0s autopkgtest [19:05:08]: starting date and time: 2025-03-15 19:05:08+0000 0s autopkgtest [19:05:08]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [19:05:08]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.26m_z3o4/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade seqprep --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-seqprep-20250315-190508-juju-7f2275-prod-proposed-migration-environment-2-40f4c3cf-b15a-44bd-a990-513501e609c3 --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/ 134s autopkgtest [19:07:22]: testbed dpkg architecture: s390x 134s autopkgtest [19:07:22]: testbed apt version: 2.9.33 135s autopkgtest [19:07:23]: @@@@@@@@@@@@@@@@@@@@ test bed setup 135s autopkgtest [19:07:23]: testbed release detected to be: None 135s autopkgtest [19:07:23]: updating testbed package index (apt update) 136s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 136s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 136s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 136s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 136s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 137s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 137s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 137s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [113 kB] 137s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1824 B] 137s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 137s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [320 kB] 137s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [13.4 kB] 137s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3776 B] 137s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [240 B] 137s Fetched 1073 kB in 1s (763 kB/s) 138s Reading package lists... 138s Reading package lists... 138s Building dependency tree... 138s Reading state information... 139s Calculating upgrade... 139s Calculating upgrade... 139s The following packages were automatically installed and are no longer required: 139s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 139s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 139s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 139s linux-tools-6.11.0-8-generic 139s Use 'sudo apt autoremove' to remove them. 139s The following packages will be upgraded: 139s pinentry-curses python3-jinja2 strace 139s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 139s Need to get 652 kB of archives. 139s After this operation, 27.6 kB of additional disk space will be used. 139s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB] 139s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pinentry-curses s390x 1.3.1-2ubuntu3 [42.9 kB] 139s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 140s Fetched 652 kB in 1s (808 kB/s) 140s (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.) 140s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ... 140s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 140s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_s390x.deb ... 140s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 140s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 140s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 140s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 140s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 140s Setting up strace (6.13+ds-1ubuntu1) ... 140s Processing triggers for man-db (2.13.0-1) ... 141s Reading package lists... 141s Building dependency tree... 141s Reading state information... 141s Solving dependencies... 141s The following packages will be REMOVED: 141s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 141s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 141s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 141s linux-tools-6.11.0-8-generic* 141s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded. 141s After this operation, 167 MB disk space will be freed. 141s (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.) 141s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 141s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 141s Removing libpython3.12t64:s390x (3.12.9-1) ... 141s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 141s Removing libnsl2:s390x (1.3.0-3build3) ... 141s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 141s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 141s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 142s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 142s Processing triggers for libc-bin (2.41-1ubuntu1) ... 142s (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.) 142s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 142s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 142s autopkgtest [19:07:30]: upgrading testbed (apt dist-upgrade and autopurge) 143s Reading package lists... 143s Building dependency tree... 143s Reading state information... 143s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 143s Starting 2 pkgProblemResolver with broken count: 0 143s Done 143s Entering ResolveByKeep 143s 143s Calculating upgrade... 143s The following packages will be upgraded: 143s libc-bin libc-dev-bin libc6 libc6-dev locales 143s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 143s Need to get 9512 kB of archives. 143s After this operation, 8192 B of additional disk space will be used. 143s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB] 145s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB] 145s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB] 147s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB] 147s 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 7s (1384 kB/s) 151s (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.) 151s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ... 151s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 151s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ... 151s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 151s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ... 151s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 151s Setting up libc6:s390x (2.41-1ubuntu2) ... 151s (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.) 151s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ... 151s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 151s Setting up libc-bin (2.41-1ubuntu2) ... 151s (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.) 151s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 151s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 151s Setting up locales (2.41-1ubuntu2) ... 151s Generating locales (this might take a while)... 152s en_US.UTF-8... done 152s Generation complete. 152s Setting up libc-dev-bin (2.41-1ubuntu2) ... 152s Setting up libc6-dev:s390x (2.41-1ubuntu2) ... 152s Processing triggers for man-db (2.13.0-1) ... 153s Processing triggers for systemd (257.3-1ubuntu3) ... 154s Reading package lists... 154s Building dependency tree... 154s Reading state information... 154s Starting pkgProblemResolver with broken count: 0 154s Starting 2 pkgProblemResolver with broken count: 0 154s Done 154s Solving dependencies... 154s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 154s autopkgtest [19:07:42]: rebooting testbed after setup commands that affected boot 159s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 174s autopkgtest [19:08:02]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025 176s autopkgtest [19:08:04]: @@@@@@@@@@@@@@@@@@@@ apt-source seqprep 204s Get:1 http://ftpmaster.internal/ubuntu plucky/universe seqprep 1.3.2-9 (dsc) [2260 B] 204s Get:2 http://ftpmaster.internal/ubuntu plucky/universe seqprep 1.3.2-9 (tar) [37.2 MB] 204s Get:3 http://ftpmaster.internal/ubuntu plucky/universe seqprep 1.3.2-9 (diff) [12.5 kB] 204s gpgv: Signature made Thu Mar 14 19:39:56 2024 UTC 204s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 204s gpgv: issuer "emollier@debian.org" 204s gpgv: Can't check signature: No public key 204s dpkg-source: warning: cannot verify inline signature for ./seqprep_1.3.2-9.dsc: no acceptable signature found 204s autopkgtest [19:08:32]: testing package seqprep version 1.3.2-9 205s autopkgtest [19:08:33]: build not needed 207s autopkgtest [19:08:35]: test run-unit-test: preparing testbed 208s Reading package lists... 208s Building dependency tree... 208s Reading state information... 208s Starting pkgProblemResolver with broken count: 0 208s Starting 2 pkgProblemResolver with broken count: 0 208s Done 208s The following NEW packages will be installed: 208s seqprep seqprep-data 208s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 208s Need to get 35.9 MB of archives. 208s After this operation, 36.9 MB of additional disk space will be used. 208s Get:1 http://ftpmaster.internal/ubuntu plucky/universe s390x seqprep s390x 1.3.2-9 [29.5 kB] 208s Get:2 http://ftpmaster.internal/ubuntu plucky/universe s390x seqprep-data all 1.3.2-9 [35.9 MB] 235s Fetched 35.9 MB in 26s (1370 kB/s) 235s Selecting previously unselected package seqprep. 235s (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.) 235s Preparing to unpack .../seqprep_1.3.2-9_s390x.deb ... 235s Unpacking seqprep (1.3.2-9) ... 235s Selecting previously unselected package seqprep-data. 235s Preparing to unpack .../seqprep-data_1.3.2-9_all.deb ... 235s Unpacking seqprep-data (1.3.2-9) ... 235s Setting up seqprep (1.3.2-9) ... 235s Setting up seqprep-data (1.3.2-9) ... 235s Processing triggers for man-db (2.13.0-1) ... 236s autopkgtest [19:09:04]: test run-unit-test: [----------------------- 237s + . RUNTEST.sh 237s ++ /usr/bin/seqprep -6 -f ./data/multiplex_bad_contam_1.fq.gz -r ./data/multiplex_bad_contam_2.fq.gz -A GATCGGAAGAGCACACGTCT -B AGATCGGAAGAGCGTCGT -1 ./out/pe_bad_contam_merged_1.fastq.gz -2 ./out/pe_bad_contam_merged_2.fastq.gz -s ./out/pe_bad_contam_merged_s.fastq.gz -E ./info/alignments_merged.txt.gz 249s fastq record not beginning with @ 249s fastq record not beginning with @ 249s 249s Pairs Processed: 0 249s Pairs Merged: 14314 249s Pairs With Adapters: 4091 249s Pairs Discarded: 2228 249s CPU Time Used (Minutes): 0.201950 249s ++ /usr/bin/seqprep -6 -f ./data/multiplex_bad_contam_1.fq.gz -r ./data/multiplex_bad_contam_2.fq.gz -A GATCGGAAGAGCACACGTCT -B AGATCGGAAGAGCGTCGT -1 ./out/pe_bad_contam_trimmed_1.fastq.gz -2 ./out/pe_bad_contam_trimmed_2.fastq.gz -E ./info/alignments_trimmed.txt.gz 261s fastq record not beginning with @ 261s fastq record not beginning with @ 261s 261s Pairs Processed: 0 261s Pairs Merged: 0 261s Pairs With Adapters: 4091 261s Pairs Discarded: 2228 261s CPU Time Used (Minutes): 0.193351 261s ++ prog=gzcat 261s ++ gzcat ./out/pe_bad_contam_trimmed_1.fastq.gz 261s ++ zcat ./out/pe_bad_contam_trimmed_1.fastq.gz 261s ++ python3 seqlens.py 261s ++ gzcat ./out/pe_bad_contam_trimmed_2.fastq.gz 261s ++ zcat ./out/pe_bad_contam_trimmed_2.fastq.gz 261s ++ python3 seqlens.py 261s ++ gzcat ./out/pe_bad_contam_merged_1.fastq.gz 261s ++ zcat ./out/pe_bad_contam_merged_1.fastq.gz 261s ++ python3 seqlens.py 261s ++ gzcat ./out/pe_bad_contam_merged_2.fastq.gz 261s ++ zcat ./out/pe_bad_contam_merged_2.fastq.gz 261s ++ python3 seqlens.py 261s ++ gzcat ./out/pe_bad_contam_merged_s.fastq.gz 261s ++ zcat ./out/pe_bad_contam_merged_s.fastq.gz 261s ++ python3 seqlens.py 261s Test OK 261s autopkgtest [19:09:29]: test run-unit-test: -----------------------] 262s autopkgtest [19:09:30]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 262s run-unit-test PASS 262s autopkgtest [19:09:30]: @@@@@@@@@@@@@@@@@@@@ summary 262s run-unit-test PASS 268s nova [W] Using flock in prodstack6-s390x 268s Creating nova instance adt-plucky-s390x-seqprep-20250315-190508-juju-7f2275-prod-proposed-migration-environment-2-40f4c3cf-b15a-44bd-a990-513501e609c3 from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 268s nova [W] Timed out waiting for 8a587791-38c3-4d07-bfa4-32a3e8a345f3 to get deleted.