0s autopkgtest [08:06:19]: starting date and time: 2024-11-13 08:06:19+0000 0s autopkgtest [08:06:19]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [08:06:19]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.xzuwl5nl/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade abpoa --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-6.secgroup --name adt-plucky-amd64-abpoa-20241113-080619-juju-7f2275-prod-proposed-migration-environment-15-bf6391ad-ba6f-4904-bc52-fe10fe6ca7d1 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 96s autopkgtest [08:07:55]: testbed dpkg architecture: amd64 96s autopkgtest [08:07:55]: testbed apt version: 2.9.8 96s autopkgtest [08:07:55]: @@@@@@@@@@@@@@@@@@@@ test bed setup 99s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 99s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [848 kB] 99s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 99s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 99s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 99s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB] 99s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.2 kB] 99s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 99s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [637 kB] 99s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [255 kB] 99s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [13.0 kB] 99s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [37.7 kB] 100s Fetched 2171 kB in 1s (2705 kB/s) 100s Reading package lists... 106s Reading package lists... 106s Building dependency tree... 106s Reading state information... 106s Calculating upgrade... 106s The following NEW packages will be installed: 106s python3.13-gdbm 106s The following packages will be upgraded: 106s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 106s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 106s Need to get 253 kB of archives. 106s After this operation, 147 kB of additional disk space will be used. 106s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 106s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 106s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 106s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 106s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 106s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.23.2-5ubuntu4 [152 kB] 107s Fetched 253 kB in 0s (616 kB/s) 107s (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 ... 75541 files and directories currently installed.) 107s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 107s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 107s Setting up python3-minimal (3.12.7-1) ... 107s (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 ... 75541 files and directories currently installed.) 107s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 107s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 107s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 107s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 107s Selecting previously unselected package python3.13-gdbm. 107s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ... 107s Unpacking python3.13-gdbm (3.13.0-2) ... 107s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ... 107s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 107s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_amd64.deb ... 107s Unpacking libgpgme11t64:amd64 (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 107s Setting up libgpgme11t64:amd64 (1.23.2-5ubuntu4) ... 107s Setting up python3.13-gdbm (3.13.0-2) ... 107s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 107s Setting up python3 (3.12.7-1) ... 107s Setting up python3-gdbm:amd64 (3.12.7-1) ... 107s Processing triggers for man-db (2.12.1-3) ... 108s Processing triggers for libc-bin (2.40-1ubuntu3) ... 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 109s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 109s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 109s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 109s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 109s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 110s Reading package lists... 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 110s Calculating upgrade... 110s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 110s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 113s autopkgtest [08:08:12]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 114s autopkgtest [08:08:13]: @@@@@@@@@@@@@@@@@@@@ apt-source abpoa 115s Get:1 http://ftpmaster.internal/ubuntu plucky/universe abpoa 1.5.3-1 (dsc) [2276 B] 115s Get:2 http://ftpmaster.internal/ubuntu plucky/universe abpoa 1.5.3-1 (tar) [163 kB] 115s Get:3 http://ftpmaster.internal/ubuntu plucky/universe abpoa 1.5.3-1 (diff) [9836 B] 116s gpgv: Signature made Wed Sep 25 19:10:18 2024 UTC 116s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 116s gpgv: issuer "emollier@debian.org" 116s gpgv: Can't check signature: No public key 116s dpkg-source: warning: cannot verify inline signature for ./abpoa_1.5.3-1.dsc: no acceptable signature found 116s autopkgtest [08:08:15]: testing package abpoa version 1.5.3-1 116s autopkgtest [08:08:15]: build not needed 118s autopkgtest [08:08:17]: test run-unit-test: preparing testbed 119s Reading package lists... 119s Building dependency tree... 119s Reading state information... 119s Starting pkgProblemResolver with broken count: 0 119s Starting 2 pkgProblemResolver with broken count: 0 119s Done 119s The following additional packages will be installed: 119s abpoa fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 119s graphviz libann0 libaom3 libcairo2 libcdt5 libcgraph6 libdatrie1 libde265-0 119s libdeflate0 libfontconfig1 libgd3 libgomp1 libgraphite2-3 libgts-0.7-5t64 119s libgvc6 libgvpr2 libharfbuzz0b libheif-plugin-aomdec libheif-plugin-libde265 119s libheif1 libice6 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 119s liblab-gamut1 liblerc4 libltdl7 libpango-1.0-0 libpangocairo-1.0-0 119s libpangoft2-1.0-0 libpathplan4 libpixman-1-0 libraqm0 libsharpyuv0 libsm6 119s libthai-data libthai0 libtiff6 libwebp7 libxaw7 libxcb-render0 libxcb-shm0 119s libxmu6 libxpm4 libxrender1 libxt6t64 python3-pyabpoa x11-common 119s Suggested packages: 119s gsfonts graphviz-doc libgd-tools libheif-plugin-x265 119s libheif-plugin-ffmpegdec libheif-plugin-jpegdec libheif-plugin-jpegenc 119s libheif-plugin-j2kdec libheif-plugin-j2kenc libheif-plugin-kvazaar 119s libheif-plugin-rav1e libheif-plugin-svtenc 119s Recommended packages: 119s fonts-liberation libgts-bin libheif-plugin-aomenc 119s The following NEW packages will be installed: 119s abpoa autopkgtest-satdep fontconfig fontconfig-config fonts-dejavu-core 119s fonts-dejavu-mono graphviz libann0 libaom3 libcairo2 libcdt5 libcgraph6 119s libdatrie1 libde265-0 libdeflate0 libfontconfig1 libgd3 libgomp1 119s libgraphite2-3 libgts-0.7-5t64 libgvc6 libgvpr2 libharfbuzz0b 119s libheif-plugin-aomdec libheif-plugin-libde265 libheif1 libice6 119s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblab-gamut1 liblerc4 119s libltdl7 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpathplan4 119s libpixman-1-0 libraqm0 libsharpyuv0 libsm6 libthai-data libthai0 libtiff6 119s libwebp7 libxaw7 libxcb-render0 libxcb-shm0 libxmu6 libxpm4 libxrender1 119s libxt6t64 python3-pyabpoa x11-common 119s 0 upgraded, 55 newly installed, 0 to remove and 0 not upgraded. 119s Need to get 13.1 MB/13.1 MB of archives. 119s After this operation, 36.7 MB of additional disk space will be used. 119s Get:1 /tmp/autopkgtest.1rn5AE/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [712 B] 120s Get:2 http://ftpmaster.internal/ubuntu plucky/universe amd64 libann0 amd64 1.1.2+doc-9build1 [25.5 kB] 120s Get:3 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcdt5 amd64 2.42.4-2build3 [22.3 kB] 120s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcgraph6 amd64 2.42.4-2build3 [45.1 kB] 120s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 120s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 120s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 120s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 120s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 120s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libaom3 amd64 3.11.0~rc1-1 [2762 kB] 120s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libheif-plugin-aomdec amd64 1.18.1-2 [11.1 kB] 120s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libde265-0 amd64 1.0.15-1build4 [168 kB] 120s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libheif-plugin-libde265 amd64 1.18.1-2 [8758 B] 120s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libheif1 amd64 1.18.1-2 [293 kB] 120s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 120s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 120s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB] 120s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 120s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 120s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB] 120s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 120s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 121s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 121s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB] 121s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 121s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 121s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libxpm4 amd64 1:3.5.17-1build2 [36.5 kB] 121s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libgd3 amd64 2.3.3-12ubuntu3 [127 kB] 121s Get:29 http://ftpmaster.internal/ubuntu plucky/universe amd64 libgts-0.7-5t64 amd64 0.7.6+darcs121130-5.2build1 [161 kB] 121s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 121s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 121s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 121s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 121s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 121s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libltdl7 amd64 2.4.7-7build1 [40.3 kB] 121s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-1.1ubuntu2 [180 kB] 121s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 121s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB] 121s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 121s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.54.0+ds-3 [252 kB] 121s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-3 [51.6 kB] 121s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-3 [29.1 kB] 121s Get:43 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpathplan4 amd64 2.42.4-2build3 [24.5 kB] 121s Get:44 http://ftpmaster.internal/ubuntu plucky/universe amd64 libgvc6 amd64 2.42.4-2build3 [721 kB] 121s Get:45 http://ftpmaster.internal/ubuntu plucky/universe amd64 libgvpr2 amd64 2.42.4-2build3 [189 kB] 121s Get:46 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblab-gamut1 amd64 2.42.4-2build3 [1898 kB] 121s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 121s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 121s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB] 121s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB] 121s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libxmu6 amd64 2:1.1.3-3build2 [47.6 kB] 121s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libxaw7 amd64 2:1.0.16-1 [207 kB] 121s Get:53 http://ftpmaster.internal/ubuntu plucky/universe amd64 graphviz amd64 2.42.4-2build3 [649 kB] 121s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 abpoa amd64 1.5.3-1 [273 kB] 121s Get:55 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyabpoa amd64 1.5.3-1 [180 kB] 122s Fetched 13.1 MB in 2s (6811 kB/s) 122s Selecting previously unselected package libann0. 122s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75548 files and directories currently installed.) 122s Preparing to unpack .../00-libann0_1.1.2+doc-9build1_amd64.deb ... 122s Unpacking libann0 (1.1.2+doc-9build1) ... 122s Selecting previously unselected package libcdt5:amd64. 122s Preparing to unpack .../01-libcdt5_2.42.4-2build3_amd64.deb ... 122s Unpacking libcdt5:amd64 (2.42.4-2build3) ... 122s Selecting previously unselected package libcgraph6:amd64. 122s Preparing to unpack .../02-libcgraph6_2.42.4-2build3_amd64.deb ... 122s Unpacking libcgraph6:amd64 (2.42.4-2build3) ... 122s Selecting previously unselected package fonts-dejavu-mono. 122s Preparing to unpack .../03-fonts-dejavu-mono_2.37-8_all.deb ... 122s Unpacking fonts-dejavu-mono (2.37-8) ... 122s Selecting previously unselected package fonts-dejavu-core. 122s Preparing to unpack .../04-fonts-dejavu-core_2.37-8_all.deb ... 122s Unpacking fonts-dejavu-core (2.37-8) ... 122s Selecting previously unselected package fontconfig-config. 122s Preparing to unpack .../05-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 122s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 122s Selecting previously unselected package libfontconfig1:amd64. 122s Preparing to unpack .../06-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 122s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 122s Selecting previously unselected package libsharpyuv0:amd64. 122s Preparing to unpack .../07-libsharpyuv0_1.4.0-0.1_amd64.deb ... 122s Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ... 122s Selecting previously unselected package libaom3:amd64. 122s Preparing to unpack .../08-libaom3_3.11.0~rc1-1_amd64.deb ... 122s Unpacking libaom3:amd64 (3.11.0~rc1-1) ... 122s Selecting previously unselected package libheif-plugin-aomdec:amd64. 122s Preparing to unpack .../09-libheif-plugin-aomdec_1.18.1-2_amd64.deb ... 122s Unpacking libheif-plugin-aomdec:amd64 (1.18.1-2) ... 122s Selecting previously unselected package libde265-0:amd64. 122s Preparing to unpack .../10-libde265-0_1.0.15-1build4_amd64.deb ... 122s Unpacking libde265-0:amd64 (1.0.15-1build4) ... 122s Selecting previously unselected package libheif-plugin-libde265:amd64. 122s Preparing to unpack .../11-libheif-plugin-libde265_1.18.1-2_amd64.deb ... 122s Unpacking libheif-plugin-libde265:amd64 (1.18.1-2) ... 122s Selecting previously unselected package libheif1:amd64. 122s Preparing to unpack .../12-libheif1_1.18.1-2_amd64.deb ... 122s Unpacking libheif1:amd64 (1.18.1-2) ... 122s Selecting previously unselected package libgomp1:amd64. 122s Preparing to unpack .../13-libgomp1_14.2.0-8ubuntu1_amd64.deb ... 122s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ... 122s Selecting previously unselected package libimagequant0:amd64. 122s Preparing to unpack .../14-libimagequant0_2.18.0-1build1_amd64.deb ... 122s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 122s Selecting previously unselected package libjpeg-turbo8:amd64. 122s Preparing to unpack .../15-libjpeg-turbo8_2.1.5-2ubuntu2_amd64.deb ... 122s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 122s Selecting previously unselected package libjpeg8:amd64. 122s Preparing to unpack .../16-libjpeg8_8c-2ubuntu11_amd64.deb ... 122s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 122s Selecting previously unselected package libgraphite2-3:amd64. 122s Preparing to unpack .../17-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 122s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 122s Selecting previously unselected package libharfbuzz0b:amd64. 122s Preparing to unpack .../18-libharfbuzz0b_10.0.1-1_amd64.deb ... 122s Unpacking libharfbuzz0b:amd64 (10.0.1-1) ... 122s Selecting previously unselected package libraqm0:amd64. 122s Preparing to unpack .../19-libraqm0_0.10.1-1build1_amd64.deb ... 122s Unpacking libraqm0:amd64 (0.10.1-1build1) ... 122s Selecting previously unselected package libdeflate0:amd64. 122s Preparing to unpack .../20-libdeflate0_1.22-1_amd64.deb ... 122s Unpacking libdeflate0:amd64 (1.22-1) ... 122s Selecting previously unselected package libjbig0:amd64. 122s Preparing to unpack .../21-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 122s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 122s Selecting previously unselected package liblerc4:amd64. 122s Preparing to unpack .../22-liblerc4_4.0.0+ds-4ubuntu2_amd64.deb ... 122s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 122s Selecting previously unselected package libwebp7:amd64. 122s Preparing to unpack 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[08:08:29]: test run-unit-test: [----------------------- 130s + for SIMDE in avx2 avx sse4.1 ssse3 sse3 generic dispatch 130s + '[' avx2 = dispatch ']' 130s + '[' avx2 = generic ']' 130s + grep -q avx2 /proc/cpuinfo 130s + command -v abpoa.avx2 130s + BINARY=abpoa.avx2 130s + abpoa.avx2 --version 130s 1.5.3 130s + abpoa.avx2 --help 130s 130s abpoa: adaptive banded Partial Order Alignment 130s 130s Version: 1.5.3 Contact: yangao@ds.dfci.harvard.edu 130s 130s Usage: abpoa [options] > cons.fa/msa.fa/abpoa.gfa 130s 130s Options: 130s Alignment: 130s -m --aln-mode INT alignment mode [0] 130s 0: global, 1: local, 2: extension 130s -M --match INT match score [2] 130s -X --mismatch INT mismatch penalty [4] 130s -t --matrix FILE scoring matrix file, '-M' and '-X' are not used when '-t' is used [Null] 130s e.g., 'HOXD70.mtx, BLOSUM62.mtx' 130s -O --gap-open INT(,INT) gap opening penalty (O1,O2) [4,24] 130s -E --gap-ext INT(,INT) gap extension penalty (E1,E2) [2,1] 130s abPOA provides three gap penalty modes, cost of a g-long gap: 130s - convex (default): min{O1+g*E1, O2+g*E2} 130s - affine (set O2 as 0): O1+g*E1 130s - linear (set O1 as 0): g*E1 130s -s --amb-strand ambiguous strand mode [False] 130s for each input sequence, try the reverse complement if the current 130s alignment score is too low, and pick the strand with a higher score 130s Adaptive banded DP: 130s -b --extra-b INT first adaptive banding parameter [10] 130s set b as < 0 to disable adaptive banded DP 130s -f --extra-f FLOAT second adaptive banding parameter [0.01] 130s the number of extra bases added on both sites of the band is 130s b+f*L, where L is the length of the aligned sequence 130s Minimizer-based seeding and partition (only effective in global alignment mode): 130s -S --seeding enable minimizer-based seeding and anchoring [False] 130s -k --k-mer INT minimizer k-mer size [19] 130s -w --window INT minimizer window size [10] 130s -n --min-poa-win INT min. size of window to perform POA [500] 130s -p --progressive build guide tree and perform progressive partial order alignment [False] 130s Input/Output: 130s -Q --use-qual-weight take base quality score from FASTQ input file as graph edge weight for consensus calling [False] 130s effective only when input sequences are in FASTQ format and consensus calling with heaviest bundling 130s -c --amino-acid input sequences are amino acid (default is nucleotide) [False] 130s -l --in-list input file is a list of sequence file names [False] 130s each line is one sequence file containing a set of sequences 130s which will be aligned by abPOA to generate a consensus sequence 130s -i --incrmnt FILE incrementally align sequences to an existing graph/MSA [Null] 130s graph could be in GFA or MSA format generated by abPOA 130s -o --output FILE output to FILE [stdout] 130s -r --result INT output result mode [0] 130s - 0: consensus in FASTA format 130s - 1: MSA in PIR format 130s - 2: both 0 & 1 130s - 3: graph in GFA format 130s - 4: graph with consensus path in GFA format 130s - 5: consensus in FASTQ format 130s -a --cons-algrm INT consensus algorithm [0] 130s - 0: heaviest bundling path in partial order graph 130s - 1: most frequent bases at each position 130s -d --maxnum-cons INT max. number of consensus sequence to generate [1] 130s -q --min-freq FLOAT min. frequency of each consensus sequence (only effective when -d/--num-cons > 1) [0.25] 130s -g --out-pog FILE dump final alignment graph to FILE (.pdf/.png) [Null] 130s 130s -h --help print this help usage information 130s -v --version show version number 130s -V --verbose INT verbose level (0-2). 0: none, 1: information, 2: debug [0] 130s 130s + test 1 = 1 130s + abpoa.avx2 ./test_data/seq.fa 130s [main] CMD: abpoa.avx2 ./test_data/seq.fa 130s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB. 130s + diff - cons.fa 130s + abpoa.avx2 ./test_data/heter.fa 130s [main] CMD: abpoa.avx2 ./test_data/heter.fa 130s [abpoa_main] Real time: 0.008 sec; CPU: 0.009 sec; Peak RSS: 0.009 GB. 130s + abpoa.avx2 -r1 ./test_data/seq.fa 130s [main] CMD: abpoa.avx2 -r1 ./test_data/seq.fa 130s [abpoa_main] Real time: 0.000 sec; CPU: 0.001 sec; Peak RSS: 0.003 GB. 130s + diff - out.msa 130s + abpoa.avx2 -r2 ./test_data/seq.fa 130s [main] CMD: abpoa.avx2 -r2 ./test_data/seq.fa 130s [abpoa_main] Real time: 0.001 sec; CPU: 0.001 sec; Peak RSS: 0.003 GB. 130s + diff - out_cons.msa 130s + abpoa.avx2 -r3 ./test_data/seq.fa 130s [main] CMD: abpoa.avx2 -r3 ./test_data/seq.fa 130s [abpoa_main] Real time: 0.001 sec; CPU: 0.001 sec; Peak RSS: 0.003 GB. 130s + diff - out.gfa 130s + abpoa.avx2 -r4 ./test_data/seq.fa 130s [main] CMD: abpoa.avx2 -r4 ./test_data/seq.fa 130s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB. 130s + diff - out4.gfa 130s + cp out.gfa in.gfa 130s + cp out.msa in.msa 130s + abpoa.avx2 -i in.gfa ./test_data/seq.fa -r3 130s [main] CMD: abpoa.avx2 -i in.gfa -r3 ./test_data/seq.fa 130s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB. 130s + diff - out.gfa 130s + abpoa.avx2 -i in.msa ./test_data/seq.fa -r1 130s [main] CMD: abpoa.avx2 -i in.msa -r1 ./test_data/seq.fa 130s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.002 GB. 130s + diff - out.msa 130s + abpoa.avx2 ./test_data/seq.fa -g poa.png 130s [main] CMD: abpoa.avx2 -g poa.png ./test_data/seq.fa 131s [abpoa_main] Real time: 0.347 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB. 131s >Consensus_sequence_1 0,2,3,4,10,13,14 131s CCATTCCCACCATCCTTACCATCAACATCACCATCCCCACCATCCCCAACACCATTCCCACCATCCCTACCATCACCATCACCATCCCCACCAACATCCCCACCACCATCCTCACTACCATCCCCACCACCATTTCCACCATTCCCACCACAGTCACCATCACCCCCACCATCCCCATCATCATCCGCACCATCCCCACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCTCCAACACCTCCCCCACCATCATCCCCACCATCCCCACCACCTTCTCCACCATCATTCTCACCATCCCCACCACCATCTCCACCACCATTCTCACCATCTCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCATCATCCCCACCATCC 131s >Consensus_sequence_2 1,5,6,7,8,9,11,12 131s CCATTCCCACCATCCTTACCATCAACATCACCATCCCCACCATCCCCAACACCATTCCCACCATCCCTACCATCACCATCACCATCCCCACCAACATCCCCACCACCATCCTCACTACCATCCCCACCACCATTTCCACCATTCCCACCACAGTCACCATCACCCCCACCATCCCCATCATCATCCGCACCATCCCCACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCATCCCCACCGCCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCTCCAACACCTCCCCCACCATCATCCCCACCATCCCCACCACCTTCTCCACCATCATTCTCACCATCCCCACCACCATCTCCACCACCATTCTCACCATCTCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCATCATCCCCACCATCC 131s + diff - cons.fa 131s + abpoa.avx2 ./test_data/heter.fa -d2 131s [main] CMD: abpoa.avx2 -d2 ./test_data/heter.fa 131s [abpoa_main] Real time: 0.009 sec; CPU: 0.010 sec; Peak RSS: 0.009 GB. 131s + for SIMDE in avx2 avx sse4.1 ssse3 sse3 generic dispatch 131s + '[' avx = dispatch ']' 131s + '[' avx = generic ']' 131s + grep -q avx /proc/cpuinfo 131s + command -v abpoa.avx 131s + BINARY=abpoa.avx 131s + abpoa.avx --version 131s + abpoa.avx --help 131s 131s abpoa: adaptive banded Partial Order Alignment 131s 131s Version: 1.5.3 Contact: yangao@ds.dfci.harvard.edu 131s 131s Usage: abpoa [options] > cons.fa/msa.fa/abpoa.gfa 131s 131s Options: 131s Alignment: 131s -m --aln-mode INT alignment mode [0] 131s 0: global, 1: local, 2: extension 131s -M --match INT match score [2] 131s -X --mismatch INT mismatch penalty [4] 131s -t --matrix FILE scoring matrix file, '-M' and '-X' are not used when '-t' is used [Null] 131s e.g., 'HOXD70.mtx, BLOSUM62.mtx' 131s -O --gap-open INT(,INT) gap opening penalty (O1,O2) [4,24] 131s -E --gap-ext INT(,INT) gap extension penalty (E1,E2) [2,1] 131s abPOA provides three gap penalty modes, cost of a g-long gap: 131s - convex (default): min{O1+g*E1, O2+g*E2} 131s - affine (set O2 as 0): O1+g*E1 131s - linear (set O1 as 0): g*E1 131s -s --amb-strand ambiguous strand mode [False] 131s for each input sequence, try the reverse complement if the current 131s alignment score is too low, and pick the strand with a higher score 131s Adaptive banded DP: 131s -b --extra-b INT first adaptive banding parameter [10] 131s set b as < 0 to disable adaptive banded DP 131s -f --extra-f FLOAT second adaptive banding parameter [0.01] 131s the number of extra bases added on both sites of the band is 131s b+f*L, where L is the length of the aligned sequence 131s Minimizer-based seeding and partition (only effective in global alignment mode): 131s -S --seeding enable minimizer-based seeding and anchoring [False] 131s -k --k-mer INT minimizer k-mer size [19] 131s -w --window INT minimizer window size [10] 131s -n --min-poa-win INT min. size of window to perform POA [500] 131s -p --progressive build guide tree and perform progressive partial order alignment [False] 131s Input/Output: 131s -Q --use-qual-weight take base quality score from FASTQ input file as graph edge weight for consensus calling [False] 131s effective only when input sequences are in FASTQ format and consensus calling with heaviest bundling 131s -c --amino-acid input sequences are amino acid (default is nucleotide) [False] 131s -l --in-list input file is a list of sequence file names [False] 131s each line is one sequence file containing a set of sequences 131s which will be aligned by abPOA to generate a consensus sequence 131s -i --incrmnt FILE incrementally align sequences to an existing graph/MSA [Null] 131s graph could be in GFA or MSA format generated by abPOA 131s -o --output FILE output to FILE [stdout] 131s -r --result INT output result mode [0] 131s - 0: consensus in FASTA format 131s - 1: MSA in PIR format 131s - 2: both 0 & 1 131s - 3: graph in GFA format 131s - 4: graph with consensus path in GFA format 131s - 5: consensus in FASTQ format 131s -a --cons-algrm INT consensus algorithm [0] 131s - 0: heaviest bundling path in partial order graph 131s - 1: most frequent bases at each position 131s -d --maxnum-cons INT max. number of consensus sequence to generate [1] 131s -q --min-freq FLOAT min. frequency of each consensus sequence (only effective when -d/--num-cons > 1) [0.25] 131s -g --out-pog FILE dump final alignment graph to FILE (.pdf/.png) [Null] 131s 131s -h --help print this help usage information 131s -v --version show version number 131s -V --verbose INT verbose level (0-2). 0: none, 1: information, 2: debug [0] 131s 131s + test 1 = 1 131s + abpoa.avx ./test_data/seq.fa 131s [main] CMD: abpoa.avx ./test_data/seq.fa 131s [abpoa_main] Real time: 0.000 sec; CPU: 0.001 sec; Peak RSS: 0.003 GB. 131s + diff - cons.fa 131s + abpoa.avx ./test_data/heter.fa 131s [main] CMD: abpoa.avx ./test_data/heter.fa 131s [abpoa_main] Real time: 0.009 sec; CPU: 0.010 sec; Peak RSS: 0.009 GB. 131s + abpoa.avx -r1 ./test_data/seq.fa 131s [main] CMD: abpoa.avx -r1 ./test_data/seq.fa 131s [abpoa_main] Real time: 0.000 sec; CPU: 0.001 sec; Peak RSS: 0.003 GB. 131s + diff - out.msa 131s + abpoa.avx -r2 ./test_data/seq.fa 131s [main] CMD: abpoa.avx -r2 ./test_data/seq.fa 131s [abpoa_main] Real time: 0.000 sec; CPU: 0.001 sec; Peak RSS: 0.003 GB. 131s + diff - out_cons.msa 131s + abpoa.avx -r3 ./test_data/seq.fa 131s [main] CMD: abpoa.avx -r3 ./test_data/seq.fa 131s [abpoa_main] Real time: 0.000 sec; CPU: 0.001 sec; Peak RSS: 0.003 GB. 131s + diff - out.gfa 131s + abpoa.avx -r4 ./test_data/seq.fa 131s [main] CMD: abpoa.avx -r4 ./test_data/seq.fa 131s [abpoa_main] Real time: 0.001 sec; CPU: 0.001 sec; Peak RSS: 0.003 GB. 131s + diff - out4.gfa 131s + cp out.gfa in.gfa 131s + cp out.msa in.msa 131s + abpoa.avx -i in.gfa ./test_data/seq.fa -r3 131s [main] CMD: abpoa.avx -i in.gfa -r3 ./test_data/seq.fa 131s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB. 131s + diff - out.gfa 131s + abpoa.avx -i in.msa ./test_data/seq.fa -r1 131s [main] CMD: abpoa.avx -i in.msa -r1 ./test_data/seq.fa 131s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB. 131s + diff - out.msa 131s + abpoa.avx ./test_data/seq.fa -g poa.png 131s [main] CMD: abpoa.avx -g poa.png ./test_data/seq.fa 131s 1.5.3 131s [abpoa_main] Real time: 0.353 sec; CPU: 0.001 sec; Peak RSS: 0.003 GB. 131s + diff - cons.fa 131s + abpoa.avx ./test_data/heter.fa -d2 131s [main] CMD: abpoa.avx -d2 ./test_data/heter.fa 131s >Consensus_sequence_1 0,2,3,4,10,13,14 131s CCATTCCCACCATCCTTACCATCAACATCACCATCCCCACCATCCCCAACACCATTCCCACCATCCCTACCATCACCATCACCATCCCCACCAACATCCCCACCACCATCCTCACTACCATCCCCACCACCATTTCCACCATTCCCACCACAGTCACCATCACCCCCACCATCCCCATCATCATCCGCACCATCCCCACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCTCCAACACCTCCCCCACCATCATCCCCACCATCCCCACCACCTTCTCCACCATCATTCTCACCATCCCCACCACCATCTCCACCACCATTCTCACCATCTCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCATCATCCCCACCATCC 131s >Consensus_sequence_2 1,5,6,7,8,9,11,12 131s CCATTCCCACCATCCTTACCATCAACATCACCATCCCCACCATCCCCAACACCATTCCCACCATCCCTACCATCACCATCACCATCCCCACCAACATCCCCACCACCATCCTCACTACCATCCCCACCACCATTTCCACCATTCCCACCACAGTCACCATCACCCCCACCATCCCCATCATCATCCGCACCATCCCCACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCATCCCCACCGCCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCTCCAACACCTCCCCCACCATCATCCCCACCATCCCCACCACCTTCTCCACCATCATTCTCACCATCCCCACCACCATCTCCACCACCATTCTCACCATCTCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCATCATCCCCACCATCC 131s [abpoa_main] Real time: 0.009 sec; CPU: 0.010 sec; Peak RSS: 0.009 GB. 131s + for SIMDE in avx2 avx sse4.1 ssse3 sse3 generic dispatch 131s + '[' sse4.1 = dispatch ']' 131s + '[' sse4.1 = generic ']' 131s + grep -q sse4.1 /proc/cpuinfo 131s + command -v abpoa.sse4.1 131s + BINARY=abpoa.sse4.1 131s + abpoa.sse4.1 --version 131s 1.5.3 131s + abpoa.sse4.1 --help 131s 131s abpoa: adaptive banded Partial Order Alignment 131s 131s Version: 1.5.3 Contact: yangao@ds.dfci.harvard.edu 131s 131s Usage: abpoa [options] > cons.fa/msa.fa/abpoa.gfa 131s 131s Options: 131s Alignment: 131s -m --aln-mode INT alignment mode [0] 131s 0: global, 1: local, 2: extension 131s -M --match INT match score [2] 131s -X --mismatch INT mismatch penalty [4] 131s -t --matrix FILE scoring matrix file, '-M' and '-X' are not used when '-t' is used [Null] 131s e.g., 'HOXD70.mtx, BLOSUM62.mtx' 131s -O --gap-open INT(,INT) gap opening penalty (O1,O2) [4,24] 131s -E --gap-ext INT(,INT) gap extension penalty (E1,E2) [2,1] 131s abPOA provides three gap penalty modes, cost of a g-long gap: 131s - convex (default): min{O1+g*E1, O2+g*E2} 131s - affine (set O2 as 0): O1+g*E1 131s - linear (set O1 as 0): g*E1 131s -s --amb-strand ambiguous strand mode [False] 131s for each input sequence, try the reverse complement if the current 131s alignment score is too low, and pick the strand with a higher score 131s Adaptive banded DP: 131s -b --extra-b INT first adaptive banding parameter [10] 131s set b as < 0 to disable adaptive banded DP 131s -f --extra-f FLOAT second adaptive banding parameter [0.01] 131s the number of extra bases added on both sites of the band is 131s b+f*L, where L is the length of the aligned sequence 131s Minimizer-based seeding and partition (only effective in global alignment mode): 131s -S --seeding enable minimizer-based seeding and anchoring [False] 131s -k --k-mer INT minimizer k-mer size [19] 131s -w --window INT minimizer window size [10] 131s -n --min-poa-win INT min. size of window to perform POA [500] 131s -p --progressive build guide tree and perform progressive partial order alignment [False] 131s Input/Output: 131s -Q --use-qual-weight take base quality score from FASTQ input file as graph edge weight for consensus calling [False] 131s effective only when input sequences are in FASTQ format and consensus calling with heaviest bundling 131s -c --amino-acid input sequences are amino acid (default is nucleotide) [False] 131s -l --in-list input file is a list of sequence file names [False] 131s each line is one sequence file containing a set of sequences 131s which will be aligned by abPOA to generate a consensus sequence 131s -i --incrmnt FILE incrementally align sequences to an existing graph/MSA [Null] 131s graph could be in GFA or MSA format generated by abPOA 131s -o --output FILE output to FILE [stdout] 131s -r --result INT output result mode [0] 131s - 0: consensus in FASTA format 131s - 1: MSA in PIR format 131s - 2: both 0 & 1 131s - 3: graph in GFA format 131s - 4: graph with consensus path in GFA format 131s - 5: consensus in FASTQ format 131s -a --cons-algrm INT consensus algorithm [0] 131s - 0: heaviest bundling path in partial order graph 131s - 1: most frequent bases at each position 131s -d --maxnum-cons INT max. number of consensus sequence to generate [1] 131s -q --min-freq FLOAT min. frequency of each consensus sequence (only effective when -d/--num-cons > 1) [0.25] 131s -g --out-pog FILE dump final alignment graph to FILE (.pdf/.png) [Null] 131s 131s -h --help print this help usage information 131s -v --version show version number 131s -V --verbose INT verbose level (0-2). 0: none, 1: information, 2: debug [0] 131s 131s + test 1 = 1 131s + abpoa.sse4.1 ./test_data/seq.fa 131s [main] CMD: abpoa.sse4.1 ./test_data/seq.fa 131s [abpoa_main] Real time: 0.001 sec; CPU: 0.001 sec; Peak RSS: 0.003 GB. 131s + diff - cons.fa 131s + abpoa.sse4.1 ./test_data/heter.fa 131s [main] CMD: abpoa.sse4.1 ./test_data/heter.fa 131s [abpoa_main] Real time: 0.008 sec; CPU: 0.009 sec; Peak RSS: 0.009 GB. 131s + abpoa.sse4.1 -r1 ./test_data/seq.fa 131s [main] CMD: abpoa.sse4.1 -r1 ./test_data/seq.fa 131s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.002 GB. 131s + diff - out.msa 131s + abpoa.sse4.1 -r2 ./test_data/seq.fa 131s [main] CMD: abpoa.sse4.1 -r2 ./test_data/seq.fa 131s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB. 131s + diff - out_cons.msa 131s + abpoa.sse4.1 -r3 ./test_data/seq.fa 131s [main] CMD: abpoa.sse4.1 -r3 ./test_data/seq.fa 131s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB. 131s + diff - out.gfa 131s + abpoa.sse4.1 -r4 ./test_data/seq.fa 131s [main] CMD: abpoa.sse4.1 -r4 ./test_data/seq.fa 131s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB. 131s + diff - out4.gfa 131s + cp out.gfa in.gfa 131s + cp out.msa in.msa 131s + abpoa.sse4.1 -i in.gfa ./test_data/seq.fa -r3 131s [main] CMD: abpoa.sse4.1 -i in.gfa -r3 ./test_data/seq.fa 131s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB. 131s + diff - out.gfa 131s + abpoa.sse4.1 -i in.msa ./test_data/seq.fa -r1 131s [main] CMD: abpoa.sse4.1 -i in.msa -r1 ./test_data/seq.fa 131s [abpoa_main] Real time: 0.001 sec; CPU: 0.001 sec; Peak RSS: 0.003 GB. 131s + diff - out.msa 131s + abpoa.sse4.1 ./test_data/seq.fa -g poa.png 131s [main] CMD: abpoa.sse4.1 -g poa.png ./test_data/seq.fa 132s [abpoa_main] Real time: 0.345 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB. 132s + diff - cons.fa 132s + abpoa.sse4.1 ./test_data/heter.fa -d2 132s [main] CMD: abpoa.sse4.1 -d2 ./test_data/heter.fa 132s >Consensus_sequence_1 0,2,3,4,10,13,14 132s CCATTCCCACCATCCTTACCATCAACATCACCATCCCCACCATCCCCAACACCATTCCCACCATCCCTACCATCACCATCACCATCCCCACCAACATCCCCACCACCATCCTCACTACCATCCCCACCACCATTTCCACCATTCCCACCACAGTCACCATCACCCCCACCATCCCCATCATCATCCGCACCATCCCCACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCTCCAACACCTCCCCCACCATCATCCCCACCATCCCCACCACCTTCTCCACCATCATTCTCACCATCCCCACCACCATCTCCACCACCATTCTCACCATCTCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCATCATCCCCACCATCC 132s >Consensus_sequence_2 1,5,6,7,8,9,11,12 132s CCATTCCCACCATCCTTACCATCAACATCACCATCCCCACCATCCCCAACACCATTCCCACCATCCCTACCATCACCATCACCATCCCCACCAACATCCCCACCACCATCCTCACTACCATCCCCACCACCATTTCCACCATTCCCACCACAGTCACCATCACCCCCACCATCCCCATCATCATCCGCACCATCCCCACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCATCCCCACCGCCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCTCCAACACCTCCCCCACCATCATCCCCACCATCCCCACCACCTTCTCCACCATCATTCTCACCATCCCCACCACCATCTCCACCACCATTCTCACCATCTCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCATCATCCCCACCATCC 132s [abpoa_main] Real time: 0.009 sec; CPU: 0.010 sec; Peak RSS: 0.009 GB. 132s + for SIMDE in avx2 avx sse4.1 ssse3 sse3 generic dispatch 132s + '[' ssse3 = dispatch ']' 132s + '[' ssse3 = generic ']' 132s + grep -q ssse3 /proc/cpuinfo 132s + command -v abpoa.ssse3 132s + BINARY=abpoa.ssse3 132s + abpoa.ssse3 --version 132s 1.5.3 132s + abpoa.ssse3 --help 132s 132s abpoa: adaptive banded Partial Order Alignment 132s 132s Version: 1.5.3 Contact: yangao@ds.dfci.harvard.edu 132s 132s Usage: abpoa [options] > cons.fa/msa.fa/abpoa.gfa 132s 132s Options: 132s Alignment: 132s -m --aln-mode INT alignment mode [0] 132s 0: global, 1: local, 2: extension 132s -M --match INT match score [2] 132s -X --mismatch INT mismatch penalty [4] 132s -t --matrix FILE scoring matrix file, '-M' and '-X' are not used when '-t' is used [Null] 132s e.g., 'HOXD70.mtx, BLOSUM62.mtx' 132s -O --gap-open INT(,INT) gap opening penalty (O1,O2) [4,24] 132s -E --gap-ext INT(,INT) gap extension penalty (E1,E2) [2,1] 132s abPOA provides three gap penalty modes, cost of a g-long gap: 132s - convex (default): min{O1+g*E1, O2+g*E2} 132s - affine (set O2 as 0): O1+g*E1 132s - linear (set O1 as 0): g*E1 132s -s --amb-strand ambiguous strand mode [False] 132s for each input sequence, try the reverse complement if the current 132s alignment score is too low, and pick the strand with a higher score 132s Adaptive banded DP: 132s -b --extra-b INT first adaptive banding parameter [10] 132s set b as < 0 to disable adaptive banded DP 132s -f --extra-f FLOAT second adaptive banding parameter [0.01] 132s the number of extra bases added on both sites of the band is 132s b+f*L, where L is the length of the aligned sequence 132s Minimizer-based seeding and partition (only effective in global alignment mode): 132s -S --seeding enable minimizer-based seeding and anchoring [False] 132s -k --k-mer INT minimizer k-mer size [19] 132s -w --window INT minimizer window size [10] 132s -n --min-poa-win INT min. size of window to perform POA [500] 132s -p --progressive build guide tree and perform progressive partial order alignment [False] 132s Input/Output: 132s -Q --use-qual-weight take base quality score from FASTQ input file as graph edge weight for consensus calling [False] 132s effective only when input sequences are in FASTQ format and consensus calling with heaviest bundling 132s -c --amino-acid input sequences are amino acid (default is nucleotide) [False] 132s -l --in-list input file is a list of sequence file names [False] 132s each line is one sequence file containing a set of sequences 132s which will be aligned by abPOA to generate a consensus sequence 132s -i --incrmnt FILE incrementally align sequences to an existing graph/MSA [Null] 132s graph could be in GFA or MSA format generated by abPOA 132s -o --output FILE output to FILE [stdout] 132s -r --result INT output result mode [0] 132s - 0: consensus in FASTA format 132s - 1: MSA in PIR format 132s - 2: both 0 & 1 132s - 3: graph in GFA format 132s - 4: graph with consensus path in GFA format 132s - 5: consensus in FASTQ format 132s -a --cons-algrm INT consensus algorithm [0] 132s - 0: heaviest bundling path in partial order graph 132s - 1: most frequent bases at each position 132s -d --maxnum-cons INT max. number of consensus sequence to generate [1] 132s -q --min-freq FLOAT min. frequency of each consensus sequence (only effective when -d/--num-cons > 1) [0.25] 132s -g --out-pog FILE dump final alignment graph to FILE (.pdf/.png) [Null] 132s 132s -h --help print this help usage information 132s -v --version show version number 132s -V --verbose INT verbose level (0-2). 0: none, 1: information, 2: debug [0] 132s 132s + test 1 = 1 132s + abpoa.ssse3 ./test_data/seq.fa 132s [main] CMD: abpoa.ssse3 ./test_data/seq.fa 132s [abpoa_main] Real time: 0.000 sec; CPU: 0.001 sec; Peak RSS: 0.003 GB. 132s + diff - cons.fa 132s + abpoa.ssse3 ./test_data/heter.fa 132s [main] CMD: abpoa.ssse3 ./test_data/heter.fa 132s [abpoa_main] Real time: 0.008 sec; CPU: 0.009 sec; Peak RSS: 0.009 GB. 132s + abpoa.ssse3 -r1 ./test_data/seq.fa 132s [main] CMD: abpoa.ssse3 -r1 ./test_data/seq.fa 132s [abpoa_main] Real time: 0.000 sec; CPU: 0.001 sec; Peak RSS: 0.003 GB. 132s + diff - out.msa 132s + abpoa.ssse3 -r2 ./test_data/seq.fa 132s [main] CMD: abpoa.ssse3 -r2 ./test_data/seq.fa 132s [abpoa_main] Real time: 0.000 sec; CPU: 0.001 sec; Peak RSS: 0.003 GB. 132s + diff - out_cons.msa 132s + abpoa.ssse3 -r3 ./test_data/seq.fa 132s [main] CMD: abpoa.ssse3 -r3 ./test_data/seq.fa 132s [abpoa_main] Real time: 0.000 sec; CPU: 0.001 sec; Peak RSS: 0.003 GB. 132s + diff - out.gfa 132s + abpoa.ssse3 -r4 ./test_data/seq.fa 132s [main] CMD: abpoa.ssse3 -r4 ./test_data/seq.fa 132s [abpoa_main] Real time: 0.000 sec; CPU: 0.001 sec; Peak RSS: 0.003 GB. 132s + diff - out4.gfa 132s + cp out.gfa in.gfa 132s + cp out.msa in.msa 132s + abpoa.ssse3 -i in.gfa ./test_data/seq.fa -r3 132s [main] CMD: abpoa.ssse3 -i in.gfa -r3 ./test_data/seq.fa 132s [abpoa_main] Real time: 0.001 sec; CPU: 0.001 sec; Peak RSS: 0.003 GB. 132s + diff - out.gfa 132s + abpoa.ssse3 -i in.msa ./test_data/seq.fa -r1 132s [main] CMD: abpoa.ssse3 -i in.msa -r1 ./test_data/seq.fa 132s [abpoa_main] Real time: 0.001 sec; CPU: 0.001 sec; Peak RSS: 0.003 GB. 132s + diff - out.msa 132s + abpoa.ssse3 ./test_data/seq.fa -g poa.png 132s [main] CMD: abpoa.ssse3 -g poa.png ./test_data/seq.fa 132s [abpoa_main] Real time: 0.336 sec; CPU: 0.001 sec; Peak RSS: 0.003 GB. 132s + diff - cons.fa 132s + abpoa.ssse3 ./test_data/heter.fa -d2 132s [main] CMD: abpoa.ssse3 -d2 ./test_data/heter.fa 132s >Consensus_sequence_1 0,2,3,4,10,13,14 132s CCATTCCCACCATCCTTACCATCAACATCACCATCCCCACCATCCCCAACACCATTCCCACCATCCCTACCATCACCATCACCATCCCCACCAACATCCCCACCACCATCCTCACTACCATCCCCACCACCATTTCCACCATTCCCACCACAGTCACCATCACCCCCACCATCCCCATCATCATCCGCACCATCCCCACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCTCCAACACCTCCCCCACCATCATCCCCACCATCCCCACCACCTTCTCCACCATCATTCTCACCATCCCCACCACCATCTCCACCACCATTCTCACCATCTCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCATCATCCCCACCATCC 132s >Consensus_sequence_2 1,5,6,7,8,9,11,12 132s CCATTCCCACCATCCTTACCATCAACATCACCATCCCCACCATCCCCAACACCATTCCCACCATCCCTACCATCACCATCACCATCCCCACCAACATCCCCACCACCATCCTCACTACCATCCCCACCACCATTTCCACCATTCCCACCACAGTCACCATCACCCCCACCATCCCCATCATCATCCGCACCATCCCCACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCATCCCCACCGCCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCTCCAACACCTCCCCCACCATCATCCCCACCATCCCCACCACCTTCTCCACCATCATTCTCACCATCCCCACCACCATCTCCACCACCATTCTCACCATCTCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCATCATCCCCACCATCC 132s [abpoa_main] Real time: 0.010 sec; CPU: 0.011 sec; Peak RSS: 0.009 GB. 132s + for SIMDE in avx2 avx sse4.1 ssse3 sse3 generic dispatch 132s + '[' sse3 = dispatch ']' 132s + '[' sse3 = generic ']' 132s + grep -q sse3 /proc/cpuinfo 132s + command -v abpoa.sse3 132s + BINARY=abpoa.sse3 132s + abpoa.sse3 --version 132s 1.5.3 132s + abpoa.sse3 --help 132s 132s abpoa: adaptive banded Partial Order Alignment 132s 132s Version: 1.5.3 Contact: yangao@ds.dfci.harvard.edu 132s 132s Usage: abpoa [options] > cons.fa/msa.fa/abpoa.gfa 132s 132s Options: 132s Alignment: 132s -m --aln-mode INT alignment mode [0] 132s 0: global, 1: local, 2: extension 132s -M --match INT match score [2] 132s -X --mismatch INT mismatch penalty [4] 132s -t --matrix FILE scoring matrix file, '-M' and '-X' are not used when '-t' is used [Null] 132s e.g., 'HOXD70.mtx, BLOSUM62.mtx' 132s -O --gap-open INT(,INT) gap opening penalty (O1,O2) [4,24] 132s -E --gap-ext INT(,INT) gap extension penalty (E1,E2) [2,1] 132s abPOA provides three gap penalty modes, cost of a g-long gap: 132s - convex (default): min{O1+g*E1, O2+g*E2} 132s - affine (set O2 as 0): O1+g*E1 132s - linear (set O1 as 0): g*E1 132s -s --amb-strand ambiguous strand mode [False] 132s for each input sequence, try the reverse complement if the current 132s alignment score is too low, and pick the strand with a higher score 132s Adaptive banded DP: 132s -b --extra-b INT first adaptive banding parameter [10] 132s set b as < 0 to disable adaptive banded DP 132s -f --extra-f FLOAT second adaptive banding parameter [0.01] 132s the number of extra bases added on both sites of the band is 132s b+f*L, where L is the length of the aligned sequence 132s Minimizer-based seeding and partition (only effective in global alignment mode): 132s -S --seeding enable minimizer-based seeding and anchoring [False] 132s -k --k-mer INT minimizer k-mer size [19] 132s -w --window INT minimizer window size [10] 132s -n --min-poa-win INT min. size of window to perform POA [500] 132s -p --progressive build guide tree and perform progressive partial order alignment [False] 132s Input/Output: 132s -Q --use-qual-weight take base quality score from FASTQ input file as graph edge weight for consensus calling [False] 132s effective only when input sequences are in FASTQ format and consensus calling with heaviest bundling 132s -c --amino-acid input sequences are amino acid (default is nucleotide) [False] 132s -l --in-list input file is a list of sequence file names [False] 132s each line is one sequence file containing a set of sequences 132s which will be aligned by abPOA to generate a consensus sequence 132s -i --incrmnt FILE incrementally align sequences to an existing graph/MSA [Null] 132s graph could be in GFA or MSA format generated by abPOA 132s -o --output FILE output to FILE [stdout] 132s -r --result INT output result mode [0] 132s - 0: consensus in FASTA format 132s - 1: MSA in PIR format 132s - 2: both 0 & 1 132s - 3: graph in GFA format 132s - 4: graph with consensus path in GFA format 132s - 5: consensus in FASTQ format 132s -a --cons-algrm INT consensus algorithm [0] 132s - 0: heaviest bundling path in partial order graph 132s - 1: most frequent bases at each position 132s -d --maxnum-cons INT max. number of consensus sequence to generate [1] 132s -q --min-freq FLOAT min. frequency of each consensus sequence (only effective when -d/--num-cons > 1) [0.25] 132s -g --out-pog FILE dump final alignment graph to FILE (.pdf/.png) [Null] 132s 132s -h --help print this help usage information 132s -v --version show version number 132s -V --verbose INT verbose level (0-2). 0: none, 1: information, 2: debug [0] 132s 132s + test 1 = 1 132s + abpoa.sse3 ./test_data/seq.fa 132s [main] CMD: abpoa.sse3 ./test_data/seq.fa 132s [abpoa_main] Real time: 0.001 sec; CPU: 0.001 sec; Peak RSS: 0.003 GB. 132s + diff - cons.fa 132s + abpoa.sse3 ./test_data/heter.fa 132s [main] CMD: abpoa.sse3 ./test_data/heter.fa 132s [abpoa_main] Real time: 0.011 sec; CPU: 0.012 sec; Peak RSS: 0.009 GB. 132s + abpoa.sse3 -r1 ./test_data/seq.fa 132s [main] CMD: abpoa.sse3 -r1 ./test_data/seq.fa 132s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB. 132s + diff - out.msa 132s + abpoa.sse3 -r2 ./test_data/seq.fa 132s [main] CMD: abpoa.sse3 -r2 ./test_data/seq.fa 132s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB. 132s + diff - out_cons.msa 132s + abpoa.sse3 -r3 ./test_data/seq.fa 132s [main] CMD: abpoa.sse3 -r3 ./test_data/seq.fa 132s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB. 132s + diff - out.gfa 132s + abpoa.sse3 -r4 ./test_data/seq.fa 132s [main] CMD: abpoa.sse3 -r4 ./test_data/seq.fa 132s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB. 132s + diff - out4.gfa 132s + cp out.gfa in.gfa 132s + cp out.msa in.msa 132s + abpoa.sse3 -i in.gfa ./test_data/seq.fa -r3 132s [main] CMD: abpoa.sse3 -i in.gfa -r3 ./test_data/seq.fa 132s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB. 132s + diff - out.gfa 132s + abpoa.sse3 -i in.msa ./test_data/seq.fa -r1 132s [main] CMD: abpoa.sse3 -i in.msa -r1 ./test_data/seq.fa 132s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB. 132s + diff - out.msa 132s + abpoa.sse3 ./test_data/seq.fa -g poa.png 132s [main] CMD: abpoa.sse3 -g poa.png ./test_data/seq.fa 132s [abpoa_main] Real time: 0.346 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB. 132s + diff - cons.fa 132s + abpoa.sse3 ./test_data/heter.fa -d2 132s [main] CMD: abpoa.sse3 -d2 ./test_data/heter.fa 132s >Consensus_sequence_1 0,2,3,4,10,13,14 132s CCATTCCCACCATCCTTACCATCAACATCACCATCCCCACCATCCCCAACACCATTCCCACCATCCCTACCATCACCATCACCATCCCCACCAACATCCCCACCACCATCCTCACTACCATCCCCACCACCATTTCCACCATTCCCACCACAGTCACCATCACCCCCACCATCCCCATCATCATCCGCACCATCCCCACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCTCCAACACCTCCCCCACCATCATCCCCACCATCCCCACCACCTTCTCCACCATCATTCTCACCATCCCCACCACCATCTCCACCACCATTCTCACCATCTCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCATCATCCCCACCATCC 132s >Consensus_sequence_2 1,5,6,7,8,9,11,12 132s CCATTCCCACCATCCTTACCATCAACATCACCATCCCCACCATCCCCAACACCATTCCCACCATCCCTACCATCACCATCACCATCCCCACCAACATCCCCACCACCATCCTCACTACCATCCCCACCACCATTTCCACCATTCCCACCACAGTCACCATCACCCCCACCATCCCCATCATCATCCGCACCATCCCCACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCATCCCCACCGCCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCTCCAACACCTCCCCCACCATCATCCCCACCATCCCCACCACCTTCTCCACCATCATTCTCACCATCCCCACCACCATCTCCACCACCATTCTCACCATCTCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCATCATCCCCACCATCC 132s [abpoa_main] Real time: 0.009 sec; CPU: 0.010 sec; Peak RSS: 0.009 GB. 132s + for SIMDE in avx2 avx sse4.1 ssse3 sse3 generic dispatch 132s + '[' generic = dispatch ']' 132s + '[' generic = generic ']' 132s + command -v abpoa.generic 132s + BINARY=abpoa.generic 132s + abpoa.generic --version 132s 1.5.3 132s + abpoa.generic --help 132s 132s abpoa: adaptive banded Partial Order Alignment 132s 132s Version: 1.5.3 Contact: yangao@ds.dfci.harvard.edu 132s 132s Usage: abpoa [options] > cons.fa/msa.fa/abpoa.gfa 132s 132s Options: 132s Alignment: 132s -m --aln-mode INT alignment mode [0] 132s 0: global, 1: local, 2: extension 132s -M --match INT match score [2] 132s -X --mismatch INT mismatch penalty [4] 132s -t --matrix FILE scoring matrix file, '-M' and '-X' are not used when '-t' is used [Null] 132s e.g., 'HOXD70.mtx, BLOSUM62.mtx' 132s -O --gap-open INT(,INT) gap opening penalty (O1,O2) [4,24] 132s -E --gap-ext INT(,INT) gap extension penalty (E1,E2) [2,1] 132s abPOA provides three gap penalty modes, cost of a g-long gap: 132s - convex (default): min{O1+g*E1, O2+g*E2} 132s - affine (set O2 as 0): O1+g*E1 132s - linear (set O1 as 0): g*E1 132s -s --amb-strand ambiguous strand mode [False] 132s for each input sequence, try the reverse complement if the current 132s alignment score is too low, and pick the strand with a higher score 132s Adaptive banded DP: 132s -b --extra-b INT first adaptive banding parameter [10] 132s set b as < 0 to disable adaptive banded DP 132s -f --extra-f FLOAT second adaptive banding parameter [0.01] 132s the number of extra bases added on both sites of the band is 132s b+f*L, where L is the length of the aligned sequence 132s Minimizer-based seeding and partition (only effective in global alignment mode): 132s -S --seeding enable minimizer-based seeding and anchoring [False] 132s -k --k-mer INT minimizer k-mer size [19] 132s -w --window INT minimizer window size [10] 132s -n --min-poa-win INT min. size of window to perform POA [500] 132s -p --progressive build guide tree and perform progressive partial order alignment [False] 132s Input/Output: 132s -Q --use-qual-weight take base quality score from FASTQ input file as graph edge weight for consensus calling [False] 132s effective only when input sequences are in FASTQ format and consensus calling with heaviest bundling 132s -c --amino-acid input sequences are amino acid (default is nucleotide) [False] 132s -l --in-list input file is a list of sequence file names [False] 132s each line is one sequence file containing a set of sequences 132s which will be aligned by abPOA to generate a consensus sequence 132s -i --incrmnt FILE incrementally align sequences to an existing graph/MSA [Null] 132s graph could be in GFA or MSA format generated by abPOA 132s -o --output FILE output to FILE [stdout] 132s -r --result INT output result mode [0] 132s - 0: consensus in FASTA format 132s - 1: MSA in PIR format 132s - 2: both 0 & 1 132s - 3: graph in GFA format 132s - 4: graph with consensus path in GFA format 132s - 5: consensus in FASTQ format 132s -a --cons-algrm INT consensus algorithm [0] 132s - 0: heaviest bundling path in partial order graph 132s - 1: most frequent bases at each position 132s -d --maxnum-cons INT max. number of consensus sequence to generate [1] 132s -q --min-freq FLOAT min. frequency of each consensus sequence (only effective when -d/--num-cons > 1) [0.25] 132s -g --out-pog FILE dump final alignment graph to FILE (.pdf/.png) [Null] 132s 132s -h --help print this help usage information 132s -v --version show version number 132s -V --verbose INT verbose level (0-2). 0: none, 1: information, 2: debug [0] 132s 132s + test 1 = 1 132s + abpoa.generic ./test_data/seq.fa 132s [main] CMD: abpoa.generic ./test_data/seq.fa 132s [abpoa_main] Real time: 0.000 sec; CPU: 0.001 sec; Peak RSS: 0.003 GB. 132s + diff - cons.fa 132s + abpoa.generic ./test_data/heter.fa 132s [main] CMD: abpoa.generic ./test_data/heter.fa 132s [abpoa_main] Real time: 0.009 sec; CPU: 0.010 sec; Peak RSS: 0.009 GB. 132s + abpoa.generic -r1 ./test_data/seq.fa 132s [main] CMD: abpoa.generic -r1 ./test_data/seq.fa 132s [abpoa_main] Real time: 0.000 sec; CPU: 0.001 sec; Peak RSS: 0.003 GB. 132s + diff - out.msa 132s + abpoa.generic -r2 ./test_data/seq.fa 132s [main] CMD: abpoa.generic -r2 ./test_data/seq.fa 132s [abpoa_main] Real time: 0.001 sec; CPU: 0.001 sec; Peak RSS: 0.003 GB. 132s + diff - out_cons.msa 132s + abpoa.generic -r3 ./test_data/seq.fa 132s [main] CMD: abpoa.generic -r3 ./test_data/seq.fa 132s [abpoa_main] Real time: 0.000 sec; CPU: 0.001 sec; Peak RSS: 0.003 GB. 132s + diff - out.gfa 132s + abpoa.generic -r4 ./test_data/seq.fa 132s [main] CMD: abpoa.generic -r4 ./test_data/seq.fa 132s [abpoa_main] Real time: 0.000 sec; CPU: 0.001 sec; Peak RSS: 0.003 GB. 132s + diff - out4.gfa 132s + cp out.gfa in.gfa 132s + cp out.msa in.msa 132s + abpoa.generic -i in.gfa ./test_data/seq.fa -r3 132s [main] CMD: abpoa.generic -i in.gfa -r3 ./test_data/seq.fa 132s [abpoa_main] Real time: 0.001 sec; CPU: 0.001 sec; Peak RSS: 0.002 GB. 132s + diff - out.gfa 132s + abpoa.generic -i in.msa ./test_data/seq.fa -r1 132s [main] CMD: abpoa.generic -i in.msa -r1 ./test_data/seq.fa 132s [abpoa_main] Real time: 0.001 sec; CPU: 0.001 sec; Peak RSS: 0.003 GB. 132s + diff - out.msa 132s + abpoa.generic ./test_data/seq.fa -g poa.png 132s [main] CMD: abpoa.generic -g poa.png ./test_data/seq.fa 133s [abpoa_main] Real time: 0.337 sec; CPU: 0.001 sec; Peak RSS: 0.003 GB. 133s + diff - cons.fa 133s + abpoa.generic ./test_data/heter.fa -d2 133s [main] CMD: abpoa.generic -d2 ./test_data/heter.fa 133s >Consensus_sequence_1 0,2,3,4,10,13,14 133s CCATTCCCACCATCCTTACCATCAACATCACCATCCCCACCATCCCCAACACCATTCCCACCATCCCTACCATCACCATCACCATCCCCACCAACATCCCCACCACCATCCTCACTACCATCCCCACCACCATTTCCACCATTCCCACCACAGTCACCATCACCCCCACCATCCCCATCATCATCCGCACCATCCCCACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCTCCAACACCTCCCCCACCATCATCCCCACCATCCCCACCACCTTCTCCACCATCATTCTCACCATCCCCACCACCATCTCCACCACCATTCTCACCATCTCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCATCATCCCCACCATCC 133s >Consensus_sequence_2 1,5,6,7,8,9,11,12 133s CCATTCCCACCATCCTTACCATCAACATCACCATCCCCACCATCCCCAACACCATTCCCACCATCCCTACCATCACCATCACCATCCCCACCAACATCCCCACCACCATCCTCACTACCATCCCCACCACCATTTCCACCATTCCCACCACAGTCACCATCACCCCCACCATCCCCATCATCATCCGCACCATCCCCACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCATCCCCACCGCCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCTCCAACACCTCCCCCACCATCATCCCCACCATCCCCACCACCTTCTCCACCATCATTCTCACCATCCCCACCACCATCTCCACCACCATTCTCACCATCTCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCATCATCCCCACCATCC 133s 1.5.3 133s [abpoa_main] Real time: 0.009 sec; CPU: 0.009 sec; Peak RSS: 0.009 GB. 133s + for SIMDE in avx2 avx sse4.1 ssse3 sse3 generic dispatch 133s + '[' dispatch = dispatch ']' 133s + BINARY=abpoa 133s + abpoa --version 133s + abpoa --help 133s 133s abpoa: adaptive banded Partial Order Alignment 133s 133s Version: 1.5.3 Contact: yangao@ds.dfci.harvard.edu 133s 133s Usage: abpoa [options] > cons.fa/msa.fa/abpoa.gfa 133s 133s Options: 133s Alignment: 133s -m --aln-mode INT alignment mode [0] 133s 0: global, 1: local, 2: extension 133s -M --match INT match score [2] 133s -X --mismatch INT mismatch penalty [4] 133s -t --matrix FILE scoring matrix file, '-M' and '-X' are not used when '-t' is used [Null] 133s e.g., 'HOXD70.mtx, BLOSUM62.mtx' 133s -O --gap-open INT(,INT) gap opening penalty (O1,O2) [4,24] 133s -E --gap-ext INT(,INT) gap extension penalty (E1,E2) [2,1] 133s abPOA provides three gap penalty modes, cost of a g-long gap: 133s - convex (default): min{O1+g*E1, O2+g*E2} 133s - affine (set O2 as 0): O1+g*E1 133s - linear (set O1 as 0): g*E1 133s -s --amb-strand ambiguous strand mode [False] 133s for each input sequence, try the reverse complement if the current 133s alignment score is too low, and pick the strand with a higher score 133s Adaptive banded DP: 133s -b --extra-b INT first adaptive banding parameter [10] 133s set b as < 0 to disable adaptive banded DP 133s -f --extra-f FLOAT second adaptive banding parameter [0.01] 133s the number of extra bases added on both sites of the band is 133s b+f*L, where L is the length of the aligned sequence 133s Minimizer-based seeding and partition (only effective in global alignment mode): 133s -S --seeding enable minimizer-based seeding and anchoring [False] 133s -k --k-mer INT minimizer k-mer size [19] 133s -w --window INT minimizer window size [10] 133s -n --min-poa-win INT min. size of window to perform POA [500] 133s -p --progressive build guide tree and perform progressive partial order alignment [False] 133s Input/Output: 133s -Q --use-qual-weight take base quality score from FASTQ input file as graph edge weight for consensus calling [False] 133s effective only when input sequences are in FASTQ format and consensus calling with heaviest bundling 133s -c --amino-acid input sequences are amino acid (default is nucleotide) [False] 133s -l --in-list input file is a list of sequence file names [False] 133s each line is one sequence file containing a set of sequences 133s which will be aligned by abPOA to generate a consensus sequence 133s -i --incrmnt FILE incrementally align sequences to an existing graph/MSA [Null] 133s graph could be in GFA or MSA format generated by abPOA 133s -o --output FILE output to FILE [stdout] 133s -r --result INT output result mode [0] 133s - 0: consensus in FASTA format 133s - 1: MSA in PIR format 133s - 2: both 0 & 1 133s - 3: graph in GFA format 133s - 4: graph with consensus path in GFA format 133s - 5: consensus in FASTQ format 133s -a --cons-algrm INT consensus algorithm [0] 133s - 0: heaviest bundling path in partial order graph 133s - 1: most frequent bases at each position 133s -d --maxnum-cons INT max. number of consensus sequence to generate [1] 133s -q --min-freq FLOAT min. frequency of each consensus sequence (only effective when -d/--num-cons > 1) [0.25] 133s -g --out-pog FILE dump final alignment graph to FILE (.pdf/.png) [Null] 133s 133s -h --help print this help usage information 133s -v --version show version number 133s -V --verbose INT verbose level (0-2). 0: none, 1: information, 2: debug [0] 133s 133s + test 1 = 1 133s + abpoa ./test_data/seq.fa 133s [main] CMD: /usr/bin/abpoa.avx2 ./test_data/seq.fa 133s [abpoa_main] Real time: 0.000 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB. 133s + diff - cons.fa 133s + abpoa ./test_data/heter.fa 133s [main] CMD: /usr/bin/abpoa.avx2 ./test_data/heter.fa 133s [abpoa_main] Real time: 0.008 sec; CPU: 0.009 sec; Peak RSS: 0.009 GB. 133s + abpoa -r1 ./test_data/seq.fa 133s [main] CMD: /usr/bin/abpoa.avx2 -r1 ./test_data/seq.fa 133s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB. 133s + diff - out.msa 133s + abpoa -r2 ./test_data/seq.fa 133s [main] CMD: /usr/bin/abpoa.avx2 -r2 ./test_data/seq.fa 133s [abpoa_main] Real time: 0.000 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB. 133s + diff - out_cons.msa 133s + abpoa -r3 ./test_data/seq.fa 133s [main] CMD: /usr/bin/abpoa.avx2 -r3 ./test_data/seq.fa 133s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB. 133s + diff - out.gfa 133s + abpoa -r4 ./test_data/seq.fa 133s [main] CMD: /usr/bin/abpoa.avx2 -r4 ./test_data/seq.fa 133s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB. 133s + diff - out4.gfa 133s + cp out.gfa in.gfa 133s + cp out.msa in.msa 133s + abpoa -i in.gfa ./test_data/seq.fa -r3 133s [main] CMD: /usr/bin/abpoa.avx2 -i in.gfa -r3 ./test_data/seq.fa 133s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB. 133s + diff - out.gfa 133s + abpoa -i in.msa ./test_data/seq.fa -r1 133s [main] CMD: /usr/bin/abpoa.avx2 -i in.msa -r1 ./test_data/seq.fa 133s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB. 133s + diff - out.msa 133s + abpoa ./test_data/seq.fa -g poa.png 133s [main] CMD: /usr/bin/abpoa.avx2 -g poa.png ./test_data/seq.fa 133s [abpoa_main] Real time: 0.336 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB. 133s + diff - cons.fa 133s + abpoa ./test_data/heter.fa -d2 133s [main] CMD: /usr/bin/abpoa.avx2 -d2 ./test_data/heter.fa 133s >Consensus_sequence_1 0,2,3,4,10,13,14 133s CCATTCCCACCATCCTTACCATCAACATCACCATCCCCACCATCCCCAACACCATTCCCACCATCCCTACCATCACCATCACCATCCCCACCAACATCCCCACCACCATCCTCACTACCATCCCCACCACCATTTCCACCATTCCCACCACAGTCACCATCACCCCCACCATCCCCATCATCATCCGCACCATCCCCACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCTCCAACACCTCCCCCACCATCATCCCCACCATCCCCACCACCTTCTCCACCATCATTCTCACCATCCCCACCACCATCTCCACCACCATTCTCACCATCTCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCATCATCCCCACCATCC 133s >Consensus_sequence_2 1,5,6,7,8,9,11,12 133s CCATTCCCACCATCCTTACCATCAACATCACCATCCCCACCATCCCCAACACCATTCCCACCATCCCTACCATCACCATCACCATCCCCACCAACATCCCCACCACCATCCTCACTACCATCCCCACCACCATTTCCACCATTCCCACCACAGTCACCATCACCCCCACCATCCCCATCATCATCCGCACCATCCCCACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCATCCCCACCGCCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCTCCAACACCTCCCCCACCATCATCCCCACCATCCCCACCACCTTCTCCACCATCATTCTCACCATCCCCACCACCATCTCCACCACCATTCTCACCATCTCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCATCATCCCCACCATCC 133s [abpoa_main] Real time: 0.009 sec; CPU: 0.010 sec; Peak RSS: 0.009 GB. 133s autopkgtest [08:08:32]: test run-unit-test: -----------------------] 134s autopkgtest [08:08:33]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 134s run-unit-test PASS 134s autopkgtest [08:08:33]: test autodep8-python3: preparing testbed 194s autopkgtest [08:09:33]: testbed dpkg architecture: amd64 194s autopkgtest [08:09:33]: testbed apt version: 2.9.8 194s autopkgtest [08:09:33]: @@@@@@@@@@@@@@@@@@@@ test bed setup 195s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 195s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 195s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 195s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 195s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [848 kB] 196s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB] 196s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.2 kB] 196s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 196s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [637 kB] 196s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [255 kB] 197s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [13.0 kB] 197s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [37.7 kB] 197s Fetched 2171 kB in 2s (1082 kB/s) 197s Reading package lists... 199s Reading package lists... 199s Building dependency tree... 199s Reading state information... 199s Calculating upgrade... 199s The following NEW packages will be installed: 199s python3.13-gdbm 199s The following packages will be upgraded: 199s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 200s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 200s Need to get 253 kB of archives. 200s After this operation, 147 kB of additional disk space will be used. 200s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 200s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 200s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 200s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 200s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 200s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.23.2-5ubuntu4 [152 kB] 200s Fetched 253 kB in 0s (624 kB/s) 200s (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 ... 75541 files and directories currently installed.) 200s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 200s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 200s Setting up python3-minimal (3.12.7-1) ... 201s (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 ... 75541 files and directories currently installed.) 201s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 201s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 201s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 201s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 201s Selecting previously unselected package python3.13-gdbm. 201s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ... 201s Unpacking python3.13-gdbm (3.13.0-2) ... 201s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ... 201s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 201s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_amd64.deb ... 201s Unpacking libgpgme11t64:amd64 (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 201s Setting up libgpgme11t64:amd64 (1.23.2-5ubuntu4) ... 201s Setting up python3.13-gdbm (3.13.0-2) ... 201s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 201s Setting up python3 (3.12.7-1) ... 201s Setting up python3-gdbm:amd64 (3.12.7-1) ... 201s Processing triggers for man-db (2.12.1-3) ... 202s Processing triggers for libc-bin (2.40-1ubuntu3) ... 202s Reading package lists... 202s Building dependency tree... 202s Reading state information... 202s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 203s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 203s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 203s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 203s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 204s Reading package lists... 204s Reading package lists... 204s Building dependency tree... 204s Reading state information... 204s Calculating upgrade... 204s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 204s Reading package lists... 205s Building dependency tree... 205s Reading state information... 205s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 208s Reading package lists... 209s Building dependency tree... 209s Reading state information... 209s Starting pkgProblemResolver with broken count: 0 209s Starting 2 pkgProblemResolver with broken count: 0 209s Done 209s The following additional packages will be installed: 209s libpython3.13-minimal libpython3.13-stdlib python3-all python3-pyabpoa 209s python3.13 python3.13-minimal 209s Suggested packages: 209s python3.13-venv python3.13-doc binfmt-support 209s The following NEW packages will be installed: 209s autopkgtest-satdep libpython3.13-minimal libpython3.13-stdlib python3-all 209s python3-pyabpoa python3.13 python3.13-minimal 209s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 209s Need to get 6074 kB/6075 kB of archives. 209s After this operation, 22.9 MB of additional disk space will be used. 209s Get:1 /tmp/autopkgtest.1rn5AE/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [720 B] 210s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.0-2 [879 kB] 210s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.0-2 [2188 kB] 211s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [2107 kB] 211s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.0-2 [719 kB] 211s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all amd64 3.12.7-1 [890 B] 211s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyabpoa amd64 1.5.3-1 [180 kB] 212s Fetched 6074 kB in 2s (3132 kB/s) 212s Selecting previously unselected package libpython3.13-minimal:amd64. 212s (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 ... 75548 files and directories currently installed.) 212s Preparing to unpack .../0-libpython3.13-minimal_3.13.0-2_amd64.deb ... 212s Unpacking libpython3.13-minimal:amd64 (3.13.0-2) ... 212s Selecting previously unselected package python3.13-minimal. 212s Preparing to unpack .../1-python3.13-minimal_3.13.0-2_amd64.deb ... 212s Unpacking python3.13-minimal (3.13.0-2) ... 212s Selecting previously unselected package libpython3.13-stdlib:amd64. 212s Preparing to unpack .../2-libpython3.13-stdlib_3.13.0-2_amd64.deb ... 212s Unpacking libpython3.13-stdlib:amd64 (3.13.0-2) ... 212s Selecting previously unselected package python3.13. 212s Preparing to unpack .../3-python3.13_3.13.0-2_amd64.deb ... 212s Unpacking python3.13 (3.13.0-2) ... 212s Selecting previously unselected package python3-all. 212s Preparing to unpack .../4-python3-all_3.12.7-1_amd64.deb ... 212s Unpacking python3-all (3.12.7-1) ... 212s Selecting previously unselected package python3-pyabpoa. 212s Preparing to unpack .../5-python3-pyabpoa_1.5.3-1_amd64.deb ... 212s Unpacking python3-pyabpoa (1.5.3-1) ... 212s Selecting previously unselected package autopkgtest-satdep. 212s Preparing to unpack .../6-2-autopkgtest-satdep.deb ... 212s Unpacking autopkgtest-satdep (0) ... 212s Setting up python3-pyabpoa (1.5.3-1) ... 212s Setting up libpython3.13-minimal:amd64 (3.13.0-2) ... 212s Setting up python3.13-minimal (3.13.0-2) ... 213s Setting up libpython3.13-stdlib:amd64 (3.13.0-2) ... 213s Setting up python3.13 (3.13.0-2) ... 213s Setting up python3-all (3.12.7-1) ... 213s Setting up autopkgtest-satdep (0) ... 214s Processing triggers for man-db (2.12.1-3) ... 214s Processing triggers for systemd (256.5-2ubuntu4) ... 216s (Reading database ... 76291 files and directories currently installed.) 216s Removing autopkgtest-satdep (0) ... 218s autopkgtest [08:09:57]: test autodep8-python3: set -e ; for py in $(py3versions -r 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c "import pyabpoa; print(pyabpoa)" ; done 218s autopkgtest [08:09:57]: test autodep8-python3: [----------------------- 218s Testing with python3.13: 218s Traceback (most recent call last): 218s File "", line 1, in 218s import pyabpoa; print(pyabpoa) 218s ^^^^^^^^^^^^^^ 218s ModuleNotFoundError: No module named 'pyabpoa' 218s autopkgtest [08:09:57]: test autodep8-python3: -----------------------] 219s autopkgtest [08:09:58]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 219s autodep8-python3 FAIL non-zero exit status 1 219s autopkgtest [08:09:58]: @@@@@@@@@@@@@@@@@@@@ summary 219s run-unit-test PASS 219s autodep8-python3 FAIL non-zero exit status 1 231s nova [W] Skipping flock for amd64 231s Creating nova instance adt-plucky-amd64-abpoa-20241113-080619-juju-7f2275-prod-proposed-migration-environment-15-bf6391ad-ba6f-4904-bc52-fe10fe6ca7d1 from image adt/ubuntu-plucky-amd64-server-20241113.img (UUID 62c21ac4-2290-4c8d-8313-dddd18eacff4)... 231s nova [W] Skipping flock for amd64 231s Creating nova instance adt-plucky-amd64-abpoa-20241113-080619-juju-7f2275-prod-proposed-migration-environment-15-bf6391ad-ba6f-4904-bc52-fe10fe6ca7d1 from image adt/ubuntu-plucky-amd64-server-20241113.img (UUID 62c21ac4-2290-4c8d-8313-dddd18eacff4)...