0s autopkgtest [19:45:39]: starting date and time: 2025-03-15 19:45:39+0000 0s autopkgtest [19:45:39]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [19:45:39]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.mvzb8_ka/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade wise --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-2@bos03-s390x-19.secgroup --name adt-plucky-s390x-wise-20250315-194538-juju-7f2275-prod-proposed-migration-environment-2-b16e132a-f515-4133-9903-fbdfc1a6dea1 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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/ 141s autopkgtest [19:48:00]: testbed dpkg architecture: s390x 141s autopkgtest [19:48:00]: testbed apt version: 2.9.33 141s autopkgtest [19:48:00]: @@@@@@@@@@@@@@@@@@@@ test bed setup 141s autopkgtest [19:48:00]: testbed release detected to be: None 142s autopkgtest [19:48:01]: updating testbed package index (apt update) 142s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 143s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 143s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 143s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 143s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [45.1 kB] 143s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [369 kB] 143s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.5 kB] 143s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [77.3 kB] 143s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1824 B] 143s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 143s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [314 kB] 144s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [13.3 kB] 144s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3532 B] 144s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [240 B] 144s Fetched 965 kB in 2s (634 kB/s) 145s Reading package lists... 145s Reading package lists... 145s Building dependency tree... 145s Reading state information... 145s Calculating upgrade... 146s Calculating upgrade... 146s The following packages were automatically installed and are no longer required: 146s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 146s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 146s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 146s linux-tools-6.11.0-8-generic 146s Use 'sudo apt autoremove' to remove them. 146s The following packages will be upgraded: 146s pinentry-curses python3-jinja2 strace 146s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 146s Need to get 652 kB of archives. 146s After this operation, 27.6 kB of additional disk space will be used. 146s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB] 146s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pinentry-curses s390x 1.3.1-2ubuntu3 [42.9 kB] 146s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 147s Fetched 652 kB in 1s (686 kB/s) 147s (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.) 147s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ... 147s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 147s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_s390x.deb ... 147s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 147s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 147s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 147s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 147s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 147s Setting up strace (6.13+ds-1ubuntu1) ... 147s Processing triggers for man-db (2.13.0-1) ... 148s Reading package lists... 148s Building dependency tree... 148s Reading state information... 148s Solving dependencies... 148s The following packages will be REMOVED: 148s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 148s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 148s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 148s linux-tools-6.11.0-8-generic* 148s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded. 148s After this operation, 167 MB disk space will be freed. 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 ... 81428 files and directories currently installed.) 148s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 148s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 148s Removing libpython3.12t64:s390x (3.12.9-1) ... 148s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 149s Removing libnsl2:s390x (1.3.0-3build3) ... 149s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 149s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 149s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 150s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 150s Processing triggers for libc-bin (2.41-1ubuntu1) ... 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 ... 56328 files and directories currently installed.) 150s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 150s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 150s autopkgtest [19:48:09]: upgrading testbed (apt dist-upgrade and autopurge) 150s Reading package lists... 150s Building dependency tree... 150s Reading state information... 150s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 150s Starting 2 pkgProblemResolver with broken count: 0 150s Done 151s Entering ResolveByKeep 151s 151s Calculating upgrade... 151s The following packages will be upgraded: 151s libc-bin libc-dev-bin libc6 libc6-dev locales 151s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 151s Need to get 9512 kB of archives. 151s After this operation, 8192 B of additional disk space will be used. 151s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB] 153s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB] 153s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB] 156s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB] 157s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB] 161s Preconfiguring packages ... 161s Fetched 9512 kB in 10s (956 kB/s) 161s (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.) 161s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ... 161s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 162s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ... 162s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 162s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ... 162s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 162s Setting up libc6:s390x (2.41-1ubuntu2) ... 162s (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.) 162s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ... 162s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 162s Setting up libc-bin (2.41-1ubuntu2) ... 162s (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.) 162s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 162s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 162s Setting up locales (2.41-1ubuntu2) ... 162s Generating locales (this might take a while)... 163s en_US.UTF-8... done 163s Generation complete. 163s Setting up libc-dev-bin (2.41-1ubuntu2) ... 163s Setting up libc6-dev:s390x (2.41-1ubuntu2) ... 163s Processing triggers for man-db (2.13.0-1) ... 164s Processing triggers for systemd (257.3-1ubuntu3) ... 165s Reading package lists... 165s Building dependency tree... 165s Reading state information... 165s Starting pkgProblemResolver with broken count: 0 165s Starting 2 pkgProblemResolver with broken count: 0 165s Done 165s Solving dependencies... 166s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 166s autopkgtest [19:48:25]: rebooting testbed after setup commands that affected boot 186s autopkgtest [19:48:45]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025 188s autopkgtest [19:48:47]: @@@@@@@@@@@@@@@@@@@@ apt-source wise 194s Get:1 http://ftpmaster.internal/ubuntu plucky/universe wise 2.4.1-25 (dsc) [2305 B] 194s Get:2 http://ftpmaster.internal/ubuntu plucky/universe wise 2.4.1-25 (tar) [3410 kB] 194s Get:3 http://ftpmaster.internal/ubuntu plucky/universe wise 2.4.1-25 (diff) [39.9 kB] 194s gpgv: Signature made Thu Aug 15 10:43:37 2024 UTC 194s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 194s gpgv: issuer "emollier@debian.org" 194s gpgv: Can't check signature: No public key 194s dpkg-source: warning: cannot verify inline signature for ./wise_2.4.1-25.dsc: no acceptable signature found 194s autopkgtest [19:48:53]: testing package wise version 2.4.1-25 194s autopkgtest [19:48:53]: build not needed 196s autopkgtest [19:48:55]: test run-unit-test: preparing testbed 197s Reading package lists... 197s Building dependency tree... 197s Reading state information... 197s Starting pkgProblemResolver with broken count: 0 197s Starting 2 pkgProblemResolver with broken count: 0 197s Done 197s The following NEW packages will be installed: 197s wise wise-data 197s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 197s Need to get 1018 kB of archives. 197s After this operation, 4372 kB of additional disk space will be used. 197s Get:1 http://ftpmaster.internal/ubuntu plucky/universe s390x wise-data all 2.4.1-25 [83.0 kB] 198s Get:2 http://ftpmaster.internal/ubuntu plucky/universe s390x wise s390x 2.4.1-25 [935 kB] 198s Fetched 1018 kB in 1s (1061 kB/s) 198s Selecting previously unselected package wise-data. 199s (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.) 199s Preparing to unpack .../wise-data_2.4.1-25_all.deb ... 199s Unpacking wise-data (2.4.1-25) ... 199s Selecting previously unselected package wise. 199s Preparing to unpack .../wise_2.4.1-25_s390x.deb ... 199s Unpacking wise (2.4.1-25) ... 199s Setting up wise-data (2.4.1-25) ... 199s Setting up wise (2.4.1-25) ... 199s Processing triggers for man-db (2.13.0-1) ... 200s autopkgtest [19:48:59]: test run-unit-test: [----------------------- 200s >>> Doing promoterwise promoterwise standard test 200s >>> Calling [promoterwise -silent pw.human pw.mouse > TEMP-PW] 200s >>> promoterwise ... Failed 200s >>> Doing basic-cdna cdna test case (protein v cdna), all outputs 200s >>> Calling [estwise short.pep short.dna -indel 1e-5 -subs 1e-5 -pretty -para -sum -alb -pal -silent -alg 333 > TEMP] 200s >>> basic-cdna ... Failed 200s >>> Doing basic-genomic genomic test case (protein v genomic), all outputs 200s >>> Calling [genewise short.pep short.dna -pretty -para -genes -sum -cdna -trans -ace -gener -alb -pal -quiet -dymem linear > TEMP] 200s Warning Error 200s Strangely truncated line in fasta file 200s Warning Error 200s Strangely truncated line in fasta file 200s Warning Error 200s Attempting to access CompMat with aminoacid numbers 190:0 (they must 200s be bound between 0:26, returning 0 here 200s Warning Error 200s Attempting to access CompMat with aminoacid numbers 190:1 (they must 200s be bound between 0:26, returning 0 here 200s Warning Error 200s Attempting to access CompMat with aminoacid numbers 190:2 (they must 200s be bound between 0:26, returning 0 here 200s Warning Error 200s Attempting to access CompMat with aminoacid numbers 190:3 (they must 200s be bound between 0:26, returning 0 here 200s Warning Error 200s Attempting to access CompMat with aminoacid numbers 190:4 (they must 200s be bound between 0:26, returning 0 here 200s Warning Error 200s Attempting to access CompMat with aminoacid numbers 190:5 (they must 200s be bound between 0:26, returning 0 here 200s Warning Error 200s Attempting to access CompMat with aminoacid numbers 190:6 (they must 200s be bound between 0:26, returning 0 here 200s Warning Error 200s Attempting to access CompMat with aminoacid numbers 190:7 (they must 200s be bound between 0:26, returning 0 here 200s Warning Error 200s Attempting to access CompMat with aminoacid numbers 190:8 (they must 200s be bound between 0:26, returning 0 here 200s Warning Error 200s Attempting to access CompMat with aminoacid numbers 190:9 (they must 200s be bound between 0:26, returning 0 here 200s Warning Error 200s Attempting to access CompMat with aminoacid numbers 190:10 (they must 200s be bound between 0:26, returning 0 here 200s Warning Error 200s Attempting to access CompMat with aminoacid numbers 190:11 (they must 200s be bound between 0:26, returning 0 here 200s Warning Error 200s Attempting to access CompMat with aminoacid numbers 190:12 (they must 200s be bound between 0:26, returning 0 here 200s Warning Error 200s Attempting to access CompMat with aminoacid numbers 190:13 (they must 200s be bound between 0:26, returning 0 here 200s Warning Error 200s Attempting to access CompMat with aminoacid numbers 190:14 (they must 200s be bound between 0:26, returning 0 here 200s Warning Error 200s Attempting to access CompMat with aminoacid numbers 190:15 (they must 200s be bound between 0:26, returning 0 here 200s Warning Error 200s Attempting to access CompMat with aminoacid numbers 190:16 (they must 200s be bound between 0:26, returning 0 here 200s Warning Error 200s Attempting to access CompMat with aminoacid numbers 190:17 (they must 200s be bound between 0:26, returning 0 here 200s Warning Error 200s Attempting to access CompMat with aminoacid numbers 190:18 (they must 200s be bound between 0:26, returning 0 here 200s Warning Error 200s Attempting to access CompMat with aminoacid numbers 190:19 (they must 200s be bound between 0:26, returning 0 here 200s Warning Error 200s Attempting to access CompMat with aminoacid numbers 190:20 (they must 200s be bound between 0:26, returning 0 here 200s Warning Error 200s Attempting to access CompMat with aminoacid numbers 190:21 (they must 200s be bound between 0:26, returning 0 here 200s Warning Error 200s Attempting to access CompMat with aminoacid numbers 190:22 (they must 200s be bound between 0:26, returning 0 here 200s Warning Error 200s Attempting to access CompMat with aminoacid numbers 190:23 (they must 200s be bound between 0:26, returning 0 here 200s Warning Error 200s Attempting to access CompMat with aminoacid numbers 190:24 (they must 200s be bound between 0:26, returning 0 here 200s Warning Error 200s Attempting to access CompMat with aminoacid numbers 190:25 (they must 200s be bound between 0:26, returning 0 here 200s >>> basic-genomic ... Failed 200s >>> Doing hmm-binary-cdna cdna test case (protein v cdna), all outputs 200s >>> Calling [estwise HMM.binary -indel 1e-5 -subs 1e-5 -hmmer short.dna -pretty -para -sum -alb -pal -quiet -alg 333L > TEMP] 200s Warning Error 200s Strangely truncated line in fasta file 200s FATAL: No support for non-protein, non-nucleic acid alphabets. 200s >>> Bad exit status - 256 (system - ) 200s >>> hmm-binary-cdna ... Failed 200s >>> Doing hmm-wrong-dna HMMs vs DNA sequence when there is no match 200s >>> Calling [genewise wrong.hmm -hmmer short.dna -alg 623 -pal > TEMP] 200s Warning Error 200s Strangely truncated line in fasta file 200s Information 200s In making HSHNCPA1 a genomic sequence, converted 3 bases (0.7%) to 200s N's from non ATGCN 200s GeneWise6 Matrix calculation: [ 0] Cells 0%[ 1000] Cells 3%[ 2000] Cells 6%[ 3000] Cells 9%[ 4000] Cells 12%[ 5000] Cells 15%[ 6000] Cells 18%[ 7000] Cells 21%[ 8000] Cells 24%[ 9000] Cells 27%[ 10000] Cells 30%[ 11000] Cells 33%[ 12000] Cells 36%[ 13000] Cells 39%[ 14000] Cells 42%[ 15000] Cells 45%[ 16000] Cells 48%[ 17000] Cells 51%[ 18000] Cells 54%[ 19000] Cells 57%[ 20000] Cells 60%[ 21000] Cells 63%[ 22000] Cells 66%[ 23000] Cells 69%[ 24000] Cells 73%[ 25000] Cells 76%[ 26000] Cells 79%[ 27000] Cells 82%[ 28000] Cells 85%[ 29000] Cells 88%[ 30000] Cells 91%[ 31000] Cells 94%[ 32000] Cells 97% 200s >>> hmm-wrong-dna ... Passed 200s >>> Doing hmm-wrong-dna-est HMMs vs DNA sequence when there is no match 200s >>> Calling [estwise wrong.hmm -hmmer short.dna -alg 333 -pal > TEMP] 200s Warning Error 200s Strangely truncated line in fasta file 200s Information 200s In making HSHNCPA1 a cdna sequence, converted 3 bases (0.7%) to N's 200s from non ATGCN 200s EstWise3 Matrix calculation: [ 0] Cells 0%[ 1000] Cells 3%[ 2000] Cells 6%[ 3000] Cells 9%[ 4000] Cells 12%[ 5000] Cells 15%[ 6000] Cells 18%[ 7000] Cells 21%[ 8000] Cells 24%[ 9000] Cells 27%[ 10000] Cells 30%[ 11000] Cells 33%[ 12000] Cells 36%[ 13000] Cells 39%[ 14000] Cells 42%[ 15000] Cells 45%[ 16000] Cells 48%[ 17000] Cells 51%[ 18000] Cells 54%[ 19000] Cells 57%[ 20000] Cells 60%[ 21000] Cells 63%[ 22000] Cells 66%[ 23000] Cells 69%[ 24000] Cells 73%[ 25000] Cells 76%[ 26000] Cells 79%[ 27000] Cells 82%[ 28000] Cells 85%[ 29000] Cells 88%[ 30000] Cells 91%[ 31000] Cells 94%[ 32000] Cells 97% 200s EstWise3 Matrix calculation: [ 0] Cells 0%[ 1000] Cells 3%[ 2000] Cells 6%[ 3000] Cells 9%[ 4000] Cells 12%[ 5000] Cells 15%[ 6000] Cells 18%[ 7000] Cells 21%[ 8000] Cells 24%[ 9000] Cells 27%[ 10000] Cells 30%[ 11000] Cells 33%[ 12000] Cells 36%[ 13000] Cells 39%[ 14000] Cells 42%[ 15000] Cells 45%[ 16000] Cells 48%[ 17000] Cells 51%[ 18000] Cells 54%[ 19000] Cells 57%[ 20000] Cells 60%[ 21000] Cells 63%[ 22000] Cells 66%[ 23000] Cells 69%[ 24000] Cells 73%[ 25000] Cells 76%[ 26000] Cells 79%[ 27000] Cells 82%[ 28000] Cells 85%[ 29000] Cells 88%[ 30000] Cells 91%[ 31000] Cells 94%[ 32000] Cells 97% 200s >>> hmm-wrong-dna-est ... Failed 200s >>> Doing hmm-ascii-genomic cdna test case (protein v cdna), all outputs 200s >>> Calling [genewise -init local HMM.ascii -hmmer short.dna -pretty -para -genes -sum -cdna -trans -ace -gener -alb -pal -quiet > TEMP] 200s Warning Error 200s Strangely truncated line in fasta file 200s FATAL: No support for non-protein, non-nucleic acid alphabets. 200s >>> Bad exit status - 256 (system - ) 200s >>> hmm-ascii-genomic ... Failed 200s >>> Doing genewise-db genewisedb hmm vs DNA sequences. Could take a while 200s >>> Calling [genewisedb rrm.HMM -hmmer dna.db -pretty -para -gener -genes -cdna -trans -ace -quiet -init global > TEMP] 200s Warning Error 200s DB searching: just finished [Query Pos: 0] [Target Pos: 5] 200s Strangely truncated line in fasta file 200s Warning Error 200s Strangely truncated line in fasta file 200s >>> genewise-db ... Passed 200s >>> Doing genewise-db-lite genewisedb hmm vs DNA sequences, using GWLITE. Could take a while 200s >>> Calling [genewisedb rrm.HMM -hmmer dna.db -pretty -para -gener -genes -cdna -trans -ace -quiet -init global -alg 6LITE > TEMP] 200s Warning Error 200s DB searching: just finished [Query Pos: 0] [Target Pos: 5] 200s Strangely truncated line in fasta file 200s Warning Error 200s Strangely truncated line in fasta file 200s >>> genewise-db-lite ... Passed 200s >>> Doing estwise-db estwisedb hmm vs DNA sequences. Could take a while 200s >>> Calling [estwisedb -init local rrm.HMM -hmmer dna.db -pretty -para -alb -quiet -alg 333 -aalg 333 > TEMP] 201s Warning Error 201s DB searching: just finished [Query Pos: 0] [Target Pos: 5] 201s Strangely truncated line in fasta file 201s Warning Error 201s Strangely truncated line in fasta file 201s >>> estwise-db ... Passed 201s >>> Doing pswdb Protein smith waterman db search 201s >>> Calling [pswdb road.pep pep.fa -quiet > TEMP ] 201s Warning Error 201s Strangely truncated line in fasta file 201s Warning Error 201s Before any actual search in db searching 201s Out of memory, trying to realloc 1696416052 bytes 201s 201s Fatal Error 201s Before any actual search in db searching 201s Cannot realloc histogram... going to die... sorry! 201s >>> Bad exit status - 512 (system - ) 201s >>> pswdb ... Failed 201s >>> Doing genewisedb-pfam-mode genewisedb designed for Pfam searching 201s >>> Calling [genewisedb -pfam rrm.HMM -dnas short.dna -pretty -para -alb -quiet -alg 623 -aalg 623L > TEMP] 201s Warning Error 201s Strangely truncated line in fasta file 201s >>> genewisedb-pfam-mode ... Failed 201s Tests failed 201s PLEASE: email ewan birney (birney@sanger.ac.uk) with the test.results file 201s 201s autopkgtest [19:49:00]: test run-unit-test: -----------------------] 201s run-unit-test PASS 201s autopkgtest [19:49:00]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 202s autopkgtest [19:49:01]: @@@@@@@@@@@@@@@@@@@@ summary 202s run-unit-test PASS 219s nova [W] Using flock in prodstack6-s390x 219s flock: timeout while waiting to get lock 219s Creating nova instance adt-plucky-s390x-wise-20250315-194538-juju-7f2275-prod-proposed-migration-environment-2-b16e132a-f515-4133-9903-fbdfc1a6dea1 from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 219s nova [W] Timed out waiting for a17a8814-1afa-4bb3-bf0e-3e5391bfce37 to get deleted.