0s autopkgtest [13:27:47]: starting date and time: 2024-07-12 13:27:47+0000
  0s autopkgtest [13:27:47]: git checkout: fd3bed09 nova: allow more retries for quota issues
  0s autopkgtest [13:27:47]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.d_pdj3i0/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade abpoa --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.39-3.1ubuntu3 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@lcy02-3.secgroup --name adt-oracular-amd64-abpoa-20240712-132747-juju-7f2275-prod-proposed-migration-environment-2-5847d891-a89c-46f1-b477-e088ecd25742 --image adt/ubuntu-oracular-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -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/
105s autopkgtest [13:29:32]: testbed dpkg architecture: amd64
105s autopkgtest [13:29:32]: testbed apt version: 2.9.6
105s autopkgtest [13:29:32]: @@@@@@@@@@@@@@@@@@@@ test bed setup
105s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB]
105s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [45.3 kB]
105s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [345 kB]
105s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8548 B]
105s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2576 B]
105s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 Packages [99.7 kB]
105s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main i386 Packages [73.0 kB]
105s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 c-n-f Metadata [2104 B]
105s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted i386 Packages [6244 B]
105s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 Packages [34.9 kB]
105s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 c-n-f Metadata [368 B]
105s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/universe i386 Packages [240 kB]
105s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 Packages [374 kB]
105s Get:14 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 c-n-f Metadata [9228 B]
105s Get:15 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 Packages [7644 B]
105s Get:16 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse i386 Packages [3052 B]
105s Get:17 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 c-n-f Metadata [276 B]
106s Fetched 1378 kB in 0s (5726 kB/s)
106s Reading package lists...
108s Reading package lists...
108s Building dependency tree...
108s Reading state information...
109s Calculating upgrade...
109s The following packages will be upgraded:
109s   binutils binutils-common binutils-x86-64-linux-gnu gir1.2-glib-2.0
109s   libbinutils libc-bin libc-dev-bin libc-devtools libc6 libc6-dev
109s   libctf-nobfd0 libctf0 libglib2.0-0t64 libglib2.0-data libgprofng0
109s   libnghttp2-14 libnss3 libsframe1 libssl3t64 locales openssl
109s 21 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
109s Need to get 21.2 MB of archives.
109s After this operation, 423 kB of additional disk space will be used.
109s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc-devtools amd64 2.39-3.1ubuntu3 [29.3 kB]
109s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc6-dev amd64 2.39-3.1ubuntu3 [2120 kB]
109s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc-dev-bin amd64 2.39-3.1ubuntu3 [20.4 kB]
109s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc6 amd64 2.39-3.1ubuntu3 [3262 kB]
109s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc-bin amd64 2.39-3.1ubuntu3 [680 kB]
109s Get:6 http://ftpmaster.internal/ubuntu oracular/main amd64 libssl3t64 amd64 3.2.2-1ubuntu1 [2138 kB]
109s Get:7 http://ftpmaster.internal/ubuntu oracular/main amd64 gir1.2-glib-2.0 amd64 2.80.4-1ubuntu1 [182 kB]
109s Get:8 http://ftpmaster.internal/ubuntu oracular/main amd64 libglib2.0-0t64 amd64 2.80.4-1ubuntu1 [1545 kB]
109s Get:9 http://ftpmaster.internal/ubuntu oracular/main amd64 libglib2.0-data all 2.80.4-1ubuntu1 [49.3 kB]
109s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 locales all 2.39-3.1ubuntu3 [4220 kB]
109s Get:11 http://ftpmaster.internal/ubuntu oracular/main amd64 openssl amd64 3.2.2-1ubuntu1 [1122 kB]
109s Get:12 http://ftpmaster.internal/ubuntu oracular/main amd64 libnghttp2-14 amd64 1.62.1-2 [75.1 kB]
109s Get:13 http://ftpmaster.internal/ubuntu oracular/main amd64 libgprofng0 amd64 2.42.50.20240710-1ubuntu1 [860 kB]
109s Get:14 http://ftpmaster.internal/ubuntu oracular/main amd64 libctf0 amd64 2.42.50.20240710-1ubuntu1 [95.6 kB]
109s Get:15 http://ftpmaster.internal/ubuntu oracular/main amd64 libctf-nobfd0 amd64 2.42.50.20240710-1ubuntu1 [97.6 kB]
109s Get:16 http://ftpmaster.internal/ubuntu oracular/main amd64 binutils-x86-64-linux-gnu amd64 2.42.50.20240710-1ubuntu1 [2477 kB]
109s Get:17 http://ftpmaster.internal/ubuntu oracular/main amd64 libbinutils amd64 2.42.50.20240710-1ubuntu1 [574 kB]
109s Get:18 http://ftpmaster.internal/ubuntu oracular/main amd64 binutils amd64 2.42.50.20240710-1ubuntu1 [18.1 kB]
109s Get:19 http://ftpmaster.internal/ubuntu oracular/main amd64 binutils-common amd64 2.42.50.20240710-1ubuntu1 [243 kB]
109s Get:20 http://ftpmaster.internal/ubuntu oracular/main amd64 libsframe1 amd64 2.42.50.20240710-1ubuntu1 [14.4 kB]
109s Get:21 http://ftpmaster.internal/ubuntu oracular/main amd64 libnss3 amd64 2:3.102-1 [1399 kB]
109s Preconfiguring packages ...
109s Fetched 21.2 MB in 0s (96.1 MB/s)
110s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 74487 files and directories currently installed.)
110s Preparing to unpack .../libc-devtools_2.39-3.1ubuntu3_amd64.deb ...
110s Unpacking libc-devtools (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ...
110s Preparing to unpack .../libc6-dev_2.39-3.1ubuntu3_amd64.deb ...
110s Unpacking libc6-dev:amd64 (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ...
110s Preparing to unpack .../libc-dev-bin_2.39-3.1ubuntu3_amd64.deb ...
110s Unpacking libc-dev-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ...
110s Preparing to unpack .../libc6_2.39-3.1ubuntu3_amd64.deb ...
110s Unpacking libc6:amd64 (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ...
110s Setting up libc6:amd64 (2.39-3.1ubuntu3) ...
111s Error: Could not restart systemd, systemd binary not working
111s (Reading database ... 
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(Reading database ... 74487 files and directories currently installed.)
111s Preparing to unpack .../libc-bin_2.39-3.1ubuntu3_amd64.deb ...
111s Unpacking libc-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ...
111s Setting up libc-bin (2.39-3.1ubuntu3) ...
111s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 74487 files and directories currently installed.)
111s Preparing to unpack .../libssl3t64_3.2.2-1ubuntu1_amd64.deb ...
111s Unpacking libssl3t64:amd64 (3.2.2-1ubuntu1) over (3.2.1-3ubuntu1) ...
111s Setting up libssl3t64:amd64 (3.2.2-1ubuntu1) ...
111s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 74487 files and directories currently installed.)
111s Preparing to unpack .../00-gir1.2-glib-2.0_2.80.4-1ubuntu1_amd64.deb ...
111s Unpacking gir1.2-glib-2.0:amd64 (2.80.4-1ubuntu1) over (2.80.3-1ubuntu1) ...
111s Preparing to unpack .../01-libglib2.0-0t64_2.80.4-1ubuntu1_amd64.deb ...
111s Unpacking libglib2.0-0t64:amd64 (2.80.4-1ubuntu1) over (2.80.3-1ubuntu1) ...
111s Preparing to unpack .../02-libglib2.0-data_2.80.4-1ubuntu1_all.deb ...
111s Unpacking libglib2.0-data (2.80.4-1ubuntu1) over (2.80.3-1ubuntu1) ...
111s Preparing to unpack .../03-locales_2.39-3.1ubuntu3_all.deb ...
111s Unpacking locales (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ...
111s Preparing to unpack .../04-openssl_3.2.2-1ubuntu1_amd64.deb ...
111s Unpacking openssl (3.2.2-1ubuntu1) over (3.2.1-3ubuntu1) ...
111s Preparing to unpack .../05-libnghttp2-14_1.62.1-2_amd64.deb ...
111s Unpacking libnghttp2-14:amd64 (1.62.1-2) over (1.62.1-1) ...
111s Preparing to unpack .../06-libgprofng0_2.42.50.20240710-1ubuntu1_amd64.deb ...
111s Unpacking libgprofng0:amd64 (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ...
111s Preparing to unpack .../07-libctf0_2.42.50.20240710-1ubuntu1_amd64.deb ...
111s Unpacking libctf0:amd64 (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ...
111s Preparing to unpack .../08-libctf-nobfd0_2.42.50.20240710-1ubuntu1_amd64.deb ...
111s Unpacking libctf-nobfd0:amd64 (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ...
112s Preparing to unpack .../09-binutils-x86-64-linux-gnu_2.42.50.20240710-1ubuntu1_amd64.deb ...
112s Unpacking binutils-x86-64-linux-gnu (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ...
112s Preparing to unpack .../10-libbinutils_2.42.50.20240710-1ubuntu1_amd64.deb ...
112s Unpacking libbinutils:amd64 (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ...
112s Preparing to unpack .../11-binutils_2.42.50.20240710-1ubuntu1_amd64.deb ...
112s Unpacking binutils (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ...
112s Preparing to unpack .../12-binutils-common_2.42.50.20240710-1ubuntu1_amd64.deb ...
112s Unpacking binutils-common:amd64 (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ...
112s Preparing to unpack .../13-libsframe1_2.42.50.20240710-1ubuntu1_amd64.deb ...
112s Unpacking libsframe1:amd64 (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ...
112s Preparing to unpack .../14-libnss3_2%3a3.102-1_amd64.deb ...
112s Unpacking libnss3:amd64 (2:3.102-1) over (2:3.101-1) ...
112s Setting up binutils-common:amd64 (2.42.50.20240710-1ubuntu1) ...
112s Setting up libnghttp2-14:amd64 (1.62.1-2) ...
112s Setting up libctf-nobfd0:amd64 (2.42.50.20240710-1ubuntu1) ...
112s Setting up libnss3:amd64 (2:3.102-1) ...
112s Setting up locales (2.39-3.1ubuntu3) ...
113s Generating locales (this might take a while)...
114s   en_US.UTF-8... done
114s Generation complete.
114s Setting up libsframe1:amd64 (2.42.50.20240710-1ubuntu1) ...
114s Setting up libglib2.0-0t64:amd64 (2.80.4-1ubuntu1) ...
114s No schema files found: doing nothing.
114s Setting up libglib2.0-data (2.80.4-1ubuntu1) ...
114s Setting up gir1.2-glib-2.0:amd64 (2.80.4-1ubuntu1) ...
114s Setting up libbinutils:amd64 (2.42.50.20240710-1ubuntu1) ...
114s Setting up libc-dev-bin (2.39-3.1ubuntu3) ...
114s Setting up openssl (3.2.2-1ubuntu1) ...
114s Installing new version of config file /etc/ssl/openssl.cnf ...
114s Setting up libc-devtools (2.39-3.1ubuntu3) ...
114s Setting up libctf0:amd64 (2.42.50.20240710-1ubuntu1) ...
114s Setting up libgprofng0:amd64 (2.42.50.20240710-1ubuntu1) ...
114s Setting up libc6-dev:amd64 (2.39-3.1ubuntu3) ...
114s Setting up binutils-x86-64-linux-gnu (2.42.50.20240710-1ubuntu1) ...
114s Setting up binutils (2.42.50.20240710-1ubuntu1) ...
114s Processing triggers for libc-bin (2.39-3.1ubuntu3) ...
114s Processing triggers for systemd (256-1ubuntu1) ...
115s Processing triggers for man-db (2.12.1-2) ...
116s Reading package lists...
117s Building dependency tree...
117s Reading state information...
117s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
117s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease
117s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease
117s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease
117s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease
119s Reading package lists...
119s Reading package lists...
119s Building dependency tree...
119s Reading state information...
119s Calculating upgrade...
120s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
120s Reading package lists...
120s Building dependency tree...
120s Reading state information...
120s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
121s autopkgtest [13:29:48]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 00:40:06 UTC 2024
121s autopkgtest [13:29:48]: @@@@@@@@@@@@@@@@@@@@ apt-source abpoa
122s Get:1 http://ftpmaster.internal/ubuntu oracular/universe abpoa 1.5.1-1build1 (dsc) [2125 B]
122s Get:2 http://ftpmaster.internal/ubuntu oracular/universe abpoa 1.5.1-1build1 (tar) [160 kB]
122s Get:3 http://ftpmaster.internal/ubuntu oracular/universe abpoa 1.5.1-1build1 (diff) [9200 B]
122s gpgv: Signature made Wed Apr 10 18:35:09 2024 UTC
122s gpgv:                using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2
122s gpgv: Can't check signature: No public key
122s dpkg-source: warning: cannot verify inline signature for ./abpoa_1.5.1-1build1.dsc: no acceptable signature found
122s autopkgtest [13:29:49]: testing package abpoa version 1.5.1-1build1
122s autopkgtest [13:29:49]: build not needed
122s autopkgtest [13:29:49]: test run-unit-test: preparing testbed
123s Reading package lists...
123s Building dependency tree...
123s Reading state information...
124s Starting pkgProblemResolver with broken count: 0
124s Starting 2 pkgProblemResolver with broken count: 0
124s Done
124s The following additional packages will be installed:
124s   abpoa fontconfig graphviz libann0 libcairo2 libcdt5 libcgraph6 libdatrie1
124s   libgraphite2-3 libgts-0.7-5t64 libgvc6 libgvpr2 libharfbuzz0b libice6
124s   liblab-gamut1 libltdl7 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
124s   libpathplan4 libpixman-1-0 libsm6 libthai-data libthai0 libxaw7
124s   libxcb-render0 libxcb-shm0 libxmu6 libxrender1 libxt6t64 python3-pyabpoa
124s   x11-common
124s Suggested packages:
124s   gsfonts graphviz-doc
124s Recommended packages:
124s   fonts-liberation libgts-bin
124s The following NEW packages will be installed:
124s   abpoa autopkgtest-satdep fontconfig graphviz libann0 libcairo2 libcdt5
124s   libcgraph6 libdatrie1 libgraphite2-3 libgts-0.7-5t64 libgvc6 libgvpr2
124s   libharfbuzz0b libice6 liblab-gamut1 libltdl7 libpango-1.0-0
124s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpathplan4 libpixman-1-0 libsm6
124s   libthai-data libthai0 libxaw7 libxcb-render0 libxcb-shm0 libxmu6 libxrender1
124s   libxt6t64 python3-pyabpoa x11-common
124s 0 upgraded, 33 newly installed, 0 to remove and 0 not upgraded.
124s Need to get 6764 kB/6765 kB of archives.
124s After this operation, 17.6 MB of additional disk space will be used.
124s Get:1 /tmp/autopkgtest.Ka7E55/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [712 B]
124s Get:2 http://ftpmaster.internal/ubuntu oracular/universe amd64 libann0 amd64 1.1.2+doc-9build1 [25.5 kB]
124s Get:3 http://ftpmaster.internal/ubuntu oracular/universe amd64 libcdt5 amd64 2.42.4-1 [21.6 kB]
124s Get:4 http://ftpmaster.internal/ubuntu oracular/universe amd64 libcgraph6 amd64 2.42.4-1 [44.7 kB]
124s Get:5 http://ftpmaster.internal/ubuntu oracular/universe amd64 libgts-0.7-5t64 amd64 0.7.6+darcs121130-5.2build1 [161 kB]
124s Get:6 http://ftpmaster.internal/ubuntu oracular/main amd64 libpixman-1-0 amd64 0.42.2-1build1 [279 kB]
124s Get:7 http://ftpmaster.internal/ubuntu oracular/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB]
124s Get:8 http://ftpmaster.internal/ubuntu oracular/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B]
124s Get:9 http://ftpmaster.internal/ubuntu oracular/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB]
124s Get:10 http://ftpmaster.internal/ubuntu oracular/main amd64 libcairo2 amd64 1.18.0-3build1 [566 kB]
124s Get:11 http://ftpmaster.internal/ubuntu oracular/main amd64 libltdl7 amd64 2.4.7-7build1 [40.3 kB]
124s Get:12 http://ftpmaster.internal/ubuntu oracular/main amd64 fontconfig amd64 2.15.0-1.1ubuntu2 [180 kB]
124s Get:13 http://ftpmaster.internal/ubuntu oracular/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB]
124s Get:14 http://ftpmaster.internal/ubuntu oracular/main amd64 libharfbuzz0b amd64 8.3.0-2build2 [469 kB]
124s Get:15 http://ftpmaster.internal/ubuntu oracular/main amd64 libthai-data all 0.1.29-2build1 [158 kB]
124s Get:16 http://ftpmaster.internal/ubuntu oracular/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB]
124s Get:17 http://ftpmaster.internal/ubuntu oracular/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB]
124s Get:18 http://ftpmaster.internal/ubuntu oracular/main amd64 libpango-1.0-0 amd64 1.54.0+ds-1 [233 kB]
124s Get:19 http://ftpmaster.internal/ubuntu oracular/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-1 [42.3 kB]
124s Get:20 http://ftpmaster.internal/ubuntu oracular/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-1 [28.7 kB]
124s Get:21 http://ftpmaster.internal/ubuntu oracular/universe amd64 libpathplan4 amd64 2.42.4-1 [24.0 kB]
124s Get:22 http://ftpmaster.internal/ubuntu oracular/universe amd64 libgvc6 amd64 2.42.4-1 [716 kB]
124s Get:23 http://ftpmaster.internal/ubuntu oracular/universe amd64 libgvpr2 amd64 2.42.4-1 [187 kB]
124s Get:24 http://ftpmaster.internal/ubuntu oracular/universe amd64 liblab-gamut1 amd64 2.42.4-1 [1898 kB]
124s Get:25 http://ftpmaster.internal/ubuntu oracular/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB]
124s Get:26 http://ftpmaster.internal/ubuntu oracular/main amd64 libice6 amd64 2:1.0.10-1build3 [41.4 kB]
124s Get:27 http://ftpmaster.internal/ubuntu oracular/main amd64 libsm6 amd64 2:1.2.3-1build3 [15.7 kB]
124s Get:28 http://ftpmaster.internal/ubuntu oracular/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB]
124s Get:29 http://ftpmaster.internal/ubuntu oracular/main amd64 libxmu6 amd64 2:1.1.3-3build2 [47.6 kB]
124s Get:30 http://ftpmaster.internal/ubuntu oracular/main amd64 libxaw7 amd64 2:1.0.14-1build2 [187 kB]
124s Get:31 http://ftpmaster.internal/ubuntu oracular/universe amd64 graphviz amd64 2.42.4-1 [641 kB]
124s Get:32 http://ftpmaster.internal/ubuntu oracular/universe amd64 abpoa amd64 1.5.1-1build1 [243 kB]
124s Get:33 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pyabpoa amd64 1.5.1-1build1 [170 kB]
125s Fetched 6764 kB in 0s (25.8 MB/s)
125s Selecting previously unselected package libann0.
125s (Reading database ... 
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125s Preparing to unpack .../00-libann0_1.1.2+doc-9build1_amd64.deb ...
125s Unpacking libann0 (1.1.2+doc-9build1) ...
125s Selecting previously unselected package libcdt5:amd64.
125s Preparing to unpack .../01-libcdt5_2.42.4-1_amd64.deb ...
125s Unpacking libcdt5:amd64 (2.42.4-1) ...
125s Selecting previously unselected package libcgraph6:amd64.
125s Preparing to unpack .../02-libcgraph6_2.42.4-1_amd64.deb ...
125s Unpacking libcgraph6:amd64 (2.42.4-1) ...
125s Selecting previously unselected package libgts-0.7-5t64:amd64.
125s Preparing to unpack .../03-libgts-0.7-5t64_0.7.6+darcs121130-5.2build1_amd64.deb ...
125s Unpacking libgts-0.7-5t64:amd64 (0.7.6+darcs121130-5.2build1) ...
125s Selecting previously unselected package libpixman-1-0:amd64.
125s Preparing to unpack .../04-libpixman-1-0_0.42.2-1build1_amd64.deb ...
125s Unpacking libpixman-1-0:amd64 (0.42.2-1build1) ...
125s Selecting previously unselected package libxcb-render0:amd64.
125s Preparing to unpack .../05-libxcb-render0_1.17.0-2_amd64.deb ...
125s Unpacking libxcb-render0:amd64 (1.17.0-2) ...
125s Selecting previously unselected package libxcb-shm0:amd64.
125s Preparing to unpack .../06-libxcb-shm0_1.17.0-2_amd64.deb ...
125s Unpacking libxcb-shm0:amd64 (1.17.0-2) ...
125s Selecting previously unselected package libxrender1:amd64.
125s Preparing to unpack .../07-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ...
125s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ...
125s Selecting previously unselected package libcairo2:amd64.
125s Preparing to unpack .../08-libcairo2_1.18.0-3build1_amd64.deb ...
125s Unpacking libcairo2:amd64 (1.18.0-3build1) ...
125s Selecting previously unselected package libltdl7:amd64.
125s Preparing to unpack .../09-libltdl7_2.4.7-7build1_amd64.deb ...
125s Unpacking libltdl7:amd64 (2.4.7-7build1) ...
125s Selecting previously unselected package fontconfig.
125s Preparing to unpack .../10-fontconfig_2.15.0-1.1ubuntu2_amd64.deb ...
125s Unpacking fontconfig (2.15.0-1.1ubuntu2) ...
125s Selecting previously unselected package libgraphite2-3:amd64.
125s Preparing to unpack .../11-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ...
125s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ...
125s Selecting previously unselected package libharfbuzz0b:amd64.
125s Preparing to unpack .../12-libharfbuzz0b_8.3.0-2build2_amd64.deb ...
125s Unpacking libharfbuzz0b:amd64 (8.3.0-2build2) ...
125s Selecting previously unselected package libthai-data.
125s Preparing to unpack .../13-libthai-data_0.1.29-2build1_all.deb ...
125s Unpacking libthai-data (0.1.29-2build1) ...
125s Selecting previously unselected package libdatrie1:amd64.
125s Preparing to unpack .../14-libdatrie1_0.2.13-3build1_amd64.deb ...
125s Unpacking libdatrie1:amd64 (0.2.13-3build1) ...
125s Selecting previously unselected package libthai0:amd64.
125s Preparing to unpack .../15-libthai0_0.1.29-2build1_amd64.deb ...
125s Unpacking libthai0:amd64 (0.1.29-2build1) ...
125s Selecting previously unselected package libpango-1.0-0:amd64.
125s Preparing to unpack .../16-libpango-1.0-0_1.54.0+ds-1_amd64.deb ...
125s Unpacking libpango-1.0-0:amd64 (1.54.0+ds-1) ...
125s Selecting previously unselected package libpangoft2-1.0-0:amd64.
125s Preparing to unpack .../17-libpangoft2-1.0-0_1.54.0+ds-1_amd64.deb ...
125s Unpacking libpangoft2-1.0-0:amd64 (1.54.0+ds-1) ...
125s Selecting previously unselected package libpangocairo-1.0-0:amd64.
125s Preparing to unpack .../18-libpangocairo-1.0-0_1.54.0+ds-1_amd64.deb ...
125s Unpacking libpangocairo-1.0-0:amd64 (1.54.0+ds-1) ...
126s Selecting previously unselected package libpathplan4:amd64.
126s Preparing to unpack .../19-libpathplan4_2.42.4-1_amd64.deb ...
126s Unpacking libpathplan4:amd64 (2.42.4-1) ...
126s Selecting previously unselected package libgvc6.
126s Preparing to unpack .../20-libgvc6_2.42.4-1_amd64.deb ...
126s Unpacking libgvc6 (2.42.4-1) ...
126s Selecting previously unselected package libgvpr2:amd64.
126s Preparing to unpack .../21-libgvpr2_2.42.4-1_amd64.deb ...
126s Unpacking libgvpr2:amd64 (2.42.4-1) ...
126s Selecting previously unselected package liblab-gamut1:amd64.
126s Preparing to unpack .../22-liblab-gamut1_2.42.4-1_amd64.deb ...
126s Unpacking liblab-gamut1:amd64 (2.42.4-1) ...
126s Selecting previously unselected package x11-common.
126s Preparing to unpack .../23-x11-common_1%3a7.7+23ubuntu3_all.deb ...
126s Unpacking x11-common (1:7.7+23ubuntu3) ...
126s Selecting previously unselected package libice6:amd64.
126s Preparing to unpack .../24-libice6_2%3a1.0.10-1build3_amd64.deb ...
126s Unpacking libice6:amd64 (2:1.0.10-1build3) ...
126s Selecting previously unselected package libsm6:amd64.
126s Preparing to unpack .../25-libsm6_2%3a1.2.3-1build3_amd64.deb ...
126s Unpacking libsm6:amd64 (2:1.2.3-1build3) ...
126s Selecting previously unselected package libxt6t64:amd64.
126s Preparing to unpack .../26-libxt6t64_1%3a1.2.1-1.2build1_amd64.deb ...
126s Unpacking libxt6t64:amd64 (1:1.2.1-1.2build1) ...
126s Selecting previously unselected package libxmu6:amd64.
126s Preparing to unpack .../27-libxmu6_2%3a1.1.3-3build2_amd64.deb ...
126s Unpacking libxmu6:amd64 (2:1.1.3-3build2) ...
126s Selecting previously unselected package libxaw7:amd64.
126s Preparing to unpack .../28-libxaw7_2%3a1.0.14-1build2_amd64.deb ...
126s Unpacking libxaw7:amd64 (2:1.0.14-1build2) ...
126s Selecting previously unselected package graphviz.
126s Preparing to unpack .../29-graphviz_2.42.4-1_amd64.deb ...
126s Unpacking graphviz (2.42.4-1) ...
126s Selecting previously unselected package abpoa.
126s Preparing to unpack .../30-abpoa_1.5.1-1build1_amd64.deb ...
126s Unpacking abpoa (1.5.1-1build1) ...
126s Selecting previously unselected package python3-pyabpoa.
126s Preparing to unpack .../31-python3-pyabpoa_1.5.1-1build1_amd64.deb ...
126s Unpacking python3-pyabpoa (1.5.1-1build1) ...
126s Selecting previously unselected package autopkgtest-satdep.
126s Preparing to unpack .../32-1-autopkgtest-satdep.deb ...
126s Unpacking autopkgtest-satdep (0) ...
126s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ...
126s Setting up libpixman-1-0:amd64 (0.42.2-1build1) ...
126s Setting up fontconfig (2.15.0-1.1ubuntu2) ...
128s Regenerating fonts cache... done.
128s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ...
128s Setting up libdatrie1:amd64 (0.2.13-3build1) ...
128s Setting up python3-pyabpoa (1.5.1-1build1) ...
128s Setting up libxcb-render0:amd64 (1.17.0-2) ...
128s Setting up liblab-gamut1:amd64 (2.42.4-1) ...
128s Setting up x11-common (1:7.7+23ubuntu3) ...
129s Setting up libxcb-shm0:amd64 (1.17.0-2) ...
129s Setting up libcairo2:amd64 (1.18.0-3build1) ...
129s Setting up libpathplan4:amd64 (2.42.4-1) ...
129s Setting up libann0 (1.1.2+doc-9build1) ...
129s Setting up libltdl7:amd64 (2.4.7-7build1) ...
129s Setting up libharfbuzz0b:amd64 (8.3.0-2build2) ...
129s Setting up libthai-data (0.1.29-2build1) ...
129s Setting up libgts-0.7-5t64:amd64 (0.7.6+darcs121130-5.2build1) ...
129s Setting up libcdt5:amd64 (2.42.4-1) ...
129s Setting up libcgraph6:amd64 (2.42.4-1) ...
129s Setting up libice6:amd64 (2:1.0.10-1build3) ...
129s Setting up libthai0:amd64 (0.1.29-2build1) ...
129s Setting up libgvpr2:amd64 (2.42.4-1) ...
129s Setting up libsm6:amd64 (2:1.2.3-1build3) ...
129s Setting up libpango-1.0-0:amd64 (1.54.0+ds-1) ...
129s Setting up libxt6t64:amd64 (1:1.2.1-1.2build1) ...
129s Setting up libpangoft2-1.0-0:amd64 (1.54.0+ds-1) ...
129s Setting up libpangocairo-1.0-0:amd64 (1.54.0+ds-1) ...
129s Setting up libxmu6:amd64 (2:1.1.3-3build2) ...
129s Setting up libxaw7:amd64 (2:1.0.14-1build2) ...
129s Setting up libgvc6 (2.42.4-1) ...
129s Setting up graphviz (2.42.4-1) ...
129s Setting up abpoa (1.5.1-1build1) ...
129s Setting up autopkgtest-satdep (0) ...
129s Processing triggers for man-db (2.12.1-2) ...
129s Processing triggers for libc-bin (2.39-3.1ubuntu3) ...
131s (Reading database ... 74847 files and directories currently installed.)
131s Removing autopkgtest-satdep (0) ...
132s autopkgtest [13:29:59]: test run-unit-test: [-----------------------
132s + for SIMDE in avx2 avx sse4.1 ssse3 sse3 generic dispatch
132s + '[' avx2 = dispatch ']'
132s + '[' avx2 = generic ']'
132s + grep -q avx2 /proc/cpuinfo
132s + command -v abpoa.avx2
132s + BINARY=abpoa.avx2
132s + abpoa.avx2 ./test_data/seq.fa
132s [main] CMD:  abpoa.avx2 ./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.avx2 ./test_data/heter.fa
132s [main] CMD:  abpoa.avx2 ./test_data/heter.fa
132s [abpoa_main] Real time: 0.014 sec; CPU: 0.015 sec; Peak RSS: 0.009 GB.
132s + abpoa.avx2 -r1 ./test_data/seq.fa
132s [main] CMD:  abpoa.avx2 -r1 ./test_data/seq.fa
132s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.002 GB.
132s + diff - out.msa
132s + abpoa.avx2 -r2 ./test_data/seq.fa
132s [main] CMD:  abpoa.avx2 -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.avx2 -r3 ./test_data/seq.fa
132s [main] CMD:  abpoa.avx2 -r3 ./test_data/seq.fa
132s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.002 GB.
132s + diff - out.gfa
132s + abpoa.avx2 -r4 ./test_data/seq.fa
132s [main] CMD:  abpoa.avx2 -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.avx2 -i in.gfa ./test_data/seq.fa -r3
132s [main] CMD:  abpoa.avx2 -i in.gfa -r3 ./test_data/seq.fa
132s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.002 GB.
132s + diff - out.gfa
132s + abpoa.avx2 -i in.msa ./test_data/seq.fa -r1
132s [main] CMD:  abpoa.avx2 -i in.msa -r1 ./test_data/seq.fa
132s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.002 GB.
132s + diff - out.msa
132s + abpoa.avx2 ./test_data/seq.fa -g poa.png
132s [main] CMD:  abpoa.avx2 -g poa.png ./test_data/seq.fa
132s [abpoa_main] Real time: 0.568 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB.
132s + diff - cons.fa
132s + abpoa.avx2 ./test_data/heter.fa -d2
132s [main] CMD:  abpoa.avx2 -d2 ./test_data/heter.fa
132s [abpoa_main] Real time: 0.015 sec; CPU: 0.016 sec; Peak RSS: 0.010 GB.
132s >Consensus_sequence
132s CCATTCCCACCATCCTTACCATCAACATCACCATCCCCACCATCCCCAACACCATTCCCACCATCCCTACCATCACCATCACCATCCCCACCAACATCCCCACCACCATCCTCACTACCATCCCCACCACCATTTCCACCATTCCCACCACAGTCACCATCACCCCCACCATCCCCATCATCATCCGCACCATCCCCACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCTCCACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCATCCCCACCGCCATCCTCGTTACCATCCCCACCACCTTTTCCACCATCCCCACCATCCCCACCACCTTCTCCACCATCATTCTCACCATCCCCACCACCATCTCCACCACCATTCTCACCATCTCCACCACCATCTCCACCATCCCCATTCTCACCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCATCATCCCCACCATCC
132s + for SIMDE in avx2 avx sse4.1 ssse3 sse3 generic dispatch
132s + '[' avx = dispatch ']'
132s + '[' avx = generic ']'
132s + grep -q avx /proc/cpuinfo
132s + command -v abpoa.avx
132s + BINARY=abpoa.avx
132s + abpoa.avx ./test_data/seq.fa
132s [main] CMD:  abpoa.avx ./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.avx ./test_data/heter.fa
132s [main] CMD:  abpoa.avx ./test_data/heter.fa
132s [abpoa_main] Real time: 0.016 sec; CPU: 0.017 sec; Peak RSS: 0.009 GB.
132s + abpoa.avx -r1 ./test_data/seq.fa
132s [main] CMD:  abpoa.avx -r1 ./test_data/seq.fa
132s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.002 GB.
132s + diff - out.msa
132s + abpoa.avx -r2 ./test_data/seq.fa
132s [main] CMD:  abpoa.avx -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.avx -r3 ./test_data/seq.fa
132s [main] CMD:  abpoa.avx -r3 ./test_data/seq.fa
132s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.002 GB.
132s + diff - out.gfa
132s + abpoa.avx -r4 ./test_data/seq.fa
132s [main] CMD:  abpoa.avx -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.avx -i in.gfa ./test_data/seq.fa -r3
132s [main] CMD:  abpoa.avx -i in.gfa -r3 ./test_data/seq.fa
132s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.002 GB.
132s + diff - out.gfa
132s + abpoa.avx -i in.msa ./test_data/seq.fa -r1
132s [main] CMD:  abpoa.avx -i in.msa -r1 ./test_data/seq.fa
132s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.002 GB.
132s + diff - out.msa
132s + abpoa.avx ./test_data/seq.fa -g poa.png
132s [main] CMD:  abpoa.avx -g poa.png ./test_data/seq.fa
133s [abpoa_main] Real time: 0.505 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB.
133s + diff - cons.fa
133s + abpoa.avx ./test_data/heter.fa -d2
133s [main] CMD:  abpoa.avx -d2 ./test_data/heter.fa
133s >Consensus_sequence_1 0,2,3,4,6,8,9,11,12
133s CCATTCCCACCATCCTTACCATCAACATCACCATCCCCACCATCCCCAACACCATTCCCACCATCCCTACCATCACCATCACCATCCCCACCAACATCCCCACCACCATCCTCACTACCATCCCCACCACCATTTCCACCATTCCCACCACAGTCACCATCACCCCCACCATCCCCATCATCATCCGCACCATCCCCACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCATCCCCACCGCCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCTCCAACACCTCCTCCACCATCATCCCCACCATCCCCACCACCTTCTCCACCATCATTCTCACCATCCCCACCACCATCTCCACCACCATTCTCACCATCTCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCATCATCCCCACCATCC
133s >Consensus_sequence_2 1,5,7,10,13,14
133s CCATTCCCACCATCCTTACCATCAACATCACCATCCCCACCATCCCCAACACCATTCCCACCATCCCTACCATCACCATCACCATCCCCACCAACATCCCCACCACCATCCTCACTACCATCCCCACCACCATTTCCACCATTCCCACCACAGTCACCATCACCCCCACCATCCCCATCAACATCCGCACCATCCCCACCATCCCCAACACCATTCCCACCATCCCTACCATCACCATCACCATCCCCACCAACATCCCCACCACCATCCTCACTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCAGTCACCATCACCACCACCATCCCCATCATCATCCCCACCACCATTTCCACCATTCCCCACCATCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCTCCAACACCTCCCCCACCATCATTCCCACCATCTCCAACACCTCCCCCACCATCATCCCCACCATCCCCACCACCTTCTCCACCATCATTCTCACCATCCCCACCACCATCTCCACCATCCCCATTCTCACCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCATCATCCCCACCATCC
133s [abpoa_main] Real time: 0.020 sec; CPU: 0.021 sec; Peak RSS: 0.009 GB.
133s + for SIMDE in avx2 avx sse4.1 ssse3 sse3 generic dispatch
133s + '[' sse4.1 = dispatch ']'
133s + '[' sse4.1 = generic ']'
133s + grep -q sse4.1 /proc/cpuinfo
133s + command -v abpoa.sse4.1
133s + BINARY=abpoa.sse4.1
133s + abpoa.sse4.1 ./test_data/seq.fa
133s [main] CMD:  abpoa.sse4.1 ./test_data/seq.fa
133s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB.
133s + diff - cons.fa
133s + abpoa.sse4.1 ./test_data/heter.fa
133s [main] CMD:  abpoa.sse4.1 ./test_data/heter.fa
133s [abpoa_main] Real time: 0.018 sec; CPU: 0.019 sec; Peak RSS: 0.009 GB.
133s + abpoa.sse4.1 -r1 ./test_data/seq.fa
133s [main] CMD:  abpoa.sse4.1 -r1 ./test_data/seq.fa
133s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.002 GB.
133s + diff - out.msa
133s + abpoa.sse4.1 -r2 ./test_data/seq.fa
133s [main] CMD:  abpoa.sse4.1 -r2 ./test_data/seq.fa
133s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB.
133s + diff - out_cons.msa
133s + abpoa.sse4.1 -r3 ./test_data/seq.fa
133s [main] CMD:  abpoa.sse4.1 -r3 ./test_data/seq.fa
133s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.002 GB.
133s + diff - out.gfa
133s + abpoa.sse4.1 -r4 ./test_data/seq.fa
133s [main] CMD:  abpoa.sse4.1 -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.sse4.1 -i in.gfa ./test_data/seq.fa -r3
133s [main] CMD:  abpoa.sse4.1 -i in.gfa -r3 ./test_data/seq.fa
133s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.002 GB.
133s + diff - out.gfa
133s + abpoa.sse4.1 -i in.msa ./test_data/seq.fa -r1
133s [main] CMD:  abpoa.sse4.1 -i in.msa -r1 ./test_data/seq.fa
133s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.002 GB.
133s + diff - out.msa
133s + abpoa.sse4.1 ./test_data/seq.fa -g poa.png
133s [main] CMD:  abpoa.sse4.1 -g poa.png ./test_data/seq.fa
134s [abpoa_main] Real time: 0.540 sec; CPU: 0.003 sec; Peak RSS: 0.003 GB.
134s + diff - cons.fa
134s + abpoa.sse4.1 ./test_data/heter.fa -d2
134s [main] CMD:  abpoa.sse4.1 -d2 ./test_data/heter.fa
134s >Consensus_sequence_1 0,2,3,4,6,8,9,11,12
134s CCATTCCCACCATCCTTACCATCAACATCACCATCCCCACCATCCCCAACACCATTCCCACCATCCCTACCATCACCATCACCATCCCCACCAACATCCCCACCACCATCCTCACTACCATCCCCACCACCATTTCCACCATTCCCACCACAGTCACCATCACCCCCACCATCCCCATCATCATCCGCACCATCCCCACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCATCCCCACCGCCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCTCCAACACCTCCTCCACCATCATCCCCACCATCCCCACCACCTTCTCCACCATCATTCTCACCATCCCCACCACCATCTCCACCACCATTCTCACCATCTCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCATCATCCCCACCATCC
134s >Consensus_sequence_2 1,5,7,10,13,14
134s CCATTCCCACCATCCTTACCATCAACATCACCATCCCCACCATCCCCAACACCATTCCCACCATCCCTACCATCACCATCACCATCCCCACCAACATCCCCACCACCATCCTCACTACCATCCCCACCACCATTTCCACCATTCCCACCACAGTCACCATCACCCCCACCATCCCCATCAACATCCGCACCATCCCCACCATCCCCAACACCATTCCCACCATCCCTACCATCACCATCACCATCCCCACCAACATCCCCACCACCATCCTCACTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCAGTCACCATCACCACCACCATCCCCATCATCATCCCCACCACCATTTCCACCATTCCCCACCATCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCTCCAACACCTCCCCCACCATCATTCCCACCATCTCCAACACCTCCCCCACCATCATCCCCACCATCCCCACCACCTTCTCCACCATCATTCTCACCATCCCCACCACCATCTCCACCATCCCCATTCTCACCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCATCATCCCCACCATCC
134s [abpoa_main] Real time: 0.016 sec; CPU: 0.017 sec; Peak RSS: 0.009 GB.
134s + for SIMDE in avx2 avx sse4.1 ssse3 sse3 generic dispatch
134s + '[' ssse3 = dispatch ']'
134s + '[' ssse3 = generic ']'
134s + grep -q ssse3 /proc/cpuinfo
134s + command -v abpoa.ssse3
134s + BINARY=abpoa.ssse3
134s + abpoa.ssse3 ./test_data/seq.fa
134s [main] CMD:  abpoa.ssse3 ./test_data/seq.fa
134s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB.
134s + diff - cons.fa
134s + abpoa.ssse3 ./test_data/heter.fa
134s [main] CMD:  abpoa.ssse3 ./test_data/heter.fa
134s [abpoa_main] Real time: 0.016 sec; CPU: 0.017 sec; Peak RSS: 0.009 GB.
134s + abpoa.ssse3 -r1 ./test_data/seq.fa
134s [main] CMD:  abpoa.ssse3 -r1 ./test_data/seq.fa
134s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.002 GB.
134s + diff - out.msa
134s + abpoa.ssse3 -r2 ./test_data/seq.fa
134s [main] CMD:  abpoa.ssse3 -r2 ./test_data/seq.fa
134s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB.
134s + diff - out_cons.msa
134s + abpoa.ssse3 -r3 ./test_data/seq.fa
134s [main] CMD:  abpoa.ssse3 -r3 ./test_data/seq.fa
134s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.002 GB.
134s + diff - out.gfa
134s + abpoa.ssse3 -r4 ./test_data/seq.fa
134s [main] CMD:  abpoa.ssse3 -r4 ./test_data/seq.fa
134s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB.
134s + diff - out4.gfa
134s + cp out.gfa in.gfa
134s + cp out.msa in.msa
134s + abpoa.ssse3 -i in.gfa ./test_data/seq.fa -r3
134s [main] CMD:  abpoa.ssse3 -i in.gfa -r3 ./test_data/seq.fa
134s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.002 GB.
134s + diff - out.gfa
134s + abpoa.ssse3 -i in.msa ./test_data/seq.fa -r1
134s [main] CMD:  abpoa.ssse3 -i in.msa -r1 ./test_data/seq.fa
134s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.002 GB.
134s + diff - out.msa
134s + abpoa.ssse3 ./test_data/seq.fa -g poa.png
134s [main] CMD:  abpoa.ssse3 -g poa.png ./test_data/seq.fa
134s [abpoa_main] Real time: 0.482 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB.
134s + diff - cons.fa
134s + abpoa.ssse3 ./test_data/heter.fa -d2
134s [main] CMD:  abpoa.ssse3 -d2 ./test_data/heter.fa
134s >Consensus_sequence_1 0,2,3,4,6,8,9,11,12
134s CCATTCCCACCATCCTTACCATCAACATCACCATCCCCACCATCCCCAACACCATTCCCACCATCCCTACCATCACCATCACCATCCCCACCAACATCCCCACCACCATCCTCACTACCATCCCCACCACCATTTCCACCATTCCCACCACAGTCACCATCACCCCCACCATCCCCATCATCATCCGCACCATCCCCACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCATCCCCACCGCCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCTCCAACACCTCCTCCACCATCATCCCCACCATCCCCACCACCTTCTCCACCATCATTCTCACCATCCCCACCACCATCTCCACCACCATTCTCACCATCTCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCATCATCCCCACCATCC
134s >Consensus_sequence_2 1,5,7,10,13,14
134s CCATTCCCACCATCCTTACCATCAACATCACCATCCCCACCATCCCCAACACCATTCCCACCATCCCTACCATCACCATCACCATCCCCACCAACATCCCCACCACCATCCTCACTACCATCCCCACCACCATTTCCACCATTCCCACCACAGTCACCATCACCCCCACCATCCCCATCAACATCCGCACCATCCCCACCATCCCCAACACCATTCCCACCATCCCTACCATCACCATCACCATCCCCACCAACATCCCCACCACCATCCTCACTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCAGTCACCATCACCACCACCATCCCCATCATCATCCCCACCACCATTTCCACCATTCCCCACCATCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCTCCAACACCTCCCCCACCATCATTCCCACCATCTCCAACACCTCCCCCACCATCATCCCCACCATCCCCACCACCTTCTCCACCATCATTCTCACCATCCCCACCACCATCTCCACCATCCCCATTCTCACCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCATCATCCCCACCATCC
134s [abpoa_main] Real time: 0.016 sec; CPU: 0.017 sec; Peak RSS: 0.009 GB.
134s + for SIMDE in avx2 avx sse4.1 ssse3 sse3 generic dispatch
134s + '[' sse3 = dispatch ']'
134s + '[' sse3 = generic ']'
134s + grep -q sse3 /proc/cpuinfo
134s + command -v abpoa.sse3
134s + BINARY=abpoa.sse3
134s + abpoa.sse3 ./test_data/seq.fa
134s [main] CMD:  abpoa.sse3 ./test_data/seq.fa
134s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB.
134s + diff - cons.fa
134s + abpoa.sse3 ./test_data/heter.fa
134s [main] CMD:  abpoa.sse3 ./test_data/heter.fa
134s [abpoa_main] Real time: 0.016 sec; CPU: 0.017 sec; Peak RSS: 0.009 GB.
134s + abpoa.sse3 -r1 ./test_data/seq.fa
134s [main] CMD:  abpoa.sse3 -r1 ./test_data/seq.fa
134s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.002 GB.
134s + diff - out.msa
134s + abpoa.sse3 -r2 ./test_data/seq.fa
134s [main] CMD:  abpoa.sse3 -r2 ./test_data/seq.fa
134s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB.
134s + diff - out_cons.msa
134s + abpoa.sse3 -r3 ./test_data/seq.fa
134s [main] CMD:  abpoa.sse3 -r3 ./test_data/seq.fa
134s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.002 GB.
134s + diff - out.gfa
134s + abpoa.sse3 -r4 ./test_data/seq.fa
134s [main] CMD:  abpoa.sse3 -r4 ./test_data/seq.fa
134s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB.
134s + diff - out4.gfa
134s + cp out.gfa in.gfa
134s + cp out.msa in.msa
134s + abpoa.sse3 -i in.gfa ./test_data/seq.fa -r3
134s [main] CMD:  abpoa.sse3 -i in.gfa -r3 ./test_data/seq.fa
134s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.002 GB.
134s + diff - out.gfa
134s + abpoa.sse3 -i in.msa ./test_data/seq.fa -r1
134s [main] CMD:  abpoa.sse3 -i in.msa -r1 ./test_data/seq.fa
134s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.002 GB.
134s + diff - out.msa
134s + abpoa.sse3 ./test_data/seq.fa -g poa.png
134s [main] CMD:  abpoa.sse3 -g poa.png ./test_data/seq.fa
135s [abpoa_main] Real time: 0.486 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB.
135s + diff - cons.fa
135s + abpoa.sse3 ./test_data/heter.fa -d2
135s [main] CMD:  abpoa.sse3 -d2 ./test_data/heter.fa
135s >Consensus_sequence_1 0,2,3,4,6,8,9,11,12
135s CCATTCCCACCATCCTTACCATCAACATCACCATCCCCACCATCCCCAACACCATTCCCACCATCCCTACCATCACCATCACCATCCCCACCAACATCCCCACCACCATCCTCACTACCATCCCCACCACCATTTCCACCATTCCCACCACAGTCACCATCACCCCCACCATCCCCATCATCATCCGCACCATCCCCACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCATCCCCACCGCCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCTCCAACACCTCCTCCACCATCATCCCCACCATCCCCACCACCTTCTCCACCATCATTCTCACCATCCCCACCACCATCTCCACCACCATTCTCACCATCTCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCATCATCCCCACCATCC
135s >Consensus_sequence_2 1,5,7,10,13,14
135s CCATTCCCACCATCCTTACCATCAACATCACCATCCCCACCATCCCCAACACCATTCCCACCATCCCTACCATCACCATCACCATCCCCACCAACATCCCCACCACCATCCTCACTACCATCCCCACCACCATTTCCACCATTCCCACCACAGTCACCATCACCCCCACCATCCCCATCAACATCCGCACCATCCCCACCATCCCCAACACCATTCCCACCATCCCTACCATCACCATCACCATCCCCACCAACATCCCCACCACCATCCTCACTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCAGTCACCATCACCACCACCATCCCCATCATCATCCCCACCACCATTTCCACCATTCCCCACCATCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCTCCAACACCTCCCCCACCATCATTCCCACCATCTCCAACACCTCCCCCACCATCATCCCCACCATCCCCACCACCTTCTCCACCATCATTCTCACCATCCCCACCACCATCTCCACCATCCCCATTCTCACCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCATCATCCCCACCATCC
135s [abpoa_main] Real time: 0.016 sec; CPU: 0.017 sec; Peak RSS: 0.009 GB.
135s + for SIMDE in avx2 avx sse4.1 ssse3 sse3 generic dispatch
135s + '[' generic = dispatch ']'
135s + '[' generic = generic ']'
135s + command -v abpoa.generic
135s + BINARY=abpoa.generic
135s + abpoa.generic ./test_data/seq.fa
135s [main] CMD:  abpoa.generic ./test_data/seq.fa
135s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB.
135s + diff - cons.fa
135s + abpoa.generic ./test_data/heter.fa
135s [main] CMD:  abpoa.generic ./test_data/heter.fa
135s [abpoa_main] Real time: 0.015 sec; CPU: 0.016 sec; Peak RSS: 0.009 GB.
135s + abpoa.generic -r1 ./test_data/seq.fa
135s [main] CMD:  abpoa.generic -r1 ./test_data/seq.fa
135s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.002 GB.
135s + diff - out.msa
135s + abpoa.generic -r2 ./test_data/seq.fa
135s [main] CMD:  abpoa.generic -r2 ./test_data/seq.fa
135s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB.
135s + diff - out_cons.msa
135s + abpoa.generic -r3 ./test_data/seq.fa
135s [main] CMD:  abpoa.generic -r3 ./test_data/seq.fa
135s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.002 GB.
135s + diff - out.gfa
135s + abpoa.generic -r4 ./test_data/seq.fa
135s [main] CMD:  abpoa.generic -r4 ./test_data/seq.fa
135s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB.
135s + diff - out4.gfa
135s + cp out.gfa in.gfa
135s + cp out.msa in.msa
135s + abpoa.generic -i in.gfa ./test_data/seq.fa -r3
135s [main] CMD:  abpoa.generic -i in.gfa -r3 ./test_data/seq.fa
135s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.002 GB.
135s + diff - out.gfa
135s + abpoa.generic -i in.msa ./test_data/seq.fa -r1
135s [main] CMD:  abpoa.generic -i in.msa -r1 ./test_data/seq.fa
135s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.002 GB.
135s + diff - out.msa
135s + abpoa.generic ./test_data/seq.fa -g poa.png
135s [main] CMD:  abpoa.generic -g poa.png ./test_data/seq.fa
135s [abpoa_main] Real time: 0.479 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB.
135s + diff - cons.fa
135s + abpoa.generic ./test_data/heter.fa -d2
135s [main] CMD:  abpoa.generic -d2 ./test_data/heter.fa
135s >Consensus_sequence_1 0,2,3,4,6,8,9,11,12
135s CCATTCCCACCATCCTTACCATCAACATCACCATCCCCACCATCCCCAACACCATTCCCACCATCCCTACCATCACCATCACCATCCCCACCAACATCCCCACCACCATCCTCACTACCATCCCCACCACCATTTCCACCATTCCCACCACAGTCACCATCACCCCCACCATCCCCATCATCATCCGCACCATCCCCACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCATCCCCACCGCCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCTCCAACACCTCCTCCACCATCATCCCCACCATCCCCACCACCTTCTCCACCATCATTCTCACCATCCCCACCACCATCTCCACCACCATTCTCACCATCTCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCATCATCCCCACCATCC
135s >Consensus_sequence_2 1,5,7,10,13,14
135s CCATTCCCACCATCCTTACCATCAACATCACCATCCCCACCATCCCCAACACCATTCCCACCATCCCTACCATCACCATCACCATCCCCACCAACATCCCCACCACCATCCTCACTACCATCCCCACCACCATTTCCACCATTCCCACCACAGTCACCATCACCCCCACCATCCCCATCAACATCCGCACCATCCCCACCATCCCCAACACCATTCCCACCATCCCTACCATCACCATCACCATCCCCACCAACATCCCCACCACCATCCTCACTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCAGTCACCATCACCACCACCATCCCCATCATCATCCCCACCACCATTTCCACCATTCCCCACCATCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCTCCAACACCTCCCCCACCATCATTCCCACCATCTCCAACACCTCCCCCACCATCATCCCCACCATCCCCACCACCTTCTCCACCATCATTCTCACCATCCCCACCACCATCTCCACCATCCCCATTCTCACCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCATCATCCCCACCATCC
135s [abpoa_main] Real time: 0.016 sec; CPU: 0.017 sec; Peak RSS: 0.009 GB.
135s + for SIMDE in avx2 avx sse4.1 ssse3 sse3 generic dispatch
135s + '[' dispatch = dispatch ']'
135s + BINARY=abpoa
135s + abpoa ./test_data/seq.fa
135s [main] CMD:  /usr/bin/abpoa.avx2 ./test_data/seq.fa
135s [abpoa_main] Real time: 0.001 sec; CPU: 0.003 sec; Peak RSS: 0.003 GB.
135s + diff - cons.fa
135s + abpoa ./test_data/heter.fa
135s [main] CMD:  /usr/bin/abpoa.avx2 ./test_data/heter.fa
135s [abpoa_main] Real time: 0.014 sec; CPU: 0.016 sec; Peak RSS: 0.009 GB.
135s + abpoa -r1 ./test_data/seq.fa
135s [main] CMD:  /usr/bin/abpoa.avx2 -r1 ./test_data/seq.fa
135s [abpoa_main] Real time: 0.001 sec; CPU: 0.003 sec; Peak RSS: 0.002 GB.
135s + diff - out.msa
135s + abpoa -r2 ./test_data/seq.fa
135s [main] CMD:  /usr/bin/abpoa.avx2 -r2 ./test_data/seq.fa
135s [abpoa_main] Real time: 0.001 sec; CPU: 0.003 sec; Peak RSS: 0.003 GB.
135s + diff - out_cons.msa
135s + abpoa -r3 ./test_data/seq.fa
135s [main] CMD:  /usr/bin/abpoa.avx2 -r3 ./test_data/seq.fa
135s [abpoa_main] Real time: 0.001 sec; CPU: 0.003 sec; Peak RSS: 0.002 GB.
135s + diff - out.gfa
135s + abpoa -r4 ./test_data/seq.fa
135s [main] CMD:  /usr/bin/abpoa.avx2 -r4 ./test_data/seq.fa
135s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB.
135s + diff - out4.gfa
135s + cp out.gfa in.gfa
135s + cp out.msa in.msa
135s + abpoa -i in.gfa ./test_data/seq.fa -r3
135s [main] CMD:  /usr/bin/abpoa.avx2 -i in.gfa -r3 ./test_data/seq.fa
135s [abpoa_main] Real time: 0.001 sec; CPU: 0.003 sec; Peak RSS: 0.002 GB.
135s + diff - out.gfa
135s + abpoa -i in.msa ./test_data/seq.fa -r1
135s [main] CMD:  /usr/bin/abpoa.avx2 -i in.msa -r1 ./test_data/seq.fa
135s [abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.002 GB.
135s + diff - out.msa
135s + abpoa ./test_data/seq.fa -g poa.png
135s [main] CMD:  /usr/bin/abpoa.avx2 -g poa.png ./test_data/seq.fa
136s [abpoa_main] Real time: 0.488 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB.
136s + diff - cons.fa
136s + abpoa ./test_data/heter.fa -d2
136s [main] CMD:  /usr/bin/abpoa.avx2 -d2 ./test_data/heter.fa
136s >Consensus_sequence
136s CCATTCCCACCATCCTTACCATCAACATCACCATCCCCACCATCCCCAACACCATTCCCACCATCCCTACCATCACCATCACCATCCCCACCAACATCCCCACCACCATCCTCACTACCATCCCCACCACCATTTCCACCATTCCCACCACAGTCACCATCACCCCCACCATCCCCATCATCATCCGCACCATCCCCACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCTCCACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCATCCCCACCGCCATCCTCGTTACCATCCCCACCACCTTTTCCACCATCCCCACCATCCCCACCACCTTCTCCACCATCATTCTCACCATCCCCACCACCATCTCCACCACCATTCTCACCATCTCCACCACCATCTCCACCATCCCCATTCTCACCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCATCATCCCCACCATCC
136s [abpoa_main] Real time: 0.016 sec; CPU: 0.018 sec; Peak RSS: 0.010 GB.
136s autopkgtest [13:30:03]: test run-unit-test: -----------------------]
136s autopkgtest [13:30:03]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
136s run-unit-test        PASS
136s autopkgtest [13:30:03]: test autodep8-python3: preparing testbed
433s autopkgtest [13:35:00]: testbed dpkg architecture: amd64
433s autopkgtest [13:35:00]: testbed apt version: 2.9.6
433s autopkgtest [13:35:00]: @@@@@@@@@@@@@@@@@@@@ test bed setup
433s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB]
434s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8548 B]
434s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [45.3 kB]
434s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [345 kB]
434s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2576 B]
434s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 Packages [99.7 kB]
434s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main i386 Packages [73.0 kB]
434s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 c-n-f Metadata [2104 B]
434s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 Packages [34.9 kB]
434s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/restricted i386 Packages [6244 B]
434s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 c-n-f Metadata [368 B]
434s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/universe i386 Packages [240 kB]
434s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 Packages [374 kB]
434s Get:14 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 c-n-f Metadata [9228 B]
434s Get:15 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 Packages [7644 B]
434s Get:16 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse i386 Packages [3052 B]
434s Get:17 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 c-n-f Metadata [276 B]
435s Fetched 1378 kB in 0s (4851 kB/s)
435s Reading package lists...
437s Reading package lists...
437s Building dependency tree...
437s Reading state information...
437s Calculating upgrade...
438s The following packages will be upgraded:
438s   binutils binutils-common binutils-x86-64-linux-gnu gir1.2-glib-2.0
438s   libbinutils libc-bin libc-dev-bin libc-devtools libc6 libc6-dev
438s   libctf-nobfd0 libctf0 libglib2.0-0t64 libglib2.0-data libgprofng0
438s   libnghttp2-14 libnss3 libsframe1 libssl3t64 locales openssl
438s 21 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
438s Need to get 21.2 MB of archives.
438s After this operation, 423 kB of additional disk space will be used.
438s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc-devtools amd64 2.39-3.1ubuntu3 [29.3 kB]
438s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc6-dev amd64 2.39-3.1ubuntu3 [2120 kB]
438s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc-dev-bin amd64 2.39-3.1ubuntu3 [20.4 kB]
438s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc6 amd64 2.39-3.1ubuntu3 [3262 kB]
438s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc-bin amd64 2.39-3.1ubuntu3 [680 kB]
438s Get:6 http://ftpmaster.internal/ubuntu oracular/main amd64 libssl3t64 amd64 3.2.2-1ubuntu1 [2138 kB]
438s Get:7 http://ftpmaster.internal/ubuntu oracular/main amd64 gir1.2-glib-2.0 amd64 2.80.4-1ubuntu1 [182 kB]
438s Get:8 http://ftpmaster.internal/ubuntu oracular/main amd64 libglib2.0-0t64 amd64 2.80.4-1ubuntu1 [1545 kB]
438s Get:9 http://ftpmaster.internal/ubuntu oracular/main amd64 libglib2.0-data all 2.80.4-1ubuntu1 [49.3 kB]
438s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 locales all 2.39-3.1ubuntu3 [4220 kB]
438s Get:11 http://ftpmaster.internal/ubuntu oracular/main amd64 openssl amd64 3.2.2-1ubuntu1 [1122 kB]
438s Get:12 http://ftpmaster.internal/ubuntu oracular/main amd64 libnghttp2-14 amd64 1.62.1-2 [75.1 kB]
438s Get:13 http://ftpmaster.internal/ubuntu oracular/main amd64 libgprofng0 amd64 2.42.50.20240710-1ubuntu1 [860 kB]
438s Get:14 http://ftpmaster.internal/ubuntu oracular/main amd64 libctf0 amd64 2.42.50.20240710-1ubuntu1 [95.6 kB]
438s Get:15 http://ftpmaster.internal/ubuntu oracular/main amd64 libctf-nobfd0 amd64 2.42.50.20240710-1ubuntu1 [97.6 kB]
438s Get:16 http://ftpmaster.internal/ubuntu oracular/main amd64 binutils-x86-64-linux-gnu amd64 2.42.50.20240710-1ubuntu1 [2477 kB]
438s Get:17 http://ftpmaster.internal/ubuntu oracular/main amd64 libbinutils amd64 2.42.50.20240710-1ubuntu1 [574 kB]
438s Get:18 http://ftpmaster.internal/ubuntu oracular/main amd64 binutils amd64 2.42.50.20240710-1ubuntu1 [18.1 kB]
438s Get:19 http://ftpmaster.internal/ubuntu oracular/main amd64 binutils-common amd64 2.42.50.20240710-1ubuntu1 [243 kB]
438s Get:20 http://ftpmaster.internal/ubuntu oracular/main amd64 libsframe1 amd64 2.42.50.20240710-1ubuntu1 [14.4 kB]
438s Get:21 http://ftpmaster.internal/ubuntu oracular/main amd64 libnss3 amd64 2:3.102-1 [1399 kB]
438s Preconfiguring packages ...
438s Fetched 21.2 MB in 0s (82.2 MB/s)
439s (Reading database ... 
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439s Preparing to unpack .../libc-devtools_2.39-3.1ubuntu3_amd64.deb ...
439s Unpacking libc-devtools (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ...
439s Preparing to unpack .../libc6-dev_2.39-3.1ubuntu3_amd64.deb ...
439s Unpacking libc6-dev:amd64 (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ...
439s Preparing to unpack .../libc-dev-bin_2.39-3.1ubuntu3_amd64.deb ...
439s Unpacking libc-dev-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ...
439s Preparing to unpack .../libc6_2.39-3.1ubuntu3_amd64.deb ...
439s Unpacking libc6:amd64 (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ...
439s Setting up libc6:amd64 (2.39-3.1ubuntu3) ...
439s Error: Could not restart systemd, systemd binary not working
439s (Reading database ... 
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439s Preparing to unpack .../libc-bin_2.39-3.1ubuntu3_amd64.deb ...
439s Unpacking libc-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ...
439s Setting up libc-bin (2.39-3.1ubuntu3) ...
440s (Reading database ... 
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440s Preparing to unpack .../libssl3t64_3.2.2-1ubuntu1_amd64.deb ...
440s Unpacking libssl3t64:amd64 (3.2.2-1ubuntu1) over (3.2.1-3ubuntu1) ...
440s Setting up libssl3t64:amd64 (3.2.2-1ubuntu1) ...
440s (Reading database ... 
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440s Preparing to unpack .../00-gir1.2-glib-2.0_2.80.4-1ubuntu1_amd64.deb ...
440s Unpacking gir1.2-glib-2.0:amd64 (2.80.4-1ubuntu1) over (2.80.3-1ubuntu1) ...
440s Preparing to unpack .../01-libglib2.0-0t64_2.80.4-1ubuntu1_amd64.deb ...
440s Unpacking libglib2.0-0t64:amd64 (2.80.4-1ubuntu1) over (2.80.3-1ubuntu1) ...
440s Preparing to unpack .../02-libglib2.0-data_2.80.4-1ubuntu1_all.deb ...
440s Unpacking libglib2.0-data (2.80.4-1ubuntu1) over (2.80.3-1ubuntu1) ...
440s Preparing to unpack .../03-locales_2.39-3.1ubuntu3_all.deb ...
440s Unpacking locales (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ...
440s Preparing to unpack .../04-openssl_3.2.2-1ubuntu1_amd64.deb ...
440s Unpacking openssl (3.2.2-1ubuntu1) over (3.2.1-3ubuntu1) ...
440s Preparing to unpack .../05-libnghttp2-14_1.62.1-2_amd64.deb ...
440s Unpacking libnghttp2-14:amd64 (1.62.1-2) over (1.62.1-1) ...
440s Preparing to unpack .../06-libgprofng0_2.42.50.20240710-1ubuntu1_amd64.deb ...
440s Unpacking libgprofng0:amd64 (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ...
440s Preparing to unpack .../07-libctf0_2.42.50.20240710-1ubuntu1_amd64.deb ...
440s Unpacking libctf0:amd64 (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ...
440s Preparing to unpack .../08-libctf-nobfd0_2.42.50.20240710-1ubuntu1_amd64.deb ...
440s Unpacking libctf-nobfd0:amd64 (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ...
440s Preparing to unpack .../09-binutils-x86-64-linux-gnu_2.42.50.20240710-1ubuntu1_amd64.deb ...
440s Unpacking binutils-x86-64-linux-gnu (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ...
440s Preparing to unpack .../10-libbinutils_2.42.50.20240710-1ubuntu1_amd64.deb ...
440s Unpacking libbinutils:amd64 (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ...
440s Preparing to unpack .../11-binutils_2.42.50.20240710-1ubuntu1_amd64.deb ...
440s Unpacking binutils (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ...
440s Preparing to unpack .../12-binutils-common_2.42.50.20240710-1ubuntu1_amd64.deb ...
440s Unpacking binutils-common:amd64 (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ...
440s Preparing to unpack .../13-libsframe1_2.42.50.20240710-1ubuntu1_amd64.deb ...
440s Unpacking libsframe1:amd64 (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ...
441s Preparing to unpack .../14-libnss3_2%3a3.102-1_amd64.deb ...
441s Unpacking libnss3:amd64 (2:3.102-1) over (2:3.101-1) ...
441s Setting up binutils-common:amd64 (2.42.50.20240710-1ubuntu1) ...
441s Setting up libnghttp2-14:amd64 (1.62.1-2) ...
441s Setting up libctf-nobfd0:amd64 (2.42.50.20240710-1ubuntu1) ...
441s Setting up libnss3:amd64 (2:3.102-1) ...
441s Setting up locales (2.39-3.1ubuntu3) ...
441s Generating locales (this might take a while)...
443s   en_US.UTF-8... done
443s Generation complete.
443s Setting up libsframe1:amd64 (2.42.50.20240710-1ubuntu1) ...
443s Setting up libglib2.0-0t64:amd64 (2.80.4-1ubuntu1) ...
443s No schema files found: doing nothing.
443s Setting up libglib2.0-data (2.80.4-1ubuntu1) ...
443s Setting up gir1.2-glib-2.0:amd64 (2.80.4-1ubuntu1) ...
443s Setting up libbinutils:amd64 (2.42.50.20240710-1ubuntu1) ...
443s Setting up libc-dev-bin (2.39-3.1ubuntu3) ...
443s Setting up openssl (3.2.2-1ubuntu1) ...
443s Installing new version of config file /etc/ssl/openssl.cnf ...
443s Setting up libc-devtools (2.39-3.1ubuntu3) ...
443s Setting up libctf0:amd64 (2.42.50.20240710-1ubuntu1) ...
443s Setting up libgprofng0:amd64 (2.42.50.20240710-1ubuntu1) ...
443s Setting up libc6-dev:amd64 (2.39-3.1ubuntu3) ...
443s Setting up binutils-x86-64-linux-gnu (2.42.50.20240710-1ubuntu1) ...
443s Setting up binutils (2.42.50.20240710-1ubuntu1) ...
443s Processing triggers for libc-bin (2.39-3.1ubuntu3) ...
443s Processing triggers for systemd (256-1ubuntu1) ...
443s Processing triggers for man-db (2.12.1-2) ...
445s Reading package lists...
445s Building dependency tree...
445s Reading state information...
446s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
446s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease
446s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease
446s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease
446s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease
447s Reading package lists...
447s Reading package lists...
447s Building dependency tree...
447s Reading state information...
448s Calculating upgrade...
448s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
448s Reading package lists...
448s Building dependency tree...
448s Reading state information...
449s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
450s Reading package lists...
450s Building dependency tree...
450s Reading state information...
450s Starting pkgProblemResolver with broken count: 0
450s Starting 2 pkgProblemResolver with broken count: 0
450s Done
451s The following additional packages will be installed:
451s   python3-all python3-pyabpoa
451s The following NEW packages will be installed:
451s   autopkgtest-satdep python3-all python3-pyabpoa
451s 0 upgraded, 3 newly installed, 0 to remove and 0 not upgraded.
451s Need to get 171 kB/172 kB of archives.
451s After this operation, 436 kB of additional disk space will be used.
451s Get:1 /tmp/autopkgtest.Ka7E55/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [716 B]
451s Get:2 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-all amd64 3.12.3-0ubuntu1 [888 B]
451s Get:3 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pyabpoa amd64 1.5.1-1build1 [170 kB]
451s Fetched 171 kB in 0s (4189 kB/s)
451s Selecting previously unselected package python3-all.
451s (Reading database ... 
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451s Preparing to unpack .../python3-all_3.12.3-0ubuntu1_amd64.deb ...
451s Unpacking python3-all (3.12.3-0ubuntu1) ...
451s Selecting previously unselected package python3-pyabpoa.
451s Preparing to unpack .../python3-pyabpoa_1.5.1-1build1_amd64.deb ...
451s Unpacking python3-pyabpoa (1.5.1-1build1) ...
451s Selecting previously unselected package autopkgtest-satdep.
451s Preparing to unpack .../2-autopkgtest-satdep.deb ...
451s Unpacking autopkgtest-satdep (0) ...
451s Setting up python3-pyabpoa (1.5.1-1build1) ...
451s Setting up python3-all (3.12.3-0ubuntu1) ...
451s Setting up autopkgtest-satdep (0) ...
453s (Reading database ... 74495 files and directories currently installed.)
453s Removing autopkgtest-satdep (0) ...
453s autopkgtest [13:35:20]: 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
453s autopkgtest [13:35:20]: test autodep8-python3: [-----------------------
454s Testing with python3.12:
454s <module 'pyabpoa' from '/usr/lib/python3/dist-packages/pyabpoa.cpython-312-x86_64-linux-gnu.so'>
454s autopkgtest [13:35:21]: test autodep8-python3: -----------------------]
454s autodep8-python3     PASS (superficial)
454s autopkgtest [13:35:21]: test autodep8-python3:  - - - - - - - - - - results - - - - - - - - - -
454s autopkgtest [13:35:21]: @@@@@@@@@@@@@@@@@@@@ summary
454s run-unit-test        PASS
454s autodep8-python3     PASS (superficial)
465s nova [W] Skipping flock for amd64
465s Creating nova instance adt-oracular-amd64-abpoa-20240712-132747-juju-7f2275-prod-proposed-migration-environment-2-5847d891-a89c-46f1-b477-e088ecd25742 from image adt/ubuntu-oracular-amd64-server-20240711.img (UUID 4d65b1cc-a829-44fc-a8ac-cdd52093f9db)...
465s nova [W] Skipping flock for amd64
465s Creating nova instance adt-oracular-amd64-abpoa-20240712-132747-juju-7f2275-prod-proposed-migration-environment-2-5847d891-a89c-46f1-b477-e088ecd25742 from image adt/ubuntu-oracular-amd64-server-20240711.img (UUID 4d65b1cc-a829-44fc-a8ac-cdd52093f9db)...