0s autopkgtest [10:48:06]: starting date and time: 2025-03-15 10:48:06+0000 0s autopkgtest [10:48:06]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [10:48:06]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.evspvivm/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade probalign --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-23.secgroup --name adt-plucky-s390x-probalign-20250315-104806-juju-7f2275-prod-proposed-migration-environment-20-05f1c957-c044-4fc2-9bce-66281657207c --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/ 128s autopkgtest [10:50:14]: testbed dpkg architecture: s390x 128s autopkgtest [10:50:14]: testbed apt version: 2.9.33 129s autopkgtest [10:50:15]: @@@@@@@@@@@@@@@@@@@@ test bed setup 129s autopkgtest [10:50:15]: testbed release detected to be: None 129s autopkgtest [10:50:15]: updating testbed package index (apt update) 130s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 130s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 130s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 130s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 130s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [410 kB] 131s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [46.2 kB] 131s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 131s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [80.7 kB] 131s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1852 B] 131s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 131s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [335 kB] 131s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [14.4 kB] 131s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3776 B] 131s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [328 B] 131s Fetched 1034 kB in 2s (588 kB/s) 132s Reading package lists... 133s Reading package lists... 133s Building dependency tree... 133s Reading state information... 133s Calculating upgrade... 133s Calculating upgrade... 133s The following packages were automatically installed and are no longer required: 133s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 133s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 133s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 133s linux-tools-6.11.0-8-generic 133s Use 'sudo apt autoremove' to remove them. 133s The following packages will be upgraded: 133s python3-jinja2 strace 133s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 133s Need to get 609 kB of archives. 133s After this operation, 27.6 kB of additional disk space will be used. 133s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB] 134s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 134s Fetched 609 kB in 1s (545 kB/s) 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 Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ... 135s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 135s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 135s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 135s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 135s Setting up strace (6.13+ds-1ubuntu1) ... 135s Processing triggers for man-db (2.13.0-1) ... 136s Reading package lists... 136s Building dependency tree... 136s Reading state information... 136s Solving dependencies... 136s The following packages will be REMOVED: 136s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 136s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 136s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 136s linux-tools-6.11.0-8-generic* 136s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded. 136s After this operation, 167 MB disk space will be freed. 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 ... 81428 files and directories currently installed.) 136s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 136s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 136s Removing libpython3.12t64:s390x (3.12.9-1) ... 136s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 136s Removing libnsl2:s390x (1.3.0-3build3) ... 136s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 136s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 136s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 137s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 137s Processing triggers for libc-bin (2.41-1ubuntu1) ... 137s (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.) 137s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 137s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 137s autopkgtest [10:50:23]: upgrading testbed (apt dist-upgrade and autopurge) 138s Reading package lists... 138s Building dependency tree... 138s Reading state information... 138s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 138s Starting 2 pkgProblemResolver with broken count: 0 138s Done 138s Entering ResolveByKeep 138s 138s Calculating upgrade... 138s The following packages will be upgraded: 138s libc-bin libc-dev-bin libc6 libc6-dev locales 139s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 139s Need to get 9512 kB of archives. 139s After this operation, 8192 B of additional disk space will be used. 139s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB] 141s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB] 141s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB] 144s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB] 145s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB] 150s Preconfiguring packages ... 150s Fetched 9512 kB in 11s (876 kB/s) 150s (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.) 150s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ... 150s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 150s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ... 150s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 150s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ... 150s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 150s Setting up libc6:s390x (2.41-1ubuntu2) ... 150s (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.) 150s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ... 150s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 150s Setting up libc-bin (2.41-1ubuntu2) ... 150s (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.) 150s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 150s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 150s Setting up locales (2.41-1ubuntu2) ... 151s Generating locales (this might take a while)... 151s en_US.UTF-8... done 151s Generation complete. 151s Setting up libc-dev-bin (2.41-1ubuntu2) ... 151s Setting up libc6-dev:s390x (2.41-1ubuntu2) ... 152s Processing triggers for man-db (2.13.0-1) ... 152s Processing triggers for systemd (257.3-1ubuntu3) ... 153s Reading package lists... 153s Building dependency tree... 153s Reading state information... 153s Starting pkgProblemResolver with broken count: 0 153s Starting 2 pkgProblemResolver with broken count: 0 153s Done 154s Solving dependencies... 154s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 154s autopkgtest [10:50:40]: rebooting testbed after setup commands that affected boot 173s autopkgtest [10:50:59]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025 175s autopkgtest [10:51:01]: @@@@@@@@@@@@@@@@@@@@ apt-source probalign 177s Get:1 http://ftpmaster.internal/ubuntu plucky/universe probalign 1.4-10 (dsc) [1971 B] 177s Get:2 http://ftpmaster.internal/ubuntu plucky/universe probalign 1.4-10 (tar) [30.1 kB] 177s Get:3 http://ftpmaster.internal/ubuntu plucky/universe probalign 1.4-10 (diff) [4916 B] 177s gpgv: Signature made Thu Jan 19 13:18:09 2023 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 ./probalign_1.4-10.dsc: no acceptable signature found 177s autopkgtest [10:51:03]: testing package probalign version 1.4-10 178s autopkgtest [10:51:04]: build not needed 178s autopkgtest [10:51:04]: 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 179s The following NEW packages will be installed: 179s probalign 179s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 179s Need to get 58.8 kB of archives. 179s After this operation, 141 kB of additional disk space will be used. 179s Get:1 http://ftpmaster.internal/ubuntu plucky/universe s390x probalign s390x 1.4-10 [58.8 kB] 179s Fetched 58.8 kB in 0s (194 kB/s) 179s Selecting previously unselected package probalign. 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 .../probalign_1.4-10_s390x.deb ... 179s Unpacking probalign (1.4-10) ... 179s Setting up probalign (1.4-10) ... 179s Processing triggers for man-db (2.13.0-1) ... 181s autopkgtest [10:51:07]: test run-unit-test: [----------------------- 181s 181s PROBALIGN Version 1.4 (Nov 2010) aligns multiple protein sequences and prints to the 181s standard output. Written by Satish Chikkagoudar and Usman Roshan using code from PROBCONS 181s version 1.1 (written by Chuong Do) and based upon probA (written by Ulrike Muckstein). 181s 181s Loading sequence file: test_data_p.fas 181s Alignment tree: ((s1 s0) (s3 s2)) 181s 181s >s1 181s 181s LLSPNGAGWVVAPITMHDSAQINMPWQRRKDFLVQACVPVLKNLYKRKYEKVIKSIVYER 181s LYIFRGLWSGGCA--RYFDPPRCYKRSPEFYLGQFHGPLVHIGTMGHTECLHYGYDIQVN 181s CNKHDNKVTPK 181s >s0 181s -----------------------------KTLCVTDEVAKPRILNRKEYERVVIYGGYQW 181s TILFTKVWNGGSG--FKCDPNRCLKQAKLYYLPLFHAPIVEAAHQAGGKSLKFELDIRQV 181s SAMNASHKSGN 181s >s3 181s -----------------------------KVYYVEEAGSPTKGTFEEDYDGLELGAGFGW 181s RTQLVRLWAKDCFNDTSKEPNTCFRKPSKLYNGEVREIVLEAAGYTKAGDMRYAAVQSVA 181s AAHTRNKTTDS 181s >s2 181s -----------------------------KTFYINVDTNPMKALYKHEYNRELSGIPLDW 181s SSLVGRLWAKDCFTTKLNDPSERFRPPTKGFNKEDCLIVLAVNVQTHGGTLRFGIPERVK 181s CDRSRSKSTGK 181s 181s PROBALIGN Version 1.4 (Nov 2010) aligns multiple protein sequences and prints to the 181s standard output. Written by Satish Chikkagoudar and Usman Roshan using code from PROBCONS 181s version 1.1 (written by Chuong Do) and based upon probA (written by Ulrike Muckstein). 181s 181s Loading sequence file: test_data_n.fas 181s Alignment tree: ((s1 s2) (s0 s3)) 181s 181s 181s >s1 181s ACGTTT-----TCGAACCCCCCGAAATTTTGGGCGCGCG-------------CACACACT 181s CATCACTCTCGACGCAAAAC------GGCT---GCACACACTCATCACTC----TCGACG 181s C-AAA--ACGGCTGCAAAACG-GCTGCACACACTCATCAC-- 181s >s0 181s A--TTTCTCTCTCAAACCCCCCGAAATTTTGGGCGCGCG-------------CACACACT 181s CATCACTCTCGACGCAAAACATTTTGGGCGCGCGCACACACTCATCACTCATTTT-G--- 181s ---------GGC-GC-------GC-GCACACACTCATCACTC 181s >s3 181s A--TTTCTCTCTCAAACCCCCCGAAATTTTGGGCGCGCG-------------CACACACT 181s CATCACTCTCGACGCAAAACATTTTGGGCGCGCGCACACACTCG----------TCG-CG 181s CGAAACTA---C-GC---ACGTGC-GCACACACTCATCACTC 181s >s2 181s ACGTTT-----TCGAACCCCCCGAAATTTT---C-CCCCCCCCCCCCCCCCCCCC-CACT 181s CATCACTCTCGACGCAAAAC------GGCT---GCACACACTCATCACTC----TCGACG 181s C-AAA--ACGGCTGCAAAACG-GCTGCACACACTCATCAC-- 181s 181s PROBALIGN Version 1.4 (Nov 2010) aligns multiple protein sequences and prints to the 181s standard output. Written by Satish Chikkagoudar and Usman Roshan using code from PROBCONS 181s version 1.1 (written by Chuong Do) and based upon probA (written by Ulrike Muckstein). 181s 181s Loading sequence file: test_data_p.fas 181s Computing posterior matrix: (1) s1 vs. (2) s0 -- 181s 0 129 181s 1 100 181s ------------- 181s 0.5564424396 181s Computing posterior matrix: (1) s1 vs. (3) s3 -- 181s 0 129 181s 2 102 181s ------------- 181s 0.2607336938 181s Computing posterior matrix: (1) s1 vs. (4) s2 -- 181s 0 129 181s 3 102 181s ------------- 181s 0.4842562675 181s Computing posterior matrix: (2) s0 vs. (3) s3 -- 181s 1 100 181s 2 102 181s ------------- 181s 0.3741489649 181s Computing posterior matrix: (2) s0 vs. (4) s2 -- 181s 1 100 181s 3 102 181s ------------- 181s 0.3683230281 181s Computing posterior matrix: (3) s3 vs. (4) s2 -- 181s 2 102 181s 3 102 181s ------------- 181s 0.8540496826 181s Relaxing (1) s1 vs. (2) s0: 654 --> 516 -- done. 181s Relaxing (1) s1 vs. (3) s3: 864 --> 608 -- done. 181s Relaxing (1) s1 vs. (4) s2: 628 --> 499 -- done. 181s Relaxing (2) s0 vs. (3) s3: 694 --> 531 -- done. 181s Relaxing (2) s0 vs. (4) s2: 766 --> 588 -- done. 181s Relaxing (3) s3 vs. (4) s2: 249 --> 227 -- done. 181s Relaxing (1) s1 vs. (2) s0: 516 --> 397 -- done. 181s Relaxing (1) s1 vs. (3) s3: 608 --> 430 -- done. 181s Relaxing (1) s1 vs. (4) s2: 499 --> 405 -- done. 181s Relaxing (2) s0 vs. (3) s3: 531 --> 402 -- done. 181s Relaxing (2) s0 vs. (4) s2: 588 --> 425 -- done. 181s Relaxing (3) s3 vs. (4) s2: 227 --> 203 -- done. 181s 181s Alignment tree: ((s1 s0) (s3 s2)) 181s 181s [0] vs. [1]: 0.2394420803 181s [2] vs. [3]: 0.3004739285 181s [0,1] vs. [2,3]: 0.2197821587 181s [0,2,3] vs. [1]: 0.2272425592 181s [0,1] vs. [2,3]: 0.2197821587 181s [0,1,3] vs. [2]: 0.2441207469 181s [1,2] vs. [0,3]: 0.2414343655 181s [0,2,3] vs. [1]: 0.2272425592 181s [3] vs. [0,1,2]: 0.2492380887 181s [0,1,2] vs. [3]: 0.2492380887 181s [2,3] vs. [0,1]: 0.2197821587 181s [0,2] vs. [1,3]: 0.2459582537 181s [1] vs. [0,2,3]: 0.2272425592 181s [0,2] vs. [1,3]: 0.2459582537 181s [0,3] vs. [1,2]: 0.2414343655 181s [3] vs. [0,1,2]: 0.2492380887 181s [0,1,3] vs. [2]: 0.2441207469 181s [1,3] vs. [0,2]: 0.2459582537 181s [0,1,3] vs. [2]: 0.2441207469 181s [1,3] vs. [0,2]: 0.2459582537 181s [2] vs. [0,1,3]: 0.2441207469 181s [0] vs. [1,2,3]: 0.2267541587 181s [2,3] vs. [0,1]: 0.2197821587 181s [1] vs. [0,2,3]: 0.2272425592 181s [2] vs. [0,1,3]: 0.2441207469 181s [3] vs. [0,1,2]: 0.2492380887 181s [0] vs. [1,2,3]: 0.2267541587 181s [0,1,2] vs. [3]: 0.2492380887 181s [0] vs. [1,2,3]: 0.2267541587 181s [0,3] vs. [1,2]: 0.2414343655 181s [0,1,3] vs. [2]: 0.2441207469 181s [1,2,3] vs. [0]: 0.2267541587 181s [0,1,2] vs. [3]: 0.2492380887 181s [0,1,3] vs. [2]: 0.2441207469 181s [1,2] vs. [0,3]: 0.2414343655 181s [1,3] vs. [0,2]: 0.2459582537 181s [0,1] vs. [2,3]: 0.2197821587 181s [1,3] vs. [0,2]: 0.2459582537 181s [1,3] vs. [0,2]: 0.2459582537 181s [1,2,3] vs. [0]: 0.2267541587 181s [0] vs. [1,2,3]: 0.2267541587 181s [0,2] vs. [1,3]: 0.2459582537 181s [0,2,3] vs. [1]: 0.2272425592 181s [0,1,2] vs. [3]: 0.2492380887 181s [1,2] vs. [0,3]: 0.2414343655 181s [0,1,3] vs. [2]: 0.2441207469 181s [1,2,3] vs. [0]: >s1 181s LLSPNGAGWVVAPITMHDSAQINMPWQRRKDFLVQACVPVLKNLYKRKYEKVIKSIVYER 181s LYIFRGLWSGGCA--RYFDPPRCYKRSPEFYLGQFHGPLVHIGTMGHTECLHYGYDIQVN 181s CNKHDNKVTPK 181s >s0 181s -----------------------------KTLCVTDEVAKPRILNRKEYERVVIYGGYQW 181s TILFTKVWNGGSG--FKCDPNRCLKQAKLYYLPLFHAPIVEAAHQAGGKSLKFELDIRQV 181s SAMNASHKSGN 181s >s3 181s -----------------------------KVYYVEEAGSPTKGTFEEDYDGLELGAGFGW 181s RTQLVRLWAKDCFNDTSKEPNTCFRKPSKLYNGEVREIVLEAAGYTKAGDMRYAAVQSVA 181s AAHTRNKTTDS 181s >s2 181s -----------------------------KTFYINVDTNPMKALYKHEYNRELSGIPLDW 181s SSLVGRLWAKDCFTTKLNDPSERFRPPTKGFNKEDCLIVLAVNVQTHGGTLRFGIPERVK 181s CDRSRSKSTGK 181s 0.2267541587 181s [0,1] vs. [2,3]: 0.2197821587 181s [0,1,3] vs. [2]: 0.2441207469 181s [2,3] vs. [0,1]: 0.2197821587 181s [0] vs. [1,2,3]: 0.2267541587 181s [0,1,2] vs. [3]: 0.2492380887 181s [1,3] vs. [0,2]: 0.2459582537 181s [1,3] vs. [0,2]: 0.2459582537 181s [2,3] vs. [0,1]: 0.2197821587 181s [2] vs. [0,1,3]: 0.2441207469 181s [2,3] vs. [0,1]: 0.2197821587 181s [0,3] vs. [1,2]: 0.2414343655 181s [2,3] vs. [0,1]: 0.2197821587 181s [0,2,3] vs. [1]: 0.2272425592 181s [0,3] vs. [1,2]: 0.2414343655 181s [1] vs. [0,2,3]: 0.2272425592 181s [3] vs. [0,1,2]: 0.2492380887 181s [1,2] vs. [0,3]: 0.2414343655 181s [1,2,3] vs. [0]: 0.2267541587 181s [0,2] vs. [1,3]: 0.2459582537 181s [1,2,3] vs. [0]: 0.2267541587 181s [0,2,3] vs. [1]: 0.2272425592 181s [0,3] vs. [1,2]: 0.2414343655 181s [1,2] vs. [0,3]: 0.2414343655 181s [0,2] vs. [1,3]: 0.2459582537 181s [2,3] vs. [0,1]: 0.2197821587 181s [3] vs. [0,1,2]: 0.2492380887 181s [1,2] vs. [0,3]: 0.2414343655 181s [0,2,3] vs. [1]: 0.2272425592 181s [1,2] vs. [0,3]: 0.2414343655 181s [0] vs. [1,2,3]: 0.2267541587 181s [3] vs. [0,1,2]: 0.2492380887 181s [1] vs. [0,2,3]: 0.2272425592 181s [0,1,3] vs. [2]: 0.2441207469 181s [3] vs. [0,1,2]: 0.2492380887 181s [0,1,2] vs. [3]: 0.2492380887 181s [1] vs. [0,2,3]: 0.2272425592 181s [0,1,2] vs. [3]: 0.2492380887 181s [1] vs. [0,2,3]: 0.2272425592 181s [0,2,3] vs. [1]: 0.2272425592 181s [0,1,3] vs. [2]: 0.2441207469 181s [0,3] vs. [1,2]: 0.2414343655 181s [1] vs. [0,2,3]: 0.2272425592 181s 181s 181s PROBALIGN Version 1.4 (Nov 2010) aligns multiple protein sequences and prints to the 181s standard output. Written by Satish Chikkagoudar and Usman Roshan using code from PROBCONS 181s version 1.1 (written by Chuong Do) and based upon probA (written by Ulrike Muckstein). 181s 181s Loading sequence file: test_data_n.fas 181s Alignment tree: ((s1 s2) (s0 s3)) 181s 181s 181s >s1 181s ACGTTT-----TCGAACCCCCCGAAATTTTGGGCGCGCG-----------CACACACTCA 181s TCACTCTCGACGCAAAAC------GGCTG----CACACACTCATCACTC---TCGACGC- 181s AAA--ACGGCTGCAAAACG-GCTGCACACACTCATCAC-- 181s >s2 181s ACGTTT-----TCGAACCCCCCGAAATTTT---CCCCCCCCCCCCCCCCCCCCCCACTCA 181s TCACTCTCGACGCAAAAC------GGCTG----CACACACTCATCACTC---TCGACGC- 181s AAA--ACGGCTGCAAAACG-GCTGCACACACTCATCAC-- 181s >s0 181s A--TTTCTCTCTCAAACCCCCCGAAATTTTGGGCGCGCG-----------CACACACTCA 181s TCACTCTCGACGCAAAACATTTTGGGC-GCGCGCACACACTCATCACTCATTTTG----- 181s -------GGC-GC-------GC-GCACACACTCATCACTC 181s >s3 181s A--TTTCTCTCTCAAACCCCCCGAAATTTTGGGCGCGCG-----------CACACACTCA 181s TCACTCTCGACGCAAAACATTTTGGGC-G----CGCGCA--CA-CACTC--GTCG-CGCG 181s AAACTA---C-GC---ACGTGC-GCACACACTCATCACTC 181s autopkgtest [10:51:07]: test run-unit-test: -----------------------] 182s run-unit-test PASS 182s autopkgtest [10:51:08]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 182s autopkgtest [10:51:08]: @@@@@@@@@@@@@@@@@@@@ summary 182s run-unit-test PASS 199s nova [W] Using flock in prodstack6-s390x 199s Creating nova instance adt-plucky-s390x-probalign-20250315-104806-juju-7f2275-prod-proposed-migration-environment-20-05f1c957-c044-4fc2-9bce-66281657207c from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 199s nova [W] Timed out waiting for 5540bfe9-7aa7-4664-b313-131c2b46688b to get deleted.