0s autopkgtest [00:25:57]: starting date and time: 2024-11-15 00:25:57+0000 0s autopkgtest [00:25:57]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [00:25:57]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.lftg_n5b/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:matplotlib --apt-upgrade ariba --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=matplotlib/3.8.3-3ubuntu1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-31.secgroup --name adt-plucky-arm64-ariba-20241115-002557-juju-7f2275-prod-proposed-migration-environment-15-83a0125b-968c-4977-aeb9-a821e5795b4b --image adt/ubuntu-plucky-arm64-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/ 1773s autopkgtest [00:55:30]: testbed dpkg architecture: arm64 1773s autopkgtest [00:55:30]: testbed apt version: 2.9.8 1773s autopkgtest [00:55:30]: @@@@@@@@@@@@@@@@@@@@ test bed setup 1774s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 1775s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [102 kB] 1779s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.5 kB] 1779s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1030 kB] 1828s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 1828s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [139 kB] 1833s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 1835s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [770 kB] 1863s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [6116 B] 1863s Fetched 2193 kB in 1min 29s (24.6 kB/s) 1863s Reading package lists... 1866s Reading package lists... 1866s Building dependency tree... 1866s Reading state information... 1866s Calculating upgrade... 1867s The following packages will be upgraded: 1867s libcap-ng0 lxd-installer man-db pastebinit python3-systemd 1867s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1867s Need to get 1402 kB of archives. 1867s After this operation, 379 kB of additional disk space will be used. 1867s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libcap-ng0 arm64 0.8.5-3build1 [15.0 kB] 1867s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 man-db arm64 2.13.0-1 [1320 kB] 1917s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 lxd-installer all 9 [5084 B] 1917s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 pastebinit all 1.7.1-1 [14.9 kB] 1918s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-systemd arm64 235-1build5 [46.7 kB] 1920s Preconfiguring packages ... 1921s Fetched 1402 kB in 53s (26.4 kB/s) 1921s (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 ... 79925 files and directories currently installed.) 1921s Preparing to unpack .../libcap-ng0_0.8.5-3build1_arm64.deb ... 1921s Unpacking libcap-ng0:arm64 (0.8.5-3build1) over (0.8.5-1) ... 1921s Setting up libcap-ng0:arm64 (0.8.5-3build1) ... 1921s (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 ... 79925 files and directories currently installed.) 1921s Preparing to unpack .../man-db_2.13.0-1_arm64.deb ... 1921s Unpacking man-db (2.13.0-1) over (2.12.1-3) ... 1921s Preparing to unpack .../lxd-installer_9_all.deb ... 1921s Unpacking lxd-installer (9) over (8) ... 1921s Preparing to unpack .../pastebinit_1.7.1-1_all.deb ... 1921s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 1922s Preparing to unpack .../python3-systemd_235-1build5_arm64.deb ... 1922s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 1922s Setting up pastebinit (1.7.1-1) ... 1922s Setting up man-db (2.13.0-1) ... 1922s Updating database of manual pages ... 1924s man-db.service is a disabled or a static unit not running, not starting it. 1924s Setting up lxd-installer (9) ... 1925s Setting up python3-systemd (235-1build5) ... 1925s Processing triggers for libc-bin (2.40-1ubuntu3) ... 1925s Reading package lists... 1925s Building dependency tree... 1925s Reading state information... 1926s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1927s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 1927s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [213 kB] 1936s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 1936s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 1938s Get:5 http://ftpmaster.internal/ubuntu plucky/universe Sources [20.8 MB] 2795s Get:6 http://ftpmaster.internal/ubuntu plucky/main Sources [1373 kB] 2851s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 Packages [1418 kB] 2903s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 Packages [15.4 MB] 3548s Fetched 39.2 MB in 27min 2s (24.2 kB/s) 3549s Reading package lists... 3549s Reading package lists... 3549s Building dependency tree... 3549s Reading state information... 3550s Calculating upgrade... 3550s The following packages will be upgraded: 3550s firmware-sof-signed xfsprogs 3551s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 3551s Need to get 8003 kB of archives. 3551s After this operation, 169 kB of additional disk space will be used. 3551s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 firmware-sof-signed all 2024.06-1ubuntu2 [7083 kB] 3837s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 xfsprogs arm64 6.8.0-2.2ubuntu2 [919 kB] 3873s Fetched 8003 kB in 5min 23s (24.8 kB/s) 3873s (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 ... 79931 files and directories currently installed.) 3873s Preparing to unpack .../firmware-sof-signed_2024.06-1ubuntu2_all.deb ... 3873s Unpacking firmware-sof-signed (2024.06-1ubuntu2) over (2024.06-1ubuntu1) ... 3873s Preparing to unpack .../xfsprogs_6.8.0-2.2ubuntu2_arm64.deb ... 3873s Unpacking xfsprogs (6.8.0-2.2ubuntu2) over (6.8.0-2.2ubuntu1) ... 3874s Setting up firmware-sof-signed (2024.06-1ubuntu2) ... 3874s Setting up xfsprogs (6.8.0-2.2ubuntu2) ... 3874s update-initramfs: deferring update (trigger activated) 3874s Processing triggers for man-db (2.13.0-1) ... 3874s Processing triggers for libc-bin (2.40-1ubuntu3) ... 3874s Processing triggers for initramfs-tools (0.142ubuntu34) ... 3874s update-initramfs: Generating /boot/initrd.img-6.11.0-8-generic 3874s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 3888s System running in EFI mode, skipping. 3888s Reading package lists... 3889s Building dependency tree... 3889s Reading state information... 3889s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 3889s autopkgtest [01:30:46]: rebooting testbed after setup commands that affected boot 3893s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 3920s autopkgtest [01:31:17]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 3927s autopkgtest [01:31:24]: @@@@@@@@@@@@@@@@@@@@ apt-source ariba 4030s Get:1 http://ftpmaster.internal/ubuntu plucky/universe ariba 2.14.7+ds-4 (dsc) [2316 B] 4030s Get:2 http://ftpmaster.internal/ubuntu plucky/universe ariba 2.14.7+ds-4 (tar) [1920 kB] 4030s Get:3 http://ftpmaster.internal/ubuntu plucky/universe ariba 2.14.7+ds-4 (diff) [10.7 kB] 4030s gpgv: Signature made Tue Nov 5 03:36:42 2024 UTC 4030s gpgv: using RSA key 13796755BBC72BB8ABE2AEB5FA9DEC5DE11C63F1 4030s gpgv: issuer "eamanu@debian.org" 4030s gpgv: Can't check signature: No public key 4030s dpkg-source: warning: cannot verify inline signature for ./ariba_2.14.7+ds-4.dsc: no acceptable signature found 4031s autopkgtest [01:33:08]: testing package ariba version 2.14.7+ds-4 4032s autopkgtest [01:33:09]: build not needed 4036s autopkgtest [01:33:13]: test test-example: preparing testbed 4038s Reading package lists... 4039s Building dependency tree... 4039s Reading state information... 4039s Starting pkgProblemResolver with broken count: 0 4039s Starting 2 pkgProblemResolver with broken count: 0 4039s Done 4040s The following additional packages will be installed: 4040s ariba blt bowtie2 cd-hit fastaq fontconfig-config fonts-dejavu-core 4040s fonts-dejavu-mono fonts-lyx fonts-urw-base35 libblas3 libcairo2 4040s libcapnp-1.0.1 libdeflate0 libfml0 libfontconfig1 libfontenc1 libgfortran5 4040s libgomp1 libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b libhts3t64 4040s libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery 4040s libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libminimap0 4040s libmurmurhash2 libopenjp2-7 libpixman-1-0 libqhull-r8.0 libraqm0 4040s libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 4040s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 mash 4040s mummer python-matplotlib-data python3-appdirs python3-biopython 4040s python3-brotli python3-bs4 python3-cairo python3-contourpy python3-cycler 4040s python3-dateutil python3-decorator python3-dendropy python3-fonttools 4040s python3-freetype python3-fs python3-kiwisolver python3-lxml python3-lz4 4040s python3-matplotlib python3-mpmath python3-numpy python3-packaging 4040s python3-pil python3-pil.imagetk python3-pymummer python3-pysam 4040s python3-reportlab python3-rlpycairo python3-scipy python3-six 4040s python3-soupsieve python3-sympy python3-tk python3-tz python3-ufolib2 4040s python3-unicodedata2 python3.12-tk samtools sgml-base tk8.6-blt2.5 4040s unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 4040s Suggested packages: 4040s spades blt-demo bowtie2-examples fonts-freefont-otf | fonts-freefont-ttf 4040s fonts-texgyre gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html 4040s libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 bwa clustalo clustalw 4040s dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons 4040s python3-mysqldb python3-mmtf python3-rdflib python3-psycopg2 raxml t-coffee 4040s wise python-cycler-doc python-lxml-doc cm-super-minimal dvipng ffmpeg 4040s fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common 4040s python-matplotlib-doc python3-cairocffi python3-gi-cairo python3-gobject 4040s python3-pyqt5 python3-sip python3-tornado texlive-extra-utils 4040s texlive-latex-extra python-mpmath-doc python3-gmpy2 gcc gfortran 4040s python-numpy-doc python3-dev python3-pytest python-pil-doc pdf-viewer 4040s python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm 4040s python-scipy-doc texlive-fonts-extra python-sympy-doc tix python3-tk-dbg 4040s python3.13-tk cwltool sgml-base-doc debhelper 4040s Recommended packages: 4040s javascript-common python-biopython-doc ncbi-blast+ python3-cssselect 4040s python3-html5lib python3-olefile fonts-dejavu-extra g++ | c++-compiler 4040s isympy-common 4040s The following NEW packages will be installed: 4040s ariba autopkgtest-satdep blt bowtie2 cd-hit fastaq fontconfig-config 4040s fonts-dejavu-core fonts-dejavu-mono fonts-lyx fonts-urw-base35 libblas3 4040s libcairo2 libcapnp-1.0.1 libdeflate0 libfml0 libfontconfig1 libfontenc1 4040s libgfortran5 libgomp1 libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b 4040s libhts3t64 libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 4040s libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblerc4 4040s libminimap0 libmurmurhash2 libopenjp2-7 libpixman-1-0 libqhull-r8.0 libraqm0 4040s libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 4040s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 mash 4040s mummer python-matplotlib-data python3-appdirs python3-biopython 4040s python3-brotli python3-bs4 python3-cairo python3-contourpy python3-cycler 4040s python3-dateutil python3-decorator python3-dendropy python3-fonttools 4040s python3-freetype python3-fs python3-kiwisolver python3-lxml python3-lz4 4040s python3-matplotlib python3-mpmath python3-numpy python3-packaging 4040s python3-pil python3-pil.imagetk python3-pymummer python3-pysam 4040s python3-reportlab python3-rlpycairo python3-scipy python3-six 4040s python3-soupsieve python3-sympy python3-tk python3-tz python3-ufolib2 4040s python3-unicodedata2 python3.12-tk samtools sgml-base tk8.6-blt2.5 4040s unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 4040s 0 upgraded, 102 newly installed, 0 to remove and 0 not upgraded. 4040s Need to get 83.5 MB/83.5 MB of archives. 4040s After this operation, 358 MB of additional disk space will be used. 4040s Get:1 /tmp/autopkgtest.v6jnk2/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [700 B] 4040s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 sgml-base all 1.31 [11.4 kB] 4040s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB] 4042s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.1-1 [82.5 kB] 4045s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts3t64 arm64 1.20+ds-1 [431 kB] 4065s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 samtools arm64 1.20-3 [590 kB] 4089s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 fastaq all 3.17.0-8 [48.2 kB] 4091s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 4098s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 4116s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 4235s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 4392s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.15+dfsg-2 [987 kB] 4441s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 4465s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 4508s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB] 4509s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 4510s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 4538s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 4545s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 5102s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB] 5105s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB] 5109s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 5110s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 5113s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 5114s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.15-1 [774 kB] 5157s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-tk arm64 3.12.7-3 [115 kB] 5162s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7build1 [618 kB] 5191s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 blt arm64 2.5.3+dfsg-7build1 [4840 B] 5192s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tk arm64 3.12.6-1ubuntu1 [9806 B] 5192s Get:30 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pil.imagetk arm64 10.4.0-1ubuntu1 [9504 B] 5194s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-8ubuntu1 [145 kB] 5202s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 5204s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu2 [163 kB] 5215s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 5215s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 5223s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu1 [182 kB] 5233s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 5236s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.0.1-1 [487 kB] 5259s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.1-1build1 [14.7 kB] 5261s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 5262s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu2 [154 kB] 5271s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [16.3 kB] 5272s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.4.0-0.1 [192 kB] 5281s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 5292s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [12.3 kB] 5295s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.4.0-0.1 [25.1 kB] 5295s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 10.4.0-1ubuntu1 [456 kB] 5318s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 5328s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 5329s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 5329s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 5355s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-cairo arm64 1.26.1-2 [121 kB] 5360s Get:53 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-freetype all 2.5.1-1 [92.3 kB] 5366s Get:54 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 5366s Get:55 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-reportlab all 4.2.5-1 [1107 kB] 5420s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 xml-core all 0.19 [20.3 kB] 5420s Get:57 http://ftpmaster.internal/ubuntu plucky/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 5439s Get:58 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biopython arm64 1.84+dfsg-4 [1689 kB] 5517s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-soupsieve all 2.6-1 [33.0 kB] 5517s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-bs4 all 4.12.3-3 [109 kB] 5517s Get:61 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-dendropy all 4.6.1-1 [278 kB] 5518s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 5519s Get:63 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 5519s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lyx all 2.4.2.1-1 [171 kB] 5519s Get:65 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python-matplotlib-data all 3.8.3-3ubuntu1 [2928 kB] 5521s Get:66 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-six all 1.16.0-7 [13.1 kB] 5521s Get:67 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-2 [80.3 kB] 5521s Get:68 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-contourpy arm64 1.3.0-2 [179 kB] 5521s Get:69 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 5521s Get:70 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-brotli arm64 1.1.0-2build2 [340 kB] 5521s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 5521s Get:72 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 5521s Get:73 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.13.1-5 [16.3 MB] 5523s Get:74 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 5523s Get:75 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 5523s Get:76 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sympy all 1.13.3-1 [4228 kB] 5524s Get:77 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2024.1-2 [31.4 kB] 5524s Get:78 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-appdirs all 1.4.4-4 [10.9 kB] 5524s Get:79 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fs all 2.4.16-4 [91.3 kB] 5524s Get:80 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu1 [167 kB] 5524s Get:81 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.0-1 [1205 kB] 5524s Get:82 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-lz4 arm64 4.0.2+dfsg-1build4 [26.7 kB] 5524s Get:83 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-unicodedata2 arm64 15.1.0+ds-1build2 [360 kB] 5524s Get:84 http://ftpmaster.internal/ubuntu plucky/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 5525s Get:85 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fonttools arm64 4.46.0-1build2 [1398 kB] 5525s Get:86 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-kiwisolver arm64 1.4.7-2build1 [62.0 kB] 5525s Get:87 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.1-1 [41.4 kB] 5525s Get:88 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 5525s Get:89 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-matplotlib arm64 3.8.3-3ubuntu1 [4612 kB] 5525s Get:90 http://ftpmaster.internal/ubuntu plucky/universe arm64 mummer arm64 3.23+dfsg-8 [673 kB] 5525s Get:91 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pymummer all 0.11.0-4 [17.1 kB] 5525s Get:92 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pysam arm64 0.22.1+ds-2 [3412 kB] 5526s Get:93 http://ftpmaster.internal/ubuntu plucky/universe arm64 libfml0 arm64 0.1+git20190320.b499514-1build1 [72.9 kB] 5526s Get:94 http://ftpmaster.internal/ubuntu plucky/universe arm64 libminimap0 arm64 0.2-8 [22.6 kB] 5526s Get:95 http://ftpmaster.internal/ubuntu plucky/universe arm64 bowtie2 arm64 2.5.4-1 [1380 kB] 5526s Get:96 http://ftpmaster.internal/ubuntu plucky/universe arm64 cd-hit arm64 4.8.1-4 [522 kB] 5526s Get:97 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcapnp-1.0.1 arm64 1.0.1-4 [1332 kB] 5527s Get:98 http://ftpmaster.internal/ubuntu plucky/universe arm64 libgslcblas0 arm64 2.8+dfsg-5 [87.3 kB] 5527s Get:99 http://ftpmaster.internal/ubuntu plucky/universe arm64 libgsl28 arm64 2.8+dfsg-5 [983 kB] 5527s Get:100 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmurmurhash2 arm64 1.6-1 [6098 B] 5527s Get:101 http://ftpmaster.internal/ubuntu plucky/universe arm64 mash arm64 2.3+dfsg-6build1 [149 kB] 5527s Get:102 http://ftpmaster.internal/ubuntu plucky/universe arm64 ariba arm64 2.14.7+ds-4 [2029 kB] 5527s Fetched 83.5 MB in 24min 47s (56.1 kB/s) 5527s Selecting previously unselected package sgml-base. 5528s (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 ... 79957 files and directories currently installed.) 5528s Preparing to unpack .../000-sgml-base_1.31_all.deb ... 5528s Unpacking sgml-base (1.31) ... 5528s Selecting previously unselected package libdeflate0:arm64. 5528s Preparing to unpack .../001-libdeflate0_1.22-1_arm64.deb ... 5528s Unpacking libdeflate0:arm64 (1.22-1) ... 5528s Selecting previously unselected package libhtscodecs2:arm64. 5528s Preparing to unpack .../002-libhtscodecs2_1.6.1-1_arm64.deb ... 5528s Unpacking libhtscodecs2:arm64 (1.6.1-1) ... 5528s Selecting previously unselected package libhts3t64:arm64. 5528s Preparing to unpack .../003-libhts3t64_1.20+ds-1_arm64.deb ... 5528s Unpacking libhts3t64:arm64 (1.20+ds-1) ... 5528s Selecting previously unselected package samtools. 5528s Preparing to unpack .../004-samtools_1.20-3_arm64.deb ... 5528s Unpacking samtools (1.20-3) ... 5528s Selecting previously unselected package fastaq. 5528s Preparing to unpack .../005-fastaq_3.17.0-8_all.deb ... 5528s Unpacking fastaq (3.17.0-8) ... 5528s Selecting previously unselected package libblas3:arm64. 5528s Preparing to unpack .../006-libblas3_3.12.0-3build2_arm64.deb ... 5528s Unpacking libblas3:arm64 (3.12.0-3build2) ... 5528s Selecting previously unselected package libgfortran5:arm64. 5528s Preparing to unpack .../007-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 5528s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 5528s Selecting previously unselected package liblapack3:arm64. 5528s Preparing to unpack .../008-liblapack3_3.12.0-3build2_arm64.deb ... 5528s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 5528s Selecting previously unselected package python3-numpy. 5528s Preparing to unpack .../009-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ... 5528s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 5528s Selecting previously unselected package libtcl8.6:arm64. 5528s Preparing to unpack .../010-libtcl8.6_8.6.15+dfsg-2_arm64.deb ... 5528s Unpacking libtcl8.6:arm64 (8.6.15+dfsg-2) ... 5528s Selecting previously unselected package fonts-dejavu-mono. 5528s Preparing to unpack .../011-fonts-dejavu-mono_2.37-8_all.deb ... 5528s Unpacking fonts-dejavu-mono (2.37-8) ... 5528s Selecting previously unselected package fonts-dejavu-core. 5528s Preparing to unpack .../012-fonts-dejavu-core_2.37-8_all.deb ... 5528s Unpacking fonts-dejavu-core (2.37-8) ... 5528s Selecting previously unselected package libfontenc1:arm64. 5528s Preparing to unpack .../013-libfontenc1_1%3a1.1.8-1build1_arm64.deb ... 5528s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ... 5528s Selecting previously unselected package x11-common. 5528s Preparing to unpack .../014-x11-common_1%3a7.7+23ubuntu3_all.deb ... 5528s Unpacking x11-common (1:7.7+23ubuntu3) ... 5528s Selecting previously unselected package xfonts-encodings. 5528s Preparing to unpack .../015-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 5528s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 5528s Selecting previously unselected package xfonts-utils. 5528s Preparing to unpack .../016-xfonts-utils_1%3a7.7+7_arm64.deb ... 5528s Unpacking xfonts-utils (1:7.7+7) ... 5528s Selecting previously unselected package fonts-urw-base35. 5528s Preparing to unpack .../017-fonts-urw-base35_20200910-8_all.deb ... 5529s Unpacking fonts-urw-base35 (20200910-8) ... 5529s Selecting previously unselected package fontconfig-config. 5529s Preparing to unpack .../018-fontconfig-config_2.15.0-1.1ubuntu2_arm64.deb ... 5529s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 5529s Selecting previously unselected package libfontconfig1:arm64. 5529s Preparing to unpack .../019-libfontconfig1_2.15.0-1.1ubuntu2_arm64.deb ... 5529s Unpacking libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 5529s Selecting previously unselected package libxrender1:arm64. 5529s Preparing to unpack .../020-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 5529s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 5529s Selecting previously unselected package libxft2:arm64. 5529s Preparing to unpack .../021-libxft2_2.3.6-1build1_arm64.deb ... 5529s Unpacking libxft2:arm64 (2.3.6-1build1) ... 5529s Selecting previously unselected package libxss1:arm64. 5529s Preparing to unpack .../022-libxss1_1%3a1.2.3-1build3_arm64.deb ... 5529s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 5529s Selecting previously unselected package libtk8.6:arm64. 5529s Preparing to unpack .../023-libtk8.6_8.6.15-1_arm64.deb ... 5529s Unpacking libtk8.6:arm64 (8.6.15-1) ... 5529s Selecting previously unselected package python3.12-tk. 5529s Preparing to unpack .../024-python3.12-tk_3.12.7-3_arm64.deb ... 5529s Unpacking python3.12-tk (3.12.7-3) ... 5529s Selecting previously unselected package tk8.6-blt2.5. 5529s Preparing to unpack .../025-tk8.6-blt2.5_2.5.3+dfsg-7build1_arm64.deb ... 5529s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 5529s Selecting previously unselected package blt. 5529s Preparing to unpack .../026-blt_2.5.3+dfsg-7build1_arm64.deb ... 5529s Unpacking blt (2.5.3+dfsg-7build1) ... 5529s Selecting previously unselected package python3-tk:arm64. 5529s Preparing to unpack .../027-python3-tk_3.12.6-1ubuntu1_arm64.deb ... 5529s Unpacking python3-tk:arm64 (3.12.6-1ubuntu1) ... 5529s Selecting previously unselected package python3-pil.imagetk:arm64. 5529s Preparing to unpack .../028-python3-pil.imagetk_10.4.0-1ubuntu1_arm64.deb ... 5529s Unpacking python3-pil.imagetk:arm64 (10.4.0-1ubuntu1) ... 5529s Selecting previously unselected package libgomp1:arm64. 5529s Preparing to unpack .../029-libgomp1_14.2.0-8ubuntu1_arm64.deb ... 5529s Unpacking libgomp1:arm64 (14.2.0-8ubuntu1) ... 5529s Selecting previously unselected package libimagequant0:arm64. 5529s Preparing to unpack .../030-libimagequant0_2.18.0-1build1_arm64.deb ... 5529s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 5529s Selecting previously unselected package libjpeg-turbo8:arm64. 5529s Preparing to unpack .../031-libjpeg-turbo8_2.1.5-2ubuntu2_arm64.deb ... 5529s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 5529s Selecting previously unselected package libjpeg8:arm64. 5529s Preparing to unpack .../032-libjpeg8_8c-2ubuntu11_arm64.deb ... 5529s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 5529s Selecting previously unselected package liblcms2-2:arm64. 5529s Preparing to unpack .../033-liblcms2-2_2.16-2_arm64.deb ... 5529s Unpacking liblcms2-2:arm64 (2.16-2) ... 5529s Selecting previously unselected package libopenjp2-7:arm64. 5529s Preparing to unpack .../034-libopenjp2-7_2.5.0-2ubuntu1_arm64.deb ... 5529s Unpacking libopenjp2-7:arm64 (2.5.0-2ubuntu1) ... 5529s Selecting previously unselected package libgraphite2-3:arm64. 5529s Preparing to unpack .../035-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 5529s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 5529s Selecting previously unselected package libharfbuzz0b:arm64. 5529s Preparing to unpack .../036-libharfbuzz0b_10.0.1-1_arm64.deb ... 5529s Unpacking libharfbuzz0b:arm64 (10.0.1-1) ... 5529s Selecting previously unselected package libraqm0:arm64. 5529s Preparing to unpack .../037-libraqm0_0.10.1-1build1_arm64.deb ... 5529s Unpacking libraqm0:arm64 (0.10.1-1build1) ... 5529s Selecting previously unselected package libjbig0:arm64. 5529s Preparing to unpack .../038-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 5529s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 5529s Selecting previously unselected package liblerc4:arm64. 5529s Preparing to unpack .../039-liblerc4_4.0.0+ds-4ubuntu2_arm64.deb ... 5529s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 5529s Selecting previously unselected package libsharpyuv0:arm64. 5529s Preparing to unpack .../040-libsharpyuv0_1.4.0-0.1_arm64.deb ... 5529s Unpacking libsharpyuv0:arm64 (1.4.0-0.1) ... 5529s Selecting previously unselected package libwebp7:arm64. 5529s Preparing to unpack .../041-libwebp7_1.4.0-0.1_arm64.deb ... 5529s Unpacking libwebp7:arm64 (1.4.0-0.1) ... 5530s Selecting previously unselected package libtiff6:arm64. 5530s Preparing to unpack .../042-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 5530s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 5530s Selecting previously unselected package libwebpdemux2:arm64. 5530s Preparing to unpack .../043-libwebpdemux2_1.4.0-0.1_arm64.deb ... 5530s Unpacking libwebpdemux2:arm64 (1.4.0-0.1) ... 5530s Selecting previously unselected package libwebpmux3:arm64. 5530s Preparing to unpack .../044-libwebpmux3_1.4.0-0.1_arm64.deb ... 5530s Unpacking libwebpmux3:arm64 (1.4.0-0.1) ... 5530s Selecting previously unselected package python3-pil:arm64. 5530s Preparing to unpack .../045-python3-pil_10.4.0-1ubuntu1_arm64.deb ... 5530s Unpacking python3-pil:arm64 (10.4.0-1ubuntu1) ... 5530s Selecting previously unselected package libpixman-1-0:arm64. 5530s Preparing to unpack .../046-libpixman-1-0_0.44.0-3_arm64.deb ... 5530s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 5530s Selecting previously unselected package libxcb-render0:arm64. 5530s Preparing to unpack .../047-libxcb-render0_1.17.0-2_arm64.deb ... 5530s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 5530s Selecting previously unselected package libxcb-shm0:arm64. 5530s Preparing to unpack .../048-libxcb-shm0_1.17.0-2_arm64.deb ... 5530s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 5530s Selecting previously unselected package libcairo2:arm64. 5530s Preparing to unpack .../049-libcairo2_1.18.2-2_arm64.deb ... 5530s Unpacking libcairo2:arm64 (1.18.2-2) ... 5530s Selecting previously unselected package python3-cairo. 5530s Preparing to unpack .../050-python3-cairo_1.26.1-2_arm64.deb ... 5530s Unpacking python3-cairo (1.26.1-2) ... 5530s Selecting previously unselected package python3-freetype. 5530s Preparing to unpack .../051-python3-freetype_2.5.1-1_all.deb ... 5530s Unpacking python3-freetype (2.5.1-1) ... 5530s Selecting previously unselected package python3-rlpycairo. 5530s Preparing to unpack .../052-python3-rlpycairo_0.3.0-3_all.deb ... 5530s Unpacking python3-rlpycairo (0.3.0-3) ... 5530s Selecting previously unselected package python3-reportlab. 5530s Preparing to unpack .../053-python3-reportlab_4.2.5-1_all.deb ... 5530s Unpacking python3-reportlab (4.2.5-1) ... 5530s Selecting previously unselected package xml-core. 5530s Preparing to unpack .../054-xml-core_0.19_all.deb ... 5530s Unpacking xml-core (0.19) ... 5530s Selecting previously unselected package w3c-sgml-lib. 5530s Preparing to unpack .../055-w3c-sgml-lib_1.3-3_all.deb ... 5530s Unpacking w3c-sgml-lib (1.3-3) ... 5530s Selecting previously unselected package python3-biopython. 5530s Preparing to unpack .../056-python3-biopython_1.84+dfsg-4_arm64.deb ... 5530s Unpacking python3-biopython (1.84+dfsg-4) ... 5530s Selecting previously unselected package python3-soupsieve. 5530s Preparing to unpack .../057-python3-soupsieve_2.6-1_all.deb ... 5530s Unpacking python3-soupsieve (2.6-1) ... 5530s Selecting previously unselected package python3-bs4. 5530s Preparing to unpack .../058-python3-bs4_4.12.3-3_all.deb ... 5530s Unpacking python3-bs4 (4.12.3-3) ... 5530s Selecting previously unselected package python3-dendropy. 5530s Preparing to unpack .../059-python3-dendropy_4.6.1-1_all.deb ... 5530s Unpacking python3-dendropy (4.6.1-1) ... 5530s Selecting previously unselected package libjs-jquery. 5530s Preparing to unpack .../060-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 5530s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 5530s Selecting previously unselected package libjs-jquery-ui. 5530s Preparing to unpack .../061-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 5530s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 5530s Selecting previously unselected package fonts-lyx. 5530s Preparing to unpack .../062-fonts-lyx_2.4.2.1-1_all.deb ... 5530s Unpacking fonts-lyx (2.4.2.1-1) ... 5530s Selecting previously unselected package python-matplotlib-data. 5530s Preparing to unpack .../063-python-matplotlib-data_3.8.3-3ubuntu1_all.deb ... 5530s Unpacking python-matplotlib-data (3.8.3-3ubuntu1) ... 5531s Selecting previously unselected package python3-six. 5531s Preparing to unpack .../064-python3-six_1.16.0-7_all.deb ... 5531s Unpacking python3-six (1.16.0-7) ... 5531s Selecting previously unselected package python3-dateutil. 5531s Preparing to unpack .../065-python3-dateutil_2.9.0-2_all.deb ... 5531s Unpacking python3-dateutil (2.9.0-2) ... 5531s Selecting previously unselected package python3-contourpy. 5531s Preparing to unpack .../066-python3-contourpy_1.3.0-2_arm64.deb ... 5531s Unpacking python3-contourpy (1.3.0-2) ... 5531s Selecting previously unselected package python3-cycler. 5531s Preparing to unpack .../067-python3-cycler_0.12.1-1_all.deb ... 5531s Unpacking python3-cycler (0.12.1-1) ... 5531s Selecting previously unselected package python3-brotli. 5531s Preparing to unpack .../068-python3-brotli_1.1.0-2build2_arm64.deb ... 5531s Unpacking python3-brotli (1.1.0-2build2) ... 5531s Selecting previously unselected package python3-decorator. 5531s Preparing to unpack .../069-python3-decorator_5.1.1-5_all.deb ... 5531s Unpacking python3-decorator (5.1.1-5) ... 5531s Selecting previously unselected package liblbfgsb0:arm64. 5531s Preparing to unpack .../070-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 5531s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 5531s Selecting previously unselected package python3-scipy. 5531s Preparing to unpack .../071-python3-scipy_1.13.1-5_arm64.deb ... 5531s Unpacking python3-scipy (1.13.1-5) ... 5531s Selecting previously unselected package python3-ufolib2. 5531s Preparing to unpack .../072-python3-ufolib2_0.16.1+dfsg1-1_all.deb ... 5531s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ... 5531s Selecting previously unselected package python3-mpmath. 5531s Preparing to unpack .../073-python3-mpmath_1.3.0-1_all.deb ... 5531s Unpacking python3-mpmath (1.3.0-1) ... 5531s Selecting previously unselected package python3-sympy. 5531s Preparing to unpack .../074-python3-sympy_1.13.3-1_all.deb ... 5531s Unpacking python3-sympy (1.13.3-1) ... 5531s Selecting previously unselected package python3-tz. 5532s Preparing to unpack .../075-python3-tz_2024.1-2_all.deb ... 5532s Unpacking python3-tz (2024.1-2) ... 5532s Selecting previously unselected package python3-appdirs. 5532s Preparing to unpack .../076-python3-appdirs_1.4.4-4_all.deb ... 5532s Unpacking python3-appdirs (1.4.4-4) ... 5532s Selecting previously unselected package python3-fs. 5532s Preparing to unpack .../077-python3-fs_2.4.16-4_all.deb ... 5532s Unpacking python3-fs (2.4.16-4) ... 5532s Selecting previously unselected package libxslt1.1:arm64. 5532s Preparing to unpack .../078-libxslt1.1_1.1.39-0exp1ubuntu1_arm64.deb ... 5532s Unpacking libxslt1.1:arm64 (1.1.39-0exp1ubuntu1) ... 5532s Selecting previously unselected package python3-lxml:arm64. 5532s Preparing to unpack .../079-python3-lxml_5.3.0-1_arm64.deb ... 5532s Unpacking python3-lxml:arm64 (5.3.0-1) ... 5532s Selecting previously unselected package python3-lz4. 5532s Preparing to unpack .../080-python3-lz4_4.0.2+dfsg-1build4_arm64.deb ... 5532s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 5532s Selecting previously unselected package python3-unicodedata2. 5532s Preparing to unpack .../081-python3-unicodedata2_15.1.0+ds-1build2_arm64.deb ... 5532s Unpacking python3-unicodedata2 (15.1.0+ds-1build2) ... 5532s Selecting previously unselected package unicode-data. 5532s Preparing to unpack .../082-unicode-data_15.1.0-1_all.deb ... 5532s Unpacking unicode-data (15.1.0-1) ... 5532s Selecting previously unselected package python3-fonttools. 5532s Preparing to unpack .../083-python3-fonttools_4.46.0-1build2_arm64.deb ... 5532s Unpacking python3-fonttools (4.46.0-1build2) ... 5532s Selecting previously unselected package python3-kiwisolver. 5532s Preparing to unpack .../084-python3-kiwisolver_1.4.7-2build1_arm64.deb ... 5532s Unpacking python3-kiwisolver (1.4.7-2build1) ... 5532s Selecting previously unselected package python3-packaging. 5532s Preparing to unpack .../085-python3-packaging_24.1-1_all.deb ... 5532s Unpacking python3-packaging (24.1-1) ... 5532s Selecting previously unselected package libqhull-r8.0:arm64. 5532s Preparing to unpack .../086-libqhull-r8.0_2020.2-6build1_arm64.deb ... 5532s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 5532s Selecting previously unselected package python3-matplotlib. 5532s Preparing to unpack .../087-python3-matplotlib_3.8.3-3ubuntu1_arm64.deb ... 5532s Unpacking python3-matplotlib (3.8.3-3ubuntu1) ... 5532s Selecting previously unselected package mummer. 5532s Preparing to unpack .../088-mummer_3.23+dfsg-8_arm64.deb ... 5532s Unpacking mummer (3.23+dfsg-8) ... 5532s Selecting previously unselected package python3-pymummer. 5532s Preparing to unpack .../089-python3-pymummer_0.11.0-4_all.deb ... 5532s Unpacking python3-pymummer (0.11.0-4) ... 5532s Selecting previously unselected package python3-pysam. 5532s Preparing to unpack .../090-python3-pysam_0.22.1+ds-2_arm64.deb ... 5532s Unpacking python3-pysam (0.22.1+ds-2) ... 5533s Selecting previously unselected package libfml0:arm64. 5533s Preparing to unpack .../091-libfml0_0.1+git20190320.b499514-1build1_arm64.deb ... 5533s Unpacking libfml0:arm64 (0.1+git20190320.b499514-1build1) ... 5533s Selecting previously unselected package libminimap0:arm64. 5533s Preparing to unpack .../092-libminimap0_0.2-8_arm64.deb ... 5533s Unpacking libminimap0:arm64 (0.2-8) ... 5533s Selecting previously unselected package bowtie2. 5533s Preparing to unpack .../093-bowtie2_2.5.4-1_arm64.deb ... 5533s Unpacking bowtie2 (2.5.4-1) ... 5533s Selecting previously unselected package cd-hit. 5533s Preparing to unpack .../094-cd-hit_4.8.1-4_arm64.deb ... 5533s Unpacking cd-hit (4.8.1-4) ... 5533s Selecting previously unselected package libcapnp-1.0.1:arm64. 5533s Preparing to unpack .../095-libcapnp-1.0.1_1.0.1-4_arm64.deb ... 5533s Unpacking libcapnp-1.0.1:arm64 (1.0.1-4) ... 5533s Selecting previously unselected package libgslcblas0:arm64. 5533s Preparing to unpack .../096-libgslcblas0_2.8+dfsg-5_arm64.deb ... 5533s Unpacking libgslcblas0:arm64 (2.8+dfsg-5) ... 5533s Selecting previously unselected package libgsl28:arm64. 5533s Preparing to unpack .../097-libgsl28_2.8+dfsg-5_arm64.deb ... 5533s Unpacking libgsl28:arm64 (2.8+dfsg-5) ... 5533s Selecting previously unselected package libmurmurhash2:arm64. 5533s Preparing to unpack .../098-libmurmurhash2_1.6-1_arm64.deb ... 5533s Unpacking libmurmurhash2:arm64 (1.6-1) ... 5533s Selecting previously unselected package mash. 5533s Preparing to unpack .../099-mash_2.3+dfsg-6build1_arm64.deb ... 5533s Unpacking mash (2.3+dfsg-6build1) ... 5533s Selecting previously unselected package ariba. 5533s Preparing to unpack .../100-ariba_2.14.7+ds-4_arm64.deb ... 5533s Unpacking ariba (2.14.7+ds-4) ... 5533s Selecting previously unselected package autopkgtest-satdep. 5533s Preparing to unpack .../101-1-autopkgtest-satdep.deb ... 5533s Unpacking autopkgtest-satdep (0) ... 5533s Setting up libhtscodecs2:arm64 (1.6.1-1) ... 5533s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 5533s Setting up liblcms2-2:arm64 (2.16-2) ... 5533s Setting up libpixman-1-0:arm64 (0.44.0-3) ... 5533s Setting up libsharpyuv0:arm64 (1.4.0-0.1) ... 5533s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 5533s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 5533s Setting up libgslcblas0:arm64 (2.8+dfsg-5) ... 5533s Setting up libmurmurhash2:arm64 (1.6-1) ... 5533s Setting up libcapnp-1.0.1:arm64 (1.0.1-4) ... 5533s Setting up python3-lz4 (4.0.2+dfsg-1build4) ... 5533s Setting up libxcb-render0:arm64 (1.17.0-2) ... 5533s Setting up python3-unicodedata2 (15.1.0+ds-1build2) ... 5533s Setting up fonts-lyx (2.4.2.1-1) ... 5533s Setting up x11-common (1:7.7+23ubuntu3) ... 5534s Setting up libdeflate0:arm64 (1.22-1) ... 5534s Setting up libqhull-r8.0:arm64 (2020.2-6build1) ... 5534s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 5534s Setting up libgomp1:arm64 (14.2.0-8ubuntu1) ... 5534s Setting up python3-freetype (2.5.1-1) ... 5534s Setting up libfml0:arm64 (0.1+git20190320.b499514-1build1) ... 5534s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 5534s Setting up python3-tz (2024.1-2) ... 5534s Setting up bowtie2 (2.5.4-1) ... 5534s Setting up unicode-data (15.1.0-1) ... 5534s Setting up python3-six (1.16.0-7) ... 5534s Setting up python3-decorator (5.1.1-5) ... 5534s Setting up libminimap0:arm64 (0.2-8) ... 5534s Setting up libfontenc1:arm64 (1:1.1.8-1build1) ... 5534s Setting up libblas3:arm64 (3.12.0-3build2) ... 5534s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 5534s Setting up python3-packaging (24.1-1) ... 5534s Setting up python3-brotli (1.1.0-2build2) ... 5534s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 5534s Setting up python3-cycler (0.12.1-1) ... 5534s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 5534s Setting up fonts-dejavu-mono (2.37-8) ... 5534s Setting up python3-kiwisolver (1.4.7-2build1) ... 5534s Setting up libtcl8.6:arm64 (8.6.15+dfsg-2) ... 5534s Setting up fonts-dejavu-core (2.37-8) ... 5535s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 5535s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 5535s Setting up libwebp7:arm64 (1.4.0-0.1) ... 5535s Setting up libxslt1.1:arm64 (1.1.39-0exp1ubuntu1) ... 5535s Setting up mummer (3.23+dfsg-8) ... 5535s Setting up libhts3t64:arm64 (1.20+ds-1) ... 5535s Setting up libopenjp2-7:arm64 (2.5.0-2ubuntu1) ... 5535s Setting up libharfbuzz0b:arm64 (10.0.1-1) ... 5535s Setting up python3-dateutil (2.9.0-2) ... 5535s Setting up sgml-base (1.31) ... 5535s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 5535s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 5535s Setting up python3-mpmath (1.3.0-1) ... 5535s Setting up libgsl28:arm64 (2.8+dfsg-5) ... 5535s Setting up python-matplotlib-data (3.8.3-3ubuntu1) ... 5535s Setting up libwebpmux3:arm64 (1.4.0-0.1) ... 5535s Setting up python3-dendropy (4.6.1-1) ... 5536s Setting up python3-appdirs (1.4.4-4) ... 5536s Setting up python3-soupsieve (2.6-1) ... 5536s Setting up cd-hit (4.8.1-4) ... 5536s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 5536s Setting up python3-sympy (1.13.3-1) ... 5542s Setting up liblapack3:arm64 (3.12.0-3build2) ... 5542s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 5542s Setting up python3-pysam (0.22.1+ds-2) ... 5542s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 5542s Setting up libwebpdemux2:arm64 (1.4.0-0.1) ... 5542s Setting up xfonts-utils (1:7.7+7) ... 5542s Setting up python3-bs4 (4.12.3-3) ... 5543s Setting up samtools (1.20-3) ... 5543s Setting up python3-fs (2.4.16-4) ... 5543s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 5543s Setting up libraqm0:arm64 (0.10.1-1build1) ... 5543s Setting up mash (2.3+dfsg-6build1) ... 5543s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 5545s Setting up python3-lxml:arm64 (5.3.0-1) ... 5545s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 5545s Setting up xml-core (0.19) ... 5545s Setting up python3-contourpy (1.3.0-2) ... 5545s Setting up libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 5545s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 5545s Setting up libxft2:arm64 (2.3.6-1build1) ... 5545s Setting up python3-scipy (1.13.1-5) ... 5549s Setting up libtk8.6:arm64 (8.6.15-1) ... 5549s Setting up fastaq (3.17.0-8) ... 5549s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:37: SyntaxWarning: invalid escape sequence '\s' 5549s phylip_regex = re.compile('^\s*[0-9]+\s+[0-9]+$') 5549s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:38: SyntaxWarning: invalid escape sequence '\s' 5549s gbk_regex = re.compile('^LOCUS\s+\S') 5549s Setting up python3.12-tk (3.12.7-3) ... 5549s Setting up fonts-urw-base35 (20200910-8) ... 5549s Setting up libcairo2:arm64 (1.18.2-2) ... 5549s Setting up python3-pymummer (0.11.0-4) ... 5549s Setting up python3-pil:arm64 (10.4.0-1ubuntu1) ... 5549s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 5549s Setting up python3-cairo (1.26.1-2) ... 5550s Setting up blt (2.5.3+dfsg-7build1) ... 5550s Setting up python3-tk:arm64 (3.12.6-1ubuntu1) ... 5550s Setting up python3-pil.imagetk:arm64 (10.4.0-1ubuntu1) ... 5550s Setting up python3-rlpycairo (0.3.0-3) ... 5550s Setting up python3-reportlab (4.2.5-1) ... 5551s Setting up python3-fonttools (4.46.0-1build2) ... 5551s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... 5552s Setting up python3-matplotlib (3.8.3-3ubuntu1) ... 5553s Processing triggers for libc-bin (2.40-1ubuntu3) ... 5553s Processing triggers for man-db (2.13.0-1) ... 5554s Processing triggers for sgml-base (1.31) ... 5554s Setting up w3c-sgml-lib (1.3-3) ... 5579s Setting up python3-biopython (1.84+dfsg-4) ... 5580s Setting up ariba (2.14.7+ds-4) ... 5581s /usr/lib/python3/dist-packages/ariba/external_progs.py:34: SyntaxWarning: invalid escape sequence '\.' 5581s 'cdhit': ('', re.compile('CD-HIT version ([0-9\.]+) \(')), 5581s /usr/lib/python3/dist-packages/ariba/external_progs.py:35: SyntaxWarning: invalid escape sequence '\.' 5581s 'nucmer': ('--version', re.compile('([0-9]+\.[0-9\.]+.*$)')), 5581s /usr/lib/python3/dist-packages/ariba/external_progs.py:36: SyntaxWarning: invalid escape sequence '\.' 5581s 'spades': ('--version', re.compile('SPAdes.*v([0-9\.]+)')) 5581s Setting up autopkgtest-satdep (0) ... 5588s (Reading database ... 90764 files and directories currently installed.) 5588s Removing autopkgtest-satdep (0) ... 5590s autopkgtest [01:59:07]: test test-example: [----------------------- 5593s ARIBA version: 2.14.6 5593s 5593s External dependencies: 5593s bowtie2 2.5.4 /usr/bin/bowtie2 5593s cdhit 4.8.1 /usr/bin/cd-hit-est 5593s nucmer 3.1 /usr/bin/nucmer 5593s 5593s External dependencies OK: True 5593s 5593s Python version: 5593s 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 5593s 5593s Python packages: 5593s ariba 2.14.6 /usr/lib/python3/dist-packages/ariba/__init__.py 5593s bs4 4.12.3 /usr/lib/python3/dist-packages/bs4/__init__.py 5593s dendropy 4.6.1 /usr/lib/python3/dist-packages/dendropy/__init__.py 5593s pyfastaq 3.17.0 /usr/lib/python3/dist-packages/pyfastaq/__init__.py 5593s pymummer 0.11.0 /usr/lib/python3/dist-packages/pymummer/__init__.py 5593s pysam 0.22.1 /usr/lib/python3/dist-packages/pysam/__init__.py 5593s 5593s Python packages OK: True 5593s 5593s Everything looks OK: True 5593s 5593s Loading and checking input data 5593s 5593s Running cdhit 5593s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.SSfcDykxLH/foo/PREPAREREF/02.cdhit.noncoding.fa -o /tmp/tmp.SSfcDykxLH/foo/tmp.run_cd-hit.uyg8gt4p/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 5593s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.SSfcDykxLH/foo/PREPAREREF/02.cdhit.noncoding.varonly.fa -o /tmp/tmp.SSfcDykxLH/foo/tmp.run_cd-hit.oay_z1gs/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 5594s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.SSfcDykxLH/foo/PREPAREREF/02.cdhit.gene.fa -o /tmp/tmp.SSfcDykxLH/foo/tmp.run_cd-hit.d2gd44xp/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 5594s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.SSfcDykxLH/foo/PREPAREREF/02.cdhit.gene.varonly.fa -o /tmp/tmp.SSfcDykxLH/foo/tmp.run_cd-hit.03ifz7f4/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 5594s 5594s Writing clusters to file. 10 in total 5595s Found reads file: reads_1.fq 5595s Found reads file: reads_2.fq 5595s ARIBA version: 2.14.6 5595s 5595s External dependencies: 5595s bowtie2 2.5.4 /usr/bin/bowtie2 5595s cdhit 4.8.1 /usr/bin/cd-hit-est 5595s nucmer 3.1 /usr/bin/nucmer 5595s 5595s External dependencies OK: True 5595s 5595s Python version: 5595s 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 5595s 5595s Python packages: 5595s ariba 2.14.6 /usr/lib/python3/dist-packages/ariba/__init__.py 5595s bs4 4.12.3 /usr/lib/python3/dist-packages/bs4/__init__.py 5595s dendropy 4.6.1 /usr/lib/python3/dist-packages/dendropy/__init__.py 5595s pyfastaq 3.17.0 /usr/lib/python3/dist-packages/pyfastaq/__init__.py 5595s pymummer 0.11.0 /usr/lib/python3/dist-packages/pymummer/__init__.py 5595s pysam 0.22.1 /usr/lib/python3/dist-packages/pysam/__init__.py 5595s 5595s Python packages OK: True 5595s 5595s Everything looks OK: True 5595s Temporary directory: /tmp/tmp.SSfcDykxLH/foo/OUT/ariba.tmp.80b9_570 5595s ______________________ Mapping reads to clustered genes _______________________ 5595s Finished mapping 5595s 5595s _____________________________ Generating clusters _____________________________ 5595s syscall: sort -k1,1 -k 2,2n /tmp/tmp.SSfcDykxLH/foo/OUT/minimap.reads > /tmp/tmp.SSfcDykxLH/foo/OUT/read_store 5595s Compressing file /tmp/tmp.SSfcDykxLH/foo/OUT/read_store 5595s Found 51 proper read pairs from minimap 5595s Total clusters to perform local assemblies: 9 5595s 5595s Insert size information from reads mapped to reference genes: 5595s Insert size: 185.0 5595s Insert sspace sd: 0.27 5595s Max insert: 220.55 5595s 5595s ___________________________ Assembling each cluster ___________________________ 5595s Will run 1 cluster(s) in parallel 5595s Not constructing cluster cluster because it only has 2 reads (1 of 9) 5595s Constructing cluster cluster_1 (2 of 9) 5595s Constructing cluster cluster_2 (3 of 9) 5595s Constructing cluster cluster_3 (4 of 9) 5595s Constructing cluster cluster_4 (5 of 9) 5595s Constructing cluster gene (6 of 9) 5595s Constructing cluster gene_1 (7 of 9) 5595s Constructing cluster noncoding (8 of 9) 5595s Constructing cluster noncoding_1 (9 of 9) 5595s Start running cluster cluster_1 in directory /tmp/tmp.SSfcDykxLH/foo/OUT/ariba.tmp.80b9_570/cluster_1 5597s cluster_1 detected 1 threads available to it 5597s cluster_1 reported completion 5597s Finished running cluster cluster_1 in directory /tmp/tmp.SSfcDykxLH/foo/OUT/ariba.tmp.80b9_570/cluster_1 5597s Deleting cluster dir /tmp/tmp.SSfcDykxLH/foo/OUT/ariba.tmp.80b9_570/cluster_1 5597s Start running cluster cluster_2 in directory /tmp/tmp.SSfcDykxLH/foo/OUT/ariba.tmp.80b9_570/cluster_2 5599s cluster_2 detected 1 threads available to it 5599s cluster_2 reported completion 5599s Finished running cluster cluster_2 in directory /tmp/tmp.SSfcDykxLH/foo/OUT/ariba.tmp.80b9_570/cluster_2 5599s Deleting cluster dir /tmp/tmp.SSfcDykxLH/foo/OUT/ariba.tmp.80b9_570/cluster_2 5599s Start running cluster cluster_3 in directory /tmp/tmp.SSfcDykxLH/foo/OUT/ariba.tmp.80b9_570/cluster_3 5600s cluster_3 detected 1 threads available to it 5600s cluster_3 reported completion 5600s Finished running cluster cluster_3 in directory /tmp/tmp.SSfcDykxLH/foo/OUT/ariba.tmp.80b9_570/cluster_3 5600s Deleting cluster dir /tmp/tmp.SSfcDykxLH/foo/OUT/ariba.tmp.80b9_570/cluster_3 5600s Start running cluster cluster_4 in directory /tmp/tmp.SSfcDykxLH/foo/OUT/ariba.tmp.80b9_570/cluster_4 5602s cluster_4 detected 1 threads available to it 5602s cluster_4 reported completion 5602s Finished running cluster cluster_4 in directory /tmp/tmp.SSfcDykxLH/foo/OUT/ariba.tmp.80b9_570/cluster_4 5602s Deleting cluster dir /tmp/tmp.SSfcDykxLH/foo/OUT/ariba.tmp.80b9_570/cluster_4 5602s Start running cluster gene in directory /tmp/tmp.SSfcDykxLH/foo/OUT/ariba.tmp.80b9_570/gene 5604s gene detected 1 threads available to it 5604s gene reported completion 5604s Finished running cluster gene in directory /tmp/tmp.SSfcDykxLH/foo/OUT/ariba.tmp.80b9_570/gene 5604s Deleting cluster dir /tmp/tmp.SSfcDykxLH/foo/OUT/ariba.tmp.80b9_570/gene 5604s Start running cluster gene_1 in directory /tmp/tmp.SSfcDykxLH/foo/OUT/ariba.tmp.80b9_570/gene_1 5606s gene_1 detected 1 threads available to it 5606s gene_1 reported completion 5606s Finished running cluster gene_1 in directory /tmp/tmp.SSfcDykxLH/foo/OUT/ariba.tmp.80b9_570/gene_1 5606s Deleting cluster dir /tmp/tmp.SSfcDykxLH/foo/OUT/ariba.tmp.80b9_570/gene_1 5606s Start running cluster noncoding in directory /tmp/tmp.SSfcDykxLH/foo/OUT/ariba.tmp.80b9_570/noncoding 5608s noncoding detected 1 threads available to it 5608s noncoding reported completion 5608s Finished running cluster noncoding in directory /tmp/tmp.SSfcDykxLH/foo/OUT/ariba.tmp.80b9_570/noncoding 5608s Deleting cluster dir /tmp/tmp.SSfcDykxLH/foo/OUT/ariba.tmp.80b9_570/noncoding 5608s Start running cluster noncoding_1 in directory /tmp/tmp.SSfcDykxLH/foo/OUT/ariba.tmp.80b9_570/noncoding_1 5610s noncoding_1 detected 1 threads available to it 5610s noncoding_1 reported completion 5610s Finished running cluster noncoding_1 in directory /tmp/tmp.SSfcDykxLH/foo/OUT/ariba.tmp.80b9_570/noncoding_1 5610s Deleting cluster dir /tmp/tmp.SSfcDykxLH/foo/OUT/ariba.tmp.80b9_570/noncoding_1 5610s Final value of remaining_clusters counter: Value('l', 0) 5610s Finished assembling clusters 5610s 5610s _______________________________ Writing reports _______________________________ 5610s Making /tmp/tmp.SSfcDykxLH/foo/OUT/debug.report.tsv 5610s Making /tmp/tmp.SSfcDykxLH/foo/OUT/report.tsv 5610s 5610s ____________________ Writing fasta of assembled sequences _____________________ 5610s /tmp/tmp.SSfcDykxLH/foo/OUT/assembled_seqs.fa.gz and /tmp/tmp.SSfcDykxLH/foo/OUT/assembled_genes.fa.gz 5610s 5610s __________________________ Catting cluster log files __________________________ 5610s Writing file /tmp/tmp.SSfcDykxLH/foo/OUT/log.clusters.gz 5610s 5610s _______________________________ Cleaning files ________________________________ 5610s Deleting Logs directory /tmp/tmp.SSfcDykxLH/foo/OUT/Logs 5610s Deleting reads store files /tmp/tmp.SSfcDykxLH/foo/OUT/read_store.gz[.tbi] 5610s 5610s All done! 5610s 5610s Running ARIBA on test data... 5610s ------------------------------------------------------------------------------- 5610s |=============================================================================| 5610s | Preparing input data | 5610s |=============================================================================| 5610s ------------------------------------------------------------------------------- 5610s Made output directory ./foo. Copying test data files into it: 5610s copied ref_seqs.fa 5610s copied metadata.tsv 5610s copied reads_1.fq 5610s copied reads_2.fq 5610s ------------------------------------------------------------------------------- 5610s |=============================================================================| 5610s | Try running ariba prepareref | 5610s |=============================================================================| 5610s ------------------------------------------------------------------------------- 5610s 5610s Running ariba prepareref with: 5610s /usr/bin/ariba prepareref --verbose -f ref_seqs.fa -m metadata.tsv --threads 1 PREPAREREF 5610s 5610s 5610s ariba prepareref finished OK 5610s ------------------------------------------------------------------------------- 5610s |=============================================================================| 5610s | Try running ariba run | 5610s |=============================================================================| 5610s ------------------------------------------------------------------------------- 5610s 5610s Running ARIBA with: 5610s /usr/bin/ariba run --verbose --threads 1 PREPAREREF reads_1.fq reads_2.fq OUT 5610s 5610s 5610s ariba run finished OK 5610s Finished run on test data OK 5610s autopkgtest [01:59:27]: test test-example: -----------------------] 5612s test-example PASS 5612s autopkgtest [01:59:29]: test test-example: - - - - - - - - - - results - - - - - - - - - - 5612s autopkgtest [01:59:29]: @@@@@@@@@@@@@@@@@@@@ summary 5612s test-example PASS 5628s nova [W] Skipping flock in bos03-arm64 5628s Creating nova instance adt-plucky-arm64-ariba-20241115-002557-juju-7f2275-prod-proposed-migration-environment-15-83a0125b-968c-4977-aeb9-a821e5795b4b from image adt/ubuntu-plucky-arm64-server-20241114.img (UUID 4472f5f7-859f-4441-9e8e-9550fb35f210)...