0s autopkgtest [21:43:56]: starting date and time: 2025-03-06 21:43:56+0000 0s autopkgtest [21:43:56]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [21:43:56]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.j13u745y/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-stdlib-extensions --apt-upgrade ariba --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-stdlib-extensions/3.13.2-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-9.secgroup --name adt-plucky-amd64-ariba-20250306-214356-juju-7f2275-prod-proposed-migration-environment-20-a41cdcfa-763f-48d8-9817-352c7c4986b6 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-amd64 -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/ 53s autopkgtest [21:44:49]: testbed dpkg architecture: amd64 53s autopkgtest [21:44:49]: testbed apt version: 2.9.31ubuntu1 54s autopkgtest [21:44:50]: @@@@@@@@@@@@@@@@@@@@ test bed setup 54s autopkgtest [21:44:50]: testbed release detected to be: None 55s autopkgtest [21:44:51]: updating testbed package index (apt update) 55s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 56s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 56s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 56s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 56s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [11.5 kB] 56s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [5496 B] 56s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [493 kB] 56s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [52.8 kB] 56s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [89.4 kB] 56s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [47.3 kB] 56s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.5 kB] 56s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [317 kB] 56s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [129 kB] 56s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [7592 B] 56s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [3536 B] 56s Fetched 1299 kB in 1s (1421 kB/s) 57s Reading package lists... 58s Reading package lists... 58s Building dependency tree... 58s Reading state information... 59s Calculating upgrade... 59s Calculating upgrade... 60s The following packages will be upgraded: 60s apparmor binutils binutils-common binutils-x86-64-linux-gnu exfatprogs 60s gcc-15-base hwdata initramfs-tools initramfs-tools-bin initramfs-tools-core 60s libapparmor1 libassuan9 libatomic1 libaudit-common libaudit1 libbinutils 60s libbrotli1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libctf-nobfd0 60s libctf0 libftdi1-2 libgcc-s1 libgpgme11t64 libgprofng0 libnewt0.52 60s libnss-systemd libpam-systemd libparted2t64 libseccomp2 libsemanage-common 60s libsemanage2 libsframe1 libstdc++6 libsystemd-shared libsystemd0 libudev1 60s libxml2 locales parted python-apt-common python3-apt python3-bcrypt 60s python3-dbus python3-gi python3-markupsafe python3-newt python3-rpds-py 60s python3-systemd systemd systemd-cryptsetup systemd-resolved systemd-sysv 60s systemd-timesyncd ubuntu-kernel-accessories ubuntu-minimal ubuntu-standard 60s udev whiptail 60s 62 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 60s Need to get 27.3 MB of archives. 60s After this operation, 1981 kB disk space will be freed. 60s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-dev-bin amd64 2.41-1ubuntu1 [24.7 kB] 60s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6-dev amd64 2.41-1ubuntu1 [2182 kB] 60s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 locales all 2.41-1ubuntu1 [4246 kB] 60s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6 amd64 2.41-1ubuntu1 [3327 kB] 60s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-bin amd64 2.41-1ubuntu1 [701 kB] 60s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libatomic1 amd64 15-20250222-0ubuntu1 [10.4 kB] 60s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-15-base amd64 15-20250222-0ubuntu1 [53.4 kB] 60s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-s1 amd64 15-20250222-0ubuntu1 [77.8 kB] 60s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++6 amd64 15-20250222-0ubuntu1 [798 kB] 61s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd0 amd64 257.3-1ubuntu3 [595 kB] 61s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libnss-systemd amd64 257.3-1ubuntu3 [199 kB] 61s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-sysv amd64 257.3-1ubuntu3 [11.9 kB] 61s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-resolved amd64 257.3-1ubuntu3 [345 kB] 61s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam-systemd amd64 257.3-1ubuntu3 [302 kB] 61s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd-shared amd64 257.3-1ubuntu3 [2371 kB] 61s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd amd64 257.3-1ubuntu3 [3052 kB] 61s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-timesyncd amd64 257.3-1ubuntu3 [42.1 kB] 61s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-cryptsetup amd64 257.3-1ubuntu3 [124 kB] 61s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 udev amd64 257.3-1ubuntu3 [1404 kB] 61s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libudev1 amd64 257.3-1ubuntu3 [215 kB] 61s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu2 [6628 B] 61s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-4build1 [15.6 kB] 61s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu2 [54.0 kB] 61s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libseccomp2 amd64 2.5.5-1ubuntu6 [53.5 kB] 61s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libapparmor1 amd64 4.1.0~beta5-0ubuntu6 [54.8 kB] 61s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage-common all 3.7-2.1build1 [7268 B] 61s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage2 amd64 3.7-2.1build1 [106 kB] 61s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libassuan9 amd64 3.0.2-2 [43.1 kB] 61s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-newt amd64 0.52.24-4ubuntu2 [21.1 kB] 61s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libnewt0.52 amd64 0.52.24-4ubuntu2 [55.7 kB] 61s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2ubuntu5 [772 kB] 61s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 python-apt-common all 2.9.9build1 [21.3 kB] 61s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-apt amd64 2.9.9build1 [172 kB] 61s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dbus amd64 1.3.2-5build5 [102 kB] 61s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-gi amd64 3.50.0-4build1 [252 kB] 61s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 whiptail amd64 0.52.24-4ubuntu2 [19.1 kB] 61s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-minimal amd64 1.549 [11.5 kB] 61s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 apparmor amd64 4.1.0~beta5-0ubuntu6 [700 kB] 61s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 parted amd64 3.6-5 [53.9 kB] 61s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libparted2t64 amd64 3.6-5 [158 kB] 61s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-standard amd64 1.549 [11.5 kB] 61s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libgprofng0 amd64 2.44-3ubuntu1 [886 kB] 61s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf0 amd64 2.44-3ubuntu1 [96.5 kB] 61s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf-nobfd0 amd64 2.44-3ubuntu1 [98.9 kB] 61s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-x86-64-linux-gnu amd64 2.44-3ubuntu1 [1108 kB] 61s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libbinutils amd64 2.44-3ubuntu1 [585 kB] 61s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils amd64 2.44-3ubuntu1 [208 kB] 61s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-common amd64 2.44-3ubuntu1 [215 kB] 61s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libsframe1 amd64 2.44-3ubuntu1 [14.8 kB] 61s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 exfatprogs amd64 1.2.8-1 [76.3 kB] 61s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 hwdata all 0.393-1 [29.5 kB] 61s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools all 0.146ubuntu1 [7920 B] 61s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-core all 0.146ubuntu1 [51.9 kB] 61s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-bin amd64 0.146ubuntu1 [26.2 kB] 61s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli1 amd64 1.1.0-2build4 [365 kB] 61s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libftdi1-2 amd64 1.5-8build1 [30.2 kB] 61s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.24.2-1ubuntu2 [155 kB] 61s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build4 [13.4 kB] 61s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-rpds-py amd64 0.21.0-2ubuntu2 [278 kB] 61s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build6 [43.9 kB] 61s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-kernel-accessories amd64 1.549 [11.2 kB] 61s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-bcrypt amd64 4.2.0-2.1build1 [221 kB] 62s Preconfiguring packages ... 62s Fetched 27.3 MB in 2s (16.2 MB/s) 62s (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 ... 109140 files and directories currently installed.) 62s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu1_amd64.deb ... 62s Unpacking libc-dev-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 63s Preparing to unpack .../libc6-dev_2.41-1ubuntu1_amd64.deb ... 63s Unpacking libc6-dev:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 63s Preparing to unpack .../locales_2.41-1ubuntu1_all.deb ... 63s Unpacking locales (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 63s Preparing to unpack .../libc6_2.41-1ubuntu1_amd64.deb ... 63s Checking for services that may need to be restarted... 63s Checking init scripts... 63s Checking for services that may need to be restarted... 63s Checking init scripts... 64s Stopping some services possibly affected by the upgrade (will be restarted later): 64s cron: stopping...done. 64s 64s Unpacking libc6:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 64s Setting up libc6:amd64 (2.41-1ubuntu1) ... 64s Checking for services that may need to be restarted... 64s Checking init scripts... 64s Restarting services possibly affected by the upgrade: 64s cron: restarting...done. 64s 64s Services restarted successfully. 64s (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 ... 109141 files and directories currently installed.) 64s Preparing to unpack .../libc-bin_2.41-1ubuntu1_amd64.deb ... 64s Unpacking libc-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 64s Setting up libc-bin (2.41-1ubuntu1) ... 65s (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 ... 109141 files and directories currently installed.) 65s Preparing to unpack .../libatomic1_15-20250222-0ubuntu1_amd64.deb ... 65s Unpacking libatomic1:amd64 (15-20250222-0ubuntu1) over (15-20250213-1ubuntu1) ... 65s Preparing to unpack .../gcc-15-base_15-20250222-0ubuntu1_amd64.deb ... 65s Unpacking gcc-15-base:amd64 (15-20250222-0ubuntu1) over (15-20250213-1ubuntu1) ... 65s Setting up gcc-15-base:amd64 (15-20250222-0ubuntu1) ... 65s (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 ... 109141 files and directories currently installed.) 65s Preparing to unpack .../libgcc-s1_15-20250222-0ubuntu1_amd64.deb ... 65s Unpacking libgcc-s1:amd64 (15-20250222-0ubuntu1) over (15-20250213-1ubuntu1) ... 65s Setting up libgcc-s1:amd64 (15-20250222-0ubuntu1) ... 65s (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 ... 109141 files and directories currently installed.) 65s Preparing to unpack .../libstdc++6_15-20250222-0ubuntu1_amd64.deb ... 65s Unpacking libstdc++6:amd64 (15-20250222-0ubuntu1) over (15-20250213-1ubuntu1) ... 65s Setting up libstdc++6:amd64 (15-20250222-0ubuntu1) ... 65s (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 ... 109141 files and directories currently installed.) 65s Preparing to unpack .../libsystemd0_257.3-1ubuntu3_amd64.deb ... 65s Unpacking libsystemd0:amd64 (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 65s Setting up libsystemd0:amd64 (257.3-1ubuntu3) ... 66s (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 ... 109141 files and directories currently installed.) 66s Preparing to unpack .../libnss-systemd_257.3-1ubuntu3_amd64.deb ... 66s Unpacking libnss-systemd:amd64 (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 66s Preparing to unpack .../systemd-sysv_257.3-1ubuntu3_amd64.deb ... 66s Unpacking systemd-sysv (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 66s Preparing to unpack .../systemd-resolved_257.3-1ubuntu3_amd64.deb ... 66s Unpacking systemd-resolved (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 66s Preparing to unpack .../libpam-systemd_257.3-1ubuntu3_amd64.deb ... 66s Unpacking libpam-systemd:amd64 (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 66s Preparing to unpack .../libsystemd-shared_257.3-1ubuntu3_amd64.deb ... 66s Unpacking libsystemd-shared:amd64 (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 66s Setting up libsystemd-shared:amd64 (257.3-1ubuntu3) ... 66s (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 ... 109141 files and directories currently installed.) 66s Preparing to unpack .../systemd_257.3-1ubuntu3_amd64.deb ... 66s Unpacking systemd (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 66s Preparing to unpack .../systemd-timesyncd_257.3-1ubuntu3_amd64.deb ... 66s Unpacking systemd-timesyncd (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 66s Preparing to unpack .../systemd-cryptsetup_257.3-1ubuntu3_amd64.deb ... 66s Unpacking systemd-cryptsetup (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 67s Preparing to unpack .../udev_257.3-1ubuntu3_amd64.deb ... 67s Unpacking udev (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 67s Preparing to unpack .../libudev1_257.3-1ubuntu3_amd64.deb ... 67s Unpacking libudev1:amd64 (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 67s Setting up libudev1:amd64 (257.3-1ubuntu3) ... 67s (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 ... 109141 files and directories currently installed.) 67s Preparing to unpack .../libaudit-common_1%3a4.0.2-2ubuntu2_all.deb ... 67s Unpacking libaudit-common (1:4.0.2-2ubuntu2) over (1:4.0.2-2ubuntu1) ... 67s Setting up libaudit-common (1:4.0.2-2ubuntu2) ... 67s (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 ... 109141 files and directories currently installed.) 67s Preparing to unpack .../libcap-ng0_0.8.5-4build1_amd64.deb ... 67s Unpacking libcap-ng0:amd64 (0.8.5-4build1) over (0.8.5-4) ... 67s Setting up libcap-ng0:amd64 (0.8.5-4build1) ... 67s (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 ... 109141 files and directories currently installed.) 67s Preparing to unpack .../libaudit1_1%3a4.0.2-2ubuntu2_amd64.deb ... 67s Unpacking libaudit1:amd64 (1:4.0.2-2ubuntu2) over (1:4.0.2-2ubuntu1) ... 67s Setting up libaudit1:amd64 (1:4.0.2-2ubuntu2) ... 67s (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 ... 109141 files and directories currently installed.) 67s Preparing to unpack .../libseccomp2_2.5.5-1ubuntu6_amd64.deb ... 67s Unpacking libseccomp2:amd64 (2.5.5-1ubuntu6) over (2.5.5-1ubuntu5) ... 67s Setting up libseccomp2:amd64 (2.5.5-1ubuntu6) ... 67s (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 ... 109141 files and directories currently installed.) 67s Preparing to unpack .../libapparmor1_4.1.0~beta5-0ubuntu6_amd64.deb ... 67s Unpacking libapparmor1:amd64 (4.1.0~beta5-0ubuntu6) over (4.1.0~beta5-0ubuntu5) ... 68s Preparing to unpack .../libsemanage-common_3.7-2.1build1_all.deb ... 68s Unpacking libsemanage-common (3.7-2.1build1) over (3.7-2.1) ... 68s Setting up libsemanage-common (3.7-2.1build1) ... 68s (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 ... 109141 files and directories currently installed.) 68s Preparing to unpack .../libsemanage2_3.7-2.1build1_amd64.deb ... 68s Unpacking libsemanage2:amd64 (3.7-2.1build1) over (3.7-2.1) ... 68s Setting up libsemanage2:amd64 (3.7-2.1build1) ... 68s (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 ... 109141 files and directories currently installed.) 68s Preparing to unpack .../libassuan9_3.0.2-2_amd64.deb ... 68s Unpacking libassuan9:amd64 (3.0.2-2) over (3.0.1-2) ... 68s Setting up libassuan9:amd64 (3.0.2-2) ... 68s (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 ... 109141 files and directories currently installed.) 68s Preparing to unpack .../00-python3-newt_0.52.24-4ubuntu2_amd64.deb ... 68s Unpacking python3-newt:amd64 (0.52.24-4ubuntu2) over (0.52.24-4ubuntu1) ... 68s Preparing to unpack .../01-libnewt0.52_0.52.24-4ubuntu2_amd64.deb ... 68s Unpacking libnewt0.52:amd64 (0.52.24-4ubuntu2) over (0.52.24-4ubuntu1) ... 68s Preparing to unpack .../02-libxml2_2.12.7+dfsg+really2.9.14-0.2ubuntu5_amd64.deb ... 68s Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2ubuntu5) over (2.12.7+dfsg+really2.9.14-0.2ubuntu4) ... 68s Preparing to unpack .../03-python-apt-common_2.9.9build1_all.deb ... 68s Unpacking python-apt-common (2.9.9build1) over (2.9.9) ... 68s Preparing to unpack .../04-python3-apt_2.9.9build1_amd64.deb ... 68s Unpacking python3-apt (2.9.9build1) over (2.9.9) ... 68s Preparing to unpack .../05-python3-dbus_1.3.2-5build5_amd64.deb ... 69s Unpacking python3-dbus (1.3.2-5build5) over (1.3.2-5build4) ... 69s Preparing to unpack .../06-python3-gi_3.50.0-4build1_amd64.deb ... 69s Unpacking python3-gi (3.50.0-4build1) over (3.50.0-4) ... 69s Preparing to unpack .../07-whiptail_0.52.24-4ubuntu2_amd64.deb ... 69s Unpacking whiptail (0.52.24-4ubuntu2) over (0.52.24-4ubuntu1) ... 69s Preparing to unpack .../08-ubuntu-minimal_1.549_amd64.deb ... 69s Unpacking ubuntu-minimal (1.549) over (1.548) ... 69s Preparing to unpack .../09-apparmor_4.1.0~beta5-0ubuntu6_amd64.deb ... 70s Unpacking apparmor (4.1.0~beta5-0ubuntu6) over (4.1.0~beta5-0ubuntu5) ... 70s Preparing to unpack .../10-parted_3.6-5_amd64.deb ... 71s Unpacking parted (3.6-5) over (3.6-4build1) ... 71s Preparing to unpack .../11-libparted2t64_3.6-5_amd64.deb ... 71s Adding 'diversion of /lib/x86_64-linux-gnu/libparted.so.2 to /lib/x86_64-linux-gnu/libparted.so.2.usr-is-merged by libparted2t64' 71s Adding 'diversion of /lib/x86_64-linux-gnu/libparted.so.2.0.5 to /lib/x86_64-linux-gnu/libparted.so.2.0.5.usr-is-merged by libparted2t64' 71s Unpacking libparted2t64:amd64 (3.6-5) over (3.6-4build1) ... 71s Preparing to unpack .../12-ubuntu-standard_1.549_amd64.deb ... 71s Unpacking ubuntu-standard (1.549) over (1.548) ... 71s Preparing to unpack .../13-libgprofng0_2.44-3ubuntu1_amd64.deb ... 71s Unpacking libgprofng0:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 71s Preparing to unpack .../14-libctf0_2.44-3ubuntu1_amd64.deb ... 71s Unpacking libctf0:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 71s Preparing to unpack .../15-libctf-nobfd0_2.44-3ubuntu1_amd64.deb ... 71s Unpacking libctf-nobfd0:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 71s Preparing to unpack .../16-binutils-x86-64-linux-gnu_2.44-3ubuntu1_amd64.deb ... 71s Unpacking binutils-x86-64-linux-gnu (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 71s Preparing to unpack .../17-libbinutils_2.44-3ubuntu1_amd64.deb ... 71s Unpacking libbinutils:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 71s Preparing to unpack .../18-binutils_2.44-3ubuntu1_amd64.deb ... 71s Unpacking binutils (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 71s Preparing to unpack .../19-binutils-common_2.44-3ubuntu1_amd64.deb ... 71s Unpacking binutils-common:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 71s Preparing to unpack .../20-libsframe1_2.44-3ubuntu1_amd64.deb ... 71s Unpacking libsframe1:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 71s Preparing to unpack .../21-exfatprogs_1.2.8-1_amd64.deb ... 71s Unpacking exfatprogs (1.2.8-1) over (1.2.7-3) ... 71s Preparing to unpack .../22-hwdata_0.393-1_all.deb ... 71s Unpacking hwdata (0.393-1) over (0.392-1) ... 71s Preparing to unpack .../23-initramfs-tools_0.146ubuntu1_all.deb ... 71s Unpacking initramfs-tools (0.146ubuntu1) over (0.145ubuntu3) ... 71s Preparing to unpack .../24-initramfs-tools-core_0.146ubuntu1_all.deb ... 71s Unpacking initramfs-tools-core (0.146ubuntu1) over (0.145ubuntu3) ... 71s Preparing to unpack .../25-initramfs-tools-bin_0.146ubuntu1_amd64.deb ... 71s Unpacking initramfs-tools-bin (0.146ubuntu1) over (0.145ubuntu3) ... 71s Preparing to unpack .../26-libbrotli1_1.1.0-2build4_amd64.deb ... 71s Unpacking libbrotli1:amd64 (1.1.0-2build4) over (1.1.0-2build3) ... 72s Preparing to unpack .../27-libftdi1-2_1.5-8build1_amd64.deb ... 72s Unpacking libftdi1-2:amd64 (1.5-8build1) over (1.5-8) ... 72s Preparing to unpack .../28-libgpgme11t64_1.24.2-1ubuntu2_amd64.deb ... 72s Unpacking libgpgme11t64:amd64 (1.24.2-1ubuntu2) over (1.24.2-1ubuntu1) ... 72s Preparing to unpack .../29-python3-markupsafe_2.1.5-1build4_amd64.deb ... 72s Unpacking python3-markupsafe (2.1.5-1build4) over (2.1.5-1build3) ... 72s Preparing to unpack .../30-python3-rpds-py_0.21.0-2ubuntu2_amd64.deb ... 72s Unpacking python3-rpds-py (0.21.0-2ubuntu2) over (0.21.0-2ubuntu1) ... 72s Preparing to unpack .../31-python3-systemd_235-1build6_amd64.deb ... 72s Unpacking python3-systemd (235-1build6) over (235-1build5) ... 72s Preparing to unpack .../32-ubuntu-kernel-accessories_1.549_amd64.deb ... 72s Unpacking ubuntu-kernel-accessories (1.549) over (1.548) ... 72s Preparing to unpack .../33-python3-bcrypt_4.2.0-2.1build1_amd64.deb ... 72s Unpacking python3-bcrypt (4.2.0-2.1build1) over (4.2.0-2.1) ... 72s Setting up python3-dbus (1.3.2-5build5) ... 72s Setting up ubuntu-kernel-accessories (1.549) ... 72s Setting up libapparmor1:amd64 (4.1.0~beta5-0ubuntu6) ... 72s Setting up libnewt0.52:amd64 (0.52.24-4ubuntu2) ... 72s Setting up exfatprogs (1.2.8-1) ... 72s Setting up python3-bcrypt (4.2.0-2.1build1) ... 72s Setting up libbrotli1:amd64 (1.1.0-2build4) ... 72s Setting up binutils-common:amd64 (2.44-3ubuntu1) ... 72s Setting up libctf-nobfd0:amd64 (2.44-3ubuntu1) ... 72s Setting up systemd (257.3-1ubuntu3) ... 73s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 73s Created symlink '/run/systemd/system/tmp.mount' → '/dev/null'. 73s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 74s Setting up libparted2t64:amd64 (3.6-5) ... 74s Removing 'diversion of /lib/x86_64-linux-gnu/libparted.so.2 to /lib/x86_64-linux-gnu/libparted.so.2.usr-is-merged by libparted2t64' 74s Removing 'diversion of /lib/x86_64-linux-gnu/libparted.so.2.0.5 to /lib/x86_64-linux-gnu/libparted.so.2.0.5.usr-is-merged by libparted2t64' 74s Setting up python3-newt:amd64 (0.52.24-4ubuntu2) ... 74s Setting up locales (2.41-1ubuntu1) ... 74s Installing new version of config file /etc/locale.alias ... 75s Generating locales (this might take a while)... 77s en_US.UTF-8... done 77s Generation complete. 77s Setting up python3-markupsafe (2.1.5-1build4) ... 77s Setting up libsframe1:amd64 (2.44-3ubuntu1) ... 77s Setting up hwdata (0.393-1) ... 77s Setting up apparmor (4.1.0~beta5-0ubuntu6) ... 77s Installing new version of config file /etc/apparmor.d/fusermount3 ... 77s Installing new version of config file /etc/apparmor.d/lsusb ... 79s Reloading AppArmor profiles 80s Setting up libftdi1-2:amd64 (1.5-8build1) ... 80s Setting up systemd-cryptsetup (257.3-1ubuntu3) ... 80s Setting up python3-gi (3.50.0-4build1) ... 80s Setting up systemd-timesyncd (257.3-1ubuntu3) ... 81s systemd-time-wait-sync.service is a disabled or a static unit not running, not starting it. 81s Setting up libatomic1:amd64 (15-20250222-0ubuntu1) ... 81s Setting up udev (257.3-1ubuntu3) ... 82s Setting up python3-rpds-py (0.21.0-2ubuntu2) ... 83s Setting up whiptail (0.52.24-4ubuntu2) ... 83s Setting up python-apt-common (2.9.9build1) ... 83s Setting up libgpgme11t64:amd64 (1.24.2-1ubuntu2) ... 83s Setting up libbinutils:amd64 (2.44-3ubuntu1) ... 83s Setting up libc-dev-bin (2.41-1ubuntu1) ... 83s Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2ubuntu5) ... 83s Setting up python3-systemd (235-1build6) ... 83s Setting up systemd-resolved (257.3-1ubuntu3) ... 83s Setting up initramfs-tools-bin (0.146ubuntu1) ... 83s Setting up libctf0:amd64 (2.44-3ubuntu1) ... 83s Setting up systemd-sysv (257.3-1ubuntu3) ... 83s Setting up ubuntu-minimal (1.549) ... 83s Setting up python3-apt (2.9.9build1) ... 84s Setting up parted (3.6-5) ... 84s Setting up libnss-systemd:amd64 (257.3-1ubuntu3) ... 84s Setting up libgprofng0:amd64 (2.44-3ubuntu1) ... 84s Setting up libpam-systemd:amd64 (257.3-1ubuntu3) ... 84s Setting up libc6-dev:amd64 (2.41-1ubuntu1) ... 84s Setting up initramfs-tools-core (0.146ubuntu1) ... 84s Setting up binutils-x86-64-linux-gnu (2.44-3ubuntu1) ... 84s Setting up initramfs-tools (0.146ubuntu1) ... 84s Installing new version of config file /etc/kernel/postinst.d/initramfs-tools ... 84s Installing new version of config file /etc/kernel/postrm.d/initramfs-tools ... 84s update-initramfs: deferring update (trigger activated) 84s Setting up binutils (2.44-3ubuntu1) ... 84s Setting up ubuntu-standard (1.549) ... 84s Processing triggers for dbus (1.16.2-1ubuntu1) ... 84s Processing triggers for shared-mime-info (2.4-5) ... 84s Warning: program compiled against libxml 212 using older 209 84s Processing triggers for libc-bin (2.41-1ubuntu1) ... 85s Processing triggers for man-db (2.13.0-1) ... 86s Processing triggers for initramfs-tools (0.146ubuntu1) ... 87s update-initramfs: Generating /boot/initrd.img-6.12.0-16-generic 87s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 102s Reading package lists... 103s Building dependency tree... 103s Reading state information... 103s Solving dependencies... 104s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 104s autopkgtest [21:45:40]: upgrading testbed (apt dist-upgrade and autopurge) 104s Reading package lists... 104s Building dependency tree... 104s Reading state information... 105s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 105s Starting 2 pkgProblemResolver with broken count: 0 105s Done 106s Entering ResolveByKeep 106s 106s Calculating upgrade... 106s The following package was automatically installed and is no longer required: 106s python3.12-gdbm 106s Use 'sudo apt autoremove' to remove it. 106s The following packages will be upgraded: 106s python3-gdbm 107s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 107s Need to get 8708 B of archives. 107s After this operation, 0 B of additional disk space will be used. 107s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.13.2-1 [8708 B] 107s Fetched 8708 B in 0s (56.0 kB/s) 107s (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 ... 109127 files and directories currently installed.) 107s Preparing to unpack .../python3-gdbm_3.13.2-1_amd64.deb ... 107s Unpacking python3-gdbm:amd64 (3.13.2-1) over (3.13.1-1) ... 107s Setting up python3-gdbm:amd64 (3.13.2-1) ... 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 108s Starting pkgProblemResolver with broken count: 0 108s Starting 2 pkgProblemResolver with broken count: 0 108s Done 109s Solving dependencies... 109s The following packages will be REMOVED: 109s python3.12-gdbm* 110s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. 110s After this operation, 99.3 kB disk space will be freed. 110s (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 ... 109127 files and directories currently installed.) 110s Removing python3.12-gdbm (3.12.9-1) ... 110s autopkgtest [21:45:46]: rebooting testbed after setup commands that affected boot 132s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 139s autopkgtest [21:46:15]: testbed running kernel: Linux 6.12.0-16-generic #16-Ubuntu SMP PREEMPT_DYNAMIC Fri Feb 14 15:11:11 UTC 2025 142s autopkgtest [21:46:18]: @@@@@@@@@@@@@@@@@@@@ apt-source ariba 145s Get:1 http://ftpmaster.internal/ubuntu plucky/universe ariba 2.14.7+ds-7 (dsc) [2435 B] 145s Get:2 http://ftpmaster.internal/ubuntu plucky/universe ariba 2.14.7+ds-7 (tar) [1920 kB] 145s Get:3 http://ftpmaster.internal/ubuntu plucky/universe ariba 2.14.7+ds-7 (diff) [11.5 kB] 145s gpgv: Signature made Thu Jan 30 21:44:32 2025 UTC 145s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 145s gpgv: issuer "emollier@debian.org" 145s gpgv: Can't check signature: No public key 145s dpkg-source: warning: cannot verify inline signature for ./ariba_2.14.7+ds-7.dsc: no acceptable signature found 145s autopkgtest [21:46:21]: testing package ariba version 2.14.7+ds-7 146s autopkgtest [21:46:22]: build not needed 147s autopkgtest [21:46:23]: test test-example: preparing testbed 147s Reading package lists... 147s Building dependency tree... 147s Reading state information... 148s Starting pkgProblemResolver with broken count: 0 148s Starting 2 pkgProblemResolver with broken count: 0 148s Done 149s The following NEW packages will be installed: 149s ariba blt bowtie2 cd-hit fastaq fontconfig-config fonts-dejavu-core 149s fonts-dejavu-mono fonts-lyx fonts-urw-base35 libblas3 libcairo2 149s libcapnp-1.1.0 libdeflate0 libfml0 libfontconfig1 libfontenc1 libgfortran5 149s libgomp1 libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b libhts3t64 149s libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery 149s libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libminimap0 149s libmurmurhash2 libopenjp2-7 libpixman-1-0 libqhull-r8.0 libraqm0 149s libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 149s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 mash 149s mummer python-matplotlib-data python3-biopython python3-brotli python3-bs4 149s python3-cairo python3-contourpy python3-cycler python3-dateutil 149s python3-decorator python3-dendropy python3-fonttools python3-freetype 149s python3-fs python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 149s python3-mpmath python3-numpy python3-numpy-dev python3-packaging python3-pil 149s python3-pil.imagetk python3-platformdirs python3-pymummer python3-pysam 149s python3-reportlab python3-rlpycairo python3-scipy python3-soupsieve 149s python3-sympy python3-tk python3-ufolib2 python3-unicodedata2 python3.13-tk 149s samtools sgml-base tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common 149s xfonts-encodings xfonts-utils xml-core 149s 0 upgraded, 100 newly installed, 0 to remove and 0 not upgraded. 149s Need to get 112 MB of archives. 149s After this operation, 484 MB of additional disk space will be used. 149s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy-dev amd64 1:2.2.3+ds-2 [147 kB] 150s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 150s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 15-20250222-0ubuntu1 [919 kB] 150s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 150s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:2.2.3+ds-2 [8537 kB] 150s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 150s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB] 150s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-2 [132 kB] 150s Get:9 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.21+ds-1 [514 kB] 150s Get:10 http://ftpmaster.internal/ubuntu plucky/universe amd64 samtools amd64 1.21-1 [655 kB] 150s Get:11 http://ftpmaster.internal/ubuntu plucky/universe amd64 fastaq all 3.17.0-9 [48.2 kB] 150s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB] 150s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 150s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 150s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 150s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 150s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 150s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 150s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 151s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-2ubuntu1 [37.4 kB] 151s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-2ubuntu1 [164 kB] 151s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 151s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 151s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 151s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB] 151s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-tk amd64 3.13.2-1 [107 kB] 151s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [694 kB] 151s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-8 [4824 B] 151s Get:29 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-tk amd64 3.13.2-1 [9818 B] 151s Get:30 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 11.1.0-5 [9936 B] 151s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250222-0ubuntu1 [148 kB] 151s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 151s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 151s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 151s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 151s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu3 [217 kB] 151s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 151s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 151s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.2-1 [17.2 kB] 151s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 151s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 151s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 151s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 151s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 151s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB] 151s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB] 151s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 11.1.0-5 [589 kB] 151s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 151s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 151s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 151s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 151s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2build2 [124 kB] 151s Get:53 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 151s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 151s Get:55 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.3.1-1 [1137 kB] 151s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 151s Get:57 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 151s Get:58 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.85+dfsg-2build1 [1739 kB] 151s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-soupsieve all 2.6-1 [33.0 kB] 151s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-bs4 all 4.13.3-1 [136 kB] 151s Get:61 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-dendropy all 4.6.1-2 [278 kB] 151s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 151s Get:63 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 151s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.3-1 [171 kB] 151s Get:65 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-7build1 [2934 kB] 151s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-3 [80.2 kB] 151s Get:67 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.1-1build1 [218 kB] 151s Get:68 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 151s Get:69 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build4 [367 kB] 151s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-platformdirs all 4.3.6-1 [16.8 kB] 151s Get:71 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-7 [90.8 kB] 151s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu2 [175 kB] 151s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.1-1build1 [1408 kB] 151s Get:74 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.4.0+dfsg-1build1 [27.0 kB] 151s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 151s Get:76 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 151s Get:77 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.14.1-4ubuntu1 [22.3 MB] 152s Get:78 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 152s Get:79 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-5 [4229 kB] 152s Get:80 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 152s Get:81 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build3 [360 kB] 152s Get:82 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 153s Get:83 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.55.3-2build1 [1536 kB] 153s Get:84 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-3build1 [55.6 kB] 153s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.2-1 [51.5 kB] 153s Get:86 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 153s Get:87 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-7build1 [17.4 MB] 154s Get:88 http://ftpmaster.internal/ubuntu plucky/universe amd64 mummer amd64 3.23+dfsg-8 [685 kB] 154s Get:89 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pymummer all 0.11.0-5 [17.3 kB] 154s Get:90 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pysam amd64 0.23.0+ds-1build1 [3966 kB] 154s Get:91 http://ftpmaster.internal/ubuntu plucky/universe amd64 libfml0 amd64 0.1+git20221215.85f159e-1 [74.4 kB] 154s Get:92 http://ftpmaster.internal/ubuntu plucky/universe amd64 libminimap0 amd64 0.2-8 [23.5 kB] 154s Get:93 http://ftpmaster.internal/ubuntu plucky/universe amd64 bowtie2 amd64 2.5.4-1 [1336 kB] 154s Get:94 http://ftpmaster.internal/ubuntu plucky/universe amd64 cd-hit amd64 4.8.1-4 [521 kB] 154s Get:95 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcapnp-1.1.0 amd64 1.1.0-2 [1533 kB] 154s Get:96 http://ftpmaster.internal/ubuntu plucky/universe amd64 libgslcblas0 amd64 2.8+dfsg-5 [290 kB] 154s Get:97 http://ftpmaster.internal/ubuntu plucky/universe amd64 libgsl28 amd64 2.8+dfsg-5 [1285 kB] 154s Get:98 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmurmurhash2 amd64 1.6-1 [5770 B] 154s Get:99 http://ftpmaster.internal/ubuntu plucky/universe amd64 mash amd64 2.3+dfsg-6build2 [160 kB] 154s Get:100 http://ftpmaster.internal/ubuntu plucky/universe amd64 ariba amd64 2.14.7+ds-7 [2034 kB] 155s Fetched 112 MB in 5s (24.0 MB/s) 155s Selecting previously unselected package python3-numpy-dev:amd64. 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 ... 109122 files and directories currently installed.) 155s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.3+ds-2_amd64.deb ... 155s Unpacking python3-numpy-dev:amd64 (1:2.2.3+ds-2) ... 155s Selecting previously unselected package libblas3:amd64. 155s Preparing to unpack .../01-libblas3_3.12.1-2_amd64.deb ... 155s Unpacking libblas3:amd64 (3.12.1-2) ... 155s Selecting previously unselected package libgfortran5:amd64. 155s Preparing to unpack .../02-libgfortran5_15-20250222-0ubuntu1_amd64.deb ... 155s Unpacking libgfortran5:amd64 (15-20250222-0ubuntu1) ... 155s Selecting previously unselected package liblapack3:amd64. 155s Preparing to unpack .../03-liblapack3_3.12.1-2_amd64.deb ... 155s Unpacking liblapack3:amd64 (3.12.1-2) ... 155s Selecting previously unselected package python3-numpy. 155s Preparing to unpack .../04-python3-numpy_1%3a2.2.3+ds-2_amd64.deb ... 156s Unpacking python3-numpy (1:2.2.3+ds-2) ... 156s Selecting previously unselected package sgml-base. 156s Preparing to unpack .../05-sgml-base_1.31_all.deb ... 156s Unpacking sgml-base (1.31) ... 156s Selecting previously unselected package libdeflate0:amd64. 156s Preparing to unpack .../06-libdeflate0_1.23-1_amd64.deb ... 156s Unpacking libdeflate0:amd64 (1.23-1) ... 156s Selecting previously unselected package libhtscodecs2:amd64. 156s Preparing to unpack .../07-libhtscodecs2_1.6.1-2_amd64.deb ... 156s Unpacking libhtscodecs2:amd64 (1.6.1-2) ... 156s Selecting previously unselected package libhts3t64:amd64. 156s Preparing to unpack .../08-libhts3t64_1.21+ds-1_amd64.deb ... 156s Unpacking libhts3t64:amd64 (1.21+ds-1) ... 156s Selecting previously unselected package samtools. 156s Preparing to unpack .../09-samtools_1.21-1_amd64.deb ... 156s Unpacking samtools (1.21-1) ... 156s Selecting previously unselected package fastaq. 156s Preparing to unpack .../10-fastaq_3.17.0-9_all.deb ... 156s Unpacking fastaq (3.17.0-9) ... 156s Selecting previously unselected package libtcl8.6:amd64. 156s Preparing to unpack .../11-libtcl8.6_8.6.16+dfsg-1_amd64.deb ... 156s Unpacking libtcl8.6:amd64 (8.6.16+dfsg-1) ... 156s Selecting previously unselected package fonts-dejavu-mono. 156s Preparing to unpack .../12-fonts-dejavu-mono_2.37-8_all.deb ... 156s Unpacking fonts-dejavu-mono (2.37-8) ... 156s Selecting previously unselected package fonts-dejavu-core. 156s Preparing to unpack .../13-fonts-dejavu-core_2.37-8_all.deb ... 156s Unpacking fonts-dejavu-core (2.37-8) ... 156s Selecting previously unselected package libfontenc1:amd64. 156s Preparing to unpack .../14-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 156s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 156s Selecting previously unselected package x11-common. 156s Preparing to unpack .../15-x11-common_1%3a7.7+23ubuntu3_all.deb ... 156s Unpacking x11-common (1:7.7+23ubuntu3) ... 157s Selecting previously unselected package xfonts-encodings. 157s Preparing to unpack .../16-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 157s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 157s Selecting previously unselected package xfonts-utils. 157s Preparing to unpack .../17-xfonts-utils_1%3a7.7+7_amd64.deb ... 157s Unpacking xfonts-utils (1:7.7+7) ... 157s Selecting previously unselected package fonts-urw-base35. 157s Preparing to unpack .../18-fonts-urw-base35_20200910-8_all.deb ... 157s Unpacking fonts-urw-base35 (20200910-8) ... 157s Selecting previously unselected package fontconfig-config. 157s Preparing to unpack .../19-fontconfig-config_2.15.0-2ubuntu1_amd64.deb ... 157s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 157s Selecting previously unselected package libfontconfig1:amd64. 157s Preparing to unpack .../20-libfontconfig1_2.15.0-2ubuntu1_amd64.deb ... 157s Unpacking libfontconfig1:amd64 (2.15.0-2ubuntu1) ... 157s Selecting previously unselected package libxrender1:amd64. 157s Preparing to unpack .../21-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 157s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 157s Selecting previously unselected package libxft2:amd64. 157s Preparing to unpack .../22-libxft2_2.3.6-1build1_amd64.deb ... 157s Unpacking libxft2:amd64 (2.3.6-1build1) ... 157s Selecting previously unselected package libxss1:amd64. 157s Preparing to unpack .../23-libxss1_1%3a1.2.3-1build3_amd64.deb ... 157s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 157s Selecting previously unselected package libtk8.6:amd64. 157s Preparing to unpack .../24-libtk8.6_8.6.16-1_amd64.deb ... 157s Unpacking libtk8.6:amd64 (8.6.16-1) ... 157s Selecting previously unselected package python3.13-tk. 157s Preparing to unpack .../25-python3.13-tk_3.13.2-1_amd64.deb ... 157s Unpacking python3.13-tk (3.13.2-1) ... 157s Selecting previously unselected package tk8.6-blt2.5. 157s Preparing to unpack .../26-tk8.6-blt2.5_2.5.3+dfsg-8_amd64.deb ... 157s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 158s Selecting previously unselected package blt. 158s Preparing to unpack .../27-blt_2.5.3+dfsg-8_amd64.deb ... 158s Unpacking blt (2.5.3+dfsg-8) ... 158s Selecting previously unselected package python3-tk:amd64. 158s Preparing to unpack .../28-python3-tk_3.13.2-1_amd64.deb ... 158s Unpacking python3-tk:amd64 (3.13.2-1) ... 158s Selecting previously unselected package python3-pil.imagetk:amd64. 158s Preparing to unpack .../29-python3-pil.imagetk_11.1.0-5_amd64.deb ... 158s Unpacking python3-pil.imagetk:amd64 (11.1.0-5) ... 158s Selecting previously unselected package libgomp1:amd64. 158s Preparing to unpack .../30-libgomp1_15-20250222-0ubuntu1_amd64.deb ... 158s Unpacking libgomp1:amd64 (15-20250222-0ubuntu1) ... 158s Selecting previously unselected package libimagequant0:amd64. 158s Preparing to unpack .../31-libimagequant0_2.18.0-1build1_amd64.deb ... 158s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 158s Selecting previously unselected package libjpeg-turbo8:amd64. 158s Preparing to unpack .../32-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ... 158s Unpacking libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 158s Selecting previously unselected package libjpeg8:amd64. 158s Preparing to unpack .../33-libjpeg8_8c-2ubuntu11_amd64.deb ... 158s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 158s Selecting previously unselected package liblcms2-2:amd64. 158s Preparing to unpack .../34-liblcms2-2_2.16-2_amd64.deb ... 158s Unpacking liblcms2-2:amd64 (2.16-2) ... 158s Selecting previously unselected package libopenjp2-7:amd64. 158s Preparing to unpack .../35-libopenjp2-7_2.5.0-2ubuntu3_amd64.deb ... 158s Unpacking libopenjp2-7:amd64 (2.5.0-2ubuntu3) ... 158s Selecting previously unselected package libgraphite2-3:amd64. 158s Preparing to unpack .../36-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 158s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 158s Selecting previously unselected package libharfbuzz0b:amd64. 158s Preparing to unpack .../37-libharfbuzz0b_10.2.0-1_amd64.deb ... 158s Unpacking libharfbuzz0b:amd64 (10.2.0-1) ... 158s Selecting previously unselected package libraqm0:amd64. 158s Preparing to unpack .../38-libraqm0_0.10.2-1_amd64.deb ... 158s Unpacking libraqm0:amd64 (0.10.2-1) ... 158s Selecting previously unselected package libjbig0:amd64. 158s Preparing to unpack .../39-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 158s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 158s Selecting previously unselected package liblerc4:amd64. 158s Preparing to unpack .../40-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 158s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 158s Selecting previously unselected package libsharpyuv0:amd64. 158s Preparing to unpack .../41-libsharpyuv0_1.5.0-0.1_amd64.deb ... 158s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 158s Selecting previously unselected package libwebp7:amd64. 158s Preparing to unpack .../42-libwebp7_1.5.0-0.1_amd64.deb ... 158s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 158s Selecting previously unselected package libtiff6:amd64. 158s Preparing to unpack .../43-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 158s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 158s Selecting previously unselected package libwebpdemux2:amd64. 158s Preparing to unpack .../44-libwebpdemux2_1.5.0-0.1_amd64.deb ... 158s Unpacking libwebpdemux2:amd64 (1.5.0-0.1) ... 158s Selecting previously unselected package libwebpmux3:amd64. 158s Preparing to unpack .../45-libwebpmux3_1.5.0-0.1_amd64.deb ... 158s Unpacking libwebpmux3:amd64 (1.5.0-0.1) ... 158s Selecting previously unselected package python3-pil:amd64. 158s Preparing to unpack .../46-python3-pil_11.1.0-5_amd64.deb ... 158s Unpacking python3-pil:amd64 (11.1.0-5) ... 158s Selecting previously unselected package libpixman-1-0:amd64. 158s Preparing to unpack .../47-libpixman-1-0_0.44.0-3_amd64.deb ... 158s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 158s Selecting previously unselected package libxcb-render0:amd64. 158s Preparing to unpack .../48-libxcb-render0_1.17.0-2_amd64.deb ... 158s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 158s Selecting previously unselected package libxcb-shm0:amd64. 158s Preparing to unpack .../49-libxcb-shm0_1.17.0-2_amd64.deb ... 158s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 159s Selecting previously unselected package libcairo2:amd64. 159s Preparing to unpack .../50-libcairo2_1.18.2-2_amd64.deb ... 159s Unpacking libcairo2:amd64 (1.18.2-2) ... 159s Selecting previously unselected package python3-cairo. 159s Preparing to unpack .../51-python3-cairo_1.26.1-2build2_amd64.deb ... 159s Unpacking python3-cairo (1.26.1-2build2) ... 159s Selecting previously unselected package python3-freetype. 159s Preparing to unpack .../52-python3-freetype_2.5.1-1_all.deb ... 159s Unpacking python3-freetype (2.5.1-1) ... 159s Selecting previously unselected package python3-rlpycairo. 159s Preparing to unpack .../53-python3-rlpycairo_0.3.0-3_all.deb ... 159s Unpacking python3-rlpycairo (0.3.0-3) ... 159s Selecting previously unselected package python3-reportlab. 159s Preparing to unpack .../54-python3-reportlab_4.3.1-1_all.deb ... 159s Unpacking python3-reportlab (4.3.1-1) ... 159s Selecting previously unselected package xml-core. 159s Preparing to unpack .../55-xml-core_0.19_all.deb ... 159s Unpacking xml-core (0.19) ... 159s Selecting previously unselected package w3c-sgml-lib. 159s Preparing to unpack .../56-w3c-sgml-lib_1.3-3_all.deb ... 159s Unpacking w3c-sgml-lib (1.3-3) ... 159s Selecting previously unselected package python3-biopython. 159s Preparing to unpack .../57-python3-biopython_1.85+dfsg-2build1_amd64.deb ... 159s Unpacking python3-biopython (1.85+dfsg-2build1) ... 159s Selecting previously unselected package python3-soupsieve. 159s Preparing to unpack .../58-python3-soupsieve_2.6-1_all.deb ... 159s Unpacking python3-soupsieve (2.6-1) ... 159s Selecting previously unselected package python3-bs4. 159s Preparing to unpack .../59-python3-bs4_4.13.3-1_all.deb ... 159s Unpacking python3-bs4 (4.13.3-1) ... 159s Selecting previously unselected package python3-dendropy. 159s Preparing to unpack .../60-python3-dendropy_4.6.1-2_all.deb ... 159s Unpacking python3-dendropy (4.6.1-2) ... 159s Selecting previously unselected package libjs-jquery. 159s Preparing to unpack .../61-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 159s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 159s Selecting previously unselected package libjs-jquery-ui. 159s Preparing to unpack .../62-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 159s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 159s Selecting previously unselected package fonts-lyx. 160s Preparing to unpack .../63-fonts-lyx_2.4.3-1_all.deb ... 160s Unpacking fonts-lyx (2.4.3-1) ... 160s Selecting previously unselected package python-matplotlib-data. 160s Preparing to unpack .../64-python-matplotlib-data_3.8.3-7build1_all.deb ... 160s Unpacking python-matplotlib-data (3.8.3-7build1) ... 160s Selecting previously unselected package python3-dateutil. 160s Preparing to unpack .../65-python3-dateutil_2.9.0-3_all.deb ... 160s Unpacking python3-dateutil (2.9.0-3) ... 160s Selecting previously unselected package python3-contourpy. 160s Preparing to unpack .../66-python3-contourpy_1.3.1-1build1_amd64.deb ... 160s Unpacking python3-contourpy (1.3.1-1build1) ... 160s Selecting previously unselected package python3-cycler. 160s Preparing to unpack .../67-python3-cycler_0.12.1-1_all.deb ... 160s Unpacking python3-cycler (0.12.1-1) ... 160s Selecting previously unselected package python3-brotli. 160s Preparing to unpack .../68-python3-brotli_1.1.0-2build4_amd64.deb ... 160s Unpacking python3-brotli (1.1.0-2build4) ... 160s Selecting previously unselected package python3-platformdirs. 160s Preparing to unpack .../69-python3-platformdirs_4.3.6-1_all.deb ... 160s Unpacking python3-platformdirs (4.3.6-1) ... 160s Selecting previously unselected package python3-fs. 160s Preparing to unpack .../70-python3-fs_2.4.16-7_all.deb ... 160s Unpacking python3-fs (2.4.16-7) ... 160s Selecting previously unselected package libxslt1.1:amd64. 160s Preparing to unpack .../71-libxslt1.1_1.1.39-0exp1ubuntu2_amd64.deb ... 160s Unpacking libxslt1.1:amd64 (1.1.39-0exp1ubuntu2) ... 160s Selecting previously unselected package python3-lxml:amd64. 160s Preparing to unpack .../72-python3-lxml_5.3.1-1build1_amd64.deb ... 160s Unpacking python3-lxml:amd64 (5.3.1-1build1) ... 160s Selecting previously unselected package python3-lz4. 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Unpacking python3-sympy (1.13.3-5) ... 161s Selecting previously unselected package python3-ufolib2. 161s Preparing to unpack .../79-python3-ufolib2_0.17.0+dfsg1-1_all.deb ... 161s Unpacking python3-ufolib2 (0.17.0+dfsg1-1) ... 161s Selecting previously unselected package python3-unicodedata2. 161s Preparing to unpack .../80-python3-unicodedata2_15.1.0+ds-1build3_amd64.deb ... 161s Unpacking python3-unicodedata2 (15.1.0+ds-1build3) ... 162s Selecting previously unselected package unicode-data. 162s Preparing to unpack .../81-unicode-data_15.1.0-1_all.deb ... 162s Unpacking unicode-data (15.1.0-1) ... 162s Selecting previously unselected package python3-fonttools. 162s Preparing to unpack .../82-python3-fonttools_4.55.3-2build1_amd64.deb ... 162s Unpacking python3-fonttools (4.55.3-2build1) ... 162s Selecting previously unselected package python3-kiwisolver. 162s Preparing to unpack .../83-python3-kiwisolver_1.4.7-3build1_amd64.deb ... 162s Unpacking python3-kiwisolver (1.4.7-3build1) ... 162s Selecting previously unselected package python3-packaging. 162s Preparing to unpack .../84-python3-packaging_24.2-1_all.deb ... 162s Unpacking python3-packaging (24.2-1) ... 162s Selecting previously unselected package libqhull-r8.0:amd64. 162s Preparing to unpack .../85-libqhull-r8.0_2020.2-6build1_amd64.deb ... 162s Unpacking libqhull-r8.0:amd64 (2020.2-6build1) ... 162s Selecting previously unselected package python3-matplotlib. 162s Preparing to unpack .../86-python3-matplotlib_3.8.3-7build1_amd64.deb ... 162s Unpacking python3-matplotlib (3.8.3-7build1) ... 163s Selecting previously unselected package mummer. 163s Preparing to unpack .../87-mummer_3.23+dfsg-8_amd64.deb ... 163s Unpacking mummer (3.23+dfsg-8) ... 163s Selecting previously unselected package python3-pymummer. 163s Preparing to unpack .../88-python3-pymummer_0.11.0-5_all.deb ... 163s Unpacking python3-pymummer (0.11.0-5) ... 163s Selecting previously unselected package python3-pysam. 163s Preparing to unpack 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unselected package libgslcblas0:amd64. 163s Preparing to unpack .../95-libgslcblas0_2.8+dfsg-5_amd64.deb ... 163s Unpacking libgslcblas0:amd64 (2.8+dfsg-5) ... 164s Selecting previously unselected package libgsl28:amd64. 164s Preparing to unpack .../96-libgsl28_2.8+dfsg-5_amd64.deb ... 164s Unpacking libgsl28:amd64 (2.8+dfsg-5) ... 164s Selecting previously unselected package libmurmurhash2:amd64. 164s Preparing to unpack .../97-libmurmurhash2_1.6-1_amd64.deb ... 164s Unpacking libmurmurhash2:amd64 (1.6-1) ... 164s Selecting previously unselected package mash. 164s Preparing to unpack .../98-mash_2.3+dfsg-6build2_amd64.deb ... 164s Unpacking mash (2.3+dfsg-6build2) ... 164s Selecting previously unselected package ariba. 164s Preparing to unpack .../99-ariba_2.14.7+ds-7_amd64.deb ... 164s Unpacking ariba (2.14.7+ds-7) ... 164s Setting up libhtscodecs2:amd64 (1.6.1-2) ... 164s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 164s Setting up liblcms2-2:amd64 (2.16-2) ... 164s Setting up libpixman-1-0:amd64 (0.44.0-3) ... 164s Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... 164s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 164s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 164s Setting up libgslcblas0:amd64 (2.8+dfsg-5) ... 164s Setting up libmurmurhash2:amd64 (1.6-1) ... 164s Setting up python3-lz4 (4.4.0+dfsg-1build1) ... 164s Setting up libxcb-render0:amd64 (1.17.0-2) ... 164s Setting up python3-unicodedata2 (15.1.0+ds-1build3) ... 164s Setting up fonts-lyx (2.4.3-1) ... 164s Setting up x11-common (1:7.7+23ubuntu3) ... 165s Setting up libdeflate0:amd64 (1.23-1) ... 165s Setting up libqhull-r8.0:amd64 (2020.2-6build1) ... 165s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 165s Setting up libgomp1:amd64 (15-20250222-0ubuntu1) ... 165s Setting up python3-freetype (2.5.1-1) ... 165s Setting up libfml0:amd64 (0.1+git20221215.85f159e-1) ... 165s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 165s Setting up python3-platformdirs (4.3.6-1) ... 165s Setting up bowtie2 (2.5.4-1) ... 165s Setting up python3-fs (2.4.16-7) ... 165s Setting up unicode-data (15.1.0-1) ... 165s Setting up python3-decorator (5.1.1-5) ... 166s Setting up libminimap0:amd64 (0.2-8) ... 166s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ... 166s Setting up libblas3:amd64 (3.12.1-2) ... 166s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 166s Setting up python3-packaging (24.2-1) ... 166s Setting up python3-brotli (1.1.0-2build4) ... 166s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 166s Setting up python3-cycler (0.12.1-1) ... 166s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 166s Setting up fonts-dejavu-mono (2.37-8) ... 166s Setting up python3-kiwisolver (1.4.7-3build1) ... 166s Setting up python3-numpy-dev:amd64 (1:2.2.3+ds-2) ... 166s Setting up libtcl8.6:amd64 (8.6.16+dfsg-1) ... 166s Setting up fonts-dejavu-core (2.37-8) ... 166s Setting up libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 166s Setting up libgfortran5:amd64 (15-20250222-0ubuntu1) ... 166s Setting up libwebp7:amd64 (1.5.0-0.1) ... 166s Setting up libxslt1.1:amd64 (1.1.39-0exp1ubuntu2) ... 166s Setting up mummer (3.23+dfsg-8) ... 166s Setting up libhts3t64:amd64 (1.21+ds-1) ... 166s Setting up libopenjp2-7:amd64 (2.5.0-2ubuntu3) ... 166s Setting up libharfbuzz0b:amd64 (10.2.0-1) ... 166s Setting up python3-dateutil (2.9.0-3) ... 166s Setting up sgml-base (1.31) ... 166s Setting up libcapnp-1.1.0:amd64 (1.1.0-2) ... 166s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 166s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 166s Setting up python3-mpmath (1.3.0-1) ... 167s Setting up libgsl28:amd64 (2.8+dfsg-5) ... 167s Setting up python-matplotlib-data (3.8.3-7build1) ... 167s Setting up libwebpmux3:amd64 (1.5.0-0.1) ... 167s Setting up python3-dendropy (4.6.1-2) ... 167s Setting up python3-soupsieve (2.6-1) ... 168s Setting up cd-hit (4.8.1-4) ... 168s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 168s Setting up python3-sympy (1.13.3-5) ... 175s Setting up liblapack3:amd64 (3.12.1-2) ... 175s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 175s Setting up python3-pysam (0.23.0+ds-1build1) ... 175s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 175s Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... 175s Setting up xfonts-utils (1:7.7+7) ... 175s Setting up python3-bs4 (4.13.3-1) ... 175s Setting up samtools (1.21-1) ... 175s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 175s Setting up libraqm0:amd64 (0.10.2-1) ... 175s Setting up mash (2.3+dfsg-6build2) ... 175s Setting up python3-numpy (1:2.2.3+ds-2) ... 178s Setting up python3-lxml:amd64 (5.3.1-1build1) ... 178s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 178s Setting up xml-core (0.19) ... 178s Setting up python3-contourpy (1.3.1-1build1) ... 178s Setting up libfontconfig1:amd64 (2.15.0-2ubuntu1) ... 178s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 178s Setting up libxft2:amd64 (2.3.6-1build1) ... 178s Setting up python3-scipy (1.14.1-4ubuntu1) ... 182s Setting up libtk8.6:amd64 (8.6.16-1) ... 182s Setting up fastaq (3.17.0-9) ... 182s Setting up fonts-urw-base35 (20200910-8) ... 182s Setting up libcairo2:amd64 (1.18.2-2) ... 182s Setting up python3.13-tk (3.13.2-1) ... 183s Setting up python3-pymummer (0.11.0-5) ... 183s Setting up python3-pil:amd64 (11.1.0-5) ... 183s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 183s Setting up python3-cairo (1.26.1-2build2) ... 183s Setting up blt (2.5.3+dfsg-8) ... 183s Setting up python3-tk:amd64 (3.13.2-1) ... 183s Setting up python3-pil.imagetk:amd64 (11.1.0-5) ... 183s Setting up python3-rlpycairo (0.3.0-3) ... 184s Setting up python3-reportlab (4.3.1-1) ... 184s Setting up python3-fonttools (4.55.3-2build1) ... 185s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 186s Setting up python3-matplotlib (3.8.3-7build1) ... 187s Processing triggers for libc-bin (2.41-1ubuntu1) ... 187s Processing triggers for man-db (2.13.0-1) ... 189s Processing triggers for sgml-base (1.31) ... 189s Setting up w3c-sgml-lib (1.3-3) ... 224s Setting up python3-biopython (1.85+dfsg-2build1) ... 226s Setting up ariba (2.14.7+ds-7) ... 227s autopkgtest [21:47:43]: test test-example: [----------------------- 230s ARIBA version: 2.14.6 230s 230s External dependencies: 230s bowtie2 2.5.4 /usr/bin/bowtie2 230s cdhit 4.8.1 /usr/bin/cd-hit-est 230s nucmer 3.1 /usr/bin/nucmer 230s 230s External dependencies OK: True 230s 230s Python version: 230s 3.13.2 (main, Feb 5 2025, 01:23:35) [GCC 14.2.0] 230s 230s Python packages: 230s ariba 2.14.6 /usr/lib/python3/dist-packages/ariba/__init__.py 230s bs4 4.13.3 /usr/lib/python3/dist-packages/bs4/__init__.py 230s dendropy 4.6.1 /usr/lib/python3/dist-packages/dendropy/__init__.py 230s pyfastaq 3.17.0 /usr/lib/python3/dist-packages/pyfastaq/__init__.py 230s pymummer 0.11.0 /usr/lib/python3/dist-packages/pymummer/__init__.py 230s pysam 0.23.0 /usr/lib/python3/dist-packages/pysam/__init__.py 230s 230s Python packages OK: True 230s 230s Everything looks OK: True 230s 230s Loading and checking input data 230s 230s Running cdhit 230s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.qdTdMd8QAU/foo/PREPAREREF/02.cdhit.noncoding.fa -o /tmp/tmp.qdTdMd8QAU/foo/tmp.run_cd-hit.flk46rvi/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 231s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.qdTdMd8QAU/foo/PREPAREREF/02.cdhit.noncoding.varonly.fa -o /tmp/tmp.qdTdMd8QAU/foo/tmp.run_cd-hit.54m2sr1x/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 231s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.qdTdMd8QAU/foo/PREPAREREF/02.cdhit.gene.fa -o /tmp/tmp.qdTdMd8QAU/foo/tmp.run_cd-hit.dzsj17fs/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 231s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.qdTdMd8QAU/foo/PREPAREREF/02.cdhit.gene.varonly.fa -o /tmp/tmp.qdTdMd8QAU/foo/tmp.run_cd-hit.bosck5bh/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 231s 231s Writing clusters to file. 10 in total 232s Found reads file: reads_1.fq 232s Found reads file: reads_2.fq 232s ARIBA version: 2.14.6 232s 232s External dependencies: 232s bowtie2 2.5.4 /usr/bin/bowtie2 232s cdhit 4.8.1 /usr/bin/cd-hit-est 232s nucmer 3.1 /usr/bin/nucmer 232s 232s External dependencies OK: True 232s 232s Python version: 232s 3.13.2 (main, Feb 5 2025, 01:23:35) [GCC 14.2.0] 232s 232s Python packages: 232s ariba 2.14.6 /usr/lib/python3/dist-packages/ariba/__init__.py 232s bs4 4.13.3 /usr/lib/python3/dist-packages/bs4/__init__.py 232s dendropy 4.6.1 /usr/lib/python3/dist-packages/dendropy/__init__.py 232s pyfastaq 3.17.0 /usr/lib/python3/dist-packages/pyfastaq/__init__.py 232s pymummer 0.11.0 /usr/lib/python3/dist-packages/pymummer/__init__.py 232s pysam 0.23.0 /usr/lib/python3/dist-packages/pysam/__init__.py 232s 232s Python packages OK: True 232s 232s Everything looks OK: True 232s Temporary directory: /tmp/tmp.qdTdMd8QAU/foo/OUT/ariba.tmp.yvglnnmu 232s ______________________ Mapping reads to clustered genes _______________________ 232s Finished mapping 232s 232s _____________________________ Generating clusters _____________________________ 232s syscall: sort -k1,1 -k 2,2n /tmp/tmp.qdTdMd8QAU/foo/OUT/minimap.reads > /tmp/tmp.qdTdMd8QAU/foo/OUT/read_store 232s Compressing file /tmp/tmp.qdTdMd8QAU/foo/OUT/read_store 232s Found 51 proper read pairs from minimap 232s Total clusters to perform local assemblies: 9 232s 232s Insert size information from reads mapped to reference genes: 232s Insert size: 185.0 232s Insert sspace sd: 0.27 232s Max insert: 220.55 232s 232s ___________________________ Assembling each cluster ___________________________ 232s Will run 1 cluster(s) in parallel 232s Not constructing cluster cluster because it only has 2 reads (1 of 9) 232s Constructing cluster cluster_1 (2 of 9) 232s Constructing cluster cluster_2 (3 of 9) 232s Constructing cluster cluster_3 (4 of 9) 232s Constructing cluster cluster_4 (5 of 9) 232s Constructing cluster gene (6 of 9) 232s Constructing cluster gene_1 (7 of 9) 232s Constructing cluster noncoding (8 of 9) 232s Constructing cluster noncoding_1 (9 of 9) 232s Start running cluster cluster_1 in directory /tmp/tmp.qdTdMd8QAU/foo/OUT/ariba.tmp.yvglnnmu/cluster_1 235s cluster_1 detected 1 threads available to it 235s cluster_1 reported completion 235s Finished running cluster cluster_1 in directory /tmp/tmp.qdTdMd8QAU/foo/OUT/ariba.tmp.yvglnnmu/cluster_1 235s Deleting cluster dir /tmp/tmp.qdTdMd8QAU/foo/OUT/ariba.tmp.yvglnnmu/cluster_1 235s Start running cluster cluster_2 in directory /tmp/tmp.qdTdMd8QAU/foo/OUT/ariba.tmp.yvglnnmu/cluster_2 237s cluster_2 detected 1 threads available to it 237s cluster_2 reported completion 237s Finished running cluster cluster_2 in directory /tmp/tmp.qdTdMd8QAU/foo/OUT/ariba.tmp.yvglnnmu/cluster_2 237s Deleting cluster dir /tmp/tmp.qdTdMd8QAU/foo/OUT/ariba.tmp.yvglnnmu/cluster_2 237s Start running cluster cluster_3 in directory /tmp/tmp.qdTdMd8QAU/foo/OUT/ariba.tmp.yvglnnmu/cluster_3 239s cluster_3 detected 1 threads available to it 239s cluster_3 reported completion 239s Finished running cluster cluster_3 in directory /tmp/tmp.qdTdMd8QAU/foo/OUT/ariba.tmp.yvglnnmu/cluster_3 239s Deleting cluster dir /tmp/tmp.qdTdMd8QAU/foo/OUT/ariba.tmp.yvglnnmu/cluster_3 239s Start running cluster cluster_4 in directory /tmp/tmp.qdTdMd8QAU/foo/OUT/ariba.tmp.yvglnnmu/cluster_4 241s cluster_4 detected 1 threads available to it 241s cluster_4 reported completion 241s Finished running cluster cluster_4 in directory /tmp/tmp.qdTdMd8QAU/foo/OUT/ariba.tmp.yvglnnmu/cluster_4 241s Deleting cluster dir /tmp/tmp.qdTdMd8QAU/foo/OUT/ariba.tmp.yvglnnmu/cluster_4 241s Start running cluster gene in directory /tmp/tmp.qdTdMd8QAU/foo/OUT/ariba.tmp.yvglnnmu/gene 243s gene detected 1 threads available to it 243s gene reported completion 243s Finished running cluster gene in directory /tmp/tmp.qdTdMd8QAU/foo/OUT/ariba.tmp.yvglnnmu/gene 243s Deleting cluster dir /tmp/tmp.qdTdMd8QAU/foo/OUT/ariba.tmp.yvglnnmu/gene 243s Start running cluster gene_1 in directory /tmp/tmp.qdTdMd8QAU/foo/OUT/ariba.tmp.yvglnnmu/gene_1 245s gene_1 detected 1 threads available to it 245s gene_1 reported completion 245s Finished running cluster gene_1 in directory /tmp/tmp.qdTdMd8QAU/foo/OUT/ariba.tmp.yvglnnmu/gene_1 245s Deleting cluster dir /tmp/tmp.qdTdMd8QAU/foo/OUT/ariba.tmp.yvglnnmu/gene_1 245s Start running cluster noncoding in directory /tmp/tmp.qdTdMd8QAU/foo/OUT/ariba.tmp.yvglnnmu/noncoding 247s noncoding detected 1 threads available to it 247s noncoding reported completion 247s Finished running cluster noncoding in directory /tmp/tmp.qdTdMd8QAU/foo/OUT/ariba.tmp.yvglnnmu/noncoding 247s Deleting cluster dir /tmp/tmp.qdTdMd8QAU/foo/OUT/ariba.tmp.yvglnnmu/noncoding 247s Start running cluster noncoding_1 in directory /tmp/tmp.qdTdMd8QAU/foo/OUT/ariba.tmp.yvglnnmu/noncoding_1 249s noncoding_1 detected 1 threads available to it 249s noncoding_1 reported completion 249s Finished running cluster noncoding_1 in directory /tmp/tmp.qdTdMd8QAU/foo/OUT/ariba.tmp.yvglnnmu/noncoding_1 249s Deleting cluster dir /tmp/tmp.qdTdMd8QAU/foo/OUT/ariba.tmp.yvglnnmu/noncoding_1 249s Final value of remaining_clusters counter: Value('l', 0) 249s Finished assembling clusters 249s 249s _______________________________ Writing reports _______________________________ 249s Making /tmp/tmp.qdTdMd8QAU/foo/OUT/debug.report.tsv 249s Making /tmp/tmp.qdTdMd8QAU/foo/OUT/report.tsv 249s 249s ____________________ Writing fasta of assembled sequences _____________________ 249s /tmp/tmp.qdTdMd8QAU/foo/OUT/assembled_seqs.fa.gz and /tmp/tmp.qdTdMd8QAU/foo/OUT/assembled_genes.fa.gz 249s 249s __________________________ Catting cluster log files __________________________ 249s Writing file /tmp/tmp.qdTdMd8QAU/foo/OUT/log.clusters.gz 249s 249s _______________________________ Cleaning files ________________________________ 249s Deleting Logs directory /tmp/tmp.qdTdMd8QAU/foo/OUT/Logs 249s Deleting reads store files /tmp/tmp.qdTdMd8QAU/foo/OUT/read_store.gz[.tbi] 249s 249s All done! 249s 249s Running ARIBA on test data... 249s ------------------------------------------------------------------------------- 249s |=============================================================================| 249s | Preparing input data | 249s |=============================================================================| 249s ------------------------------------------------------------------------------- 249s Made output directory ./foo. Copying test data files into it: 249s copied ref_seqs.fa 249s copied metadata.tsv 249s copied reads_1.fq 249s copied reads_2.fq 249s ------------------------------------------------------------------------------- 249s |=============================================================================| 249s | Try running ariba prepareref | 249s |=============================================================================| 249s ------------------------------------------------------------------------------- 249s 249s Running ariba prepareref with: 249s /usr/bin/ariba prepareref --verbose -f ref_seqs.fa -m metadata.tsv --threads 1 PREPAREREF 249s 249s 249s ariba prepareref finished OK 249s ------------------------------------------------------------------------------- 249s |=============================================================================| 249s | Try running ariba run | 249s |=============================================================================| 249s ------------------------------------------------------------------------------- 249s 249s Running ARIBA with: 249s /usr/bin/ariba run --verbose --threads 1 PREPAREREF reads_1.fq reads_2.fq OUT 249s 249s 249s ariba run finished OK 249s Finished run on test data OK 250s autopkgtest [21:48:06]: test test-example: -----------------------] 250s test-example PASS 250s autopkgtest [21:48:06]: test test-example: - - - - - - - - - - results - - - - - - - - - - 251s autopkgtest [21:48:07]: @@@@@@@@@@@@@@@@@@@@ summary 251s test-example PASS 256s nova [W] Skipping flock for amd64 256s Creating nova instance adt-plucky-amd64-ariba-20250306-214356-juju-7f2275-prod-proposed-migration-environment-20-a41cdcfa-763f-48d8-9817-352c7c4986b6 from image adt/ubuntu-plucky-amd64-server-20250304.img (UUID 9c7d4da5-d95f-4c85-ac1f-51eb37e75c4c)... 256s nova [W] Timed out waiting for 10e8fe33-94e1-4d29-8637-9adacf48950f to get deleted.