0s autopkgtest [23:00:46]: starting date and time: 2025-12-03 23:00:46+0000 0s autopkgtest [23:00:46]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [23:00:46]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work._g4esnzt/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade gasic --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-20@sto01-1.secgroup --name adt-resolute-amd64-gasic-20251203-230046-juju-7f2275-prod-proposed-migration-environment-20-0723cc5b-46cb-4b8a-ab4c-168da26b005f --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-amd64-gasic-20251203-230046-juju-7f2275-prod-proposed-migration-environment-20-0723cc5b-46cb-4b8a-ab4c-168da26b005f from image adt/ubuntu-resolute-amd64-server-20251203.img (UUID c6e78f39-c16c-48bb-9815-0096f6be052e)... 40s autopkgtest [23:01:26]: testbed dpkg architecture: amd64 40s autopkgtest [23:01:26]: testbed apt version: 3.1.12 40s autopkgtest [23:01:26]: @@@@@@@@@@@@@@@@@@@@ test bed setup 40s autopkgtest [23:01:26]: testbed release detected to be: None 41s autopkgtest [23:01:27]: updating testbed package index (apt update) 41s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 41s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 41s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 41s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 41s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [23.1 kB] 41s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [931 kB] 41s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [155 kB] 41s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [220 kB] 41s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [163 kB] 41s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [6432 B] 41s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [120 B] 41s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [757 kB] 41s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [345 kB] 41s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [23.6 kB] 41s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [4040 B] 42s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [9636 B] 42s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [748 B] 42s Fetched 2762 kB in 1s (4173 kB/s) 43s Reading package lists... 43s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 43s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 43s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 43s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 44s Reading package lists... 44s Reading package lists... 44s Building dependency tree... 44s Reading state information... 44s Calculating upgrade... 44s The following packages will be upgraded: 44s libpython3-stdlib python3 python3-gdbm python3-minimal 44s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 44s Need to get 72.9 kB of archives. 44s After this operation, 2048 B of additional disk space will be used. 44s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-minimal amd64 3.13.9-2 [28.1 kB] 44s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3 amd64 3.13.9-2 [23.0 kB] 44s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libpython3-stdlib amd64 3.13.9-2 [10.8 kB] 44s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-gdbm amd64 3.13.9-2 [11.0 kB] 44s dpkg-preconfigure: unable to re-open stdin: No such file or directory 44s Fetched 72.9 kB in 0s (2196 kB/s) 44s (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.) 44s Preparing to unpack .../python3-minimal_3.13.9-2_amd64.deb ... 44s Unpacking python3-minimal (3.13.9-2) over (3.13.7-1) ... 44s Setting up python3-minimal (3.13.9-2) ... 45s (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.) 45s Preparing to unpack .../python3_3.13.9-2_amd64.deb ... 45s running python pre-rtupdate hooks for python3.13... 45s Unpacking python3 (3.13.9-2) over (3.13.7-1) ... 45s Preparing to unpack .../libpython3-stdlib_3.13.9-2_amd64.deb ... 45s Unpacking libpython3-stdlib:amd64 (3.13.9-2) over (3.13.7-1) ... 45s Preparing to unpack .../python3-gdbm_3.13.9-2_amd64.deb ... 45s Unpacking python3-gdbm (3.13.9-2) over (3.13.9-1) ... 45s Setting up python3-gdbm (3.13.9-2) ... 45s Setting up libpython3-stdlib:amd64 (3.13.9-2) ... 45s Setting up python3 (3.13.9-2) ... 45s running python rtupdate hooks for python3.13... 45s running python post-rtupdate hooks for python3.13... 45s Processing triggers for man-db (2.13.1-1) ... 45s autopkgtest [23:01:31]: upgrading testbed (apt dist-upgrade and autopurge) 45s Reading package lists... 45s Building dependency tree... 45s Reading state information... 46s Calculating upgrade... 46s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 46s Reading package lists... 46s Building dependency tree... 46s Reading state information... 46s Solving dependencies... 46s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 48s autopkgtest [23:01:34]: testbed running kernel: Linux 6.17.0-6-generic #6-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 7 13:34:17 UTC 2025 48s autopkgtest [23:01:34]: @@@@@@@@@@@@@@@@@@@@ apt-source gasic 50s Get:1 http://ftpmaster.internal/ubuntu resolute/universe gasic 0.0.r19-8 (dsc) [2112 B] 50s Get:2 http://ftpmaster.internal/ubuntu resolute/universe gasic 0.0.r19-8 (tar) [12.4 kB] 50s Get:3 http://ftpmaster.internal/ubuntu resolute/universe gasic 0.0.r19-8 (diff) [7305 kB] 50s gpgv: Signature made Thu Dec 29 18:00:34 2022 UTC 50s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 50s gpgv: issuer "tille@debian.org" 50s gpgv: Can't check signature: No public key 50s dpkg-source: warning: cannot verify inline signature for ./gasic_0.0.r19-8.dsc: no acceptable signature found 50s autopkgtest [23:01:36]: testing package gasic version 0.0.r19-8 50s autopkgtest [23:01:36]: build not needed 51s autopkgtest [23:01:37]: test run-unit-test: preparing testbed 51s Reading package lists... 51s Building dependency tree... 51s Reading state information... 51s Solving dependencies... 51s The following NEW packages will be installed: 51s bowtie bowtie2 bwa fontconfig-config fonts-dejavu-core fonts-dejavu-mono 51s fonts-lyx fonts-urw-base35 gasic gasic-examples libblas3 libcairo2 51s libdeflate0 libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 51s libharfbuzz0b libhts3t64 libhtscodecs2 libimagequant0 libjbig0 51s libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4 libopenjp2-7 51s libpixman-1-0 libqhull-r8.0 libraqm0 libsharpyuv0 libtcl8.6 libtiff6 51s libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 51s libxft2 libxrender1 libxslt1.1 libxss1 libzopfli1 python-matplotlib-data 51s python3-biopython python3-brotli python3-cairo python3-charset-normalizer 51s python3-contourpy python3-cycler python3-decorator python3-fonttools 51s python3-freetype python3-fs python3-kiwisolver python3-lxml python3-lz4 51s python3-matplotlib python3-mpmath python3-numpy python3-numpy-dev 51s python3-pil python3-pil.imagetk python3-platformdirs python3-pysam 51s python3-reportlab python3-rlpycairo python3-scipy python3-sympy python3-tk 51s python3-ufolib2 python3-unicodedata2 python3-zopfli python3.13-tk 51s python3.14-tk seqan-apps sgml-base unicode-data w3c-sgml-lib x11-common 51s xfonts-encodings xfonts-utils xml-core 51s 0 upgraded, 86 newly installed, 0 to remove and 0 not upgraded. 51s Need to get 119 MB of archives. 51s After this operation, 503 MB of additional disk space will be used. 51s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1ubuntu1 [147 kB] 51s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7 [259 kB] 51s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-9ubuntu1 [939 kB] 52s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7 [2739 kB] 52s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.2.4+ds-1ubuntu1 [5377 kB] 52s Get:6 http://ftpmaster.internal/ubuntu resolute/universe amd64 bwa amd64 0.7.19-1 [200 kB] 52s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 52s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 52s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontenc1 amd64 1:1.1.8-1build2 [14.1 kB] 52s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 52s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu3 [576 kB] 52s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 52s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 52s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.15.0-2.3ubuntu1 [38.0 kB] 52s Get:15 http://ftpmaster.internal/ubuntu resolute/universe amd64 fonts-lyx all 2.4.4-2 [171 kB] 52s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-decorator all 5.2.1-2 [28.1 kB] 52s Get:17 http://ftpmaster.internal/ubuntu resolute/universe amd64 libqhull-r8.0 amd64 2020.2-7 [197 kB] 52s Get:18 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-scipy amd64 1.16.3-1 [18.8 MB] 53s Get:19 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-charset-normalizer amd64 3.4.4-1 [175 kB] 53s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1 [1036 kB] 53s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.15.0-2.3ubuntu1 [141 kB] 53s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB] 53s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 53s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 53s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libtk8.6 amd64 8.6.17-1 [823 kB] 53s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.13-tk amd64 3.13.9-1 [108 kB] 53s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14-tk amd64 3.14.0-4 [108 kB] 53s Get:28 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-tk amd64 3.13.9-2 [11.1 kB] 53s Get:29 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pil.imagetk amd64 12.0.0-1ubuntu1 [9700 B] 53s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 15.2.0-9ubuntu1 [151 kB] 53s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 53s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu2 [152 kB] 53s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 53s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 liblcms2-2 amd64 2.17-1 [170 kB] 53s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 libopenjp2-7 amd64 2.5.3-2.1 [188 kB] 53s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 53s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.1.0-1 [535 kB] 53s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libraqm0 amd64 0.10.3-1 [15.4 kB] 53s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 53s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 53s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 53s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 53s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 53s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB] 53s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB] 53s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB] 53s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-pil amd64 12.0.0-1ubuntu1 [494 kB] 53s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.46.4-1 [287 kB] 53s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2build1 [17.4 kB] 53s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2build1 [6120 B] 53s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-1build1 [611 kB] 53s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-cairo amd64 1.27.0-2build1 [140 kB] 53s Get:53 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-freetype all 2.5.1-2 [92.2 kB] 53s Get:54 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-rlpycairo all 0.3.0-4 [9332 B] 53s Get:55 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-reportlab all 4.4.5-1 [1148 kB] 53s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 sgml-base all 1.31+nmu1 [11.0 kB] 53s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 xml-core all 0.19 [20.3 kB] 53s Get:58 http://ftpmaster.internal/ubuntu resolute/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 53s Get:59 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-biopython amd64 1.86+dfsg-1 [1682 kB] 53s Get:60 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhtscodecs2 amd64 1.6.1-2 [132 kB] 53s Get:61 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhts3t64 amd64 1.22.1+ds2-1 [461 kB] 53s Get:62 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pysam amd64 0.23.3+ds-2 [4536 kB] 53s Get:63 http://ftpmaster.internal/ubuntu resolute/universe amd64 python-matplotlib-data all 3.10.7+dfsg1-1 [2930 kB] 54s Get:64 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-contourpy amd64 1.3.3-1 [255 kB] 54s Get:65 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-cycler all 0.12.1-2 [9850 B] 54s Get:66 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-brotli amd64 1.1.0-2build6 [340 kB] 54s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-platformdirs all 4.4.0-1 [16.9 kB] 54s Get:68 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-fs all 2.4.16-9ubuntu1 [91.5 kB] 54s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 libxslt1.1 amd64 1.1.43-0.3 [172 kB] 54s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-lxml amd64 6.0.2-1 [2333 kB] 54s Get:71 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-lz4 amd64 4.4.4+dfsg-3 [27.5 kB] 54s Get:72 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-mpmath all 1.3.0-2 [423 kB] 54s Get:73 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-sympy all 1.14.0-2 [4306 kB] 54s Get:74 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.5 kB] 54s Get:75 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-unicodedata2 amd64 16.0.0+ds-1build1 [400 kB] 54s Get:76 http://ftpmaster.internal/ubuntu resolute/universe amd64 libzopfli1 amd64 1.0.3-3 [141 kB] 54s Get:77 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-zopfli amd64 0.4.0-1 [11.1 kB] 54s Get:78 http://ftpmaster.internal/ubuntu resolute/universe amd64 unicode-data all 16.0.0-1 [9513 kB] 54s Get:79 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-fonttools amd64 4.57.0-3 [1705 kB] 54s Get:80 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-kiwisolver amd64 1.4.10~rc0-1 [65.5 kB] 54s Get:81 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-matplotlib amd64 3.10.7+dfsg1-1 [17.2 MB] 55s Get:82 http://ftpmaster.internal/ubuntu resolute/universe amd64 bowtie amd64 1.3.1-3 [1562 kB] 55s Get:83 http://ftpmaster.internal/ubuntu resolute/universe amd64 bowtie2 amd64 2.5.4-1 [1336 kB] 55s Get:84 http://ftpmaster.internal/ubuntu resolute/universe amd64 seqan-apps amd64 2.4.0+dfsg-16 [12.3 MB] 57s Get:85 http://ftpmaster.internal/ubuntu resolute/universe amd64 gasic all 0.0.r19-8 [21.1 kB] 57s Get:86 http://ftpmaster.internal/ubuntu resolute/universe amd64 gasic-examples all 0.0.r19-8 [7270 kB] 57s Fetched 119 MB in 6s (20.3 MB/s) 57s Selecting previously unselected package python3-numpy-dev:amd64. 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 .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 58s Unpacking python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 58s Selecting previously unselected package libblas3:amd64. 58s Preparing to unpack .../01-libblas3_3.12.1-7_amd64.deb ... 58s Unpacking libblas3:amd64 (3.12.1-7) ... 58s Selecting previously unselected package libgfortran5:amd64. 58s Preparing to unpack .../02-libgfortran5_15.2.0-9ubuntu1_amd64.deb ... 58s Unpacking libgfortran5:amd64 (15.2.0-9ubuntu1) ... 58s Selecting previously unselected package liblapack3:amd64. 58s Preparing to unpack .../03-liblapack3_3.12.1-7_amd64.deb ... 58s Unpacking liblapack3:amd64 (3.12.1-7) ... 58s Selecting previously unselected package python3-numpy. 58s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 58s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 58s Selecting previously unselected package bwa. 58s Preparing to unpack .../05-bwa_0.7.19-1_amd64.deb ... 58s Unpacking bwa (0.7.19-1) ... 58s Selecting previously unselected package fonts-dejavu-mono. 58s Preparing to unpack .../06-fonts-dejavu-mono_2.37-8_all.deb ... 58s Unpacking fonts-dejavu-mono (2.37-8) ... 58s Selecting previously unselected package fonts-dejavu-core. 58s Preparing to unpack .../07-fonts-dejavu-core_2.37-8_all.deb ... 58s Unpacking fonts-dejavu-core (2.37-8) ... 58s Selecting previously unselected package libfontenc1:amd64. 58s Preparing to unpack .../08-libfontenc1_1%3a1.1.8-1build2_amd64.deb ... 58s Unpacking libfontenc1:amd64 (1:1.1.8-1build2) ... 58s Selecting previously unselected package x11-common. 58s Preparing to unpack .../09-x11-common_1%3a7.7+24ubuntu1_all.deb ... 58s Unpacking x11-common (1:7.7+24ubuntu1) ... 58s Selecting previously unselected package xfonts-encodings. 58s Preparing to unpack .../10-xfonts-encodings_1%3a1.0.5-0ubuntu3_all.deb ... 58s Unpacking xfonts-encodings (1:1.0.5-0ubuntu3) ... 58s Selecting previously unselected package xfonts-utils. 58s Preparing to unpack .../11-xfonts-utils_1%3a7.7+7_amd64.deb ... 58s Unpacking xfonts-utils (1:7.7+7) ... 58s Selecting previously unselected package fonts-urw-base35. 58s Preparing to unpack .../12-fonts-urw-base35_20200910-8_all.deb ... 58s Unpacking fonts-urw-base35 (20200910-8) ... 58s Selecting previously unselected package fontconfig-config. 58s Preparing to unpack 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... 58s Selecting previously unselected package libtcl8.6:amd64. 58s Preparing to unpack .../19-libtcl8.6_8.6.17+dfsg-1_amd64.deb ... 58s Unpacking libtcl8.6:amd64 (8.6.17+dfsg-1) ... 58s Selecting previously unselected package libfontconfig1:amd64. 58s Preparing to unpack .../20-libfontconfig1_2.15.0-2.3ubuntu1_amd64.deb ... 58s Unpacking libfontconfig1:amd64 (2.15.0-2.3ubuntu1) ... 58s Selecting previously unselected package libxrender1:amd64. 58s Preparing to unpack .../21-libxrender1_1%3a0.9.12-1_amd64.deb ... 58s Unpacking libxrender1:amd64 (1:0.9.12-1) ... 58s Selecting previously unselected package libxft2:amd64. 58s Preparing to unpack .../22-libxft2_2.3.6-1build1_amd64.deb ... 58s Unpacking libxft2:amd64 (2.3.6-1build1) ... 58s Selecting previously unselected package libxss1:amd64. 58s Preparing to unpack .../23-libxss1_1%3a1.2.3-1build3_amd64.deb ... 58s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 58s Selecting previously unselected package libtk8.6:amd64. 58s Preparing to unpack .../24-libtk8.6_8.6.17-1_amd64.deb ... 58s Unpacking libtk8.6:amd64 (8.6.17-1) ... 58s Selecting previously unselected package python3.13-tk. 58s Preparing to unpack .../25-python3.13-tk_3.13.9-1_amd64.deb ... 58s Unpacking python3.13-tk (3.13.9-1) ... 58s Selecting previously unselected package python3.14-tk. 58s Preparing to unpack .../26-python3.14-tk_3.14.0-4_amd64.deb ... 58s Unpacking python3.14-tk (3.14.0-4) ... 58s Selecting previously unselected package python3-tk. 58s Preparing to unpack .../27-python3-tk_3.13.9-2_amd64.deb ... 58s Unpacking python3-tk (3.13.9-2) ... 58s Selecting previously unselected package python3-pil.imagetk:amd64. 58s Preparing to unpack .../28-python3-pil.imagetk_12.0.0-1ubuntu1_amd64.deb ... 58s Unpacking python3-pil.imagetk:amd64 (12.0.0-1ubuntu1) ... 58s Selecting previously unselected package libgomp1:amd64. 58s Preparing to unpack .../29-libgomp1_15.2.0-9ubuntu1_amd64.deb ... 58s Unpacking libgomp1:amd64 (15.2.0-9ubuntu1) ... 58s Selecting previously unselected package libimagequant0:amd64. 58s Preparing to unpack .../30-libimagequant0_2.18.0-1build1_amd64.deb ... 58s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 58s Selecting previously unselected package libjpeg-turbo8:amd64. 58s Preparing to unpack .../31-libjpeg-turbo8_2.1.5-4ubuntu2_amd64.deb ... 58s Unpacking libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 58s Selecting previously unselected package libjpeg8:amd64. 58s Preparing to unpack .../32-libjpeg8_8c-2ubuntu11_amd64.deb ... 58s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 58s Selecting previously unselected package liblcms2-2:amd64. 58s Preparing to unpack .../33-liblcms2-2_2.17-1_amd64.deb ... 58s Unpacking liblcms2-2:amd64 (2.17-1) ... 58s Selecting previously unselected package libopenjp2-7:amd64. 59s Preparing to unpack .../34-libopenjp2-7_2.5.3-2.1_amd64.deb ... 59s Unpacking libopenjp2-7:amd64 (2.5.3-2.1) ... 59s Selecting previously unselected package libgraphite2-3:amd64. 59s Preparing to unpack .../35-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 59s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 59s Selecting previously unselected package libharfbuzz0b:amd64. 59s Preparing to unpack .../36-libharfbuzz0b_12.1.0-1_amd64.deb ... 59s Unpacking libharfbuzz0b:amd64 (12.1.0-1) ... 59s Selecting previously unselected package libraqm0:amd64. 59s Preparing to unpack .../37-libraqm0_0.10.3-1_amd64.deb ... 59s Unpacking libraqm0:amd64 (0.10.3-1) ... 59s Selecting previously unselected package libdeflate0:amd64. 59s Preparing to unpack .../38-libdeflate0_1.23-2_amd64.deb ... 59s Unpacking libdeflate0:amd64 (1.23-2) ... 59s Selecting previously unselected package libjbig0:amd64. 59s Preparing to unpack .../39-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 59s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 59s Selecting previously unselected package liblerc4:amd64. 59s Preparing to unpack .../40-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 59s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 59s Selecting previously unselected package libsharpyuv0:amd64. 59s Preparing to unpack .../41-libsharpyuv0_1.5.0-0.1_amd64.deb ... 59s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 59s Selecting previously unselected package libwebp7:amd64. 59s Preparing to unpack .../42-libwebp7_1.5.0-0.1_amd64.deb ... 59s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 59s Selecting previously unselected package libtiff6:amd64. 59s Preparing to unpack .../43-libtiff6_4.7.0-3ubuntu3_amd64.deb ... 59s Unpacking libtiff6:amd64 (4.7.0-3ubuntu3) ... 59s Selecting previously unselected package libwebpdemux2:amd64. 59s Preparing to unpack .../44-libwebpdemux2_1.5.0-0.1_amd64.deb ... 59s Unpacking libwebpdemux2:amd64 (1.5.0-0.1) ... 59s Selecting previously unselected package libwebpmux3:amd64. 59s Preparing to unpack .../45-libwebpmux3_1.5.0-0.1_amd64.deb ... 59s Unpacking libwebpmux3:amd64 (1.5.0-0.1) ... 59s Selecting previously unselected package python3-pil:amd64. 59s Preparing to unpack .../46-python3-pil_12.0.0-1ubuntu1_amd64.deb ... 59s Unpacking python3-pil:amd64 (12.0.0-1ubuntu1) ... 59s Selecting previously unselected package libpixman-1-0:amd64. 59s Preparing to unpack .../47-libpixman-1-0_0.46.4-1_amd64.deb ... 59s Unpacking libpixman-1-0:amd64 (0.46.4-1) ... 59s Selecting previously unselected package libxcb-render0:amd64. 59s Preparing to unpack .../48-libxcb-render0_1.17.0-2build1_amd64.deb ... 59s Unpacking libxcb-render0:amd64 (1.17.0-2build1) ... 59s Selecting previously unselected package libxcb-shm0:amd64. 59s Preparing to unpack .../49-libxcb-shm0_1.17.0-2build1_amd64.deb ... 59s Unpacking libxcb-shm0:amd64 (1.17.0-2build1) ... 59s Selecting previously unselected package libcairo2:amd64. 59s Preparing to unpack .../50-libcairo2_1.18.4-1build1_amd64.deb ... 59s Unpacking libcairo2:amd64 (1.18.4-1build1) ... 59s Selecting previously unselected package python3-cairo. 59s Preparing to unpack .../51-python3-cairo_1.27.0-2build1_amd64.deb ... 59s Unpacking python3-cairo (1.27.0-2build1) ... 59s Selecting previously unselected package python3-freetype. 59s Preparing to unpack .../52-python3-freetype_2.5.1-2_all.deb ... 59s Unpacking python3-freetype (2.5.1-2) ... 59s Selecting previously unselected package python3-rlpycairo. 59s Preparing to unpack .../53-python3-rlpycairo_0.3.0-4_all.deb ... 59s Unpacking python3-rlpycairo (0.3.0-4) ... 59s Selecting previously unselected package python3-reportlab. 59s Preparing to unpack .../54-python3-reportlab_4.4.5-1_all.deb ... 59s Unpacking python3-reportlab (4.4.5-1) ... 59s Selecting previously unselected package sgml-base. 59s Preparing to unpack .../55-sgml-base_1.31+nmu1_all.deb ... 59s Unpacking sgml-base (1.31+nmu1) ... 59s Selecting previously unselected package xml-core. 59s Preparing to unpack .../56-xml-core_0.19_all.deb ... 59s Unpacking xml-core (0.19) ... 59s Selecting previously unselected package w3c-sgml-lib. 59s Preparing to unpack .../57-w3c-sgml-lib_1.3-3_all.deb ... 59s Unpacking w3c-sgml-lib (1.3-3) ... 59s Selecting previously unselected package python3-biopython. 59s Preparing to unpack .../58-python3-biopython_1.86+dfsg-1_amd64.deb ... 59s Unpacking python3-biopython (1.86+dfsg-1) ... 59s Selecting previously unselected package libhtscodecs2:amd64. 59s Preparing to unpack .../59-libhtscodecs2_1.6.1-2_amd64.deb ... 59s Unpacking libhtscodecs2:amd64 (1.6.1-2) ... 59s Selecting previously unselected package libhts3t64:amd64. 59s Preparing to unpack .../60-libhts3t64_1.22.1+ds2-1_amd64.deb ... 59s Unpacking libhts3t64:amd64 (1.22.1+ds2-1) ... 59s Selecting previously unselected package python3-pysam. 59s Preparing to unpack .../61-python3-pysam_0.23.3+ds-2_amd64.deb ... 59s Unpacking python3-pysam (0.23.3+ds-2) ... 59s Selecting previously unselected package python-matplotlib-data. 59s Preparing to unpack .../62-python-matplotlib-data_3.10.7+dfsg1-1_all.deb ... 59s Unpacking python-matplotlib-data (3.10.7+dfsg1-1) ... 59s Selecting previously unselected package python3-contourpy. 59s Preparing to unpack .../63-python3-contourpy_1.3.3-1_amd64.deb ... 59s Unpacking python3-contourpy (1.3.3-1) ... 59s Selecting previously unselected package python3-cycler. 59s Preparing to unpack .../64-python3-cycler_0.12.1-2_all.deb ... 59s Unpacking python3-cycler (0.12.1-2) ... 59s Selecting previously unselected package python3-brotli. 59s Preparing to unpack .../65-python3-brotli_1.1.0-2build6_amd64.deb ... 59s Unpacking python3-brotli (1.1.0-2build6) ... 59s Selecting previously unselected package python3-platformdirs. 59s Preparing to unpack .../66-python3-platformdirs_4.4.0-1_all.deb ... 59s Unpacking python3-platformdirs (4.4.0-1) ... 59s Selecting previously unselected package python3-fs. 59s Preparing to unpack .../67-python3-fs_2.4.16-9ubuntu1_all.deb ... 59s Unpacking python3-fs (2.4.16-9ubuntu1) ... 59s Selecting previously unselected package libxslt1.1:amd64. 59s Preparing to unpack .../68-libxslt1.1_1.1.43-0.3_amd64.deb ... 59s Unpacking libxslt1.1:amd64 (1.1.43-0.3) ... 59s Selecting previously unselected package python3-lxml:amd64. 59s Preparing to unpack .../69-python3-lxml_6.0.2-1_amd64.deb ... 59s Unpacking python3-lxml:amd64 (6.0.2-1) ... 59s Selecting previously unselected package python3-lz4. 59s Preparing to unpack .../70-python3-lz4_4.4.4+dfsg-3_amd64.deb ... 59s Unpacking python3-lz4 (4.4.4+dfsg-3) ... 59s Selecting previously unselected package python3-mpmath. 59s Preparing to unpack .../71-python3-mpmath_1.3.0-2_all.deb ... 59s Unpacking python3-mpmath (1.3.0-2) ... 59s Selecting previously unselected package python3-sympy. 59s Preparing to unpack .../72-python3-sympy_1.14.0-2_all.deb ... 59s Unpacking python3-sympy (1.14.0-2) ... 59s Selecting previously unselected package python3-ufolib2. 59s Preparing to unpack .../73-python3-ufolib2_0.17.1+dfsg1-1_all.deb ... 59s Unpacking python3-ufolib2 (0.17.1+dfsg1-1) ... 59s Selecting previously unselected package python3-unicodedata2. 59s Preparing to unpack .../74-python3-unicodedata2_16.0.0+ds-1build1_amd64.deb ... 59s Unpacking python3-unicodedata2 (16.0.0+ds-1build1) ... 59s Selecting previously unselected package libzopfli1. 59s Preparing to unpack .../75-libzopfli1_1.0.3-3_amd64.deb ... 59s Unpacking libzopfli1 (1.0.3-3) ... 59s Selecting previously unselected package python3-zopfli. 59s Preparing to unpack .../76-python3-zopfli_0.4.0-1_amd64.deb ... 59s Unpacking python3-zopfli (0.4.0-1) ... 59s Selecting previously unselected package unicode-data. 59s Preparing to unpack .../77-unicode-data_16.0.0-1_all.deb ... 59s Unpacking unicode-data (16.0.0-1) ... 59s Selecting previously unselected package python3-fonttools. 59s Preparing to unpack .../78-python3-fonttools_4.57.0-3_amd64.deb ... 59s Unpacking python3-fonttools (4.57.0-3) ... 60s Selecting previously unselected package python3-kiwisolver. 60s Preparing to unpack .../79-python3-kiwisolver_1.4.10~rc0-1_amd64.deb ... 60s Unpacking python3-kiwisolver (1.4.10~rc0-1) ... 60s Selecting previously unselected package python3-matplotlib. 60s Preparing to unpack .../80-python3-matplotlib_3.10.7+dfsg1-1_amd64.deb ... 60s Unpacking python3-matplotlib (3.10.7+dfsg1-1) ... 60s Selecting previously unselected package bowtie. 60s Preparing to unpack .../81-bowtie_1.3.1-3_amd64.deb ... 60s Unpacking bowtie (1.3.1-3) ... 60s Selecting previously unselected package bowtie2. 60s Preparing to unpack .../82-bowtie2_2.5.4-1_amd64.deb ... 60s Unpacking bowtie2 (2.5.4-1) ... 60s Selecting previously unselected package seqan-apps. 60s Preparing to unpack .../83-seqan-apps_2.4.0+dfsg-16_amd64.deb ... 60s Unpacking seqan-apps (2.4.0+dfsg-16) ... 60s Selecting previously unselected package gasic. 60s Preparing to unpack .../84-gasic_0.0.r19-8_all.deb ... 60s Unpacking gasic (0.0.r19-8) ... 60s Selecting previously unselected package gasic-examples. 60s Preparing to unpack .../85-gasic-examples_0.0.r19-8_all.deb ... 60s Unpacking gasic-examples (0.0.r19-8) ... 60s Setting up libhtscodecs2:amd64 (1.6.1-2) ... 60s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 60s Setting up liblcms2-2:amd64 (2.17-1) ... 60s Setting up libpixman-1-0:amd64 (0.46.4-1) ... 60s Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... 60s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 60s Setting up bowtie (1.3.1-3) ... 60s Setting up libxrender1:amd64 (1:0.9.12-1) ... 60s Setting up python3-lz4 (4.4.4+dfsg-3) ... 60s Setting up libxcb-render0:amd64 (1.17.0-2build1) ... 60s Setting up python3-charset-normalizer (3.4.4-1) ... 60s Setting up bwa (0.7.19-1) ... 60s Setting up python3-unicodedata2 (16.0.0+ds-1build1) ... 60s Setting up fonts-lyx (2.4.4-2) ... 60s Setting up gasic-examples (0.0.r19-8) ... 60s Setting up x11-common (1:7.7+24ubuntu1) ... 60s Setting up libdeflate0:amd64 (1.23-2) ... 60s Setting up libqhull-r8.0:amd64 (2020.2-7) ... 60s Setting up libxcb-shm0:amd64 (1.17.0-2build1) ... 60s Setting up libgomp1:amd64 (15.2.0-9ubuntu1) ... 60s Setting up python3-freetype (2.5.1-2) ... 60s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 60s Setting up python3-platformdirs (4.4.0-1) ... 60s Setting up bowtie2 (2.5.4-1) ... 60s Setting up python3-fs (2.4.16-9ubuntu1) ... 61s Setting up unicode-data (16.0.0-1) ... 61s Setting up python3-decorator (5.2.1-2) ... 61s Setting up libfontenc1:amd64 (1:1.1.8-1build2) ... 61s Setting up libblas3:amd64 (3.12.1-7) ... 61s 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 61s Setting up libzopfli1 (1.0.3-3) ... 61s Setting up python3-brotli (1.1.0-2build6) ... 61s Setting up xfonts-encodings (1:1.0.5-0ubuntu3) ... 61s Setting up python3-cycler (0.12.1-2) ... 61s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 61s Setting up seqan-apps (2.4.0+dfsg-16) ... 61s Setting up fonts-dejavu-mono (2.37-8) ... 61s Setting up python3-kiwisolver (1.4.10~rc0-1) ... 61s Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 61s Setting up libtcl8.6:amd64 (8.6.17+dfsg-1) ... 61s Setting up fonts-dejavu-core (2.37-8) ... 61s Setting up libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 61s Setting up libgfortran5:amd64 (15.2.0-9ubuntu1) ... 61s Setting up libwebp7:amd64 (1.5.0-0.1) ... 61s Setting up libxslt1.1:amd64 (1.1.43-0.3) ... 61s Setting up libhts3t64:amd64 (1.22.1+ds2-1) ... 61s Setting up libopenjp2-7:amd64 (2.5.3-2.1) ... 61s Setting up libharfbuzz0b:amd64 (12.1.0-1) ... 61s Setting up sgml-base (1.31+nmu1) ... 61s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 61s Setting up python3-mpmath (1.3.0-2) ... 61s Setting up python-matplotlib-data (3.10.7+dfsg1-1) ... 61s Setting up libwebpmux3:amd64 (1.5.0-0.1) ... 61s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 61s Setting up python3-sympy (1.14.0-2) ... 65s Setting up liblapack3:amd64 (3.12.1-7) ... 65s 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 65s Setting up python3-pysam (0.23.3+ds-2) ... 65s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ... 65s Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... 65s Setting up xfonts-utils (1:7.7+7) ... 65s Setting up python3-zopfli (0.4.0-1) ... 65s Setting up libraqm0:amd64 (0.10.3-1) ... 65s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 66s Setting up python3-lxml:amd64 (6.0.2-1) ... 66s Setting up libtiff6:amd64 (4.7.0-3ubuntu3) ... 66s Setting up xml-core (0.19) ... 66s Setting up python3-contourpy (1.3.3-1) ... 66s Setting up libfontconfig1:amd64 (2.15.0-2.3ubuntu1) ... 66s Setting up libxft2:amd64 (2.3.6-1build1) ... 66s Setting up python3-scipy (1.16.3-1) ... 68s Setting up libtk8.6:amd64 (8.6.17-1) ... 68s Setting up fonts-urw-base35 (20200910-8) ... 68s Setting up libcairo2:amd64 (1.18.4-1build1) ... 68s Setting up python3.13-tk (3.13.9-1) ... 68s Setting up python3-pil:amd64 (12.0.0-1ubuntu1) ... 69s Setting up python3.14-tk (3.14.0-4) ... 69s Setting up python3-cairo (1.27.0-2build1) ... 69s Setting up python3-tk (3.13.9-2) ... 69s Setting up python3-pil.imagetk:amd64 (12.0.0-1ubuntu1) ... 69s Setting up python3-rlpycairo (0.3.0-4) ... 69s Setting up python3-reportlab (4.4.5-1) ... 69s Setting up python3-fonttools (4.57.0-3) ... 70s Setting up python3-ufolib2 (0.17.1+dfsg1-1) ... 70s Setting up python3-matplotlib (3.10.7+dfsg1-1) ... 71s Processing triggers for libc-bin (2.42-2ubuntu2) ... 71s Processing triggers for man-db (2.13.1-1) ... 71s Processing triggers for sgml-base (1.31+nmu1) ... 71s Setting up w3c-sgml-lib (1.3-3) ... 87s Setting up python3-biopython (1.86+dfsg-1) ... 87s Setting up gasic (0.0.r19-8) ... 88s autopkgtest [23:02:14]: test run-unit-test: [----------------------- 89s [bwa_index] Pack FASTA... Test 0: Create Genome Indices 89s 0.00 sec 89s [bwa_index] Construct BWT for the packed sequence... 89s [bwa_index] 0.00 seconds elapse. 89s [bwa_index] Update BWT... 0.00 sec 89s [bwa_index] Pack forward-only FASTA... 0.00 sec 89s [bwa_index] Construct SA from BWT and Occ... 0.00 sec 89s [main] Version: 0.7.19-r1273 89s [main] CMD: bwa index dwv.fasta 89s [main] Real time: 0.024 sec; CPU: 0.003 sec 89s [bwa_index] Pack FASTA... 0.00 sec 89s [bwa_index] Construct BWT for the packed sequence... 89s [bwa_index] 0.00 seconds elapse. 89s [bwa_index] Update BWT... 0.00 sec 89s [bwa_index] Pack forward-only FASTA... 0.00 sec 89s [bwa_index] Construct SA from BWT and Occ... 0.00 sec 89s [main] Version: 0.7.19-r1273 89s [main] CMD: bwa index vdv1.fasta 89s [main] Real time: 0.014 sec; CPU: 0.003 sec 89s [bwa_index] Pack FASTA... 0.00 sec 89s [bwa_index] Construct BWT for the packed sequence... 89s [bwa_index] 0.00 seconds elapse. 89s [bwa_index] Update BWT... 0.00 sec 89s [bwa_index] Pack forward-only FASTA... 0.00 sec 89s [bwa_index] Construct SA from BWT and Occ... 0.00 sec 89s [main] Version: 0.7.19-r1273 89s [main] CMD: bwa index vdv1dwv9.fasta 89s [main] Real time: 0.013 sec; CPU: 0.003 sec 89s [bwa_index] Pack FASTA... 0.00 sec 89s [bwa_index] Construct BWT for the packed sequence... 89s [bwa_index] 0.00 seconds elapse. 89s [bwa_index] Update BWT... 0.00 sec 89s [bwa_index] Pack forward-only FASTA... 0.00 sec 89s [bwa_index] Construct SA from BWT and Occ... 0.00 sec 89s [main] Version: 0.7.19-r1273 89s [main] CMD: bwa index vdv1dwv5.fasta 89s [main] Real time: 0.010 sec; CPU: 0.003 sec 89s Passed 89s 89s Test 1: run_mappers 89s [bwa_aln] 17bp reads: max_diff = 2 89s [bwa_aln] 38bp reads: max_diff = 3 89s [bwa_aln] 64bp reads: max_diff = 4 89s [bwa_aln] 93bp reads: max_diff = 5 89s [bwa_aln] 124bp reads: max_diff = 6 89s [bwa_aln] 157bp reads: max_diff = 7 89s [bwa_aln] 190bp reads: max_diff = 8 89s [bwa_aln] 225bp reads: max_diff = 9 89s [bwa_aln_core] calculate SA coordinate... 0.64 sec 89s [bwa_aln_core] write to the disk... 0.00 sec 89s [bwa_aln_core] 100000 sequences have been processed. 89s [main] Version: 0.7.19-r1273 89s [main] CMD: bwa aln ./genomes/dwv.fasta reads/SRR059298_subset.fastq 89s [main] Real time: 0.696 sec; CPU: 0.692 sec 90s [bwa_aln_core] convert to sequence coordinate... 0.04 sec 90s [bwa_aln_core] refine gapped alignments... 0.02 sec 90s [bwa_aln_core] print alignments... 0.04 sec 90s [bwa_aln_core] 100000 sequences have been processed. 90s [main] Version: 0.7.19-r1273 90s [main] CMD: bwa samse ./genomes/dwv.fasta /tmp/res.sai reads/SRR059298_subset.fastq 90s [main] Real time: 0.174 sec; CPU: 0.167 sec 90s [bwa_aln] 17bp reads: max_diff = 2 90s [bwa_aln] 38bp reads: max_diff = 3 90s [bwa_aln] 64bp reads: max_diff = 4 90s [bwa_aln] 93bp reads: max_diff = 5 90s [bwa_aln] 124bp reads: max_diff = 6 90s [bwa_aln] 157bp reads: max_diff = 7 90s [bwa_aln] 190bp reads: max_diff = 8 90s [bwa_aln] 225bp reads: max_diff = 9 90s [bwa_aln_core] calculate SA coordinate... 0.48 sec 90s [bwa_aln_core] write to the disk... 0.00 sec 90s [bwa_aln_core] 100000 sequences have been processed. 90s [main] Version: 0.7.19-r1273 90s [main] CMD: bwa aln ./genomes/vdv1.fasta reads/SRR059298_subset.fastq 90s [main] Real time: 0.541 sec; CPU: 0.538 sec 90s [bwa_aln_core] convert to sequence coordinate... 0.03 sec 90s [bwa_aln_core] refine gapped alignments... 0.01 sec 90s [bwa_aln_core] print alignments... 0.03 sec 90s [bwa_aln_core] 100000 sequences have been processed. 90s [main] Version: 0.7.19-r1273 90s [main] CMD: bwa samse ./genomes/vdv1.fasta /tmp/res.sai reads/SRR059298_subset.fastq 90s [main] Real time: 0.139 sec; CPU: 0.131 sec 90s [bwa_aln] 17bp reads: max_diff = 2 90s [bwa_aln] 38bp reads: max_diff = 3 90s [bwa_aln] 64bp reads: max_diff = 4 90s [bwa_aln] 93bp reads: max_diff = 5 90s [bwa_aln] 124bp reads: max_diff = 6 90s [bwa_aln] 157bp reads: max_diff = 7 90s [bwa_aln] 190bp reads: max_diff = 8 90s [bwa_aln] 225bp reads: max_diff = 9 91s [bwa_aln_core] calculate SA coordinate... 0.81 sec 91s [bwa_aln_core] write to the disk... 0.00 sec 91s [bwa_aln_core] 100000 sequences have been processed. 91s [main] Version: 0.7.19-r1273 91s [main] CMD: bwa aln ./genomes/vdv1dwv5.fasta reads/SRR059298_subset.fastq 91s [main] Real time: 0.875 sec; CPU: 0.870 sec 91s [bwa_aln_core] convert to sequence coordinate... 0.07 sec 91s [bwa_aln_core] refine gapped alignments... 0.02 sec 91s [bwa_aln_core] print alignments... 0.05 sec 91s [bwa_aln_core] 100000 sequences have been processed. 91s [main] Version: 0.7.19-r1273 91s [main] CMD: bwa samse ./genomes/vdv1dwv5.fasta /tmp/res.sai reads/SRR059298_subset.fastq 91s [main] Real time: 0.210 sec; CPU: 0.203 sec 91s [bwa_aln] 17bp reads: max_diff = 2 91s [bwa_aln] 38bp reads: max_diff = 3 91s [bwa_aln] 64bp reads: max_diff = 4 91s [bwa_aln] 93bp reads: max_diff = 5 91s [bwa_aln] 124bp reads: max_diff = 6 91s [bwa_aln] 157bp reads: max_diff = 7 91s [bwa_aln] 190bp reads: max_diff = 8 91s [bwa_aln] 225bp reads: max_diff = 9 92s [bwa_aln_core] calculate SA coordinate... 0.73 sec 92s [bwa_aln_core] write to the disk... 0.00 sec 92s [bwa_aln_core] 100000 sequences have been processed. 92s [main] Version: 0.7.19-r1273 92s [main] CMD: bwa aln ./genomes/vdv1dwv9.fasta reads/SRR059298_subset.fastq 92s [main] Real time: 0.795 sec; CPU: 0.791 sec 92s [bwa_aln_core] convert to sequence coordinate... 0.05 sec 92s [bwa_aln_core] refine gapped alignments... 0.02 sec 92s [bwa_aln_core] print alignments... 0.05 sec 92s [bwa_aln_core] 100000 sequences have been processed. 92s [main] Version: 0.7.19-r1273 92s [main] CMD: bwa samse ./genomes/vdv1dwv9.fasta /tmp/res.sai reads/SRR059298_subset.fastq 92s [main] Real time: 0.186 sec; CPU: 0.180 sec 92s --- mapping reads with bwa to ./genomes/dwv.fasta 92s Executing: bwa aln ./genomes/dwv.fasta reads/SRR059298_subset.fastq > /tmp/res.sai 92s --- mapping reads with bwa to ./genomes/vdv1.fasta 92s Executing: bwa aln ./genomes/vdv1.fasta reads/SRR059298_subset.fastq > /tmp/res.sai 92s --- mapping reads with bwa to ./genomes/vdv1dwv5.fasta 92s Executing: bwa aln ./genomes/vdv1dwv5.fasta reads/SRR059298_subset.fastq > /tmp/res.sai 92s --- mapping reads with bwa to ./genomes/vdv1dwv9.fasta 92s Executing: bwa aln ./genomes/vdv1dwv9.fasta reads/SRR059298_subset.fastq > /tmp/res.sai 92s 92s Mapping done. 92s 92s Passed 92s 92s Test 2: create_matrix 92s MASON SIMULATOR 92s =============== 92s 92s ____INITIALIZING______________________________________________________________ 92s 92s Opening reference and variants file ... OK 92s Initializing fragment-to-contig distribution ... OK 92s Initializing simulation threads ... OK 92s Opening output file ./SAM/dwv.fastq ... OK 92s 92s ____READ SIMULATION___________________________________________________________ 92s 92s Distributing fragments to 1 contigs (1 haplotypes each) ... OK 92s 92s Simulating Reads: 93s gi|71480055|ref|NC_004830.2| (allele 1) .. (10000 fragments) OK 93s Done simulating reads. 93s 93s Joining temporary files ... OK 93s rm: cannot remove './SAM/dwv.fastq.sam': No such file or directory 93s MASON SIMULATOR 93s =============== 93s 93s ____INITIALIZING______________________________________________________________ 93s 93s Opening reference and variants file ... OK 93s Initializing fragment-to-contig distribution ... OK 93s Initializing simulation threads ... OK 93s Opening output file ./SAM/vdv1.fastq ... OK 93s 93s ____READ SIMULATION___________________________________________________________ 93s 93s Distributing fragments to 1 contigs (1 haplotypes each) ... OK 93s 93s Simulating Reads: 93s gi|56121875|ref|NC_006494.1| (allele 1) .. (10000 fragments) OK 93s Done simulating reads. 93s 93s Joining temporary files ... OK 93s rm: cannot remove './SAM/vdv1.fastq.sam': No such file or directory 93s MASON SIMULATOR 93s =============== 93s 93s ____INITIALIZING______________________________________________________________ 93s 93s Opening reference and variants file ... OK 93s Initializing fragment-to-contig distribution ... OK 93s Initializing simulation threads ... OK 93s Opening output file ./SAM/vdv1dwv5.fastq ... OK 93s 93s ____READ SIMULATION___________________________________________________________ 93s 93s Distributing fragments to 1 contigs (1 haplotypes each) ... OK 93s 93s Simulating Reads: 93s gi|301070167|gb|HM067437.1| (allele 1) .. (10000 fragments) OK 93s Done simulating reads. 93s 93s Joining temporary files ... OK 93s rm: cannot remove './SAM/vdv1dwv5.fastq.sam': No such file or directory 93s MASON SIMULATOR 93s =============== 93s 93s ____INITIALIZING______________________________________________________________ 93s 93s Opening reference and variants file ... OK 93s Initializing fragment-to-contig distribution ... OK 93s Initializing simulation threads ... OK 93s Opening output file ./SAM/vdv1dwv9.fastq ... OK 93s 93s ____READ SIMULATION___________________________________________________________ 93s 93s Distributing fragments to 1 contigs (1 haplotypes each) ... OK 93s 93s Simulating Reads: 93s gi|301070169|gb|HM067438.1| (allele 1) .. (10000 fragments) OK 93s Done simulating reads. 93s 93s Joining temporary files ... OK 93s rm: cannot remove './SAM/vdv1dwv9.fastq.sam': No such file or directory 93s [bwa_aln] 17bp reads: max_diff = 2 93s [bwa_aln] 38bp reads: max_diff = 3 93s [bwa_aln] 64bp reads: max_diff = 4 93s [bwa_aln] 93bp reads: max_diff = 5 93s [bwa_aln] 124bp reads: max_diff = 6 93s [bwa_aln] 157bp reads: max_diff = 7 93s [bwa_aln] 190bp reads: max_diff = 8 93s [bwa_aln] 225bp reads: max_diff = 9 93s [bwa_aln_core] calculate SA coordinate... 0.08 sec 93s [bwa_aln_core] write to the disk... 0.00 sec 93s [bwa_aln_core] 10000 sequences have been processed. 93s [main] Version: 0.7.19-r1273 93s [main] CMD: bwa aln genomes/dwv.fasta ./SAM/dwv.fastq 93s [main] Real time: 0.092 sec; CPU: 0.090 sec 93s [bwa_aln_core] convert to sequence coordinate... 0.01 sec 93s [bwa_aln_core] refine gapped alignments... 0.00 sec 93s [bwa_aln_core] print alignments... 0.01 sec 93s [bwa_aln_core] 10000 sequences have been processed. 93s [main] Version: 0.7.19-r1273 93s [main] CMD: bwa samse genomes/dwv.fasta /tmp/res.sai ./SAM/dwv.fastq 93s [main] Real time: 0.028 sec; CPU: 0.024 sec 93s [bwa_aln] 17bp reads: max_diff = 2 93s [bwa_aln] 38bp reads: max_diff = 3 93s [bwa_aln] 64bp reads: max_diff = 4 93s [bwa_aln] 93bp reads: max_diff = 5 93s [bwa_aln] 124bp reads: max_diff = 6 93s [bwa_aln] 157bp reads: max_diff = 7 93s [bwa_aln] 190bp reads: max_diff = 8 93s [bwa_aln] 225bp reads: max_diff = 9 93s [bwa_aln_core] calculate SA coordinate... 0.02 sec 93s [bwa_aln_core] write to the disk... 0.00 sec 93s [bwa_aln_core] 10000 sequences have been processed. 93s [main] Version: 0.7.19-r1273 93s [main] CMD: bwa aln genomes/vdv1.fasta ./SAM/dwv.fastq 93s [main] Real time: 0.030 sec; CPU: 0.029 sec 93s [bwa_aln_core] convert to sequence coordinate... 0.00 sec 93s [bwa_aln_core] refine gapped alignments... 0.00 sec 93s [bwa_aln_core] print alignments... 0.00 sec 93s [bwa_aln_core] 10000 sequences have been processed. 93s [main] Version: 0.7.19-r1273 93s [main] CMD: bwa samse genomes/vdv1.fasta /tmp/res.sai ./SAM/dwv.fastq 93s [main] Real time: 0.011 sec; CPU: 0.007 sec 93s [bwa_aln] 17bp reads: max_diff = 2 93s [bwa_aln] 38bp reads: max_diff = 3 93s [bwa_aln] 64bp reads: max_diff = 4 93s [bwa_aln] 93bp reads: max_diff = 5 93s [bwa_aln] 124bp reads: max_diff = 6 93s [bwa_aln] 157bp reads: max_diff = 7 93s [bwa_aln] 190bp reads: max_diff = 8 93s [bwa_aln] 225bp reads: max_diff = 9 93s [bwa_aln_core] calculate SA coordinate... 0.05 sec 93s [bwa_aln_core] write to the disk... 0.00 sec 93s [bwa_aln_core] 10000 sequences have been processed. 93s [main] Version: 0.7.19-r1273 93s [main] CMD: bwa aln genomes/vdv1dwv5.fasta ./SAM/dwv.fastq 93s [main] Real time: 0.060 sec; CPU: 0.058 sec 93s [bwa_aln_core] convert to sequence coordinate... 0.00 sec 93s [bwa_aln_core] refine gapped alignments... 0.00 sec 93s [bwa_aln_core] print alignments... 0.00 sec 93s [bwa_aln_core] 10000 sequences have been processed. 93s [main] Version: 0.7.19-r1273 93s [main] CMD: bwa samse genomes/vdv1dwv5.fasta /tmp/res.sai ./SAM/dwv.fastq 93s [main] Real time: 0.017 sec; CPU: 0.015 sec 93s [bwa_aln] 17bp reads: max_diff = 2 93s [bwa_aln] 38bp reads: max_diff = 3 93s [bwa_aln] 64bp reads: max_diff = 4 93s [bwa_aln] 93bp reads: max_diff = 5 93s [bwa_aln] 124bp reads: max_diff = 6 93s [bwa_aln] 157bp reads: max_diff = 7 93s [bwa_aln] 190bp reads: max_diff = 8 93s [bwa_aln] 225bp reads: max_diff = 9 93s [bwa_aln_core] calculate SA coordinate... 0.05 sec 93s [bwa_aln_core] write to the disk... 0.00 sec 93s [bwa_aln_core] 10000 sequences have been processed. 93s [main] Version: 0.7.19-r1273 93s [main] CMD: bwa aln genomes/vdv1dwv9.fasta ./SAM/dwv.fastq 93s [main] Real time: 0.060 sec; CPU: 0.057 sec 93s [bwa_aln_core] convert to sequence coordinate... 0.00 sec 93s [bwa_aln_core] refine gapped alignments... 0.00 sec 93s [bwa_aln_core] print alignments... 0.00 sec 93s [bwa_aln_core] 10000 sequences have been processed. 93s [main] Version: 0.7.19-r1273 93s [main] CMD: bwa samse genomes/vdv1dwv9.fasta /tmp/res.sai ./SAM/dwv.fastq 93s [main] Real time: 0.018 sec; CPU: 0.014 sec 93s [bwa_aln] 17bp reads: max_diff = 2 93s [bwa_aln] 38bp reads: max_diff = 3 93s [bwa_aln] 64bp reads: max_diff = 4 93s [bwa_aln] 93bp reads: max_diff = 5 93s [bwa_aln] 124bp reads: max_diff = 6 93s [bwa_aln] 157bp reads: max_diff = 7 93s [bwa_aln] 190bp reads: max_diff = 8 93s [bwa_aln] 225bp reads: max_diff = 9 93s [bwa_aln_core] calculate SA coordinate... 0.03 sec 93s [bwa_aln_core] write to the disk... 0.00 sec 93s [bwa_aln_core] 10000 sequences have been processed. 93s [main] Version: 0.7.19-r1273 93s [main] CMD: bwa aln genomes/dwv.fasta ./SAM/vdv1.fastq 93s [main] Real time: 0.032 sec; CPU: 0.030 sec 93s [bwa_aln_core] convert to sequence coordinate... 0.00 sec 93s [bwa_aln_core] refine gapped alignments... 0.00 sec 93s [bwa_aln_core] print alignments... 0.00 sec 93s [bwa_aln_core] 10000 sequences have been processed. 93s [main] Version: 0.7.19-r1273 93s [main] CMD: bwa samse genomes/dwv.fasta /tmp/res.sai ./SAM/vdv1.fastq 93s [main] Real time: 0.010 sec; CPU: 0.007 sec 93s [bwa_aln] 17bp reads: max_diff = 2 93s [bwa_aln] 38bp reads: max_diff = 3 93s [bwa_aln] 64bp reads: max_diff = 4 93s [bwa_aln] 93bp reads: max_diff = 5 93s [bwa_aln] 124bp reads: max_diff = 6 93s [bwa_aln] 157bp reads: max_diff = 7 93s [bwa_aln] 190bp reads: max_diff = 8 93s [bwa_aln] 225bp reads: max_diff = 9 93s [bwa_aln_core] calculate SA coordinate... 0.08 sec 93s [bwa_aln_core] write to the disk... 0.00 sec 93s [bwa_aln_core] 10000 sequences have been processed. 93s [main] Version: 0.7.19-r1273 93s [main] CMD: bwa aln genomes/vdv1.fasta ./SAM/vdv1.fastq 93s [main] Real time: 0.090 sec; CPU: 0.088 sec 93s [bwa_aln_core] convert to sequence coordinate... 0.01 sec 93s [bwa_aln_core] refine gapped alignments... 0.00 sec 93s [bwa_aln_core] print alignments... 0.01 sec 93s [bwa_aln_core] 10000 sequences have been processed. 93s [main] Version: 0.7.19-r1273 93s [main] CMD: bwa samse genomes/vdv1.fasta /tmp/res.sai ./SAM/vdv1.fastq 93s [main] Real time: 0.026 sec; CPU: 0.023 sec 93s [bwa_aln] 17bp reads: max_diff = 2 93s [bwa_aln] 38bp reads: max_diff = 3 93s [bwa_aln] 64bp reads: max_diff = 4 93s [bwa_aln] 93bp reads: max_diff = 5 93s [bwa_aln] 124bp reads: max_diff = 6 93s [bwa_aln] 157bp reads: max_diff = 7 93s [bwa_aln] 190bp reads: max_diff = 8 93s [bwa_aln] 225bp reads: max_diff = 9 93s [bwa_aln_core] calculate SA coordinate... 0.06 sec 93s [bwa_aln_core] write to the disk... 0.00 sec 93s [bwa_aln_core] 10000 sequences have been processed. 93s [main] Version: 0.7.19-r1273 93s [main] CMD: bwa aln genomes/vdv1dwv5.fasta ./SAM/vdv1.fastq 93s [main] Real time: 0.066 sec; CPU: 0.065 sec 93s [bwa_aln_core] convert to sequence coordinate... 0.00 sec 93s [bwa_aln_core] refine gapped alignments... 0.00 sec 93s [bwa_aln_core] print alignments... 0.00 sec 93s [bwa_aln_core] 10000 sequences have been processed. 93s [main] Version: 0.7.19-r1273 93s [main] CMD: bwa samse genomes/vdv1dwv5.fasta /tmp/res.sai ./SAM/vdv1.fastq 93s [main] Real time: 0.020 sec; CPU: 0.016 sec 93s [bwa_aln] 17bp reads: max_diff = 2 93s [bwa_aln] 38bp reads: max_diff = 3 93s [bwa_aln] 64bp reads: max_diff = 4 93s [bwa_aln] 93bp reads: max_diff = 5 93s [bwa_aln] 124bp reads: max_diff = 6 93s [bwa_aln] 157bp reads: max_diff = 7 93s [bwa_aln] 190bp reads: max_diff = 8 93s [bwa_aln] 225bp reads: max_diff = 9 93s [bwa_aln_core] calculate SA coordinate... 0.06 sec 93s [bwa_aln_core] write to the disk... 0.00 sec 93s [bwa_aln_core] 10000 sequences have been processed. 93s [main] Version: 0.7.19-r1273 93s [main] CMD: bwa aln genomes/vdv1dwv9.fasta ./SAM/vdv1.fastq 93s [main] Real time: 0.066 sec; CPU: 0.064 sec 93s [bwa_aln_core] convert to sequence coordinate... 0.00 sec 93s [bwa_aln_core] refine gapped alignments... 0.00 sec 93s [bwa_aln_core] print alignments... 0.00 sec 93s [bwa_aln_core] 10000 sequences have been processed. 93s [main] Version: 0.7.19-r1273 93s [main] CMD: bwa samse genomes/vdv1dwv9.fasta /tmp/res.sai ./SAM/vdv1.fastq 93s [main] Real time: 0.019 sec; CPU: 0.017 sec 93s [bwa_aln] 17bp reads: max_diff = 2 93s [bwa_aln] 38bp reads: max_diff = 3 93s [bwa_aln] 64bp reads: max_diff = 4 93s [bwa_aln] 93bp reads: max_diff = 5 93s [bwa_aln] 124bp reads: max_diff = 6 93s [bwa_aln] 157bp reads: max_diff = 7 93s [bwa_aln] 190bp reads: max_diff = 8 93s [bwa_aln] 225bp reads: max_diff = 9 93s [bwa_aln_core] calculate SA coordinate... 0.06 sec 93s [bwa_aln_core] write to the disk... 0.00 sec 93s [bwa_aln_core] 10000 sequences have been processed. 93s [main] Version: 0.7.19-r1273 93s [main] CMD: bwa aln genomes/dwv.fasta ./SAM/vdv1dwv5.fastq 93s [main] Real time: 0.062 sec; CPU: 0.060 sec 93s [bwa_aln_core] convert to sequence coordinate... 0.00 sec 93s [bwa_aln_core] refine gapped alignments... 0.00 sec 93s [bwa_aln_core] print alignments... 0.00 sec 93s [bwa_aln_core] 10000 sequences have been processed. 93s [main] Version: 0.7.19-r1273 93s [main] CMD: bwa samse genomes/dwv.fasta /tmp/res.sai ./SAM/vdv1dwv5.fastq 93s [main] Real time: 0.020 sec; CPU: 0.016 sec 93s [bwa_aln] 17bp reads: max_diff = 2 93s [bwa_aln] 38bp reads: max_diff = 3 93s [bwa_aln] 64bp reads: max_diff = 4 93s [bwa_aln] 93bp reads: max_diff = 5 93s [bwa_aln] 124bp reads: max_diff = 6 93s [bwa_aln] 157bp reads: max_diff = 7 93s [bwa_aln] 190bp reads: max_diff = 8 93s [bwa_aln] 225bp reads: max_diff = 9 94s [bwa_aln_core] calculate SA coordinate... 0.06 sec 94s [bwa_aln_core] write to the disk... 0.00 sec 94s [bwa_aln_core] 10000 sequences have been processed. 94s [main] Version: 0.7.19-r1273 94s [main] CMD: bwa aln genomes/vdv1.fasta ./SAM/vdv1dwv5.fastq 94s [main] Real time: 0.067 sec; CPU: 0.065 sec 94s [bwa_aln_core] convert to sequence coordinate... 0.00 sec 94s [bwa_aln_core] refine gapped alignments... 0.00 sec 94s [bwa_aln_core] print alignments... 0.00 sec 94s [bwa_aln_core] 10000 sequences have been processed. 94s [main] Version: 0.7.19-r1273 94s [main] CMD: bwa samse genomes/vdv1.fasta /tmp/res.sai ./SAM/vdv1dwv5.fastq 94s [main] Real time: 0.020 sec; CPU: 0.017 sec 94s [bwa_aln] 17bp reads: max_diff = 2 94s [bwa_aln] 38bp reads: max_diff = 3 94s [bwa_aln] 64bp reads: max_diff = 4 94s [bwa_aln] 93bp reads: max_diff = 5 94s [bwa_aln] 124bp reads: max_diff = 6 94s [bwa_aln] 157bp reads: max_diff = 7 94s [bwa_aln] 190bp reads: max_diff = 8 94s [bwa_aln] 225bp reads: max_diff = 9 94s [bwa_aln_core] calculate SA coordinate... 0.08 sec 94s [bwa_aln_core] write to the disk... 0.00 sec 94s [bwa_aln_core] 10000 sequences have been processed. 94s [main] Version: 0.7.19-r1273 94s [main] CMD: bwa aln genomes/vdv1dwv5.fasta ./SAM/vdv1dwv5.fastq 94s [main] Real time: 0.090 sec; CPU: 0.088 sec 94s [bwa_aln_core] convert to sequence coordinate... 0.01 sec 94s [bwa_aln_core] refine gapped alignments... 0.00 sec 94s [bwa_aln_core] print alignments... 0.01 sec 94s [bwa_aln_core] 10000 sequences have been processed. 94s [main] Version: 0.7.19-r1273 94s [main] CMD: bwa samse genomes/vdv1dwv5.fasta /tmp/res.sai ./SAM/vdv1dwv5.fastq 94s [main] Real time: 0.028 sec; CPU: 0.023 sec 94s [bwa_aln] 17bp reads: max_diff = 2 94s [bwa_aln] 38bp reads: max_diff = 3 94s [bwa_aln] 64bp reads: max_diff = 4 94s [bwa_aln] 93bp reads: max_diff = 5 94s [bwa_aln] 124bp reads: max_diff = 6 94s [bwa_aln] 157bp reads: max_diff = 7 94s [bwa_aln] 190bp reads: max_diff = 8 94s [bwa_aln] 225bp reads: max_diff = 9 94s [bwa_aln_core] calculate SA coordinate... 0.08 sec 94s [bwa_aln_core] write to the disk... 0.00 sec 94s [bwa_aln_core] 10000 sequences have been processed. 94s [main] Version: 0.7.19-r1273 94s [main] CMD: bwa aln genomes/vdv1dwv9.fasta ./SAM/vdv1dwv5.fastq 94s [main] Real time: 0.084 sec; CPU: 0.083 sec 94s [bwa_aln_core] convert to sequence coordinate... 0.01 sec 94s [bwa_aln_core] refine gapped alignments... 0.00 sec 94s [bwa_aln_core] print alignments... 0.01 sec 94s [bwa_aln_core] 10000 sequences have been processed. 94s [main] Version: 0.7.19-r1273 94s [main] CMD: bwa samse genomes/vdv1dwv9.fasta /tmp/res.sai ./SAM/vdv1dwv5.fastq 94s [main] Real time: 0.025 sec; CPU: 0.021 sec 94s [bwa_aln] 17bp reads: max_diff = 2 94s [bwa_aln] 38bp reads: max_diff = 3 94s [bwa_aln] 64bp reads: max_diff = 4 94s [bwa_aln] 93bp reads: max_diff = 5 94s [bwa_aln] 124bp reads: max_diff = 6 94s [bwa_aln] 157bp reads: max_diff = 7 94s [bwa_aln] 190bp reads: max_diff = 8 94s [bwa_aln] 225bp reads: max_diff = 9 94s [bwa_aln_core] calculate SA coordinate... 0.05 sec 94s [bwa_aln_core] write to the disk... 0.00 sec 94s [bwa_aln_core] 10000 sequences have been processed. 94s [main] Version: 0.7.19-r1273 94s [main] CMD: bwa aln genomes/dwv.fasta ./SAM/vdv1dwv9.fastq 94s [main] Real time: 0.061 sec; CPU: 0.059 sec 94s [bwa_aln_core] convert to sequence coordinate... 0.00 sec 94s [bwa_aln_core] refine gapped alignments... 0.00 sec 94s [bwa_aln_core] print alignments... 0.00 sec 94s [bwa_aln_core] 10000 sequences have been processed. 94s [main] Version: 0.7.19-r1273 94s [main] CMD: bwa samse genomes/dwv.fasta /tmp/res.sai ./SAM/vdv1dwv9.fastq 94s [main] Real time: 0.019 sec; CPU: 0.016 sec 94s [bwa_aln] 17bp reads: max_diff = 2 94s [bwa_aln] 38bp reads: max_diff = 3 94s [bwa_aln] 64bp reads: max_diff = 4 94s [bwa_aln] 93bp reads: max_diff = 5 94s [bwa_aln] 124bp reads: max_diff = 6 94s [bwa_aln] 157bp reads: max_diff = 7 94s [bwa_aln] 190bp reads: max_diff = 8 94s [bwa_aln] 225bp reads: max_diff = 9 94s [bwa_aln_core] calculate SA coordinate... 0.06 sec 94s [bwa_aln_core] write to the disk... 0.00 sec 94s [bwa_aln_core] 10000 sequences have been processed. 94s [main] Version: 0.7.19-r1273 94s [main] CMD: bwa aln genomes/vdv1.fasta ./SAM/vdv1dwv9.fastq 94s [main] Real time: 0.068 sec; CPU: 0.065 sec 94s [bwa_aln_core] convert to sequence coordinate... 0.00 sec 94s [bwa_aln_core] refine gapped alignments... 0.00 sec 94s [bwa_aln_core] print alignments... 0.00 sec 94s [bwa_aln_core] 10000 sequences have been processed. 94s [main] Version: 0.7.19-r1273 94s [main] CMD: bwa samse genomes/vdv1.fasta /tmp/res.sai ./SAM/vdv1dwv9.fastq 94s [main] Real time: 0.021 sec; CPU: 0.017 sec 94s [bwa_aln] 17bp reads: max_diff = 2 94s [bwa_aln] 38bp reads: max_diff = 3 94s [bwa_aln] 64bp reads: max_diff = 4 94s [bwa_aln] 93bp reads: max_diff = 5 94s [bwa_aln] 124bp reads: max_diff = 6 94s [bwa_aln] 157bp reads: max_diff = 7 94s [bwa_aln] 190bp reads: max_diff = 8 94s [bwa_aln] 225bp reads: max_diff = 9 94s [bwa_aln_core] calculate SA coordinate... 0.08 sec 94s [bwa_aln_core] write to the disk... 0.00 sec 94s [bwa_aln_core] 10000 sequences have been processed. 94s [main] Version: 0.7.19-r1273 94s [main] CMD: bwa aln genomes/vdv1dwv5.fasta ./SAM/vdv1dwv9.fastq 94s [main] Real time: 0.085 sec; CPU: 0.082 sec 94s [bwa_aln_core] convert to sequence coordinate... 0.01 sec 94s [bwa_aln_core] refine gapped alignments... 0.00 sec 94s [bwa_aln_core] print alignments... 0.01 sec 94s [bwa_aln_core] 10000 sequences have been processed. 94s [main] Version: 0.7.19-r1273 94s [main] CMD: bwa samse genomes/vdv1dwv5.fasta /tmp/res.sai ./SAM/vdv1dwv9.fastq 94s [main] Real time: 0.027 sec; CPU: 0.021 sec 94s [bwa_aln] 17bp reads: max_diff = 2 94s [bwa_aln] 38bp reads: max_diff = 3 94s [bwa_aln] 64bp reads: max_diff = 4 94s [bwa_aln] 93bp reads: max_diff = 5 94s [bwa_aln] 124bp reads: max_diff = 6 94s [bwa_aln] 157bp reads: max_diff = 7 94s [bwa_aln] 190bp reads: max_diff = 8 94s [bwa_aln] 225bp reads: max_diff = 9 94s [bwa_aln_core] calculate SA coordinate... 0.08 sec 94s [bwa_aln_core] write to the disk... 0.00 sec 94s [bwa_aln_core] 10000 sequences have been processed. 94s [main] Version: 0.7.19-r1273 94s [main] CMD: bwa aln genomes/vdv1dwv9.fasta ./SAM/vdv1dwv9.fastq 94s [main] Real time: 0.091 sec; CPU: 0.088 sec 94s [bwa_aln_core] convert to sequence coordinate... 0.01 sec 94s [bwa_aln_core] refine gapped alignments... 0.00 sec 94s [bwa_aln_core] print alignments... 0.01 sec 94s [bwa_aln_core] 10000 sequences have been processed. 94s [main] Version: 0.7.19-r1273 94s [main] CMD: bwa samse genomes/vdv1dwv9.fasta /tmp/res.sai ./SAM/vdv1dwv9.fastq 94s [main] Real time: 0.028 sec; CPU: 0.024 sec 94s 94s --- Simulating reads for each reference genome with mason_illumina 94s 94s Original command with mason from SeQan 1 was 94s mason illumina -N 10000 -hi 0 -hs 0 -n 72 -sq -o ./SAM/dwv.fastq genomes/dwv.fasta 94s Please verify that the following call of mason_simulator fits your needs. If not 94s please use 94s reportbug gasic 94s to propose enhancements. 94s 94s Executing: /usr/lib/seqan/bin/mason_simulator --seq-technology illumina -n 10000 --illumina-read-length 72 -o ./SAM/dwv.fastq -ir genomes/dwv.fasta 94s Original command with mason from SeQan 1 was 94s mason illumina -N 10000 -hi 0 -hs 0 -n 72 -sq -o ./SAM/vdv1.fastq genomes/vdv1.fasta 94s Please verify that the following call of mason_simulator fits your needs. If not 94s please use 94s reportbug gasic 94s to propose enhancements. 94s 94s Executing: /usr/lib/seqan/bin/mason_simulator --seq-technology illumina -n 10000 --illumina-read-length 72 -o ./SAM/vdv1.fastq -ir genomes/vdv1.fasta 94s Original command with mason from SeQan 1 was 94s mason illumina -N 10000 -hi 0 -hs 0 -n 72 -sq -o ./SAM/vdv1dwv5.fastq genomes/vdv1dwv5.fasta 94s Please verify that the following call of mason_simulator fits your needs. If not 94s please use 94s reportbug gasic 94s to propose enhancements. 94s 94s Executing: /usr/lib/seqan/bin/mason_simulator --seq-technology illumina -n 10000 --illumina-read-length 72 -o ./SAM/vdv1dwv5.fastq -ir genomes/vdv1dwv5.fasta 94s Original command with mason from SeQan 1 was 94s mason illumina -N 10000 -hi 0 -hs 0 -n 72 -sq -o ./SAM/vdv1dwv9.fastq genomes/vdv1dwv9.fasta 94s Please verify that the following call of mason_simulator fits your needs. If not 94s please use 94s reportbug gasic 94s to propose enhancements. 94s 94s Executing: /usr/lib/seqan/bin/mason_simulator --seq-technology illumina -n 10000 --illumina-read-length 72 -o ./SAM/vdv1dwv9.fastq -ir genomes/vdv1dwv9.fasta 94s 94s --- Mapping simulated reads to reference genomes with bwa 94s 94s Executing: bwa aln genomes/dwv.fasta ./SAM/dwv.fastq > /tmp/res.sai 94s Executing: bwa aln genomes/vdv1.fasta ./SAM/dwv.fastq > /tmp/res.sai 94s Executing: bwa aln genomes/vdv1dwv5.fasta ./SAM/dwv.fastq > /tmp/res.sai 94s Executing: bwa aln genomes/vdv1dwv9.fasta ./SAM/dwv.fastq > /tmp/res.sai 94s Executing: bwa aln genomes/dwv.fasta ./SAM/vdv1.fastq > /tmp/res.sai 94s Executing: bwa aln genomes/vdv1.fasta ./SAM/vdv1.fastq > /tmp/res.sai 94s Executing: bwa aln genomes/vdv1dwv5.fasta ./SAM/vdv1.fastq > /tmp/res.sai 94s Executing: bwa aln genomes/vdv1dwv9.fasta ./SAM/vdv1.fastq > /tmp/res.sai 94s Executing: bwa aln genomes/dwv.fasta ./SAM/vdv1dwv5.fastq > /tmp/res.sai 94s Executing: bwa aln genomes/vdv1.fasta ./SAM/vdv1dwv5.fastq > /tmp/res.sai 94s Executing: bwa aln genomes/vdv1dwv5.fasta ./SAM/vdv1dwv5.fastq > /tmp/res.sai 94s Executing: bwa aln genomes/vdv1dwv9.fasta ./SAM/vdv1dwv5.fastq > /tmp/res.sai 94s Executing: bwa aln genomes/dwv.fasta ./SAM/vdv1dwv9.fastq > /tmp/res.sai 94s Executing: bwa aln genomes/vdv1.fasta ./SAM/vdv1dwv9.fastq > /tmp/res.sai 94s Executing: bwa aln genomes/vdv1dwv5.fasta ./SAM/vdv1dwv9.fastq > /tmp/res.sai 94s Executing: bwa aln genomes/vdv1dwv9.fasta ./SAM/vdv1dwv9.fastq > /tmp/res.sai 94s 94s --- Parsing SAM files 94s 94s SAM file 1 of 16 SAM file 2 of 16 SAM file 3 of 16 SAM file 4 of 16 SAM file 5 of 16 SAM file 6 of 16 SAM file 7 of 16 SAM file 8 of 16 SAM file 9 of 16 SAM file 10 of 16 SAM file 11 of 16 SAM file 12 of 16 SAM file 13 of 16 SAM file 14 of 16 SAM file 15 of 16 SAM file 16 of 16 94s 94s Matrix creation done 94s 94s Wrote similarity matrix to ./similarity_matrix.npy 94s Passed 94s 94s Test 3: correct_abundances 95s 95s --- GASiC correction 95s 95s found 100000 reads 95s 95s --- Analyzing SAM files 95s 95s SAM file 1 of 4 SAM file 2 of 4 SAM file 3 of 4 SAM file 4 of 4 95s 95s --- Bootstrapping abundances 95s 224s bootstrapping 1 of 100 bootstrapping 2 of 100 bootstrapping 3 of 100 bootstrapping 4 of 100 bootstrapping 5 of 100 bootstrapping 6 of 100 bootstrapping 7 of 100 bootstrapping 8 of 100 bootstrapping 9 of 100 bootstrapping 10 of 100 bootstrapping 11 of 100 bootstrapping 12 of 100 bootstrapping 13 of 100 bootstrapping 14 of 100 bootstrapping 15 of 100 bootstrapping 16 of 100 bootstrapping 17 of 100 bootstrapping 18 of 100 bootstrapping 19 of 100 bootstrapping 20 of 100 bootstrapping 21 of 100 bootstrapping 22 of 100 bootstrapping 23 of 100 bootstrapping 24 of 100 bootstrapping 25 of 100 bootstrapping 26 of 100 bootstrapping 27 of 100 bootstrapping 28 of 100 bootstrapping 29 of 100 bootstrapping 30 of 100 bootstrapping 31 of 100 bootstrapping 32 of 100 bootstrapping 33 of 100 bootstrapping 34 of 100 bootstrapping 35 of 100 bootstrapping 36 of 100 bootstrapping 37 of 100 bootstrapping 38 of 100 bootstrapping 39 of 100 bootstrapping 40 of 100 bootstrapping 41 of 100 bootstrapping 42 of 100 bootstrapping 43 of 100 bootstrapping 44 of 100 bootstrapping 45 of 100 bootstrapping 46 of 100 bootstrapping 47 of 100 bootstrapping 48 of 100 bootstrapping 49 of 100 bootstrapping 50 of 100 bootstrapping 51 of 100 bootstrapping 52 of 100 bootstrapping 53 of 100 bootstrapping 54 of 100 bootstrapping 55 of 100 bootstrapping 56 of 100 bootstrapping 57 of 100 bootstrapping 58 of 100 bootstrapping 59 of 100 bootstrapping 60 of 100 bootstrapping 61 of 100 bootstrapping 62 of 100 bootstrapping 63 of 100 bootstrapping 64 of 100 bootstrapping 65 of 100 bootstrapping 66 of 100 bootstrapping 67 of 100 bootstrapping 68 of 100 bootstrapping 69 of 100 bootstrapping 70 of 100 bootstrapping 71 of 100 bootstrapping 72 of 100 bootstrapping 73 of 100 bootstrapping 74 of 100 bootstrapping 75 of 100 bootstrapping 76 of 100 bootstrapping 77 of 100 bootstrapping 78 of 100 bootstrapping 79 of 100 bootstrapping 80 of 100 bootstrapping 81 of 100 bootstrapping 82 of 100 bootstrapping 83 of 100 bootstrapping 84 of 100 bootstrapping 85 of 100 bootstrapping 86 of 100 bootstrapping 87 of 100 bootstrapping 88 of 100 bootstrapping 89 of 100 bootstrapping 90 of 100 bootstrapping 91 of 100 bootstrapping 92 of 100 bootstrapping 93 of 100 bootstrapping 94 of 100 bootstrapping 95 of 100 bootstrapping 96 of 100 bootstrapping 97 of 100 bootstrapping 98 of 100 bootstrapping 99 of 100 bootstrapping 100 of 100 224s 224s Done estimating abundances 224s 224s --- wrote results to results.txt 224s Passed 224s 224s Test 4: quality_check 225s Passed 225s 226s autopkgtest [23:04:32]: test run-unit-test: -----------------------] 226s autopkgtest [23:04:32]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 226s run-unit-test PASS 226s autopkgtest [23:04:32]: @@@@@@@@@@@@@@@@@@@@ summary 226s run-unit-test PASS