0s autopkgtest [16:46:19]: starting date and time: 2026-01-24 16:46:19+0000 0s autopkgtest [16:46:19]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [16:46:19]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.n2rs74mt/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade seqsero --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.14.2-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-9.secgroup --name adt-resolute-amd64-seqsero-20260124-164619-juju-7f2275-prod-proposed-migration-environment-2-d5d563ea-d851-42f7-90e4-6fb3a2ea72f5 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-amd64-seqsero-20260124-164619-juju-7f2275-prod-proposed-migration-environment-2-d5d563ea-d851-42f7-90e4-6fb3a2ea72f5 from image adt/ubuntu-resolute-amd64-server-20260124.img (UUID 46811f22-3700-43f4-953b-ee3c613d71bb)... 102s autopkgtest [16:48:01]: testbed dpkg architecture: amd64 102s autopkgtest [16:48:01]: testbed apt version: 3.1.13 102s autopkgtest [16:48:01]: @@@@@@@@@@@@@@@@@@@@ test bed setup 102s autopkgtest [16:48:01]: testbed release detected to be: None 103s autopkgtest [16:48:02]: updating testbed package index (apt update) 104s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 104s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 104s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 104s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 104s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [92.4 kB] 104s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [991 kB] 104s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [24.3 kB] 104s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [2820 B] 104s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [113 kB] 104s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [96.9 kB] 104s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [3712 B] 104s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [12.3 kB] 104s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3696 B] 104s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [336 B] 104s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [897 kB] 104s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [378 kB] 104s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [24.5 kB] 104s Get:18 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [4704 B] 104s Get:19 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [12.4 kB] 104s Get:20 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [824 B] 105s Fetched 2781 kB in 1s (2143 kB/s) 106s Reading package lists... 107s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 107s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 107s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 107s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 108s Reading package lists... 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 109s Calculating upgrade... 109s The following packages were automatically installed and are no longer required: 109s python3.13 python3.13-minimal 109s Use 'sudo apt autoremove' to remove them. 109s The following NEW packages will be installed: 109s libpython3.14-minimal libpython3.14-stdlib python3.14 python3.14-minimal 109s The following packages will be upgraded: 109s libpython3-stdlib python3 python3-gdbm python3-minimal rust-coreutils 109s 5 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 109s Need to get 10.4 MB of archives. 109s After this operation, 25.2 MB of additional disk space will be used. 109s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-minimal amd64 3.14.2-1 [920 kB] 109s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14-minimal amd64 3.14.2-1 [2563 kB] 109s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-minimal amd64 3.14.2-1 [28.2 kB] 109s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3 amd64 3.14.2-1 [22.9 kB] 109s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.2-1 [2398 kB] 109s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14 amd64 3.14.2-1 [816 kB] 109s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libpython3-stdlib amd64 3.14.2-1 [10.9 kB] 109s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 rust-coreutils amd64 0.5.0-0ubuntu1 [3628 kB] 110s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-gdbm amd64 3.14.2-1 [11.1 kB] 110s dpkg-preconfigure: unable to re-open stdin: No such file or directory 110s Fetched 10.4 MB in 1s (11.5 MB/s) 110s Selecting previously unselected package libpython3.14-minimal:amd64. 110s (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 ... 124177 files and directories currently installed.) 110s Preparing to unpack .../libpython3.14-minimal_3.14.2-1_amd64.deb ... 110s Unpacking libpython3.14-minimal:amd64 (3.14.2-1) ... 110s Selecting previously unselected package python3.14-minimal. 110s Preparing to unpack .../python3.14-minimal_3.14.2-1_amd64.deb ... 110s Unpacking python3.14-minimal (3.14.2-1) ... 111s Setting up libpython3.14-minimal:amd64 (3.14.2-1) ... 111s Setting up python3.14-minimal (3.14.2-1) ... 112s (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 ... 124519 files and directories currently installed.) 112s Preparing to unpack .../python3-minimal_3.14.2-1_amd64.deb ... 112s Unpacking python3-minimal (3.14.2-1) over (3.13.9-3) ... 112s Setting up python3-minimal (3.14.2-1) ... 112s (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 ... 124519 files and directories currently installed.) 112s Preparing to unpack .../python3_3.14.2-1_amd64.deb ... 112s running python pre-rtupdate hooks for python3.14... 112s Unpacking python3 (3.14.2-1) over (3.13.9-3) ... 112s Selecting previously unselected package libpython3.14-stdlib:amd64. 112s Preparing to unpack .../libpython3.14-stdlib_3.14.2-1_amd64.deb ... 112s Unpacking libpython3.14-stdlib:amd64 (3.14.2-1) ... 112s Selecting previously unselected package python3.14. 112s Preparing to unpack .../python3.14_3.14.2-1_amd64.deb ... 112s Unpacking python3.14 (3.14.2-1) ... 112s Preparing to unpack .../libpython3-stdlib_3.14.2-1_amd64.deb ... 112s Unpacking libpython3-stdlib:amd64 (3.14.2-1) over (3.13.9-3) ... 113s Preparing to unpack .../rust-coreutils_0.5.0-0ubuntu1_amd64.deb ... 113s Unpacking rust-coreutils (0.5.0-0ubuntu1) over (0.2.2-0ubuntu2) ... 113s Setting up rust-coreutils (0.5.0-0ubuntu1) ... 113s (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 ... 124980 files and directories currently installed.) 113s Preparing to unpack .../python3-gdbm_3.14.2-1_amd64.deb ... 113s Unpacking python3-gdbm (3.14.2-1) over (3.13.9-3) ... 113s Setting up libpython3.14-stdlib:amd64 (3.14.2-1) ... 113s Setting up python3.14 (3.14.2-1) ... 114s Setting up libpython3-stdlib:amd64 (3.14.2-1) ... 114s Setting up python3-gdbm (3.14.2-1) ... 114s Setting up python3 (3.14.2-1) ... 114s running python rtupdate hooks for python3.14... 114s running python post-rtupdate hooks for python3.14... 114s Processing triggers for man-db (2.13.1-1) ... 115s Processing triggers for systemd (259-1ubuntu2) ... 115s autopkgtest [16:48:14]: upgrading testbed (apt dist-upgrade and autopurge) 115s Reading package lists... 116s Building dependency tree... 116s Reading state information... 116s Calculating upgrade... 116s The following packages were automatically installed and are no longer required: 116s python3.13 python3.13-minimal 116s Use 'sudo apt autoremove' to remove them. 116s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 116s Reading package lists... 116s Building dependency tree... 116s Reading state information... 116s Solving dependencies... 117s The following packages will be REMOVED: 117s python3.13* python3.13-minimal* 117s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 117s After this operation, 7860 kB disk space will be freed. 117s (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 ... 124978 files and directories currently installed.) 117s Removing python3.13 (3.13.11-1) ... 117s Removing python3.13-minimal (3.13.11-1) ... 118s Processing triggers for man-db (2.13.1-1) ... 118s Processing triggers for systemd (259-1ubuntu2) ... 118s (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 ... 124951 files and directories currently installed.) 118s Purging configuration files for python3.13-minimal (3.13.11-1) ... 121s autopkgtest [16:48:20]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:49:02 UTC 2026 121s autopkgtest [16:48:20]: @@@@@@@@@@@@@@@@@@@@ apt-source seqsero 123s Get:1 http://ftpmaster.internal/ubuntu resolute/universe seqsero 1.0.1+dfsg-6build1 (dsc) [2023 B] 123s Get:2 http://ftpmaster.internal/ubuntu resolute/universe seqsero 1.0.1+dfsg-6build1 (tar) [356 kB] 123s Get:3 http://ftpmaster.internal/ubuntu resolute/universe seqsero 1.0.1+dfsg-6build1 (diff) [43.2 kB] 123s gpgv: Signature made Fri Jan 9 20:22:15 2026 UTC 123s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 123s gpgv: Can't check signature: No public key 123s dpkg-source: warning: cannot verify inline signature for ./seqsero_1.0.1+dfsg-6build1.dsc: no acceptable signature found 123s autopkgtest [16:48:22]: testing package seqsero version 1.0.1+dfsg-6build1 123s autopkgtest [16:48:22]: build not needed 123s autopkgtest [16:48:22]: test run-unit-test: preparing testbed 124s Reading package lists... 124s Building dependency tree... 124s Reading state information... 124s Solving dependencies... 124s The following NEW packages will be installed: 124s bwa fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono 124s fonts-urw-base35 libabsl20240722 libaec0 libblas3 libcairo2 libdeflate0 124s libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 124s libharfbuzz0b libhdf5-310 libhts3t64 libhtscodecs2 libimagequant0 libjbig0 124s libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4 libmbedcrypto16 124s libmbedtls21 libmbedx509-7 libncbi-vdb3 libncbi-wvdb3 libopenjp2-7 124s libpixman-1-0 libraqm0 libre2-11 libsharpyuv0 libsz2 libtiff6 libwebp7 124s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 124s ncbi-vdb-data python3-biopython python3-cairo python3-charset-normalizer 124s python3-freetype python3-numpy python3-numpy-dev python3-pil 124s python3-reportlab python3-rlpycairo samtools seqsero sgml-base sra-toolkit 124s w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 124s 0 upgraded, 64 newly installed, 0 to remove and 0 not upgraded. 124s Need to get 49.1 MB of archives. 124s After this operation, 162 MB of additional disk space will be used. 124s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.3.5+ds-3 [147 kB] 124s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7ubuntu1 [260 kB] 124s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-11ubuntu1 [939 kB] 125s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7ubuntu1 [2739 kB] 125s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.3.5+ds-3 [8129 kB] 125s Get:6 http://ftpmaster.internal/ubuntu resolute/universe amd64 bwa amd64 0.7.19-1 [200 kB] 125s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8build1 [502 kB] 125s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8build1 [834 kB] 125s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontenc1 amd64 1:1.1.8-1build2 [14.1 kB] 125s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 125s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu3 [576 kB] 125s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 xfonts-utils amd64 1:7.7+7build1 [97.1 kB] 125s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-urw-base35 all 20200910-8build1 [10.9 MB] 125s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.17.1-3ubuntu1 [38.5 kB] 125s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-extra all 2.37-8build1 [1944 kB] 125s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 libabsl20240722 amd64 20240722.0-4ubuntu1 [528 kB] 125s Get:17 http://ftpmaster.internal/ubuntu resolute/universe amd64 libaec0 amd64 1.1.4-2 [22.9 kB] 125s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.17.1-3ubuntu1 [144 kB] 125s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.46.4-1 [287 kB] 125s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2build1 [17.4 kB] 125s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2build1 [6120 B] 125s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB] 125s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-3 [579 kB] 125s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 125s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 15.2.0-11ubuntu1 [151 kB] 125s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-11ubuntu1 [73.7 kB] 125s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.3.0-4 [529 kB] 125s Get:28 http://ftpmaster.internal/ubuntu resolute/universe amd64 libsz2 amd64 1.1.4-2 [5516 B] 125s Get:29 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhdf5-310 amd64 1.14.6+repack-2 [1433 kB] 125s Get:30 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhtscodecs2 amd64 1.6.1-2build1 [108 kB] 125s Get:31 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhts3t64 amd64 1.22.1+ds2-1 [461 kB] 125s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 125s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu2 [152 kB] 125s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 125s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 liblcms2-2 amd64 2.17-1 [170 kB] 125s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu2 [207 kB] 125s Get:37 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmbedcrypto16 amd64 3.6.5-0.1ubuntu2 [259 kB] 125s Get:38 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmbedx509-7 amd64 3.6.5-0.1ubuntu2 [35.4 kB] 125s Get:39 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmbedtls21 amd64 3.6.5-0.1ubuntu2 [130 kB] 125s Get:40 http://ftpmaster.internal/ubuntu resolute/universe amd64 ncbi-vdb-data all 3.2.1+dfsg-2 [81.3 kB] 125s Get:41 http://ftpmaster.internal/ubuntu resolute/universe amd64 libncbi-vdb3 amd64 3.2.1+dfsg-2 [1376 kB] 125s Get:42 http://ftpmaster.internal/ubuntu resolute/universe amd64 libncbi-wvdb3 amd64 3.2.1+dfsg-2 [1386 kB] 125s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 libraqm0 amd64 0.10.3-1 [15.4 kB] 125s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 libre2-11 amd64 20250805-1build1 [175 kB] 125s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1build1 [17.6 kB] 125s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu3 [30.0 kB] 125s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1build1 [264 kB] 125s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB] 125s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpdemux2 amd64 1.5.0-0.1build1 [12.8 kB] 125s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpmux3 amd64 1.5.0-0.1build1 [26.4 kB] 125s Get:51 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-charset-normalizer amd64 3.4.4-2 [173 kB] 125s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libopenjp2-7 amd64 2.5.4-1 [188 kB] 125s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-pil amd64 12.0.0-1ubuntu1 [494 kB] 125s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-cairo amd64 1.27.0-2build1 [140 kB] 125s Get:55 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-freetype all 2.5.1-2 [92.2 kB] 125s Get:56 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-rlpycairo all 0.3.0-4 [9332 B] 126s Get:57 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-reportlab all 4.4.9-1 [1149 kB] 126s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 sgml-base all 1.31+nmu1 [11.0 kB] 126s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 xml-core all 0.19build1 [20.3 kB] 126s Get:60 http://ftpmaster.internal/ubuntu resolute/universe amd64 w3c-sgml-lib all 1.3-3build1 [278 kB] 126s Get:61 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-biopython amd64 1.86+dfsg-1 [1682 kB] 126s Get:62 http://ftpmaster.internal/ubuntu resolute/universe amd64 samtools amd64 1.22.1-1 [645 kB] 126s Get:63 http://ftpmaster.internal/ubuntu resolute/universe amd64 sra-toolkit amd64 3.2.1+dfsg-4ubuntu5 [7502 kB] 126s Get:64 http://ftpmaster.internal/ubuntu resolute/universe amd64 seqsero amd64 1.0.1+dfsg-6build1 [369 kB] 126s Fetched 49.1 MB in 2s (29.6 MB/s) 126s Selecting previously unselected package python3-numpy-dev:amd64. 126s (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 ... 124953 files and directories currently installed.) 126s Preparing to unpack .../00-python3-numpy-dev_1%3a2.3.5+ds-3_amd64.deb ... 126s Unpacking python3-numpy-dev:amd64 (1:2.3.5+ds-3) ... 126s Selecting previously unselected package libblas3:amd64. 126s Preparing to unpack .../01-libblas3_3.12.1-7ubuntu1_amd64.deb ... 126s Unpacking libblas3:amd64 (3.12.1-7ubuntu1) ... 126s Selecting previously unselected package libgfortran5:amd64. 126s Preparing to unpack .../02-libgfortran5_15.2.0-11ubuntu1_amd64.deb ... 126s Unpacking libgfortran5:amd64 (15.2.0-11ubuntu1) ... 126s Selecting previously unselected package liblapack3:amd64. 126s Preparing to unpack .../03-liblapack3_3.12.1-7ubuntu1_amd64.deb ... 126s Unpacking liblapack3:amd64 (3.12.1-7ubuntu1) ... 126s Selecting previously unselected package python3-numpy. 127s Preparing to unpack .../04-python3-numpy_1%3a2.3.5+ds-3_amd64.deb ... 127s Unpacking python3-numpy (1:2.3.5+ds-3) ... 127s Selecting previously unselected package bwa. 127s Preparing to unpack .../05-bwa_0.7.19-1_amd64.deb ... 127s Unpacking bwa (0.7.19-1) ... 127s Selecting previously unselected package fonts-dejavu-mono. 127s Preparing to unpack .../06-fonts-dejavu-mono_2.37-8build1_all.deb ... 127s Unpacking fonts-dejavu-mono (2.37-8build1) ... 127s Selecting previously unselected package fonts-dejavu-core. 127s Preparing to unpack .../07-fonts-dejavu-core_2.37-8build1_all.deb ... 127s Unpacking fonts-dejavu-core 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previously unselected package liblcms2-2:amd64. 128s Preparing to unpack .../34-liblcms2-2_2.17-1_amd64.deb ... 128s Unpacking liblcms2-2:amd64 (2.17-1) ... 128s Selecting previously unselected package liblerc4:amd64. 128s Preparing to unpack .../35-liblerc4_4.0.0+ds-5ubuntu2_amd64.deb ... 128s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu2) ... 128s Selecting previously unselected package libmbedcrypto16:amd64. 128s Preparing to unpack .../36-libmbedcrypto16_3.6.5-0.1ubuntu2_amd64.deb ... 128s Unpacking libmbedcrypto16:amd64 (3.6.5-0.1ubuntu2) ... 128s Selecting previously unselected package libmbedx509-7:amd64. 128s Preparing to unpack .../37-libmbedx509-7_3.6.5-0.1ubuntu2_amd64.deb ... 128s Unpacking libmbedx509-7:amd64 (3.6.5-0.1ubuntu2) ... 128s Selecting previously unselected package libmbedtls21:amd64. 128s Preparing to unpack .../38-libmbedtls21_3.6.5-0.1ubuntu2_amd64.deb ... 128s Unpacking libmbedtls21:amd64 (3.6.5-0.1ubuntu2) ... 128s Selecting previously unselected package ncbi-vdb-data. 128s Preparing to unpack .../39-ncbi-vdb-data_3.2.1+dfsg-2_all.deb ... 128s Unpacking ncbi-vdb-data (3.2.1+dfsg-2) ... 128s Selecting previously unselected package libncbi-vdb3:amd64. 128s Preparing to unpack .../40-libncbi-vdb3_3.2.1+dfsg-2_amd64.deb ... 128s Unpacking libncbi-vdb3:amd64 (3.2.1+dfsg-2) ... 128s Selecting previously unselected package libncbi-wvdb3:amd64. 128s Preparing to unpack .../41-libncbi-wvdb3_3.2.1+dfsg-2_amd64.deb ... 128s Unpacking libncbi-wvdb3:amd64 (3.2.1+dfsg-2) ... 128s Selecting previously unselected package libraqm0:amd64. 128s Preparing to unpack .../42-libraqm0_0.10.3-1_amd64.deb ... 128s Unpacking libraqm0:amd64 (0.10.3-1) ... 128s Selecting previously unselected package libre2-11:amd64. 128s Preparing to unpack .../43-libre2-11_20250805-1build1_amd64.deb ... 128s Unpacking libre2-11:amd64 (20250805-1build1) ... 128s Selecting previously unselected package libsharpyuv0:amd64. 128s Preparing to unpack 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Selecting previously unselected package python3-rlpycairo. 129s Preparing to unpack .../55-python3-rlpycairo_0.3.0-4_all.deb ... 129s Unpacking python3-rlpycairo (0.3.0-4) ... 129s Selecting previously unselected package python3-reportlab. 129s Preparing to unpack .../56-python3-reportlab_4.4.9-1_all.deb ... 129s Unpacking python3-reportlab (4.4.9-1) ... 129s Selecting previously unselected package sgml-base. 129s Preparing to unpack .../57-sgml-base_1.31+nmu1_all.deb ... 129s Unpacking sgml-base (1.31+nmu1) ... 129s Selecting previously unselected package xml-core. 129s Preparing to unpack .../58-xml-core_0.19build1_all.deb ... 129s Unpacking xml-core (0.19build1) ... 129s Selecting previously unselected package w3c-sgml-lib. 129s Preparing to unpack .../59-w3c-sgml-lib_1.3-3build1_all.deb ... 129s Unpacking w3c-sgml-lib (1.3-3build1) ... 129s Selecting previously unselected package python3-biopython. 129s Preparing to unpack .../60-python3-biopython_1.86+dfsg-1_amd64.deb ... 129s Unpacking python3-biopython (1.86+dfsg-1) ... 129s Selecting previously unselected package samtools. 129s Preparing to unpack .../61-samtools_1.22.1-1_amd64.deb ... 129s Unpacking samtools (1.22.1-1) ... 129s Selecting previously unselected package sra-toolkit. 129s Preparing to unpack .../62-sra-toolkit_3.2.1+dfsg-4ubuntu5_amd64.deb ... 129s Unpacking sra-toolkit (3.2.1+dfsg-4ubuntu5) ... 129s Selecting previously unselected package seqsero. 129s Preparing to unpack .../63-seqsero_1.0.1+dfsg-6build1_amd64.deb ... 129s Unpacking seqsero (1.0.1+dfsg-6build1) ... 129s Setting up libhtscodecs2:amd64 (1.6.1-2build1) ... 129s Setting up libgraphite2-3:amd64 (1.3.14-11ubuntu1) ... 129s Setting up liblcms2-2:amd64 (2.17-1) ... 129s Setting up libpixman-1-0:amd64 (0.46.4-1) ... 129s Setting up libsharpyuv0:amd64 (1.5.0-0.1build1) ... 129s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu2) ... 129s Setting up libxrender1:amd64 (1:0.9.12-1) ... 129s Setting up libxcb-render0:amd64 (1.17.0-2build1) ... 129s Setting up python3-charset-normalizer (3.4.4-2) ... 129s Setting up bwa (0.7.19-1) ... 129s Setting up x11-common (1:7.7+24ubuntu1) ... 130s Setting up libdeflate0:amd64 (1.23-2) ... 130s Setting up libxcb-shm0:amd64 (1.17.0-2build1) ... 130s Setting up libgomp1:amd64 (15.2.0-11ubuntu1) ... 130s Setting up python3-freetype (2.5.1-2) ... 130s Setting up libabsl20240722:amd64 (20240722.0-4ubuntu1) ... 130s Setting up libjbig0:amd64 (2.1-6.1ubuntu3) ... 130s Setting up libaec0:amd64 (1.1.4-2) ... 130s Setting up libfontenc1:amd64 (1:1.1.8-1build2) ... 130s Setting up libblas3:amd64 (3.12.1-7ubuntu1) ... 130s 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 130s Setting up xfonts-encodings (1:1.0.5-0ubuntu3) ... 130s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 130s Setting up fonts-dejavu-mono (2.37-8build1) ... 130s Setting up python3-numpy-dev:amd64 (1:2.3.5+ds-3) ... 130s Setting up fonts-dejavu-core (2.37-8build1) ... 130s Setting up libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 130s Setting up libgfortran5:amd64 (15.2.0-11ubuntu1) ... 130s Setting up libwebp7:amd64 (1.5.0-0.1build1) ... 130s Setting up fonts-dejavu-extra (2.37-8build1) ... 130s Setting up libhts3t64:amd64 (1.22.1+ds2-1) ... 130s Setting up libopenjp2-7:amd64 (2.5.4-1) ... 130s Setting up libharfbuzz0b:amd64 (12.3.0-4) ... 130s Setting up ncbi-vdb-data (3.2.1+dfsg-2) ... 130s Setting up sgml-base (1.31+nmu1) ... 130s Setting up libmbedcrypto16:amd64 (3.6.5-0.1ubuntu2) ... 130s Setting up libwebpmux3:amd64 (1.5.0-0.1build1) ... 130s Setting up libsz2:amd64 (1.1.4-2) ... 130s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 130s Setting up libre2-11:amd64 (20250805-1build1) ... 130s Setting up liblapack3:amd64 (3.12.1-7ubuntu1) ... 130s 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 130s Setting up fontconfig-config (2.17.1-3ubuntu1) ... 131s Setting up libwebpdemux2:amd64 (1.5.0-0.1build1) ... 131s Setting up xfonts-utils (1:7.7+7build1) ... 131s Setting up samtools (1.22.1-1) ... 131s Setting up libmbedx509-7:amd64 (3.6.5-0.1ubuntu2) ... 131s Setting up libraqm0:amd64 (0.10.3-1) ... 131s Setting up python3-numpy (1:2.3.5+ds-3) ... 133s Setting up libmbedtls21:amd64 (3.6.5-0.1ubuntu2) ... 133s Setting up libhdf5-310:amd64 (1.14.6+repack-2) ... 133s Setting up libtiff6:amd64 (4.7.0-3ubuntu3) ... 133s Setting up xml-core (0.19build1) ... 133s Setting up libfontconfig1:amd64 (2.17.1-3ubuntu1) ... 133s Setting up libncbi-vdb3:amd64 (3.2.1+dfsg-2) ... 133s Setting up fonts-urw-base35 (20200910-8build1) ... 133s Setting up libcairo2:amd64 (1.18.4-3) ... 133s Setting up python3-pil:amd64 (12.0.0-1ubuntu1) ... 134s Setting up libncbi-wvdb3:amd64 (3.2.1+dfsg-2) ... 134s Setting up sra-toolkit (3.2.1+dfsg-4ubuntu5) ... 134s Setting up python3-cairo (1.27.0-2build1) ... 134s Setting up python3-rlpycairo (0.3.0-4) ... 134s Setting up python3-reportlab (4.4.9-1) ... 135s Processing triggers for libc-bin (2.42-2ubuntu4) ... 135s Processing triggers for man-db (2.13.1-1) ... 136s Processing triggers for sgml-base (1.31+nmu1) ... 136s Setting up w3c-sgml-lib (1.3-3build1) ... 166s Setting up python3-biopython (1.86+dfsg-1) ... 167s Setting up seqsero (1.0.1+dfsg-6build1) ... 168s autopkgtest [16:49:07]: test run-unit-test: [----------------------- 168s Test for checking functionality 169s Traceback (most recent call last): 169s File "", line 1, in 169s from multiprocessing.forkserver import main; main(4, 6, ['__main__'], **{'sys_path': ['/usr/share/seqsero/libs', '/usr/lib/python314.zip', '/usr/lib/python3.14', '/usr/lib/python3.14/lib-dynload', '/usr/local/lib/python3.14/dist-packages', '/usr/lib/python3/dist-packages'], 'main_path': '/usr/share/seqsero/libs/run_auto_All_for_web_multi_revise.py', 'authkey_r': 8}) 169s ~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 169s File "/usr/lib/python3.14/multiprocessing/forkserver.py", line 217, in main 169s spawn.import_main_path(main_path) 169s ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^ 169s File "/usr/lib/python3.14/multiprocessing/spawn.py", line 307, in import_main_path 169s _fixup_main_from_path(main_path) 169s ~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^ 169s File "/usr/lib/python3.14/multiprocessing/spawn.py", line 297, in _fixup_main_from_path 169s main_content = runpy.run_path(main_path, 169s run_name="__mp_main__") 169s File "", line 287, in run_path 169s File "", line 98, in _run_module_code 169s File "", line 88, in _run_code 169s File "/usr/share/seqsero/libs/run_auto_All_for_web_multi_revise.py", line 19, in 169s file_name=sys.argv[1] 169s ~~~~~~~~^^^ 169s IndexError: list index out of range 170s Traceback (most recent call last): 170s File "/usr/share/seqsero/libs/run_auto_All_for_web_multi_revise.py", line 315, in 170s main() 170s ~~~~^^ 170s File "/usr/share/seqsero/libs/run_auto_All_for_web_multi_revise.py", line 261, in main 170s p.start() 170s ~~~~~~~^^ 170s File "/usr/lib/python3.14/multiprocessing/process.py", line 121, in start 170s self._popen = self._Popen(self) 170s ~~~~~~~~~~~^^^^^^ 170s File "/usr/lib/python3.14/multiprocessing/context.py", line 224, in _Popen 170s return _default_context.get_context().Process._Popen(process_obj) 170s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^ 170s File "/usr/lib/python3.14/multiprocessing/context.py", line 300, in _Popen 170s return Popen(process_obj) 170s File "/usr/lib/python3.14/multiprocessing/popen_forkserver.py", line 35, in __init__ 170s super().__init__(process_obj) 170s ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^ 170s File "/usr/lib/python3.14/multiprocessing/popen_fork.py", line 20, in __init__ 170s self._launch(process_obj) 170s ~~~~~~~~~~~~^^^^^^^^^^^^^ 170s File "/usr/lib/python3.14/multiprocessing/popen_forkserver.py", line 51, in _launch 170s self.sentinel, w = forkserver.connect_to_new_process(self._fds) 170s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^ 170s File "/usr/lib/python3.14/multiprocessing/forkserver.py", line 106, in connect_to_new_process 170s connection.answer_challenge( 170s ~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 170s wrapped_client, self._forkserver_authkey) 170s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 170s File "/usr/lib/python3.14/multiprocessing/connection.py", line 970, in answer_challenge 170s message = connection.recv_bytes(256) # reject large message 170s File "/usr/lib/python3.14/multiprocessing/connection.py", line 222, in recv_bytes 170s buf = self._recv_bytes(maxlength) 170s File "/usr/lib/python3.14/multiprocessing/connection.py", line 447, in _recv_bytes 170s buf = self._recv(4) 170s File "/usr/lib/python3.14/multiprocessing/connection.py", line 412, in _recv 170s chunk = read(handle, to_read) 170s ConnectionResetError: [Errno 104] Connection reset by peer 170s cat: Seqsero_result.txt: No such file or directory (os error 2) 170s 170s 170s 170s Result: 170s 171s autopkgtest [16:49:10]: test run-unit-test: -----------------------] 171s autopkgtest [16:49:10]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 171s run-unit-test FAIL non-zero exit status 1 171s autopkgtest [16:49:10]: @@@@@@@@@@@@@@@@@@@@ summary 171s run-unit-test FAIL non-zero exit status 1