0s autopkgtest [02:53:59]: starting date and time: 2025-12-06 02:53:59+0000 0s autopkgtest [02:53:59]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [02:53:59]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.fdbqv7sg/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-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@sto01-ppc64el-3.secgroup --name adt-resolute-ppc64el-gasic-20251206-025359-juju-7f2275-prod-proposed-migration-environment-20-031a0284-753e-465c-8b09-9e34fbc5055d --image adt/ubuntu-resolute-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-autopkgtest-workers-ppc64el -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-ppc64el-gasic-20251206-025359-juju-7f2275-prod-proposed-migration-environment-20-031a0284-753e-465c-8b09-9e34fbc5055d from image adt/ubuntu-resolute-ppc64el-server-20251205.img (UUID ec8e7418-51bb-4f88-80fc-4d434bdc97c2)... 55s autopkgtest [02:54:54]: testbed dpkg architecture: ppc64el 56s autopkgtest [02:54:55]: testbed apt version: 3.1.12 56s autopkgtest [02:54:55]: @@@@@@@@@@@@@@@@@@@@ test bed setup 56s autopkgtest [02:54:55]: testbed release detected to be: None 57s autopkgtest [02:54:56]: updating testbed package index (apt update) 57s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 57s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 57s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 57s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 57s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [852 kB] 57s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [22.8 kB] 57s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [139 kB] 57s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el Packages [224 kB] 57s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el Packages [700 kB] 57s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse ppc64el Packages [6648 B] 58s Fetched 2067 kB in 0s (4363 kB/s) 58s Reading package lists... 60s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 60s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 60s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 60s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 60s Reading package lists... 60s Reading package lists... 61s Building dependency tree... 61s Reading state information... 61s Calculating upgrade... 61s The following packages will be upgraded: 61s libnftnl11 libpython3-stdlib lxd-installer python3 python3-attr python3-gdbm 61s python3-minimal 61s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 61s Need to get 212 kB of archives. 61s After this operation, 16.4 kB of additional disk space will be used. 61s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el python3-minimal ppc64el 3.13.9-2 [28.1 kB] 61s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el python3 ppc64el 3.13.9-2 [23.0 kB] 61s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el libpython3-stdlib ppc64el 3.13.9-2 [10.8 kB] 61s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el libnftnl11 ppc64el 1.3.1-1 [80.0 kB] 61s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el python3-gdbm ppc64el 3.13.9-2 [11.0 kB] 61s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el lxd-installer all 14ubuntu0 [5428 B] 61s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-attr all 25.4.0-1 [53.6 kB] 61s dpkg-preconfigure: unable to re-open stdin: No such file or directory 61s Fetched 212 kB in 0s (9840 kB/s) 62s (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 ... 81185 files and directories currently installed.) 62s Preparing to unpack .../python3-minimal_3.13.9-2_ppc64el.deb ... 62s Unpacking python3-minimal (3.13.9-2) over (3.13.7-1) ... 62s Setting up python3-minimal (3.13.9-2) ... 62s (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 ... 81185 files and directories currently installed.) 62s Preparing to unpack .../0-python3_3.13.9-2_ppc64el.deb ... 62s running python pre-rtupdate hooks for python3.13... 62s Unpacking python3 (3.13.9-2) over (3.13.7-1) ... 62s Preparing to unpack .../1-libpython3-stdlib_3.13.9-2_ppc64el.deb ... 62s Unpacking libpython3-stdlib:ppc64el (3.13.9-2) over (3.13.7-1) ... 63s Preparing to unpack .../2-libnftnl11_1.3.1-1_ppc64el.deb ... 63s Unpacking libnftnl11:ppc64el (1.3.1-1) over (1.3.0-1) ... 63s Preparing to unpack .../3-python3-gdbm_3.13.9-2_ppc64el.deb ... 63s Unpacking python3-gdbm (3.13.9-2) over (3.13.9-1) ... 63s Preparing to unpack .../4-lxd-installer_14ubuntu0_all.deb ... 63s Unpacking lxd-installer (14ubuntu0) over (13ubuntu0) ... 63s Preparing to unpack .../5-python3-attr_25.4.0-1_all.deb ... 63s Unpacking python3-attr (25.4.0-1) over (25.3.0-1) ... 63s Setting up python3-gdbm (3.13.9-2) ... 63s Setting up libnftnl11:ppc64el (1.3.1-1) ... 63s Setting up lxd-installer (14ubuntu0) ... 64s Setting up libpython3-stdlib:ppc64el (3.13.9-2) ... 64s Setting up python3 (3.13.9-2) ... 64s running python rtupdate hooks for python3.13... 64s running python post-rtupdate hooks for python3.13... 64s Setting up python3-attr (25.4.0-1) ... 64s Processing triggers for man-db (2.13.1-1) ... 65s Processing triggers for libc-bin (2.42-2ubuntu2) ... 65s autopkgtest [02:55:04]: upgrading testbed (apt dist-upgrade and autopurge) 65s Reading package lists... 65s Building dependency tree... 65s Reading state information... 65s Calculating upgrade... 65s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 66s Reading package lists... 66s Building dependency tree... 66s Reading state information... 66s Solving dependencies... 66s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 66s autopkgtest [02:55:05]: rebooting testbed after setup commands that affected boot 104s autopkgtest [02:55:43]: testbed running kernel: Linux 6.17.0-6-generic #6-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 7 13:47:32 UTC 2025 106s autopkgtest [02:55:45]: @@@@@@@@@@@@@@@@@@@@ apt-source gasic 108s Get:1 http://ftpmaster.internal/ubuntu resolute/universe gasic 0.0.r19-8 (dsc) [2112 B] 108s Get:2 http://ftpmaster.internal/ubuntu resolute/universe gasic 0.0.r19-8 (tar) [12.4 kB] 108s Get:3 http://ftpmaster.internal/ubuntu resolute/universe gasic 0.0.r19-8 (diff) [7305 kB] 108s gpgv: Signature made Thu Dec 29 18:00:34 2022 UTC 108s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 108s gpgv: issuer "tille@debian.org" 108s gpgv: Can't check signature: No public key 108s dpkg-source: warning: cannot verify inline signature for ./gasic_0.0.r19-8.dsc: no acceptable signature found 108s autopkgtest [02:55:47]: testing package gasic version 0.0.r19-8 109s autopkgtest [02:55:48]: build not needed 110s autopkgtest [02:55:49]: test run-unit-test: preparing testbed 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 110s Solving dependencies... 111s The following NEW packages will be installed: 111s bowtie bowtie2 bwa fontconfig-config fonts-dejavu-core fonts-dejavu-mono 111s fonts-lyx fonts-urw-base35 gasic gasic-examples libblas3 libcairo2 111s libdeflate0 libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 111s libharfbuzz0b libhts3t64 libhtscodecs2 libimagequant0 libjbig0 111s libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4 libopenjp2-7 111s libpixman-1-0 libqhull-r8.0 libraqm0 libsharpyuv0 libtcl8.6 libtiff6 111s libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 111s libxft2 libxrender1 libxslt1.1 libxss1 libzopfli1 python-matplotlib-data 111s python3-biopython python3-brotli python3-cairo python3-charset-normalizer 111s python3-contourpy python3-cycler python3-decorator python3-fonttools 111s python3-freetype python3-fs python3-kiwisolver python3-lxml python3-lz4 111s python3-matplotlib python3-mpmath python3-numpy python3-numpy-dev 111s python3-pil python3-pil.imagetk python3-platformdirs python3-pysam 111s python3-reportlab python3-rlpycairo python3-scipy python3-sympy python3-tk 111s python3-ufolib2 python3-unicodedata2 python3-zopfli python3.13-tk 111s python3.14-tk seqan-apps sgml-base unicode-data w3c-sgml-lib x11-common 111s xfonts-encodings xfonts-utils xml-core 111s 0 upgraded, 86 newly installed, 0 to remove and 0 not upgraded. 111s Need to get 123 MB of archives. 111s After this operation, 553 MB of additional disk space will be used. 111s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-numpy-dev ppc64el 1:2.2.4+ds-1ubuntu1 [153 kB] 111s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el libblas3 ppc64el 3.12.1-7 [291 kB] 111s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgfortran5 ppc64el 15.2.0-9ubuntu1 [620 kB] 111s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblapack3 ppc64el 3.12.1-7 [2960 kB] 111s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-numpy ppc64el 1:2.2.4+ds-1ubuntu1 [4887 kB] 111s Get:6 http://ftpmaster.internal/ubuntu resolute/universe ppc64el bwa ppc64el 0.7.19-1 [230 kB] 111s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB] 111s Get:8 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB] 111s Get:9 http://ftpmaster.internal/ubuntu resolute/main ppc64el libfontenc1 ppc64el 1:1.1.8-1build2 [16.1 kB] 111s Get:10 http://ftpmaster.internal/ubuntu resolute/main ppc64el x11-common all 1:7.7+24ubuntu1 [22.4 kB] 111s Get:11 http://ftpmaster.internal/ubuntu resolute/main ppc64el xfonts-encodings all 1:1.0.5-0ubuntu3 [576 kB] 111s Get:12 http://ftpmaster.internal/ubuntu resolute/main ppc64el xfonts-utils ppc64el 1:7.7+7 [114 kB] 111s Get:13 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-urw-base35 all 20200910-8 [11.0 MB] 112s Get:14 http://ftpmaster.internal/ubuntu resolute/main ppc64el fontconfig-config ppc64el 2.15.0-2.3ubuntu1 [38.1 kB] 112s Get:15 http://ftpmaster.internal/ubuntu resolute/universe ppc64el fonts-lyx all 2.4.4-2 [171 kB] 112s Get:16 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-decorator all 5.2.1-2 [28.1 kB] 112s Get:17 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libqhull-r8.0 ppc64el 2020.2-7 [227 kB] 112s Get:18 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-scipy ppc64el 1.16.3-1 [20.6 MB] 113s Get:19 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-charset-normalizer ppc64el 3.4.4-2 [175 kB] 113s Get:20 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtcl8.6 ppc64el 8.6.17+dfsg-1 [1239 kB] 113s Get:21 http://ftpmaster.internal/ubuntu resolute/main ppc64el libfontconfig1 ppc64el 2.15.0-2.3ubuntu1 [188 kB] 113s Get:22 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxrender1 ppc64el 1:0.9.12-1 [23.0 kB] 113s Get:23 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxft2 ppc64el 2.3.6-1build2 [61.6 kB] 113s Get:24 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxss1 ppc64el 1:1.2.3-1build4 [7470 B] 113s Get:25 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtk8.6 ppc64el 8.6.17-1 [968 kB] 113s Get:26 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3.13-tk ppc64el 3.13.9-1 [108 kB] 113s Get:27 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3.14-tk ppc64el 3.14.0-4 [109 kB] 113s Get:28 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el python3-tk ppc64el 3.13.9-2 [11.1 kB] 113s Get:29 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-pil.imagetk ppc64el 12.0.0-1ubuntu1 [10.1 kB] 113s Get:30 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgomp1 ppc64el 15.2.0-9ubuntu1 [169 kB] 113s Get:31 http://ftpmaster.internal/ubuntu resolute/main ppc64el libimagequant0 ppc64el 2.18.0-1build1 [43.2 kB] 113s Get:32 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-4ubuntu2 [215 kB] 113s Get:33 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 113s Get:34 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblcms2-2 ppc64el 2.17-1 [246 kB] 113s Get:35 http://ftpmaster.internal/ubuntu resolute/main ppc64el libopenjp2-7 ppc64el 2.5.3-2.1 [251 kB] 113s Get:36 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgraphite2-3 ppc64el 1.3.14-2ubuntu1 [84.6 kB] 113s Get:37 http://ftpmaster.internal/ubuntu resolute/main ppc64el libharfbuzz0b ppc64el 12.1.0-1 [679 kB] 113s Get:38 http://ftpmaster.internal/ubuntu resolute/main ppc64el libraqm0 ppc64el 0.10.3-1 [19.6 kB] 113s Get:39 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdeflate0 ppc64el 1.23-2 [63.3 kB] 113s Get:40 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu2 [35.9 kB] 113s Get:41 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblerc4 ppc64el 4.0.0+ds-5ubuntu1 [298 kB] 113s Get:42 http://ftpmaster.internal/ubuntu resolute/main ppc64el libsharpyuv0 ppc64el 1.5.0-0.1 [22.3 kB] 113s Get:43 http://ftpmaster.internal/ubuntu resolute/main ppc64el libwebp7 ppc64el 1.5.0-0.1 [315 kB] 113s Get:44 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtiff6 ppc64el 4.7.0-3ubuntu3 [307 kB] 113s Get:45 http://ftpmaster.internal/ubuntu resolute/main ppc64el libwebpdemux2 ppc64el 1.5.0-0.1 [14.6 kB] 113s Get:46 http://ftpmaster.internal/ubuntu resolute/main ppc64el libwebpmux3 ppc64el 1.5.0-0.1 [31.1 kB] 113s Get:47 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-pil ppc64el 12.0.0-1ubuntu1 [645 kB] 113s Get:48 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpixman-1-0 ppc64el 0.46.4-1 [347 kB] 113s Get:49 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxcb-render0 ppc64el 1.17.0-2build1 [17.2 kB] 113s Get:50 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxcb-shm0 ppc64el 1.17.0-2build1 [6078 B] 113s Get:51 http://ftpmaster.internal/ubuntu resolute/main ppc64el libcairo2 ppc64el 1.18.4-1build1 [759 kB] 113s Get:52 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-cairo ppc64el 1.27.0-2build1 [150 kB] 113s Get:53 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-freetype all 2.5.1-2 [92.2 kB] 113s Get:54 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-rlpycairo all 0.3.0-4 [9332 B] 113s Get:55 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-reportlab all 4.4.5-1 [1148 kB] 113s Get:56 http://ftpmaster.internal/ubuntu resolute/main ppc64el sgml-base all 1.31+nmu1 [11.0 kB] 113s Get:57 http://ftpmaster.internal/ubuntu resolute/main ppc64el xml-core all 0.19 [20.3 kB] 113s Get:58 http://ftpmaster.internal/ubuntu resolute/universe ppc64el w3c-sgml-lib all 1.3-3 [280 kB] 113s Get:59 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-biopython ppc64el 1.86+dfsg-1 [1726 kB] 113s Get:60 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhtscodecs2 ppc64el 1.6.1-2 [113 kB] 113s Get:61 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhts3t64 ppc64el 1.22.1+ds2-1 [617 kB] 113s Get:62 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-pysam ppc64el 0.23.3+ds-2 [5011 kB] 113s Get:63 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python-matplotlib-data all 3.10.7+dfsg1-1 [2930 kB] 113s Get:64 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-contourpy ppc64el 1.3.3-1 [274 kB] 113s Get:65 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-cycler all 0.12.1-2 [9850 B] 113s Get:66 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-brotli ppc64el 1.1.0-2build6 [430 kB] 113s Get:67 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-platformdirs all 4.4.0-1 [16.9 kB] 113s Get:68 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-fs all 2.4.16-9ubuntu1 [91.5 kB] 113s Get:69 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxslt1.1 ppc64el 1.1.43-0.3 [190 kB] 113s Get:70 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-lxml ppc64el 6.0.2-1 [2452 kB] 113s Get:71 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-lz4 ppc64el 4.4.4+dfsg-3 [28.9 kB] 113s Get:72 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-mpmath all 1.3.0-2 [423 kB] 114s Get:73 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-sympy all 1.14.0-2 [4306 kB] 114s Get:74 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-ufolib2 all 0.17.1+dfsg1-1 [33.5 kB] 114s Get:75 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-unicodedata2 ppc64el 16.0.0+ds-1build1 [400 kB] 114s Get:76 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libzopfli1 ppc64el 1.0.3-3 [160 kB] 114s Get:77 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-zopfli ppc64el 0.4.0-1 [11.3 kB] 114s Get:78 http://ftpmaster.internal/ubuntu resolute/universe ppc64el unicode-data all 16.0.0-1 [9513 kB] 114s Get:79 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-fonttools ppc64el 4.57.0-3 [1749 kB] 114s Get:80 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-kiwisolver ppc64el 1.4.10~rc0-1 [72.4 kB] 114s Get:81 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-matplotlib ppc64el 3.10.7+dfsg1-1 [17.2 MB] 115s Get:82 http://ftpmaster.internal/ubuntu resolute/universe ppc64el bowtie ppc64el 1.3.1-3 [1698 kB] 115s Get:83 http://ftpmaster.internal/ubuntu resolute/universe ppc64el bowtie2 ppc64el 2.5.4-1 [1437 kB] 115s Get:84 http://ftpmaster.internal/ubuntu resolute/universe ppc64el seqan-apps ppc64el 2.4.0+dfsg-16 [12.7 MB] 115s Get:85 http://ftpmaster.internal/ubuntu resolute/universe ppc64el gasic all 0.0.r19-8 [21.1 kB] 115s Get:86 http://ftpmaster.internal/ubuntu resolute/universe ppc64el gasic-examples all 0.0.r19-8 [7270 kB] 116s Fetched 123 MB in 5s (25.2 MB/s) 116s Selecting previously unselected package python3-numpy-dev:ppc64el. 116s (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 ... 81185 files and directories currently installed.) 116s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_ppc64el.deb ... 116s Unpacking python3-numpy-dev:ppc64el (1:2.2.4+ds-1ubuntu1) ... 116s Selecting previously unselected package libblas3:ppc64el. 116s Preparing to unpack .../01-libblas3_3.12.1-7_ppc64el.deb ... 116s Unpacking libblas3:ppc64el (3.12.1-7) ... 116s Selecting previously unselected package libgfortran5:ppc64el. 116s Preparing to unpack .../02-libgfortran5_15.2.0-9ubuntu1_ppc64el.deb ... 116s Unpacking libgfortran5:ppc64el (15.2.0-9ubuntu1) ... 116s Selecting previously unselected package liblapack3:ppc64el. 116s Preparing to unpack .../03-liblapack3_3.12.1-7_ppc64el.deb ... 116s Unpacking liblapack3:ppc64el (3.12.1-7) ... 116s Selecting previously unselected package python3-numpy. 116s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_ppc64el.deb ... 116s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 117s Selecting previously unselected package bwa. 117s Preparing to unpack .../05-bwa_0.7.19-1_ppc64el.deb ... 117s Unpacking bwa (0.7.19-1) ... 117s Selecting previously unselected package fonts-dejavu-mono. 117s Preparing to unpack .../06-fonts-dejavu-mono_2.37-8_all.deb ... 117s Unpacking fonts-dejavu-mono (2.37-8) ... 117s Selecting previously unselected package fonts-dejavu-core. 117s Preparing to unpack .../07-fonts-dejavu-core_2.37-8_all.deb ... 117s Unpacking fonts-dejavu-core (2.37-8) ... 117s Selecting previously unselected package libfontenc1:ppc64el. 117s Preparing to unpack .../08-libfontenc1_1%3a1.1.8-1build2_ppc64el.deb ... 117s Unpacking libfontenc1:ppc64el (1:1.1.8-1build2) ... 117s Selecting previously unselected package x11-common. 117s Preparing to unpack .../09-x11-common_1%3a7.7+24ubuntu1_all.deb ... 117s Unpacking x11-common (1:7.7+24ubuntu1) ... 117s Selecting previously unselected package xfonts-encodings. 117s Preparing to unpack .../10-xfonts-encodings_1%3a1.0.5-0ubuntu3_all.deb ... 117s Unpacking xfonts-encodings (1:1.0.5-0ubuntu3) ... 117s Selecting previously unselected package xfonts-utils. 117s Preparing to unpack .../11-xfonts-utils_1%3a7.7+7_ppc64el.deb ... 117s Unpacking xfonts-utils (1:7.7+7) ... 117s Selecting previously unselected package fonts-urw-base35. 117s Preparing to unpack .../12-fonts-urw-base35_20200910-8_all.deb ... 117s Unpacking fonts-urw-base35 (20200910-8) ... 117s Selecting previously unselected package fontconfig-config. 117s Preparing to unpack .../13-fontconfig-config_2.15.0-2.3ubuntu1_ppc64el.deb ... 117s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 117s Selecting previously unselected package fonts-lyx. 117s Preparing to unpack .../14-fonts-lyx_2.4.4-2_all.deb ... 117s Unpacking fonts-lyx (2.4.4-2) ... 117s Selecting previously unselected package python3-decorator. 117s Preparing to unpack .../15-python3-decorator_5.2.1-2_all.deb ... 117s Unpacking python3-decorator (5.2.1-2) ... 117s Selecting previously unselected package libqhull-r8.0:ppc64el. 117s Preparing to unpack .../16-libqhull-r8.0_2020.2-7_ppc64el.deb ... 117s Unpacking libqhull-r8.0:ppc64el (2020.2-7) ... 117s Selecting previously unselected package python3-scipy. 117s Preparing to unpack .../17-python3-scipy_1.16.3-1_ppc64el.deb ... 117s Unpacking python3-scipy (1.16.3-1) ... 118s Selecting previously unselected package python3-charset-normalizer. 118s Preparing to unpack .../18-python3-charset-normalizer_3.4.4-2_ppc64el.deb ... 118s Unpacking python3-charset-normalizer (3.4.4-2) ... 118s Selecting previously unselected package libtcl8.6:ppc64el. 118s Preparing to unpack .../19-libtcl8.6_8.6.17+dfsg-1_ppc64el.deb ... 118s Unpacking libtcl8.6:ppc64el (8.6.17+dfsg-1) ... 118s Selecting previously unselected package libfontconfig1:ppc64el. 118s Preparing to unpack .../20-libfontconfig1_2.15.0-2.3ubuntu1_ppc64el.deb ... 118s Unpacking libfontconfig1:ppc64el (2.15.0-2.3ubuntu1) ... 118s Selecting previously unselected package libxrender1:ppc64el. 118s Preparing to unpack .../21-libxrender1_1%3a0.9.12-1_ppc64el.deb ... 118s Unpacking libxrender1:ppc64el (1:0.9.12-1) ... 118s Selecting previously unselected package libxft2:ppc64el. 118s Preparing to unpack .../22-libxft2_2.3.6-1build2_ppc64el.deb ... 118s Unpacking libxft2:ppc64el (2.3.6-1build2) ... 118s Selecting previously unselected package libxss1:ppc64el. 118s Preparing to unpack .../23-libxss1_1%3a1.2.3-1build4_ppc64el.deb ... 118s Unpacking libxss1:ppc64el (1:1.2.3-1build4) ... 118s Selecting previously unselected package libtk8.6:ppc64el. 118s Preparing to unpack .../24-libtk8.6_8.6.17-1_ppc64el.deb ... 118s Unpacking libtk8.6:ppc64el (8.6.17-1) ... 118s Selecting previously unselected package python3.13-tk. 118s Preparing to unpack .../25-python3.13-tk_3.13.9-1_ppc64el.deb ... 118s Unpacking python3.13-tk (3.13.9-1) ... 118s Selecting previously unselected package python3.14-tk. 118s Preparing to unpack .../26-python3.14-tk_3.14.0-4_ppc64el.deb ... 118s Unpacking python3.14-tk (3.14.0-4) ... 118s Selecting previously unselected package python3-tk. 118s Preparing to unpack .../27-python3-tk_3.13.9-2_ppc64el.deb ... 118s Unpacking python3-tk (3.13.9-2) ... 118s Selecting previously unselected package python3-pil.imagetk:ppc64el. 118s Preparing to unpack .../28-python3-pil.imagetk_12.0.0-1ubuntu1_ppc64el.deb ... 118s Unpacking python3-pil.imagetk:ppc64el (12.0.0-1ubuntu1) ... 118s Selecting previously unselected package libgomp1:ppc64el. 118s Preparing to unpack .../29-libgomp1_15.2.0-9ubuntu1_ppc64el.deb ... 118s Unpacking libgomp1:ppc64el (15.2.0-9ubuntu1) ... 118s Selecting previously unselected package libimagequant0:ppc64el. 118s Preparing to unpack .../30-libimagequant0_2.18.0-1build1_ppc64el.deb ... 118s Unpacking libimagequant0:ppc64el (2.18.0-1build1) ... 118s Selecting previously unselected package libjpeg-turbo8:ppc64el. 118s Preparing to unpack .../31-libjpeg-turbo8_2.1.5-4ubuntu2_ppc64el.deb ... 118s Unpacking libjpeg-turbo8:ppc64el (2.1.5-4ubuntu2) ... 118s Selecting previously unselected package libjpeg8:ppc64el. 118s Preparing to unpack .../32-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 118s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 118s Selecting previously unselected package liblcms2-2:ppc64el. 118s Preparing to unpack .../33-liblcms2-2_2.17-1_ppc64el.deb ... 118s Unpacking liblcms2-2:ppc64el (2.17-1) ... 118s Selecting previously unselected package libopenjp2-7:ppc64el. 118s Preparing to unpack .../34-libopenjp2-7_2.5.3-2.1_ppc64el.deb ... 118s Unpacking libopenjp2-7:ppc64el (2.5.3-2.1) ... 118s Selecting previously unselected package libgraphite2-3:ppc64el. 118s Preparing to unpack .../35-libgraphite2-3_1.3.14-2ubuntu1_ppc64el.deb ... 118s Unpacking libgraphite2-3:ppc64el (1.3.14-2ubuntu1) ... 118s Selecting previously unselected package libharfbuzz0b:ppc64el. 118s Preparing to unpack .../36-libharfbuzz0b_12.1.0-1_ppc64el.deb ... 118s Unpacking libharfbuzz0b:ppc64el (12.1.0-1) ... 118s Selecting previously unselected package libraqm0:ppc64el. 118s Preparing to unpack .../37-libraqm0_0.10.3-1_ppc64el.deb ... 118s Unpacking libraqm0:ppc64el (0.10.3-1) ... 118s Selecting previously unselected package libdeflate0:ppc64el. 118s Preparing to unpack .../38-libdeflate0_1.23-2_ppc64el.deb ... 118s Unpacking libdeflate0:ppc64el (1.23-2) ... 118s Selecting previously unselected package libjbig0:ppc64el. 118s Preparing to unpack .../39-libjbig0_2.1-6.1ubuntu2_ppc64el.deb ... 118s Unpacking libjbig0:ppc64el (2.1-6.1ubuntu2) ... 118s Selecting previously unselected package liblerc4:ppc64el. 118s Preparing to unpack .../40-liblerc4_4.0.0+ds-5ubuntu1_ppc64el.deb ... 118s Unpacking liblerc4:ppc64el (4.0.0+ds-5ubuntu1) ... 118s Selecting previously unselected package libsharpyuv0:ppc64el. 118s Preparing to unpack .../41-libsharpyuv0_1.5.0-0.1_ppc64el.deb ... 118s Unpacking libsharpyuv0:ppc64el (1.5.0-0.1) ... 118s Selecting previously unselected package libwebp7:ppc64el. 118s Preparing to unpack .../42-libwebp7_1.5.0-0.1_ppc64el.deb ... 118s Unpacking libwebp7:ppc64el (1.5.0-0.1) ... 118s Selecting previously unselected package libtiff6:ppc64el. 118s Preparing to unpack .../43-libtiff6_4.7.0-3ubuntu3_ppc64el.deb ... 118s Unpacking libtiff6:ppc64el (4.7.0-3ubuntu3) ... 118s Selecting previously unselected package libwebpdemux2:ppc64el. 118s Preparing to unpack .../44-libwebpdemux2_1.5.0-0.1_ppc64el.deb ... 118s Unpacking libwebpdemux2:ppc64el (1.5.0-0.1) ... 118s Selecting previously unselected package libwebpmux3:ppc64el. 118s Preparing to unpack .../45-libwebpmux3_1.5.0-0.1_ppc64el.deb ... 118s Unpacking libwebpmux3:ppc64el (1.5.0-0.1) ... 118s Selecting previously unselected package python3-pil:ppc64el. 118s Preparing to unpack .../46-python3-pil_12.0.0-1ubuntu1_ppc64el.deb ... 118s Unpacking python3-pil:ppc64el (12.0.0-1ubuntu1) ... 118s Selecting previously unselected package libpixman-1-0:ppc64el. 118s Preparing to unpack .../47-libpixman-1-0_0.46.4-1_ppc64el.deb ... 118s Unpacking libpixman-1-0:ppc64el (0.46.4-1) ... 118s Selecting previously unselected package libxcb-render0:ppc64el. 118s Preparing to unpack .../48-libxcb-render0_1.17.0-2build1_ppc64el.deb ... 118s Unpacking libxcb-render0:ppc64el (1.17.0-2build1) ... 118s Selecting previously unselected package libxcb-shm0:ppc64el. 118s Preparing to unpack .../49-libxcb-shm0_1.17.0-2build1_ppc64el.deb ... 118s Unpacking libxcb-shm0:ppc64el (1.17.0-2build1) ... 118s Selecting previously unselected package libcairo2:ppc64el. 118s Preparing to unpack .../50-libcairo2_1.18.4-1build1_ppc64el.deb ... 118s Unpacking libcairo2:ppc64el (1.18.4-1build1) ... 118s Selecting previously unselected package python3-cairo. 118s Preparing to unpack .../51-python3-cairo_1.27.0-2build1_ppc64el.deb ... 118s Unpacking python3-cairo (1.27.0-2build1) ... 119s Selecting previously unselected package python3-freetype. 119s Preparing to unpack .../52-python3-freetype_2.5.1-2_all.deb ... 119s Unpacking python3-freetype (2.5.1-2) ... 119s Selecting previously unselected package python3-rlpycairo. 119s Preparing to unpack .../53-python3-rlpycairo_0.3.0-4_all.deb ... 119s Unpacking python3-rlpycairo (0.3.0-4) ... 119s Selecting previously unselected package python3-reportlab. 119s Preparing to unpack .../54-python3-reportlab_4.4.5-1_all.deb ... 119s Unpacking python3-reportlab (4.4.5-1) ... 119s Selecting previously unselected package sgml-base. 119s Preparing to unpack .../55-sgml-base_1.31+nmu1_all.deb ... 119s Unpacking sgml-base (1.31+nmu1) ... 119s Selecting previously unselected package xml-core. 119s Preparing to unpack .../56-xml-core_0.19_all.deb ... 119s Unpacking xml-core (0.19) ... 119s Selecting previously unselected package w3c-sgml-lib. 119s Preparing to unpack .../57-w3c-sgml-lib_1.3-3_all.deb ... 119s Unpacking w3c-sgml-lib (1.3-3) ... 119s Selecting previously unselected package python3-biopython. 119s Preparing to unpack .../58-python3-biopython_1.86+dfsg-1_ppc64el.deb ... 119s Unpacking python3-biopython (1.86+dfsg-1) ... 119s Selecting previously unselected package libhtscodecs2:ppc64el. 119s Preparing to unpack .../59-libhtscodecs2_1.6.1-2_ppc64el.deb ... 119s Unpacking libhtscodecs2:ppc64el (1.6.1-2) ... 119s Selecting previously unselected package libhts3t64:ppc64el. 119s Preparing to unpack .../60-libhts3t64_1.22.1+ds2-1_ppc64el.deb ... 119s Unpacking libhts3t64:ppc64el (1.22.1+ds2-1) ... 119s Selecting previously unselected package python3-pysam. 119s Preparing to unpack .../61-python3-pysam_0.23.3+ds-2_ppc64el.deb ... 119s Unpacking python3-pysam (0.23.3+ds-2) ... 119s Selecting previously unselected package python-matplotlib-data. 119s Preparing to unpack .../62-python-matplotlib-data_3.10.7+dfsg1-1_all.deb ... 119s Unpacking python-matplotlib-data (3.10.7+dfsg1-1) ... 119s Selecting previously unselected package python3-contourpy. 119s Preparing to unpack .../63-python3-contourpy_1.3.3-1_ppc64el.deb ... 119s Unpacking python3-contourpy (1.3.3-1) ... 119s Selecting previously unselected package python3-cycler. 119s Preparing to unpack .../64-python3-cycler_0.12.1-2_all.deb ... 119s Unpacking python3-cycler (0.12.1-2) ... 119s Selecting previously unselected package python3-brotli. 119s Preparing to unpack .../65-python3-brotli_1.1.0-2build6_ppc64el.deb ... 119s Unpacking python3-brotli (1.1.0-2build6) ... 119s Selecting previously unselected package python3-platformdirs. 119s Preparing to unpack .../66-python3-platformdirs_4.4.0-1_all.deb ... 119s Unpacking python3-platformdirs (4.4.0-1) ... 119s Selecting previously unselected package python3-fs. 119s Preparing to unpack .../67-python3-fs_2.4.16-9ubuntu1_all.deb ... 119s Unpacking python3-fs (2.4.16-9ubuntu1) ... 119s Selecting previously unselected package libxslt1.1:ppc64el. 119s Preparing to unpack .../68-libxslt1.1_1.1.43-0.3_ppc64el.deb ... 119s Unpacking libxslt1.1:ppc64el (1.1.43-0.3) ... 119s Selecting previously unselected package python3-lxml:ppc64el. 119s Preparing to unpack .../69-python3-lxml_6.0.2-1_ppc64el.deb ... 119s Unpacking python3-lxml:ppc64el (6.0.2-1) ... 119s Selecting previously unselected package python3-lz4. 119s Preparing to unpack .../70-python3-lz4_4.4.4+dfsg-3_ppc64el.deb ... 119s Unpacking python3-lz4 (4.4.4+dfsg-3) ... 119s Selecting previously unselected package python3-mpmath. 119s Preparing to unpack .../71-python3-mpmath_1.3.0-2_all.deb ... 119s Unpacking python3-mpmath (1.3.0-2) ... 119s Selecting previously unselected package python3-sympy. 119s Preparing to unpack .../72-python3-sympy_1.14.0-2_all.deb ... 119s Unpacking python3-sympy (1.14.0-2) ... 120s Selecting previously unselected package python3-ufolib2. 120s Preparing to unpack .../73-python3-ufolib2_0.17.1+dfsg1-1_all.deb ... 120s Unpacking python3-ufolib2 (0.17.1+dfsg1-1) ... 120s Selecting previously unselected package python3-unicodedata2. 120s Preparing to unpack .../74-python3-unicodedata2_16.0.0+ds-1build1_ppc64el.deb ... 120s Unpacking python3-unicodedata2 (16.0.0+ds-1build1) ... 120s Selecting previously unselected package libzopfli1. 120s Preparing to unpack .../75-libzopfli1_1.0.3-3_ppc64el.deb ... 120s Unpacking libzopfli1 (1.0.3-3) ... 120s Selecting previously unselected package python3-zopfli. 120s Preparing to unpack .../76-python3-zopfli_0.4.0-1_ppc64el.deb ... 120s Unpacking python3-zopfli (0.4.0-1) ... 120s Selecting previously unselected package unicode-data. 120s Preparing to unpack .../77-unicode-data_16.0.0-1_all.deb ... 120s Unpacking unicode-data (16.0.0-1) ... 120s Selecting previously unselected package python3-fonttools. 120s Preparing to unpack .../78-python3-fonttools_4.57.0-3_ppc64el.deb ... 120s Unpacking python3-fonttools (4.57.0-3) ... 120s Selecting previously unselected package python3-kiwisolver. 120s Preparing to unpack .../79-python3-kiwisolver_1.4.10~rc0-1_ppc64el.deb ... 120s Unpacking python3-kiwisolver (1.4.10~rc0-1) ... 120s Selecting previously unselected package python3-matplotlib. 120s Preparing to unpack .../80-python3-matplotlib_3.10.7+dfsg1-1_ppc64el.deb ... 120s Unpacking python3-matplotlib (3.10.7+dfsg1-1) ... 121s Selecting previously unselected package bowtie. 121s Preparing to unpack .../81-bowtie_1.3.1-3_ppc64el.deb ... 121s Unpacking bowtie (1.3.1-3) ... 121s Selecting previously unselected package bowtie2. 121s Preparing to unpack .../82-bowtie2_2.5.4-1_ppc64el.deb ... 121s Unpacking bowtie2 (2.5.4-1) ... 121s Selecting previously unselected package seqan-apps. 121s Preparing to unpack .../83-seqan-apps_2.4.0+dfsg-16_ppc64el.deb ... 121s Unpacking seqan-apps (2.4.0+dfsg-16) ... 121s Selecting previously unselected package gasic. 121s Preparing to unpack .../84-gasic_0.0.r19-8_all.deb ... 121s Unpacking gasic (0.0.r19-8) ... 121s Selecting previously unselected package gasic-examples. 121s Preparing to unpack .../85-gasic-examples_0.0.r19-8_all.deb ... 121s Unpacking gasic-examples (0.0.r19-8) ... 121s Setting up libhtscodecs2:ppc64el (1.6.1-2) ... 121s Setting up libgraphite2-3:ppc64el (1.3.14-2ubuntu1) ... 121s Setting up liblcms2-2:ppc64el (2.17-1) ... 121s Setting up libpixman-1-0:ppc64el (0.46.4-1) ... 121s Setting up libsharpyuv0:ppc64el (1.5.0-0.1) ... 121s Setting up liblerc4:ppc64el (4.0.0+ds-5ubuntu1) ... 121s Setting up bowtie (1.3.1-3) ... 121s Setting up libxrender1:ppc64el (1:0.9.12-1) ... 121s Setting up python3-lz4 (4.4.4+dfsg-3) ... 121s Setting up libxcb-render0:ppc64el (1.17.0-2build1) ... 121s Setting up python3-charset-normalizer (3.4.4-2) ... 121s Setting up bwa (0.7.19-1) ... 121s Setting up python3-unicodedata2 (16.0.0+ds-1build1) ... 121s Setting up fonts-lyx (2.4.4-2) ... 121s Setting up gasic-examples (0.0.r19-8) ... 121s Setting up x11-common (1:7.7+24ubuntu1) ... 122s Setting up libdeflate0:ppc64el (1.23-2) ... 122s Setting up libqhull-r8.0:ppc64el (2020.2-7) ... 122s Setting up libxcb-shm0:ppc64el (1.17.0-2build1) ... 122s Setting up libgomp1:ppc64el (15.2.0-9ubuntu1) ... 122s Setting up python3-freetype (2.5.1-2) ... 122s Setting up libjbig0:ppc64el (2.1-6.1ubuntu2) ... 122s Setting up python3-platformdirs (4.4.0-1) ... 122s Setting up bowtie2 (2.5.4-1) ... 122s Setting up python3-fs (2.4.16-9ubuntu1) ... 122s Setting up unicode-data (16.0.0-1) ... 122s Setting up python3-decorator (5.2.1-2) ... 122s Setting up libfontenc1:ppc64el (1:1.1.8-1build2) ... 122s Setting up libblas3:ppc64el (3.12.1-7) ... 122s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 122s Setting up libzopfli1 (1.0.3-3) ... 122s Setting up python3-brotli (1.1.0-2build6) ... 122s Setting up xfonts-encodings (1:1.0.5-0ubuntu3) ... 122s Setting up python3-cycler (0.12.1-2) ... 122s Setting up libimagequant0:ppc64el (2.18.0-1build1) ... 122s Setting up seqan-apps (2.4.0+dfsg-16) ... 122s Setting up fonts-dejavu-mono (2.37-8) ... 122s Setting up python3-kiwisolver (1.4.10~rc0-1) ... 122s Setting up python3-numpy-dev:ppc64el (1:2.2.4+ds-1ubuntu1) ... 122s Setting up libtcl8.6:ppc64el (8.6.17+dfsg-1) ... 122s Setting up fonts-dejavu-core (2.37-8) ... 122s Setting up libjpeg-turbo8:ppc64el (2.1.5-4ubuntu2) ... 122s Setting up libgfortran5:ppc64el (15.2.0-9ubuntu1) ... 122s Setting up libwebp7:ppc64el (1.5.0-0.1) ... 122s Setting up libxslt1.1:ppc64el (1.1.43-0.3) ... 122s Setting up libhts3t64:ppc64el (1.22.1+ds2-1) ... 122s Setting up libopenjp2-7:ppc64el (2.5.3-2.1) ... 122s Setting up libharfbuzz0b:ppc64el (12.1.0-1) ... 122s Setting up sgml-base (1.31+nmu1) ... 122s Setting up libxss1:ppc64el (1:1.2.3-1build4) ... 122s Setting up python3-mpmath (1.3.0-2) ... 123s Setting up python-matplotlib-data (3.10.7+dfsg1-1) ... 123s Setting up libwebpmux3:ppc64el (1.5.0-0.1) ... 123s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 123s Setting up python3-sympy (1.14.0-2) ... 129s Setting up liblapack3:ppc64el (3.12.1-7) ... 129s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 129s Setting up python3-pysam (0.23.3+ds-2) ... 129s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ... 129s Setting up libwebpdemux2:ppc64el (1.5.0-0.1) ... 129s Setting up xfonts-utils (1:7.7+7) ... 129s Setting up python3-zopfli (0.4.0-1) ... 129s Setting up libraqm0:ppc64el (0.10.3-1) ... 129s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 131s Setting up python3-lxml:ppc64el (6.0.2-1) ... 131s Setting up libtiff6:ppc64el (4.7.0-3ubuntu3) ... 131s Setting up xml-core (0.19) ... 131s Setting up python3-contourpy (1.3.3-1) ... 132s Setting up libfontconfig1:ppc64el (2.15.0-2.3ubuntu1) ... 132s Setting up libxft2:ppc64el (2.3.6-1build2) ... 132s Setting up python3-scipy (1.16.3-1) ... 135s Setting up libtk8.6:ppc64el (8.6.17-1) ... 135s Setting up fonts-urw-base35 (20200910-8) ... 135s Setting up libcairo2:ppc64el (1.18.4-1build1) ... 135s Setting up python3.13-tk (3.13.9-1) ... 135s Setting up python3-pil:ppc64el (12.0.0-1ubuntu1) ... 136s Setting up python3.14-tk (3.14.0-4) ... 136s Setting up python3-cairo (1.27.0-2build1) ... 136s Setting up python3-tk (3.13.9-2) ... 136s Setting up python3-pil.imagetk:ppc64el (12.0.0-1ubuntu1) ... 136s Setting up python3-rlpycairo (0.3.0-4) ... 136s Setting up python3-reportlab (4.4.5-1) ... 137s Setting up python3-fonttools (4.57.0-3) ... 138s Setting up python3-ufolib2 (0.17.1+dfsg1-1) ... 138s Setting up python3-matplotlib (3.10.7+dfsg1-1) ... 139s Processing triggers for libc-bin (2.42-2ubuntu2) ... 139s Processing triggers for man-db (2.13.1-1) ... 142s Processing triggers for sgml-base (1.31+nmu1) ... 142s Setting up w3c-sgml-lib (1.3-3) ... 172s Setting up python3-biopython (1.86+dfsg-1) ... 172s Setting up gasic (0.0.r19-8) ... 174s autopkgtest [02:56:53]: test run-unit-test: [----------------------- 174s Test 0: Create Genome Indices 174s [bwa_index] Pack FASTA... 0.00 sec 174s [bwa_index] Construct BWT for the packed sequence... 174s [bwa_index] 0.00 seconds elapse. 174s [bwa_index] Update BWT... 0.00 sec 174s [bwa_index] Pack forward-only FASTA... 0.00 sec 174s [bwa_index] Construct SA from BWT and Occ... 0.00 sec 174s [main] Version: 0.7.19-r1273 174s [main] CMD: bwa index dwv.fasta 174s [main] Real time: 0.195 sec; CPU: 0.005 sec 174s [bwa_index] Pack FASTA... 0.00 sec 174s [bwa_index] Construct BWT for the packed sequence... 174s [bwa_index] 0.00 seconds elapse. 174s [bwa_index] Update BWT... 0.00 sec 174s [bwa_index] Pack forward-only FASTA... 0.00 sec 174s [bwa_index] Construct SA from BWT and Occ... 0.00 sec 174s [main] Version: 0.7.19-r1273 174s [main] CMD: bwa index vdv1.fasta 174s [main] Real time: 0.073 sec; CPU: 0.004 sec 174s [bwa_index] Pack FASTA... 0.00 sec 174s [bwa_index] Construct BWT for the packed sequence... 174s [bwa_index] 0.00 seconds elapse. 174s [bwa_index] Update BWT... 0.00 sec 175s [bwa_index] Pack forward-only FASTA... 0.00 sec 175s [bwa_index] Construct SA from BWT and Occ... 0.00 sec 175s [main] Version: 0.7.19-r1273 175s [main] CMD: bwa index vdv1dwv9.fasta 175s [main] Real time: 0.123 sec; CPU: 0.004 sec 175s [bwa_index] Pack FASTA... 0.00 sec 175s [bwa_index] Construct BWT for the packed sequence... 175s [bwa_index] 0.00 seconds elapse. 175s [bwa_index] Update BWT... 0.00 sec 175s [bwa_index] Pack forward-only FASTA... 0.00 sec 175s [bwa_index] Construct SA from BWT and Occ... 0.00 sec 175s [main] Version: 0.7.19-r1273 175s [main] CMD: bwa index vdv1dwv5.fasta 175s [main] Real time: 0.082 sec; CPU: 0.004 sec 175s Passed 175s 175s Test 1: run_mappers 175s [bwa_aln] 17bp reads: max_diff = 2 175s [bwa_aln] 38bp reads: max_diff = 3 175s [bwa_aln] 64bp reads: max_diff = 4 175s [bwa_aln] 93bp reads: max_diff = 5 175s [bwa_aln] 124bp reads: max_diff = 6 175s [bwa_aln] 157bp reads: max_diff = 7 175s [bwa_aln] 190bp reads: max_diff = 8 175s [bwa_aln] 225bp reads: max_diff = 9 176s [bwa_aln_core] calculate SA coordinate... 1.08 sec 176s [bwa_aln_core] write to the disk... 0.00 sec 176s [bwa_aln_core] 100000 sequences have been processed. 176s [main] Version: 0.7.19-r1273 176s [main] CMD: bwa aln ./genomes/dwv.fasta reads/SRR059298_subset.fastq 176s [main] Real time: 1.162 sec; CPU: 1.139 sec 176s [bwa_aln_core] convert to sequence coordinate... 0.11 sec 177s [bwa_aln_core] refine gapped alignments... 0.03 sec 177s [bwa_aln_core] print alignments... 0.10 sec 177s [bwa_aln_core] 100000 sequences have been processed. 177s [main] Version: 0.7.19-r1273 177s [main] CMD: bwa samse ./genomes/dwv.fasta /tmp/res.sai reads/SRR059298_subset.fastq 177s [main] Real time: 0.372 sec; CPU: 0.297 sec 177s [bwa_aln] 17bp reads: max_diff = 2 177s [bwa_aln] 38bp reads: max_diff = 3 177s [bwa_aln] 64bp reads: max_diff = 4 177s [bwa_aln] 93bp reads: max_diff = 5 177s [bwa_aln] 124bp reads: max_diff = 6 177s [bwa_aln] 157bp reads: max_diff = 7 177s [bwa_aln] 190bp reads: max_diff = 8 177s [bwa_aln] 225bp reads: max_diff = 9 177s [bwa_aln_core] calculate SA coordinate... 0.86 sec 177s [bwa_aln_core] write to the disk... 0.00 sec 177s [bwa_aln_core] 100000 sequences have been processed. 177s [main] Version: 0.7.19-r1273 177s [main] CMD: bwa aln ./genomes/vdv1.fasta reads/SRR059298_subset.fastq 177s [main] Real time: 0.935 sec; CPU: 0.923 sec 177s [bwa_aln_core] convert to sequence coordinate... 0.06 sec 177s [bwa_aln_core] refine gapped alignments... 0.02 sec 177s [bwa_aln_core] print alignments... 0.07 sec 177s [bwa_aln_core] 100000 sequences have been processed. 177s [main] Version: 0.7.19-r1273 177s [main] CMD: bwa samse ./genomes/vdv1.fasta /tmp/res.sai reads/SRR059298_subset.fastq 177s [main] Real time: 0.274 sec; CPU: 0.221 sec 177s [bwa_aln] 17bp reads: max_diff = 2 177s [bwa_aln] 38bp reads: max_diff = 3 177s [bwa_aln] 64bp reads: max_diff = 4 177s [bwa_aln] 93bp reads: max_diff = 5 177s [bwa_aln] 124bp reads: max_diff = 6 177s [bwa_aln] 157bp reads: max_diff = 7 177s [bwa_aln] 190bp reads: max_diff = 8 177s [bwa_aln] 225bp reads: max_diff = 9 179s [bwa_aln_core] calculate SA coordinate... 1.42 sec 179s [bwa_aln_core] write to the disk... 0.01 sec 179s [bwa_aln_core] 100000 sequences have been processed. 179s [main] Version: 0.7.19-r1273 179s [main] CMD: bwa aln ./genomes/vdv1dwv5.fasta reads/SRR059298_subset.fastq 179s [main] Real time: 1.507 sec; CPU: 1.487 sec 179s [bwa_aln_core] convert to sequence coordinate... 0.16 sec 179s [bwa_aln_core] refine gapped alignments... 0.03 sec 179s [bwa_aln_core] print alignments... 0.12 sec 179s [bwa_aln_core] 100000 sequences have been processed. 179s [main] Version: 0.7.19-r1273 179s [main] CMD: bwa samse ./genomes/vdv1dwv5.fasta /tmp/res.sai reads/SRR059298_subset.fastq 179s [main] Real time: 0.479 sec; CPU: 0.379 sec 179s [bwa_aln] 17bp reads: max_diff = 2 179s [bwa_aln] 38bp reads: max_diff = 3 179s [bwa_aln] 64bp reads: max_diff = 4 179s [bwa_aln] 93bp reads: max_diff = 5 179s [bwa_aln] 124bp reads: max_diff = 6 179s [bwa_aln] 157bp reads: max_diff = 7 179s [bwa_aln] 190bp reads: max_diff = 8 179s [bwa_aln] 225bp reads: max_diff = 9 181s [bwa_aln_core] calculate SA coordinate... 1.27 sec 181s [bwa_aln_core] write to the disk... 0.00 sec 181s [bwa_aln_core] 100000 sequences have been processed. 181s [main] Version: 0.7.19-r1273 181s [main] CMD: bwa aln ./genomes/vdv1dwv9.fasta reads/SRR059298_subset.fastq 181s [main] Real time: 1.356 sec; CPU: 1.338 sec 181s [bwa_aln_core] convert to sequence coordinate... 0.12 sec 181s [bwa_aln_core] refine gapped alignments... 0.03 sec 181s [bwa_aln_core] print alignments... 0.11 sec 181s [bwa_aln_core] 100000 sequences have been processed. 181s [main] Version: 0.7.19-r1273 181s [main] CMD: bwa samse ./genomes/vdv1dwv9.fasta /tmp/res.sai reads/SRR059298_subset.fastq 181s [main] Real time: 0.407 sec; CPU: 0.329 sec 181s --- mapping reads with bwa to ./genomes/dwv.fasta 181s Executing: bwa aln ./genomes/dwv.fasta reads/SRR059298_subset.fastq > /tmp/res.sai 181s --- mapping reads with bwa to ./genomes/vdv1.fasta 181s Executing: bwa aln ./genomes/vdv1.fasta reads/SRR059298_subset.fastq > /tmp/res.sai 181s --- mapping reads with bwa to ./genomes/vdv1dwv5.fasta 181s Executing: bwa aln ./genomes/vdv1dwv5.fasta reads/SRR059298_subset.fastq > /tmp/res.sai 181s --- mapping reads with bwa to ./genomes/vdv1dwv9.fasta 181s Executing: bwa aln ./genomes/vdv1dwv9.fasta reads/SRR059298_subset.fastq > /tmp/res.sai 181s 181s Mapping done. 181s 181s Passed 181s 181s Test 2: create_matrix 181s MASON SIMULATOR 181s =============== 181s 181s ____INITIALIZING______________________________________________________________ 181s 181s Opening reference and variants file ... OK 181s Initializing fragment-to-contig distribution ... OK 181s Initializing simulation threads ... OK 181s Opening output file ./SAM/dwv.fastq ... OK 181s 181s ____READ SIMULATION___________________________________________________________ 181s 181s Distributing fragments to 1 contigs (1 haplotypes each) ... OK 181s 181s Simulating Reads: 181s gi|71480055|ref|NC_004830.2| (allele 1) .. (10000 fragments) OK 181s Done simulating reads. 181s 181s Joining temporary files ... OK 181s rm: cannot remove './SAM/dwv.fastq.sam': No such file or directory 181s MASON SIMULATOR 181s =============== 181s 181s ____INITIALIZING______________________________________________________________ 181s 181s Opening reference and variants file ... OK 181s Initializing fragment-to-contig distribution ... OK 181s Initializing simulation threads ... OK 181s Opening output file ./SAM/vdv1.fastq ... OK 181s 181s ____READ SIMULATION___________________________________________________________ 181s 181s Distributing fragments to 1 contigs (1 haplotypes each) ... OK 181s 181s Simulating Reads: 182s gi|56121875|ref|NC_006494.1| (allele 1) .. (10000 fragments) OK 182s Done simulating reads. 182s 182s Joining temporary files ... OK 182s rm: cannot remove './SAM/vdv1.fastq.sam': No such file or directory 182s MASON SIMULATOR 182s =============== 182s 182s ____INITIALIZING______________________________________________________________ 182s 182s Opening reference and variants file ... OK 182s Initializing fragment-to-contig distribution ... OK 182s Initializing simulation threads ... OK 182s Opening output file ./SAM/vdv1dwv5.fastq ... OK 182s 182s ____READ SIMULATION___________________________________________________________ 182s 182s Distributing fragments to 1 contigs (1 haplotypes each) ... OK 182s 182s Simulating Reads: 182s gi|301070167|gb|HM067437.1| (allele 1) .. (10000 fragments) OK 182s Done simulating reads. 182s 182s Joining temporary files ... OK 182s rm: cannot remove './SAM/vdv1dwv5.fastq.sam': No such file or directory 182s MASON SIMULATOR 182s =============== 182s 182s ____INITIALIZING______________________________________________________________ 182s 182s Opening reference and variants file ... OK 182s Initializing fragment-to-contig distribution ... OK 182s Initializing simulation threads ... OK 182s Opening output file ./SAM/vdv1dwv9.fastq ... OK 182s 182s ____READ SIMULATION___________________________________________________________ 182s 182s Distributing fragments to 1 contigs (1 haplotypes each) ... OK 182s 182s Simulating Reads: 182s gi|301070169|gb|HM067438.1| (allele 1) .. (10000 fragments) OK 182s Done simulating reads. 182s 182s Joining temporary files ... OK 182s rm: cannot remove './SAM/vdv1dwv9.fastq.sam': No such file or directory 182s [bwa_aln] 17bp reads: max_diff = 2 182s [bwa_aln] 38bp reads: max_diff = 3 182s [bwa_aln] 64bp reads: max_diff = 4 182s [bwa_aln] 93bp reads: max_diff = 5 182s [bwa_aln] 124bp reads: max_diff = 6 182s [bwa_aln] 157bp reads: max_diff = 7 182s [bwa_aln] 190bp reads: max_diff = 8 182s [bwa_aln] 225bp reads: max_diff = 9 182s [bwa_aln_core] calculate SA coordinate... 0.15 sec 182s [bwa_aln_core] write to the disk... 0.00 sec 182s [bwa_aln_core] 10000 sequences have been processed. 182s [main] Version: 0.7.19-r1273 182s [main] CMD: bwa aln genomes/dwv.fasta ./SAM/dwv.fastq 182s [main] Real time: 0.163 sec; CPU: 0.155 sec 182s [bwa_aln_core] convert to sequence coordinate... 0.02 sec 182s [bwa_aln_core] refine gapped alignments... 0.00 sec 182s [bwa_aln_core] print alignments... 0.02 sec 182s [bwa_aln_core] 10000 sequences have been processed. 182s [main] Version: 0.7.19-r1273 182s [main] CMD: bwa samse genomes/dwv.fasta /tmp/res.sai ./SAM/dwv.fastq 182s [main] Real time: 0.066 sec; CPU: 0.049 sec 182s [bwa_aln] 17bp reads: max_diff = 2 182s [bwa_aln] 38bp reads: max_diff = 3 182s [bwa_aln] 64bp reads: max_diff = 4 182s [bwa_aln] 93bp reads: max_diff = 5 182s [bwa_aln] 124bp reads: max_diff = 6 182s [bwa_aln] 157bp reads: max_diff = 7 182s [bwa_aln] 190bp reads: max_diff = 8 182s [bwa_aln] 225bp reads: max_diff = 9 182s [bwa_aln_core] calculate SA coordinate... 0.05 sec 182s [bwa_aln_core] write to the disk... 0.00 sec 182s [bwa_aln_core] 10000 sequences have been processed. 182s [main] Version: 0.7.19-r1273 182s [main] CMD: bwa aln genomes/vdv1.fasta ./SAM/dwv.fastq 182s [main] Real time: 0.059 sec; CPU: 0.054 sec 182s [bwa_aln_core] convert to sequence coordinate... 0.00 sec 182s [bwa_aln_core] refine gapped alignments... 0.00 sec 182s [bwa_aln_core] print alignments... 0.00 sec 182s [bwa_aln_core] 10000 sequences have been processed. 182s [main] Version: 0.7.19-r1273 182s [main] CMD: bwa samse genomes/vdv1.fasta /tmp/res.sai ./SAM/dwv.fastq 182s [main] Real time: 0.022 sec; CPU: 0.011 sec 182s [bwa_aln] 17bp reads: max_diff = 2 182s [bwa_aln] 38bp reads: max_diff = 3 182s [bwa_aln] 64bp reads: max_diff = 4 182s [bwa_aln] 93bp reads: max_diff = 5 182s [bwa_aln] 124bp reads: max_diff = 6 182s [bwa_aln] 157bp reads: max_diff = 7 182s [bwa_aln] 190bp reads: max_diff = 8 182s [bwa_aln] 225bp reads: max_diff = 9 182s [bwa_aln_core] calculate SA coordinate... 0.09 sec 182s [bwa_aln_core] write to the disk... 0.00 sec 182s [bwa_aln_core] 10000 sequences have been processed. 182s [main] Version: 0.7.19-r1273 182s [main] CMD: bwa aln genomes/vdv1dwv5.fasta ./SAM/dwv.fastq 182s [main] Real time: 0.105 sec; CPU: 0.100 sec 182s [bwa_aln_core] convert to sequence coordinate... 0.01 sec 182s [bwa_aln_core] refine gapped alignments... 0.00 sec 182s [bwa_aln_core] print alignments... 0.01 sec 182s [bwa_aln_core] 10000 sequences have been processed. 182s [main] Version: 0.7.19-r1273 182s [main] CMD: bwa samse genomes/vdv1dwv5.fasta /tmp/res.sai ./SAM/dwv.fastq 182s [main] Real time: 0.052 sec; CPU: 0.027 sec 182s [bwa_aln] 17bp reads: max_diff = 2 182s [bwa_aln] 38bp reads: max_diff = 3 182s [bwa_aln] 64bp reads: max_diff = 4 182s [bwa_aln] 93bp reads: max_diff = 5 182s [bwa_aln] 124bp reads: max_diff = 6 182s [bwa_aln] 157bp reads: max_diff = 7 182s [bwa_aln] 190bp reads: max_diff = 8 182s [bwa_aln] 225bp reads: max_diff = 9 182s [bwa_aln_core] calculate SA coordinate... 0.09 sec 182s [bwa_aln_core] write to the disk... 0.00 sec 182s [bwa_aln_core] 10000 sequences have been processed. 182s [main] Version: 0.7.19-r1273 182s [main] CMD: bwa aln genomes/vdv1dwv9.fasta ./SAM/dwv.fastq 182s [main] Real time: 0.106 sec; CPU: 0.098 sec 182s [bwa_aln_core] convert to sequence coordinate... 0.01 sec 182s [bwa_aln_core] refine gapped alignments... 0.00 sec 182s [bwa_aln_core] print alignments... 0.01 sec 182s [bwa_aln_core] 10000 sequences have been processed. 182s [main] Version: 0.7.19-r1273 182s [main] CMD: bwa samse genomes/vdv1dwv9.fasta /tmp/res.sai ./SAM/dwv.fastq 182s [main] Real time: 0.042 sec; CPU: 0.025 sec 182s [bwa_aln] 17bp reads: max_diff = 2 182s [bwa_aln] 38bp reads: max_diff = 3 182s [bwa_aln] 64bp reads: max_diff = 4 182s [bwa_aln] 93bp reads: max_diff = 5 182s [bwa_aln] 124bp reads: max_diff = 6 182s [bwa_aln] 157bp reads: max_diff = 7 182s [bwa_aln] 190bp reads: max_diff = 8 182s [bwa_aln] 225bp reads: max_diff = 9 182s [bwa_aln_core] calculate SA coordinate... 0.05 sec 182s [bwa_aln_core] write to the disk... 0.00 sec 182s [bwa_aln_core] 10000 sequences have been processed. 182s [main] Version: 0.7.19-r1273 182s [main] CMD: bwa aln genomes/dwv.fasta ./SAM/vdv1.fastq 182s [main] Real time: 0.063 sec; CPU: 0.055 sec 182s [bwa_aln_core] convert to sequence coordinate... 0.00 sec 182s [bwa_aln_core] refine gapped alignments... 0.00 sec 183s [bwa_aln_core] print alignments... 0.00 sec 183s [bwa_aln_core] 10000 sequences have been processed. 183s [main] Version: 0.7.19-r1273 183s [main] CMD: bwa samse genomes/dwv.fasta /tmp/res.sai ./SAM/vdv1.fastq 183s [main] Real time: 0.023 sec; CPU: 0.011 sec 183s [bwa_aln] 17bp reads: max_diff = 2 183s [bwa_aln] 38bp reads: max_diff = 3 183s [bwa_aln] 64bp reads: max_diff = 4 183s [bwa_aln] 93bp reads: max_diff = 5 183s [bwa_aln] 124bp reads: max_diff = 6 183s [bwa_aln] 157bp reads: max_diff = 7 183s [bwa_aln] 190bp reads: max_diff = 8 183s [bwa_aln] 225bp reads: max_diff = 9 183s [bwa_aln_core] calculate SA coordinate... 0.15 sec 183s [bwa_aln_core] write to the disk... 0.00 sec 183s [bwa_aln_core] 10000 sequences have been processed. 183s [main] Version: 0.7.19-r1273 183s [main] CMD: bwa aln genomes/vdv1.fasta ./SAM/vdv1.fastq 183s [main] Real time: 0.169 sec; CPU: 0.155 sec 183s [bwa_aln_core] convert to sequence coordinate... 0.02 sec 183s [bwa_aln_core] refine gapped alignments... 0.00 sec 183s [bwa_aln_core] print alignments... 0.02 sec 183s [bwa_aln_core] 10000 sequences have been processed. 183s [main] Version: 0.7.19-r1273 183s [main] CMD: bwa samse genomes/vdv1.fasta /tmp/res.sai ./SAM/vdv1.fastq 183s [main] Real time: 0.063 sec; CPU: 0.046 sec 183s [bwa_aln] 17bp reads: max_diff = 2 183s [bwa_aln] 38bp reads: max_diff = 3 183s [bwa_aln] 64bp reads: max_diff = 4 183s [bwa_aln] 93bp reads: max_diff = 5 183s [bwa_aln] 124bp reads: max_diff = 6 183s [bwa_aln] 157bp reads: max_diff = 7 183s [bwa_aln] 190bp reads: max_diff = 8 183s [bwa_aln] 225bp reads: max_diff = 9 183s [bwa_aln_core] calculate SA coordinate... 0.11 sec 183s [bwa_aln_core] write to the disk... 0.00 sec 183s [bwa_aln_core] 10000 sequences have been processed. 183s [main] Version: 0.7.19-r1273 183s [main] CMD: bwa aln genomes/vdv1dwv5.fasta ./SAM/vdv1.fastq 183s [main] Real time: 0.126 sec; CPU: 0.113 sec 183s [bwa_aln_core] convert to sequence coordinate... 0.01 sec 183s [bwa_aln_core] refine gapped alignments... 0.00 sec 183s [bwa_aln_core] print alignments... 0.01 sec 183s [bwa_aln_core] 10000 sequences have been processed. 183s [main] Version: 0.7.19-r1273 183s [main] CMD: bwa samse genomes/vdv1dwv5.fasta /tmp/res.sai ./SAM/vdv1.fastq 183s [main] Real time: 0.041 sec; CPU: 0.031 sec 183s [bwa_aln] 17bp reads: max_diff = 2 183s [bwa_aln] 38bp reads: max_diff = 3 183s [bwa_aln] 64bp reads: max_diff = 4 183s [bwa_aln] 93bp reads: max_diff = 5 183s [bwa_aln] 124bp reads: max_diff = 6 183s [bwa_aln] 157bp reads: max_diff = 7 183s [bwa_aln] 190bp reads: max_diff = 8 183s [bwa_aln] 225bp reads: max_diff = 9 183s [bwa_aln_core] calculate SA coordinate... 0.11 sec 183s [bwa_aln_core] write to the disk... 0.00 sec 183s [bwa_aln_core] 10000 sequences have been processed. 183s [main] Version: 0.7.19-r1273 183s [main] CMD: bwa aln genomes/vdv1dwv9.fasta ./SAM/vdv1.fastq 183s [main] Real time: 0.129 sec; CPU: 0.116 sec 183s [bwa_aln_core] convert to sequence coordinate... 0.01 sec 183s [bwa_aln_core] refine gapped alignments... 0.00 sec 183s [bwa_aln_core] print alignments... 0.01 sec 183s [bwa_aln_core] 10000 sequences have been processed. 183s [main] Version: 0.7.19-r1273 183s [main] CMD: bwa samse genomes/vdv1dwv9.fasta /tmp/res.sai ./SAM/vdv1.fastq 183s [main] Real time: 0.065 sec; CPU: 0.033 sec 183s [bwa_aln] 17bp reads: max_diff = 2 183s [bwa_aln] 38bp reads: max_diff = 3 183s [bwa_aln] 64bp reads: max_diff = 4 183s [bwa_aln] 93bp reads: max_diff = 5 183s [bwa_aln] 124bp reads: max_diff = 6 183s [bwa_aln] 157bp reads: max_diff = 7 183s [bwa_aln] 190bp reads: max_diff = 8 183s [bwa_aln] 225bp reads: max_diff = 9 183s [bwa_aln_core] calculate SA coordinate... 0.10 sec 183s [bwa_aln_core] write to the disk... 0.00 sec 183s [bwa_aln_core] 10000 sequences have been processed. 183s [main] Version: 0.7.19-r1273 183s [main] CMD: bwa aln genomes/dwv.fasta ./SAM/vdv1dwv5.fastq 183s [main] Real time: 0.111 sec; CPU: 0.106 sec 183s [bwa_aln_core] convert to sequence coordinate... 0.01 sec 183s [bwa_aln_core] refine gapped alignments... 0.00 sec 183s [bwa_aln_core] print alignments... 0.01 sec 183s [bwa_aln_core] 10000 sequences have been processed. 183s [main] Version: 0.7.19-r1273 183s [main] CMD: bwa samse genomes/dwv.fasta /tmp/res.sai ./SAM/vdv1dwv5.fastq 183s [main] Real time: 0.041 sec; CPU: 0.029 sec 183s [bwa_aln] 17bp reads: max_diff = 2 183s [bwa_aln] 38bp reads: max_diff = 3 183s [bwa_aln] 64bp reads: max_diff = 4 183s [bwa_aln] 93bp reads: max_diff = 5 183s [bwa_aln] 124bp reads: max_diff = 6 183s [bwa_aln] 157bp reads: max_diff = 7 183s [bwa_aln] 190bp reads: max_diff = 8 183s [bwa_aln] 225bp reads: max_diff = 9 183s [bwa_aln_core] calculate SA coordinate... 0.11 sec 183s [bwa_aln_core] write to the disk... 0.00 sec 183s [bwa_aln_core] 10000 sequences have been processed. 183s [main] Version: 0.7.19-r1273 183s [main] CMD: bwa aln genomes/vdv1.fasta ./SAM/vdv1dwv5.fastq 183s [main] Real time: 0.116 sec; CPU: 0.111 sec 183s [bwa_aln_core] convert to sequence coordinate... 0.01 sec 183s [bwa_aln_core] refine gapped alignments... 0.00 sec 183s [bwa_aln_core] print alignments... 0.01 sec 183s [bwa_aln_core] 10000 sequences have been processed. 183s [main] Version: 0.7.19-r1273 183s [main] CMD: bwa samse genomes/vdv1.fasta /tmp/res.sai ./SAM/vdv1dwv5.fastq 183s [main] Real time: 0.044 sec; CPU: 0.030 sec 183s [bwa_aln] 17bp reads: max_diff = 2 183s [bwa_aln] 38bp reads: max_diff = 3 183s [bwa_aln] 64bp reads: max_diff = 4 183s [bwa_aln] 93bp reads: max_diff = 5 183s [bwa_aln] 124bp reads: max_diff = 6 183s [bwa_aln] 157bp reads: max_diff = 7 183s [bwa_aln] 190bp reads: max_diff = 8 183s [bwa_aln] 225bp reads: max_diff = 9 184s [bwa_aln_core] calculate SA coordinate... 0.15 sec 184s [bwa_aln_core] write to the disk... 0.00 sec 184s [bwa_aln_core] 10000 sequences have been processed. 184s [main] Version: 0.7.19-r1273 184s [main] CMD: bwa aln genomes/vdv1dwv5.fasta ./SAM/vdv1dwv5.fastq 184s [main] Real time: 0.163 sec; CPU: 0.155 sec 184s [bwa_aln_core] convert to sequence coordinate... 0.02 sec 184s [bwa_aln_core] refine gapped alignments... 0.00 sec 184s [bwa_aln_core] print alignments... 0.02 sec 184s [bwa_aln_core] 10000 sequences have been processed. 184s [main] Version: 0.7.19-r1273 184s [main] CMD: bwa samse genomes/vdv1dwv5.fasta /tmp/res.sai ./SAM/vdv1dwv5.fastq 184s [main] Real time: 0.061 sec; CPU: 0.047 sec 184s [bwa_aln] 17bp reads: max_diff = 2 184s [bwa_aln] 38bp reads: max_diff = 3 184s [bwa_aln] 64bp reads: max_diff = 4 184s [bwa_aln] 93bp reads: max_diff = 5 184s [bwa_aln] 124bp reads: max_diff = 6 184s [bwa_aln] 157bp reads: max_diff = 7 184s [bwa_aln] 190bp reads: max_diff = 8 184s [bwa_aln] 225bp reads: max_diff = 9 184s [bwa_aln_core] calculate SA coordinate... 0.13 sec 184s [bwa_aln_core] write to the disk... 0.00 sec 184s [bwa_aln_core] 10000 sequences have been processed. 184s [main] Version: 0.7.19-r1273 184s [main] CMD: bwa aln genomes/vdv1dwv9.fasta ./SAM/vdv1dwv5.fastq 184s [main] Real time: 0.145 sec; CPU: 0.140 sec 184s [bwa_aln_core] convert to sequence coordinate... 0.02 sec 184s [bwa_aln_core] refine gapped alignments... 0.00 sec 184s [bwa_aln_core] print alignments... 0.01 sec 184s [bwa_aln_core] 10000 sequences have been processed. 184s [main] Version: 0.7.19-r1273 184s [main] CMD: bwa samse genomes/vdv1dwv9.fasta /tmp/res.sai ./SAM/vdv1dwv5.fastq 184s [main] Real time: 0.054 sec; CPU: 0.039 sec 184s [bwa_aln] 17bp reads: max_diff = 2 184s [bwa_aln] 38bp reads: max_diff = 3 184s [bwa_aln] 64bp reads: max_diff = 4 184s [bwa_aln] 93bp reads: max_diff = 5 184s [bwa_aln] 124bp reads: max_diff = 6 184s [bwa_aln] 157bp reads: max_diff = 7 184s [bwa_aln] 190bp reads: max_diff = 8 184s [bwa_aln] 225bp reads: max_diff = 9 184s [bwa_aln_core] calculate SA coordinate... 0.10 sec 184s [bwa_aln_core] write to the disk... 0.00 sec 184s [bwa_aln_core] 10000 sequences have been processed. 184s [main] Version: 0.7.19-r1273 184s [main] CMD: bwa aln genomes/dwv.fasta ./SAM/vdv1dwv9.fastq 184s [main] Real time: 0.107 sec; CPU: 0.103 sec 184s [bwa_aln_core] convert to sequence coordinate... 0.01 sec 184s [bwa_aln_core] refine gapped alignments... 0.00 sec 184s [bwa_aln_core] print alignments... 0.01 sec 184s [bwa_aln_core] 10000 sequences have been processed. 184s [main] Version: 0.7.19-r1273 184s [main] CMD: bwa samse genomes/dwv.fasta /tmp/res.sai ./SAM/vdv1dwv9.fastq 184s [main] Real time: 0.047 sec; CPU: 0.028 sec 184s [bwa_aln] 17bp reads: max_diff = 2 184s [bwa_aln] 38bp reads: max_diff = 3 184s [bwa_aln] 64bp reads: max_diff = 4 184s [bwa_aln] 93bp reads: max_diff = 5 184s [bwa_aln] 124bp reads: max_diff = 6 184s [bwa_aln] 157bp reads: max_diff = 7 184s [bwa_aln] 190bp reads: max_diff = 8 184s [bwa_aln] 225bp reads: max_diff = 9 184s [bwa_aln_core] calculate SA coordinate... 0.11 sec 184s [bwa_aln_core] write to the disk... 0.00 sec 184s [bwa_aln_core] 10000 sequences have been processed. 184s [main] Version: 0.7.19-r1273 184s [main] CMD: bwa aln genomes/vdv1.fasta ./SAM/vdv1dwv9.fastq 184s [main] Real time: 0.118 sec; CPU: 0.114 sec 184s [bwa_aln_core] convert to sequence coordinate... 0.01 sec 184s [bwa_aln_core] refine gapped alignments... 0.00 sec 184s [bwa_aln_core] print alignments... 0.01 sec 184s [bwa_aln_core] 10000 sequences have been processed. 184s [main] Version: 0.7.19-r1273 184s [main] CMD: bwa samse genomes/vdv1.fasta /tmp/res.sai ./SAM/vdv1dwv9.fastq 184s [main] Real time: 0.047 sec; CPU: 0.032 sec 184s [bwa_aln] 17bp reads: max_diff = 2 184s [bwa_aln] 38bp reads: max_diff = 3 184s [bwa_aln] 64bp reads: max_diff = 4 184s [bwa_aln] 93bp reads: max_diff = 5 184s [bwa_aln] 124bp reads: max_diff = 6 184s [bwa_aln] 157bp reads: max_diff = 7 184s [bwa_aln] 190bp reads: max_diff = 8 184s [bwa_aln] 225bp reads: max_diff = 9 184s [bwa_aln_core] calculate SA coordinate... 0.14 sec 184s [bwa_aln_core] write to the disk... 0.00 sec 184s [bwa_aln_core] 10000 sequences have been processed. 184s [main] Version: 0.7.19-r1273 184s [main] CMD: bwa aln genomes/vdv1dwv5.fasta ./SAM/vdv1dwv9.fastq 184s [main] Real time: 0.145 sec; CPU: 0.141 sec 184s [bwa_aln_core] convert to sequence coordinate... 0.02 sec 184s [bwa_aln_core] refine gapped alignments... 0.00 sec 184s [bwa_aln_core] print alignments... 0.01 sec 184s [bwa_aln_core] 10000 sequences have been processed. 184s [main] Version: 0.7.19-r1273 184s [main] CMD: bwa samse genomes/vdv1dwv5.fasta /tmp/res.sai ./SAM/vdv1dwv9.fastq 184s [main] Real time: 0.053 sec; CPU: 0.040 sec 184s [bwa_aln] 17bp reads: max_diff = 2 184s [bwa_aln] 38bp reads: max_diff = 3 184s [bwa_aln] 64bp reads: max_diff = 4 184s [bwa_aln] 93bp reads: max_diff = 5 184s [bwa_aln] 124bp reads: max_diff = 6 184s [bwa_aln] 157bp reads: max_diff = 7 184s [bwa_aln] 190bp reads: max_diff = 8 184s [bwa_aln] 225bp reads: max_diff = 9 185s [bwa_aln_core] calculate SA coordinate... 0.15 sec 185s [bwa_aln_core] write to the disk... 0.00 sec 185s [bwa_aln_core] 10000 sequences have been processed. 185s [main] Version: 0.7.19-r1273 185s [main] CMD: bwa aln genomes/vdv1dwv9.fasta ./SAM/vdv1dwv9.fastq 185s [main] Real time: 0.160 sec; CPU: 0.156 sec 185s [bwa_aln_core] convert to sequence coordinate... 0.02 sec 185s [bwa_aln_core] refine gapped alignments... 0.00 sec 185s [bwa_aln_core] print alignments... 0.02 sec 185s [bwa_aln_core] 10000 sequences have been processed. 185s [main] Version: 0.7.19-r1273 185s [main] CMD: bwa samse genomes/vdv1dwv9.fasta /tmp/res.sai ./SAM/vdv1dwv9.fastq 185s [main] Real time: 0.064 sec; CPU: 0.046 sec 185s 185s --- Simulating reads for each reference genome with mason_illumina 185s 185s Original command with mason from SeQan 1 was 185s mason illumina -N 10000 -hi 0 -hs 0 -n 72 -sq -o ./SAM/dwv.fastq genomes/dwv.fasta 185s Please verify that the following call of mason_simulator fits your needs. If not 185s please use 185s reportbug gasic 185s to propose enhancements. 185s 185s Executing: /usr/lib/seqan/bin/mason_simulator --seq-technology illumina -n 10000 --illumina-read-length 72 -o ./SAM/dwv.fastq -ir genomes/dwv.fasta 185s Original command with mason from SeQan 1 was 185s mason illumina -N 10000 -hi 0 -hs 0 -n 72 -sq -o ./SAM/vdv1.fastq genomes/vdv1.fasta 185s Please verify that the following call of mason_simulator fits your needs. If not 185s please use 185s reportbug gasic 185s to propose enhancements. 185s 185s Executing: /usr/lib/seqan/bin/mason_simulator --seq-technology illumina -n 10000 --illumina-read-length 72 -o ./SAM/vdv1.fastq -ir genomes/vdv1.fasta 185s Original command with mason from SeQan 1 was 185s mason illumina -N 10000 -hi 0 -hs 0 -n 72 -sq -o ./SAM/vdv1dwv5.fastq genomes/vdv1dwv5.fasta 185s Please verify that the following call of mason_simulator fits your needs. If not 185s please use 185s reportbug gasic 185s to propose enhancements. 185s 185s Executing: /usr/lib/seqan/bin/mason_simulator --seq-technology illumina -n 10000 --illumina-read-length 72 -o ./SAM/vdv1dwv5.fastq -ir genomes/vdv1dwv5.fasta 185s Original command with mason from SeQan 1 was 185s mason illumina -N 10000 -hi 0 -hs 0 -n 72 -sq -o ./SAM/vdv1dwv9.fastq genomes/vdv1dwv9.fasta 185s Please verify that the following call of mason_simulator fits your needs. If not 185s please use 185s reportbug gasic 185s to propose enhancements. 185s 185s Executing: /usr/lib/seqan/bin/mason_simulator --seq-technology illumina -n 10000 --illumina-read-length 72 -o ./SAM/vdv1dwv9.fastq -ir genomes/vdv1dwv9.fasta 185s 185s --- Mapping simulated reads to reference genomes with bwa 185s 185s Executing: bwa aln genomes/dwv.fasta ./SAM/dwv.fastq > /tmp/res.sai 185s Executing: bwa aln genomes/vdv1.fasta ./SAM/dwv.fastq > /tmp/res.sai 185s Executing: bwa aln genomes/vdv1dwv5.fasta ./SAM/dwv.fastq > /tmp/res.sai 185s Executing: bwa aln genomes/vdv1dwv9.fasta ./SAM/dwv.fastq > /tmp/res.sai 185s Executing: bwa aln genomes/dwv.fasta ./SAM/vdv1.fastq > /tmp/res.sai 185s Executing: bwa aln genomes/vdv1.fasta ./SAM/vdv1.fastq > /tmp/res.sai 185s Executing: bwa aln genomes/vdv1dwv5.fasta ./SAM/vdv1.fastq > /tmp/res.sai 185s Executing: bwa aln genomes/vdv1dwv9.fasta ./SAM/vdv1.fastq > /tmp/res.sai 185s Executing: bwa aln genomes/dwv.fasta ./SAM/vdv1dwv5.fastq > /tmp/res.sai 185s Executing: bwa aln genomes/vdv1.fasta ./SAM/vdv1dwv5.fastq > /tmp/res.sai 185s Executing: bwa aln genomes/vdv1dwv5.fasta ./SAM/vdv1dwv5.fastq > /tmp/res.sai 185s Executing: bwa aln genomes/vdv1dwv9.fasta ./SAM/vdv1dwv5.fastq > /tmp/res.sai 185s Executing: bwa aln genomes/dwv.fasta ./SAM/vdv1dwv9.fastq > /tmp/res.sai 185s Executing: bwa aln genomes/vdv1.fasta ./SAM/vdv1dwv9.fastq > /tmp/res.sai 185s Executing: bwa aln genomes/vdv1dwv5.fasta ./SAM/vdv1dwv9.fastq > /tmp/res.sai 185s Executing: bwa aln genomes/vdv1dwv9.fasta ./SAM/vdv1dwv9.fastq > /tmp/res.sai 185s 185s --- Parsing SAM files 185s 185s 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 185s 185s Matrix creation done 185s 185s Wrote similarity matrix to ./similarity_matrix.npy 185s Passed 185s 185s Test 3: correct_abundances 185s 185s --- GASiC correction 185s 185s found 100000 reads 185s 185s --- Analyzing SAM files 185s 186s SAM file 1 of 4 SAM file 2 of 4 SAM file 3 of 4 SAM file 4 of 4 186s 186s --- Bootstrapping abundances 186s 514s 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 514s 514s Done estimating abundances 514s 514s --- wrote results to results.txt 514s Passed 514s 514s Test 4: quality_check 517s Passed 517s 517s autopkgtest [03:02:36]: test run-unit-test: -----------------------] 517s autopkgtest [03:02:36]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 517s run-unit-test PASS 518s autopkgtest [03:02:37]: @@@@@@@@@@@@@@@@@@@@ summary 518s run-unit-test PASS