0s autopkgtest [13:26:03]: starting date and time: 2025-12-03 13:26:03+0000 0s autopkgtest [13:26:03]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [13:26:03]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.z9yxjdff/out --timeout-copy=6000 -a i386 --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@sto01-2.secgroup --name adt-resolute-i386-gasic-20251203-132603-juju-7f2275-prod-proposed-migration-environment-20-98849828-9c41-497d-84d3-cbac2d3a6105 --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-i386-gasic-20251203-132603-juju-7f2275-prod-proposed-migration-environment-20-98849828-9c41-497d-84d3-cbac2d3a6105 from image adt/ubuntu-resolute-amd64-server-20251203.img (UUID c6e78f39-c16c-48bb-9815-0096f6be052e)... 49s autopkgtest [13:26:52]: testbed dpkg architecture: amd64 49s autopkgtest [13:26:52]: testbed apt version: 3.1.12 50s autopkgtest [13:26:53]: @@@@@@@@@@@@@@@@@@@@ test bed setup 50s autopkgtest [13:26:53]: testbed release detected to be: None 50s autopkgtest [13:26:53]: updating testbed package index (apt update) 51s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 51s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 51s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 51s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 51s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [147 kB] 51s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [25.2 kB] 51s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [981 kB] 51s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [205 kB] 51s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [158 kB] 51s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [6168 B] 51s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [120 B] 51s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [742 kB] 51s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [343 kB] 51s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [23.3 kB] 51s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [11.5 kB] 51s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [5224 B] 51s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [828 B] 52s Fetched 2774 kB in 1s (2956 kB/s) 53s Reading package lists... 53s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 53s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 53s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 53s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 54s Reading package lists... 54s Reading package lists... 54s Building dependency tree... 54s Reading state information... 54s Calculating upgrade... 54s The following packages will be upgraded: 54s libpython3-stdlib python3 python3-gdbm python3-minimal 54s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 54s Need to get 72.9 kB of archives. 54s After this operation, 2048 B of additional disk space will be used. 54s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-minimal amd64 3.13.9-2 [28.1 kB] 54s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3 amd64 3.13.9-2 [23.0 kB] 54s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libpython3-stdlib amd64 3.13.9-2 [10.8 kB] 54s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-gdbm amd64 3.13.9-2 [11.0 kB] 54s dpkg-preconfigure: unable to re-open stdin: No such file or directory 54s Fetched 72.9 kB in 0s (5168 kB/s) 54s (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.) 54s Preparing to unpack .../python3-minimal_3.13.9-2_amd64.deb ... 54s Unpacking python3-minimal (3.13.9-2) over (3.13.7-1) ... 54s Setting up python3-minimal (3.13.9-2) ... 55s (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.) 55s Preparing to unpack .../python3_3.13.9-2_amd64.deb ... 55s running python pre-rtupdate hooks for python3.13... 55s Unpacking python3 (3.13.9-2) over (3.13.7-1) ... 55s Preparing to unpack .../libpython3-stdlib_3.13.9-2_amd64.deb ... 55s Unpacking libpython3-stdlib:amd64 (3.13.9-2) over (3.13.7-1) ... 55s Preparing to unpack .../python3-gdbm_3.13.9-2_amd64.deb ... 55s Unpacking python3-gdbm (3.13.9-2) over (3.13.9-1) ... 55s Setting up python3-gdbm (3.13.9-2) ... 55s Setting up libpython3-stdlib:amd64 (3.13.9-2) ... 55s Setting up python3 (3.13.9-2) ... 55s running python rtupdate hooks for python3.13... 55s running python post-rtupdate hooks for python3.13... 55s Processing triggers for man-db (2.13.1-1) ... 55s autopkgtest [13:26:58]: upgrading testbed (apt dist-upgrade and autopurge) 55s Reading package lists... 55s Building dependency tree... 55s Reading state information... 56s Calculating upgrade... 56s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 56s Reading package lists... 56s Building dependency tree... 56s Reading state information... 56s Solving dependencies... 56s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 58s autopkgtest [13:27:01]: testbed running kernel: Linux 6.17.0-6-generic #6-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 7 13:34:17 UTC 2025 58s autopkgtest [13:27:01]: @@@@@@@@@@@@@@@@@@@@ apt-source gasic 60s Get:1 http://ftpmaster.internal/ubuntu resolute/universe gasic 0.0.r19-8 (dsc) [2112 B] 60s Get:2 http://ftpmaster.internal/ubuntu resolute/universe gasic 0.0.r19-8 (tar) [12.4 kB] 60s Get:3 http://ftpmaster.internal/ubuntu resolute/universe gasic 0.0.r19-8 (diff) [7305 kB] 60s gpgv: Signature made Thu Dec 29 18:00:34 2022 UTC 60s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 60s gpgv: issuer "tille@debian.org" 60s gpgv: Can't check signature: No public key 60s dpkg-source: warning: cannot verify inline signature for ./gasic_0.0.r19-8.dsc: no acceptable signature found 60s autopkgtest [13:27:03]: testing package gasic version 0.0.r19-8 61s autopkgtest [13:27:04]: build not needed 61s autopkgtest [13:27:04]: test run-unit-test: preparing testbed 61s Reading package lists... 62s Building dependency tree... 62s Reading state information... 62s Solving dependencies... 62s The following NEW packages will be installed: 62s bowtie bowtie2 bwa fontconfig-config fonts-dejavu-core fonts-dejavu-mono 62s fonts-lyx fonts-urw-base35 gasic gasic-examples libblas3 libcairo2 62s libdeflate0 libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 62s libharfbuzz0b libhts3t64 libhtscodecs2 libimagequant0 libjbig0 62s libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4 libopenjp2-7 62s libpixman-1-0 libqhull-r8.0 libraqm0 libsharpyuv0 libtcl8.6 libtiff6 62s libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 62s libxft2 libxrender1 libxslt1.1 libxss1 libzopfli1 python-matplotlib-data 62s python3-biopython python3-brotli python3-cairo python3-charset-normalizer 62s python3-contourpy python3-cycler python3-decorator python3-fonttools 62s python3-freetype python3-fs python3-kiwisolver python3-lxml python3-lz4 62s python3-matplotlib python3-mpmath python3-numpy python3-numpy-dev 62s python3-pil python3-pil.imagetk python3-platformdirs python3-pysam 62s python3-reportlab python3-rlpycairo python3-scipy python3-sympy python3-tk 62s python3-ufolib2 python3-unicodedata2 python3-zopfli python3.13-tk 62s python3.14-tk seqan-apps sgml-base unicode-data w3c-sgml-lib x11-common 62s xfonts-encodings xfonts-utils xml-core 62s 0 upgraded, 86 newly installed, 0 to remove and 0 not upgraded. 62s Need to get 119 MB of archives. 62s After this operation, 503 MB of additional disk space will be used. 62s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1ubuntu1 [147 kB] 62s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7 [259 kB] 62s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-9ubuntu1 [939 kB] 62s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7 [2739 kB] 62s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.2.4+ds-1ubuntu1 [5377 kB] 63s Get:6 http://ftpmaster.internal/ubuntu resolute/universe amd64 bwa amd64 0.7.19-1 [200 kB] 63s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 63s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 63s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontenc1 amd64 1:1.1.8-1build2 [14.1 kB] 63s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 63s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu3 [576 kB] 63s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 63s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 63s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.15.0-2.3ubuntu1 [38.0 kB] 63s Get:15 http://ftpmaster.internal/ubuntu resolute/universe amd64 fonts-lyx all 2.4.4-2 [171 kB] 63s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-decorator all 5.2.1-2 [28.1 kB] 63s Get:17 http://ftpmaster.internal/ubuntu resolute/universe amd64 libqhull-r8.0 amd64 2020.2-7 [197 kB] 64s Get:18 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-scipy amd64 1.16.3-1 [18.8 MB] 64s Get:19 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-charset-normalizer amd64 3.4.4-1 [175 kB] 64s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1 [1036 kB] 64s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.15.0-2.3ubuntu1 [141 kB] 64s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB] 64s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 64s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 64s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libtk8.6 amd64 8.6.17-1 [823 kB] 64s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.13-tk amd64 3.13.9-1 [108 kB] 64s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14-tk amd64 3.14.0-4 [108 kB] 64s Get:28 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-tk amd64 3.13.9-2 [11.1 kB] 64s Get:29 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pil.imagetk amd64 12.0.0-1ubuntu1 [9700 B] 64s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 15.2.0-9ubuntu1 [151 kB] 64s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 64s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu2 [152 kB] 64s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 64s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 liblcms2-2 amd64 2.17-1 [170 kB] 64s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 libopenjp2-7 amd64 2.5.3-2.1 [188 kB] 64s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 64s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.1.0-1 [535 kB] 64s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libraqm0 amd64 0.10.3-1 [15.4 kB] 64s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 64s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 64s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 64s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 64s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 64s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB] 64s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB] 64s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB] 64s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-pil amd64 12.0.0-1ubuntu1 [494 kB] 64s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.46.4-1 [287 kB] 64s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2build1 [17.4 kB] 64s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2build1 [6120 B] 64s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-1build1 [611 kB] 64s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-cairo amd64 1.27.0-2build1 [140 kB] 64s Get:53 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-freetype all 2.5.1-2 [92.2 kB] 64s Get:54 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-rlpycairo all 0.3.0-4 [9332 B] 64s Get:55 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-reportlab all 4.4.5-1 [1148 kB] 64s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 sgml-base all 1.31+nmu1 [11.0 kB] 64s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 xml-core all 0.19 [20.3 kB] 64s Get:58 http://ftpmaster.internal/ubuntu resolute/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 64s Get:59 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-biopython amd64 1.86+dfsg-1 [1682 kB] 64s Get:60 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhtscodecs2 amd64 1.6.1-2 [132 kB] 64s Get:61 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhts3t64 amd64 1.22.1+ds2-1 [461 kB] 64s Get:62 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pysam amd64 0.23.3+ds-2 [4536 kB] 65s Get:63 http://ftpmaster.internal/ubuntu resolute/universe amd64 python-matplotlib-data all 3.10.7+dfsg1-1 [2930 kB] 65s Get:64 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-contourpy amd64 1.3.3-1 [255 kB] 65s Get:65 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-cycler all 0.12.1-2 [9850 B] 65s Get:66 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-brotli amd64 1.1.0-2build6 [340 kB] 65s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-platformdirs all 4.4.0-1 [16.9 kB] 65s Get:68 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-fs all 2.4.16-9ubuntu1 [91.5 kB] 65s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 libxslt1.1 amd64 1.1.43-0.3 [172 kB] 65s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-lxml amd64 6.0.2-1 [2333 kB] 65s Get:71 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-lz4 amd64 4.4.4+dfsg-3 [27.5 kB] 65s Get:72 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-mpmath all 1.3.0-2 [423 kB] 65s Get:73 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-sympy all 1.14.0-2 [4306 kB] 65s Get:74 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.5 kB] 65s Get:75 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-unicodedata2 amd64 16.0.0+ds-1build1 [400 kB] 65s Get:76 http://ftpmaster.internal/ubuntu resolute/universe amd64 libzopfli1 amd64 1.0.3-3 [141 kB] 65s Get:77 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-zopfli amd64 0.4.0-1 [11.1 kB] 65s Get:78 http://ftpmaster.internal/ubuntu resolute/universe amd64 unicode-data all 16.0.0-1 [9513 kB] 65s Get:79 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-fonttools amd64 4.57.0-3 [1705 kB] 65s Get:80 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-kiwisolver amd64 1.4.10~rc0-1 [65.5 kB] 65s Get:81 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-matplotlib amd64 3.10.7+dfsg1-1 [17.2 MB] 65s Get:82 http://ftpmaster.internal/ubuntu resolute/universe amd64 bowtie amd64 1.3.1-3 [1562 kB] 65s Get:83 http://ftpmaster.internal/ubuntu resolute/universe amd64 bowtie2 amd64 2.5.4-1 [1336 kB] 66s Get:84 http://ftpmaster.internal/ubuntu resolute/universe amd64 seqan-apps amd64 2.4.0+dfsg-16 [12.3 MB] 66s Get:85 http://ftpmaster.internal/ubuntu resolute/universe amd64 gasic all 0.0.r19-8 [21.1 kB] 66s Get:86 http://ftpmaster.internal/ubuntu resolute/universe amd64 gasic-examples all 0.0.r19-8 [7270 kB] 66s Fetched 119 MB in 4s (27.8 MB/s) 66s Selecting previously unselected package python3-numpy-dev:amd64. 66s (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.) 66s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 66s Unpacking python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 66s Selecting previously unselected package libblas3:amd64. 66s Preparing to unpack .../01-libblas3_3.12.1-7_amd64.deb ... 66s Unpacking libblas3:amd64 (3.12.1-7) ... 66s Selecting previously unselected package libgfortran5:amd64. 66s Preparing to unpack .../02-libgfortran5_15.2.0-9ubuntu1_amd64.deb ... 66s Unpacking libgfortran5:amd64 (15.2.0-9ubuntu1) ... 66s Selecting previously unselected package liblapack3:amd64. 66s Preparing to unpack .../03-liblapack3_3.12.1-7_amd64.deb ... 66s Unpacking liblapack3:amd64 (3.12.1-7) ... 66s Selecting previously unselected package python3-numpy. 66s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 66s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 67s Selecting previously unselected package bwa. 67s Preparing to unpack .../05-bwa_0.7.19-1_amd64.deb ... 67s Unpacking bwa (0.7.19-1) ... 67s Selecting previously unselected package fonts-dejavu-mono. 67s Preparing to unpack .../06-fonts-dejavu-mono_2.37-8_all.deb ... 67s Unpacking fonts-dejavu-mono (2.37-8) ... 67s Selecting previously unselected package fonts-dejavu-core. 67s Preparing to unpack .../07-fonts-dejavu-core_2.37-8_all.deb ... 67s Unpacking fonts-dejavu-core (2.37-8) ... 67s Selecting previously unselected package libfontenc1:amd64. 67s Preparing to unpack .../08-libfontenc1_1%3a1.1.8-1build2_amd64.deb ... 67s Unpacking libfontenc1:amd64 (1:1.1.8-1build2) ... 67s Selecting previously unselected package x11-common. 67s Preparing to unpack .../09-x11-common_1%3a7.7+24ubuntu1_all.deb ... 67s Unpacking x11-common (1:7.7+24ubuntu1) ... 67s Selecting previously unselected package xfonts-encodings. 67s Preparing to unpack .../10-xfonts-encodings_1%3a1.0.5-0ubuntu3_all.deb ... 67s Unpacking xfonts-encodings (1:1.0.5-0ubuntu3) ... 67s Selecting previously unselected package xfonts-utils. 67s Preparing to unpack .../11-xfonts-utils_1%3a7.7+7_amd64.deb ... 67s Unpacking xfonts-utils (1:7.7+7) ... 67s Selecting previously unselected package fonts-urw-base35. 67s Preparing to unpack .../12-fonts-urw-base35_20200910-8_all.deb ... 67s Unpacking fonts-urw-base35 (20200910-8) ... 67s Selecting previously unselected package fontconfig-config. 67s Preparing to unpack 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... 67s Selecting previously unselected package libtcl8.6:amd64. 67s Preparing to unpack .../19-libtcl8.6_8.6.17+dfsg-1_amd64.deb ... 67s Unpacking libtcl8.6:amd64 (8.6.17+dfsg-1) ... 67s Selecting previously unselected package libfontconfig1:amd64. 67s Preparing to unpack .../20-libfontconfig1_2.15.0-2.3ubuntu1_amd64.deb ... 67s Unpacking libfontconfig1:amd64 (2.15.0-2.3ubuntu1) ... 67s Selecting previously unselected package libxrender1:amd64. 67s Preparing to unpack .../21-libxrender1_1%3a0.9.12-1_amd64.deb ... 67s Unpacking libxrender1:amd64 (1:0.9.12-1) ... 67s Selecting previously unselected package libxft2:amd64. 67s Preparing to unpack .../22-libxft2_2.3.6-1build1_amd64.deb ... 67s Unpacking libxft2:amd64 (2.3.6-1build1) ... 67s Selecting previously unselected package libxss1:amd64. 67s Preparing to unpack .../23-libxss1_1%3a1.2.3-1build3_amd64.deb ... 67s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 67s Selecting previously unselected package libtk8.6:amd64. 67s Preparing to unpack .../24-libtk8.6_8.6.17-1_amd64.deb ... 67s Unpacking libtk8.6:amd64 (8.6.17-1) ... 67s Selecting previously unselected package python3.13-tk. 67s Preparing to unpack .../25-python3.13-tk_3.13.9-1_amd64.deb ... 67s Unpacking python3.13-tk (3.13.9-1) ... 67s Selecting previously unselected package python3.14-tk. 67s Preparing to unpack .../26-python3.14-tk_3.14.0-4_amd64.deb ... 67s Unpacking python3.14-tk (3.14.0-4) ... 67s Selecting previously unselected package python3-tk. 67s Preparing to unpack .../27-python3-tk_3.13.9-2_amd64.deb ... 67s Unpacking python3-tk (3.13.9-2) ... 67s Selecting previously unselected package python3-pil.imagetk:amd64. 67s Preparing to unpack .../28-python3-pil.imagetk_12.0.0-1ubuntu1_amd64.deb ... 67s Unpacking python3-pil.imagetk:amd64 (12.0.0-1ubuntu1) ... 67s Selecting previously unselected package libgomp1:amd64. 67s Preparing to unpack .../29-libgomp1_15.2.0-9ubuntu1_amd64.deb ... 67s Unpacking libgomp1:amd64 (15.2.0-9ubuntu1) ... 67s Selecting previously unselected package libimagequant0:amd64. 67s Preparing to unpack .../30-libimagequant0_2.18.0-1build1_amd64.deb ... 67s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 67s Selecting previously unselected package libjpeg-turbo8:amd64. 67s Preparing to unpack .../31-libjpeg-turbo8_2.1.5-4ubuntu2_amd64.deb ... 67s Unpacking libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 67s Selecting previously unselected package libjpeg8:amd64. 67s Preparing to unpack .../32-libjpeg8_8c-2ubuntu11_amd64.deb ... 67s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 67s Selecting previously unselected package liblcms2-2:amd64. 67s Preparing to unpack .../33-liblcms2-2_2.17-1_amd64.deb ... 67s Unpacking liblcms2-2:amd64 (2.17-1) ... 67s Selecting previously unselected package libopenjp2-7:amd64. 67s Preparing to unpack .../34-libopenjp2-7_2.5.3-2.1_amd64.deb ... 67s Unpacking libopenjp2-7:amd64 (2.5.3-2.1) ... 67s Selecting previously unselected package libgraphite2-3:amd64. 67s Preparing to unpack .../35-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 67s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 67s Selecting previously unselected package libharfbuzz0b:amd64. 67s Preparing to unpack .../36-libharfbuzz0b_12.1.0-1_amd64.deb ... 67s Unpacking libharfbuzz0b:amd64 (12.1.0-1) ... 67s Selecting previously unselected package libraqm0:amd64. 67s Preparing to unpack .../37-libraqm0_0.10.3-1_amd64.deb ... 67s Unpacking libraqm0:amd64 (0.10.3-1) ... 67s Selecting previously unselected package libdeflate0:amd64. 67s Preparing to unpack .../38-libdeflate0_1.23-2_amd64.deb ... 67s Unpacking libdeflate0:amd64 (1.23-2) ... 67s Selecting previously unselected package libjbig0:amd64. 67s Preparing to unpack .../39-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 67s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 67s Selecting previously unselected package liblerc4:amd64. 67s Preparing to unpack .../40-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 67s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 67s Selecting previously unselected package libsharpyuv0:amd64. 67s Preparing to unpack .../41-libsharpyuv0_1.5.0-0.1_amd64.deb ... 67s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 67s Selecting previously unselected package libwebp7:amd64. 67s Preparing to unpack .../42-libwebp7_1.5.0-0.1_amd64.deb ... 67s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 67s Selecting previously unselected package libtiff6:amd64. 67s Preparing to unpack .../43-libtiff6_4.7.0-3ubuntu3_amd64.deb ... 67s Unpacking libtiff6:amd64 (4.7.0-3ubuntu3) ... 67s Selecting previously unselected package libwebpdemux2:amd64. 67s Preparing to unpack .../44-libwebpdemux2_1.5.0-0.1_amd64.deb ... 67s Unpacking libwebpdemux2:amd64 (1.5.0-0.1) ... 67s Selecting previously unselected package libwebpmux3:amd64. 67s Preparing to unpack .../45-libwebpmux3_1.5.0-0.1_amd64.deb ... 67s Unpacking libwebpmux3:amd64 (1.5.0-0.1) ... 67s Selecting previously unselected package python3-pil:amd64. 67s Preparing to unpack .../46-python3-pil_12.0.0-1ubuntu1_amd64.deb ... 67s Unpacking python3-pil:amd64 (12.0.0-1ubuntu1) ... 67s Selecting previously unselected package libpixman-1-0:amd64. 67s Preparing to unpack .../47-libpixman-1-0_0.46.4-1_amd64.deb ... 67s Unpacking libpixman-1-0:amd64 (0.46.4-1) ... 67s Selecting previously unselected package libxcb-render0:amd64. 67s Preparing to unpack .../48-libxcb-render0_1.17.0-2build1_amd64.deb ... 67s Unpacking libxcb-render0:amd64 (1.17.0-2build1) ... 68s Selecting previously unselected package libxcb-shm0:amd64. 68s Preparing to unpack .../49-libxcb-shm0_1.17.0-2build1_amd64.deb ... 68s Unpacking libxcb-shm0:amd64 (1.17.0-2build1) ... 68s Selecting previously unselected package libcairo2:amd64. 68s Preparing to unpack .../50-libcairo2_1.18.4-1build1_amd64.deb ... 68s Unpacking libcairo2:amd64 (1.18.4-1build1) ... 68s Selecting previously unselected package python3-cairo. 68s Preparing to unpack .../51-python3-cairo_1.27.0-2build1_amd64.deb ... 68s Unpacking python3-cairo (1.27.0-2build1) ... 68s Selecting previously unselected package python3-freetype. 68s Preparing to unpack .../52-python3-freetype_2.5.1-2_all.deb ... 68s Unpacking python3-freetype (2.5.1-2) ... 68s Selecting previously unselected package python3-rlpycairo. 68s Preparing to unpack .../53-python3-rlpycairo_0.3.0-4_all.deb ... 68s Unpacking python3-rlpycairo (0.3.0-4) ... 68s Selecting previously unselected package python3-reportlab. 68s Preparing to unpack .../54-python3-reportlab_4.4.5-1_all.deb ... 68s Unpacking python3-reportlab (4.4.5-1) ... 68s Selecting previously unselected package sgml-base. 68s Preparing to unpack .../55-sgml-base_1.31+nmu1_all.deb ... 68s Unpacking sgml-base (1.31+nmu1) ... 68s Selecting previously unselected package xml-core. 68s Preparing to unpack .../56-xml-core_0.19_all.deb ... 68s Unpacking xml-core (0.19) ... 68s Selecting previously unselected package w3c-sgml-lib. 68s Preparing to unpack .../57-w3c-sgml-lib_1.3-3_all.deb ... 68s Unpacking w3c-sgml-lib (1.3-3) ... 68s Selecting previously unselected package python3-biopython. 68s Preparing to unpack .../58-python3-biopython_1.86+dfsg-1_amd64.deb ... 68s Unpacking python3-biopython (1.86+dfsg-1) ... 68s Selecting previously unselected package libhtscodecs2:amd64. 68s Preparing to unpack .../59-libhtscodecs2_1.6.1-2_amd64.deb ... 68s Unpacking libhtscodecs2:amd64 (1.6.1-2) ... 68s Selecting previously unselected package libhts3t64:amd64. 68s Preparing to unpack .../60-libhts3t64_1.22.1+ds2-1_amd64.deb ... 68s Unpacking libhts3t64:amd64 (1.22.1+ds2-1) ... 68s Selecting previously unselected package python3-pysam. 68s Preparing to unpack .../61-python3-pysam_0.23.3+ds-2_amd64.deb ... 68s Unpacking python3-pysam (0.23.3+ds-2) ... 68s Selecting previously unselected package python-matplotlib-data. 68s Preparing to unpack .../62-python-matplotlib-data_3.10.7+dfsg1-1_all.deb ... 68s Unpacking python-matplotlib-data (3.10.7+dfsg1-1) ... 68s Selecting previously unselected package python3-contourpy. 68s Preparing to unpack .../63-python3-contourpy_1.3.3-1_amd64.deb ... 68s Unpacking python3-contourpy (1.3.3-1) ... 68s Selecting previously unselected package python3-cycler. 68s Preparing to unpack .../64-python3-cycler_0.12.1-2_all.deb ... 68s Unpacking python3-cycler (0.12.1-2) ... 68s Selecting previously unselected package python3-brotli. 68s Preparing to unpack .../65-python3-brotli_1.1.0-2build6_amd64.deb ... 68s Unpacking python3-brotli (1.1.0-2build6) ... 68s Selecting previously unselected package python3-platformdirs. 68s Preparing to unpack .../66-python3-platformdirs_4.4.0-1_all.deb ... 68s Unpacking python3-platformdirs (4.4.0-1) ... 68s Selecting previously unselected package python3-fs. 68s Preparing to unpack .../67-python3-fs_2.4.16-9ubuntu1_all.deb ... 68s Unpacking python3-fs (2.4.16-9ubuntu1) ... 68s Selecting previously unselected package libxslt1.1:amd64. 68s Preparing to unpack .../68-libxslt1.1_1.1.43-0.3_amd64.deb ... 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to unpack .../74-python3-unicodedata2_16.0.0+ds-1build1_amd64.deb ... 68s Unpacking python3-unicodedata2 (16.0.0+ds-1build1) ... 68s Selecting previously unselected package libzopfli1. 68s Preparing to unpack .../75-libzopfli1_1.0.3-3_amd64.deb ... 68s Unpacking libzopfli1 (1.0.3-3) ... 68s Selecting previously unselected package python3-zopfli. 68s Preparing to unpack .../76-python3-zopfli_0.4.0-1_amd64.deb ... 68s Unpacking python3-zopfli (0.4.0-1) ... 68s Selecting previously unselected package unicode-data. 68s Preparing to unpack .../77-unicode-data_16.0.0-1_all.deb ... 68s Unpacking unicode-data (16.0.0-1) ... 68s Selecting previously unselected package python3-fonttools. 68s Preparing to unpack .../78-python3-fonttools_4.57.0-3_amd64.deb ... 68s Unpacking python3-fonttools (4.57.0-3) ... 68s Selecting previously unselected package python3-kiwisolver. 68s Preparing to unpack .../79-python3-kiwisolver_1.4.10~rc0-1_amd64.deb ... 68s Unpacking python3-kiwisolver (1.4.10~rc0-1) ... 68s Selecting previously unselected package python3-matplotlib. 68s Preparing to unpack .../80-python3-matplotlib_3.10.7+dfsg1-1_amd64.deb ... 68s Unpacking python3-matplotlib (3.10.7+dfsg1-1) ... 69s Selecting previously unselected package bowtie. 69s Preparing to unpack .../81-bowtie_1.3.1-3_amd64.deb ... 69s Unpacking bowtie (1.3.1-3) ... 69s Selecting previously unselected package bowtie2. 69s Preparing to unpack .../82-bowtie2_2.5.4-1_amd64.deb ... 69s Unpacking bowtie2 (2.5.4-1) ... 69s Selecting previously unselected package seqan-apps. 69s Preparing to unpack .../83-seqan-apps_2.4.0+dfsg-16_amd64.deb ... 69s Unpacking seqan-apps (2.4.0+dfsg-16) ... 69s Selecting previously unselected package gasic. 69s Preparing to unpack .../84-gasic_0.0.r19-8_all.deb ... 69s Unpacking gasic (0.0.r19-8) ... 69s Selecting previously unselected package gasic-examples. 69s Preparing to unpack .../85-gasic-examples_0.0.r19-8_all.deb ... 69s Unpacking gasic-examples (0.0.r19-8) ... 69s Setting up libhtscodecs2:amd64 (1.6.1-2) ... 69s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 69s Setting up liblcms2-2:amd64 (2.17-1) ... 69s Setting up libpixman-1-0:amd64 (0.46.4-1) ... 69s Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... 69s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 69s Setting up bowtie (1.3.1-3) ... 69s Setting up libxrender1:amd64 (1:0.9.12-1) ... 69s Setting up python3-lz4 (4.4.4+dfsg-3) ... 69s Setting up libxcb-render0:amd64 (1.17.0-2build1) ... 69s Setting up python3-charset-normalizer (3.4.4-1) ... 69s Setting up bwa (0.7.19-1) ... 69s Setting up python3-unicodedata2 (16.0.0+ds-1build1) ... 69s Setting up fonts-lyx (2.4.4-2) ... 69s Setting up gasic-examples (0.0.r19-8) ... 69s Setting up x11-common (1:7.7+24ubuntu1) ... 69s Setting up libdeflate0:amd64 (1.23-2) ... 69s Setting up libqhull-r8.0:amd64 (2020.2-7) ... 69s Setting up libxcb-shm0:amd64 (1.17.0-2build1) ... 69s Setting up libgomp1:amd64 (15.2.0-9ubuntu1) ... 69s Setting up python3-freetype (2.5.1-2) ... 69s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 69s Setting up python3-platformdirs (4.4.0-1) ... 69s Setting up bowtie2 (2.5.4-1) ... 69s Setting up python3-fs (2.4.16-9ubuntu1) ... 70s Setting up unicode-data (16.0.0-1) ... 70s Setting up python3-decorator (5.2.1-2) ... 70s Setting up libfontenc1:amd64 (1:1.1.8-1build2) ... 70s Setting up libblas3:amd64 (3.12.1-7) ... 70s 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 70s Setting up libzopfli1 (1.0.3-3) ... 70s Setting up python3-brotli (1.1.0-2build6) ... 70s Setting up xfonts-encodings (1:1.0.5-0ubuntu3) ... 70s Setting up python3-cycler (0.12.1-2) ... 70s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 70s Setting up seqan-apps (2.4.0+dfsg-16) ... 70s Setting up fonts-dejavu-mono (2.37-8) ... 70s Setting up python3-kiwisolver (1.4.10~rc0-1) ... 70s Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 70s Setting up libtcl8.6:amd64 (8.6.17+dfsg-1) ... 70s Setting up fonts-dejavu-core (2.37-8) ... 70s Setting up libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 70s Setting up libgfortran5:amd64 (15.2.0-9ubuntu1) ... 70s Setting up libwebp7:amd64 (1.5.0-0.1) ... 70s Setting up libxslt1.1:amd64 (1.1.43-0.3) ... 70s Setting up libhts3t64:amd64 (1.22.1+ds2-1) ... 70s Setting up libopenjp2-7:amd64 (2.5.3-2.1) ... 70s Setting up libharfbuzz0b:amd64 (12.1.0-1) ... 70s Setting up sgml-base (1.31+nmu1) ... 70s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 70s Setting up python3-mpmath (1.3.0-2) ... 70s Setting up python-matplotlib-data (3.10.7+dfsg1-1) ... 70s Setting up libwebpmux3:amd64 (1.5.0-0.1) ... 70s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 70s Setting up python3-sympy (1.14.0-2) ... 74s Setting up liblapack3:amd64 (3.12.1-7) ... 74s 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 74s Setting up python3-pysam (0.23.3+ds-2) ... 74s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ... 74s Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... 74s Setting up xfonts-utils (1:7.7+7) ... 74s Setting up python3-zopfli (0.4.0-1) ... 74s Setting up libraqm0:amd64 (0.10.3-1) ... 74s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 75s Setting up python3-lxml:amd64 (6.0.2-1) ... 75s Setting up libtiff6:amd64 (4.7.0-3ubuntu3) ... 75s Setting up xml-core (0.19) ... 75s Setting up python3-contourpy (1.3.3-1) ... 75s Setting up libfontconfig1:amd64 (2.15.0-2.3ubuntu1) ... 75s Setting up libxft2:amd64 (2.3.6-1build1) ... 75s Setting up python3-scipy (1.16.3-1) ... 78s Setting up libtk8.6:amd64 (8.6.17-1) ... 78s Setting up fonts-urw-base35 (20200910-8) ... 78s Setting up libcairo2:amd64 (1.18.4-1build1) ... 78s Setting up python3.13-tk (3.13.9-1) ... 78s Setting up python3-pil:amd64 (12.0.0-1ubuntu1) ... 78s Setting up python3.14-tk (3.14.0-4) ... 78s Setting up python3-cairo (1.27.0-2build1) ... 78s Setting up python3-tk (3.13.9-2) ... 78s Setting up python3-pil.imagetk:amd64 (12.0.0-1ubuntu1) ... 78s Setting up python3-rlpycairo (0.3.0-4) ... 78s Setting up python3-reportlab (4.4.5-1) ... 79s Setting up python3-fonttools (4.57.0-3) ... 79s Setting up python3-ufolib2 (0.17.1+dfsg1-1) ... 79s Setting up python3-matplotlib (3.10.7+dfsg1-1) ... 81s Processing triggers for libc-bin (2.42-2ubuntu2) ... 81s Processing triggers for man-db (2.13.1-1) ... 81s Processing triggers for sgml-base (1.31+nmu1) ... 81s Setting up w3c-sgml-lib (1.3-3) ... 97s Setting up python3-biopython (1.86+dfsg-1) ... 98s Setting up gasic (0.0.r19-8) ... 99s autopkgtest [13:27:42]: test environment configured for cross building 99s autopkgtest [13:27:42]: test run-unit-test: [----------------------- 99s Test 0: Create Genome Indices 99s [bwa_index] Pack FASTA... 0.00 sec 99s [bwa_index] Construct BWT for the packed sequence... 99s [bwa_index] 0.00 seconds elapse. 99s [bwa_index] Update BWT... 0.00 sec 99s [bwa_index] Pack forward-only FASTA... 0.00 sec 99s [bwa_index] Construct SA from BWT and Occ... 0.00 sec 99s [main] Version: 0.7.19-r1273 99s [main] CMD: bwa index dwv.fasta 99s [main] Real time: 0.017 sec; CPU: 0.003 sec 99s [bwa_index] Pack FASTA... 0.00 sec 99s [bwa_index] Construct BWT for the packed sequence... 99s [bwa_index] 0.00 seconds elapse. 99s [bwa_index] Update BWT... 0.00 sec 99s [bwa_index] Pack forward-only FASTA... 0.00 sec 99s [bwa_index] Construct SA from BWT and Occ... 0.00 sec 99s [main] Version: 0.7.19-r1273 99s [main] CMD: bwa index vdv1.fasta 99s [main] Real time: 0.017 sec; CPU: 0.003 sec 99s [bwa_index] Pack FASTA... 0.00 sec 99s [bwa_index] Construct BWT for the packed sequence... 99s [bwa_index] 0.00 seconds elapse. 99s [bwa_index] Update BWT... 0.00 sec 99s [bwa_index] Pack forward-only FASTA... 0.00 sec 99s [bwa_index] Construct SA from BWT and Occ... 0.00 sec 99s [main] Version: 0.7.19-r1273 99s [main] CMD: bwa index vdv1dwv9.fasta 99s [main] Real time: 0.012 sec; CPU: 0.003 sec 99s [bwa_index] Pack FASTA... 0.00 sec 99s [bwa_index] Construct BWT for the packed sequence... 99s [bwa_index] 0.00 seconds elapse. 99s [bwa_index] Update BWT... 0.00 sec 99s [bwa_index] Pack forward-only FASTA... 0.00 sec 99s [bwa_index] Construct SA from BWT and Occ... Passed 99s 99s 0.00 sec 99s [main] Version: 0.7.19-r1273 99s [main] CMD: bwa index vdv1dwv5.fasta 99s [main] Real time: 0.013 sec; CPU: 0.003 sec 99s Test 1: run_mappers 99s [bwa_aln] 17bp reads: max_diff = 2 99s [bwa_aln] 38bp reads: max_diff = 3 99s [bwa_aln] 64bp reads: max_diff = 4 99s [bwa_aln] 93bp reads: max_diff = 5 99s [bwa_aln] 124bp reads: max_diff = 6 99s [bwa_aln] 157bp reads: max_diff = 7 99s [bwa_aln] 190bp reads: max_diff = 8 99s [bwa_aln] 225bp reads: max_diff = 9 100s [bwa_aln_core] calculate SA coordinate... 0.68 sec 100s [bwa_aln_core] write to the disk... 0.00 sec 100s [bwa_aln_core] 100000 sequences have been processed. 100s [main] Version: 0.7.19-r1273 100s [main] CMD: bwa aln ./genomes/dwv.fasta reads/SRR059298_subset.fastq 100s [main] Real time: 0.749 sec; CPU: 0.745 sec 100s [bwa_aln_core] convert to sequence coordinate... 0.05 sec 100s [bwa_aln_core] refine gapped alignments... 0.02 sec 100s [bwa_aln_core] print alignments... 0.04 sec 100s [bwa_aln_core] 100000 sequences have been processed. 100s [main] Version: 0.7.19-r1273 100s [main] CMD: bwa samse ./genomes/dwv.fasta /tmp/res.sai reads/SRR059298_subset.fastq 100s [main] Real time: 0.182 sec; CPU: 0.176 sec 100s [bwa_aln] 17bp reads: max_diff = 2 100s [bwa_aln] 38bp reads: max_diff = 3 100s [bwa_aln] 64bp reads: max_diff = 4 100s [bwa_aln] 93bp reads: max_diff = 5 100s [bwa_aln] 124bp reads: max_diff = 6 100s [bwa_aln] 157bp reads: max_diff = 7 100s [bwa_aln] 190bp reads: max_diff = 8 100s [bwa_aln] 225bp reads: max_diff = 9 101s [bwa_aln_core] calculate SA coordinate... 0.50 sec 101s [bwa_aln_core] write to the disk... 0.00 sec 101s [bwa_aln_core] 100000 sequences have been processed. 101s [main] Version: 0.7.19-r1273 101s [main] CMD: bwa aln ./genomes/vdv1.fasta reads/SRR059298_subset.fastq 101s [main] Real time: 0.561 sec; CPU: 0.556 sec 101s [bwa_aln_core] convert to sequence coordinate... 0.03 sec 101s [bwa_aln_core] refine gapped alignments... 0.01 sec 101s [bwa_aln_core] print alignments... 0.03 sec 101s [bwa_aln_core] 100000 sequences have been processed. 101s [main] Version: 0.7.19-r1273 101s [main] CMD: bwa samse ./genomes/vdv1.fasta /tmp/res.sai reads/SRR059298_subset.fastq 101s [main] Real time: 0.142 sec; CPU: 0.134 sec 101s [bwa_aln] 17bp reads: max_diff = 2 101s [bwa_aln] 38bp reads: max_diff = 3 101s [bwa_aln] 64bp reads: max_diff = 4 101s [bwa_aln] 93bp reads: max_diff = 5 101s [bwa_aln] 124bp reads: max_diff = 6 101s [bwa_aln] 157bp reads: max_diff = 7 101s [bwa_aln] 190bp reads: max_diff = 8 101s [bwa_aln] 225bp reads: max_diff = 9 102s [bwa_aln_core] calculate SA coordinate... 0.82 sec 102s [bwa_aln_core] write to the disk... 0.00 sec 102s [bwa_aln_core] 100000 sequences have been processed. 102s [main] Version: 0.7.19-r1273 102s [main] CMD: bwa aln ./genomes/vdv1dwv5.fasta reads/SRR059298_subset.fastq 102s [main] Real time: 0.888 sec; CPU: 0.883 sec 102s [bwa_aln_core] convert to sequence coordinate... 0.07 sec 102s [bwa_aln_core] refine gapped alignments... 0.02 sec 102s [bwa_aln_core] print alignments... 0.05 sec 102s [bwa_aln_core] 100000 sequences have been processed. 102s [main] Version: 0.7.19-r1273 102s [main] CMD: bwa samse ./genomes/vdv1dwv5.fasta /tmp/res.sai reads/SRR059298_subset.fastq 102s [main] Real time: 0.211 sec; CPU: 0.203 sec 102s [bwa_aln] 17bp reads: max_diff = 2 102s [bwa_aln] 38bp reads: max_diff = 3 102s [bwa_aln] 64bp reads: max_diff = 4 102s [bwa_aln] 93bp reads: max_diff = 5 102s [bwa_aln] 124bp reads: max_diff = 6 102s [bwa_aln] 157bp reads: max_diff = 7 102s [bwa_aln] 190bp reads: max_diff = 8 102s [bwa_aln] 225bp reads: max_diff = 9 103s [bwa_aln_core] calculate SA coordinate... 0.74 sec 103s [bwa_aln_core] write to the disk... 0.00 sec 103s [bwa_aln_core] 100000 sequences have been processed. 103s [main] Version: 0.7.19-r1273 103s [main] CMD: bwa aln ./genomes/vdv1dwv9.fasta reads/SRR059298_subset.fastq 103s [main] Real time: 0.805 sec; CPU: 0.801 sec 103s [bwa_aln_core] convert to sequence coordinate... 0.05 sec 103s [bwa_aln_core] refine gapped alignments... 0.02 sec 103s [bwa_aln_core] print alignments... 0.05 sec 103s [bwa_aln_core] 100000 sequences have been processed. 103s [main] Version: 0.7.19-r1273 103s [main] CMD: bwa samse ./genomes/vdv1dwv9.fasta /tmp/res.sai reads/SRR059298_subset.fastq 103s [main] Real time: 0.188 sec; CPU: 0.182 sec 103s --- mapping reads with bwa to ./genomes/dwv.fasta 103s Executing: bwa aln ./genomes/dwv.fasta reads/SRR059298_subset.fastq > /tmp/res.sai 103s --- mapping reads with bwa to ./genomes/vdv1.fasta 103s Executing: bwa aln ./genomes/vdv1.fasta reads/SRR059298_subset.fastq > /tmp/res.sai 103s --- mapping reads with bwa to ./genomes/vdv1dwv5.fasta 103s Executing: bwa aln ./genomes/vdv1dwv5.fasta reads/SRR059298_subset.fastq > /tmp/res.sai 103s --- mapping reads with bwa to ./genomes/vdv1dwv9.fasta 103s Executing: bwa aln ./genomes/vdv1dwv9.fasta reads/SRR059298_subset.fastq > /tmp/res.sai 103s 103s Mapping done. 103s 103s Passed 103s 103s Test 2: create_matrix 103s MASON SIMULATOR 103s =============== 103s 103s ____INITIALIZING______________________________________________________________ 103s 103s Opening reference and variants file ... OK 103s Initializing fragment-to-contig distribution ... OK 103s Initializing simulation threads ... OK 103s Opening output file ./SAM/dwv.fastq ... OK 103s 103s ____READ SIMULATION___________________________________________________________ 103s 103s Distributing fragments to 1 contigs (1 haplotypes each) ... OK 103s 103s Simulating Reads: 103s gi|71480055|ref|NC_004830.2| (allele 1) .. (10000 fragments) OK 103s Done simulating reads. 103s 103s Joining temporary files ... OK 103s rm: cannot remove './SAM/dwv.fastq.sam': No such file or directory 103s MASON SIMULATOR 103s =============== 103s 103s ____INITIALIZING______________________________________________________________ 103s 103s Opening reference and variants file ... OK 103s Initializing fragment-to-contig distribution ... OK 103s Initializing simulation threads ... OK 103s Opening output file ./SAM/vdv1.fastq ... OK 103s 103s ____READ SIMULATION___________________________________________________________ 103s 103s Distributing fragments to 1 contigs (1 haplotypes each) ... OK 103s 103s Simulating Reads: 103s gi|56121875|ref|NC_006494.1| (allele 1) .. (10000 fragments) OK 103s Done simulating reads. 103s 103s Joining temporary files ... OK 103s rm: cannot remove './SAM/vdv1.fastq.sam': No such file or directory 103s MASON SIMULATOR 103s =============== 103s 103s ____INITIALIZING______________________________________________________________ 103s 103s Opening reference and variants file ... OK 103s Initializing fragment-to-contig distribution ... OK 103s Initializing simulation threads ... OK 103s Opening output file ./SAM/vdv1dwv5.fastq ... OK 103s 103s ____READ SIMULATION___________________________________________________________ 103s 103s Distributing fragments to 1 contigs (1 haplotypes each) ... OK 103s 103s Simulating Reads: 103s gi|301070167|gb|HM067437.1| (allele 1) .. (10000 fragments) OK 103s Done simulating reads. 103s 103s Joining temporary files ... OK 103s rm: cannot remove './SAM/vdv1dwv5.fastq.sam': No such file or directory 103s MASON SIMULATOR 103s =============== 103s 103s ____INITIALIZING______________________________________________________________ 103s 103s Opening reference and variants file ... OK 103s Initializing fragment-to-contig distribution ... OK 103s Initializing simulation threads ... OK 103s Opening output file ./SAM/vdv1dwv9.fastq ... OK 103s 103s ____READ SIMULATION___________________________________________________________ 103s 103s Distributing fragments to 1 contigs (1 haplotypes each) ... OK 103s 103s Simulating Reads: 104s gi|301070169|gb|HM067438.1| (allele 1) .. (10000 fragments) OK 104s Done simulating reads. 104s 104s Joining temporary files ... OK 104s rm: cannot remove './SAM/vdv1dwv9.fastq.sam': No such file or directory 104s [bwa_aln] 17bp reads: max_diff = 2 104s [bwa_aln] 38bp reads: max_diff = 3 104s [bwa_aln] 64bp reads: max_diff = 4 104s [bwa_aln] 93bp reads: max_diff = 5 104s [bwa_aln] 124bp reads: max_diff = 6 104s [bwa_aln] 157bp reads: max_diff = 7 104s [bwa_aln] 190bp reads: max_diff = 8 104s [bwa_aln] 225bp reads: max_diff = 9 104s [bwa_aln_core] calculate SA coordinate... 0.08 sec 104s [bwa_aln_core] write to the disk... 0.00 sec 104s [bwa_aln_core] 10000 sequences have been processed. 104s [main] Version: 0.7.19-r1273 104s [main] CMD: bwa aln genomes/dwv.fasta ./SAM/dwv.fastq 104s [main] Real time: 0.093 sec; CPU: 0.090 sec 104s [bwa_aln_core] convert to sequence coordinate... 0.01 sec 104s [bwa_aln_core] refine gapped alignments... 0.00 sec 104s [bwa_aln_core] print alignments... 0.01 sec 104s [bwa_aln_core] 10000 sequences have been processed. 104s [main] Version: 0.7.19-r1273 104s [main] CMD: bwa samse genomes/dwv.fasta /tmp/res.sai ./SAM/dwv.fastq 104s [main] Real time: 0.027 sec; CPU: 0.025 sec 104s [bwa_aln] 17bp reads: max_diff = 2 104s [bwa_aln] 38bp reads: max_diff = 3 104s [bwa_aln] 64bp reads: max_diff = 4 104s [bwa_aln] 93bp reads: max_diff = 5 104s [bwa_aln] 124bp reads: max_diff = 6 104s [bwa_aln] 157bp reads: max_diff = 7 104s [bwa_aln] 190bp reads: max_diff = 8 104s [bwa_aln] 225bp reads: max_diff = 9 104s [bwa_aln_core] calculate SA coordinate... 0.02 sec 104s [bwa_aln_core] write to the disk... 0.00 sec 104s [bwa_aln_core] 10000 sequences have been processed. 104s [main] Version: 0.7.19-r1273 104s [main] CMD: bwa aln genomes/vdv1.fasta ./SAM/dwv.fastq 104s [main] Real time: 0.030 sec; CPU: 0.029 sec 104s [bwa_aln_core] convert to sequence coordinate... 0.00 sec 104s [bwa_aln_core] refine gapped alignments... 0.00 sec 104s [bwa_aln_core] print alignments... 0.00 sec 104s [bwa_aln_core] 10000 sequences have been processed. 104s [main] Version: 0.7.19-r1273 104s [main] CMD: bwa samse genomes/vdv1.fasta /tmp/res.sai ./SAM/dwv.fastq 104s [main] Real time: 0.012 sec; CPU: 0.008 sec 104s [bwa_aln] 17bp reads: max_diff = 2 104s [bwa_aln] 38bp reads: max_diff = 3 104s [bwa_aln] 64bp reads: max_diff = 4 104s [bwa_aln] 93bp reads: max_diff = 5 104s [bwa_aln] 124bp reads: max_diff = 6 104s [bwa_aln] 157bp reads: max_diff = 7 104s [bwa_aln] 190bp reads: max_diff = 8 104s [bwa_aln] 225bp reads: max_diff = 9 104s [bwa_aln_core] calculate SA coordinate... 0.05 sec 104s [bwa_aln_core] write to the disk... 0.00 sec 104s [bwa_aln_core] 10000 sequences have been processed. 104s [main] Version: 0.7.19-r1273 104s [main] CMD: bwa aln genomes/vdv1dwv5.fasta ./SAM/dwv.fastq 104s [main] Real time: 0.060 sec; CPU: 0.059 sec 104s [bwa_aln_core] convert to sequence coordinate... 0.00 sec 104s [bwa_aln_core] refine gapped alignments... 0.00 sec 104s [bwa_aln_core] print alignments... 0.00 sec 104s [bwa_aln_core] 10000 sequences have been processed. 104s [main] Version: 0.7.19-r1273 104s [main] CMD: bwa samse genomes/vdv1dwv5.fasta /tmp/res.sai ./SAM/dwv.fastq 104s [main] Real time: 0.020 sec; CPU: 0.015 sec 104s [bwa_aln] 17bp reads: max_diff = 2 104s [bwa_aln] 38bp reads: max_diff = 3 104s [bwa_aln] 64bp reads: max_diff = 4 104s [bwa_aln] 93bp reads: max_diff = 5 104s [bwa_aln] 124bp reads: max_diff = 6 104s [bwa_aln] 157bp reads: max_diff = 7 104s [bwa_aln] 190bp reads: max_diff = 8 104s [bwa_aln] 225bp reads: max_diff = 9 104s [bwa_aln_core] calculate SA coordinate... 0.05 sec 104s [bwa_aln_core] write to the disk... 0.00 sec 104s [bwa_aln_core] 10000 sequences have been processed. 104s [main] Version: 0.7.19-r1273 104s [main] CMD: bwa aln genomes/vdv1dwv9.fasta ./SAM/dwv.fastq 104s [main] Real time: 0.062 sec; CPU: 0.058 sec 104s [bwa_aln_core] convert to sequence coordinate... 0.00 sec 104s [bwa_aln_core] refine gapped alignments... 0.00 sec 104s [bwa_aln_core] print alignments... 0.00 sec 104s [bwa_aln_core] 10000 sequences have been processed. 104s [main] Version: 0.7.19-r1273 104s [main] CMD: bwa samse genomes/vdv1dwv9.fasta /tmp/res.sai ./SAM/dwv.fastq 104s [main] Real time: 0.017 sec; CPU: 0.015 sec 104s [bwa_aln] 17bp reads: max_diff = 2 104s [bwa_aln] 38bp reads: max_diff = 3 104s [bwa_aln] 64bp reads: max_diff = 4 104s [bwa_aln] 93bp reads: max_diff = 5 104s [bwa_aln] 124bp reads: max_diff = 6 104s [bwa_aln] 157bp reads: max_diff = 7 104s [bwa_aln] 190bp reads: max_diff = 8 104s [bwa_aln] 225bp reads: max_diff = 9 104s [bwa_aln_core] calculate SA coordinate... 0.03 sec 104s [bwa_aln_core] write to the disk... 0.00 sec 104s [bwa_aln_core] 10000 sequences have been processed. 104s [main] Version: 0.7.19-r1273 104s [main] CMD: bwa aln genomes/dwv.fasta ./SAM/vdv1.fastq 104s [main] Real time: 0.032 sec; CPU: 0.030 sec 104s [bwa_aln_core] convert to sequence coordinate... 0.00 sec 104s [bwa_aln_core] refine gapped alignments... 0.00 sec 104s [bwa_aln_core] print alignments... 0.00 sec 104s [bwa_aln_core] 10000 sequences have been processed. 104s [main] Version: 0.7.19-r1273 104s [main] CMD: bwa samse genomes/dwv.fasta /tmp/res.sai ./SAM/vdv1.fastq 104s [main] Real time: 0.011 sec; CPU: 0.008 sec 104s [bwa_aln] 17bp reads: max_diff = 2 104s [bwa_aln] 38bp reads: max_diff = 3 104s [bwa_aln] 64bp reads: max_diff = 4 104s [bwa_aln] 93bp reads: max_diff = 5 104s [bwa_aln] 124bp reads: max_diff = 6 104s [bwa_aln] 157bp reads: max_diff = 7 104s [bwa_aln] 190bp reads: max_diff = 8 104s [bwa_aln] 225bp reads: max_diff = 9 104s [bwa_aln_core] calculate SA coordinate... 0.08 sec 104s [bwa_aln_core] write to the disk... 0.00 sec 104s [bwa_aln_core] 10000 sequences have been processed. 104s [main] Version: 0.7.19-r1273 104s [main] CMD: bwa aln genomes/vdv1.fasta ./SAM/vdv1.fastq 104s [main] Real time: 0.092 sec; CPU: 0.089 sec 104s [bwa_aln_core] convert to sequence coordinate... 0.01 sec 104s [bwa_aln_core] refine gapped alignments... 0.00 sec 104s [bwa_aln_core] print alignments... 0.01 sec 104s [bwa_aln_core] 10000 sequences have been processed. 104s [main] Version: 0.7.19-r1273 104s [main] CMD: bwa samse genomes/vdv1.fasta /tmp/res.sai ./SAM/vdv1.fastq 104s [main] Real time: 0.026 sec; CPU: 0.024 sec 104s [bwa_aln] 17bp reads: max_diff = 2 104s [bwa_aln] 38bp reads: max_diff = 3 104s [bwa_aln] 64bp reads: max_diff = 4 104s [bwa_aln] 93bp reads: max_diff = 5 104s [bwa_aln] 124bp reads: max_diff = 6 104s [bwa_aln] 157bp reads: max_diff = 7 104s [bwa_aln] 190bp reads: max_diff = 8 104s [bwa_aln] 225bp reads: max_diff = 9 104s [bwa_aln_core] calculate SA coordinate... 0.06 sec 104s [bwa_aln_core] write to the disk... 0.00 sec 104s [bwa_aln_core] 10000 sequences have been processed. 104s [main] Version: 0.7.19-r1273 104s [main] CMD: bwa aln genomes/vdv1dwv5.fasta ./SAM/vdv1.fastq 104s [main] Real time: 0.067 sec; CPU: 0.065 sec 104s [bwa_aln_core] convert to sequence coordinate... 0.00 sec 104s [bwa_aln_core] refine gapped alignments... 0.00 sec 104s [bwa_aln_core] print alignments... 0.00 sec 104s [bwa_aln_core] 10000 sequences have been processed. 104s [main] Version: 0.7.19-r1273 104s [main] CMD: bwa samse genomes/vdv1dwv5.fasta /tmp/res.sai ./SAM/vdv1.fastq 104s [main] Real time: 0.019 sec; CPU: 0.016 sec 104s [bwa_aln] 17bp reads: max_diff = 2 104s [bwa_aln] 38bp reads: max_diff = 3 104s [bwa_aln] 64bp reads: max_diff = 4 104s [bwa_aln] 93bp reads: max_diff = 5 104s [bwa_aln] 124bp reads: max_diff = 6 104s [bwa_aln] 157bp reads: max_diff = 7 104s [bwa_aln] 190bp reads: max_diff = 8 104s [bwa_aln] 225bp reads: max_diff = 9 104s [bwa_aln_core] calculate SA coordinate... 0.06 sec 104s [bwa_aln_core] write to the disk... 0.00 sec 104s [bwa_aln_core] 10000 sequences have been processed. 104s [main] Version: 0.7.19-r1273 104s [main] CMD: bwa aln genomes/vdv1dwv9.fasta ./SAM/vdv1.fastq 104s [main] Real time: 0.066 sec; CPU: 0.064 sec 104s [bwa_aln_core] convert to sequence coordinate... 0.00 sec 104s [bwa_aln_core] refine gapped alignments... 0.00 sec 104s [bwa_aln_core] print alignments... 0.00 sec 104s [bwa_aln_core] 10000 sequences have been processed. 104s [main] Version: 0.7.19-r1273 104s [main] CMD: bwa samse genomes/vdv1dwv9.fasta /tmp/res.sai ./SAM/vdv1.fastq 104s [main] Real time: 0.021 sec; CPU: 0.017 sec 104s [bwa_aln] 17bp reads: max_diff = 2 104s [bwa_aln] 38bp reads: max_diff = 3 104s [bwa_aln] 64bp reads: max_diff = 4 104s [bwa_aln] 93bp reads: max_diff = 5 104s [bwa_aln] 124bp reads: max_diff = 6 104s [bwa_aln] 157bp reads: max_diff = 7 104s [bwa_aln] 190bp reads: max_diff = 8 104s [bwa_aln] 225bp reads: max_diff = 9 104s [bwa_aln_core] calculate SA coordinate... 0.06 sec 104s [bwa_aln_core] write to the disk... 0.00 sec 104s [bwa_aln_core] 10000 sequences have been processed. 104s [main] Version: 0.7.19-r1273 104s [main] CMD: bwa aln genomes/dwv.fasta ./SAM/vdv1dwv5.fastq 104s [main] Real time: 0.063 sec; CPU: 0.060 sec 104s [bwa_aln_core] convert to sequence coordinate... 0.00 sec 104s [bwa_aln_core] refine gapped alignments... 0.00 sec 104s [bwa_aln_core] print alignments... 0.00 sec 104s [bwa_aln_core] 10000 sequences have been processed. 104s [main] Version: 0.7.19-r1273 104s [main] CMD: bwa samse genomes/dwv.fasta /tmp/res.sai ./SAM/vdv1dwv5.fastq 104s [main] Real time: 0.021 sec; CPU: 0.016 sec 104s [bwa_aln] 17bp reads: max_diff = 2 104s [bwa_aln] 38bp reads: max_diff = 3 104s [bwa_aln] 64bp reads: max_diff = 4 104s [bwa_aln] 93bp reads: max_diff = 5 104s [bwa_aln] 124bp reads: max_diff = 6 104s [bwa_aln] 157bp reads: max_diff = 7 104s [bwa_aln] 190bp reads: max_diff = 8 104s [bwa_aln] 225bp reads: max_diff = 9 104s [bwa_aln_core] calculate SA coordinate... 0.06 sec 104s [bwa_aln_core] write to the disk... 0.00 sec 104s [bwa_aln_core] 10000 sequences have been processed. 104s [main] Version: 0.7.19-r1273 104s [main] CMD: bwa aln genomes/vdv1.fasta ./SAM/vdv1dwv5.fastq 104s [main] Real time: 0.066 sec; CPU: 0.064 sec 104s [bwa_aln_core] convert to sequence coordinate... 0.00 sec 104s [bwa_aln_core] refine gapped alignments... 0.00 sec 104s [bwa_aln_core] print alignments... 0.00 sec 104s [bwa_aln_core] 10000 sequences have been processed. 104s [main] Version: 0.7.19-r1273 104s [main] CMD: bwa samse genomes/vdv1.fasta /tmp/res.sai ./SAM/vdv1dwv5.fastq 104s [main] Real time: 0.037 sec; CPU: 0.017 sec 104s [bwa_aln] 17bp reads: max_diff = 2 104s [bwa_aln] 38bp reads: max_diff = 3 104s [bwa_aln] 64bp reads: max_diff = 4 104s [bwa_aln] 93bp reads: max_diff = 5 104s [bwa_aln] 124bp reads: max_diff = 6 104s [bwa_aln] 157bp reads: max_diff = 7 104s [bwa_aln] 190bp reads: max_diff = 8 104s [bwa_aln] 225bp reads: max_diff = 9 105s [bwa_aln_core] calculate SA coordinate... 0.08 sec 105s [bwa_aln_core] write to the disk... 0.00 sec 105s [bwa_aln_core] 10000 sequences have been processed. 105s [main] Version: 0.7.19-r1273 105s [main] CMD: bwa aln genomes/vdv1dwv5.fasta ./SAM/vdv1dwv5.fastq 105s [main] Real time: 0.091 sec; CPU: 0.088 sec 105s [bwa_aln_core] convert to sequence coordinate... 0.01 sec 105s [bwa_aln_core] refine gapped alignments... 0.00 sec 105s [bwa_aln_core] print alignments... 0.01 sec 105s [bwa_aln_core] 10000 sequences have been processed. 105s [main] Version: 0.7.19-r1273 105s [main] CMD: bwa samse genomes/vdv1dwv5.fasta /tmp/res.sai ./SAM/vdv1dwv5.fastq 105s [main] Real time: 0.027 sec; CPU: 0.024 sec 105s [bwa_aln] 17bp reads: max_diff = 2 105s [bwa_aln] 38bp reads: max_diff = 3 105s [bwa_aln] 64bp reads: max_diff = 4 105s [bwa_aln] 93bp reads: max_diff = 5 105s [bwa_aln] 124bp reads: max_diff = 6 105s [bwa_aln] 157bp reads: max_diff = 7 105s [bwa_aln] 190bp reads: max_diff = 8 105s [bwa_aln] 225bp reads: max_diff = 9 105s [bwa_aln_core] calculate SA coordinate... 0.08 sec 105s [bwa_aln_core] write to the disk... 0.00 sec 105s [bwa_aln_core] 10000 sequences have been processed. 105s [main] Version: 0.7.19-r1273 105s [main] CMD: bwa aln genomes/vdv1dwv9.fasta ./SAM/vdv1dwv5.fastq 105s [main] Real time: 0.085 sec; CPU: 0.082 sec 105s [bwa_aln_core] convert to sequence coordinate... 0.01 sec 105s [bwa_aln_core] refine gapped alignments... 0.00 sec 105s [bwa_aln_core] print alignments... 0.01 sec 105s [bwa_aln_core] 10000 sequences have been processed. 105s [main] Version: 0.7.19-r1273 105s [main] CMD: bwa samse genomes/vdv1dwv9.fasta /tmp/res.sai ./SAM/vdv1dwv5.fastq 105s [main] Real time: 0.025 sec; CPU: 0.021 sec 105s [bwa_aln] 17bp reads: max_diff = 2 105s [bwa_aln] 38bp reads: max_diff = 3 105s [bwa_aln] 64bp reads: max_diff = 4 105s [bwa_aln] 93bp reads: max_diff = 5 105s [bwa_aln] 124bp reads: max_diff = 6 105s [bwa_aln] 157bp reads: max_diff = 7 105s [bwa_aln] 190bp reads: max_diff = 8 105s [bwa_aln] 225bp reads: max_diff = 9 105s [bwa_aln_core] calculate SA coordinate... 0.05 sec 105s [bwa_aln_core] write to the disk... 0.00 sec 105s [bwa_aln_core] 10000 sequences have been processed. 105s [main] Version: 0.7.19-r1273 105s [main] CMD: bwa aln genomes/dwv.fasta ./SAM/vdv1dwv9.fastq 105s [main] Real time: 0.061 sec; CPU: 0.059 sec 105s [bwa_aln_core] convert to sequence coordinate... 0.00 sec 105s [bwa_aln_core] refine gapped alignments... 0.00 sec 105s [bwa_aln_core] print alignments... 0.00 sec 105s [bwa_aln_core] 10000 sequences have been processed. 105s [main] Version: 0.7.19-r1273 105s [main] CMD: bwa samse genomes/dwv.fasta /tmp/res.sai ./SAM/vdv1dwv9.fastq 105s [main] Real time: 0.021 sec; CPU: 0.015 sec 105s [bwa_aln] 17bp reads: max_diff = 2 105s [bwa_aln] 38bp reads: max_diff = 3 105s [bwa_aln] 64bp reads: max_diff = 4 105s [bwa_aln] 93bp reads: max_diff = 5 105s [bwa_aln] 124bp reads: max_diff = 6 105s [bwa_aln] 157bp reads: max_diff = 7 105s [bwa_aln] 190bp reads: max_diff = 8 105s [bwa_aln] 225bp reads: max_diff = 9 105s [bwa_aln_core] calculate SA coordinate... 0.06 sec 105s [bwa_aln_core] write to the disk... 0.00 sec 105s [bwa_aln_core] 10000 sequences have been processed. 105s [main] Version: 0.7.19-r1273 105s [main] CMD: bwa aln genomes/vdv1.fasta ./SAM/vdv1dwv9.fastq 105s [main] Real time: 0.066 sec; CPU: 0.065 sec 105s [bwa_aln_core] convert to sequence coordinate... 0.00 sec 105s [bwa_aln_core] refine gapped alignments... 0.00 sec 105s [bwa_aln_core] print alignments... 0.00 sec 105s [bwa_aln_core] 10000 sequences have been processed. 105s [main] Version: 0.7.19-r1273 105s [main] CMD: bwa samse genomes/vdv1.fasta /tmp/res.sai ./SAM/vdv1dwv9.fastq 105s [main] Real time: 0.020 sec; CPU: 0.017 sec 105s [bwa_aln] 17bp reads: max_diff = 2 105s [bwa_aln] 38bp reads: max_diff = 3 105s [bwa_aln] 64bp reads: max_diff = 4 105s [bwa_aln] 93bp reads: max_diff = 5 105s [bwa_aln] 124bp reads: max_diff = 6 105s [bwa_aln] 157bp reads: max_diff = 7 105s [bwa_aln] 190bp reads: max_diff = 8 105s [bwa_aln] 225bp reads: max_diff = 9 105s [bwa_aln_core] calculate SA coordinate... 0.08 sec 105s [bwa_aln_core] write to the disk... 0.00 sec 105s [bwa_aln_core] 10000 sequences have been processed. 105s [main] Version: 0.7.19-r1273 105s [main] CMD: bwa aln genomes/vdv1dwv5.fasta ./SAM/vdv1dwv9.fastq 105s [main] Real time: 0.084 sec; CPU: 0.082 sec 105s [bwa_aln_core] convert to sequence coordinate... 0.01 sec 105s [bwa_aln_core] refine gapped alignments... 0.00 sec 105s [bwa_aln_core] print alignments... 0.01 sec 105s [bwa_aln_core] 10000 sequences have been processed. 105s [main] Version: 0.7.19-r1273 105s [main] CMD: bwa samse genomes/vdv1dwv5.fasta /tmp/res.sai ./SAM/vdv1dwv9.fastq 105s [main] Real time: 0.023 sec; CPU: 0.021 sec 105s [bwa_aln] 17bp reads: max_diff = 2 105s [bwa_aln] 38bp reads: max_diff = 3 105s [bwa_aln] 64bp reads: max_diff = 4 105s [bwa_aln] 93bp reads: max_diff = 5 105s [bwa_aln] 124bp reads: max_diff = 6 105s [bwa_aln] 157bp reads: max_diff = 7 105s [bwa_aln] 190bp reads: max_diff = 8 105s [bwa_aln] 225bp reads: max_diff = 9 105s [bwa_aln_core] calculate SA coordinate... 0.09 sec 105s [bwa_aln_core] write to the disk... 0.00 sec 105s [bwa_aln_core] 10000 sequences have been processed. 105s [main] Version: 0.7.19-r1273 105s [main] CMD: bwa aln genomes/vdv1dwv9.fasta ./SAM/vdv1dwv9.fastq 105s [main] Real time: 0.092 sec; CPU: 0.090 sec 105s [bwa_aln_core] convert to sequence coordinate... 0.01 sec 105s [bwa_aln_core] refine gapped alignments... 0.00 sec 105s [bwa_aln_core] print alignments... 0.01 sec 105s [bwa_aln_core] 10000 sequences have been processed. 105s [main] Version: 0.7.19-r1273 105s [main] CMD: bwa samse genomes/vdv1dwv9.fasta /tmp/res.sai ./SAM/vdv1dwv9.fastq 105s [main] Real time: 0.027 sec; CPU: 0.023 sec 105s 105s --- Simulating reads for each reference genome with mason_illumina 105s 105s Original command with mason from SeQan 1 was 105s mason illumina -N 10000 -hi 0 -hs 0 -n 72 -sq -o ./SAM/dwv.fastq genomes/dwv.fasta 105s Please verify that the following call of mason_simulator fits your needs. If not 105s please use 105s reportbug gasic 105s to propose enhancements. 105s 105s Executing: /usr/lib/seqan/bin/mason_simulator --seq-technology illumina -n 10000 --illumina-read-length 72 -o ./SAM/dwv.fastq -ir genomes/dwv.fasta 105s Original command with mason from SeQan 1 was 105s mason illumina -N 10000 -hi 0 -hs 0 -n 72 -sq -o ./SAM/vdv1.fastq genomes/vdv1.fasta 105s Please verify that the following call of mason_simulator fits your needs. If not 105s please use 105s reportbug gasic 105s to propose enhancements. 105s 105s Executing: /usr/lib/seqan/bin/mason_simulator --seq-technology illumina -n 10000 --illumina-read-length 72 -o ./SAM/vdv1.fastq -ir genomes/vdv1.fasta 105s Original command with mason from SeQan 1 was 105s mason illumina -N 10000 -hi 0 -hs 0 -n 72 -sq -o ./SAM/vdv1dwv5.fastq genomes/vdv1dwv5.fasta 105s Please verify that the following call of mason_simulator fits your needs. If not 105s please use 105s reportbug gasic 105s to propose enhancements. 105s 105s Executing: /usr/lib/seqan/bin/mason_simulator --seq-technology illumina -n 10000 --illumina-read-length 72 -o ./SAM/vdv1dwv5.fastq -ir genomes/vdv1dwv5.fasta 105s Original command with mason from SeQan 1 was 105s mason illumina -N 10000 -hi 0 -hs 0 -n 72 -sq -o ./SAM/vdv1dwv9.fastq genomes/vdv1dwv9.fasta 105s Please verify that the following call of mason_simulator fits your needs. If not 105s please use 105s reportbug gasic 105s to propose enhancements. 105s 105s Executing: /usr/lib/seqan/bin/mason_simulator --seq-technology illumina -n 10000 --illumina-read-length 72 -o ./SAM/vdv1dwv9.fastq -ir genomes/vdv1dwv9.fasta 105s 105s --- Mapping simulated reads to reference genomes with bwa 105s 105s Executing: bwa aln genomes/dwv.fasta ./SAM/dwv.fastq > /tmp/res.sai 105s Executing: bwa aln genomes/vdv1.fasta ./SAM/dwv.fastq > /tmp/res.sai 105s Executing: bwa aln genomes/vdv1dwv5.fasta ./SAM/dwv.fastq > /tmp/res.sai 105s Executing: bwa aln genomes/vdv1dwv9.fasta ./SAM/dwv.fastq > /tmp/res.sai 105s Executing: bwa aln genomes/dwv.fasta ./SAM/vdv1.fastq > /tmp/res.sai 105s Executing: bwa aln genomes/vdv1.fasta ./SAM/vdv1.fastq > /tmp/res.sai 105s Executing: bwa aln genomes/vdv1dwv5.fasta ./SAM/vdv1.fastq > /tmp/res.sai 105s Executing: bwa aln genomes/vdv1dwv9.fasta ./SAM/vdv1.fastq > /tmp/res.sai 105s Executing: bwa aln genomes/dwv.fasta ./SAM/vdv1dwv5.fastq > /tmp/res.sai 105s Executing: bwa aln genomes/vdv1.fasta ./SAM/vdv1dwv5.fastq > /tmp/res.sai 105s Executing: bwa aln genomes/vdv1dwv5.fasta ./SAM/vdv1dwv5.fastq > /tmp/res.sai 105s Executing: bwa aln genomes/vdv1dwv9.fasta ./SAM/vdv1dwv5.fastq > /tmp/res.sai 105s Executing: bwa aln genomes/dwv.fasta ./SAM/vdv1dwv9.fastq > /tmp/res.sai 105s Executing: bwa aln genomes/vdv1.fasta ./SAM/vdv1dwv9.fastq > /tmp/res.sai 105s Executing: bwa aln genomes/vdv1dwv5.fasta ./SAM/vdv1dwv9.fastq > /tmp/res.sai 105s Executing: bwa aln genomes/vdv1dwv9.fasta ./SAM/vdv1dwv9.fastq > /tmp/res.sai 105s 105s --- Parsing SAM files 105s 105s 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 105s 105s Matrix creation done 105s 105s Wrote similarity matrix to ./similarity_matrix.npy 105s Passed 105s 105s Test 3: correct_abundances 105s 105s --- GASiC correction 105s 105s found 100000 reads 105s 105s --- Analyzing SAM files 105s 106s SAM file 1 of 4 SAM file 2 of 4 SAM file 3 of 4 SAM file 4 of 4 106s 106s --- Bootstrapping abundances 106s 236s 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 236s 236s Done estimating abundances 236s 236s --- wrote results to results.txt 236s Passed 236s 236s Test 4: quality_check 237s Passed 237s 238s autopkgtest [13:30:01]: test run-unit-test: -----------------------] 238s autopkgtest [13:30:01]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 238s run-unit-test PASS 238s autopkgtest [13:30:01]: @@@@@@@@@@@@@@@@@@@@ summary 238s run-unit-test PASS