0s autopkgtest [02:53:17]: starting date and time: 2024-03-26 02:53:17+0000 0s autopkgtest [02:53:17]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [02:53:17]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.gx4w8k06/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed --apt-upgrade exonerate --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glib2.0/2.79.3-3ubuntu5 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@lcy02-55.secgroup --name adt-noble-amd64-exonerate-20240326-025317-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-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,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 886s autopkgtest [03:08:03]: testbed dpkg architecture: amd64 886s autopkgtest [03:08:03]: testbed apt version: 2.7.12 886s autopkgtest [03:08:03]: @@@@@@@@@@@@@@@@@@@@ test bed setup 886s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 886s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.0 kB] 886s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 886s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4027 kB] 886s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [7592 B] 886s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main i386 Packages [483 kB] 886s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 Packages [731 kB] 886s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 c-n-f Metadata [3508 B] 886s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted i386 Packages [6700 B] 886s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 Packages [37.9 kB] 886s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 c-n-f Metadata [116 B] 886s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 Packages [4390 kB] 886s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/universe i386 Packages [1260 kB] 886s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 c-n-f Metadata [9396 B] 886s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 Packages [96.8 kB] 886s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/multiverse i386 Packages [28.6 kB] 886s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 c-n-f Metadata [196 B] 889s Fetched 11.7 MB in 1s (7900 kB/s) 890s Reading package lists... 891s Reading package lists... 891s Building dependency tree... 891s Reading state information... 892s Calculating upgrade... 892s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 892s Reading package lists... 892s Building dependency tree... 892s Reading state information... 893s 0 upgraded, 0 newly installed, 0 to remove and 248 not upgraded. 893s sh: Attempting to set up Debian/Ubuntu apt sources automatically 893s sh: Distribution appears to be Ubuntu 894s Reading package lists... 894s Building dependency tree... 894s Reading state information... 895s eatmydata is already the newest version (131-1). 895s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 895s Reading package lists... 895s Building dependency tree... 895s Reading state information... 895s dbus is already the newest version (1.14.10-4ubuntu1). 895s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 896s Reading package lists... 896s Building dependency tree... 896s Reading state information... 896s rng-tools-debian is already the newest version (2.4). 896s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 896s Reading package lists... 897s Building dependency tree... 897s Reading state information... 897s The following packages will be REMOVED: 897s cloud-init* python3-configobj* python3-debconf* 897s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 897s After this operation, 3256 kB disk space will be freed. 897s (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 ... 71864 files and directories currently installed.) 897s Removing cloud-init (24.1.2-0ubuntu1) ... 898s Removing python3-configobj (5.0.8-3) ... 898s Removing python3-debconf (1.5.86) ... 898s Processing triggers for man-db (2.12.0-3) ... 899s (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 ... 71475 files and directories currently installed.) 899s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 899s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 899s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 899s invoke-rc.d: policy-rc.d denied execution of try-restart. 900s Reading package lists... 900s Building dependency tree... 900s Reading state information... 900s linux-generic is already the newest version (6.8.0-11.11+1). 900s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 900s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 900s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 900s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 903s Reading package lists... 903s Reading package lists... 903s Building dependency tree... 903s Reading state information... 903s Calculating upgrade... 903s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 903s Reading package lists... 904s Building dependency tree... 904s Reading state information... 904s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 904s autopkgtest [03:08:21]: rebooting testbed after setup commands that affected boot 930s autopkgtest [03:08:47]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 00:29:05 UTC 2024 931s autopkgtest [03:08:48]: @@@@@@@@@@@@@@@@@@@@ apt-source exonerate 932s Get:1 http://ftpmaster.internal/ubuntu noble/universe exonerate 2.4.0-5 (dsc) [2109 B] 932s Get:2 http://ftpmaster.internal/ubuntu noble/universe exonerate 2.4.0-5 (tar) [521 kB] 932s Get:3 http://ftpmaster.internal/ubuntu noble/universe exonerate 2.4.0-5 (diff) [9192 B] 932s gpgv: Signature made Thu Dec 3 21:18:18 2020 UTC 932s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 932s gpgv: issuer "tille@debian.org" 932s gpgv: Can't check signature: No public key 932s dpkg-source: warning: cannot verify inline signature for ./exonerate_2.4.0-5.dsc: no acceptable signature found 932s autopkgtest [03:08:49]: testing package exonerate version 2.4.0-5 932s autopkgtest [03:08:49]: build not needed 932s autopkgtest [03:08:49]: test run-unit-test: preparing testbed 932s Reading package lists... 933s Building dependency tree... 933s Reading state information... 933s Starting pkgProblemResolver with broken count: 0 933s Starting 2 pkgProblemResolver with broken count: 0 933s Done 933s The following additional packages will be installed: 933s exonerate 933s Suggested packages: 933s wise 933s The following NEW packages will be installed: 933s autopkgtest-satdep exonerate 933s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 933s Need to get 1608 kB/1609 kB of archives. 933s After this operation, 8491 kB of additional disk space will be used. 933s Get:1 /tmp/autopkgtest.GHegd4/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [704 B] 933s Get:2 http://ftpmaster.internal/ubuntu noble/universe amd64 exonerate amd64 2.4.0-5 [1608 kB] 934s Fetched 1608 kB in 0s (25.2 MB/s) 934s Selecting previously unselected package exonerate. 934s (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 ... 71420 files and directories currently installed.) 934s Preparing to unpack .../exonerate_2.4.0-5_amd64.deb ... 934s Unpacking exonerate (2.4.0-5) ... 934s Selecting previously unselected package autopkgtest-satdep. 934s Preparing to unpack .../1-autopkgtest-satdep.deb ... 934s Unpacking autopkgtest-satdep (0) ... 934s Setting up exonerate (2.4.0-5) ... 934s Setting up autopkgtest-satdep (0) ... 934s Processing triggers for man-db (2.12.0-3) ... 937s (Reading database ... 71518 files and directories currently installed.) 937s Removing autopkgtest-satdep (0) ... 937s autopkgtest [03:08:54]: test run-unit-test: [----------------------- 937s 937s /tmp/autopkgtest.GHegd4/autopkgtest_tmp/util/fastaexpode.test.sh 937s Made input file for fastaexplode 937s Make output directory for fastaexplode 937s Successfully ran fastaexplode on: fastaexplode.test.fasta 937s Expected number of seqs in output: 4 937s 937s /tmp/autopkgtest.GHegd4/autopkgtest_tmp/util/fastasort.test.sh 937s Sorted CALM_HUMAN 149 937s Sorted P53_HUMAN 393 937s Sorted TUBE_DROME 462 937s Sorted AF01595 1132 937s 937s /tmp/autopkgtest.GHegd4/autopkgtest_tmp/util/fastaremove.test.sh 937s Have calmodulin in input 937s ** FATAL ERROR **: Could not open list for removal [CALM_HUMAN] 937s exiting ... 937s Calmodulin successfully removed 937s 937s /tmp/autopkgtest.GHegd4/autopkgtest_tmp/util/fastaclip.test.sh 937s Clipped OK 937s >test:subseq(0,4) 937s ACGT 937s Clipped input correctly 937s 937s /tmp/autopkgtest.GHegd4/autopkgtest_tmp/util/fastaindex.fastafetch.test.sh 937s Made index fastafetch.test.idx 937s /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx CALM_HUMAN 937s expect 0 937s >CALM_HUMAN 937s MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFL 937s TMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYE 937s EFVQMMTAK 937s /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx P53_HUMAN 937s expect 0 937s >P53_HUMAN 937s MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAA 937s PPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKT 937s CPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRN 937s TFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVHVCACPGR 937s DRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALEL 937s KDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD 937s /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx A_MISSING_FROM_START 937s expect 1 937s ** FATAL ERROR **: Could not find identifier [A_MISSING_FROM_START] (missing -F ?) 937s exiting ... 937s /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx M_MISSING_FROM_MIDDLE 937s expect 1 937s ** FATAL ERROR **: Could not find identifier [M_MISSING_FROM_MIDDLE] (missing -F ?) 937s exiting ... 937s /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx z_MISSING_FROM_END 937s expect 1 937s ** FATAL ERROR **: Could not find identifier [z_MISSING_FROM_END] (missing -F ?) 937s exiting ... 937s fastaindex fastafetch test OK 937s 937s /tmp/autopkgtest.GHegd4/autopkgtest_tmp/util/fastaoverlap.test.sh 937s /usr/bin/fastaoverlap working OK 937s Generated 15 937s 937s /tmp/autopkgtest.GHegd4/autopkgtest_tmp/util/fastarevcomp.test.sh 937s Reverse complement created : ./data/cdna/calm.human.dna.fasta 937s Reverse complement created : fastarevcomp.rc.test.fasta 937s RC length is the same 937s RC length is the same 937s 2nd reverse complement same as original 937s 937s /tmp/autopkgtest.GHegd4/autopkgtest_tmp/util/fastanrdb.test.sh 937s Made input file for fastanrdb 937s Successfully ran fastanrdb on: fastanrdb.input.test.fasta 937s Expected number of seqs in output: 4 937s 937s /tmp/autopkgtest.GHegd4/autopkgtest_tmp/util/fastacomposition.test.sh 937s Calmodulin cDNA composition correct 937s 937s /tmp/autopkgtest.GHegd4/autopkgtest_tmp/util/fastarefomat.test.sh 937s Reformatted OK 937s >test 937s ACGTAACCGGTTAAACCCGGGTTTAAAACCCCGGGGTTTT 937s Reformatted length consistent 937s 937s /tmp/autopkgtest.GHegd4/autopkgtest_tmp/util/fastalength.test.sh 937s 149 CALM_HUMAN 937s Calmodulin length OK 937s Calmodulin identifier OK 937s 937s /tmp/autopkgtest.GHegd4/autopkgtest_tmp/util/fastasoftmask.fastahardmask.test.sh 937s Softmasked OK 937s >test 937s ACGNAACCGGNNAAACCCGGGNNNAAAACCCCGGGGNNNN 937s Hardmasked OK 937s Hardmasked file is same as original masked file 937s 937s /tmp/autopkgtest.GHegd4/autopkgtest_tmp/util/fastadiff.test.sh 937s fastadiff: id mismatch: CALM_HUMAN P53_HUMAN 937s Different seqs recognised as different 937s Identity test OK 937s 937s /tmp/autopkgtest.GHegd4/autopkgtest_tmp/util/fastasubseq.test.sh 937s Generated correct subseq 937s 937s /tmp/autopkgtest.GHegd4/autopkgtest_tmp/util/fastaclean.test.sh 937s >CALM_HUMAN:filter(clean) 937s MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFL 937s TMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYE 937s EFVQMMTAK 937s 937s /tmp/autopkgtest.GHegd4/autopkgtest_tmp/util/fastavalidcds.test.sh 937s 937s ** (process:1346): WARNING **: 03:08:54.560: odd_length length (7) not divisible by 3 937s 937s ** (process:1346): WARNING **: 03:08:54.561: too_short length (4) not divisible by 3 937s 937s ** (process:1346): WARNING **: 03:08:54.561: no_start missing start codon (has:AAA) 937s 937s ** (process:1346): WARNING **: 03:08:54.561: no_end missing stop codon (has:TTT) 937s 937s ** (process:1346): WARNING **: 03:08:54.561: in_frame_stop contains in-frame stop codon (pos:9, codon:TAG) 937s 937s ** (process:1346): WARNING **: 03:08:54.561: non_acgt_base contains non-ACGT base: [pos: 5 base: N] 937s Validiated CDS sequences OK 937s >valid_seq 937s ATGAAACCCGGGTTTTAA 937s Validated correctly a single seq from input 937s 937s /tmp/autopkgtest.GHegd4/autopkgtest_tmp/util/fastatranslate.test.sh 937s Extraced CDS for translation 937s Tranlated sequence 937s Tranlsated sequence correct 937s 937s /tmp/autopkgtest.GHegd4/autopkgtest_tmp/util/fastasplit.test.sh 937s Split fastasplit.test.fasta OK 937s Split into two files as expected 937s Input len 2136 937s Output len 2136 937s Input and output lengths match 937s 937s /tmp/autopkgtest.GHegd4/autopkgtest_tmp/ipcress/ipcress.simple.test.sh 937s ** Message: 03:08:54.608: Loaded [1] experiments 937s Ipcress run successfully 937s Found 1 product, as expected 937s 937s /tmp/autopkgtest.GHegd4/autopkgtest_tmp/exonerate/exonerate.simple.test.sh 937s Exonerate simple test OK 937s Score as expected: 10875 937s PASS 938s autopkgtest [03:08:55]: test run-unit-test: -----------------------] 938s autopkgtest [03:08:55]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 938s run-unit-test PASS 938s autopkgtest [03:08:55]: @@@@@@@@@@@@@@@@@@@@ summary 938s run-unit-test PASS 948s Creating nova instance adt-noble-amd64-exonerate-20240326-025317-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-amd64-server-20240325.img (UUID ba43860b-557a-4db2-b3f0-378a99bca08c)...