0s autopkgtest [18:30:12]: starting date and time: 2025-12-03 18:30:12+0000 0s autopkgtest [18:30:12]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [18:30:12]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.2h02ft3f/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade ariba --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.13.9-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@sto01-2.secgroup --name adt-resolute-amd64-ariba-20251203-183012-juju-7f2275-prod-proposed-migration-environment-15-82b3c7ae-e3c2-4bcf-8530-32026a76d1b5 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-amd64-ariba-20251203-183012-juju-7f2275-prod-proposed-migration-environment-15-82b3c7ae-e3c2-4bcf-8530-32026a76d1b5 from image adt/ubuntu-resolute-amd64-server-20251203.img (UUID c6e78f39-c16c-48bb-9815-0096f6be052e)... 53s autopkgtest [18:31:05]: testbed dpkg architecture: amd64 53s autopkgtest [18:31:05]: testbed apt version: 3.1.12 53s autopkgtest [18:31:05]: @@@@@@@@@@@@@@@@@@@@ test bed setup 53s autopkgtest [18:31:05]: testbed release detected to be: None 54s autopkgtest [18:31:06]: updating testbed package index (apt update) 54s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 54s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 54s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 54s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 54s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [157 kB] 54s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [23.1 kB] 54s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [954 kB] 55s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [220 kB] 55s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [161 kB] 55s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [6252 B] 55s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [120 B] 55s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [764 kB] 55s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [349 kB] 55s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [23.0 kB] 55s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [4040 B] 55s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [9636 B] 55s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [764 B] 55s Fetched 2796 kB in 1s (3218 kB/s) 56s Reading package lists... 57s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 57s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 57s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 57s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 57s Reading package lists... 57s Reading package lists... 57s Building dependency tree... 57s Reading state information... 57s Calculating upgrade... 58s The following packages will be upgraded: 58s libpython3-stdlib python3 python3-gdbm python3-minimal 58s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 58s Need to get 72.9 kB of archives. 58s After this operation, 2048 B of additional disk space will be used. 58s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-minimal amd64 3.13.9-2 [28.1 kB] 58s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3 amd64 3.13.9-2 [23.0 kB] 58s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libpython3-stdlib amd64 3.13.9-2 [10.8 kB] 58s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-gdbm amd64 3.13.9-2 [11.0 kB] 58s dpkg-preconfigure: unable to re-open stdin: No such file or directory 58s Fetched 72.9 kB in 0s (0 B/s) 58s (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 ... 83538 files and directories currently installed.) 58s Preparing to unpack .../python3-minimal_3.13.9-2_amd64.deb ... 58s Unpacking python3-minimal (3.13.9-2) over (3.13.7-1) ... 58s Setting up python3-minimal (3.13.9-2) ... 58s (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 ... 83538 files and directories currently installed.) 58s Preparing to unpack .../python3_3.13.9-2_amd64.deb ... 58s running python pre-rtupdate hooks for python3.13... 58s Unpacking python3 (3.13.9-2) over (3.13.7-1) ... 58s Preparing to unpack .../libpython3-stdlib_3.13.9-2_amd64.deb ... 58s Unpacking libpython3-stdlib:amd64 (3.13.9-2) over (3.13.7-1) ... 58s Preparing to unpack .../python3-gdbm_3.13.9-2_amd64.deb ... 58s Unpacking python3-gdbm (3.13.9-2) over (3.13.9-1) ... 58s Setting up python3-gdbm (3.13.9-2) ... 58s Setting up libpython3-stdlib:amd64 (3.13.9-2) ... 58s Setting up python3 (3.13.9-2) ... 58s running python rtupdate hooks for python3.13... 58s running python post-rtupdate hooks for python3.13... 58s Processing triggers for man-db (2.13.1-1) ... 59s autopkgtest [18:31:11]: upgrading testbed (apt dist-upgrade and autopurge) 59s Reading package lists... 59s Building dependency tree... 59s Reading state information... 59s Calculating upgrade... 59s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 59s Reading package lists... 59s Building dependency tree... 59s Reading state information... 59s Solving dependencies... 59s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 62s autopkgtest [18:31:14]: testbed running kernel: Linux 6.17.0-6-generic #6-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 7 13:34:17 UTC 2025 62s autopkgtest [18:31:14]: @@@@@@@@@@@@@@@@@@@@ apt-source ariba 63s Get:1 http://ftpmaster.internal/ubuntu resolute/universe ariba 2.14.7+ds-7syncable1build1 (dsc) [2430 B] 63s Get:2 http://ftpmaster.internal/ubuntu resolute/universe ariba 2.14.7+ds-7syncable1build1 (tar) [1920 kB] 63s Get:3 http://ftpmaster.internal/ubuntu resolute/universe ariba 2.14.7+ds-7syncable1build1 (diff) [11.9 kB] 63s gpgv: Signature made Tue Oct 21 17:40:02 2025 UTC 63s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 63s gpgv: Can't check signature: No public key 63s dpkg-source: warning: cannot verify inline signature for ./ariba_2.14.7+ds-7syncable1build1.dsc: no acceptable signature found 63s autopkgtest [18:31:15]: testing package ariba version 2.14.7+ds-7syncable1build1 63s autopkgtest [18:31:15]: build not needed 65s autopkgtest [18:31:17]: test test-example: preparing testbed 66s Reading package lists... 66s Building dependency tree... 66s Reading state information... 66s Solving dependencies... 66s The following NEW packages will be installed: 66s ariba bowtie2 cd-hit fastaq fontconfig-config fonts-dejavu-core 66s fonts-dejavu-mono fonts-lyx fonts-urw-base35 libblas3 libcairo2 66s libcapnp-1.1.0 libdeflate0 libfml0 libfontconfig1 libfontenc1 libgfortran5 66s libgomp1 libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b libhts3t64 66s libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 66s liblcms2-2 liblerc4 libminimap0 libmurmurhash2 libopenjp2-7 libpixman-1-0 66s libqhull-r8.0 libraqm0 libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 66s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 libxrender1 66s libxslt1.1 libxss1 libzopfli1 mash mummer python-matplotlib-data 66s python3-biopython python3-brotli python3-bs4 python3-cairo 66s python3-charset-normalizer python3-contourpy python3-cycler python3-dendropy 66s python3-fonttools python3-freetype python3-fs python3-kiwisolver 66s python3-lxml python3-lz4 python3-matplotlib python3-mpmath python3-munkres 66s python3-numpy python3-numpy-dev python3-pil python3-pil.imagetk 66s python3-platformdirs python3-pymummer python3-pysam python3-reportlab 66s python3-rlpycairo python3-soupsieve python3-sympy python3-tk python3-ufolib2 66s python3-unicodedata2 python3-zopfli python3.13-tk python3.14-tk samtools 66s sgml-base unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils 66s xml-core 66s 0 upgraded, 96 newly installed, 0 to remove and 0 not upgraded. 66s Need to get 86.2 MB of archives. 66s After this operation, 358 MB of additional disk space will be used. 66s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1ubuntu1 [147 kB] 66s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7 [259 kB] 66s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-9ubuntu1 [939 kB] 66s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7 [2739 kB] 67s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.2.4+ds-1ubuntu1 [5377 kB] 67s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 67s Get:7 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhtscodecs2 amd64 1.6.1-2 [132 kB] 67s Get:8 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhts3t64 amd64 1.22.1+ds2-1 [461 kB] 67s Get:9 http://ftpmaster.internal/ubuntu resolute/universe amd64 samtools amd64 1.22.1-1 [645 kB] 67s Get:10 http://ftpmaster.internal/ubuntu resolute/universe amd64 fastaq all 3.17.0-9 [48.2 kB] 67s Get:11 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-charset-normalizer amd64 3.4.4-1 [175 kB] 67s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1 [1036 kB] 68s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 68s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 68s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontenc1 amd64 1:1.1.8-1build2 [14.1 kB] 68s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 68s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu3 [576 kB] 68s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 68s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 68s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.15.0-2.3ubuntu1 [38.0 kB] 68s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.15.0-2.3ubuntu1 [141 kB] 68s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB] 68s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 68s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 68s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libtk8.6 amd64 8.6.17-1 [823 kB] 68s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.13-tk amd64 3.13.9-1 [108 kB] 68s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14-tk amd64 3.14.0-4 [108 kB] 68s Get:28 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-tk amd64 3.13.9-2 [11.1 kB] 68s Get:29 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pil.imagetk amd64 12.0.0-1ubuntu1 [9700 B] 68s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 15.2.0-9ubuntu1 [151 kB] 68s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 68s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu2 [152 kB] 68s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 68s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 liblcms2-2 amd64 2.17-1 [170 kB] 68s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 libopenjp2-7 amd64 2.5.3-2.1 [188 kB] 68s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 68s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.1.0-1 [535 kB] 68s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libraqm0 amd64 0.10.3-1 [15.4 kB] 68s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 68s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 68s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 68s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 68s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB] 68s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB] 68s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB] 68s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-pil amd64 12.0.0-1ubuntu1 [494 kB] 68s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.46.4-1 [287 kB] 68s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2build1 [17.4 kB] 68s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2build1 [6120 B] 68s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-1build1 [611 kB] 68s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-cairo amd64 1.27.0-2build1 [140 kB] 68s Get:52 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-freetype all 2.5.1-2 [92.2 kB] 68s Get:53 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-rlpycairo all 0.3.0-4 [9332 B] 68s Get:54 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-reportlab all 4.4.5-1 [1148 kB] 68s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 sgml-base all 1.31+nmu1 [11.0 kB] 68s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 xml-core all 0.19 [20.3 kB] 68s Get:57 http://ftpmaster.internal/ubuntu resolute/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 68s Get:58 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-biopython amd64 1.86+dfsg-1 [1682 kB] 68s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-soupsieve all 2.7-2 [33.6 kB] 68s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-bs4 all 4.14.2-1 [82.8 kB] 68s Get:61 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-dendropy all 4.6.1-2 [278 kB] 68s Get:62 http://ftpmaster.internal/ubuntu resolute/universe amd64 fonts-lyx all 2.4.4-2 [171 kB] 68s Get:63 http://ftpmaster.internal/ubuntu resolute/universe amd64 python-matplotlib-data all 3.10.7+dfsg1-1 [2930 kB] 69s Get:64 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-contourpy amd64 1.3.3-1 [255 kB] 69s Get:65 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-cycler all 0.12.1-2 [9850 B] 69s Get:66 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-brotli amd64 1.1.0-2build6 [340 kB] 69s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-platformdirs all 4.4.0-1 [16.9 kB] 69s Get:68 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-fs all 2.4.16-9ubuntu1 [91.5 kB] 69s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 libxslt1.1 amd64 1.1.43-0.3 [172 kB] 69s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-lxml amd64 6.0.2-1 [2333 kB] 69s Get:71 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-lz4 amd64 4.4.4+dfsg-3 [27.5 kB] 69s Get:72 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-munkres all 1.1.4-3 [9236 B] 69s Get:73 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-mpmath all 1.3.0-2 [423 kB] 69s Get:74 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-sympy all 1.14.0-2 [4306 kB] 69s Get:75 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.5 kB] 69s Get:76 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-unicodedata2 amd64 16.0.0+ds-1build1 [400 kB] 69s Get:77 http://ftpmaster.internal/ubuntu resolute/universe amd64 libzopfli1 amd64 1.0.3-3 [141 kB] 69s Get:78 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-zopfli amd64 0.4.0-1 [11.1 kB] 69s Get:79 http://ftpmaster.internal/ubuntu resolute/universe amd64 unicode-data all 16.0.0-1 [9513 kB] 69s Get:80 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-fonttools amd64 4.57.0-3 [1705 kB] 69s Get:81 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-kiwisolver amd64 1.4.10~rc0-1 [65.5 kB] 69s Get:82 http://ftpmaster.internal/ubuntu resolute/universe amd64 libqhull-r8.0 amd64 2020.2-7 [197 kB] 69s Get:83 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-matplotlib amd64 3.10.7+dfsg1-1 [17.2 MB] 70s Get:84 http://ftpmaster.internal/ubuntu resolute/universe amd64 mummer amd64 3.23+dfsg-8 [685 kB] 70s Get:85 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pymummer all 0.12.0-1 [13.3 kB] 70s Get:86 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pysam amd64 0.23.3+ds-2 [4536 kB] 70s Get:87 http://ftpmaster.internal/ubuntu resolute/universe amd64 libfml0 amd64 0.1+git20221215.85f159e-1 [74.4 kB] 70s Get:88 http://ftpmaster.internal/ubuntu resolute/universe amd64 libminimap0 amd64 0.2-8 [23.5 kB] 70s Get:89 http://ftpmaster.internal/ubuntu resolute/universe amd64 bowtie2 amd64 2.5.4-1 [1336 kB] 70s Get:90 http://ftpmaster.internal/ubuntu resolute/universe amd64 cd-hit amd64 4.8.1-4build1 [524 kB] 70s Get:91 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcapnp-1.1.0 amd64 1.1.0-2.1 [1445 kB] 70s Get:92 http://ftpmaster.internal/ubuntu resolute/universe amd64 libgslcblas0 amd64 2.8+dfsg-5.1ubuntu1 [133 kB] 70s Get:93 http://ftpmaster.internal/ubuntu resolute/universe amd64 libgsl28 amd64 2.8+dfsg-5.1ubuntu1 [1104 kB] 70s Get:94 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmurmurhash2 amd64 1.6-1 [5770 B] 71s Get:95 http://ftpmaster.internal/ubuntu resolute/universe amd64 mash amd64 2.3+dfsg-6build2 [160 kB] 71s Get:96 http://ftpmaster.internal/ubuntu resolute/universe amd64 ariba amd64 2.14.7+ds-7syncable1build1 [2035 kB] 71s Fetched 86.2 MB in 5s (17.2 MB/s) 71s Selecting previously unselected package python3-numpy-dev:amd64. 71s (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 ... 83538 files and directories currently installed.) 71s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 71s Unpacking python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 71s Selecting previously unselected package libblas3:amd64. 71s Preparing to unpack .../01-libblas3_3.12.1-7_amd64.deb ... 71s Unpacking libblas3:amd64 (3.12.1-7) ... 71s Selecting previously unselected package libgfortran5:amd64. 71s Preparing to unpack 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... 71s Selecting previously unselected package samtools. 71s Preparing to unpack .../08-samtools_1.22.1-1_amd64.deb ... 71s Unpacking samtools (1.22.1-1) ... 71s Selecting previously unselected package fastaq. 71s Preparing to unpack .../09-fastaq_3.17.0-9_all.deb ... 71s Unpacking fastaq (3.17.0-9) ... 71s Selecting previously unselected package python3-charset-normalizer. 71s Preparing to unpack .../10-python3-charset-normalizer_3.4.4-1_amd64.deb ... 71s Unpacking python3-charset-normalizer (3.4.4-1) ... 71s Selecting previously unselected package libtcl8.6:amd64. 71s Preparing to unpack .../11-libtcl8.6_8.6.17+dfsg-1_amd64.deb ... 71s Unpacking libtcl8.6:amd64 (8.6.17+dfsg-1) ... 71s Selecting previously unselected package fonts-dejavu-mono. 71s Preparing to unpack .../12-fonts-dejavu-mono_2.37-8_all.deb ... 71s Unpacking fonts-dejavu-mono (2.37-8) ... 71s Selecting previously unselected package fonts-dejavu-core. 71s Preparing to unpack .../13-fonts-dejavu-core_2.37-8_all.deb ... 71s Unpacking fonts-dejavu-core (2.37-8) ... 71s Selecting previously unselected package libfontenc1:amd64. 71s Preparing to unpack .../14-libfontenc1_1%3a1.1.8-1build2_amd64.deb ... 71s Unpacking libfontenc1:amd64 (1:1.1.8-1build2) ... 71s Selecting previously unselected package x11-common. 71s Preparing to unpack .../15-x11-common_1%3a7.7+24ubuntu1_all.deb ... 71s Unpacking x11-common (1:7.7+24ubuntu1) ... 71s Selecting previously unselected package xfonts-encodings. 71s Preparing to unpack .../16-xfonts-encodings_1%3a1.0.5-0ubuntu3_all.deb ... 71s Unpacking xfonts-encodings (1:1.0.5-0ubuntu3) ... 71s Selecting previously unselected package xfonts-utils. 71s Preparing to unpack .../17-xfonts-utils_1%3a7.7+7_amd64.deb ... 71s Unpacking xfonts-utils (1:7.7+7) ... 71s Selecting previously unselected package fonts-urw-base35. 71s Preparing to unpack .../18-fonts-urw-base35_20200910-8_all.deb ... 71s Unpacking fonts-urw-base35 (20200910-8) ... 71s Selecting previously unselected package fontconfig-config. 71s Preparing to unpack .../19-fontconfig-config_2.15.0-2.3ubuntu1_amd64.deb ... 72s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 72s Selecting previously unselected package libfontconfig1:amd64. 72s Preparing to unpack .../20-libfontconfig1_2.15.0-2.3ubuntu1_amd64.deb ... 72s Unpacking libfontconfig1:amd64 (2.15.0-2.3ubuntu1) ... 72s Selecting previously unselected package libxrender1:amd64. 72s Preparing to unpack .../21-libxrender1_1%3a0.9.12-1_amd64.deb ... 72s Unpacking libxrender1:amd64 (1:0.9.12-1) ... 72s Selecting previously unselected package libxft2:amd64. 72s Preparing to unpack .../22-libxft2_2.3.6-1build1_amd64.deb ... 72s Unpacking libxft2:amd64 (2.3.6-1build1) ... 72s Selecting previously unselected package libxss1:amd64. 72s Preparing to unpack .../23-libxss1_1%3a1.2.3-1build3_amd64.deb ... 72s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 72s Selecting previously unselected package libtk8.6:amd64. 72s Preparing to unpack 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previously unselected package libimagequant0:amd64. 72s Preparing to unpack .../30-libimagequant0_2.18.0-1build1_amd64.deb ... 72s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 72s Selecting previously unselected package libjpeg-turbo8:amd64. 72s Preparing to unpack .../31-libjpeg-turbo8_2.1.5-4ubuntu2_amd64.deb ... 72s Unpacking libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 72s Selecting previously unselected package libjpeg8:amd64. 72s Preparing to unpack .../32-libjpeg8_8c-2ubuntu11_amd64.deb ... 72s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 72s Selecting previously unselected package liblcms2-2:amd64. 72s Preparing to unpack .../33-liblcms2-2_2.17-1_amd64.deb ... 72s Unpacking liblcms2-2:amd64 (2.17-1) ... 72s Selecting previously unselected package libopenjp2-7:amd64. 72s Preparing to unpack .../34-libopenjp2-7_2.5.3-2.1_amd64.deb ... 72s Unpacking libopenjp2-7:amd64 (2.5.3-2.1) ... 72s Selecting previously unselected package libgraphite2-3:amd64. 72s Preparing to unpack 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... 72s Selecting previously unselected package libwebp7:amd64. 72s Preparing to unpack .../41-libwebp7_1.5.0-0.1_amd64.deb ... 72s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 72s Selecting previously unselected package libtiff6:amd64. 72s Preparing to unpack .../42-libtiff6_4.7.0-3ubuntu3_amd64.deb ... 72s Unpacking libtiff6:amd64 (4.7.0-3ubuntu3) ... 72s Selecting previously unselected package libwebpdemux2:amd64. 72s Preparing to unpack .../43-libwebpdemux2_1.5.0-0.1_amd64.deb ... 72s Unpacking libwebpdemux2:amd64 (1.5.0-0.1) ... 72s Selecting previously unselected package libwebpmux3:amd64. 72s Preparing to unpack .../44-libwebpmux3_1.5.0-0.1_amd64.deb ... 72s Unpacking libwebpmux3:amd64 (1.5.0-0.1) ... 72s Selecting previously unselected package python3-pil:amd64. 72s Preparing to unpack .../45-python3-pil_12.0.0-1ubuntu1_amd64.deb ... 72s Unpacking python3-pil:amd64 (12.0.0-1ubuntu1) ... 72s Selecting previously unselected package libpixman-1-0:amd64. 72s Preparing to unpack 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python3-freetype (2.5.1-2) ... 72s Selecting previously unselected package python3-rlpycairo. 72s Preparing to unpack .../52-python3-rlpycairo_0.3.0-4_all.deb ... 72s Unpacking python3-rlpycairo (0.3.0-4) ... 72s Selecting previously unselected package python3-reportlab. 72s Preparing to unpack .../53-python3-reportlab_4.4.5-1_all.deb ... 72s Unpacking python3-reportlab (4.4.5-1) ... 72s Selecting previously unselected package sgml-base. 72s Preparing to unpack .../54-sgml-base_1.31+nmu1_all.deb ... 72s Unpacking sgml-base (1.31+nmu1) ... 72s Selecting previously unselected package xml-core. 72s Preparing to unpack .../55-xml-core_0.19_all.deb ... 72s Unpacking xml-core (0.19) ... 72s Selecting previously unselected package w3c-sgml-lib. 72s Preparing to unpack .../56-w3c-sgml-lib_1.3-3_all.deb ... 72s Unpacking w3c-sgml-lib (1.3-3) ... 72s Selecting previously unselected package python3-biopython. 72s Preparing to unpack .../57-python3-biopython_1.86+dfsg-1_amd64.deb ... 72s Unpacking python3-biopython (1.86+dfsg-1) ... 72s Selecting previously unselected package python3-soupsieve. 72s Preparing to unpack .../58-python3-soupsieve_2.7-2_all.deb ... 72s Unpacking python3-soupsieve (2.7-2) ... 72s Selecting previously unselected package python3-bs4. 72s Preparing to unpack .../59-python3-bs4_4.14.2-1_all.deb ... 72s Unpacking python3-bs4 (4.14.2-1) ... 72s Selecting previously unselected package python3-dendropy. 72s Preparing to unpack .../60-python3-dendropy_4.6.1-2_all.deb ... 72s Unpacking python3-dendropy (4.6.1-2) ... 72s Selecting previously unselected package fonts-lyx. 72s Preparing to unpack .../61-fonts-lyx_2.4.4-2_all.deb ... 72s Unpacking fonts-lyx (2.4.4-2) ... 72s Selecting previously unselected package python-matplotlib-data. 72s Preparing to unpack .../62-python-matplotlib-data_3.10.7+dfsg1-1_all.deb ... 72s Unpacking python-matplotlib-data (3.10.7+dfsg1-1) ... 72s Selecting previously unselected package python3-contourpy. 72s Preparing to unpack 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previously unselected package python3-lxml:amd64. 72s Preparing to unpack .../69-python3-lxml_6.0.2-1_amd64.deb ... 72s Unpacking python3-lxml:amd64 (6.0.2-1) ... 72s Selecting previously unselected package python3-lz4. 72s Preparing to unpack .../70-python3-lz4_4.4.4+dfsg-3_amd64.deb ... 72s Unpacking python3-lz4 (4.4.4+dfsg-3) ... 72s Selecting previously unselected package python3-munkres. 72s Preparing to unpack .../71-python3-munkres_1.1.4-3_all.deb ... 72s Unpacking python3-munkres (1.1.4-3) ... 72s Selecting previously unselected package python3-mpmath. 72s Preparing to unpack .../72-python3-mpmath_1.3.0-2_all.deb ... 72s Unpacking python3-mpmath (1.3.0-2) ... 72s Selecting previously unselected package python3-sympy. 72s Preparing to unpack .../73-python3-sympy_1.14.0-2_all.deb ... 72s Unpacking python3-sympy (1.14.0-2) ... 72s Selecting previously unselected package python3-ufolib2. 72s Preparing to unpack .../74-python3-ufolib2_0.17.1+dfsg1-1_all.deb ... 72s Unpacking python3-ufolib2 (0.17.1+dfsg1-1) ... 72s Selecting previously unselected package python3-unicodedata2. 72s Preparing to unpack .../75-python3-unicodedata2_16.0.0+ds-1build1_amd64.deb ... 72s Unpacking python3-unicodedata2 (16.0.0+ds-1build1) ... 72s Selecting previously unselected package libzopfli1. 72s Preparing to unpack .../76-libzopfli1_1.0.3-3_amd64.deb ... 72s Unpacking libzopfli1 (1.0.3-3) ... 72s Selecting previously unselected package python3-zopfli. 72s Preparing to unpack .../77-python3-zopfli_0.4.0-1_amd64.deb ... 72s Unpacking python3-zopfli (0.4.0-1) ... 72s Selecting previously unselected package unicode-data. 72s Preparing to unpack .../78-unicode-data_16.0.0-1_all.deb ... 72s Unpacking unicode-data (16.0.0-1) ... 73s Selecting previously unselected package python3-fonttools. 73s Preparing to unpack .../79-python3-fonttools_4.57.0-3_amd64.deb ... 73s Unpacking python3-fonttools (4.57.0-3) ... 73s Selecting previously unselected package python3-kiwisolver. 73s Preparing 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... 73s Selecting previously unselected package libfml0:amd64. 73s Preparing to unpack .../86-libfml0_0.1+git20221215.85f159e-1_amd64.deb ... 73s Unpacking libfml0:amd64 (0.1+git20221215.85f159e-1) ... 73s Selecting previously unselected package libminimap0:amd64. 73s Preparing to unpack .../87-libminimap0_0.2-8_amd64.deb ... 73s Unpacking libminimap0:amd64 (0.2-8) ... 73s Selecting previously unselected package bowtie2. 73s Preparing to unpack .../88-bowtie2_2.5.4-1_amd64.deb ... 73s Unpacking bowtie2 (2.5.4-1) ... 73s Selecting previously unselected package cd-hit. 73s Preparing to unpack .../89-cd-hit_4.8.1-4build1_amd64.deb ... 73s Unpacking cd-hit (4.8.1-4build1) ... 73s Selecting previously unselected package libcapnp-1.1.0:amd64. 73s Preparing to unpack .../90-libcapnp-1.1.0_1.1.0-2.1_amd64.deb ... 73s Unpacking libcapnp-1.1.0:amd64 (1.1.0-2.1) ... 73s Selecting previously unselected package libgslcblas0:amd64. 73s Preparing to unpack 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libpixman-1-0:amd64 (0.46.4-1) ... 73s Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... 73s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 73s Setting up libxrender1:amd64 (1:0.9.12-1) ... 73s Setting up libgslcblas0:amd64 (2.8+dfsg-5.1ubuntu1) ... 73s Setting up libmurmurhash2:amd64 (1.6-1) ... 73s Setting up python3-lz4 (4.4.4+dfsg-3) ... 73s Setting up libxcb-render0:amd64 (1.17.0-2build1) ... 73s Setting up python3-charset-normalizer (3.4.4-1) ... 73s Setting up python3-unicodedata2 (16.0.0+ds-1build1) ... 73s Setting up fonts-lyx (2.4.4-2) ... 73s Setting up x11-common (1:7.7+24ubuntu1) ... 74s Setting up libdeflate0:amd64 (1.23-2) ... 74s Setting up libqhull-r8.0:amd64 (2020.2-7) ... 74s Setting up libxcb-shm0:amd64 (1.17.0-2build1) ... 74s Setting up libgomp1:amd64 (15.2.0-9ubuntu1) ... 74s Setting up python3-freetype (2.5.1-2) ... 74s Setting up libfml0:amd64 (0.1+git20221215.85f159e-1) ... 74s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 74s Setting up python3-platformdirs (4.4.0-1) ... 74s Setting up bowtie2 (2.5.4-1) ... 74s Setting up python3-fs (2.4.16-9ubuntu1) ... 74s Setting up unicode-data (16.0.0-1) ... 74s Setting up libminimap0:amd64 (0.2-8) ... 74s Setting up libfontenc1:amd64 (1:1.1.8-1build2) ... 74s Setting up libblas3:amd64 (3.12.1-7) ... 74s 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 74s Setting up libzopfli1 (1.0.3-3) ... 74s Setting up python3-brotli (1.1.0-2build6) ... 74s Setting up xfonts-encodings (1:1.0.5-0ubuntu3) ... 74s Setting up python3-cycler (0.12.1-2) ... 74s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 74s Setting up fonts-dejavu-mono (2.37-8) ... 74s Setting up python3-kiwisolver (1.4.10~rc0-1) ... 74s Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 74s Setting up libtcl8.6:amd64 (8.6.17+dfsg-1) ... 74s Setting up fonts-dejavu-core (2.37-8) ... 74s Setting up libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 74s Setting up libgfortran5:amd64 (15.2.0-9ubuntu1) ... 74s Setting up libwebp7:amd64 (1.5.0-0.1) ... 74s Setting up libxslt1.1:amd64 (1.1.43-0.3) ... 74s Setting up mummer (3.23+dfsg-8) ... 74s Setting up python3-munkres (1.1.4-3) ... 74s Setting up libhts3t64:amd64 (1.22.1+ds2-1) ... 74s Setting up libopenjp2-7:amd64 (2.5.3-2.1) ... 74s Setting up libharfbuzz0b:amd64 (12.1.0-1) ... 74s Setting up sgml-base (1.31+nmu1) ... 74s Setting up libcapnp-1.1.0:amd64 (1.1.0-2.1) ... 74s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 74s Setting up python3-mpmath (1.3.0-2) ... 74s Setting up libgsl28:amd64 (2.8+dfsg-5.1ubuntu1) ... 74s Setting up python-matplotlib-data (3.10.7+dfsg1-1) ... 74s Setting up libwebpmux3:amd64 (1.5.0-0.1) ... 74s Setting up python3-dendropy (4.6.1-2) ... 75s Setting up python3-soupsieve (2.7-2) ... 75s Setting up cd-hit (4.8.1-4build1) ... 75s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 75s Setting up python3-sympy (1.14.0-2) ... 78s Setting up liblapack3:amd64 (3.12.1-7) ... 78s 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 78s Setting up python3-pysam (0.23.3+ds-2) ... 78s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ... 78s Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... 78s Setting up xfonts-utils (1:7.7+7) ... 78s Setting up python3-bs4 (4.14.2-1) ... 78s Setting up python3-zopfli (0.4.0-1) ... 78s Setting up samtools (1.22.1-1) ... 78s Setting up libraqm0:amd64 (0.10.3-1) ... 78s Setting up mash (2.3+dfsg-6build2) ... 78s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 79s Setting up python3-lxml:amd64 (6.0.2-1) ... 80s Setting up libtiff6:amd64 (4.7.0-3ubuntu3) ... 80s Setting up xml-core (0.19) ... 80s Setting up python3-contourpy (1.3.3-1) ... 80s Setting up libfontconfig1:amd64 (2.15.0-2.3ubuntu1) ... 80s Setting up libxft2:amd64 (2.3.6-1build1) ... 80s Setting up libtk8.6:amd64 (8.6.17-1) ... 80s Setting up fastaq (3.17.0-9) ... 80s Setting up fonts-urw-base35 (20200910-8) ... 80s Setting up libcairo2:amd64 (1.18.4-1build1) ... 80s Setting up python3.13-tk (3.13.9-1) ... 80s Setting up python3-pymummer (0.12.0-1) ... 80s Setting up python3-pil:amd64 (12.0.0-1ubuntu1) ... 80s Setting up python3.14-tk (3.14.0-4) ... 80s Setting up python3-cairo (1.27.0-2build1) ... 80s Setting up python3-tk (3.13.9-2) ... 80s Setting up python3-pil.imagetk:amd64 (12.0.0-1ubuntu1) ... 80s Setting up python3-rlpycairo (0.3.0-4) ... 80s Setting up python3-reportlab (4.4.5-1) ... 81s Setting up python3-fonttools (4.57.0-3) ... 81s Setting up python3-ufolib2 (0.17.1+dfsg1-1) ... 81s Setting up python3-matplotlib (3.10.7+dfsg1-1) ... 82s Processing triggers for libc-bin (2.42-2ubuntu2) ... 82s Processing triggers for man-db (2.13.1-1) ... 83s Processing triggers for sgml-base (1.31+nmu1) ... 83s Setting up w3c-sgml-lib (1.3-3) ... 98s Setting up python3-biopython (1.86+dfsg-1) ... 99s Setting up ariba (2.14.7+ds-7syncable1build1) ... 100s autopkgtest [18:31:52]: test test-example: [----------------------- 101s ARIBA version: 2.14.6 101s 101s External dependencies: 101s bowtie2 2.5.4 /usr/bin/bowtie2 101s cdhit 4.8.1 /usr/bin/cd-hit-est 101s nucmer 3.1 /usr/bin/nucmer 101s 101s External dependencies OK: True 101s 101s Python version: 101s 3.13.9 (main, Oct 15 2025, 14:56:22) [GCC 15.2.0] 101s 101s Python packages: 101s ariba 2.14.6 /usr/lib/python3/dist-packages/ariba/__init__.py 101s bs4 4.14.2 /usr/lib/python3/dist-packages/bs4/__init__.py 101s dendropy 4.6.1 /usr/lib/python3/dist-packages/dendropy/__init__.py 101s pyfastaq 3.17.0 /usr/lib/python3/dist-packages/pyfastaq/__init__.py 101s pymummer 0.12.0 /usr/lib/python3/dist-packages/pymummer/__init__.py 101s pysam 0.23.3 /usr/lib/python3/dist-packages/pysam/__init__.py 101s 101s Python packages OK: True 101s 101s Everything looks OK: True 101s 101s Loading and checking input data 101s 101s Running cdhit 101s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.F8LIhMPYx4/foo/PREPAREREF/02.cdhit.noncoding.fa -o /tmp/tmp.F8LIhMPYx4/foo/tmp.run_cd-hit.59ts3ghg/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 101s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.F8LIhMPYx4/foo/PREPAREREF/02.cdhit.noncoding.varonly.fa -o /tmp/tmp.F8LIhMPYx4/foo/tmp.run_cd-hit.c7e3h_y7/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 101s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.F8LIhMPYx4/foo/PREPAREREF/02.cdhit.gene.fa -o /tmp/tmp.F8LIhMPYx4/foo/tmp.run_cd-hit.dz1ax8ud/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 102s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.F8LIhMPYx4/foo/PREPAREREF/02.cdhit.gene.varonly.fa -o /tmp/tmp.F8LIhMPYx4/foo/tmp.run_cd-hit.kfq9mfhi/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 102s 102s Writing clusters to file. 10 in total 102s Found reads file: reads_1.fq 102s Found reads file: reads_2.fq 102s ARIBA version: 2.14.6 102s 102s External dependencies: 102s bowtie2 2.5.4 /usr/bin/bowtie2 102s cdhit 4.8.1 /usr/bin/cd-hit-est 102s nucmer 3.1 /usr/bin/nucmer 102s 102s External dependencies OK: True 102s 102s Python version: 102s 3.13.9 (main, Oct 15 2025, 14:56:22) [GCC 15.2.0] 102s 102s Python packages: 102s ariba 2.14.6 /usr/lib/python3/dist-packages/ariba/__init__.py 102s bs4 4.14.2 /usr/lib/python3/dist-packages/bs4/__init__.py 102s dendropy 4.6.1 /usr/lib/python3/dist-packages/dendropy/__init__.py 102s pyfastaq 3.17.0 /usr/lib/python3/dist-packages/pyfastaq/__init__.py 102s pymummer 0.12.0 /usr/lib/python3/dist-packages/pymummer/__init__.py 102s pysam 0.23.3 /usr/lib/python3/dist-packages/pysam/__init__.py 102s 102s Python packages OK: True 102s 102s Everything looks OK: True 102s Temporary directory: /tmp/tmp.F8LIhMPYx4/foo/OUT/ariba.tmp.ss_fmzap 102s ______________________ Mapping reads to clustered genes _______________________ 102s Finished mapping 102s 102s _____________________________ Generating clusters _____________________________ 102s syscall: sort -k1,1 -k 2,2n /tmp/tmp.F8LIhMPYx4/foo/OUT/minimap.reads > /tmp/tmp.F8LIhMPYx4/foo/OUT/read_store 102s Compressing file /tmp/tmp.F8LIhMPYx4/foo/OUT/read_store 102s Found 51 proper read pairs from minimap 102s Total clusters to perform local assemblies: 9 102s 102s Insert size information from reads mapped to reference genes: 102s Insert size: 185.0 102s Insert sspace sd: 0.27 102s Max insert: 220.55 102s 102s ___________________________ Assembling each cluster ___________________________ 102s Will run 1 cluster(s) in parallel 102s Not constructing cluster cluster because it only has 2 reads (1 of 9) 102s Constructing cluster cluster_1 (2 of 9) 102s Constructing cluster cluster_2 (3 of 9) 102s Constructing cluster cluster_3 (4 of 9) 102s Constructing cluster cluster_4 (5 of 9) 102s Constructing cluster gene (6 of 9) 102s Constructing cluster gene_1 (7 of 9) 102s Constructing cluster noncoding (8 of 9) 102s Constructing cluster noncoding_1 (9 of 9) 102s Start running cluster cluster_1 in directory /tmp/tmp.F8LIhMPYx4/foo/OUT/ariba.tmp.ss_fmzap/cluster_1 103s cluster_1 detected 1 threads available to it 103s cluster_1 reported completion 103s Finished running cluster cluster_1 in directory /tmp/tmp.F8LIhMPYx4/foo/OUT/ariba.tmp.ss_fmzap/cluster_1 103s Deleting cluster dir /tmp/tmp.F8LIhMPYx4/foo/OUT/ariba.tmp.ss_fmzap/cluster_1 103s Start running cluster cluster_2 in directory /tmp/tmp.F8LIhMPYx4/foo/OUT/ariba.tmp.ss_fmzap/cluster_2 104s cluster_2 detected 1 threads available to it 104s cluster_2 reported completion 104s Finished running cluster cluster_2 in directory /tmp/tmp.F8LIhMPYx4/foo/OUT/ariba.tmp.ss_fmzap/cluster_2 104s Deleting cluster dir /tmp/tmp.F8LIhMPYx4/foo/OUT/ariba.tmp.ss_fmzap/cluster_2 104s Start running cluster cluster_3 in directory /tmp/tmp.F8LIhMPYx4/foo/OUT/ariba.tmp.ss_fmzap/cluster_3 105s cluster_3 detected 1 threads available to it 105s cluster_3 reported completion 105s Finished running cluster cluster_3 in directory /tmp/tmp.F8LIhMPYx4/foo/OUT/ariba.tmp.ss_fmzap/cluster_3 105s Deleting cluster dir /tmp/tmp.F8LIhMPYx4/foo/OUT/ariba.tmp.ss_fmzap/cluster_3 105s Start running cluster cluster_4 in directory /tmp/tmp.F8LIhMPYx4/foo/OUT/ariba.tmp.ss_fmzap/cluster_4 106s cluster_4 detected 1 threads available to it 106s cluster_4 reported completion 106s Finished running cluster cluster_4 in directory /tmp/tmp.F8LIhMPYx4/foo/OUT/ariba.tmp.ss_fmzap/cluster_4 106s Deleting cluster dir /tmp/tmp.F8LIhMPYx4/foo/OUT/ariba.tmp.ss_fmzap/cluster_4 106s Start running cluster gene in directory /tmp/tmp.F8LIhMPYx4/foo/OUT/ariba.tmp.ss_fmzap/gene 107s gene detected 1 threads available to it 107s gene reported completion 107s Finished running cluster gene in directory /tmp/tmp.F8LIhMPYx4/foo/OUT/ariba.tmp.ss_fmzap/gene 107s Deleting cluster dir /tmp/tmp.F8LIhMPYx4/foo/OUT/ariba.tmp.ss_fmzap/gene 107s Start running cluster gene_1 in directory /tmp/tmp.F8LIhMPYx4/foo/OUT/ariba.tmp.ss_fmzap/gene_1 108s gene_1 detected 1 threads available to it 108s gene_1 reported completion 108s Finished running cluster gene_1 in directory /tmp/tmp.F8LIhMPYx4/foo/OUT/ariba.tmp.ss_fmzap/gene_1 108s Deleting cluster dir /tmp/tmp.F8LIhMPYx4/foo/OUT/ariba.tmp.ss_fmzap/gene_1 108s Start running cluster noncoding in directory /tmp/tmp.F8LIhMPYx4/foo/OUT/ariba.tmp.ss_fmzap/noncoding 109s noncoding detected 1 threads available to it 109s noncoding reported completion 109s Finished running cluster noncoding in directory /tmp/tmp.F8LIhMPYx4/foo/OUT/ariba.tmp.ss_fmzap/noncoding 109s Deleting cluster dir /tmp/tmp.F8LIhMPYx4/foo/OUT/ariba.tmp.ss_fmzap/noncoding 109s Start running cluster noncoding_1 in directory /tmp/tmp.F8LIhMPYx4/foo/OUT/ariba.tmp.ss_fmzap/noncoding_1 111s noncoding_1 detected 1 threads available to it 111s noncoding_1 reported completion 111s Finished running cluster noncoding_1 in directory /tmp/tmp.F8LIhMPYx4/foo/OUT/ariba.tmp.ss_fmzap/noncoding_1 111s Deleting cluster dir /tmp/tmp.F8LIhMPYx4/foo/OUT/ariba.tmp.ss_fmzap/noncoding_1 111s Final value of remaining_clusters counter: Value('l', 0) 111s Finished assembling clusters 111s 111s _______________________________ Writing reports _______________________________ 111s Making /tmp/tmp.F8LIhMPYx4/foo/OUT/debug.report.tsv 111s Making /tmp/tmp.F8LIhMPYx4/foo/OUT/report.tsv 111s 111s ____________________ Writing fasta of assembled sequences _____________________ 111s /tmp/tmp.F8LIhMPYx4/foo/OUT/assembled_seqs.fa.gz and /tmp/tmp.F8LIhMPYx4/foo/OUT/assembled_genes.fa.gz 111s 111s __________________________ Catting cluster log files __________________________ 111s Writing file /tmp/tmp.F8LIhMPYx4/foo/OUT/log.clusters.gz 111s 111s _______________________________ Cleaning files ________________________________ 111s Deleting Logs directory /tmp/tmp.F8LIhMPYx4/foo/OUT/Logs 111s Deleting reads store files /tmp/tmp.F8LIhMPYx4/foo/OUT/read_store.gz[.tbi] 111s 111s All done! 111s 111s Running ARIBA on test data... 111s ------------------------------------------------------------------------------- 111s |=============================================================================| 111s | Preparing input data | 111s |=============================================================================| 111s ------------------------------------------------------------------------------- 111s Made output directory ./foo. Copying test data files into it: 111s copied ref_seqs.fa 111s copied metadata.tsv 111s copied reads_1.fq 111s copied reads_2.fq 111s ------------------------------------------------------------------------------- 111s |=============================================================================| 111s | Try running ariba prepareref | 111s |=============================================================================| 111s ------------------------------------------------------------------------------- 111s 111s Running ariba prepareref with: 111s /usr/bin/ariba prepareref --verbose -f ref_seqs.fa -m metadata.tsv --threads 1 PREPAREREF 111s 111s 111s ariba prepareref finished OK 111s ------------------------------------------------------------------------------- 111s |=============================================================================| 111s | Try running ariba run | 111s |=============================================================================| 111s ------------------------------------------------------------------------------- 111s 111s Running ARIBA with: 111s /usr/bin/ariba run --verbose --threads 1 PREPAREREF reads_1.fq reads_2.fq OUT 111s 111s 111s ariba run finished OK 111s Finished run on test data OK 111s autopkgtest [18:32:03]: test test-example: -----------------------] 111s test-example PASS 111s autopkgtest [18:32:03]: test test-example: - - - - - - - - - - results - - - - - - - - - - 112s autopkgtest [18:32:04]: @@@@@@@@@@@@@@@@@@@@ summary 112s test-example PASS