0s autopkgtest [13:50:48]: starting date and time: 2025-12-04 13:50:48+0000 0s autopkgtest [13:50:48]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [13:50:48]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.flehi785/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-3.secgroup --name adt-resolute-arm64-ariba-20251204-135048-juju-7f2275-prod-proposed-migration-environment-2-069b824e-fb3b-41ac-a922-5b619da1d27d --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-arm64-ariba-20251204-135048-juju-7f2275-prod-proposed-migration-environment-2-069b824e-fb3b-41ac-a922-5b619da1d27d from image adt/ubuntu-resolute-arm64-server-20251204.img (UUID d10d485b-270b-4b77-bdc2-f40c1cd474cf)... 64s autopkgtest [13:51:52]: testbed dpkg architecture: arm64 65s autopkgtest [13:51:53]: testbed apt version: 3.1.12 65s autopkgtest [13:51:53]: @@@@@@@@@@@@@@@@@@@@ test bed setup 65s autopkgtest [13:51:53]: testbed release detected to be: None 66s autopkgtest [13:51:54]: updating testbed package index (apt update) 66s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 67s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 67s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 67s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 67s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [935 kB] 68s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [23.1 kB] 68s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [156 kB] 68s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [219 kB] 68s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [6632 B] 68s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [120 B] 68s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [727 kB] 68s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [20.6 kB] 68s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [8768 B] 68s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [644 B] 71s Fetched 2221 kB in 2s (1049 kB/s) 72s Reading package lists... 73s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 73s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 74s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 74s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 74s Reading package lists... 74s Reading package lists... 75s Building dependency tree... 75s Reading state information... 75s Calculating upgrade... 75s The following packages will be upgraded: 75s libpython3-stdlib python3 python3-gdbm python3-minimal 76s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 76s Need to get 72.9 kB of archives. 76s After this operation, 2048 B of additional disk space will be used. 76s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-minimal arm64 3.13.9-2 [28.1 kB] 76s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3 arm64 3.13.9-2 [23.0 kB] 76s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libpython3-stdlib arm64 3.13.9-2 [10.8 kB] 76s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-gdbm arm64 3.13.9-2 [11.0 kB] 76s dpkg-preconfigure: unable to re-open stdin: No such file or directory 76s Fetched 72.9 kB in 0s (197 kB/s) 76s (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 ... 88300 files and directories currently installed.) 76s Preparing to unpack .../python3-minimal_3.13.9-2_arm64.deb ... 76s Unpacking python3-minimal (3.13.9-2) over (3.13.7-1) ... 76s Setting up python3-minimal (3.13.9-2) ... 77s (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 ... 88300 files and directories currently installed.) 77s Preparing to unpack .../python3_3.13.9-2_arm64.deb ... 77s running python pre-rtupdate hooks for python3.13... 77s Unpacking python3 (3.13.9-2) over (3.13.7-1) ... 77s Preparing to unpack .../libpython3-stdlib_3.13.9-2_arm64.deb ... 77s Unpacking libpython3-stdlib:arm64 (3.13.9-2) over (3.13.7-1) ... 77s Preparing to unpack .../python3-gdbm_3.13.9-2_arm64.deb ... 77s Unpacking python3-gdbm (3.13.9-2) over (3.13.9-1) ... 77s Setting up python3-gdbm (3.13.9-2) ... 77s Setting up libpython3-stdlib:arm64 (3.13.9-2) ... 77s Setting up python3 (3.13.9-2) ... 77s running python rtupdate hooks for python3.13... 77s running python post-rtupdate hooks for python3.13... 77s Processing triggers for man-db (2.13.1-1) ... 78s autopkgtest [13:52:06]: upgrading testbed (apt dist-upgrade and autopurge) 78s Reading package lists... 78s Building dependency tree... 78s Reading state information... 79s Calculating upgrade... 79s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 79s Reading package lists... 80s Building dependency tree... 80s Reading state information... 80s Solving dependencies... 80s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 83s autopkgtest [13:52:11]: testbed running kernel: Linux 6.17.0-6-generic #6-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 7 14:22:06 UTC 2025 83s autopkgtest [13:52:11]: @@@@@@@@@@@@@@@@@@@@ apt-source ariba 88s Get:1 http://ftpmaster.internal/ubuntu resolute/universe ariba 2.14.7+ds-7syncable1build1 (dsc) [2430 B] 88s Get:2 http://ftpmaster.internal/ubuntu resolute/universe ariba 2.14.7+ds-7syncable1build1 (tar) [1920 kB] 88s Get:3 http://ftpmaster.internal/ubuntu resolute/universe ariba 2.14.7+ds-7syncable1build1 (diff) [11.9 kB] 88s gpgv: Signature made Tue Oct 21 17:40:02 2025 UTC 88s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 88s gpgv: Can't check signature: No public key 88s dpkg-source: warning: cannot verify inline signature for ./ariba_2.14.7+ds-7syncable1build1.dsc: no acceptable signature found 88s autopkgtest [13:52:16]: testing package ariba version 2.14.7+ds-7syncable1build1 88s autopkgtest [13:52:16]: build not needed 94s autopkgtest [13:52:22]: test test-example: preparing testbed 95s Reading package lists... 96s Building dependency tree... 96s Reading state information... 96s Solving dependencies... 97s The following NEW packages will be installed: 97s ariba bowtie2 cd-hit fastaq fontconfig-config fonts-dejavu-core 97s fonts-dejavu-mono fonts-lyx fonts-urw-base35 libblas3 libcairo2 97s libcapnp-1.1.0 libdeflate0 libfml0 libfontconfig1 libfontenc1 libgfortran5 97s libgomp1 libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b libhts3t64 97s libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 97s liblcms2-2 liblerc4 libminimap0 libmurmurhash2 libopenjp2-7 libpixman-1-0 97s libqhull-r8.0 libraqm0 libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 97s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 libxrender1 97s libxslt1.1 libxss1 libzopfli1 mash mummer python-matplotlib-data 97s python3-biopython python3-brotli python3-bs4 python3-cairo 97s python3-charset-normalizer python3-contourpy python3-cycler python3-dendropy 97s python3-fonttools python3-freetype python3-fs python3-kiwisolver 97s python3-lxml python3-lz4 python3-matplotlib python3-mpmath python3-munkres 97s python3-numpy python3-numpy-dev python3-pil python3-pil.imagetk 97s python3-platformdirs python3-pymummer python3-pysam python3-reportlab 97s python3-rlpycairo python3-soupsieve python3-sympy python3-tk python3-ufolib2 97s python3-unicodedata2 python3-zopfli python3.13-tk python3.14-tk samtools 97s sgml-base unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils 97s xml-core 98s 0 upgraded, 96 newly installed, 0 to remove and 0 not upgraded. 98s Need to get 82.5 MB of archives. 98s After this operation, 350 MB of additional disk space will be used. 98s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy-dev arm64 1:2.2.4+ds-1ubuntu1 [146 kB] 98s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-7 [181 kB] 98s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-9ubuntu1 [450 kB] 99s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-7 [2300 kB] 100s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy arm64 1:2.2.4+ds-1ubuntu1 [3986 kB] 101s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB] 101s Get:7 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhtscodecs2 arm64 1.6.1-2 [82.7 kB] 101s Get:8 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhts3t64 arm64 1.22.1+ds2-1 [442 kB] 101s Get:9 http://ftpmaster.internal/ubuntu resolute/universe arm64 samtools arm64 1.22.1-1 [631 kB] 101s Get:10 http://ftpmaster.internal/ubuntu resolute/universe arm64 fastaq all 3.17.0-9 [48.2 kB] 101s Get:11 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-charset-normalizer arm64 3.4.4-1 [164 kB] 101s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 libtcl8.6 arm64 8.6.17+dfsg-1 [1024 kB] 102s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 102s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 102s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontenc1 arm64 1:1.1.8-1build2 [13.9 kB] 102s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 102s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu3 [576 kB] 102s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 102s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 105s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig-config arm64 2.15.0-2.3ubuntu1 [38.1 kB] 105s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontconfig1 arm64 2.15.0-2.3ubuntu1 [144 kB] 105s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 libxrender1 arm64 1:0.9.12-1 [19.5 kB] 105s Get:23 http://ftpmaster.internal/ubuntu resolute/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 105s Get:24 http://ftpmaster.internal/ubuntu resolute/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 105s Get:25 http://ftpmaster.internal/ubuntu resolute/main arm64 libtk8.6 arm64 8.6.17-1 [811 kB] 105s Get:26 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.13-tk arm64 3.13.9-1 [106 kB] 105s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14-tk arm64 3.14.0-4 [107 kB] 106s Get:28 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-tk arm64 3.13.9-2 [11.1 kB] 106s Get:29 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pil.imagetk arm64 12.0.0-1ubuntu1 [9532 B] 106s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-9ubuntu1 [147 kB] 106s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 106s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8 arm64 2.1.5-4ubuntu2 [165 kB] 106s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 106s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 liblcms2-2 arm64 2.17-1 [170 kB] 106s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 libopenjp2-7 arm64 2.5.3-2.1 [179 kB] 106s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 106s Get:37 http://ftpmaster.internal/ubuntu resolute/main arm64 libharfbuzz0b arm64 12.1.0-1 [523 kB] 106s Get:38 http://ftpmaster.internal/ubuntu resolute/main arm64 libraqm0 arm64 0.10.3-1 [15.0 kB] 106s Get:39 http://ftpmaster.internal/ubuntu resolute/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 106s Get:40 http://ftpmaster.internal/ubuntu resolute/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 106s Get:41 http://ftpmaster.internal/ubuntu resolute/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 106s Get:42 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 106s Get:43 http://ftpmaster.internal/ubuntu resolute/main arm64 libtiff6 arm64 4.7.0-3ubuntu3 [196 kB] 106s Get:44 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [12.5 kB] 106s Get:45 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebpmux3 arm64 1.5.0-0.1 [25.4 kB] 106s Get:46 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-pil arm64 12.0.0-1ubuntu1 [486 kB] 106s Get:47 http://ftpmaster.internal/ubuntu resolute/main arm64 libpixman-1-0 arm64 0.46.4-1 [204 kB] 106s Get:48 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-render0 arm64 1.17.0-2build1 [18.1 kB] 106s Get:49 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-shm0 arm64 1.17.0-2build1 [6234 B] 106s Get:50 http://ftpmaster.internal/ubuntu resolute/main arm64 libcairo2 arm64 1.18.4-1build1 [592 kB] 106s Get:51 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-cairo arm64 1.27.0-2build1 [141 kB] 106s Get:52 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-freetype all 2.5.1-2 [92.2 kB] 106s Get:53 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-rlpycairo all 0.3.0-4 [9332 B] 106s Get:54 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-reportlab all 4.4.5-1 [1148 kB] 107s Get:55 http://ftpmaster.internal/ubuntu resolute/main arm64 sgml-base all 1.31+nmu1 [11.0 kB] 107s Get:56 http://ftpmaster.internal/ubuntu resolute/main arm64 xml-core all 0.19 [20.3 kB] 107s Get:57 http://ftpmaster.internal/ubuntu resolute/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 107s Get:58 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-biopython arm64 1.86+dfsg-1 [1675 kB] 107s Get:59 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-soupsieve all 2.7-2 [33.6 kB] 107s Get:60 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-bs4 all 4.14.2-1 [82.8 kB] 107s Get:61 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-dendropy all 4.6.1-2 [278 kB] 107s Get:62 http://ftpmaster.internal/ubuntu resolute/universe arm64 fonts-lyx all 2.4.4-2 [171 kB] 107s Get:63 http://ftpmaster.internal/ubuntu resolute/universe arm64 python-matplotlib-data all 3.10.7+dfsg1-1 [2930 kB] 108s Get:64 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-contourpy arm64 1.3.3-1 [245 kB] 108s Get:65 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-cycler all 0.12.1-2 [9850 B] 108s Get:66 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-brotli arm64 1.1.0-2build6 [343 kB] 108s Get:67 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-platformdirs all 4.4.0-1 [16.9 kB] 108s Get:68 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-fs all 2.4.16-9ubuntu1 [91.5 kB] 108s Get:69 http://ftpmaster.internal/ubuntu resolute/main arm64 libxslt1.1 arm64 1.1.43-0.3 [172 kB] 108s Get:70 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-lxml arm64 6.0.2-1 [2155 kB] 109s Get:71 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-lz4 arm64 4.4.4+dfsg-3 [27.6 kB] 109s Get:72 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-munkres all 1.1.4-3 [9236 B] 109s Get:73 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-mpmath all 1.3.0-2 [423 kB] 109s Get:74 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-sympy all 1.14.0-2 [4306 kB] 110s Get:75 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.5 kB] 110s Get:76 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-unicodedata2 arm64 16.0.0+ds-1build1 [398 kB] 110s Get:77 http://ftpmaster.internal/ubuntu resolute/universe arm64 libzopfli1 arm64 1.0.3-3 [108 kB] 110s Get:78 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-zopfli arm64 0.4.0-1 [10.8 kB] 110s Get:79 http://ftpmaster.internal/ubuntu resolute/universe arm64 unicode-data all 16.0.0-1 [9513 kB] 113s Get:80 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-fonttools arm64 4.57.0-3 [1643 kB] 113s Get:81 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-kiwisolver arm64 1.4.10~rc0-1 [60.1 kB] 113s Get:82 http://ftpmaster.internal/ubuntu resolute/universe arm64 libqhull-r8.0 arm64 2020.2-7 [190 kB] 113s Get:83 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-matplotlib arm64 3.10.7+dfsg1-1 [17.1 MB] 118s Get:84 http://ftpmaster.internal/ubuntu resolute/universe arm64 mummer arm64 3.23+dfsg-8 [673 kB] 118s Get:85 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pymummer all 0.12.0-1 [13.3 kB] 118s Get:86 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pysam arm64 0.23.3+ds-2 [4348 kB] 120s Get:87 http://ftpmaster.internal/ubuntu resolute/universe arm64 libfml0 arm64 0.1+git20221215.85f159e-1 [74.4 kB] 120s Get:88 http://ftpmaster.internal/ubuntu resolute/universe arm64 libminimap0 arm64 0.2-8 [22.6 kB] 120s Get:89 http://ftpmaster.internal/ubuntu resolute/universe arm64 bowtie2 arm64 2.5.4-1 [1380 kB] 120s Get:90 http://ftpmaster.internal/ubuntu resolute/universe arm64 cd-hit arm64 4.8.1-4build1 [521 kB] 120s Get:91 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcapnp-1.1.0 arm64 1.1.0-2.1 [1357 kB] 121s Get:92 http://ftpmaster.internal/ubuntu resolute/universe arm64 libgslcblas0 arm64 2.8+dfsg-5.1ubuntu1 [96.3 kB] 121s Get:93 http://ftpmaster.internal/ubuntu resolute/universe arm64 libgsl28 arm64 2.8+dfsg-5.1ubuntu1 [1029 kB] 121s Get:94 http://ftpmaster.internal/ubuntu resolute/universe arm64 libmurmurhash2 arm64 1.6-1 [6098 B] 121s Get:95 http://ftpmaster.internal/ubuntu resolute/universe arm64 mash arm64 2.3+dfsg-6build2 [149 kB] 121s Get:96 http://ftpmaster.internal/ubuntu resolute/universe arm64 ariba arm64 2.14.7+ds-7syncable1build1 [2031 kB] 122s Fetched 82.5 MB in 25s (3368 kB/s) 122s Selecting previously unselected package python3-numpy-dev:arm64. 122s (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 ... 88300 files and directories currently installed.) 122s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 122s Unpacking python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 122s Selecting previously unselected package libblas3:arm64. 122s Preparing to unpack .../01-libblas3_3.12.1-7_arm64.deb ... 122s Unpacking libblas3:arm64 (3.12.1-7) ... 122s Selecting previously unselected package libgfortran5:arm64. 122s Preparing to unpack .../02-libgfortran5_15.2.0-9ubuntu1_arm64.deb ... 122s Unpacking libgfortran5:arm64 (15.2.0-9ubuntu1) ... 122s Selecting previously unselected package liblapack3:arm64. 122s Preparing to unpack .../03-liblapack3_3.12.1-7_arm64.deb ... 122s Unpacking liblapack3:arm64 (3.12.1-7) ... 122s Selecting previously unselected package python3-numpy. 122s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 122s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 122s Selecting previously unselected package libdeflate0:arm64. 122s Preparing to unpack .../05-libdeflate0_1.23-2_arm64.deb ... 122s Unpacking libdeflate0:arm64 (1.23-2) ... 122s Selecting previously unselected package libhtscodecs2:arm64. 122s Preparing to unpack .../06-libhtscodecs2_1.6.1-2_arm64.deb ... 122s Unpacking libhtscodecs2:arm64 (1.6.1-2) ... 123s Selecting previously unselected package libhts3t64:arm64. 123s Preparing to unpack .../07-libhts3t64_1.22.1+ds2-1_arm64.deb ... 123s Unpacking libhts3t64:arm64 (1.22.1+ds2-1) ... 123s Selecting previously unselected package samtools. 123s Preparing to unpack .../08-samtools_1.22.1-1_arm64.deb ... 123s Unpacking samtools (1.22.1-1) ... 123s Selecting previously unselected package fastaq. 123s Preparing to unpack .../09-fastaq_3.17.0-9_all.deb ... 123s Unpacking fastaq (3.17.0-9) ... 123s Selecting previously unselected package python3-charset-normalizer. 123s Preparing to unpack .../10-python3-charset-normalizer_3.4.4-1_arm64.deb ... 123s Unpacking python3-charset-normalizer (3.4.4-1) ... 123s Selecting previously unselected package libtcl8.6:arm64. 123s Preparing to unpack .../11-libtcl8.6_8.6.17+dfsg-1_arm64.deb ... 123s Unpacking libtcl8.6:arm64 (8.6.17+dfsg-1) ... 123s Selecting previously unselected package fonts-dejavu-mono. 123s Preparing to unpack .../12-fonts-dejavu-mono_2.37-8_all.deb ... 123s Unpacking fonts-dejavu-mono (2.37-8) ... 123s Selecting previously unselected package fonts-dejavu-core. 123s Preparing to unpack .../13-fonts-dejavu-core_2.37-8_all.deb ... 123s Unpacking fonts-dejavu-core (2.37-8) ... 123s Selecting previously unselected package libfontenc1:arm64. 123s Preparing to unpack .../14-libfontenc1_1%3a1.1.8-1build2_arm64.deb ... 123s Unpacking libfontenc1:arm64 (1:1.1.8-1build2) ... 123s Selecting previously unselected package x11-common. 123s Preparing to unpack .../15-x11-common_1%3a7.7+24ubuntu1_all.deb ... 123s Unpacking x11-common (1:7.7+24ubuntu1) ... 123s Selecting previously unselected package xfonts-encodings. 123s Preparing to unpack .../16-xfonts-encodings_1%3a1.0.5-0ubuntu3_all.deb ... 123s Unpacking xfonts-encodings (1:1.0.5-0ubuntu3) ... 123s Selecting previously unselected package xfonts-utils. 123s Preparing to unpack .../17-xfonts-utils_1%3a7.7+7_arm64.deb ... 123s Unpacking xfonts-utils (1:7.7+7) ... 123s Selecting previously unselected package fonts-urw-base35. 123s Preparing to unpack .../18-fonts-urw-base35_20200910-8_all.deb ... 123s Unpacking fonts-urw-base35 (20200910-8) ... 123s Selecting previously unselected package fontconfig-config. 123s Preparing to unpack .../19-fontconfig-config_2.15.0-2.3ubuntu1_arm64.deb ... 123s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 123s Selecting previously unselected package libfontconfig1:arm64. 123s Preparing to unpack .../20-libfontconfig1_2.15.0-2.3ubuntu1_arm64.deb ... 123s Unpacking libfontconfig1:arm64 (2.15.0-2.3ubuntu1) ... 123s Selecting previously unselected package libxrender1:arm64. 124s Preparing to unpack .../21-libxrender1_1%3a0.9.12-1_arm64.deb ... 124s Unpacking libxrender1:arm64 (1:0.9.12-1) ... 124s Selecting previously unselected package libxft2:arm64. 124s Preparing to unpack .../22-libxft2_2.3.6-1build1_arm64.deb ... 124s Unpacking libxft2:arm64 (2.3.6-1build1) ... 124s Selecting previously unselected package libxss1:arm64. 124s Preparing to unpack .../23-libxss1_1%3a1.2.3-1build3_arm64.deb ... 124s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 124s Selecting previously unselected package libtk8.6:arm64. 124s Preparing to unpack .../24-libtk8.6_8.6.17-1_arm64.deb ... 124s Unpacking libtk8.6:arm64 (8.6.17-1) ... 124s Selecting previously unselected package python3.13-tk. 124s Preparing to unpack .../25-python3.13-tk_3.13.9-1_arm64.deb ... 124s Unpacking python3.13-tk (3.13.9-1) ... 124s Selecting previously unselected package python3.14-tk. 124s Preparing to unpack .../26-python3.14-tk_3.14.0-4_arm64.deb ... 124s Unpacking python3.14-tk (3.14.0-4) ... 124s Selecting previously unselected package python3-tk. 124s Preparing to unpack .../27-python3-tk_3.13.9-2_arm64.deb ... 124s Unpacking python3-tk (3.13.9-2) ... 124s Selecting previously unselected package python3-pil.imagetk:arm64. 124s Preparing to unpack .../28-python3-pil.imagetk_12.0.0-1ubuntu1_arm64.deb ... 124s Unpacking python3-pil.imagetk:arm64 (12.0.0-1ubuntu1) ... 124s Selecting previously unselected package libgomp1:arm64. 124s Preparing to unpack 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libopenjp2-7:arm64 (2.5.3-2.1) ... 124s Selecting previously unselected package libgraphite2-3:arm64. 124s Preparing to unpack .../35-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 124s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 124s Selecting previously unselected package libharfbuzz0b:arm64. 124s Preparing to unpack .../36-libharfbuzz0b_12.1.0-1_arm64.deb ... 124s Unpacking libharfbuzz0b:arm64 (12.1.0-1) ... 124s Selecting previously unselected package libraqm0:arm64. 124s Preparing to unpack .../37-libraqm0_0.10.3-1_arm64.deb ... 124s Unpacking libraqm0:arm64 (0.10.3-1) ... 124s Selecting previously unselected package libjbig0:arm64. 124s Preparing to unpack .../38-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 124s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 124s Selecting previously unselected package liblerc4:arm64. 124s Preparing to unpack .../39-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 124s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 124s Selecting previously unselected package libsharpyuv0:arm64. 124s Preparing to unpack .../40-libsharpyuv0_1.5.0-0.1_arm64.deb ... 124s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 124s Selecting previously unselected package libwebp7:arm64. 124s Preparing to unpack .../41-libwebp7_1.5.0-0.1_arm64.deb ... 124s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 124s Selecting previously unselected package libtiff6:arm64. 124s Preparing to unpack .../42-libtiff6_4.7.0-3ubuntu3_arm64.deb ... 124s Unpacking libtiff6:arm64 (4.7.0-3ubuntu3) ... 124s Selecting previously unselected package libwebpdemux2:arm64. 124s Preparing to unpack .../43-libwebpdemux2_1.5.0-0.1_arm64.deb ... 124s Unpacking libwebpdemux2:arm64 (1.5.0-0.1) ... 124s Selecting previously unselected package libwebpmux3:arm64. 124s Preparing to unpack .../44-libwebpmux3_1.5.0-0.1_arm64.deb ... 124s Unpacking libwebpmux3:arm64 (1.5.0-0.1) ... 124s Selecting previously unselected package python3-pil:arm64. 125s Preparing to unpack .../45-python3-pil_12.0.0-1ubuntu1_arm64.deb ... 125s Unpacking python3-pil:arm64 (12.0.0-1ubuntu1) ... 125s Selecting previously unselected package libpixman-1-0:arm64. 125s Preparing to unpack .../46-libpixman-1-0_0.46.4-1_arm64.deb ... 125s Unpacking libpixman-1-0:arm64 (0.46.4-1) ... 125s Selecting previously unselected package libxcb-render0:arm64. 125s Preparing to unpack .../47-libxcb-render0_1.17.0-2build1_arm64.deb ... 125s Unpacking libxcb-render0:arm64 (1.17.0-2build1) ... 125s Selecting previously unselected package libxcb-shm0:arm64. 125s Preparing to unpack .../48-libxcb-shm0_1.17.0-2build1_arm64.deb ... 125s Unpacking libxcb-shm0:arm64 (1.17.0-2build1) ... 125s Selecting previously unselected package libcairo2:arm64. 125s Preparing to unpack .../49-libcairo2_1.18.4-1build1_arm64.deb ... 125s Unpacking libcairo2:arm64 (1.18.4-1build1) ... 125s Selecting previously unselected package python3-cairo. 125s Preparing to unpack .../50-python3-cairo_1.27.0-2build1_arm64.deb ... 125s Unpacking python3-cairo (1.27.0-2build1) ... 125s Selecting previously unselected package python3-freetype. 125s Preparing to unpack .../51-python3-freetype_2.5.1-2_all.deb ... 125s Unpacking python3-freetype (2.5.1-2) ... 125s Selecting previously unselected package python3-rlpycairo. 125s Preparing to unpack .../52-python3-rlpycairo_0.3.0-4_all.deb ... 125s Unpacking python3-rlpycairo (0.3.0-4) ... 125s Selecting previously unselected package python3-reportlab. 125s Preparing to unpack .../53-python3-reportlab_4.4.5-1_all.deb ... 125s Unpacking python3-reportlab (4.4.5-1) ... 125s Selecting previously unselected package sgml-base. 125s Preparing to unpack .../54-sgml-base_1.31+nmu1_all.deb ... 125s Unpacking sgml-base (1.31+nmu1) ... 125s Selecting previously unselected package xml-core. 125s Preparing to unpack .../55-xml-core_0.19_all.deb ... 125s Unpacking xml-core (0.19) ... 125s Selecting previously unselected package w3c-sgml-lib. 125s Preparing to unpack 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python-matplotlib-data. 125s Preparing to unpack .../62-python-matplotlib-data_3.10.7+dfsg1-1_all.deb ... 125s Unpacking python-matplotlib-data (3.10.7+dfsg1-1) ... 125s Selecting previously unselected package python3-contourpy. 125s Preparing to unpack .../63-python3-contourpy_1.3.3-1_arm64.deb ... 125s Unpacking python3-contourpy (1.3.3-1) ... 125s Selecting previously unselected package python3-cycler. 125s Preparing to unpack .../64-python3-cycler_0.12.1-2_all.deb ... 125s Unpacking python3-cycler (0.12.1-2) ... 125s Selecting previously unselected package python3-brotli. 125s Preparing to unpack .../65-python3-brotli_1.1.0-2build6_arm64.deb ... 125s Unpacking python3-brotli (1.1.0-2build6) ... 125s Selecting previously unselected package python3-platformdirs. 125s Preparing to unpack .../66-python3-platformdirs_4.4.0-1_all.deb ... 125s Unpacking python3-platformdirs (4.4.0-1) ... 125s Selecting previously unselected package python3-fs. 125s Preparing to unpack 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previously unselected package python3-sympy. 126s Preparing to unpack .../73-python3-sympy_1.14.0-2_all.deb ... 126s Unpacking python3-sympy (1.14.0-2) ... 126s Selecting previously unselected package python3-ufolib2. 126s Preparing to unpack .../74-python3-ufolib2_0.17.1+dfsg1-1_all.deb ... 126s Unpacking python3-ufolib2 (0.17.1+dfsg1-1) ... 126s Selecting previously unselected package python3-unicodedata2. 126s Preparing to unpack .../75-python3-unicodedata2_16.0.0+ds-1build1_arm64.deb ... 126s Unpacking python3-unicodedata2 (16.0.0+ds-1build1) ... 126s Selecting previously unselected package libzopfli1. 126s Preparing to unpack .../76-libzopfli1_1.0.3-3_arm64.deb ... 126s Unpacking libzopfli1 (1.0.3-3) ... 126s Selecting previously unselected package python3-zopfli. 126s Preparing to unpack .../77-python3-zopfli_0.4.0-1_arm64.deb ... 126s Unpacking python3-zopfli (0.4.0-1) ... 126s Selecting previously unselected package unicode-data. 126s Preparing to unpack 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(2.3+dfsg-6build2) ... 128s Selecting previously unselected package ariba. 128s Preparing to unpack .../95-ariba_2.14.7+ds-7syncable1build1_arm64.deb ... 128s Unpacking ariba (2.14.7+ds-7syncable1build1) ... 128s Setting up libhtscodecs2:arm64 (1.6.1-2) ... 128s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 128s Setting up liblcms2-2:arm64 (2.17-1) ... 128s Setting up libpixman-1-0:arm64 (0.46.4-1) ... 128s Setting up libsharpyuv0:arm64 (1.5.0-0.1) ... 128s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 128s Setting up libxrender1:arm64 (1:0.9.12-1) ... 128s Setting up libgslcblas0:arm64 (2.8+dfsg-5.1ubuntu1) ... 128s Setting up libmurmurhash2:arm64 (1.6-1) ... 128s Setting up python3-lz4 (4.4.4+dfsg-3) ... 128s Setting up libxcb-render0:arm64 (1.17.0-2build1) ... 128s Setting up python3-charset-normalizer (3.4.4-1) ... 128s Setting up python3-unicodedata2 (16.0.0+ds-1build1) ... 128s Setting up fonts-lyx (2.4.4-2) ... 128s Setting up x11-common (1:7.7+24ubuntu1) ... 128s Setting up libdeflate0:arm64 (1.23-2) ... 128s Setting up libqhull-r8.0:arm64 (2020.2-7) ... 128s Setting up libxcb-shm0:arm64 (1.17.0-2build1) ... 128s Setting up libgomp1:arm64 (15.2.0-9ubuntu1) ... 128s Setting up python3-freetype (2.5.1-2) ... 128s Setting up libfml0:arm64 (0.1+git20221215.85f159e-1) ... 128s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 128s Setting up python3-platformdirs (4.4.0-1) ... 129s Setting up bowtie2 (2.5.4-1) ... 129s Setting up python3-fs (2.4.16-9ubuntu1) ... 129s Setting up unicode-data (16.0.0-1) ... 129s Setting up libminimap0:arm64 (0.2-8) ... 129s Setting up libfontenc1:arm64 (1:1.1.8-1build2) ... 129s Setting up libblas3:arm64 (3.12.1-7) ... 129s 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 129s Setting up libzopfli1 (1.0.3-3) ... 129s Setting up python3-brotli (1.1.0-2build6) ... 129s Setting up xfonts-encodings (1:1.0.5-0ubuntu3) ... 129s Setting up python3-cycler (0.12.1-2) ... 129s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 129s Setting up fonts-dejavu-mono (2.37-8) ... 129s Setting up python3-kiwisolver (1.4.10~rc0-1) ... 129s Setting up python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 129s Setting up libtcl8.6:arm64 (8.6.17+dfsg-1) ... 129s Setting up fonts-dejavu-core (2.37-8) ... 129s Setting up libjpeg-turbo8:arm64 (2.1.5-4ubuntu2) ... 129s Setting up libgfortran5:arm64 (15.2.0-9ubuntu1) ... 129s Setting up libwebp7:arm64 (1.5.0-0.1) ... 129s Setting up libxslt1.1:arm64 (1.1.43-0.3) ... 129s Setting up mummer (3.23+dfsg-8) ... 129s Setting up python3-munkres (1.1.4-3) ... 129s Setting up libhts3t64:arm64 (1.22.1+ds2-1) ... 129s Setting up libopenjp2-7:arm64 (2.5.3-2.1) ... 129s Setting up libharfbuzz0b:arm64 (12.1.0-1) ... 129s Setting up sgml-base (1.31+nmu1) ... 129s Setting up libcapnp-1.1.0:arm64 (1.1.0-2.1) ... 129s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 129s Setting up python3-mpmath (1.3.0-2) ... 130s Setting up libgsl28:arm64 (2.8+dfsg-5.1ubuntu1) ... 130s Setting up python-matplotlib-data (3.10.7+dfsg1-1) ... 130s Setting up libwebpmux3:arm64 (1.5.0-0.1) ... 130s Setting up python3-dendropy (4.6.1-2) ... 130s Setting up python3-soupsieve (2.7-2) ... 130s Setting up cd-hit (4.8.1-4build1) ... 130s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 130s Setting up python3-sympy (1.14.0-2) ... 136s Setting up liblapack3:arm64 (3.12.1-7) ... 136s 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 136s Setting up python3-pysam (0.23.3+ds-2) ... 136s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ... 136s Setting up libwebpdemux2:arm64 (1.5.0-0.1) ... 136s Setting up xfonts-utils (1:7.7+7) ... 136s Setting up python3-bs4 (4.14.2-1) ... 137s Setting up python3-zopfli (0.4.0-1) ... 137s Setting up samtools (1.22.1-1) ... 137s Setting up libraqm0:arm64 (0.10.3-1) ... 137s Setting up mash (2.3+dfsg-6build2) ... 137s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 138s Setting up python3-lxml:arm64 (6.0.2-1) ... 139s Setting up libtiff6:arm64 (4.7.0-3ubuntu3) ... 139s Setting up xml-core (0.19) ... 139s Setting up python3-contourpy (1.3.3-1) ... 139s Setting up libfontconfig1:arm64 (2.15.0-2.3ubuntu1) ... 139s Setting up libxft2:arm64 (2.3.6-1build1) ... 139s Setting up libtk8.6:arm64 (8.6.17-1) ... 139s Setting up fastaq (3.17.0-9) ... 139s Setting up fonts-urw-base35 (20200910-8) ... 139s Setting up libcairo2:arm64 (1.18.4-1build1) ... 139s Setting up python3.13-tk (3.13.9-1) ... 139s Setting up python3-pymummer (0.12.0-1) ... 139s Setting up python3-pil:arm64 (12.0.0-1ubuntu1) ... 140s Setting up python3.14-tk (3.14.0-4) ... 140s Setting up python3-cairo (1.27.0-2build1) ... 140s Setting up python3-tk (3.13.9-2) ... 140s Setting up python3-pil.imagetk:arm64 (12.0.0-1ubuntu1) ... 140s Setting up python3-rlpycairo (0.3.0-4) ... 140s Setting up python3-reportlab (4.4.5-1) ... 141s Setting up python3-fonttools (4.57.0-3) ... 142s Setting up python3-ufolib2 (0.17.1+dfsg1-1) ... 142s Setting up python3-matplotlib (3.10.7+dfsg1-1) ... 143s Processing triggers for libc-bin (2.42-2ubuntu2) ... 143s Processing triggers for man-db (2.13.1-1) ... 144s Processing triggers for sgml-base (1.31+nmu1) ... 144s Setting up w3c-sgml-lib (1.3-3) ... 169s Setting up python3-biopython (1.86+dfsg-1) ... 170s Setting up ariba (2.14.7+ds-7syncable1build1) ... 172s autopkgtest [13:53:40]: test test-example: [----------------------- 174s ARIBA version: 2.14.6 174s 174s External dependencies: 174s bowtie2 2.5.4 /usr/bin/bowtie2 174s cdhit 4.8.1 /usr/bin/cd-hit-est 174s nucmer 3.1 /usr/bin/nucmer 174s 174s External dependencies OK: True 174s 174s Python version: 174s 3.13.9 (main, Oct 15 2025, 14:56:22) [GCC 15.2.0] 174s 174s Python packages: 174s ariba 2.14.6 /usr/lib/python3/dist-packages/ariba/__init__.py 174s bs4 4.14.2 /usr/lib/python3/dist-packages/bs4/__init__.py 174s dendropy 4.6.1 /usr/lib/python3/dist-packages/dendropy/__init__.py 174s pyfastaq 3.17.0 /usr/lib/python3/dist-packages/pyfastaq/__init__.py 174s pymummer 0.12.0 /usr/lib/python3/dist-packages/pymummer/__init__.py 174s pysam 0.23.3 /usr/lib/python3/dist-packages/pysam/__init__.py 174s 174s Python packages OK: True 174s 174s Everything looks OK: True 174s 174s Loading and checking input data 174s 174s Running cdhit 174s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.37it7tSHtA/foo/PREPAREREF/02.cdhit.noncoding.fa -o /tmp/tmp.37it7tSHtA/foo/tmp.run_cd-hit.ateakkj2/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 174s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.37it7tSHtA/foo/PREPAREREF/02.cdhit.noncoding.varonly.fa -o /tmp/tmp.37it7tSHtA/foo/tmp.run_cd-hit.0d5_z3fd/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 174s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.37it7tSHtA/foo/PREPAREREF/02.cdhit.gene.fa -o /tmp/tmp.37it7tSHtA/foo/tmp.run_cd-hit.bl5osqv8/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 175s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.37it7tSHtA/foo/PREPAREREF/02.cdhit.gene.varonly.fa -o /tmp/tmp.37it7tSHtA/foo/tmp.run_cd-hit.9r_yewsq/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 175s 175s Writing clusters to file. 10 in total 176s Found reads file: reads_1.fq 176s Found reads file: reads_2.fq 176s ARIBA version: 2.14.6 176s 176s External dependencies: 176s bowtie2 2.5.4 /usr/bin/bowtie2 176s cdhit 4.8.1 /usr/bin/cd-hit-est 176s nucmer 3.1 /usr/bin/nucmer 176s 176s External dependencies OK: True 176s 176s Python version: 176s 3.13.9 (main, Oct 15 2025, 14:56:22) [GCC 15.2.0] 176s 176s Python packages: 176s ariba 2.14.6 /usr/lib/python3/dist-packages/ariba/__init__.py 176s bs4 4.14.2 /usr/lib/python3/dist-packages/bs4/__init__.py 176s dendropy 4.6.1 /usr/lib/python3/dist-packages/dendropy/__init__.py 176s pyfastaq 3.17.0 /usr/lib/python3/dist-packages/pyfastaq/__init__.py 176s pymummer 0.12.0 /usr/lib/python3/dist-packages/pymummer/__init__.py 176s pysam 0.23.3 /usr/lib/python3/dist-packages/pysam/__init__.py 176s 176s Python packages OK: True 176s 176s Everything looks OK: True 176s Temporary directory: /tmp/tmp.37it7tSHtA/foo/OUT/ariba.tmp.bi_iad53 176s ______________________ Mapping reads to clustered genes _______________________ 176s Finished mapping 176s 176s _____________________________ Generating clusters _____________________________ 176s syscall: sort -k1,1 -k 2,2n /tmp/tmp.37it7tSHtA/foo/OUT/minimap.reads > /tmp/tmp.37it7tSHtA/foo/OUT/read_store 176s Compressing file /tmp/tmp.37it7tSHtA/foo/OUT/read_store 176s Found 51 proper read pairs from minimap 176s Total clusters to perform local assemblies: 9 176s 176s Insert size information from reads mapped to reference genes: 176s Insert size: 185.0 176s Insert sspace sd: 0.27 176s Max insert: 220.55 176s 176s ___________________________ Assembling each cluster ___________________________ 176s Will run 1 cluster(s) in parallel 176s Not constructing cluster cluster because it only has 2 reads (1 of 9) 176s Constructing cluster cluster_1 (2 of 9) 176s Constructing cluster cluster_2 (3 of 9) 176s Constructing cluster cluster_3 (4 of 9) 176s Constructing cluster cluster_4 (5 of 9) 176s Constructing cluster gene (6 of 9) 176s Constructing cluster gene_1 (7 of 9) 176s Constructing cluster noncoding (8 of 9) 176s Constructing cluster noncoding_1 (9 of 9) 176s Start running cluster cluster_1 in directory /tmp/tmp.37it7tSHtA/foo/OUT/ariba.tmp.bi_iad53/cluster_1 177s cluster_1 detected 1 threads available to it 177s cluster_1 reported completion 177s Finished running cluster cluster_1 in directory /tmp/tmp.37it7tSHtA/foo/OUT/ariba.tmp.bi_iad53/cluster_1 177s Deleting cluster dir /tmp/tmp.37it7tSHtA/foo/OUT/ariba.tmp.bi_iad53/cluster_1 177s Start running cluster cluster_2 in directory /tmp/tmp.37it7tSHtA/foo/OUT/ariba.tmp.bi_iad53/cluster_2 179s cluster_2 detected 1 threads available to it 179s cluster_2 reported completion 179s Finished running cluster cluster_2 in directory /tmp/tmp.37it7tSHtA/foo/OUT/ariba.tmp.bi_iad53/cluster_2 179s Deleting cluster dir /tmp/tmp.37it7tSHtA/foo/OUT/ariba.tmp.bi_iad53/cluster_2 179s Start running cluster cluster_3 in directory /tmp/tmp.37it7tSHtA/foo/OUT/ariba.tmp.bi_iad53/cluster_3 181s cluster_3 detected 1 threads available to it 181s cluster_3 reported completion 181s Finished running cluster cluster_3 in directory /tmp/tmp.37it7tSHtA/foo/OUT/ariba.tmp.bi_iad53/cluster_3 181s Deleting cluster dir /tmp/tmp.37it7tSHtA/foo/OUT/ariba.tmp.bi_iad53/cluster_3 181s Start running cluster cluster_4 in directory /tmp/tmp.37it7tSHtA/foo/OUT/ariba.tmp.bi_iad53/cluster_4 182s cluster_4 detected 1 threads available to it 182s cluster_4 reported completion 182s Finished running cluster cluster_4 in directory /tmp/tmp.37it7tSHtA/foo/OUT/ariba.tmp.bi_iad53/cluster_4 182s Deleting cluster dir /tmp/tmp.37it7tSHtA/foo/OUT/ariba.tmp.bi_iad53/cluster_4 182s Start running cluster gene in directory /tmp/tmp.37it7tSHtA/foo/OUT/ariba.tmp.bi_iad53/gene 184s gene detected 1 threads available to it 184s gene reported completion 184s Finished running cluster gene in directory /tmp/tmp.37it7tSHtA/foo/OUT/ariba.tmp.bi_iad53/gene 184s Deleting cluster dir /tmp/tmp.37it7tSHtA/foo/OUT/ariba.tmp.bi_iad53/gene 184s Start running cluster gene_1 in directory /tmp/tmp.37it7tSHtA/foo/OUT/ariba.tmp.bi_iad53/gene_1 186s gene_1 detected 1 threads available to it 186s gene_1 reported completion 186s Finished running cluster gene_1 in directory /tmp/tmp.37it7tSHtA/foo/OUT/ariba.tmp.bi_iad53/gene_1 186s Deleting cluster dir /tmp/tmp.37it7tSHtA/foo/OUT/ariba.tmp.bi_iad53/gene_1 186s Start running cluster noncoding in directory /tmp/tmp.37it7tSHtA/foo/OUT/ariba.tmp.bi_iad53/noncoding 188s noncoding detected 1 threads available to it 188s noncoding reported completion 188s Finished running cluster noncoding in directory /tmp/tmp.37it7tSHtA/foo/OUT/ariba.tmp.bi_iad53/noncoding 188s Deleting cluster dir /tmp/tmp.37it7tSHtA/foo/OUT/ariba.tmp.bi_iad53/noncoding 188s Start running cluster noncoding_1 in directory /tmp/tmp.37it7tSHtA/foo/OUT/ariba.tmp.bi_iad53/noncoding_1 189s noncoding_1 detected 1 threads available to it 189s noncoding_1 reported completion 189s Finished running cluster noncoding_1 in directory /tmp/tmp.37it7tSHtA/foo/OUT/ariba.tmp.bi_iad53/noncoding_1 189s Deleting cluster dir /tmp/tmp.37it7tSHtA/foo/OUT/ariba.tmp.bi_iad53/noncoding_1 189s Final value of remaining_clusters counter: Value('l', 0) 189s Finished assembling clusters 189s 189s _______________________________ Writing reports _______________________________ 189s Making /tmp/tmp.37it7tSHtA/foo/OUT/debug.report.tsv 189s Making /tmp/tmp.37it7tSHtA/foo/OUT/report.tsv 189s 189s ____________________ Writing fasta of assembled sequences _____________________ 189s /tmp/tmp.37it7tSHtA/foo/OUT/assembled_seqs.fa.gz and /tmp/tmp.37it7tSHtA/foo/OUT/assembled_genes.fa.gz 189s 189s __________________________ Catting cluster log files __________________________ 189s Writing file /tmp/tmp.37it7tSHtA/foo/OUT/log.clusters.gz 189s 189s _______________________________ Cleaning files ________________________________ 189s Deleting Logs directory /tmp/tmp.37it7tSHtA/foo/OUT/Logs 189s Deleting reads store files /tmp/tmp.37it7tSHtA/foo/OUT/read_store.gz[.tbi] 189s 189s All done! 189s 190s Running ARIBA on test data... 190s ------------------------------------------------------------------------------- 190s |=============================================================================| 190s | Preparing input data | 190s |=============================================================================| 190s ------------------------------------------------------------------------------- 190s Made output directory ./foo. Copying test data files into it: 190s copied ref_seqs.fa 190s copied metadata.tsv 190s copied reads_1.fq 190s copied reads_2.fq 190s ------------------------------------------------------------------------------- 190s |=============================================================================| 190s | Try running ariba prepareref | 190s |=============================================================================| 190s ------------------------------------------------------------------------------- 190s 190s Running ariba prepareref with: 190s /usr/bin/ariba prepareref --verbose -f ref_seqs.fa -m metadata.tsv --threads 1 PREPAREREF 190s 190s 190s ariba prepareref finished OK 190s ------------------------------------------------------------------------------- 190s |=============================================================================| 190s | Try running ariba run | 190s |=============================================================================| 190s ------------------------------------------------------------------------------- 190s 190s Running ARIBA with: 190s /usr/bin/ariba run --verbose --threads 1 PREPAREREF reads_1.fq reads_2.fq OUT 190s 190s 190s ariba run finished OK 190s Finished run on test data OK 190s autopkgtest [13:53:58]: test test-example: -----------------------] 191s autopkgtest [13:53:59]: test test-example: - - - - - - - - - - results - - - - - - - - - - 191s test-example PASS 191s autopkgtest [13:53:59]: @@@@@@@@@@@@@@@@@@@@ summary 191s test-example PASS