0s autopkgtest [15:54:21]: starting date and time: 2025-03-15 15:54:21+0000 0s autopkgtest [15:54:21]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [15:54:21]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.iqm7hobb/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade probcons --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-s390x-2.secgroup --name adt-plucky-s390x-probcons-20250315-155420-juju-7f2275-prod-proposed-migration-environment-20-1bec3787-c276-4f4d-a0cd-763d830974bd --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-s390x -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,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 126s autopkgtest [15:56:27]: testbed dpkg architecture: s390x 127s autopkgtest [15:56:28]: testbed apt version: 2.9.33 127s autopkgtest [15:56:28]: @@@@@@@@@@@@@@@@@@@@ test bed setup 127s autopkgtest [15:56:28]: testbed release detected to be: None 128s autopkgtest [15:56:29]: updating testbed package index (apt update) 128s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 128s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 128s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 128s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 129s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 129s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 129s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 129s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [113 kB] 129s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1824 B] 129s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 129s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [320 kB] 130s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [13.4 kB] 130s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3776 B] 130s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [240 B] 130s Fetched 1073 kB in 2s (636 kB/s) 130s Reading package lists... 131s Reading package lists... 131s Building dependency tree... 131s Reading state information... 131s Calculating upgrade... 131s Calculating upgrade... 131s The following packages were automatically installed and are no longer required: 131s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 131s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 131s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 131s linux-tools-6.11.0-8-generic 131s Use 'sudo apt autoremove' to remove them. 131s The following packages will be upgraded: 131s pinentry-curses python3-jinja2 strace 132s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 132s Need to get 652 kB of archives. 132s After this operation, 27.6 kB of additional disk space will be used. 132s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB] 132s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pinentry-curses s390x 1.3.1-2ubuntu3 [42.9 kB] 133s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 133s Fetched 652 kB in 1s (504 kB/s) 133s (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 ... 81428 files and directories currently installed.) 133s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ... 133s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 133s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_s390x.deb ... 133s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 133s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 133s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 133s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 133s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 133s Setting up strace (6.13+ds-1ubuntu1) ... 133s Processing triggers for man-db (2.13.0-1) ... 134s Reading package lists... 134s Building dependency tree... 134s Reading state information... 134s Solving dependencies... 134s The following packages will be REMOVED: 134s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 134s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 134s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 134s linux-tools-6.11.0-8-generic* 134s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded. 134s After this operation, 167 MB disk space will be freed. 135s (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 ... 81428 files and directories currently installed.) 135s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 135s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 135s Removing libpython3.12t64:s390x (3.12.9-1) ... 135s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 135s Removing libnsl2:s390x (1.3.0-3build3) ... 135s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 135s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 135s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 136s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 136s Processing triggers for libc-bin (2.41-1ubuntu1) ... 136s (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 ... 56328 files and directories currently installed.) 136s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 136s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 136s autopkgtest [15:56:37]: upgrading testbed (apt dist-upgrade and autopurge) 136s Reading package lists... 136s Building dependency tree... 136s Reading state information... 137s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 137s Starting 2 pkgProblemResolver with broken count: 0 137s Done 137s Entering ResolveByKeep 137s 137s Calculating upgrade... 137s The following packages will be upgraded: 137s libc-bin libc-dev-bin libc6 libc6-dev locales 137s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 137s Need to get 9512 kB of archives. 137s After this operation, 8192 B of additional disk space will be used. 137s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB] 139s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB] 139s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB] 143s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB] 144s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB] 148s Preconfiguring packages ... 148s Fetched 9512 kB in 11s (874 kB/s) 148s (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 ... 56326 files and directories currently installed.) 148s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ... 148s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 148s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ... 148s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 148s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ... 149s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 149s Setting up libc6:s390x (2.41-1ubuntu2) ... 149s (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 ... 56326 files and directories currently installed.) 149s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ... 149s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 149s Setting up libc-bin (2.41-1ubuntu2) ... 149s (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 ... 56326 files and directories currently installed.) 149s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 149s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 149s Setting up locales (2.41-1ubuntu2) ... 149s Generating locales (this might take a while)... 150s en_US.UTF-8... done 150s Generation complete. 150s Setting up libc-dev-bin (2.41-1ubuntu2) ... 150s Setting up libc6-dev:s390x (2.41-1ubuntu2) ... 150s Processing triggers for man-db (2.13.0-1) ... 151s Processing triggers for systemd (257.3-1ubuntu3) ... 152s Reading package lists... 152s Building dependency tree... 152s Reading state information... 152s Starting pkgProblemResolver with broken count: 0 152s Starting 2 pkgProblemResolver with broken count: 0 152s Done 153s Solving dependencies... 153s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 153s autopkgtest [15:56:54]: rebooting testbed after setup commands that affected boot 162s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 172s autopkgtest [15:57:13]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025 175s autopkgtest [15:57:16]: @@@@@@@@@@@@@@@@@@@@ apt-source probcons 177s Get:1 http://ftpmaster.internal/ubuntu plucky/universe probcons 1.12-14 (dsc) [2049 B] 177s Get:2 http://ftpmaster.internal/ubuntu plucky/universe probcons 1.12-14 (tar) [43.2 kB] 177s Get:3 http://ftpmaster.internal/ubuntu plucky/universe probcons 1.12-14 (diff) [13.2 kB] 177s gpgv: Signature made Thu Aug 26 08:43:07 2021 UTC 177s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 177s gpgv: issuer "tille@debian.org" 177s gpgv: Can't check signature: No public key 177s dpkg-source: warning: cannot verify inline signature for ./probcons_1.12-14.dsc: no acceptable signature found 177s autopkgtest [15:57:18]: testing package probcons version 1.12-14 177s autopkgtest [15:57:18]: build not needed 178s autopkgtest [15:57:19]: test run-unit-test: preparing testbed 178s Reading package lists... 178s Building dependency tree... 178s Reading state information... 178s Starting pkgProblemResolver with broken count: 0 178s Starting 2 pkgProblemResolver with broken count: 0 178s Done 178s The following NEW packages will be installed: 178s probcons probcons-extra 179s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 179s Need to get 145 kB of archives. 179s After this operation, 455 kB of additional disk space will be used. 179s Get:1 http://ftpmaster.internal/ubuntu plucky/universe s390x probcons s390x 1.12-14 [109 kB] 179s Get:2 http://ftpmaster.internal/ubuntu plucky/universe s390x probcons-extra s390x 1.12-14 [35.7 kB] 179s Fetched 145 kB in 0s (298 kB/s) 179s Selecting previously unselected package probcons. 179s (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 ... 56326 files and directories currently installed.) 179s Preparing to unpack .../probcons_1.12-14_s390x.deb ... 179s Unpacking probcons (1.12-14) ... 179s Selecting previously unselected package probcons-extra. 179s Preparing to unpack .../probcons-extra_1.12-14_s390x.deb ... 179s Unpacking probcons-extra (1.12-14) ... 179s Setting up probcons (1.12-14) ... 179s Setting up probcons-extra (1.12-14) ... 179s Processing triggers for man-db (2.13.0-1) ... 182s autopkgtest [15:57:23]: test run-unit-test: [----------------------- 182s 182s PROBCONS version 1.12 - align multiple protein sequences and print to standard output 182s Written by Chuong Do 182s 182s Using parameter set: 182s initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 } 182s gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } 182s gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } 182s 182s Loading sequence file: example.fa 182s Alignment tree: ((CALM_HUMAN P53_HUMAN) (AF01595 Human telomerase reverse transcriptase (hTRT) mRNA TUBE_DROME)) 182s 182s 182s 182s PROBCONS version 1.12 - align multiple protein sequences and print to standard output 182s Written by Chuong Do 182s 182s Using parameter set: 182s initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 } 182s gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } 182s gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } 182s 182s Loading sequence file: example.fa 182s Alignment tree: ((CALM_HUMAN P53_HUMAN) (AF01595 Human telomerase reverse transcriptase (hTRT) mRNA TUBE_DROME)) 182s 183s 183s 183s PROBCONS version 1.12 - align multiple protein sequences and print to standard output 183s Written by Chuong Do 183s 183s Using parameter set: 183s initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 } 183s gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } 183s gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } 183s 183s Loading sequence file: example.fa 183s Alignment tree: ((CALM_HUMAN P53_HUMAN) (AF01595 Human telomerase reverse transcriptase (hTRT) mRNA TUBE_DROME)) 183s 183s 183s 183s PROBCONS version 1.12 - align multiple protein sequences and print to standard output 183s Written by Chuong Do 183s 183s Using parameter set: 183s initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 } 183s gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } 183s gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } 183s 183s Loading sequence file: example.fa 183s Alignment tree: ((CALM_HUMAN P53_HUMAN) (AF01595 Human telomerase reverse transcriptase (hTRT) mRNA TUBE_DROME)) 183s 183s 183s 183s PROBCONS version 1.12 - align multiple protein sequences and print to standard output 183s Written by Chuong Do 183s 183s Using parameter set: 183s initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 } 183s gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } 183s gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } 183s 183s Loading sequence file: example.fa 184s Alignment tree: ((CALM_HUMAN P53_HUMAN) (AF01595 Human telomerase reverse transcriptase (hTRT) mRNA TUBE_DROME)) 184s 185s 185s 185s PROBCONS version 1.12 - align multiple protein sequences and print to standard output 185s Written by Chuong Do 185s 185s Using parameter set: 185s initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 } 185s gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } 185s gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } 186s 186s Loading sequence file: example.fa 186s Alignment tree: ((CALM_HUMAN P53_HUMAN) (AF01595 Human telomerase reverse transcriptase (hTRT) mRNA TUBE_DROME)) 186s 188s 188s 188s PROBCONS version 1.12 - align multiple protein sequences and print to standard output 188s Written by Chuong Do 188s 188s Using parameter set: 188s initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 } 188s gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } 188s gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } 188s 188s Loading sequence file: example.fa 188s Recomputed parameter set: 188s initDistrib[] = { 0.6472518444 8.226895261e-06 8.226895261e-06 0.1763658673 0.1763658673 } 188s gapOpen[] = { 0.01773866639 0.01773866639 0.03061322309 0.03061322309 } 188s gapExtend[] = { 0.413000226 0.413000226 0.941649437 0.941649437 } 188s 188s Alignment tree: ((CALM_HUMAN P53_HUMAN) (AF01595 Human telomerase reverse transcriptase (hTRT) mRNA TUBE_DROME)) 188s 188s 188s 188s PROBCONS version 1.12 - align multiple protein sequences and print to standard output 188s Written by Chuong Do 188s 188s Using parameter set: 188s initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 } 188s gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } 188s gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } 188s 188s Loading sequence file: example.fa 189s Recomputed parameter set: 189s initDistrib[] = { 0.6472518444 8.226895261e-06 8.226895261e-06 0.1763658673 0.1763658673 } 189s gapOpen[] = { 0.01773866639 0.01773866639 0.03061322309 0.03061322309 } 189s gapExtend[] = { 0.413000226 0.413000226 0.941649437 0.941649437 } 189s 189s Alignment tree: ((CALM_HUMAN P53_HUMAN) (AF01595 Human telomerase reverse transcriptase (hTRT) mRNA TUBE_DROME)) 189s 189s 189s 189s PROBCONS version 1.12 - align multiple protein sequences and print to standard output 189s Written by Chuong Do 189s 189s Using parameter set: 189s initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 } 189s gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } 189s gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } 189s 189s Loading sequence file: example.fa 189s 189s PROBCONS version 1.12 - align multiple protein sequences and print to standard output 189s Written by Chuong Do 189s 189s Using parameter set: 189s initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 } 189s gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } 189s gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } 189s 189s Loading sequence file: example.fa 189s 189s PROBCONS version 1.12 - align multiple protein sequences and print to standard output 189s Written by Chuong Do 189s 189s Using parameter set: 189s initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 } 189s gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } 189s gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } 189s 189s Loading sequence file: example.fa 189s Computing posterior matrix: (1) CALM_HUMAN vs. (2) AF01595 Human telomerase reverse transcriptase (hTRT) mRNA -- 0.220677346 189s Computing posterior matrix: (1) CALM_HUMAN vs. (3) P53_HUMAN -- 0.3983216584 189s Computing posterior matrix: (1) CALM_HUMAN vs. (4) TUBE_DROME -- 0.2310655862 190s Computing posterior matrix: (2) AF01595 Human telomerase reverse transcriptase (hTRT) mRNA vs. (3) P53_HUMAN -- 0.2095304132 190s Computing posterior matrix: (2) AF01595 Human telomerase reverse transcriptase (hTRT) mRNA vs. (4) TUBE_DROME -- 0.2289323211 190s Computing posterior matrix: (3) P53_HUMAN vs. (4) TUBE_DROME -- 0.2899678648 190s Relaxing (1) CALM_HUMAN vs. (2) AF01595 Human telomerase reverse transcriptase (hTRT) mRNA: 2141 --> 1139 -- done. 190s Relaxing (1) CALM_HUMAN vs. (3) P53_HUMAN: 1369 --> 864 -- done. 190s Relaxing (1) CALM_HUMAN vs. (4) TUBE_DROME: 2094 --> 1268 -- done. 190s Relaxing (2) AF01595 Human telomerase reverse transcriptase (hTRT) mRNA vs. (3) P53_HUMAN: 5476 --> 3181 -- done. 190s Relaxing (2) AF01595 Human telomerase reverse transcriptase (hTRT) mRNA vs. (4) TUBE_DROME: 5680 --> 3332 -- done. 190s Relaxing (3) P53_HUMAN vs. (4) TUBE_DROME: 3329 --> 2222 -- done. 190s Relaxing (1) CALM_HUMAN vs. (2) AF01595 Human telomerase reverse transcriptase (hTRT) mRNA: 1139 --> 557 -- done. 190s Relaxing (1) CALM_HUMAN vs. (3) P53_HUMAN: 864 --> 525 -- done. 190s Relaxing (1) CALM_HUMAN vs. (4) TUBE_DROME: 1268 --> 732 -- done. 190s Relaxing (2) AF01595 Human telomerase reverse transcriptase (hTRT) mRNA vs. (3) P53_HUMAN: 3181 --> 1744 -- done. 190s Relaxing (2) AF01595 Human telomerase reverse transcriptase (hTRT) mRNA vs. (4) TUBE_DROME: 3332 --> 1803 -- done. 190s Relaxing (3) P53_HUMAN vs. (4) TUBE_DROME: 2222 --> 1486 -- done. 190s 190s Alignment tree: ((CALM_HUMAN P53_HUMAN) (AF01595 Human telomerase reverse transcriptase (hTRT) mRNA TUBE_DROME)) 190s 190s [0] vs. [2]: 0.1050620601 190s [1] vs. [3]: 0.05934812129 190s [0,2] vs. [1,3]: 0.02306902781 190s [0,2,3] vs. [1]: 0.02062231861 190s [0,1] vs. [2,3]: 0.0215531718 190s [0,1,3] vs. [2]: 0.03732775152 190s [1,2] vs. [0,3]: 0.03665437922 190s [0,2,3] vs. [1]: 0.02072408795 190s [3] vs. [0,1,2]: 0.04131478816 190s [0,1,2] vs. [3]: 0.04131478816 190s [2,3] vs. [0,1]: 0.02140655369 190s [0,2] vs. [1,3]: 0.0238978155 190s [1] vs. [0,2,3]: 0.02052048407 190s [0,2] vs. [1,3]: 0.02381537855 190s [0,3] vs. [1,2]: 0.03669665754 190s [3] vs. [0,1,2]: 0.04147393256 190s [0,1,3] vs. [2]: 0.03778945655 190s [1,3] vs. [0,2]: 0.02382831834 190s [0,1,3] vs. [2]: 0.03782599792 190s [1,3] vs. [0,2]: 0.02382831834 190s [2] vs. [0,1,3]: 0.03782599792 190s [0] vs. [1,2,3]: 0.05896024778 190s [2,3] vs. [0,1]: 0.02192944102 190s [1] vs. [0,2,3]: 0.02071446367 190s [2] vs. [0,1,3]: 0.03613902256 190s [3] vs. [0,1,2]: 0.04358047619 190s [0] vs. [1,2,3]: 0.05896024778 190s [0,1,2] vs. [3]: 0.04358047619 190s [0] vs. [1,2,3]: 0.05896024778 190s [0,3] vs. [1,2]: 0.03590458632 190s [0,1,3] vs. [2]: 0.03613902256 190s [1,2,3] vs. [0]: 0.05896024778 190s [0,1,2] vs. [3]: 0.04358047619 190s [0,1,3] vs. [2]: 0.03613902256 190s [1,2] vs. [0,3]: 0.03590458632 190s [1,3] vs. [0,2]: 0.02533986792 190s [0,1] vs. [2,3]: 0.02192944102 190s [1,3] vs. [0,2]: 0.02533986792 190s [1,3] vs. [0,2]: 0.02533986792 190s [1,2,3] vs. [0]: 0.05896024778 190s [0] vs. [1,2,3]: 0.05896024778 190s [0,2] vs. [1,3]: 0.02533986792 190s [0,2,3] vs. [1]: 0.02071446367 190s [0,1,2] vs. [3]: 0.04358047619 190s [1,2] vs. [0,3]: 0.03590458632 190s [0,1,3] vs. [2]: 0.03613902256 190s [1,2,3] vs. [0]: 0.05896024778 190s [0,1] vs. [2,3]: 0.02192944102 190s [0,1,3] vs. [2]: 0.03613902256 190s [2,3] vs. [0,1]: 0.02192944102 190s [0] vs. [1,2,3]: 0.05896024778 190s [0,1,2] vs. [3]: 0.04358047619 190s [1,3] vs. [0,2]: 0.02533986792 190s [1,3] vs. [0,2]: 0.02533986792 190s [2,3] vs. [0,1]: 0.02192944102 190s [2] vs. [0,1,3]: 0.03613902256 190s [2,3] vs. [0,1]: 0.02192944102 190s [0,3] vs. [1,2]: 0.03590458632 190s [2,3] vs. [0,1]: 0.02192944102 190s [0,2,3] vs. [1]: 0.02071446367 190s [0,3] vs. [1,2]: 0.03590458632 190s [1] vs. [0,2,3]: 0.02071446367 190s [3] vs. [0,1,2]: 0.04358047619 190s [1,2] vs. [0,3]: 0.03590458632 190s [1,2,3] vs. [0]: 0.05896024778 190s [0,2] vs. [1,3]: 0.02533986792 190s [1,2,3] vs. [0]: 0.05896024778 190s [0,2,3] vs. [1]: 0.02071446367 190s [0,3] vs. [1,2]: 0.03590458632 190s [1,2] vs. [0,3]: 0.03590458632 190s [0,2] vs. [1,3]: 0.02533986792 190s [2,3] vs. [0,1]: 0.02192944102 190s [3] vs. [0,1,2]: 0.04358047619 190s [1,2] vs. [0,3]: 0.03590458632 190s [0,2,3] vs. [1]: 0.02071446367 190s [1,2] vs. [0,3]: 0.03590458632 190s [0] vs. [1,2,3]: 0.05896024778 190s [3] vs. [0,1,2]: 0.04358047619 190s [1] vs. [0,2,3]: 0.02071446367 190s [0,1,3] vs. [2]: 0.03613902256 190s [3] vs. [0,1,2]: 0.04358047619 190s [0,1,2] vs. [3]: 0.04358047619 190s [1] vs. [0,2,3]: 0.02071446367 190s [0,1,2] vs. [3]: 0.04358047619 190s [1] vs. [0,2,3]: 0.02071446367 190s [0,2,3] vs. [1]: 0.02071446367 190s [0,1,3] vs. [2]: 0.03613902256 190s [0,3] vs. [1,2]: 0.03590458632 190s [1] vs. [0,2,3]: 0.02071446367 190s 190s 190s PROBCONS version 1.12 - align multiple protein sequences and print to standard output 190s Written by Chuong Do 190s 190s Using parameter set: 190s initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 } 190s gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } 190s gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } 190s 190s Loading sequence file: example.fa 190s Computing posterior matrix: (1) CALM_HUMAN vs. (2) AF01595 Human telomerase reverse transcriptase (hTRT) mRNA -- 0.220677346 190s Computing posterior matrix: (1) CALM_HUMAN vs. (3) P53_HUMAN -- 0.3983216584 190s Computing posterior matrix: (1) CALM_HUMAN vs. (4) TUBE_DROME -- 0.2310655862 190s Computing posterior matrix: (2) AF01595 Human telomerase reverse transcriptase (hTRT) mRNA vs. (3) P53_HUMAN -- 0.2095304132 190s Computing posterior matrix: (2) AF01595 Human telomerase reverse transcriptase (hTRT) mRNA vs. (4) TUBE_DROME -- 0.2289323211 190s Computing posterior matrix: (3) P53_HUMAN vs. (4) TUBE_DROME -- 0.2899678648 190s Relaxing (1) CALM_HUMAN vs. (2) AF01595 Human telomerase reverse transcriptase (hTRT) mRNA: 2141 --> 1139 -- done. 190s Relaxing (1) CALM_HUMAN vs. (3) P53_HUMAN: 1369 --> 864 -- done. 190s Relaxing (1) CALM_HUMAN vs. (4) TUBE_DROME: 2094 --> 1268 -- done. 190s Relaxing (2) AF01595 Human telomerase reverse transcriptase (hTRT) mRNA vs. (3) P53_HUMAN: 5476 --> 3181 -- done. 190s Relaxing (2) AF01595 Human telomerase reverse transcriptase (hTRT) mRNA vs. (4) TUBE_DROME: 5680 --> 3332 -- done. 190s Relaxing (3) P53_HUMAN vs. (4) TUBE_DROME: 3329 --> 2222 -- done. 190s Relaxing (1) CALM_HUMAN vs. (2) AF01595 Human telomerase reverse transcriptase (hTRT) mRNA: 1139 --> 557 -- done. 190s Relaxing (1) CALM_HUMAN vs. (3) P53_HUMAN: 864 --> 525 -- done. 190s Relaxing (1) CALM_HUMAN vs. (4) TUBE_DROME: 1268 --> 732 -- done. 190s Relaxing (2) AF01595 Human telomerase reverse transcriptase (hTRT) mRNA vs. (3) P53_HUMAN: 3181 --> 1744 -- done. 190s Relaxing (2) AF01595 Human telomerase reverse transcriptase (hTRT) mRNA vs. (4) TUBE_DROME: 3332 --> 1803 -- done. 190s Relaxing (3) P53_HUMAN vs. (4) TUBE_DROME: 2222 --> 1486 -- done. 190s 190s Alignment tree: ((CALM_HUMAN P53_HUMAN) (AF01595 Human telomerase reverse transcriptase (hTRT) mRNA TUBE_DROME)) 190s 190s [0] vs. [2]: 0.1050620601 190s [1] vs. [3]: 0.05934812129 190s [0,2] vs. [1,3]: 0.02306902781 190s [0,2,3] vs. [1]: 0.02062231861 190s [0,1] vs. [2,3]: 0.0215531718 190s [0,1,3] vs. [2]: 0.03732775152 190s [1,2] vs. [0,3]: 0.03665437922 190s [0,2,3] vs. [1]: 0.02072408795 190s [3] vs. [0,1,2]: 0.04131478816 190s [0,1,2] vs. [3]: 0.04131478816 190s [2,3] vs. [0,1]: 0.02140655369 190s [0,2] vs. [1,3]: 0.0238978155 190s [1] vs. [0,2,3]: 0.02052048407 190s [0,2] vs. [1,3]: 0.02381537855 190s [0,3] vs. [1,2]: 0.03669665754 190s [3] vs. [0,1,2]: 0.04147393256 190s [0,1,3] vs. [2]: 0.03778945655 190s [1,3] vs. [0,2]: 0.02382831834 190s [0,1,3] vs. [2]: 0.03782599792 190s [1,3] vs. [0,2]: 0.02382831834 190s [2] vs. [0,1,3]: 0.03782599792 190s [0] vs. [1,2,3]: 0.05896024778 190s [2,3] vs. [0,1]: 0.02192944102 190s [1] vs. [0,2,3]: 0.02071446367 190s [2] vs. [0,1,3]: 0.03613902256 190s [3] vs. [0,1,2]: 0.04358047619 190s [0] vs. [1,2,3]: 0.05896024778 190s [0,1,2] vs. [3]: 0.04358047619 190s [0] vs. [1,2,3]: 0.05896024778 190s [0,3] vs. [1,2]: 0.03590458632 190s [0,1,3] vs. [2]: 0.03613902256 190s [1,2,3] vs. [0]: 0.05896024778 190s [0,1,2] vs. [3]: 0.04358047619 190s [0,1,3] vs. [2]: 0.03613902256 190s [1,2] vs. [0,3]: 0.03590458632 190s [1,3] vs. [0,2]: 0.02533986792 190s [0,1] vs. [2,3]: 0.02192944102 190s [1,3] vs. [0,2]: 0.02533986792 190s [1,3] vs. [0,2]: 0.02533986792 190s [1,2,3] vs. [0]: 0.05896024778 190s [0] vs. [1,2,3]: 0.05896024778 190s [0,2] vs. [1,3]: 0.02533986792 190s [0,2,3] vs. [1]: 0.02071446367 190s [0,1,2] vs. [3]: 0.04358047619 190s [1,2] vs. [0,3]: 0.03590458632 190s [0,1,3] vs. [2]: 0.03613902256 190s [1,2,3] vs. [0]: 0.05896024778 190s [0,1] vs. [2,3]: 0.02192944102 190s [0,1,3] vs. [2]: 0.03613902256 190s [2,3] vs. [0,1]: 0.02192944102 190s [0] vs. [1,2,3]: 0.05896024778 190s [0,1,2] vs. [3]: 0.04358047619 190s [1,3] vs. [0,2]: 0.02533986792 190s [1,3] vs. [0,2]: 0.02533986792 190s [2,3] vs. [0,1]: 0.02192944102 190s [2] vs. [0,1,3]: 0.03613902256 190s [2,3] vs. [0,1]: 0.02192944102 190s [0,3] vs. [1,2]: 0.03590458632 190s [2,3] vs. [0,1]: 0.02192944102 190s [0,2,3] vs. [1]: 0.02071446367 190s [0,3] vs. [1,2]: 0.03590458632 190s [1] vs. [0,2,3]: 0.02071446367 190s [3] vs. [0,1,2]: 0.04358047619 190s [1,2] vs. [0,3]: 0.03590458632 190s [1,2,3] vs. [0]: 0.05896024778 190s [0,2] vs. [1,3]: 0.02533986792 190s [1,2,3] vs. [0]: 0.05896024778 190s [0,2,3] vs. [1]: 0.02071446367 190s [0,3] vs. [1,2]: 0.03590458632 190s [1,2] vs. [0,3]: 0.03590458632 190s [0,2] vs. [1,3]: 0.02533986792 190s [2,3] vs. [0,1]: 0.02192944102 190s [3] vs. [0,1,2]: 0.04358047619 190s [1,2] vs. [0,3]: 0.03590458632 190s [0,2,3] vs. [1]: 0.02071446367 190s [1,2] vs. [0,3]: 0.03590458632 190s [0] vs. [1,2,3]: 0.05896024778 190s [3] vs. [0,1,2]: 0.04358047619 190s [1] vs. [0,2,3]: 0.02071446367 190s [0,1,3] vs. [2]: 0.03613902256 190s [3] vs. [0,1,2]: 0.04358047619 190s [0,1,2] vs. [3]: 0.04358047619 190s [1] vs. [0,2,3]: 0.02071446367 190s [0,1,2] vs. [3]: 0.04358047619 190s [1] vs. [0,2,3]: 0.02071446367 190s [0,2,3] vs. [1]: 0.02071446367 190s [0,1,3] vs. [2]: 0.03613902256 190s [0,3] vs. [1,2]: 0.03590458632 190s [1] vs. [0,2,3]: 0.02071446367 190s 190s PASS 191s autopkgtest [15:57:32]: test run-unit-test: -----------------------] 191s autopkgtest [15:57:32]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 191s run-unit-test PASS 191s autopkgtest [15:57:32]: @@@@@@@@@@@@@@@@@@@@ summary 191s run-unit-test PASS 209s nova [W] Using flock in prodstack6-s390x 209s Creating nova instance adt-plucky-s390x-probcons-20250315-155420-juju-7f2275-prod-proposed-migration-environment-20-1bec3787-c276-4f4d-a0cd-763d830974bd from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 209s nova [W] Timed out waiting for 1d3a2a05-d56a-419e-ba50-fb78324aca0b to get deleted.