0s autopkgtest [08:06:30]: starting date and time: 2024-11-13 08:06:30+0000 0s autopkgtest [08:06:30]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [08:06:30]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.vc5liwkc/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade ariba --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@lcy02-34.secgroup --name adt-plucky-amd64-ariba-20241113-080628-juju-7f2275-prod-proposed-migration-environment-15-1494d410-39cc-41e4-9544-02e0310e1379 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -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/ 526s autopkgtest [08:15:16]: testbed dpkg architecture: amd64 526s autopkgtest [08:15:16]: testbed apt version: 2.9.8 526s autopkgtest [08:15:16]: @@@@@@@@@@@@@@@@@@@@ test bed setup 527s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 527s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [848 kB] 527s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 527s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 527s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 527s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.2 kB] 527s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB] 527s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 527s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [637 kB] 527s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [255 kB] 527s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [37.7 kB] 527s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [13.0 kB] 527s Fetched 2171 kB in 0s (6979 kB/s) 527s Reading package lists... 528s Reading package lists... 529s Building dependency tree... 529s Reading state information... 529s Calculating upgrade... 529s The following NEW packages will be installed: 529s python3.13-gdbm 529s The following packages will be upgraded: 529s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 529s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 529s Need to get 253 kB of archives. 529s After this operation, 147 kB of additional disk space will be used. 529s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 529s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 529s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 529s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 529s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 529s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.23.2-5ubuntu4 [152 kB] 529s Fetched 253 kB in 0s (8635 kB/s) 530s (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 ... 75541 files and directories currently installed.) 530s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 530s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 530s Setting up python3-minimal (3.12.7-1) ... 530s (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 ... 75541 files and directories currently installed.) 530s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 530s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 530s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 530s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 530s Selecting previously unselected package python3.13-gdbm. 530s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ... 530s Unpacking python3.13-gdbm (3.13.0-2) ... 530s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ... 530s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 530s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_amd64.deb ... 530s Unpacking libgpgme11t64:amd64 (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 530s Setting up libgpgme11t64:amd64 (1.23.2-5ubuntu4) ... 530s Setting up python3.13-gdbm (3.13.0-2) ... 530s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 530s Setting up python3 (3.12.7-1) ... 530s Setting up python3-gdbm:amd64 (3.12.7-1) ... 530s Processing triggers for man-db (2.12.1-3) ... 531s Processing triggers for libc-bin (2.40-1ubuntu3) ... 531s Reading package lists... 531s Building dependency tree... 531s Reading state information... 532s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 532s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 532s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 532s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 532s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 533s Reading package lists... 533s Reading package lists... 533s Building dependency tree... 533s Reading state information... 534s Calculating upgrade... 534s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 534s Reading package lists... 534s Building dependency tree... 534s Reading state information... 535s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 535s autopkgtest [08:15:25]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 535s autopkgtest [08:15:25]: @@@@@@@@@@@@@@@@@@@@ apt-source ariba 536s Get:1 http://ftpmaster.internal/ubuntu plucky/universe ariba 2.14.7+ds-4 (dsc) [2316 B] 536s Get:2 http://ftpmaster.internal/ubuntu plucky/universe ariba 2.14.7+ds-4 (tar) [1920 kB] 536s Get:3 http://ftpmaster.internal/ubuntu plucky/universe ariba 2.14.7+ds-4 (diff) [10.7 kB] 536s gpgv: Signature made Tue Nov 5 03:36:42 2024 UTC 536s gpgv: using RSA key 13796755BBC72BB8ABE2AEB5FA9DEC5DE11C63F1 536s gpgv: issuer "eamanu@debian.org" 536s gpgv: Can't check signature: No public key 536s dpkg-source: warning: cannot verify inline signature for ./ariba_2.14.7+ds-4.dsc: no acceptable signature found 536s autopkgtest [08:15:26]: testing package ariba version 2.14.7+ds-4 536s autopkgtest [08:15:26]: build not needed 536s autopkgtest [08:15:26]: test test-example: preparing testbed 538s Reading package lists... 538s Building dependency tree... 538s Reading state information... 539s Starting pkgProblemResolver with broken count: 0 539s Starting 2 pkgProblemResolver with broken count: 0 539s Done 539s The following additional packages will be installed: 539s ariba blt bowtie2 cd-hit fastaq fontconfig-config fonts-dejavu-core 539s fonts-dejavu-mono fonts-lyx fonts-urw-base35 libblas3 libcairo2 539s libcapnp-1.0.1 libdeflate0 libfml0 libfontconfig1 libfontenc1 libgfortran5 539s libgomp1 libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b libhts3t64 539s libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery 539s libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libminimap0 539s libmurmurhash2 libopenjp2-7 libpixman-1-0 libqhull-r8.0 libraqm0 539s libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 539s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 mash 539s mummer python-matplotlib-data python3-appdirs python3-biopython 539s python3-brotli python3-bs4 python3-cairo python3-contourpy python3-cycler 539s python3-dateutil python3-decorator python3-dendropy python3-fonttools 539s python3-freetype python3-fs python3-kiwisolver python3-lxml python3-lz4 539s python3-matplotlib python3-mpmath python3-numpy python3-packaging 539s python3-pil python3-pil.imagetk python3-pymummer python3-pysam 539s python3-reportlab python3-rlpycairo python3-scipy python3-six 539s python3-soupsieve python3-sympy python3-tk python3-tz python3-ufolib2 539s python3-unicodedata2 python3.12-tk python3.13-tk samtools sgml-base 539s tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings 539s xfonts-utils xml-core 539s Suggested packages: 539s spades blt-demo bowtie2-examples fonts-freefont-otf | fonts-freefont-ttf 539s fonts-texgyre gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html 539s libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 bwa clustalo clustalw 539s dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons 539s python3-mysqldb python3-mmtf python3-rdflib python3-psycopg2 raxml t-coffee 539s wise python-cycler-doc python-lxml-doc cm-super-minimal dvipng ffmpeg 539s fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common 539s python-matplotlib-doc python3-cairocffi python3-gi-cairo python3-gobject 539s python3-pyqt5 python3-sip python3-tornado texlive-extra-utils 539s texlive-latex-extra python-mpmath-doc python3-gmpy2 gcc gfortran 539s python-numpy-doc python3-dev python3-pytest python-pil-doc pdf-viewer 539s python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm 539s python-scipy-doc texlive-fonts-extra python-sympy-doc tix python3-tk-dbg 539s cwltool sgml-base-doc debhelper 539s Recommended packages: 539s javascript-common python-biopython-doc ncbi-blast+ python3-cssselect 539s python3-html5lib python3-olefile fonts-dejavu-extra g++ | c++-compiler 539s isympy-common 539s The following NEW packages will be installed: 539s ariba autopkgtest-satdep blt bowtie2 cd-hit fastaq fontconfig-config 539s fonts-dejavu-core fonts-dejavu-mono fonts-lyx fonts-urw-base35 libblas3 539s libcairo2 libcapnp-1.0.1 libdeflate0 libfml0 libfontconfig1 libfontenc1 539s libgfortran5 libgomp1 libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b 539s libhts3t64 libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 539s libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblerc4 539s libminimap0 libmurmurhash2 libopenjp2-7 libpixman-1-0 libqhull-r8.0 libraqm0 539s libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 539s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 mash 539s mummer python-matplotlib-data python3-appdirs python3-biopython 539s python3-brotli python3-bs4 python3-cairo python3-contourpy python3-cycler 539s python3-dateutil python3-decorator python3-dendropy python3-fonttools 539s python3-freetype python3-fs python3-kiwisolver python3-lxml python3-lz4 539s python3-matplotlib python3-mpmath python3-numpy python3-packaging 539s python3-pil python3-pil.imagetk python3-pymummer python3-pysam 539s python3-reportlab python3-rlpycairo python3-scipy python3-six 539s python3-soupsieve python3-sympy python3-tk python3-tz python3-ufolib2 539s python3-unicodedata2 python3.12-tk python3.13-tk samtools sgml-base 539s tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings 539s xfonts-utils xml-core 539s 0 upgraded, 103 newly installed, 0 to remove and 0 not upgraded. 539s Need to get 88.7 MB/88.7 MB of archives. 539s After this operation, 370 MB of additional disk space will be used. 539s Get:1 /tmp/autopkgtest.yzTCcf/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [700 B] 539s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 539s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 539s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-1 [132 kB] 539s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.20+ds-1 [439 kB] 539s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 samtools amd64 1.20-3 [599 kB] 539s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 fastaq all 3.17.0-8 [48.2 kB] 539s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 539s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 539s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 539s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 539s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1085 kB] 539s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 539s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 540s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 540s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 540s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 540s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 540s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 540s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 540s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 540s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 540s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 540s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 540s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.15-1 [862 kB] 540s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.7-3 [116 kB] 540s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-tk amd64 3.13.0-2 [106 kB] 540s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB] 540s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B] 540s Get:30 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-tk amd64 3.12.7-1 [9752 B] 540s Get:31 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 10.4.0-1ubuntu1 [9394 B] 540s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 540s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 540s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB] 540s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 540s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 540s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB] 540s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 540s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB] 540s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 540s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 540s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB] 540s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 540s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 540s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 540s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 540s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 540s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu1 [463 kB] 540s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 540s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 540s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 540s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 540s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2 [119 kB] 540s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 540s Get:55 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 540s Get:56 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.2.5-1 [1107 kB] 540s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 540s Get:58 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 540s Get:59 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.84+dfsg-4 [1714 kB] 540s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-soupsieve all 2.6-1 [33.0 kB] 540s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-bs4 all 4.12.3-3 [109 kB] 540s Get:62 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-dendropy all 4.6.1-1 [278 kB] 540s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 540s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 540s Get:65 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.2.1-1 [171 kB] 540s Get:66 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-3 [2928 kB] 540s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.16.0-7 [13.1 kB] 540s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB] 540s Get:69 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.0-2 [217 kB] 540s Get:70 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 540s Get:71 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build2 [332 kB] 540s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 540s Get:73 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 540s Get:74 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5 [18.2 MB] 540s Get:75 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 540s Get:76 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 540s Get:77 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-1 [4228 kB] 540s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB] 540s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-appdirs all 1.4.4-4 [10.9 kB] 540s Get:80 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-4 [91.3 kB] 540s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu1 [169 kB] 540s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.0-1 [1282 kB] 540s Get:83 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.0.2+dfsg-1build4 [26.2 kB] 540s Get:84 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build1 [362 kB] 540s Get:85 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 540s Get:86 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.46.0-1build2 [1436 kB] 540s Get:87 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-2 [55.1 kB] 540s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 540s Get:89 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 540s Get:90 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-3 [4545 kB] 540s Get:91 http://ftpmaster.internal/ubuntu plucky/universe amd64 mummer amd64 3.23+dfsg-8 [685 kB] 540s Get:92 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pymummer all 0.11.0-4 [17.1 kB] 540s Get:93 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pysam amd64 0.22.1+ds-2 [3504 kB] 540s Get:94 http://ftpmaster.internal/ubuntu plucky/universe amd64 libfml0 amd64 0.1+git20190320.b499514-1build1 [74.2 kB] 540s Get:95 http://ftpmaster.internal/ubuntu plucky/universe amd64 libminimap0 amd64 0.2-8 [23.5 kB] 540s Get:96 http://ftpmaster.internal/ubuntu plucky/universe amd64 bowtie2 amd64 2.5.4-1 [1336 kB] 540s Get:97 http://ftpmaster.internal/ubuntu plucky/universe amd64 cd-hit amd64 4.8.1-4 [521 kB] 540s Get:98 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcapnp-1.0.1 amd64 1.0.1-4 [1400 kB] 540s Get:99 http://ftpmaster.internal/ubuntu plucky/universe amd64 libgslcblas0 amd64 2.8+dfsg-5 [290 kB] 540s Get:100 http://ftpmaster.internal/ubuntu plucky/universe amd64 libgsl28 amd64 2.8+dfsg-5 [1285 kB] 540s Get:101 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmurmurhash2 amd64 1.6-1 [5770 B] 540s Get:102 http://ftpmaster.internal/ubuntu plucky/universe amd64 mash amd64 2.3+dfsg-6build1 [160 kB] 540s Get:103 http://ftpmaster.internal/ubuntu plucky/universe amd64 ariba amd64 2.14.7+ds-4 [2033 kB] 541s Fetched 88.7 MB in 1s (84.9 MB/s) 541s Selecting previously unselected package sgml-base. 541s (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 ... 75548 files and directories currently installed.) 541s Preparing to unpack .../000-sgml-base_1.31_all.deb ... 541s Unpacking sgml-base (1.31) ... 541s Selecting previously unselected package libdeflate0:amd64. 541s Preparing to unpack .../001-libdeflate0_1.22-1_amd64.deb ... 541s Unpacking libdeflate0:amd64 (1.22-1) ... 541s Selecting previously unselected package libhtscodecs2:amd64. 541s Preparing to unpack .../002-libhtscodecs2_1.6.1-1_amd64.deb ... 541s Unpacking libhtscodecs2:amd64 (1.6.1-1) ... 541s Selecting previously unselected package libhts3t64:amd64. 541s Preparing to unpack .../003-libhts3t64_1.20+ds-1_amd64.deb ... 541s Unpacking libhts3t64:amd64 (1.20+ds-1) ... 541s Selecting previously unselected package samtools. 541s Preparing to unpack .../004-samtools_1.20-3_amd64.deb ... 541s Unpacking samtools (1.20-3) ... 541s Selecting previously unselected package fastaq. 541s Preparing to unpack .../005-fastaq_3.17.0-8_all.deb ... 541s Unpacking fastaq (3.17.0-8) ... 541s Selecting previously unselected package libblas3:amd64. 541s Preparing to unpack .../006-libblas3_3.12.0-3build2_amd64.deb ... 541s Unpacking libblas3:amd64 (3.12.0-3build2) ... 541s Selecting previously unselected package libgfortran5:amd64. 541s Preparing to unpack .../007-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 541s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 541s Selecting previously unselected package liblapack3:amd64. 541s Preparing to unpack .../008-liblapack3_3.12.0-3build2_amd64.deb ... 541s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 541s Selecting previously unselected package python3-numpy. 541s Preparing to unpack .../009-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 541s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 541s Selecting previously unselected package libtcl8.6:amd64. 541s Preparing to unpack .../010-libtcl8.6_8.6.15+dfsg-2_amd64.deb ... 541s Unpacking libtcl8.6:amd64 (8.6.15+dfsg-2) ... 541s Selecting previously unselected package fonts-dejavu-mono. 541s Preparing to unpack .../011-fonts-dejavu-mono_2.37-8_all.deb ... 541s Unpacking fonts-dejavu-mono (2.37-8) ... 542s Selecting previously unselected package fonts-dejavu-core. 542s Preparing to unpack .../012-fonts-dejavu-core_2.37-8_all.deb ... 542s Unpacking fonts-dejavu-core (2.37-8) ... 542s Selecting previously unselected package libfontenc1:amd64. 542s Preparing to unpack .../013-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 542s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 542s Selecting previously unselected package x11-common. 542s Preparing to unpack .../014-x11-common_1%3a7.7+23ubuntu3_all.deb ... 542s Unpacking x11-common (1:7.7+23ubuntu3) ... 542s Selecting previously unselected package xfonts-encodings. 542s Preparing to unpack .../015-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 542s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 542s Selecting previously unselected package xfonts-utils. 542s Preparing to unpack .../016-xfonts-utils_1%3a7.7+7_amd64.deb ... 542s Unpacking xfonts-utils (1:7.7+7) ... 542s Selecting previously unselected package fonts-urw-base35. 542s Preparing to unpack .../017-fonts-urw-base35_20200910-8_all.deb ... 542s Unpacking fonts-urw-base35 (20200910-8) ... 542s Selecting previously unselected package fontconfig-config. 542s Preparing to unpack .../018-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 542s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 542s Selecting previously unselected package libfontconfig1:amd64. 542s Preparing to unpack .../019-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 542s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 542s Selecting previously unselected package libxrender1:amd64. 542s Preparing to unpack .../020-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 542s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 542s Selecting previously unselected package libxft2:amd64. 542s Preparing to unpack .../021-libxft2_2.3.6-1build1_amd64.deb ... 542s Unpacking libxft2:amd64 (2.3.6-1build1) ... 542s Selecting previously unselected package libxss1:amd64. 542s Preparing to unpack .../022-libxss1_1%3a1.2.3-1build3_amd64.deb ... 542s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 542s Selecting previously unselected package libtk8.6:amd64. 542s Preparing to unpack .../023-libtk8.6_8.6.15-1_amd64.deb ... 542s Unpacking libtk8.6:amd64 (8.6.15-1) ... 542s Selecting previously unselected package python3.12-tk. 542s Preparing to unpack .../024-python3.12-tk_3.12.7-3_amd64.deb ... 542s Unpacking python3.12-tk (3.12.7-3) ... 542s Selecting previously unselected package python3.13-tk. 542s Preparing to unpack .../025-python3.13-tk_3.13.0-2_amd64.deb ... 542s Unpacking python3.13-tk (3.13.0-2) ... 542s Selecting previously unselected package tk8.6-blt2.5. 542s Preparing to unpack .../026-tk8.6-blt2.5_2.5.3+dfsg-7build1_amd64.deb ... 542s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 542s Selecting previously unselected package blt. 542s Preparing to unpack .../027-blt_2.5.3+dfsg-7build1_amd64.deb ... 542s Unpacking blt (2.5.3+dfsg-7build1) ... 542s Selecting previously unselected package python3-tk:amd64. 542s Preparing to unpack .../028-python3-tk_3.12.7-1_amd64.deb ... 542s Unpacking python3-tk:amd64 (3.12.7-1) ... 543s Selecting previously unselected package python3-pil.imagetk:amd64. 543s Preparing to unpack .../029-python3-pil.imagetk_10.4.0-1ubuntu1_amd64.deb ... 543s Unpacking python3-pil.imagetk:amd64 (10.4.0-1ubuntu1) ... 543s Selecting previously unselected package libgomp1:amd64. 543s Preparing to unpack .../030-libgomp1_14.2.0-8ubuntu1_amd64.deb ... 543s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ... 543s Selecting previously unselected package libimagequant0:amd64. 543s Preparing to unpack .../031-libimagequant0_2.18.0-1build1_amd64.deb ... 543s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 543s Selecting previously unselected package libjpeg-turbo8:amd64. 543s Preparing to unpack .../032-libjpeg-turbo8_2.1.5-2ubuntu2_amd64.deb ... 543s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 543s Selecting previously unselected package libjpeg8:amd64. 543s Preparing to unpack .../033-libjpeg8_8c-2ubuntu11_amd64.deb ... 543s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 543s Selecting previously unselected package liblcms2-2:amd64. 543s Preparing to unpack .../034-liblcms2-2_2.16-2_amd64.deb ... 543s Unpacking liblcms2-2:amd64 (2.16-2) ... 543s Selecting previously unselected package libopenjp2-7:amd64. 543s Preparing to unpack .../035-libopenjp2-7_2.5.0-2ubuntu1_amd64.deb ... 543s Unpacking libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 543s Selecting previously unselected package libgraphite2-3:amd64. 543s Preparing to unpack .../036-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 543s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 543s Selecting previously unselected package libharfbuzz0b:amd64. 543s Preparing to unpack .../037-libharfbuzz0b_10.0.1-1_amd64.deb ... 543s Unpacking libharfbuzz0b:amd64 (10.0.1-1) ... 543s Selecting previously unselected package libraqm0:amd64. 543s Preparing to unpack .../038-libraqm0_0.10.1-1build1_amd64.deb ... 543s Unpacking libraqm0:amd64 (0.10.1-1build1) ... 543s Selecting previously unselected package libjbig0:amd64. 543s Preparing to unpack .../039-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 543s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 543s Selecting previously unselected package liblerc4:amd64. 543s Preparing to unpack .../040-liblerc4_4.0.0+ds-4ubuntu2_amd64.deb ... 543s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 543s Selecting previously unselected package libsharpyuv0:amd64. 543s Preparing to unpack .../041-libsharpyuv0_1.4.0-0.1_amd64.deb ... 543s Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ... 543s Selecting previously unselected package libwebp7:amd64. 543s Preparing to unpack .../042-libwebp7_1.4.0-0.1_amd64.deb ... 543s Unpacking libwebp7:amd64 (1.4.0-0.1) ... 543s Selecting previously unselected package libtiff6:amd64. 543s Preparing to unpack .../043-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 543s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 543s Selecting previously unselected package libwebpdemux2:amd64. 543s Preparing to unpack .../044-libwebpdemux2_1.4.0-0.1_amd64.deb ... 543s Unpacking libwebpdemux2:amd64 (1.4.0-0.1) ... 543s Selecting previously unselected package libwebpmux3:amd64. 543s Preparing to unpack .../045-libwebpmux3_1.4.0-0.1_amd64.deb ... 543s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ... 543s Selecting previously unselected package python3-pil:amd64. 543s Preparing to unpack .../046-python3-pil_10.4.0-1ubuntu1_amd64.deb ... 543s Unpacking python3-pil:amd64 (10.4.0-1ubuntu1) ... 543s Selecting previously unselected package libpixman-1-0:amd64. 543s Preparing to unpack .../047-libpixman-1-0_0.44.0-3_amd64.deb ... 543s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 543s Selecting previously unselected package libxcb-render0:amd64. 543s Preparing to unpack .../048-libxcb-render0_1.17.0-2_amd64.deb ... 543s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 543s Selecting previously unselected package libxcb-shm0:amd64. 543s Preparing to unpack .../049-libxcb-shm0_1.17.0-2_amd64.deb ... 543s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 543s Selecting previously unselected package libcairo2:amd64. 543s Preparing to unpack .../050-libcairo2_1.18.2-2_amd64.deb ... 543s Unpacking libcairo2:amd64 (1.18.2-2) ... 543s Selecting previously unselected package python3-cairo. 543s Preparing to unpack .../051-python3-cairo_1.26.1-2_amd64.deb ... 543s Unpacking python3-cairo (1.26.1-2) ... 543s Selecting previously unselected package python3-freetype. 543s Preparing to unpack .../052-python3-freetype_2.5.1-1_all.deb ... 543s Unpacking python3-freetype (2.5.1-1) ... 543s Selecting previously unselected package python3-rlpycairo. 543s Preparing to unpack .../053-python3-rlpycairo_0.3.0-3_all.deb ... 543s Unpacking python3-rlpycairo (0.3.0-3) ... 543s Selecting previously unselected package python3-reportlab. 543s Preparing to unpack .../054-python3-reportlab_4.2.5-1_all.deb ... 543s Unpacking python3-reportlab (4.2.5-1) ... 543s Selecting previously unselected package xml-core. 543s Preparing to unpack .../055-xml-core_0.19_all.deb ... 543s Unpacking xml-core (0.19) ... 543s Selecting previously unselected package w3c-sgml-lib. 543s Preparing to unpack .../056-w3c-sgml-lib_1.3-3_all.deb ... 543s Unpacking w3c-sgml-lib (1.3-3) ... 543s Selecting previously unselected package python3-biopython. 543s Preparing to unpack .../057-python3-biopython_1.84+dfsg-4_amd64.deb ... 543s Unpacking python3-biopython (1.84+dfsg-4) ... 544s Selecting previously unselected package python3-soupsieve. 544s Preparing to unpack .../058-python3-soupsieve_2.6-1_all.deb ... 544s Unpacking python3-soupsieve (2.6-1) ... 544s Selecting previously unselected package python3-bs4. 544s Preparing to unpack .../059-python3-bs4_4.12.3-3_all.deb ... 544s Unpacking python3-bs4 (4.12.3-3) ... 544s Selecting previously unselected package python3-dendropy. 544s Preparing to unpack .../060-python3-dendropy_4.6.1-1_all.deb ... 544s Unpacking python3-dendropy (4.6.1-1) ... 544s Selecting previously unselected package libjs-jquery. 544s Preparing to unpack .../061-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 544s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 544s Selecting previously unselected package libjs-jquery-ui. 544s Preparing to unpack .../062-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 544s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 544s Selecting previously unselected package fonts-lyx. 544s Preparing to unpack .../063-fonts-lyx_2.4.2.1-1_all.deb ... 544s Unpacking fonts-lyx (2.4.2.1-1) ... 544s Selecting previously unselected package python-matplotlib-data. 544s Preparing to unpack .../064-python-matplotlib-data_3.8.3-3_all.deb ... 544s Unpacking python-matplotlib-data (3.8.3-3) ... 544s Selecting previously unselected package python3-six. 544s Preparing to unpack .../065-python3-six_1.16.0-7_all.deb ... 544s Unpacking python3-six (1.16.0-7) ... 544s Selecting previously unselected package python3-dateutil. 544s Preparing to unpack .../066-python3-dateutil_2.9.0-2_all.deb ... 544s Unpacking python3-dateutil (2.9.0-2) ... 544s Selecting previously unselected package python3-contourpy. 544s Preparing to unpack .../067-python3-contourpy_1.3.0-2_amd64.deb ... 544s Unpacking python3-contourpy (1.3.0-2) ... 544s Selecting previously unselected package python3-cycler. 544s Preparing to unpack .../068-python3-cycler_0.12.1-1_all.deb ... 544s Unpacking python3-cycler (0.12.1-1) ... 544s Selecting previously unselected package python3-brotli. 544s Preparing to unpack .../069-python3-brotli_1.1.0-2build2_amd64.deb ... 544s Unpacking python3-brotli (1.1.0-2build2) ... 544s Selecting previously unselected package python3-decorator. 544s Preparing to unpack .../070-python3-decorator_5.1.1-5_all.deb ... 544s Unpacking python3-decorator (5.1.1-5) ... 544s Selecting previously unselected package liblbfgsb0:amd64. 544s Preparing to unpack .../071-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 544s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 544s Selecting previously unselected package python3-scipy. 544s Preparing to unpack .../072-python3-scipy_1.13.1-5_amd64.deb ... 544s Unpacking python3-scipy (1.13.1-5) ... 545s Selecting previously unselected package python3-ufolib2. 545s Preparing to unpack .../073-python3-ufolib2_0.16.1+dfsg1-1_all.deb ... 545s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ... 545s Selecting previously unselected package python3-mpmath. 545s Preparing to unpack .../074-python3-mpmath_1.3.0-1_all.deb ... 545s Unpacking python3-mpmath (1.3.0-1) ... 545s Selecting previously unselected package python3-sympy. 545s Preparing to unpack .../075-python3-sympy_1.13.3-1_all.deb ... 545s Unpacking python3-sympy (1.13.3-1) ... 545s Selecting previously unselected package python3-tz. 545s Preparing to unpack .../076-python3-tz_2024.1-2_all.deb ... 545s Unpacking python3-tz (2024.1-2) ... 545s Selecting previously unselected package python3-appdirs. 545s Preparing to unpack .../077-python3-appdirs_1.4.4-4_all.deb ... 545s Unpacking python3-appdirs (1.4.4-4) ... 545s Selecting previously unselected package python3-fs. 545s Preparing to unpack .../078-python3-fs_2.4.16-4_all.deb ... 545s Unpacking python3-fs (2.4.16-4) ... 545s Selecting previously unselected package libxslt1.1:amd64. 545s Preparing to unpack .../079-libxslt1.1_1.1.39-0exp1ubuntu1_amd64.deb ... 545s Unpacking libxslt1.1:amd64 (1.1.39-0exp1ubuntu1) ... 545s Selecting previously unselected package python3-lxml:amd64. 545s Preparing to unpack .../080-python3-lxml_5.3.0-1_amd64.deb ... 545s Unpacking python3-lxml:amd64 (5.3.0-1) ... 545s Selecting previously unselected package python3-lz4. 545s Preparing to unpack .../081-python3-lz4_4.0.2+dfsg-1build4_amd64.deb ... 545s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 545s Selecting previously unselected package python3-unicodedata2. 545s Preparing to unpack .../082-python3-unicodedata2_15.1.0+ds-1build1_amd64.deb ... 545s Unpacking python3-unicodedata2 (15.1.0+ds-1build1) ... 545s Selecting previously unselected package unicode-data. 545s Preparing to unpack .../083-unicode-data_15.1.0-1_all.deb ... 545s Unpacking unicode-data (15.1.0-1) ... 546s Selecting previously unselected package python3-fonttools. 546s Preparing to unpack .../084-python3-fonttools_4.46.0-1build2_amd64.deb ... 546s Unpacking python3-fonttools (4.46.0-1build2) ... 546s Selecting previously unselected package python3-kiwisolver. 546s Preparing to unpack .../085-python3-kiwisolver_1.4.7-2_amd64.deb ... 546s Unpacking python3-kiwisolver (1.4.7-2) ... 546s Selecting previously unselected package python3-packaging. 546s Preparing to unpack .../086-python3-packaging_24.1-1_all.deb ... 546s Unpacking python3-packaging (24.1-1) ... 546s Selecting previously unselected package libqhull-r8.0:amd64. 546s Preparing to unpack .../087-libqhull-r8.0_2020.2-6build1_amd64.deb ... 546s Unpacking libqhull-r8.0:amd64 (2020.2-6build1) ... 546s Selecting previously unselected package python3-matplotlib. 546s Preparing to unpack .../088-python3-matplotlib_3.8.3-3_amd64.deb ... 546s Unpacking python3-matplotlib (3.8.3-3) ... 546s Selecting previously unselected package mummer. 546s Preparing to unpack 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previously unselected package cd-hit. 546s Preparing to unpack .../095-cd-hit_4.8.1-4_amd64.deb ... 546s Unpacking cd-hit (4.8.1-4) ... 546s Selecting previously unselected package libcapnp-1.0.1:amd64. 546s Preparing to unpack .../096-libcapnp-1.0.1_1.0.1-4_amd64.deb ... 546s Unpacking libcapnp-1.0.1:amd64 (1.0.1-4) ... 546s Selecting previously unselected package libgslcblas0:amd64. 546s Preparing to unpack .../097-libgslcblas0_2.8+dfsg-5_amd64.deb ... 546s Unpacking libgslcblas0:amd64 (2.8+dfsg-5) ... 546s Selecting previously unselected package libgsl28:amd64. 546s Preparing to unpack .../098-libgsl28_2.8+dfsg-5_amd64.deb ... 546s Unpacking libgsl28:amd64 (2.8+dfsg-5) ... 546s Selecting previously unselected package libmurmurhash2:amd64. 546s Preparing to unpack .../099-libmurmurhash2_1.6-1_amd64.deb ... 546s Unpacking libmurmurhash2:amd64 (1.6-1) ... 546s Selecting previously unselected package mash. 546s Preparing to unpack .../100-mash_2.3+dfsg-6build1_amd64.deb ... 546s Unpacking mash (2.3+dfsg-6build1) ... 547s Selecting previously unselected package ariba. 547s Preparing to unpack .../101-ariba_2.14.7+ds-4_amd64.deb ... 547s Unpacking ariba (2.14.7+ds-4) ... 547s Selecting previously unselected package autopkgtest-satdep. 547s Preparing to unpack .../102-1-autopkgtest-satdep.deb ... 547s Unpacking autopkgtest-satdep (0) ... 547s Setting up libhtscodecs2:amd64 (1.6.1-1) ... 547s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 547s Setting up liblcms2-2:amd64 (2.16-2) ... 547s Setting up libpixman-1-0:amd64 (0.44.0-3) ... 547s Setting up libsharpyuv0:amd64 (1.4.0-0.1) ... 547s Setting up liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 547s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 547s Setting up libgslcblas0:amd64 (2.8+dfsg-5) ... 547s Setting up libmurmurhash2:amd64 (1.6-1) ... 547s Setting up libcapnp-1.0.1:amd64 (1.0.1-4) ... 547s Setting up python3-lz4 (4.0.2+dfsg-1build4) ... 547s Setting up libxcb-render0:amd64 (1.17.0-2) ... 547s Setting up python3-unicodedata2 (15.1.0+ds-1build1) ... 547s Setting up fonts-lyx (2.4.2.1-1) ... 547s Setting up x11-common (1:7.7+23ubuntu3) ... 547s Setting up libdeflate0:amd64 (1.22-1) ... 547s Setting up libqhull-r8.0:amd64 (2020.2-6build1) ... 547s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 547s Setting up libgomp1:amd64 (14.2.0-8ubuntu1) ... 547s Setting up python3-freetype (2.5.1-1) ... 547s Setting up libfml0:amd64 (0.1+git20190320.b499514-1build1) ... 547s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 547s Setting up python3-tz (2024.1-2) ... 547s Setting up bowtie2 (2.5.4-1) ... 547s Setting up unicode-data (15.1.0-1) ... 547s Setting up python3-six (1.16.0-7) ... 548s Setting up python3-decorator (5.1.1-5) ... 548s Setting up libminimap0:amd64 (0.2-8) ... 548s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ... 548s Setting up libblas3:amd64 (3.12.0-3build2) ... 548s 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 548s Setting up python3-packaging (24.1-1) ... 548s Setting up python3-brotli (1.1.0-2build2) ... 548s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 548s Setting up python3-cycler (0.12.1-1) ... 548s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 548s Setting up fonts-dejavu-mono (2.37-8) ... 548s Setting up python3-kiwisolver (1.4.7-2) ... 548s Setting up libtcl8.6:amd64 (8.6.15+dfsg-2) ... 548s Setting up fonts-dejavu-core (2.37-8) ... 548s Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 548s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 548s Setting up libwebp7:amd64 (1.4.0-0.1) ... 548s Setting up libxslt1.1:amd64 (1.1.39-0exp1ubuntu1) ... 548s Setting up mummer (3.23+dfsg-8) ... 548s Setting up libhts3t64:amd64 (1.20+ds-1) ... 548s Setting up libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 548s Setting up libharfbuzz0b:amd64 (10.0.1-1) ... 548s Setting up python3-dateutil (2.9.0-2) ... 548s Setting up sgml-base (1.31) ... 548s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 548s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 548s Setting up python3-mpmath (1.3.0-1) ... 549s Setting up libgsl28:amd64 (2.8+dfsg-5) ... 549s Setting up python-matplotlib-data (3.8.3-3) ... 549s Setting up libwebpmux3:amd64 (1.4.0-0.1) ... 549s Setting up python3-dendropy (4.6.1-1) ... 549s Setting up python3-appdirs (1.4.4-4) ... 549s Setting up python3-soupsieve (2.6-1) ... 549s Setting up cd-hit (4.8.1-4) ... 549s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 549s Setting up python3-sympy (1.13.3-1) ... 555s Setting up liblapack3:amd64 (3.12.0-3build2) ... 555s 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 555s Setting up python3-pysam (0.22.1+ds-2) ... 555s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 555s Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... 555s Setting up xfonts-utils (1:7.7+7) ... 555s Setting up python3-bs4 (4.12.3-3) ... 556s Setting up samtools (1.20-3) ... 556s Setting up python3-fs (2.4.16-4) ... 556s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 556s Setting up libraqm0:amd64 (0.10.1-1build1) ... 556s Setting up mash (2.3+dfsg-6build1) ... 556s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 557s Setting up python3-lxml:amd64 (5.3.0-1) ... 558s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 558s Setting up xml-core (0.19) ... 558s Setting up python3-contourpy (1.3.0-2) ... 558s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 558s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 558s Setting up libxft2:amd64 (2.3.6-1build1) ... 558s Setting up python3-scipy (1.13.1-5) ... 561s Setting up libtk8.6:amd64 (8.6.15-1) ... 561s Setting up fastaq (3.17.0-8) ... 561s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:37: SyntaxWarning: invalid escape sequence '\s' 561s phylip_regex = re.compile('^\s*[0-9]+\s+[0-9]+$') 561s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:38: SyntaxWarning: invalid escape sequence '\s' 561s gbk_regex = re.compile('^LOCUS\s+\S') 561s Setting up python3.12-tk (3.12.7-3) ... 561s Setting up fonts-urw-base35 (20200910-8) ... 561s Setting up libcairo2:amd64 (1.18.2-2) ... 561s Setting up python3.13-tk (3.13.0-2) ... 561s Setting up python3-pymummer (0.11.0-4) ... 562s Setting up python3-pil:amd64 (10.4.0-1ubuntu1) ... 562s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 562s Setting up python3-cairo (1.26.1-2) ... 562s Setting up blt (2.5.3+dfsg-7build1) ... 562s Setting up python3-tk:amd64 (3.12.7-1) ... 562s Setting up python3-pil.imagetk:amd64 (10.4.0-1ubuntu1) ... 562s Setting up python3-rlpycairo (0.3.0-3) ... 562s Setting up python3-reportlab (4.2.5-1) ... 563s Setting up python3-fonttools (4.46.0-1build2) ... 564s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... 564s Setting up python3-matplotlib (3.8.3-3) ... 565s Processing triggers for libc-bin (2.40-1ubuntu3) ... 565s Processing triggers for man-db (2.12.1-3) ... 566s Processing triggers for sgml-base (1.31) ... 566s Setting up w3c-sgml-lib (1.3-3) ... 593s Setting up python3-biopython (1.84+dfsg-4) ... 594s Setting up ariba (2.14.7+ds-4) ... 594s /usr/lib/python3/dist-packages/ariba/external_progs.py:34: SyntaxWarning: invalid escape sequence '\.' 594s 'cdhit': ('', re.compile('CD-HIT version ([0-9\.]+) \(')), 594s /usr/lib/python3/dist-packages/ariba/external_progs.py:35: SyntaxWarning: invalid escape sequence '\.' 594s 'nucmer': ('--version', re.compile('([0-9]+\.[0-9\.]+.*$)')), 594s /usr/lib/python3/dist-packages/ariba/external_progs.py:36: SyntaxWarning: invalid escape sequence '\.' 594s 'spades': ('--version', re.compile('SPAdes.*v([0-9\.]+)')) 594s Setting up autopkgtest-satdep (0) ... 597s (Reading database ... 86366 files and directories currently installed.) 597s Removing autopkgtest-satdep (0) ... 597s autopkgtest [08:16:27]: test test-example: [----------------------- 599s ARIBA version: 2.14.6 599s 599s External dependencies: 599s bowtie2 2.5.4 /usr/bin/bowtie2 599s cdhit 4.8.1 /usr/bin/cd-hit-est 599s nucmer 3.1 /usr/bin/nucmer 599s 599s External dependencies OK: True 599s 599s Python version: 599s 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 599s 599s Python packages: 599s ariba 2.14.6 /usr/lib/python3/dist-packages/ariba/__init__.py 599s bs4 4.12.3 /usr/lib/python3/dist-packages/bs4/__init__.py 599s dendropy 4.6.1 /usr/lib/python3/dist-packages/dendropy/__init__.py 599s pyfastaq 3.17.0 /usr/lib/python3/dist-packages/pyfastaq/__init__.py 599s pymummer 0.11.0 /usr/lib/python3/dist-packages/pymummer/__init__.py 599s pysam 0.22.1 /usr/lib/python3/dist-packages/pysam/__init__.py 599s 599s Python packages OK: True 599s 599s Everything looks OK: True 599s 599s Loading and checking input data 599s 599s Running cdhit 600s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.BJm4gXB3UQ/foo/PREPAREREF/02.cdhit.noncoding.fa -o /tmp/tmp.BJm4gXB3UQ/foo/tmp.run_cd-hit.juhd49hx/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 600s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.BJm4gXB3UQ/foo/PREPAREREF/02.cdhit.noncoding.varonly.fa -o /tmp/tmp.BJm4gXB3UQ/foo/tmp.run_cd-hit.n7ef1wiy/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 600s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.BJm4gXB3UQ/foo/PREPAREREF/02.cdhit.gene.fa -o /tmp/tmp.BJm4gXB3UQ/foo/tmp.run_cd-hit.yiznc_d5/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 600s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.BJm4gXB3UQ/foo/PREPAREREF/02.cdhit.gene.varonly.fa -o /tmp/tmp.BJm4gXB3UQ/foo/tmp.run_cd-hit.tvepxkqa/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 600s 600s Writing clusters to file. 10 in total 601s Found reads file: reads_1.fq 601s Found reads file: reads_2.fq 601s ARIBA version: 2.14.6 601s 601s External dependencies: 601s bowtie2 2.5.4 /usr/bin/bowtie2 601s cdhit 4.8.1 /usr/bin/cd-hit-est 601s nucmer 3.1 /usr/bin/nucmer 601s 601s External dependencies OK: True 601s 601s Python version: 601s 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 601s 601s Python packages: 601s ariba 2.14.6 /usr/lib/python3/dist-packages/ariba/__init__.py 601s bs4 4.12.3 /usr/lib/python3/dist-packages/bs4/__init__.py 601s dendropy 4.6.1 /usr/lib/python3/dist-packages/dendropy/__init__.py 601s pyfastaq 3.17.0 /usr/lib/python3/dist-packages/pyfastaq/__init__.py 601s pymummer 0.11.0 /usr/lib/python3/dist-packages/pymummer/__init__.py 601s pysam 0.22.1 /usr/lib/python3/dist-packages/pysam/__init__.py 601s 601s Python packages OK: True 601s 601s Everything looks OK: True 601s Temporary directory: /tmp/tmp.BJm4gXB3UQ/foo/OUT/ariba.tmp.7mzbs15w 601s ______________________ Mapping reads to clustered genes _______________________ 601s Finished mapping 601s 601s _____________________________ Generating clusters _____________________________ 601s syscall: sort -k1,1 -k 2,2n /tmp/tmp.BJm4gXB3UQ/foo/OUT/minimap.reads > /tmp/tmp.BJm4gXB3UQ/foo/OUT/read_store 601s Compressing file /tmp/tmp.BJm4gXB3UQ/foo/OUT/read_store 601s Found 51 proper read pairs from minimap 601s Total clusters to perform local assemblies: 9 601s 601s Insert size information from reads mapped to reference genes: 601s Insert size: 185.0 601s Insert sspace sd: 0.27 601s Max insert: 220.55 601s 601s ___________________________ Assembling each cluster ___________________________ 601s Will run 1 cluster(s) in parallel 601s Not constructing cluster cluster because it only has 2 reads (1 of 9) 601s Constructing cluster cluster_1 (2 of 9) 601s Constructing cluster cluster_2 (3 of 9) 601s Constructing cluster cluster_3 (4 of 9) 601s Constructing cluster cluster_4 (5 of 9) 601s Constructing cluster gene (6 of 9) 601s Constructing cluster gene_1 (7 of 9) 601s Constructing cluster noncoding (8 of 9) 601s Constructing cluster noncoding_1 (9 of 9) 601s Start running cluster cluster_1 in directory /tmp/tmp.BJm4gXB3UQ/foo/OUT/ariba.tmp.7mzbs15w/cluster_1 605s cluster_1 detected 1 threads available to it 605s cluster_1 reported completion 605s Finished running cluster cluster_1 in directory /tmp/tmp.BJm4gXB3UQ/foo/OUT/ariba.tmp.7mzbs15w/cluster_1 605s Deleting cluster dir /tmp/tmp.BJm4gXB3UQ/foo/OUT/ariba.tmp.7mzbs15w/cluster_1 605s Start running cluster cluster_2 in directory /tmp/tmp.BJm4gXB3UQ/foo/OUT/ariba.tmp.7mzbs15w/cluster_2 605s cluster_2 detected 1 threads available to it 605s cluster_2 reported completion 605s Finished running cluster cluster_2 in directory /tmp/tmp.BJm4gXB3UQ/foo/OUT/ariba.tmp.7mzbs15w/cluster_2 605s Deleting cluster dir /tmp/tmp.BJm4gXB3UQ/foo/OUT/ariba.tmp.7mzbs15w/cluster_2 605s Start running cluster cluster_3 in directory /tmp/tmp.BJm4gXB3UQ/foo/OUT/ariba.tmp.7mzbs15w/cluster_3 606s cluster_3 detected 1 threads available to it 606s cluster_3 reported completion 606s Finished running cluster cluster_3 in directory /tmp/tmp.BJm4gXB3UQ/foo/OUT/ariba.tmp.7mzbs15w/cluster_3 606s Deleting cluster dir /tmp/tmp.BJm4gXB3UQ/foo/OUT/ariba.tmp.7mzbs15w/cluster_3 606s Start running cluster cluster_4 in directory /tmp/tmp.BJm4gXB3UQ/foo/OUT/ariba.tmp.7mzbs15w/cluster_4 608s cluster_4 detected 1 threads available to it 608s cluster_4 reported completion 608s Finished running cluster cluster_4 in directory /tmp/tmp.BJm4gXB3UQ/foo/OUT/ariba.tmp.7mzbs15w/cluster_4 608s Deleting cluster dir /tmp/tmp.BJm4gXB3UQ/foo/OUT/ariba.tmp.7mzbs15w/cluster_4 608s Start running cluster gene in directory /tmp/tmp.BJm4gXB3UQ/foo/OUT/ariba.tmp.7mzbs15w/gene 610s gene detected 1 threads available to it 610s gene reported completion 610s Finished running cluster gene in directory /tmp/tmp.BJm4gXB3UQ/foo/OUT/ariba.tmp.7mzbs15w/gene 610s Deleting cluster dir /tmp/tmp.BJm4gXB3UQ/foo/OUT/ariba.tmp.7mzbs15w/gene 610s Start running cluster gene_1 in directory /tmp/tmp.BJm4gXB3UQ/foo/OUT/ariba.tmp.7mzbs15w/gene_1 612s gene_1 detected 1 threads available to it 612s gene_1 reported completion 612s Finished running cluster gene_1 in directory /tmp/tmp.BJm4gXB3UQ/foo/OUT/ariba.tmp.7mzbs15w/gene_1 612s Deleting cluster dir /tmp/tmp.BJm4gXB3UQ/foo/OUT/ariba.tmp.7mzbs15w/gene_1 612s Start running cluster noncoding in directory /tmp/tmp.BJm4gXB3UQ/foo/OUT/ariba.tmp.7mzbs15w/noncoding 613s noncoding detected 1 threads available to it 613s noncoding reported completion 613s Finished running cluster noncoding in directory /tmp/tmp.BJm4gXB3UQ/foo/OUT/ariba.tmp.7mzbs15w/noncoding 613s Deleting cluster dir /tmp/tmp.BJm4gXB3UQ/foo/OUT/ariba.tmp.7mzbs15w/noncoding 613s Start running cluster noncoding_1 in directory /tmp/tmp.BJm4gXB3UQ/foo/OUT/ariba.tmp.7mzbs15w/noncoding_1 615s noncoding_1 detected 1 threads available to it 615s noncoding_1 reported completion 615s Finished running cluster noncoding_1 in directory /tmp/tmp.BJm4gXB3UQ/foo/OUT/ariba.tmp.7mzbs15w/noncoding_1 615s Deleting cluster dir /tmp/tmp.BJm4gXB3UQ/foo/OUT/ariba.tmp.7mzbs15w/noncoding_1 615s Final value of remaining_clusters counter: Value('l', 0) 615s Finished assembling clusters 615s 615s _______________________________ Writing reports _______________________________ 615s Making /tmp/tmp.BJm4gXB3UQ/foo/OUT/debug.report.tsv 615s Making /tmp/tmp.BJm4gXB3UQ/foo/OUT/report.tsv 615s 615s ____________________ Writing fasta of assembled sequences _____________________ 615s /tmp/tmp.BJm4gXB3UQ/foo/OUT/assembled_seqs.fa.gz and /tmp/tmp.BJm4gXB3UQ/foo/OUT/assembled_genes.fa.gz 615s 615s __________________________ Catting cluster log files __________________________ 615s Writing file /tmp/tmp.BJm4gXB3UQ/foo/OUT/log.clusters.gz 615s 615s _______________________________ Cleaning files ________________________________ 615s Deleting Logs directory /tmp/tmp.BJm4gXB3UQ/foo/OUT/Logs 615s Deleting reads store files /tmp/tmp.BJm4gXB3UQ/foo/OUT/read_store.gz[.tbi] 615s 615s All done! 615s 615s Running ARIBA on test data... 615s ------------------------------------------------------------------------------- 615s |=============================================================================| 615s | Preparing input data | 615s |=============================================================================| 615s ------------------------------------------------------------------------------- 615s Made output directory ./foo. Copying test data files into it: 615s copied ref_seqs.fa 615s copied metadata.tsv 615s copied reads_1.fq 615s copied reads_2.fq 615s ------------------------------------------------------------------------------- 615s |=============================================================================| 615s | Try running ariba prepareref | 615s |=============================================================================| 615s ------------------------------------------------------------------------------- 615s 615s Running ariba prepareref with: 615s /usr/bin/ariba prepareref --verbose -f ref_seqs.fa -m metadata.tsv --threads 1 PREPAREREF 615s 615s 615s ariba prepareref finished OK 615s ------------------------------------------------------------------------------- 615s |=============================================================================| 615s | Try running ariba run | 615s |=============================================================================| 615s ------------------------------------------------------------------------------- 615s 615s Running ARIBA with: 615s /usr/bin/ariba run --verbose --threads 1 PREPAREREF reads_1.fq reads_2.fq OUT 615s 615s 615s ariba run finished OK 615s Finished run on test data OK 616s autopkgtest [08:16:46]: test test-example: -----------------------] 616s test-example PASS 616s autopkgtest [08:16:46]: test test-example: - - - - - - - - - - results - - - - - - - - - - 616s autopkgtest [08:16:46]: @@@@@@@@@@@@@@@@@@@@ summary 616s test-example PASS 629s nova [W] Skipping flock for amd64 629s Creating nova instance adt-plucky-amd64-ariba-20241113-080628-juju-7f2275-prod-proposed-migration-environment-15-1494d410-39cc-41e4-9544-02e0310e1379 from image adt/ubuntu-plucky-amd64-server-20241113.img (UUID 76b850f9-98f4-4b79-af06-fa11000b95b2)...