0s autopkgtest [16:41:50]: starting date and time: 2025-03-15 16:41:50+0000 0s autopkgtest [16:41:50]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [16:41:50]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.4v3oudgc/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-10.secgroup --name adt-plucky-arm64-seqprep-20250315-164150-juju-7f2275-prod-proposed-migration-environment-2-bb35fef5-3026-42c7-85aa-1966bdad40f5 --image adt/ubuntu-plucky-arm64-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,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/ 143s autopkgtest [16:44:13]: testbed dpkg architecture: arm64 143s autopkgtest [16:44:13]: testbed apt version: 2.9.33 143s autopkgtest [16:44:13]: @@@@@@@@@@@@@@@@@@@@ test bed setup 144s autopkgtest [16:44:14]: testbed release detected to be: None 144s autopkgtest [16:44:14]: updating testbed package index (apt update) 145s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 145s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 145s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 145s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 146s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 146s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 146s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 146s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [111 kB] 147s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1856 B] 147s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 147s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [324 kB] 147s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [14.7 kB] 147s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 147s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [268 B] 148s Fetched 1078 kB in 3s (387 kB/s) 148s Reading package lists... 149s Reading package lists... 149s Building dependency tree... 149s Reading state information... 150s Calculating upgrade... 150s Calculating upgrade... 150s The following packages will be upgraded: 150s pinentry-curses python3-jinja2 strace 151s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 151s Need to get 647 kB of archives. 151s After this operation, 11.3 kB of additional disk space will be used. 151s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 151s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pinentry-curses arm64 1.3.1-2ubuntu3 [39.2 kB] 151s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 152s Fetched 647 kB in 1s (604 kB/s) 152s (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 ... 117701 files and directories currently installed.) 152s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 152s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 152s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_arm64.deb ... 152s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 152s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 152s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 152s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 152s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 153s Setting up strace (6.13+ds-1ubuntu1) ... 153s Processing triggers for man-db (2.13.0-1) ... 153s Reading package lists... 154s Building dependency tree... 154s Reading state information... 154s Solving dependencies... 154s The following packages will be REMOVED: 154s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 154s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 154s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 154s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 155s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 155s After this operation, 267 MB disk space will be freed. 155s (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 ... 117701 files and directories currently installed.) 155s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 155s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 155s Removing libpython3.12t64:arm64 (3.12.9-1) ... 155s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 155s Removing libnsl2:arm64 (1.3.0-3build3) ... 155s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 155s Removing libunwind8:arm64 (1.6.2-3.1) ... 155s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 155s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 157s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 157s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 157s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 157s /etc/kernel/postrm.d/initramfs-tools: 157s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 157s /etc/kernel/postrm.d/zz-flash-kernel: 157s flash-kernel: Kernel 6.11.0-8-generic has been removed. 157s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 158s /etc/kernel/postrm.d/zz-update-grub: 158s Sourcing file `/etc/default/grub' 158s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 158s Generating grub configuration file ... 158s Found linux image: /boot/vmlinuz-6.14.0-10-generic 158s Found initrd image: /boot/initrd.img-6.14.0-10-generic 158s Warning: os-prober will not be executed to detect other bootable partitions. 158s Systems on them will not be added to the GRUB boot configuration. 158s Check GRUB_DISABLE_OS_PROBER documentation entry. 158s Adding boot menu entry for UEFI Firmware Settings ... 158s done 158s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 158s Processing triggers for libc-bin (2.41-1ubuntu1) ... 158s (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 ... 81650 files and directories currently installed.) 158s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 159s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 159s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 159s autopkgtest [16:44:29]: upgrading testbed (apt dist-upgrade and autopurge) 159s Reading package lists... 159s Building dependency tree... 159s Reading state information... 160s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 160s Starting 2 pkgProblemResolver with broken count: 0 160s Done 161s Entering ResolveByKeep 161s 161s Calculating upgrade... 161s The following packages will be upgraded: 161s libc-bin libc-dev-bin libc6 libc6-dev locales 162s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 162s Need to get 9530 kB of archives. 162s After this operation, 0 B of additional disk space will be used. 162s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 164s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 164s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 167s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 167s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 172s Preconfiguring packages ... 172s Fetched 9530 kB in 10s (945 kB/s) 172s (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 ... 81647 files and directories currently installed.) 172s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 172s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 172s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 172s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 172s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 172s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 173s Setting up libc6:arm64 (2.41-1ubuntu2) ... 173s (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 ... 81647 files and directories currently installed.) 173s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 173s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 173s Setting up libc-bin (2.41-1ubuntu2) ... 173s (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 ... 81647 files and directories currently installed.) 173s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 173s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 173s Setting up locales (2.41-1ubuntu2) ... 174s Generating locales (this might take a while)... 176s en_US.UTF-8... done 176s Generation complete. 176s Setting up libc-dev-bin (2.41-1ubuntu2) ... 176s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 176s Processing triggers for man-db (2.13.0-1) ... 177s Processing triggers for systemd (257.3-1ubuntu3) ... 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 Solving dependencies... 179s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 179s autopkgtest [16:44:49]: rebooting testbed after setup commands that affected boot 203s autopkgtest [16:45:13]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 206s autopkgtest [16:45:16]: @@@@@@@@@@@@@@@@@@@@ apt-source seqprep 250s Get:1 http://ftpmaster.internal/ubuntu plucky/universe seqprep 1.3.2-9 (dsc) [2260 B] 250s Get:2 http://ftpmaster.internal/ubuntu plucky/universe seqprep 1.3.2-9 (tar) [37.2 MB] 250s Get:3 http://ftpmaster.internal/ubuntu plucky/universe seqprep 1.3.2-9 (diff) [12.5 kB] 251s gpgv: Signature made Thu Mar 14 19:39:56 2024 UTC 251s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 251s gpgv: issuer "emollier@debian.org" 251s gpgv: Can't check signature: No public key 251s dpkg-source: warning: cannot verify inline signature for ./seqprep_1.3.2-9.dsc: no acceptable signature found 251s autopkgtest [16:46:01]: testing package seqprep version 1.3.2-9 252s autopkgtest [16:46:02]: build not needed 255s autopkgtest [16:46:05]: test run-unit-test: preparing testbed 255s Reading package lists... 256s Building dependency tree... 256s Reading state information... 256s Starting pkgProblemResolver with broken count: 0 256s Starting 2 pkgProblemResolver with broken count: 0 256s Done 257s The following NEW packages will be installed: 257s seqprep seqprep-data 257s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 257s Need to get 35.9 MB of archives. 257s After this operation, 36.9 MB of additional disk space will be used. 257s Get:1 http://ftpmaster.internal/ubuntu plucky/universe arm64 seqprep arm64 1.3.2-9 [29.3 kB] 257s Get:2 http://ftpmaster.internal/ubuntu plucky/universe arm64 seqprep-data all 1.3.2-9 [35.9 MB] 297s Fetched 35.9 MB in 40s (899 kB/s) 297s Selecting previously unselected package seqprep. 297s (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 ... 81647 files and directories currently installed.) 297s Preparing to unpack .../seqprep_1.3.2-9_arm64.deb ... 297s Unpacking seqprep (1.3.2-9) ... 297s Selecting previously unselected package seqprep-data. 297s Preparing to unpack .../seqprep-data_1.3.2-9_all.deb ... 297s Unpacking seqprep-data (1.3.2-9) ... 298s Setting up seqprep (1.3.2-9) ... 298s Setting up seqprep-data (1.3.2-9) ... 298s Processing triggers for man-db (2.13.0-1) ... 299s autopkgtest [16:46:49]: test run-unit-test: [----------------------- 300s + . RUNTEST.sh 300s ++ /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 313s fastq record not beginning with @ 313s fastq record not beginning with @ 313s 313s Pairs Processed: 0 313s Pairs Merged: 14314 313s Pairs With Adapters: 4091 313s Pairs Discarded: 2228 313s CPU Time Used (Minutes): 0.224422 313s ++ /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 326s fastq record not beginning with @ 326s fastq record not beginning with @ 326s 326s Pairs Processed: 0 326s Pairs Merged: 0 326s Pairs With Adapters: 4091 326s Pairs Discarded: 2228 326s CPU Time Used (Minutes): 0.211325 326s ++ prog=gzcat 326s ++ gzcat ./out/pe_bad_contam_trimmed_1.fastq.gz 326s ++ zcat ./out/pe_bad_contam_trimmed_1.fastq.gz 326s ++ python3 seqlens.py 326s ++ gzcat ./out/pe_bad_contam_trimmed_2.fastq.gz 326s ++ zcat ./out/pe_bad_contam_trimmed_2.fastq.gz 326s ++ python3 seqlens.py 326s ++ gzcat ./out/pe_bad_contam_merged_1.fastq.gz 326s ++ python3 seqlens.py 326s ++ zcat ./out/pe_bad_contam_merged_1.fastq.gz 326s ++ gzcat ./out/pe_bad_contam_merged_2.fastq.gz 326s ++ zcat ./out/pe_bad_contam_merged_2.fastq.gz 326s ++ python3 seqlens.py 327s ++ gzcat ./out/pe_bad_contam_merged_s.fastq.gz 327s ++ zcat ./out/pe_bad_contam_merged_s.fastq.gz 327s ++ python3 seqlens.py 327s Test OK 327s autopkgtest [16:47:17]: test run-unit-test: -----------------------] 328s autopkgtest [16:47:18]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 328s run-unit-test PASS 328s autopkgtest [16:47:18]: @@@@@@@@@@@@@@@@@@@@ summary 328s run-unit-test PASS 347s nova [W] Using flock in prodstack6-arm64 347s Creating nova instance adt-plucky-arm64-seqprep-20250315-164150-juju-7f2275-prod-proposed-migration-environment-2-bb35fef5-3026-42c7-85aa-1966bdad40f5 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 347s nova [W] Timed out waiting for fcab2f61-f5df-460e-8df8-21965be82f1c to get deleted.