0s autopkgtest [20:44:19]: starting date and time: 2026-02-06 20:44:19+0000 0s autopkgtest [20:44:19]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [20:44:19]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.21iedhl9/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade mothur --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.42-2ubuntu5 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@sto01-29.secgroup --name adt-resolute-amd64-mothur-20260206-204418-juju-7f2275-prod-proposed-migration-environment-20-2c781b97-fc0b-4333-98c6-f1297cb63920 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-amd64-mothur-20260206-204418-juju-7f2275-prod-proposed-migration-environment-20-2c781b97-fc0b-4333-98c6-f1297cb63920 from image adt/ubuntu-resolute-amd64-server-20260204.img (UUID fedf54b4-458b-493e-8072-6425c19717b4)... 83s autopkgtest [20:45:42]: testbed dpkg architecture: amd64 83s autopkgtest [20:45:42]: testbed apt version: 3.1.14 84s autopkgtest [20:45:43]: @@@@@@@@@@@@@@@@@@@@ test bed setup 84s autopkgtest [20:45:43]: testbed release detected to be: None 84s autopkgtest [20:45:43]: updating testbed package index (apt update) 85s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 85s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 85s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 85s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 85s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [201 kB] 85s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [32.7 kB] 85s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [10.7 kB] 85s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1547 kB] 85s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [189 kB] 85s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [266 kB] 85s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [6500 B] 85s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3692 B] 85s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [80.4 kB] 85s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [336 B] 85s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [1433 kB] 86s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [550 kB] 86s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [36.8 kB] 86s Get:18 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [28.2 kB] 86s Get:19 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [4892 B] 86s Get:20 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [1104 B] 86s Fetched 4516 kB in 1s (4022 kB/s) 87s Reading package lists... 87s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 87s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 87s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 88s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 88s Reading package lists... 88s Reading package lists... 88s Building dependency tree... 88s Reading state information... 88s Calculating upgrade... 88s The following packages will be upgraded: 88s amd64-microcode apt busybox-initramfs busybox-static dmsetup findutils less 88s libapt-pkg7.0 libattr1 libc-bin libc-gconv-modules-extra libc6 88s libdevmapper1.02.1 libdrm-amdgpu1 libdrm-common libdrm2 libgpm2 libkeyutils1 88s libmaxminddb0 libnpth0t64 libsensors-config libsensors5 locales mawk patch 88s pollinate python3-linkify-it python3-markdown-it python3-referencing sed tar 88s 31 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 88s Need to get 14.4 MB of archives. 88s After this operation, 270 kB disk space will be freed. 88s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 findutils amd64 4.10.0-3build2 [307 kB] 88s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 sed amd64 4.9-2build3 [195 kB] 88s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 tar amd64 1.35+dfsg-3.1build2 [257 kB] 89s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libc-gconv-modules-extra amd64 2.42-2ubuntu5 [1394 kB] 89s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libc6 amd64 2.42-2ubuntu5 [2041 kB] 89s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libc-bin amd64 2.42-2ubuntu5 [702 kB] 89s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 libattr1 amd64 1:2.5.2-3build2 [11.4 kB] 89s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 mawk amd64 1.3.4.20260129-1 [133 kB] 89s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libapt-pkg7.0 amd64 3.1.15 [1151 kB] 89s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 apt amd64 3.1.15 [1479 kB] 89s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libdevmapper1.02.1 amd64 2:1.02.205-2ubuntu3 [142 kB] 89s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 dmsetup amd64 2:1.02.205-2ubuntu3 [79.4 kB] 89s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 less amd64 668-1build1 [172 kB] 89s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libkeyutils1 amd64 1.6.3-6ubuntu3 [10.6 kB] 89s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 locales all 2.42-2ubuntu5 [4255 kB] 89s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-linkify-it all 2.0.3-1ubuntu3 [19.4 kB] 89s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-markdown-it all 3.0.0-3build1 [54.4 kB] 89s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-static amd64 1:1.37.0-7ubuntu1 [1034 kB] 89s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-common all 2.4.131-1 [9774 B] 89s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm2 amd64 2.4.131-1 [42.3 kB] 89s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libgpm2 amd64 1.20.7-12build1 [14.4 kB] 89s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 libmaxminddb0 amd64 1.12.2-1build2 [18.9 kB] 89s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors-config all 1:3.6.2-2build1 [6862 B] 89s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors5 amd64 1:3.6.2-2build1 [28.9 kB] 89s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-initramfs amd64 1:1.37.0-7ubuntu1 [191 kB] 89s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-amdgpu1 amd64 2.4.131-1 [23.2 kB] 89s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 libnpth0t64 amd64 1.8-3build1 [9302 B] 89s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 patch amd64 2.8-2build1 [95.7 kB] 89s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 pollinate all 4.33-4ubuntu5 [14.0 kB] 89s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-referencing all 0.36.2-1ubuntu2 [22.2 kB] 89s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 amd64-microcode amd64 3.20251202.1ubuntu1 [459 kB] 90s dpkg-preconfigure: unable to re-open stdin: No such file or directory 90s Fetched 14.4 MB in 1s (14.1 MB/s) 90s (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 ... 83957 files and directories currently installed.) 90s Preparing to unpack .../findutils_4.10.0-3build2_amd64.deb ... 90s Unpacking findutils (4.10.0-3build2) over (4.10.0-3build1) ... 90s Setting up findutils (4.10.0-3build2) ... 90s (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 ... 83957 files and directories currently installed.) 90s Preparing to unpack .../sed_4.9-2build3_amd64.deb ... 90s Unpacking sed (4.9-2build3) over (4.9-2build2) ... 90s Setting up sed (4.9-2build3) ... 90s (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 ... 83957 files and directories currently installed.) 90s Preparing to unpack .../tar_1.35+dfsg-3.1build2_amd64.deb ... 90s Unpacking tar (1.35+dfsg-3.1build2) over (1.35+dfsg-3.1build1) ... 90s Setting up tar (1.35+dfsg-3.1build2) ... 90s (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 ... 83957 files and directories currently installed.) 90s Preparing to unpack .../libc-gconv-modules-extra_2.42-2ubuntu5_amd64.deb ... 90s Unpacking libc-gconv-modules-extra:amd64 (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 90s Setting up libc-gconv-modules-extra:amd64 (2.42-2ubuntu5) ... 90s (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 ... 83957 files and directories currently installed.) 90s Preparing to unpack .../libc6_2.42-2ubuntu5_amd64.deb ... 90s Unpacking libc6:amd64 (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 90s Setting up libc6:amd64 (2.42-2ubuntu5) ... 90s (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 ... 83957 files and directories currently installed.) 90s Preparing to unpack .../libc-bin_2.42-2ubuntu5_amd64.deb ... 90s Unpacking libc-bin (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 91s Setting up libc-bin (2.42-2ubuntu5) ... 91s (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 ... 83957 files and directories currently installed.) 91s Preparing to unpack .../libattr1_1%3a2.5.2-3build2_amd64.deb ... 91s Unpacking libattr1:amd64 (1:2.5.2-3build2) over (1:2.5.2-3build1) ... 91s Setting up libattr1:amd64 (1:2.5.2-3build2) ... 91s (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 ... 83957 files and directories currently installed.) 91s Preparing to unpack .../00-mawk_1.3.4.20260129-1_amd64.deb ... 91s Unpacking mawk (1.3.4.20260129-1) over (1.3.4.20250131-2) ... 91s Preparing to unpack .../01-libapt-pkg7.0_3.1.15_amd64.deb ... 91s Unpacking libapt-pkg7.0:amd64 (3.1.15) over (3.1.14) ... 91s Preparing to unpack .../02-apt_3.1.15_amd64.deb ... 91s Unpacking apt (3.1.15) over (3.1.14) ... 91s Preparing to unpack .../03-libdevmapper1.02.1_2%3a1.02.205-2ubuntu3_amd64.deb ... 91s Unpacking libdevmapper1.02.1:amd64 (2:1.02.205-2ubuntu3) over (2:1.02.205-2ubuntu2) ... 91s Preparing to unpack .../04-dmsetup_2%3a1.02.205-2ubuntu3_amd64.deb ... 91s Unpacking dmsetup (2:1.02.205-2ubuntu3) over (2:1.02.205-2ubuntu2) ... 91s Preparing to unpack .../05-less_668-1build1_amd64.deb ... 91s Unpacking less (668-1build1) over (668-1) ... 91s Preparing to unpack .../06-libkeyutils1_1.6.3-6ubuntu3_amd64.deb ... 91s Unpacking libkeyutils1:amd64 (1.6.3-6ubuntu3) over (1.6.3-6ubuntu2) ... 91s Preparing to unpack .../07-locales_2.42-2ubuntu5_all.deb ... 91s Unpacking locales (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 91s Preparing to unpack .../08-python3-linkify-it_2.0.3-1ubuntu3_all.deb ... 91s Unpacking python3-linkify-it (2.0.3-1ubuntu3) over (2.0.3-1ubuntu2) ... 91s Preparing to unpack .../09-python3-markdown-it_3.0.0-3build1_all.deb ... 91s Unpacking python3-markdown-it (3.0.0-3build1) over (3.0.0-3) ... 91s Preparing to unpack .../10-busybox-static_1%3a1.37.0-7ubuntu1_amd64.deb ... 91s Unpacking busybox-static (1:1.37.0-7ubuntu1) over (1:1.37.0-4ubuntu1) ... 91s Preparing to unpack .../11-libdrm-common_2.4.131-1_all.deb ... 91s Unpacking libdrm-common (2.4.131-1) over (2.4.129-1) ... 91s Preparing to unpack .../12-libdrm2_2.4.131-1_amd64.deb ... 91s Unpacking libdrm2:amd64 (2.4.131-1) over (2.4.129-1) ... 91s Preparing to unpack .../13-libgpm2_1.20.7-12build1_amd64.deb ... 91s Unpacking libgpm2:amd64 (1.20.7-12build1) over (1.20.7-12) ... 91s Preparing to unpack .../14-libmaxminddb0_1.12.2-1build2_amd64.deb ... 91s Unpacking libmaxminddb0:amd64 (1.12.2-1build2) over (1.12.2-1build1) ... 91s Preparing to unpack .../15-libsensors-config_1%3a3.6.2-2build1_all.deb ... 91s Unpacking libsensors-config (1:3.6.2-2build1) over (1:3.6.2-2) ... 91s Preparing to unpack .../16-libsensors5_1%3a3.6.2-2build1_amd64.deb ... 91s Unpacking libsensors5:amd64 (1:3.6.2-2build1) over (1:3.6.2-2) ... 92s Preparing to unpack .../17-busybox-initramfs_1%3a1.37.0-7ubuntu1_amd64.deb ... 92s Unpacking busybox-initramfs (1:1.37.0-7ubuntu1) over (1:1.37.0-4ubuntu1) ... 92s Preparing to unpack .../18-libdrm-amdgpu1_2.4.131-1_amd64.deb ... 92s Unpacking libdrm-amdgpu1:amd64 (2.4.131-1) over (2.4.129-1) ... 92s Preparing to unpack .../19-libnpth0t64_1.8-3build1_amd64.deb ... 92s Unpacking libnpth0t64:amd64 (1.8-3build1) over (1.8-3) ... 92s Preparing to unpack .../20-patch_2.8-2build1_amd64.deb ... 92s Unpacking patch (2.8-2build1) over (2.8-2) ... 92s Preparing to unpack .../21-pollinate_4.33-4ubuntu5_all.deb ... 92s Unpacking pollinate (4.33-4ubuntu5) over (4.33-4ubuntu4) ... 92s Preparing to unpack .../22-python3-referencing_0.36.2-1ubuntu2_all.deb ... 92s Unpacking python3-referencing (0.36.2-1ubuntu2) over (0.36.2-1ubuntu1) ... 92s Preparing to unpack .../23-amd64-microcode_3.20251202.1ubuntu1_amd64.deb ... 92s Unpacking amd64-microcode (3.20251202.1ubuntu1) over (3.20250708.1ubuntu1) ... 92s Setting up libnpth0t64:amd64 (1.8-3build1) ... 92s Setting up libkeyutils1:amd64 (1.6.3-6ubuntu3) ... 92s Setting up libgpm2:amd64 (1.20.7-12build1) ... 92s Setting up libmaxminddb0:amd64 (1.12.2-1build2) ... 92s Setting up libsensors-config (1:3.6.2-2build1) ... 92s Setting up less (668-1build1) ... 92s Setting up amd64-microcode (3.20251202.1ubuntu1) ... 92s amd64-microcode: microcode will be updated at next boot 92s Setting up locales (2.42-2ubuntu5) ... 92s Generating locales (this might take a while)... 93s en_US.UTF-8... done 93s Generation complete. 93s Setting up pollinate (4.33-4ubuntu5) ... 106s Setting up busybox-static (1:1.37.0-7ubuntu1) ... 106s Setting up patch (2.8-2build1) ... 106s Setting up libsensors5:amd64 (1:3.6.2-2build1) ... 106s Setting up busybox-initramfs (1:1.37.0-7ubuntu1) ... 106s Setting up libdevmapper1.02.1:amd64 (2:1.02.205-2ubuntu3) ... 106s Setting up dmsetup (2:1.02.205-2ubuntu3) ... 106s Setting up python3-linkify-it (2.0.3-1ubuntu3) ... 106s Setting up mawk (1.3.4.20260129-1) ... 106s Setting up libapt-pkg7.0:amd64 (3.1.15) ... 106s Setting up libdrm-common (2.4.131-1) ... 113s Setting up python3-referencing (0.36.2-1ubuntu2) ... 113s Setting up apt (3.1.15) ... 113s Setting up python3-markdown-it (3.0.0-3build1) ... 113s Setting up libdrm2:amd64 (2.4.131-1) ... 113s Setting up libdrm-amdgpu1:amd64 (2.4.131-1) ... 113s Processing triggers for libc-bin (2.42-2ubuntu5) ... 113s Processing triggers for systemd (259-1ubuntu3) ... 113s Processing triggers for man-db (2.13.1-1) ... 113s Processing triggers for install-info (7.2-5) ... 113s Processing triggers for initramfs-tools (0.150ubuntu7) ... 113s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic 113s autopkgtest [20:46:12]: upgrading testbed (apt dist-upgrade and autopurge) 113s Reading package lists... 114s Building dependency tree... 114s Reading state information... 114s Calculating upgrade... 114s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 114s Reading package lists... 114s Building dependency tree... 114s Reading state information... 114s Solving dependencies... 114s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 114s autopkgtest [20:46:13]: rebooting testbed after setup commands that affected boot 143s autopkgtest [20:46:42]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:49:02 UTC 2026 145s autopkgtest [20:46:44]: @@@@@@@@@@@@@@@@@@@@ apt-source mothur 146s Get:1 http://ftpmaster.internal/ubuntu resolute/universe mothur 1.48.1-1build1 (dsc) [2074 B] 146s Get:2 http://ftpmaster.internal/ubuntu resolute/universe mothur 1.48.1-1build1 (tar) [1654 kB] 146s Get:3 http://ftpmaster.internal/ubuntu resolute/universe mothur 1.48.1-1build1 (diff) [21.7 kB] 146s gpgv: Signature made Mon Jan 26 19:31:04 2026 UTC 146s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 146s gpgv: Can't check signature: No public key 146s dpkg-source: warning: cannot verify inline signature for ./mothur_1.48.1-1build1.dsc: no acceptable signature found 146s autopkgtest [20:46:45]: testing package mothur version 1.48.1-1build1 147s autopkgtest [20:46:46]: build not needed 147s autopkgtest [20:46:46]: test run-unit-test: preparing testbed 148s Reading package lists... 148s Building dependency tree... 148s Reading state information... 148s Solving dependencies... 148s The following NEW packages will be installed: 148s mothur 148s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 148s Need to get 4800 kB of archives. 148s After this operation, 14.6 MB of additional disk space will be used. 148s Get:1 http://ftpmaster.internal/ubuntu resolute/universe amd64 mothur amd64 1.48.1-1build1 [4800 kB] 148s Fetched 4800 kB in 0s (22.8 MB/s) 148s Selecting previously unselected package mothur. 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 ... 83962 files and directories currently installed.) 148s Preparing to unpack .../mothur_1.48.1-1build1_amd64.deb ... 148s Unpacking mothur (1.48.1-1build1) ... 148s Setting up mothur (1.48.1-1build1) ... 148s Processing triggers for man-db (2.13.1-1) ... 149s autopkgtest [20:46:48]: test run-unit-test: [----------------------- 150s Linux version 150s 150s Using ReadLine 150s mothur v.1.48.1 150s Last updated: 5/15/24 150s by 150s Patrick D. Schloss 150s 150s Department of Microbiology & Immunology 150s 150s University of Michigan 150s http://www.mothur.org 150s 150s When using, please cite: 150s Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41. 150s 150s Distributed under the GNU General Public License 150s 150s Type 'help()' for information on the commands that are available 150s 150s For questions and analysis support, please visit our forum at https://forum.mothur.org 150s 150s Type 'quit()' to exit program 150s 150s [NOTE]: Setting random seed to 19760620. 150s 150s Batch Mode 150s 150s 150s 150s mothur > unique.seqs(fasta=HA.fasta) 150s 599 259 150s 150s Output File Names: 150s HA.unique.fasta 150s HA.count_table 150s 150s 150s mothur > dist.seqs(fasta=HA.unique.fasta, countends=F, cutoff=0.01) 150s 150s Using 2 processors. 150s 150s Sequence Time Num_Dists_Below_Cutoff 150s 0 0 0 150s 200 0 3443 150s 100 0 5025 150s 258 0 15965 150s 182 0 16617 150s 150s It took 0 secs to find distances for 259 sequences. 32582 distances below cutoff 0.01. 150s 150s 150s Output File Names: 150s HA.unique.dist 150s 150s 150s mothur > cluster(method=furthest, column=HA.unique.dist, count=current, cutoff=0.01, precision=1000) 150s Using HA.count_table as input file for the count parameter. 150s 150s Using 2 processors. 150s unique 154 211 18 2 6 0 4 2 0 2 0 0 0 1 0 0 0 0 2 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 150s 0.001 155 161 28 5 3 4 2 4 0 0 1 0 1 0 1 0 0 0 0 2 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 150s 0.002 206 56 9 8 2 0 4 2 2 0 0 0 0 0 2 0 0 0 0 1 1 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 150s 0.003 236 26 4 2 1 1 0 2 2 1 0 0 0 0 1 1 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 150s 0.004 270 15 3 0 1 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 150s 0.005 272 7 2 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 150s 0.006 274 5 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 150s 0.007 274 5 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 150s 0.008 552 3 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 150s 0.009 592 3 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 150s It took 0 seconds to cluster 150s 150s Output File Names: 150s HA.unique.fn.list 150s 150s 150s mothur > summary.single(list=HA.unique.fn.list, calc=nseqs-sobs-chao, label=unique-0.001-0.003-0.005-0.008) 150s unique 150s 0.001 150s 0.003 150s 0.005 150s 0.008 150s 150s Output File Names: 150s HA.unique.fn.summary 150s 150s 150s mothur > heatmap.bin(scale=linear, label=unique-0.001-0.003) 150s Using HA.unique.fn.list as input file for the list parameter. 150s unique 150s 0.001 150s 0.003 150s 150s Output File Names: 150s HA.unique.fn.unique.heatmap.bin.svg 150s HA.unique.fn.0.001.heatmap.bin.svg 150s HA.unique.fn.0.003.heatmap.bin.svg 150s HA.unique.fn.0.004.heatmap.bin.svg 150s HA.unique.fn.0.005.heatmap.bin.svg 150s HA.unique.fn.0.006.heatmap.bin.svg 150s HA.unique.fn.0.007.heatmap.bin.svg 150s HA.unique.fn.0.008.heatmap.bin.svg 150s HA.unique.fn.0.009.heatmap.bin.svg 150s 150s 150s mothur > rarefaction.single(calc=sobs-chao, label=unique-0.001-0.003, freq=10) 150s Using HA.unique.fn.list as input file for the list parameter. 150s 150s Using 2 processors. 150s unique 150s 0.001 150s 0.003 150s 150s It took 0 secs to run rarefaction.single. 150s 150s Output File Names: 150s HA.unique.fn.rarefaction 150s HA.unique.fn.r_chao 150s 150s 150s mothur > quit() 150s 150s 150s It took 0 seconds to run 7 commands from test.batch batch file. 150s 150s Logfile : mothur.1770410808.logfile 150s 150s autopkgtest [20:46:49]: test run-unit-test: -----------------------] 150s autopkgtest [20:46:49]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 150s run-unit-test PASS 151s autopkgtest [20:46:50]: @@@@@@@@@@@@@@@@@@@@ summary 151s run-unit-test PASS