0s autopkgtest [01:59:27]: starting date and time: 2024-11-04 01:59:27+0000 0s autopkgtest [01:59:27]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [01:59:27]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ni20krp9/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:tm-align --apt-upgrade tm-align --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=tm-align/20190822+dfsg-3 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@lcy02-42.secgroup --name adt-plucky-amd64-tm-align-20241104-015927-juju-7f2275-prod-proposed-migration-environment-15-c174c754-aa4a-4ebe-a737-47131b08d287 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --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/ 68s autopkgtest [02:00:35]: testbed dpkg architecture: amd64 68s autopkgtest [02:00:35]: testbed apt version: 2.9.8 68s autopkgtest [02:00:35]: @@@@@@@@@@@@@@@@@@@@ test bed setup 68s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 68s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [31.2 kB] 68s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [177 kB] 68s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [2268 kB] 68s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 68s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [165 kB] 68s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [238 kB] 68s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 68s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [833 kB] 68s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [1715 kB] 68s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [58.6 kB] 68s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [18.1 kB] 69s Fetched 5618 kB in 1s (9502 kB/s) 69s Reading package lists... 70s Reading package lists... 71s Building dependency tree... 71s Reading state information... 71s Calculating upgrade... 71s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 71s Reading package lists... 72s Building dependency tree... 72s Reading state information... 72s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 72s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 72s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 72s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 72s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 73s Reading package lists... 73s Reading package lists... 74s Building dependency tree... 74s Reading state information... 74s Calculating upgrade... 74s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 74s Reading package lists... 75s Building dependency tree... 75s Reading state information... 75s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 76s autopkgtest [02:00:43]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 76s autopkgtest [02:00:43]: @@@@@@@@@@@@@@@@@@@@ apt-source tm-align 77s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/universe tm-align 20190822+dfsg-3 (dsc) [2077 B] 77s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe tm-align 20190822+dfsg-3 (tar) [52.8 kB] 77s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe tm-align 20190822+dfsg-3 (diff) [818 kB] 77s gpgv: Signature made Mon Sep 16 11:21:36 2024 UTC 77s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 77s gpgv: issuer "tille@debian.org" 77s gpgv: Can't check signature: No public key 77s dpkg-source: warning: cannot verify inline signature for ./tm-align_20190822+dfsg-3.dsc: no acceptable signature found 77s autopkgtest [02:00:44]: testing package tm-align version 20190822+dfsg-3 77s autopkgtest [02:00:44]: build not needed 77s autopkgtest [02:00:44]: test run-unit-test: preparing testbed 78s Reading package lists... 78s Building dependency tree... 78s Reading state information... 79s Starting pkgProblemResolver with broken count: 0 79s Starting 2 pkgProblemResolver with broken count: 0 79s Done 79s The following additional packages will be installed: 79s libgfortran5 tm-align 79s Suggested packages: 79s pymol rasmol 79s The following NEW packages will be installed: 79s autopkgtest-satdep libgfortran5 tm-align 79s 0 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. 79s Need to get 1795 kB/1796 kB of archives. 79s After this operation, 4412 kB of additional disk space will be used. 79s Get:1 /tmp/autopkgtest.CJwpDv/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [708 B] 79s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-7ubuntu1 [909 kB] 79s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 tm-align amd64 20190822+dfsg-3 [886 kB] 80s Fetched 1795 kB in 0s (26.2 MB/s) 80s Selecting previously unselected package libgfortran5:amd64. 80s (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 ... 75323 files and directories currently installed.) 80s Preparing to unpack .../libgfortran5_14.2.0-7ubuntu1_amd64.deb ... 80s Unpacking libgfortran5:amd64 (14.2.0-7ubuntu1) ... 80s Selecting previously unselected package tm-align. 80s Preparing to unpack .../tm-align_20190822+dfsg-3_amd64.deb ... 80s Unpacking tm-align (20190822+dfsg-3) ... 80s Selecting previously unselected package autopkgtest-satdep. 80s Preparing to unpack .../1-autopkgtest-satdep.deb ... 80s Unpacking autopkgtest-satdep (0) ... 80s Setting up libgfortran5:amd64 (14.2.0-7ubuntu1) ... 80s Setting up tm-align (20190822+dfsg-3) ... 80s Setting up autopkgtest-satdep (0) ... 80s Processing triggers for man-db (2.12.1-3) ... 81s Processing triggers for libc-bin (2.40-1ubuntu3) ... 83s (Reading database ... 75339 files and directories currently installed.) 83s Removing autopkgtest-satdep (0) ... 84s autopkgtest [02:00:51]: test run-unit-test: [----------------------- 84s Run TMalign... 84s 84s ************************************************************************** 84s * TM-align (Version 20190822) * 84s * An algorithm for protein structure alignment and comparison * 84s * Based on statistics: * 84s * 0.0 < TM-score < 0.30, random structural similarity * 84s * 0.5 < TM-score < 1.00, in about the same fold * 84s * Reference: Y Zhang and J Skolnick, Nucl Acids Res 33, 2302-9 (2005) * 84s * Please email your comments and suggestions to: zhng@umich.edu * 84s ************************************************************************** 84s 84s Name of Chain_1: 1ni7.pdb 84s Name of Chain_2: 5eep.pdb 84s Length of Chain_1: 149 residues 84s Length of Chain_2: 140 residues 84s 84s Aligned length= 140, RMSD= 1.60, Seq_ID=n_identical/n_aligned= 0.986 84s TM-score= 0.85044 (if normalized by length of Chain_1) 84s TM-score= 0.90009 (if normalized by length of Chain_2) 84s (You should use TM-score normalized by length of the reference protein) 84s 84s (":" denotes aligned residue pairs of d < 5.0 A, "." denotes other aligned residues) 84s MTNPQFAGHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAATKQVLE 84s : ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 84s ------G-HPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAAAKQV-- 84s 84s Run TMscore... 84s 84s ***************************************************************************** 84s * TM-SCORE * 84s * A scoring function to assess the similarity of protein structures * 84s * Based on statistics: * 84s * 0.0 < TM-score < 0.17, random structural similarity * 84s * 0.5 < TM-score < 1.00, in about the same fold * 84s * Reference: Yang Zhang and Jeffrey Skolnick, Proteins 2004 57: 702-710 * 84s * For comments, please email to: zhng@umich.edu * 84s ***************************************************************************** 84s 84s Structure1: 1ni7.pdb Length= 149 84s Structure2: 5eep.pdb Length= 140 (by which all scores are normalized) 84s Number of residues in common= 140 84s RMSD of the common residues= 1.616 84s 84s TM-score = 0.8987 (d0= 4.40) 84s MaxSub-score= 0.8459 (d0= 3.50) 84s GDT-TS-score= 0.8321 %(d<1)=0.4786 %(d<2)=0.8571 %(d<4)=0.9929 %(d<8)=1.0000 84s GDT-HA-score= 0.6214 %(d<0.5)=0.1571 %(d<1)=0.4786 %(d<2)=0.8571 %(d<4)=0.9929 84s 84s -------- rotation matrix to rotate Chain-1 to Chain-2 ------ 84s i t(i) u(i,1) u(i,2) u(i,3) 84s 1 0.9977278941 -0.2584957318 -0.9156232244 -0.3079189302 84s 2 13.5083713477 -0.8848339137 0.0965207762 0.4557989522 84s 3 45.5856492856 -0.3876195322 0.3902791958 -0.8351246898 84s 84s Superposition in the TM-score: Length(d<5.0)=140 RMSD= 1.62 84s (":" denotes the residue pairs of distance < 5.0 Angstrom) 84s MTNPQFAGHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAATKQVLE 84s :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 84s -------GHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAAAKQV-- 84s 12345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789 84s 84s autopkgtest [02:00:51]: test run-unit-test: -----------------------] 84s autopkgtest [02:00:51]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 84s run-unit-test PASS 84s autopkgtest [02:00:51]: @@@@@@@@@@@@@@@@@@@@ summary 84s run-unit-test PASS 105s nova [W] Skipping flock for amd64 105s Creating nova instance adt-plucky-amd64-tm-align-20241104-015927-juju-7f2275-prod-proposed-migration-environment-15-c174c754-aa4a-4ebe-a737-47131b08d287 from image adt/ubuntu-plucky-amd64-server-20241103.img (UUID 35ab818c-a1b8-49b0-b1ec-61e6c5b42b5f)...