster_4 in directory /tmp/tmp.yl3K3bNiuP/foo/OUT/ariba.tmp.rlt542no/cluster_4 235s Deleting cluster dir /tmp/tmp.yl3K3bNiuP/foo/OUT/ariba.tmp.rlt542no/cluster_4 235s Start running cluster gene in directory /tmp/tmp.yl3K3bNiuP/foo/OUT/ariba.tmp.rlt542no/gene 237s gene detected 1 threads available to it 237s gene reported completion 237s Finished running cluster gene in directory /tmp/tmp.yl3K3bNiuP/foo/OUT/ariba.tmp.rlt542no/gene 237s Deleting cluster dir /tmp/tmp.yl3K3bNiuP/foo/OUT/ariba.tmp.rlt542no/gene 237s Start running cluster gene_1 in directory /tmp/tmp.yl3K3bNiuP/foo/OUT/ariba.tmp.rlt542no/gene_1 240s gene_1 detected 1 threads available to it 240s gene_1 reported completion 240s Finished running cluster gene_1 in directory /tmp/tmp.yl3K3bNiuP/foo/OUT/ariba.tmp.rlt542no/gene_1 240s Deleting cluster dir /tmp/tmp.yl3K3bNiuP/foo/OUT/ariba.tmp.rlt542no/gene_1 240s Start running cluster noncoding in directory /tmp/tmp.yl3K3bNiuP/foo/OUT/ariba.tmp.rlt542no/noncoding 242s noncoding detected 1 threads available to it 242s noncoding reported completion 242s Finished running cluster noncoding in directory /tmp/tmp.yl3K3bNiuP/foo/OUT/ariba.tmp.rlt542no/noncoding 242s Deleting cluster dir /tmp/tmp.yl3K3bNiuP/foo/OUT/ariba.tmp.rlt542no/noncoding 242s Start running cluster noncoding_1 in directory /tmp/tmp.yl3K3bNiuP/foo/OUT/ariba.tmp.rlt542no/noncoding_1 244s noncoding_1 detected 1 threads available to it 244s noncoding_1 reported completion 244s Finished running cluster noncoding_1 in directory /tmp/tmp.yl3K3bNiuP/foo/OUT/ariba.tmp.rlt542no/noncoding_1 244s Deleting cluster dir /tmp/tmp.yl3K3bNiuP/foo/OUT/ariba.tmp.rlt542no/noncoding_1 244s Final value of remaining_clusters counter: Value('l', 0) 244s Finished assembling clusters 244s 244s _______________________________ Writing reports _______________________________ 244s Making /tmp/tmp.yl3K3bNiuP/foo/OUT/debug.report.tsv 244s Making /tmp/tmp.yl3K3bNiuP/foo/OUT/report.tsv 244s 244s ____________________ Writing fasta of assembled sequences _____________________ 244s /tmp/tmp.yl3K3bNiuP/foo/OUT/assembled_seqs.fa.gz and /tmp/tmp.yl3K3bNiuP/foo/OUT/assembled_genes.fa.gz 244s 244s __________________________ Catting cluster log files __________________________ 244s Writing file /tmp/tmp.yl3K3bNiuP/foo/OUT/log.clusters.gz 244s 244s _______________________________ Cleaning files ________________________________ 244s Deleting Logs directory /tmp/tmp.yl3K3bNiuP/foo/OUT/Logs 244s Deleting reads store files /tmp/tmp.yl3K3bNiuP/foo/OUT/read_store.gz[.tbi] 244s 244s All done! 244s 244s Running ARIBA on test data... 244s ------------------------------------------------------------------------------- 244s |=============================================================================| 244s | Preparing input data | 244s |=============================================================================| 244s ------------------------------------------------------------------------------- 244s Made output directory ./foo. Copying test data files into it: 244s copied ref_seqs.fa 244s copied metadata.tsv 244s copied reads_1.fq 244s copied reads_2.fq 244s ------------------------------------------------------------------------------- 244s |=============================================================================| 244s | Try running ariba prepareref | 244s |=============================================================================| 244s ------------------------------------------------------------------------------- 244s 244s Running ariba prepareref with: 244s /usr/bin/ariba prepareref --verbose -f ref_seqs.fa -m metadata.tsv --threads 1 PREPAREREF 244s 244s 244s ariba prepareref finished OK 244s ------------------------------------------------------------------------------- 244s |=============================================================================| 244s | Try running ariba run | 244s |=============================================================================| 244s ------------------------------------------------------------------------------- 244s 244s Running ARIBA with: 244s /usr/bin/ariba run --verbose --threads 1 PREPAREREF reads_1.fq reads_2.fq OUT 244s 244s 244s ariba run finished OK 244s Finished run on test data OK 245s autopkgtest [23:43:26]: test test-example: -----------------------] 245s test-example PASS 245s autopkgtest [23:43:26]: test test-example: - - - - - - - - - - results - - - - - - - - - - 245s autopkgtest [23:43:26]: @@@@@@@@@@@@@@@@@@@@ summary 245s test-example PASS 257s nova [W] Using flock in prodstack6-ppc64el 257s Creating nova instance adt-plucky-ppc64el-ariba-20241114-233126-juju-7f2275-prod-proposed-migration-environment-15-960a3276-6f42-4dbc-a8f6-e4e06cc9dc20 from image adt/ubuntu-plucky-ppc64el-server-20241113.img (UUID 0c5715b6-5cca-4485-b8bf-b85dfd917a5f)...