0s autopkgtest [13:02:06]: starting date and time: 2024-11-15 13:02:06+0000 0s autopkgtest [13:02:06]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [13:02:06]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.sr72_2xg/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 builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-15.secgroup --name adt-plucky-amd64-ariba-20241115-130206-juju-7f2275-prod-proposed-migration-environment-15-caad0e7b-107a-4942-af76-bd9d6d994714 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-amd64 -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/ 41s autopkgtest [13:02:47]: testbed dpkg architecture: amd64 42s autopkgtest [13:02:48]: testbed apt version: 2.9.8 42s autopkgtest [13:02:48]: @@@@@@@@@@@@@@@@@@@@ test bed setup 42s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 43s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1052 kB] 43s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [94.5 kB] 43s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 43s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.5 kB] 43s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [176 kB] 43s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [109 kB] 43s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 43s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [831 kB] 43s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [295 kB] 43s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [740 B] 43s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [9416 B] 43s Fetched 2696 kB in 1s (3198 kB/s) 43s Reading package lists... 46s Reading package lists... 46s Building dependency tree... 46s Reading state information... 46s Calculating upgrade... 46s The following packages will be upgraded: 46s firmware-sof-signed grub-common grub-pc grub-pc-bin grub2-common libcap-ng0 46s libexpat1 lxd-installer man-db pastebinit python3-markupsafe python3-systemd 46s xfsprogs 46s 13 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 46s Need to get 13.6 MB of archives. 46s After this operation, 493 kB of additional disk space will be used. 46s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 firmware-sof-signed all 2024.06-1ubuntu2 [7083 kB] 48s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-3build1 [15.6 kB] 48s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libexpat1 amd64 2.6.4-1 [94.9 kB] 48s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 man-db amd64 2.13.0-1 [1352 kB] 48s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 grub2-common amd64 2.12-5ubuntu7 [672 kB] 48s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-pc amd64 2.12-5ubuntu7 [137 kB] 48s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-pc-bin amd64 2.12-5ubuntu7 [1127 kB] 48s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-common amd64 2.12-5ubuntu7 [2110 kB] 48s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 lxd-installer all 9 [5084 B] 48s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 pastebinit all 1.7.1-1 [14.9 kB] 48s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build3 [13.0 kB] 48s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build5 [45.7 kB] 48s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 xfsprogs amd64 6.8.0-2.2ubuntu2 [926 kB] 48s Preconfiguring packages ... 49s Fetched 13.6 MB in 2s (6306 kB/s) 49s (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 ... 75542 files and directories currently installed.) 49s Preparing to unpack .../firmware-sof-signed_2024.06-1ubuntu2_all.deb ... 49s Unpacking firmware-sof-signed (2024.06-1ubuntu2) over (2024.06-1ubuntu1) ... 49s Preparing to unpack .../libcap-ng0_0.8.5-3build1_amd64.deb ... 49s Unpacking libcap-ng0:amd64 (0.8.5-3build1) over (0.8.5-1) ... 49s Setting up libcap-ng0:amd64 (0.8.5-3build1) ... 49s (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 ... 75568 files and directories currently installed.) 49s Preparing to unpack .../00-libexpat1_2.6.4-1_amd64.deb ... 49s Unpacking libexpat1:amd64 (2.6.4-1) over (2.6.2-2) ... 49s Preparing to unpack .../01-man-db_2.13.0-1_amd64.deb ... 49s Unpacking man-db (2.13.0-1) over (2.12.1-3) ... 49s Preparing to unpack .../02-grub2-common_2.12-5ubuntu7_amd64.deb ... 49s Unpacking grub2-common (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ... 49s Preparing to unpack .../03-grub-pc_2.12-5ubuntu7_amd64.deb ... 49s Unpacking grub-pc (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ... 49s Preparing to unpack .../04-grub-pc-bin_2.12-5ubuntu7_amd64.deb ... 49s Unpacking grub-pc-bin (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ... 49s Preparing to unpack .../05-grub-common_2.12-5ubuntu7_amd64.deb ... 49s Unpacking grub-common (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ... 50s Preparing to unpack .../06-lxd-installer_9_all.deb ... 50s Unpacking lxd-installer (9) over (8) ... 50s Preparing to unpack .../07-pastebinit_1.7.1-1_all.deb ... 50s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 50s Preparing to unpack .../08-python3-markupsafe_2.1.5-1build3_amd64.deb ... 50s Unpacking python3-markupsafe (2.1.5-1build3) over (2.1.5-1build2) ... 50s Preparing to unpack .../09-python3-systemd_235-1build5_amd64.deb ... 50s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 50s Preparing to unpack .../10-xfsprogs_6.8.0-2.2ubuntu2_amd64.deb ... 50s Unpacking xfsprogs (6.8.0-2.2ubuntu2) over (6.8.0-2.2ubuntu1) ... 50s Setting up libexpat1:amd64 (2.6.4-1) ... 50s Setting up firmware-sof-signed (2024.06-1ubuntu2) ... 50s Setting up pastebinit (1.7.1-1) ... 50s Setting up man-db (2.13.0-1) ... 50s Updating database of manual pages ... 52s man-db.service is a disabled or a static unit not running, not starting it. 52s Setting up python3-markupsafe (2.1.5-1build3) ... 52s Setting up grub-common (2.12-5ubuntu7) ... 52s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 53s Setting up xfsprogs (6.8.0-2.2ubuntu2) ... 53s update-initramfs: deferring update (trigger activated) 53s Setting up lxd-installer (9) ... 53s Setting up python3-systemd (235-1build5) ... 54s Setting up grub2-common (2.12-5ubuntu7) ... 54s Setting up grub-pc-bin (2.12-5ubuntu7) ... 54s Setting up grub-pc (2.12-5ubuntu7) ... 54s Installing for i386-pc platform. 54s Installation finished. No error reported. 54s Sourcing file `/etc/default/grub' 54s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 54s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 54s Generating grub configuration file ... 54s Found linux image: /boot/vmlinuz-6.11.0-8-generic 55s Found initrd image: /boot/initrd.img-6.11.0-8-generic 55s Warning: os-prober will not be executed to detect other bootable partitions. 55s Systems on them will not be added to the GRUB boot configuration. 55s Check GRUB_DISABLE_OS_PROBER documentation entry. 55s Adding boot menu entry for UEFI Firmware Settings ... 55s done 55s Processing triggers for libc-bin (2.40-1ubuntu3) ... 55s Processing triggers for install-info (7.1.1-1) ... 55s Processing triggers for initramfs-tools (0.142ubuntu34) ... 55s update-initramfs: Generating /boot/initrd.img-6.11.0-8-generic 55s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 63s Reading package lists... 63s Building dependency tree... 63s Reading state information... 63s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 63s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 64s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 64s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 64s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 64s Reading package lists... 64s Reading package lists... 65s Building dependency tree... 65s Reading state information... 65s Calculating upgrade... 65s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 65s Reading package lists... 65s Building dependency tree... 65s Reading state information... 65s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 65s autopkgtest [13:03:11]: rebooting testbed after setup commands that affected boot 82s autopkgtest [13:03:28]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 85s autopkgtest [13:03:31]: @@@@@@@@@@@@@@@@@@@@ apt-source ariba 87s Get:1 http://ftpmaster.internal/ubuntu plucky/universe ariba 2.14.7+ds-4 (dsc) [2316 B] 87s Get:2 http://ftpmaster.internal/ubuntu plucky/universe ariba 2.14.7+ds-4 (tar) [1920 kB] 87s Get:3 http://ftpmaster.internal/ubuntu plucky/universe ariba 2.14.7+ds-4 (diff) [10.7 kB] 87s gpgv: Signature made Tue Nov 5 03:36:42 2024 UTC 87s gpgv: using RSA key 13796755BBC72BB8ABE2AEB5FA9DEC5DE11C63F1 87s gpgv: issuer "eamanu@debian.org" 87s gpgv: Can't check signature: No public key 87s dpkg-source: warning: cannot verify inline signature for ./ariba_2.14.7+ds-4.dsc: no acceptable signature found 87s autopkgtest [13:03:33]: testing package ariba version 2.14.7+ds-4 87s autopkgtest [13:03:33]: build not needed 89s autopkgtest [13:03:35]: test test-example: preparing testbed 90s Reading package lists... 90s Building dependency tree... 90s Reading state information... 90s Starting pkgProblemResolver with broken count: 0 91s Starting 2 pkgProblemResolver with broken count: 0 91s Done 91s The following additional packages will be installed: 91s ariba blt bowtie2 cd-hit fastaq fontconfig-config fonts-dejavu-core 91s fonts-dejavu-mono fonts-lyx fonts-urw-base35 libblas3 libcairo2 91s libcapnp-1.0.1 libdeflate0 libfml0 libfontconfig1 libfontenc1 libgfortran5 91s libgomp1 libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b libhts3t64 91s libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery 91s libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libminimap0 91s libmurmurhash2 libopenjp2-7 libpixman-1-0 libqhull-r8.0 libraqm0 91s libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 91s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 mash 91s mummer python-matplotlib-data python3-appdirs python3-biopython 91s python3-brotli python3-bs4 python3-cairo python3-contourpy python3-cycler 91s python3-dateutil python3-decorator python3-dendropy python3-fonttools 91s python3-freetype python3-fs python3-kiwisolver python3-lxml python3-lz4 91s python3-matplotlib python3-mpmath python3-numpy python3-packaging 91s python3-pil python3-pil.imagetk python3-pymummer python3-pysam 91s python3-reportlab python3-rlpycairo python3-scipy python3-six 91s python3-soupsieve python3-sympy python3-tk python3-tz python3-ufolib2 91s python3-unicodedata2 python3.12-tk samtools sgml-base tk8.6-blt2.5 91s unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 91s Suggested packages: 91s spades blt-demo bowtie2-examples fonts-freefont-otf | fonts-freefont-ttf 91s fonts-texgyre gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html 91s libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 bwa clustalo clustalw 91s dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons 91s python3-mysqldb python3-mmtf python3-rdflib python3-psycopg2 raxml t-coffee 91s wise python-cycler-doc python-lxml-doc cm-super-minimal dvipng ffmpeg 91s fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common 91s python-matplotlib-doc python3-cairocffi python3-gi-cairo python3-gobject 91s python3-pyqt5 python3-sip python3-tornado texlive-extra-utils 91s texlive-latex-extra python-mpmath-doc python3-gmpy2 gcc gfortran 91s python-numpy-doc python3-dev python3-pytest python-pil-doc pdf-viewer 91s python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm 91s python-scipy-doc texlive-fonts-extra python-sympy-doc tix python3-tk-dbg 91s python3.13-tk cwltool sgml-base-doc debhelper 91s Recommended packages: 91s javascript-common python-biopython-doc ncbi-blast+ python3-cssselect 91s python3-html5lib python3-olefile fonts-dejavu-extra g++ | c++-compiler 91s isympy-common 91s The following NEW packages will be installed: 91s ariba autopkgtest-satdep blt bowtie2 cd-hit fastaq fontconfig-config 91s fonts-dejavu-core fonts-dejavu-mono fonts-lyx fonts-urw-base35 libblas3 91s libcairo2 libcapnp-1.0.1 libdeflate0 libfml0 libfontconfig1 libfontenc1 91s libgfortran5 libgomp1 libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b 91s libhts3t64 libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 91s libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblerc4 91s libminimap0 libmurmurhash2 libopenjp2-7 libpixman-1-0 libqhull-r8.0 libraqm0 91s libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 91s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 mash 91s mummer python-matplotlib-data python3-appdirs python3-biopython 91s python3-brotli python3-bs4 python3-cairo python3-contourpy python3-cycler 91s python3-dateutil python3-decorator python3-dendropy python3-fonttools 91s python3-freetype python3-fs python3-kiwisolver python3-lxml python3-lz4 91s python3-matplotlib python3-mpmath python3-numpy python3-packaging 91s python3-pil python3-pil.imagetk python3-pymummer python3-pysam 91s python3-reportlab python3-rlpycairo python3-scipy python3-six 91s python3-soupsieve python3-sympy python3-tk python3-tz python3-ufolib2 91s python3-unicodedata2 python3.12-tk samtools sgml-base tk8.6-blt2.5 91s unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 91s 0 upgraded, 102 newly installed, 0 to remove and 0 not upgraded. 91s Need to get 88.6 MB/88.6 MB of archives. 91s After this operation, 372 MB of additional disk space will be used. 91s Get:1 /tmp/autopkgtest.m42ESS/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [700 B] 91s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 91s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 91s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-1 [132 kB] 91s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.20+ds-1 [439 kB] 92s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 samtools amd64 1.20-3 [599 kB] 92s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 fastaq all 3.17.0-8 [48.2 kB] 92s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 92s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 92s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 92s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 92s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1085 kB] 93s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 93s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 93s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 93s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 93s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 93s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 93s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 93s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 93s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 93s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 93s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 93s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 93s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.15-1 [862 kB] 93s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.7-3 [116 kB] 93s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB] 93s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B] 93s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tk amd64 3.12.6-1ubuntu1 [9806 B] 93s Get:30 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 10.4.0-1ubuntu1 [9394 B] 93s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 93s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 93s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB] 93s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 93s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 93s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB] 93s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 93s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB] 93s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 93s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 93s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB] 93s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 93s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 93s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 93s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 94s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 94s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu1 [463 kB] 94s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 94s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 94s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 94s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 94s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2 [119 kB] 94s Get:53 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 94s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 94s Get:55 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.2.5-1 [1107 kB] 94s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 94s Get:57 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 94s Get:58 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-biopython amd64 1.84+dfsg-4build1 [1719 kB] 94s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-soupsieve all 2.6-1 [33.0 kB] 94s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-bs4 all 4.12.3-3 [109 kB] 94s Get:61 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-dendropy all 4.6.1-1 [278 kB] 94s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 94s Get:63 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 94s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.2.1-1 [171 kB] 94s Get:65 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-3 [2928 kB] 94s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.16.0-7 [13.1 kB] 94s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB] 94s Get:68 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.0-2 [217 kB] 94s Get:69 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 94s Get:70 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build2 [332 kB] 94s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 94s Get:72 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 94s Get:73 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5 [18.2 MB] 95s Get:74 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 95s Get:75 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 95s Get:76 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-1 [4228 kB] 95s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB] 95s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-appdirs all 1.4.4-4 [10.9 kB] 95s Get:79 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-4 [91.3 kB] 95s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu1 [169 kB] 95s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.0-1 [1282 kB] 95s Get:82 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.0.2+dfsg-1build4 [26.2 kB] 95s Get:83 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build2 [360 kB] 95s Get:84 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 96s Get:85 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.46.0-1build2 [1436 kB] 96s Get:86 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-2build1 [70.3 kB] 96s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 96s Get:88 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 96s Get:89 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-3 [4545 kB] 96s Get:90 http://ftpmaster.internal/ubuntu plucky/universe amd64 mummer amd64 3.23+dfsg-8 [685 kB] 96s Get:91 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pymummer all 0.11.0-4 [17.1 kB] 96s Get:92 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pysam amd64 0.22.1+ds-2 [3504 kB] 96s Get:93 http://ftpmaster.internal/ubuntu plucky/universe amd64 libfml0 amd64 0.1+git20190320.b499514-1build1 [74.2 kB] 96s Get:94 http://ftpmaster.internal/ubuntu plucky/universe amd64 libminimap0 amd64 0.2-8 [23.5 kB] 96s Get:95 http://ftpmaster.internal/ubuntu plucky/universe amd64 bowtie2 amd64 2.5.4-1 [1336 kB] 96s Get:96 http://ftpmaster.internal/ubuntu plucky/universe amd64 cd-hit amd64 4.8.1-4 [521 kB] 96s Get:97 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcapnp-1.0.1 amd64 1.0.1-4 [1400 kB] 96s Get:98 http://ftpmaster.internal/ubuntu plucky/universe amd64 libgslcblas0 amd64 2.8+dfsg-5 [290 kB] 96s Get:99 http://ftpmaster.internal/ubuntu plucky/universe amd64 libgsl28 amd64 2.8+dfsg-5 [1285 kB] 96s Get:100 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmurmurhash2 amd64 1.6-1 [5770 B] 96s Get:101 http://ftpmaster.internal/ubuntu plucky/universe amd64 mash amd64 2.3+dfsg-6build1 [160 kB] 96s Get:102 http://ftpmaster.internal/ubuntu plucky/universe amd64 ariba amd64 2.14.7+ds-4 [2033 kB] 97s Fetched 88.6 MB in 5s (16.5 MB/s) 97s Selecting previously unselected package sgml-base. 97s (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 ... 75576 files and directories currently installed.) 97s Preparing to unpack .../000-sgml-base_1.31_all.deb ... 97s Unpacking sgml-base (1.31) ... 97s Selecting previously unselected package libdeflate0:amd64. 97s Preparing to unpack .../001-libdeflate0_1.22-1_amd64.deb ... 97s Unpacking libdeflate0:amd64 (1.22-1) ... 97s Selecting previously unselected package libhtscodecs2:amd64. 97s Preparing to unpack .../002-libhtscodecs2_1.6.1-1_amd64.deb ... 97s Unpacking libhtscodecs2:amd64 (1.6.1-1) ... 97s Selecting previously unselected package libhts3t64:amd64. 97s Preparing to unpack .../003-libhts3t64_1.20+ds-1_amd64.deb ... 97s Unpacking libhts3t64:amd64 (1.20+ds-1) ... 97s Selecting previously unselected package samtools. 97s Preparing to unpack .../004-samtools_1.20-3_amd64.deb ... 97s Unpacking samtools (1.20-3) ... 97s Selecting previously unselected package fastaq. 97s Preparing to unpack .../005-fastaq_3.17.0-8_all.deb ... 97s Unpacking fastaq (3.17.0-8) ... 97s Selecting previously unselected package libblas3:amd64. 97s Preparing to unpack .../006-libblas3_3.12.0-3build2_amd64.deb ... 97s Unpacking libblas3:amd64 (3.12.0-3build2) ... 97s Selecting previously unselected package libgfortran5:amd64. 97s Preparing to unpack .../007-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 97s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 97s Selecting previously unselected package liblapack3:amd64. 97s Preparing to unpack .../008-liblapack3_3.12.0-3build2_amd64.deb ... 97s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 97s Selecting previously unselected package python3-numpy. 97s Preparing to unpack .../009-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 97s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 98s Selecting previously unselected package libtcl8.6:amd64. 98s Preparing to unpack .../010-libtcl8.6_8.6.15+dfsg-2_amd64.deb ... 98s Unpacking libtcl8.6:amd64 (8.6.15+dfsg-2) ... 98s Selecting previously unselected package fonts-dejavu-mono. 98s Preparing to unpack .../011-fonts-dejavu-mono_2.37-8_all.deb ... 98s Unpacking fonts-dejavu-mono (2.37-8) ... 98s Selecting previously unselected package fonts-dejavu-core. 98s Preparing to unpack .../012-fonts-dejavu-core_2.37-8_all.deb ... 98s Unpacking fonts-dejavu-core (2.37-8) ... 98s Selecting previously unselected package libfontenc1:amd64. 98s Preparing to unpack .../013-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 98s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 98s Selecting previously unselected package x11-common. 98s Preparing to unpack .../014-x11-common_1%3a7.7+23ubuntu3_all.deb ... 98s Unpacking x11-common (1:7.7+23ubuntu3) ... 98s Selecting previously unselected package xfonts-encodings. 98s Preparing to unpack .../015-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 98s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 98s Selecting previously unselected package xfonts-utils. 98s Preparing to unpack .../016-xfonts-utils_1%3a7.7+7_amd64.deb ... 98s Unpacking xfonts-utils (1:7.7+7) ... 98s Selecting previously unselected package fonts-urw-base35. 98s Preparing to unpack .../017-fonts-urw-base35_20200910-8_all.deb ... 98s Unpacking fonts-urw-base35 (20200910-8) ... 98s Selecting previously unselected package fontconfig-config. 98s Preparing to unpack .../018-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 98s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 98s Selecting previously unselected package libfontconfig1:amd64. 98s Preparing to unpack .../019-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 98s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 98s Selecting previously unselected package libxrender1:amd64. 98s Preparing to unpack .../020-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 98s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 98s Selecting previously unselected package libxft2:amd64. 98s Preparing to unpack .../021-libxft2_2.3.6-1build1_amd64.deb ... 98s Unpacking libxft2:amd64 (2.3.6-1build1) ... 98s Selecting previously unselected package libxss1:amd64. 98s Preparing to unpack .../022-libxss1_1%3a1.2.3-1build3_amd64.deb ... 98s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 98s Selecting previously unselected package libtk8.6:amd64. 98s Preparing to unpack .../023-libtk8.6_8.6.15-1_amd64.deb ... 98s Unpacking libtk8.6:amd64 (8.6.15-1) ... 98s Selecting previously unselected package python3.12-tk. 98s Preparing to unpack .../024-python3.12-tk_3.12.7-3_amd64.deb ... 98s Unpacking python3.12-tk (3.12.7-3) ... 98s Selecting previously unselected package tk8.6-blt2.5. 98s Preparing to unpack .../025-tk8.6-blt2.5_2.5.3+dfsg-7build1_amd64.deb ... 98s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 98s Selecting previously unselected package blt. 98s Preparing to unpack .../026-blt_2.5.3+dfsg-7build1_amd64.deb ... 98s Unpacking blt (2.5.3+dfsg-7build1) ... 99s Selecting previously unselected package python3-tk:amd64. 99s Preparing to unpack .../027-python3-tk_3.12.6-1ubuntu1_amd64.deb ... 99s Unpacking python3-tk:amd64 (3.12.6-1ubuntu1) ... 99s Selecting previously unselected package python3-pil.imagetk:amd64. 99s Preparing to unpack .../028-python3-pil.imagetk_10.4.0-1ubuntu1_amd64.deb ... 99s Unpacking python3-pil.imagetk:amd64 (10.4.0-1ubuntu1) ... 99s Selecting previously unselected package libgomp1:amd64. 99s Preparing to unpack .../029-libgomp1_14.2.0-8ubuntu1_amd64.deb ... 99s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ... 99s Selecting previously unselected package libimagequant0:amd64. 99s Preparing to unpack .../030-libimagequant0_2.18.0-1build1_amd64.deb ... 99s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 99s Selecting previously unselected package libjpeg-turbo8:amd64. 99s Preparing to unpack .../031-libjpeg-turbo8_2.1.5-2ubuntu2_amd64.deb ... 99s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 99s Selecting previously unselected package libjpeg8:amd64. 99s Preparing to unpack .../032-libjpeg8_8c-2ubuntu11_amd64.deb ... 99s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 99s Selecting previously unselected package liblcms2-2:amd64. 99s Preparing to unpack .../033-liblcms2-2_2.16-2_amd64.deb ... 99s Unpacking liblcms2-2:amd64 (2.16-2) ... 99s Selecting previously unselected package libopenjp2-7:amd64. 99s Preparing to unpack .../034-libopenjp2-7_2.5.0-2ubuntu1_amd64.deb ... 99s Unpacking libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 99s Selecting previously unselected package libgraphite2-3:amd64. 99s Preparing to unpack .../035-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 99s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 99s Selecting previously unselected package libharfbuzz0b:amd64. 99s Preparing to unpack .../036-libharfbuzz0b_10.0.1-1_amd64.deb ... 99s Unpacking libharfbuzz0b:amd64 (10.0.1-1) ... 99s Selecting previously unselected package libraqm0:amd64. 99s Preparing to unpack .../037-libraqm0_0.10.1-1build1_amd64.deb ... 99s Unpacking libraqm0:amd64 (0.10.1-1build1) ... 99s Selecting previously unselected package libjbig0:amd64. 99s Preparing to unpack .../038-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 99s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 99s Selecting previously unselected package liblerc4:amd64. 99s Preparing to unpack .../039-liblerc4_4.0.0+ds-4ubuntu2_amd64.deb ... 99s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 99s Selecting previously unselected package libsharpyuv0:amd64. 99s Preparing to unpack .../040-libsharpyuv0_1.4.0-0.1_amd64.deb ... 99s Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ... 99s Selecting previously unselected package libwebp7:amd64. 99s Preparing to unpack .../041-libwebp7_1.4.0-0.1_amd64.deb ... 99s Unpacking libwebp7:amd64 (1.4.0-0.1) ... 99s Selecting previously unselected package libtiff6:amd64. 99s Preparing to unpack .../042-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 99s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 99s Selecting previously unselected package libwebpdemux2:amd64. 99s Preparing to unpack .../043-libwebpdemux2_1.4.0-0.1_amd64.deb ... 99s Unpacking libwebpdemux2:amd64 (1.4.0-0.1) ... 99s Selecting previously unselected package libwebpmux3:amd64. 99s Preparing to unpack .../044-libwebpmux3_1.4.0-0.1_amd64.deb ... 99s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ... 99s Selecting previously unselected package python3-pil:amd64. 99s Preparing to unpack .../045-python3-pil_10.4.0-1ubuntu1_amd64.deb ... 99s Unpacking python3-pil:amd64 (10.4.0-1ubuntu1) ... 99s Selecting previously unselected package libpixman-1-0:amd64. 99s Preparing to unpack .../046-libpixman-1-0_0.44.0-3_amd64.deb ... 99s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 99s Selecting previously unselected package libxcb-render0:amd64. 99s Preparing to unpack .../047-libxcb-render0_1.17.0-2_amd64.deb ... 99s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 99s Selecting previously unselected package libxcb-shm0:amd64. 99s Preparing to unpack .../048-libxcb-shm0_1.17.0-2_amd64.deb ... 99s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 99s Selecting previously unselected package libcairo2:amd64. 99s Preparing to unpack .../049-libcairo2_1.18.2-2_amd64.deb ... 99s Unpacking libcairo2:amd64 (1.18.2-2) ... 99s Selecting previously unselected package python3-cairo. 99s Preparing to unpack .../050-python3-cairo_1.26.1-2_amd64.deb ... 99s Unpacking python3-cairo (1.26.1-2) ... 99s Selecting previously unselected package python3-freetype. 99s Preparing to unpack .../051-python3-freetype_2.5.1-1_all.deb ... 99s Unpacking python3-freetype (2.5.1-1) ... 99s Selecting previously unselected package python3-rlpycairo. 99s Preparing to unpack .../052-python3-rlpycairo_0.3.0-3_all.deb ... 99s Unpacking python3-rlpycairo (0.3.0-3) ... 99s Selecting previously unselected package python3-reportlab. 99s Preparing to unpack .../053-python3-reportlab_4.2.5-1_all.deb ... 99s Unpacking python3-reportlab (4.2.5-1) ... 99s Selecting previously unselected package xml-core. 99s Preparing to unpack .../054-xml-core_0.19_all.deb ... 99s Unpacking xml-core (0.19) ... 99s Selecting previously unselected package w3c-sgml-lib. 99s Preparing to unpack .../055-w3c-sgml-lib_1.3-3_all.deb ... 99s Unpacking w3c-sgml-lib (1.3-3) ... 99s Selecting previously unselected package python3-biopython. 99s Preparing to unpack .../056-python3-biopython_1.84+dfsg-4build1_amd64.deb ... 99s Unpacking python3-biopython (1.84+dfsg-4build1) ... 100s Selecting previously unselected package python3-soupsieve. 100s Preparing to unpack .../057-python3-soupsieve_2.6-1_all.deb ... 100s Unpacking python3-soupsieve (2.6-1) ... 100s Selecting previously unselected package python3-bs4. 100s Preparing to unpack .../058-python3-bs4_4.12.3-3_all.deb ... 100s Unpacking python3-bs4 (4.12.3-3) ... 100s Selecting previously unselected package python3-dendropy. 100s Preparing to unpack .../059-python3-dendropy_4.6.1-1_all.deb ... 100s Unpacking python3-dendropy (4.6.1-1) ... 100s Selecting previously unselected package libjs-jquery. 100s Preparing to unpack .../060-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 100s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 100s Selecting previously unselected package libjs-jquery-ui. 100s Preparing to unpack .../061-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 100s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 100s Selecting previously unselected package fonts-lyx. 100s Preparing to unpack .../062-fonts-lyx_2.4.2.1-1_all.deb ... 100s Unpacking fonts-lyx (2.4.2.1-1) ... 100s Selecting previously unselected package python-matplotlib-data. 100s Preparing to unpack .../063-python-matplotlib-data_3.8.3-3_all.deb ... 100s Unpacking python-matplotlib-data (3.8.3-3) ... 100s Selecting previously unselected package python3-six. 100s Preparing to unpack .../064-python3-six_1.16.0-7_all.deb ... 100s Unpacking python3-six (1.16.0-7) ... 100s Selecting previously unselected package python3-dateutil. 100s Preparing to unpack .../065-python3-dateutil_2.9.0-2_all.deb ... 100s Unpacking python3-dateutil (2.9.0-2) ... 100s Selecting previously unselected package python3-contourpy. 100s Preparing to unpack .../066-python3-contourpy_1.3.0-2_amd64.deb ... 100s Unpacking python3-contourpy (1.3.0-2) ... 100s Selecting previously unselected package python3-cycler. 100s Preparing to unpack .../067-python3-cycler_0.12.1-1_all.deb ... 100s Unpacking python3-cycler (0.12.1-1) ... 100s Selecting previously unselected package python3-brotli. 100s Preparing to unpack .../068-python3-brotli_1.1.0-2build2_amd64.deb ... 100s Unpacking python3-brotli (1.1.0-2build2) ... 100s Selecting previously unselected package python3-decorator. 100s Preparing to unpack .../069-python3-decorator_5.1.1-5_all.deb ... 100s Unpacking python3-decorator (5.1.1-5) ... 100s Selecting previously unselected package liblbfgsb0:amd64. 100s Preparing to unpack .../070-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 100s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 100s Selecting previously unselected package python3-scipy. 100s Preparing to unpack .../071-python3-scipy_1.13.1-5_amd64.deb ... 100s Unpacking python3-scipy (1.13.1-5) ... 100s Selecting previously unselected package python3-ufolib2. 100s Preparing to unpack .../072-python3-ufolib2_0.16.1+dfsg1-1_all.deb ... 100s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ... 101s Selecting previously unselected package python3-mpmath. 101s Preparing to unpack .../073-python3-mpmath_1.3.0-1_all.deb ... 101s Unpacking python3-mpmath (1.3.0-1) ... 101s Selecting previously unselected package python3-sympy. 101s Preparing to unpack .../074-python3-sympy_1.13.3-1_all.deb ... 101s Unpacking python3-sympy (1.13.3-1) ... 101s Selecting previously unselected package python3-tz. 101s Preparing to unpack .../075-python3-tz_2024.1-2_all.deb ... 101s Unpacking python3-tz (2024.1-2) ... 101s Selecting previously unselected package python3-appdirs. 101s Preparing to unpack .../076-python3-appdirs_1.4.4-4_all.deb ... 101s Unpacking python3-appdirs (1.4.4-4) ... 101s Selecting previously unselected package python3-fs. 101s Preparing to unpack .../077-python3-fs_2.4.16-4_all.deb ... 101s Unpacking python3-fs (2.4.16-4) ... 101s Selecting previously unselected package libxslt1.1:amd64. 101s Preparing to unpack .../078-libxslt1.1_1.1.39-0exp1ubuntu1_amd64.deb ... 101s Unpacking libxslt1.1:amd64 (1.1.39-0exp1ubuntu1) ... 101s Selecting previously unselected package python3-lxml:amd64. 101s Preparing to unpack .../079-python3-lxml_5.3.0-1_amd64.deb ... 101s Unpacking python3-lxml:amd64 (5.3.0-1) ... 101s Selecting previously unselected package python3-lz4. 101s Preparing to unpack .../080-python3-lz4_4.0.2+dfsg-1build4_amd64.deb ... 101s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 101s Selecting previously unselected package python3-unicodedata2. 101s Preparing to unpack .../081-python3-unicodedata2_15.1.0+ds-1build2_amd64.deb ... 101s Unpacking python3-unicodedata2 (15.1.0+ds-1build2) ... 101s Selecting previously unselected package unicode-data. 101s Preparing to unpack .../082-unicode-data_15.1.0-1_all.deb ... 101s Unpacking unicode-data (15.1.0-1) ... 101s Selecting previously unselected package python3-fonttools. 101s Preparing to unpack .../083-python3-fonttools_4.46.0-1build2_amd64.deb ... 101s Unpacking python3-fonttools (4.46.0-1build2) ... 101s Selecting previously unselected package python3-kiwisolver. 101s Preparing to unpack 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(0.11.0-4) ... 102s Selecting previously unselected package python3-pysam. 102s Preparing to unpack .../090-python3-pysam_0.22.1+ds-2_amd64.deb ... 102s Unpacking python3-pysam (0.22.1+ds-2) ... 102s Selecting previously unselected package libfml0:amd64. 102s Preparing to unpack .../091-libfml0_0.1+git20190320.b499514-1build1_amd64.deb ... 102s Unpacking libfml0:amd64 (0.1+git20190320.b499514-1build1) ... 102s Selecting previously unselected package libminimap0:amd64. 102s Preparing to unpack .../092-libminimap0_0.2-8_amd64.deb ... 102s Unpacking libminimap0:amd64 (0.2-8) ... 102s Selecting previously unselected package bowtie2. 102s Preparing to unpack .../093-bowtie2_2.5.4-1_amd64.deb ... 102s Unpacking bowtie2 (2.5.4-1) ... 102s Selecting previously unselected package cd-hit. 102s Preparing to unpack .../094-cd-hit_4.8.1-4_amd64.deb ... 102s Unpacking cd-hit (4.8.1-4) ... 102s Selecting previously unselected package libcapnp-1.0.1:amd64. 102s Preparing to unpack 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package autopkgtest-satdep. 102s Preparing to unpack .../101-1-autopkgtest-satdep.deb ... 102s Unpacking autopkgtest-satdep (0) ... 102s Setting up libhtscodecs2:amd64 (1.6.1-1) ... 102s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 102s Setting up liblcms2-2:amd64 (2.16-2) ... 102s Setting up libpixman-1-0:amd64 (0.44.0-3) ... 102s Setting up libsharpyuv0:amd64 (1.4.0-0.1) ... 102s Setting up liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 102s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 102s Setting up libgslcblas0:amd64 (2.8+dfsg-5) ... 102s Setting up libmurmurhash2:amd64 (1.6-1) ... 102s Setting up libcapnp-1.0.1:amd64 (1.0.1-4) ... 102s Setting up python3-lz4 (4.0.2+dfsg-1build4) ... 102s Setting up libxcb-render0:amd64 (1.17.0-2) ... 102s Setting up python3-unicodedata2 (15.1.0+ds-1build2) ... 102s Setting up fonts-lyx (2.4.2.1-1) ... 102s Setting up x11-common (1:7.7+23ubuntu3) ... 103s Setting up libdeflate0:amd64 (1.22-1) ... 103s Setting up libqhull-r8.0:amd64 (2020.2-6build1) ... 103s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 103s Setting up libgomp1:amd64 (14.2.0-8ubuntu1) ... 103s Setting up python3-freetype (2.5.1-1) ... 103s Setting up libfml0:amd64 (0.1+git20190320.b499514-1build1) ... 103s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 103s Setting up python3-tz (2024.1-2) ... 103s Setting up bowtie2 (2.5.4-1) ... 103s Setting up unicode-data (15.1.0-1) ... 103s Setting up python3-six (1.16.0-7) ... 103s Setting up python3-decorator (5.1.1-5) ... 103s Setting up libminimap0:amd64 (0.2-8) ... 103s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ... 103s Setting up libblas3:amd64 (3.12.0-3build2) ... 103s 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 103s Setting up python3-packaging (24.1-1) ... 103s Setting up python3-brotli (1.1.0-2build2) ... 103s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 103s Setting up python3-cycler (0.12.1-1) ... 103s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 103s Setting up fonts-dejavu-mono (2.37-8) ... 103s Setting up python3-kiwisolver (1.4.7-2build1) ... 103s Setting up libtcl8.6:amd64 (8.6.15+dfsg-2) ... 103s Setting up fonts-dejavu-core (2.37-8) ... 103s Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 103s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 103s Setting up libwebp7:amd64 (1.4.0-0.1) ... 103s Setting up libxslt1.1:amd64 (1.1.39-0exp1ubuntu1) ... 103s Setting up mummer (3.23+dfsg-8) ... 103s Setting up libhts3t64:amd64 (1.20+ds-1) ... 103s Setting up libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 103s Setting up libharfbuzz0b:amd64 (10.0.1-1) ... 103s Setting up python3-dateutil (2.9.0-2) ... 104s Setting up sgml-base (1.31) ... 104s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 104s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 104s Setting up python3-mpmath (1.3.0-1) ... 104s Setting up libgsl28:amd64 (2.8+dfsg-5) ... 104s Setting up python-matplotlib-data (3.8.3-3) ... 104s Setting up libwebpmux3:amd64 (1.4.0-0.1) ... 104s Setting up python3-dendropy (4.6.1-1) ... 104s Setting up python3-appdirs (1.4.4-4) ... 104s Setting up python3-soupsieve (2.6-1) ... 104s Setting up cd-hit (4.8.1-4) ... 104s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 104s Setting up python3-sympy (1.13.3-1) ... 109s Setting up liblapack3:amd64 (3.12.0-3build2) ... 109s 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 109s Setting up python3-pysam (0.22.1+ds-2) ... 109s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 109s Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... 109s Setting up xfonts-utils (1:7.7+7) ... 109s Setting up python3-bs4 (4.12.3-3) ... 110s Setting up samtools (1.20-3) ... 110s Setting up python3-fs (2.4.16-4) ... 110s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 110s Setting up libraqm0:amd64 (0.10.1-1build1) ... 110s Setting up mash (2.3+dfsg-6build1) ... 110s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 111s Setting up python3-lxml:amd64 (5.3.0-1) ... 111s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 111s Setting up xml-core (0.19) ... 112s Setting up python3-contourpy (1.3.0-2) ... 112s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 112s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 112s Setting up libxft2:amd64 (2.3.6-1build1) ... 112s Setting up python3-scipy (1.13.1-5) ... 114s Setting up libtk8.6:amd64 (8.6.15-1) ... 114s Setting up fastaq (3.17.0-8) ... 114s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:37: SyntaxWarning: invalid escape sequence '\s' 114s phylip_regex = re.compile('^\s*[0-9]+\s+[0-9]+$') 114s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:38: SyntaxWarning: invalid escape sequence '\s' 114s gbk_regex = re.compile('^LOCUS\s+\S') 114s Setting up python3.12-tk (3.12.7-3) ... 114s Setting up fonts-urw-base35 (20200910-8) ... 115s Setting up libcairo2:amd64 (1.18.2-2) ... 115s Setting up python3-pymummer (0.11.0-4) ... 115s Setting up python3-pil:amd64 (10.4.0-1ubuntu1) ... 115s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 115s Setting up python3-cairo (1.26.1-2) ... 115s Setting up blt (2.5.3+dfsg-7build1) ... 115s Setting up python3-tk:amd64 (3.12.6-1ubuntu1) ... 115s Setting up python3-pil.imagetk:amd64 (10.4.0-1ubuntu1) ... 115s Setting up python3-rlpycairo (0.3.0-3) ... 115s Setting up python3-reportlab (4.2.5-1) ... 116s Setting up python3-fonttools (4.46.0-1build2) ... 116s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... 117s Setting up python3-matplotlib (3.8.3-3) ... 118s Processing triggers for libc-bin (2.40-1ubuntu3) ... 118s Processing triggers for man-db (2.13.0-1) ... 119s Processing triggers for sgml-base (1.31) ... 119s Setting up w3c-sgml-lib (1.3-3) ... 141s Setting up python3-biopython (1.84+dfsg-4build1) ... 142s Setting up ariba (2.14.7+ds-4) ... 142s /usr/lib/python3/dist-packages/ariba/external_progs.py:34: SyntaxWarning: invalid escape sequence '\.' 142s 'cdhit': ('', re.compile('CD-HIT version ([0-9\.]+) \(')), 142s /usr/lib/python3/dist-packages/ariba/external_progs.py:35: SyntaxWarning: invalid escape sequence '\.' 142s 'nucmer': ('--version', re.compile('([0-9]+\.[0-9\.]+.*$)')), 142s /usr/lib/python3/dist-packages/ariba/external_progs.py:36: SyntaxWarning: invalid escape sequence '\.' 142s 'spades': ('--version', re.compile('SPAdes.*v([0-9\.]+)')) 142s Setting up autopkgtest-satdep (0) ... 146s (Reading database ... 86385 files and directories currently installed.) 146s Removing autopkgtest-satdep (0) ... 147s autopkgtest [13:04:33]: test test-example: [----------------------- 148s ARIBA version: 2.14.6 148s 148s External dependencies: 148s bowtie2 2.5.4 /usr/bin/bowtie2 148s cdhit 4.8.1 /usr/bin/cd-hit-est 148s nucmer 3.1 /usr/bin/nucmer 148s 148s External dependencies OK: True 148s 148s Python version: 148s 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 148s 148s Python packages: 148s ariba 2.14.6 /usr/lib/python3/dist-packages/ariba/__init__.py 148s bs4 4.12.3 /usr/lib/python3/dist-packages/bs4/__init__.py 148s dendropy 4.6.1 /usr/lib/python3/dist-packages/dendropy/__init__.py 148s pyfastaq 3.17.0 /usr/lib/python3/dist-packages/pyfastaq/__init__.py 148s pymummer 0.11.0 /usr/lib/python3/dist-packages/pymummer/__init__.py 148s pysam 0.22.1 /usr/lib/python3/dist-packages/pysam/__init__.py 148s 148s Python packages OK: True 148s 148s Everything looks OK: True 148s 148s Loading and checking input data 148s 148s Running cdhit 149s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.46BCFrwQvV/foo/PREPAREREF/02.cdhit.noncoding.fa -o /tmp/tmp.46BCFrwQvV/foo/tmp.run_cd-hit.yqxpxyl3/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 149s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.46BCFrwQvV/foo/PREPAREREF/02.cdhit.noncoding.varonly.fa -o /tmp/tmp.46BCFrwQvV/foo/tmp.run_cd-hit.336z92nz/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 149s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.46BCFrwQvV/foo/PREPAREREF/02.cdhit.gene.fa -o /tmp/tmp.46BCFrwQvV/foo/tmp.run_cd-hit.ela5_qid/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 149s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.46BCFrwQvV/foo/PREPAREREF/02.cdhit.gene.varonly.fa -o /tmp/tmp.46BCFrwQvV/foo/tmp.run_cd-hit.56jwzgrd/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 149s 149s Writing clusters to file. 10 in total 150s Found reads file: reads_1.fq 150s Found reads file: reads_2.fq 150s ARIBA version: 2.14.6 150s 150s External dependencies: 150s bowtie2 2.5.4 /usr/bin/bowtie2 150s cdhit 4.8.1 /usr/bin/cd-hit-est 150s nucmer 3.1 /usr/bin/nucmer 150s 150s External dependencies OK: True 150s 150s Python version: 150s 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 150s 150s Python packages: 150s ariba 2.14.6 /usr/lib/python3/dist-packages/ariba/__init__.py 150s bs4 4.12.3 /usr/lib/python3/dist-packages/bs4/__init__.py 150s dendropy 4.6.1 /usr/lib/python3/dist-packages/dendropy/__init__.py 150s pyfastaq 3.17.0 /usr/lib/python3/dist-packages/pyfastaq/__init__.py 150s pymummer 0.11.0 /usr/lib/python3/dist-packages/pymummer/__init__.py 150s pysam 0.22.1 /usr/lib/python3/dist-packages/pysam/__init__.py 150s 150s Python packages OK: True 150s 150s Everything looks OK: True 150s Temporary directory: /tmp/tmp.46BCFrwQvV/foo/OUT/ariba.tmp.v_o92vfe 150s ______________________ Mapping reads to clustered genes _______________________ 150s Finished mapping 150s 150s _____________________________ Generating clusters _____________________________ 150s syscall: sort -k1,1 -k 2,2n /tmp/tmp.46BCFrwQvV/foo/OUT/minimap.reads > /tmp/tmp.46BCFrwQvV/foo/OUT/read_store 150s Compressing file /tmp/tmp.46BCFrwQvV/foo/OUT/read_store 150s Found 51 proper read pairs from minimap 150s Total clusters to perform local assemblies: 9 150s 150s Insert size information from reads mapped to reference genes: 150s Insert size: 185.0 150s Insert sspace sd: 0.27 150s Max insert: 220.55 150s 150s ___________________________ Assembling each cluster ___________________________ 150s Will run 1 cluster(s) in parallel 150s Not constructing cluster cluster because it only has 2 reads (1 of 9) 150s Constructing cluster cluster_1 (2 of 9) 150s Constructing cluster cluster_2 (3 of 9) 150s Constructing cluster cluster_3 (4 of 9) 150s Constructing cluster cluster_4 (5 of 9) 150s Constructing cluster gene (6 of 9) 150s Constructing cluster gene_1 (7 of 9) 150s Constructing cluster noncoding (8 of 9) 150s Constructing cluster noncoding_1 (9 of 9) 150s Start running cluster cluster_1 in directory /tmp/tmp.46BCFrwQvV/foo/OUT/ariba.tmp.v_o92vfe/cluster_1 151s cluster_1 detected 1 threads available to it 151s cluster_1 reported completion 151s Finished running cluster cluster_1 in directory /tmp/tmp.46BCFrwQvV/foo/OUT/ariba.tmp.v_o92vfe/cluster_1 151s Deleting cluster dir /tmp/tmp.46BCFrwQvV/foo/OUT/ariba.tmp.v_o92vfe/cluster_1 151s Start running cluster cluster_2 in directory /tmp/tmp.46BCFrwQvV/foo/OUT/ariba.tmp.v_o92vfe/cluster_2 153s cluster_2 detected 1 threads available to it 153s cluster_2 reported completion 153s Finished running cluster cluster_2 in directory /tmp/tmp.46BCFrwQvV/foo/OUT/ariba.tmp.v_o92vfe/cluster_2 153s Deleting cluster dir /tmp/tmp.46BCFrwQvV/foo/OUT/ariba.tmp.v_o92vfe/cluster_2 153s Start running cluster cluster_3 in directory /tmp/tmp.46BCFrwQvV/foo/OUT/ariba.tmp.v_o92vfe/cluster_3 154s cluster_3 detected 1 threads available to it 154s cluster_3 reported completion 154s Finished running cluster cluster_3 in directory /tmp/tmp.46BCFrwQvV/foo/OUT/ariba.tmp.v_o92vfe/cluster_3 154s Deleting cluster dir /tmp/tmp.46BCFrwQvV/foo/OUT/ariba.tmp.v_o92vfe/cluster_3 154s Start running cluster cluster_4 in directory /tmp/tmp.46BCFrwQvV/foo/OUT/ariba.tmp.v_o92vfe/cluster_4 156s cluster_4 detected 1 threads available to it 156s cluster_4 reported completion 156s Finished running cluster cluster_4 in directory /tmp/tmp.46BCFrwQvV/foo/OUT/ariba.tmp.v_o92vfe/cluster_4 156s Deleting cluster dir /tmp/tmp.46BCFrwQvV/foo/OUT/ariba.tmp.v_o92vfe/cluster_4 156s Start running cluster gene in directory /tmp/tmp.46BCFrwQvV/foo/OUT/ariba.tmp.v_o92vfe/gene 158s gene detected 1 threads available to it 158s gene reported completion 158s Finished running cluster gene in directory /tmp/tmp.46BCFrwQvV/foo/OUT/ariba.tmp.v_o92vfe/gene 158s Deleting cluster dir /tmp/tmp.46BCFrwQvV/foo/OUT/ariba.tmp.v_o92vfe/gene 158s Start running cluster gene_1 in directory /tmp/tmp.46BCFrwQvV/foo/OUT/ariba.tmp.v_o92vfe/gene_1 159s gene_1 detected 1 threads available to it 159s gene_1 reported completion 159s Finished running cluster gene_1 in directory /tmp/tmp.46BCFrwQvV/foo/OUT/ariba.tmp.v_o92vfe/gene_1 159s Deleting cluster dir /tmp/tmp.46BCFrwQvV/foo/OUT/ariba.tmp.v_o92vfe/gene_1 159s Start running cluster noncoding in directory /tmp/tmp.46BCFrwQvV/foo/OUT/ariba.tmp.v_o92vfe/noncoding 160s noncoding detected 1 threads available to it 160s noncoding reported completion 160s Finished running cluster noncoding in directory /tmp/tmp.46BCFrwQvV/foo/OUT/ariba.tmp.v_o92vfe/noncoding 160s Deleting cluster dir /tmp/tmp.46BCFrwQvV/foo/OUT/ariba.tmp.v_o92vfe/noncoding 160s Start running cluster noncoding_1 in directory /tmp/tmp.46BCFrwQvV/foo/OUT/ariba.tmp.v_o92vfe/noncoding_1 162s noncoding_1 detected 1 threads available to it 162s noncoding_1 reported completion 162s Finished running cluster noncoding_1 in directory /tmp/tmp.46BCFrwQvV/foo/OUT/ariba.tmp.v_o92vfe/noncoding_1 162s Deleting cluster dir /tmp/tmp.46BCFrwQvV/foo/OUT/ariba.tmp.v_o92vfe/noncoding_1 162s Final value of remaining_clusters counter: Value('l', 0) 162s Finished assembling clusters 162s 162s _______________________________ Writing reports _______________________________ 162s Making /tmp/tmp.46BCFrwQvV/foo/OUT/debug.report.tsv 162s Making /tmp/tmp.46BCFrwQvV/foo/OUT/report.tsv 162s 162s ____________________ Writing fasta of assembled sequences _____________________ 162s /tmp/tmp.46BCFrwQvV/foo/OUT/assembled_seqs.fa.gz and /tmp/tmp.46BCFrwQvV/foo/OUT/assembled_genes.fa.gz 162s 162s __________________________ Catting cluster log files __________________________ 162s Writing file /tmp/tmp.46BCFrwQvV/foo/OUT/log.clusters.gz 162s 162s _______________________________ Cleaning files ________________________________ 162s Deleting Logs directory /tmp/tmp.46BCFrwQvV/foo/OUT/Logs 162s Deleting reads store files /tmp/tmp.46BCFrwQvV/foo/OUT/read_store.gz[.tbi] 162s 162s All done! 162s 162s Running ARIBA on test data... 162s ------------------------------------------------------------------------------- 162s |=============================================================================| 162s | Preparing input data | 162s |=============================================================================| 162s ------------------------------------------------------------------------------- 162s Made output directory ./foo. Copying test data files into it: 162s copied ref_seqs.fa 162s copied metadata.tsv 162s copied reads_1.fq 162s copied reads_2.fq 162s ------------------------------------------------------------------------------- 162s |=============================================================================| 162s | Try running ariba prepareref | 162s |=============================================================================| 162s ------------------------------------------------------------------------------- 162s 162s Running ariba prepareref with: 162s /usr/bin/ariba prepareref --verbose -f ref_seqs.fa -m metadata.tsv --threads 1 PREPAREREF 162s 162s 162s ariba prepareref finished OK 162s ------------------------------------------------------------------------------- 162s |=============================================================================| 162s | Try running ariba run | 162s |=============================================================================| 162s ------------------------------------------------------------------------------- 162s 162s Running ARIBA with: 162s /usr/bin/ariba run --verbose --threads 1 PREPAREREF reads_1.fq reads_2.fq OUT 162s 162s 162s ariba run finished OK 162s Finished run on test data OK 162s autopkgtest [13:04:48]: test test-example: -----------------------] 163s test-example PASS 163s autopkgtest [13:04:49]: test test-example: - - - - - - - - - - results - - - - - - - - - - 163s autopkgtest [13:04:49]: @@@@@@@@@@@@@@@@@@@@ summary 163s test-example PASS 176s nova [W] Skipping flock for amd64 176s Creating nova instance adt-plucky-amd64-ariba-20241115-130206-juju-7f2275-prod-proposed-migration-environment-15-caad0e7b-107a-4942-af76-bd9d6d994714 from image adt/ubuntu-plucky-amd64-server-20241114.img (UUID 79d80331-8736-463c-82c6-8c9e13c0a4ca)...