0s autopkgtest [02:45:09]: starting date and time: 2025-02-17 02:45:09+0000
  0s autopkgtest [02:45:09]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production'
  0s autopkgtest [02:45:09]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.k56ej94y/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:spades --apt-upgrade circlator --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=spades/4.0.0+dfsg1-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-ppc64el-2.secgroup --name adt-plucky-ppc64el-circlator-20250217-024508-juju-7f2275-prod-proposed-migration-environment-15-9d1b909a-b15b-414f-b90f-ab440500ec45 --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-ppc64el -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/
 63s autopkgtest [02:46:12]: testbed dpkg architecture: ppc64el
 63s autopkgtest [02:46:12]: testbed apt version: 2.9.28
 63s autopkgtest [02:46:12]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 64s autopkgtest [02:46:13]: testbed release detected to be: None
 64s autopkgtest [02:46:13]: updating testbed package index (apt update)
 65s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB]
 65s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
 65s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
 65s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
 65s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [698 kB]
 65s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [61.5 kB]
 65s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B]
 65s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.9 kB]
 65s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [78.2 kB]
 65s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted ppc64el Packages [760 B]
 65s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [597 kB]
 65s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [5164 B]
 66s Fetched 1569 kB in 1s (1669 kB/s)
 67s Reading package lists...
 67s + lsb_release --codename --short
 67s + RELEASE=plucky
 67s + cat
 67s + [ plucky != trusty ]
 67s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade
 67s Reading package lists...
 67s Building dependency tree...
 67s Reading state information...
 68s Calculating upgrade...
 68s The following NEW packages will be installed:
 68s   gcc-15-base
 68s The following packages will be upgraded:
 68s   libatomic1 libgcc-s1 libstdc++6
 68s 3 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
 68s Need to get 1006 kB of archives.
 68s After this operation, 184 kB of additional disk space will be used.
 68s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el gcc-15-base ppc64el 15-20250213-1ubuntu1 [53.3 kB]
 68s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgcc-s1 ppc64el 15-20250213-1ubuntu1 [40.0 kB]
 68s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el libstdc++6 ppc64el 15-20250213-1ubuntu1 [902 kB]
 68s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libatomic1 ppc64el 15-20250213-1ubuntu1 [10.8 kB]
 69s Fetched 1006 kB in 1s (1816 kB/s)
 69s Selecting previously unselected package gcc-15-base:ppc64el.
 70s (Reading database ... 
(Reading database ... 5%
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(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 ... 106311 files and directories currently installed.)
 70s Preparing to unpack .../gcc-15-base_15-20250213-1ubuntu1_ppc64el.deb ...
 70s Unpacking gcc-15-base:ppc64el (15-20250213-1ubuntu1) ...
 70s Setting up gcc-15-base:ppc64el (15-20250213-1ubuntu1) ...
 70s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
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(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 ... 106316 files and directories currently installed.)
 70s Preparing to unpack .../libgcc-s1_15-20250213-1ubuntu1_ppc64el.deb ...
 70s Unpacking libgcc-s1:ppc64el (15-20250213-1ubuntu1) over (14.2.0-17ubuntu1) ...
 70s Setting up libgcc-s1:ppc64el (15-20250213-1ubuntu1) ...
 70s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
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(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 ... 106316 files and directories currently installed.)
 70s Preparing to unpack .../libstdc++6_15-20250213-1ubuntu1_ppc64el.deb ...
 70s Unpacking libstdc++6:ppc64el (15-20250213-1ubuntu1) over (14.2.0-17ubuntu1) ...
 70s Setting up libstdc++6:ppc64el (15-20250213-1ubuntu1) ...
 70s (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 ... 106316 files and directories currently installed.)
 70s Preparing to unpack .../libatomic1_15-20250213-1ubuntu1_ppc64el.deb ...
 70s Unpacking libatomic1:ppc64el (15-20250213-1ubuntu1) over (14.2.0-17ubuntu1) ...
 70s Setting up libatomic1:ppc64el (15-20250213-1ubuntu1) ...
 70s Processing triggers for libc-bin (2.40-4ubuntu1) ...
 70s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref
 70s + /usr/lib/apt/apt-helper analyze-pattern ?true
 70s + uname -r
 70s + sed s/\./\\./g
 70s + running_kernel_pattern=^linux-.*6\.12\.0-15-generic.*
 70s + apt list ?obsolete
 70s + tail -n+2
 70s + cut -d/ -f1
 70s + grep -v ^linux-.*6\.12\.0-15-generic.*
 71s + true
 71s + obsolete_pkgs=
 71s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove
 71s Reading package lists...
 71s Building dependency tree...
 71s Reading state information...
 71s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 71s + grep -q trusty /etc/lsb-release
 71s + [ ! -d /usr/share/doc/unattended-upgrades ]
 71s + [ ! -d /usr/share/doc/lxd ]
 71s + [ ! -d /usr/share/doc/lxd-client ]
 71s + [ ! -d /usr/share/doc/snapd ]
 71s + type iptables
 71s + cat
 71s + chmod 755 /etc/rc.local
 71s + . /etc/rc.local
 71s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu
 71s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP
 71s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP
 71s + uname -m
 71s + [ ppc64le = ppc64le ]
 71s + systemctl is-active keyboard-setup.service
 71s + [ active = failed ]
 71s + [ -d /run/systemd/system ]
 71s + systemd-detect-virt --quiet --vm
 71s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/
 71s + cat
 71s + grep -q lz4 /etc/initramfs-tools/initramfs.conf
 71s + echo COMPRESS=lz4
 71s autopkgtest [02:46:20]: upgrading testbed (apt dist-upgrade and autopurge)
 71s Reading package lists...
 72s Building dependency tree...
 72s Reading state information...
 72s Calculating upgrade...Starting pkgProblemResolver with broken count: 0
 72s Starting 2 pkgProblemResolver with broken count: 0
 72s Done
 72s Entering ResolveByKeep
 73s 
 73s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 73s Reading package lists...
 73s Building dependency tree...
 73s Reading state information...
 73s Starting pkgProblemResolver with broken count: 0
 73s Starting 2 pkgProblemResolver with broken count: 0
 73s Done
 74s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 76s autopkgtest [02:46:25]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP Tue Feb  4 16:32:08 UTC 2025
 77s autopkgtest [02:46:26]: @@@@@@@@@@@@@@@@@@@@ apt-source circlator
 78s Get:1 http://ftpmaster.internal/ubuntu plucky/universe circlator 1.5.6-12 (dsc) [2302 B]
 78s Get:2 http://ftpmaster.internal/ubuntu plucky/universe circlator 1.5.6-12 (tar) [5724 kB]
 78s Get:3 http://ftpmaster.internal/ubuntu plucky/universe circlator 1.5.6-12 (diff) [6412 B]
 79s gpgv: Signature made Fri Dec  6 09:53:32 2024 UTC
 79s gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
 79s gpgv:                issuer "tille@debian.org"
 79s gpgv: Can't check signature: No public key
 79s dpkg-source: warning: cannot verify inline signature for ./circlator_1.5.6-12.dsc: no acceptable signature found
 79s autopkgtest [02:46:28]: testing package circlator version 1.5.6-12
 79s autopkgtest [02:46:28]: build not needed
 80s autopkgtest [02:46:29]: test run-unit-test: preparing testbed
 80s Reading package lists...
 80s Building dependency tree...
 80s Reading state information...
 81s Starting pkgProblemResolver with broken count: 0
 81s Starting 2 pkgProblemResolver with broken count: 0
 81s Done
 81s The following NEW packages will be installed:
 81s   aglfn binfmt-support bwa ca-certificates-java canu circlator
 81s   default-jre-headless fastaq fastjar fontconfig fontconfig-config
 81s   fonts-dejavu-core fonts-dejavu-mono gnuplot-data gnuplot-nox jaligner
 81s   jarwrapper java-common libaom3 libapache-pom-java
 81s   libatinject-jsr330-api-java libcairo2 libcommons-codec-java
 81s   libcommons-compress-java libcommons-io-java libcommons-parent-java
 81s   libdatrie1 libde265-0 libdeflate0 liberror-prone-java libfastutil-java
 81s   libfilesys-df-perl libfontconfig1 libgd3 libgomp1 libgraphite2-3
 81s   libguava-java libharfbuzz0b libheif-plugin-aomdec libheif-plugin-libde265
 81s   libheif1 libhts3t64 libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8
 81s   libjpeg8 libjsr305-java liblcms2-2 liblerc4 liblua5.4-0 libpango-1.0-0
 81s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpcsclite1 libpixman-1-0 libraqm0
 81s   libsharpyuv0 libsnappy1v5 libssw-java libthai-data libthai0 libtiff6
 81s   libwebp7 libwebpmux3 libxcb-render0 libxcb-shm0 libxpm4 libxrender1
 81s   libxslt1.1 mhap mummer openjdk-21-jre-headless prodigal python3-all
 81s   python3-et-xmlfile python3-iniconfig python3-lxml python3-openpyxl
 81s   python3-packaging python3-pluggy python3-pymummer python3-pysam
 81s   python3-pytest python3.12 python3.12-minimal samtools
 81s 0 upgraded, 87 newly installed, 0 to remove and 0 not upgraded.
 81s Need to get 102 MB of archives.
 81s After this operation, 390 MB of additional disk space will be used.
 81s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.12-minimal ppc64el 3.12.9-1 [2465 kB]
 82s Get:2 http://ftpmaster.internal/ubuntu plucky/universe ppc64el binfmt-support ppc64el 2.2.2-7 [66.8 kB]
 82s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.12 ppc64el 3.12.9-1 [671 kB]
 82s Get:4 http://ftpmaster.internal/ubuntu plucky/universe ppc64el bwa ppc64el 0.7.18-1 [231 kB]
 82s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el ca-certificates-java all 20240118 [11.6 kB]
 82s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgomp1 ppc64el 15-20250213-1ubuntu1 [168 kB]
 82s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el libsnappy1v5 ppc64el 1.2.1-1 [33.4 kB]
 82s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfilesys-df-perl ppc64el 0.92-7build5 [11.2 kB]
 82s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el java-common all 0.76 [6852 B]
 82s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblcms2-2 ppc64el 2.16-2 [243 kB]
 82s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-3ubuntu2 [215 kB]
 82s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B]
 82s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpcsclite1 ppc64el 2.3.1-1 [31.4 kB]
 82s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el openjdk-21-jre-headless ppc64el 21.0.6+7-1 [45.6 MB]
 84s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el default-jre-headless ppc64el 2:1.21-76 [3184 B]
 84s Get:16 http://ftpmaster.internal/ubuntu plucky/universe ppc64el fastjar ppc64el 2:0.98-7 [79.7 kB]
 84s Get:17 http://ftpmaster.internal/ubuntu plucky/universe ppc64el jarwrapper all 0.80 [9800 B]
 84s Get:18 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libapache-pom-java all 33-2 [5874 B]
 84s Get:19 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libcommons-parent-java all 56-1 [10.7 kB]
 84s Get:20 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libcommons-codec-java all 1.17.1-1 [302 kB]
 84s Get:21 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libcommons-io-java all 2.18.0-1 [477 kB]
 84s Get:22 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libcommons-compress-java all 1.27.1-2 [610 kB]
 84s Get:23 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libfastutil-java all 8.5.15+dfsg-1 [20.2 MB]
 84s Get:24 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libatinject-jsr330-api-java all 1.0+ds1-6 [5076 B]
 84s Get:25 http://ftpmaster.internal/ubuntu plucky/universe ppc64el liberror-prone-java all 2.18.0-1 [22.5 kB]
 84s Get:26 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libjsr305-java all 0.1~+svn49-12 [27.0 kB]
 84s Get:27 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libguava-java all 32.0.1-1 [2692 kB]
 84s Get:28 http://ftpmaster.internal/ubuntu plucky/universe ppc64el jaligner all 1.0+dfsg-11 [136 kB]
 84s Get:29 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libssw-java ppc64el 1.1-15 [20.4 kB]
 84s Get:30 http://ftpmaster.internal/ubuntu plucky/universe ppc64el mhap all 2.1.3+dfsg-3 [160 kB]
 85s Get:31 http://ftpmaster.internal/ubuntu plucky/universe ppc64el aglfn all 1.7+git20191031.4036a9c-2 [30.6 kB]
 85s Get:32 http://ftpmaster.internal/ubuntu plucky/universe ppc64el gnuplot-data all 6.0.0+dfsg1-1ubuntu3 [75.3 kB]
 85s Get:33 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB]
 85s Get:34 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB]
 85s Get:35 http://ftpmaster.internal/ubuntu plucky/main ppc64el fontconfig-config ppc64el 2.15.0-1.1ubuntu2 [37.4 kB]
 85s Get:36 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfontconfig1 ppc64el 2.15.0-1.1ubuntu2 [190 kB]
 85s Get:37 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpixman-1-0 ppc64el 0.44.0-3 [334 kB]
 85s Get:38 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcb-render0 ppc64el 1.17.0-2 [17.2 kB]
 85s Get:39 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcb-shm0 ppc64el 1.17.0-2 [5980 B]
 85s Get:40 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1build1 [23.1 kB]
 85s Get:41 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcairo2 ppc64el 1.18.2-2 [747 kB]
 85s Get:42 http://ftpmaster.internal/ubuntu plucky/main ppc64el libsharpyuv0 ppc64el 1.5.0-0.1 [22.3 kB]
 85s Get:43 http://ftpmaster.internal/ubuntu plucky/main ppc64el libaom3 ppc64el 3.12.0-1 [2940 kB]
 85s Get:44 http://ftpmaster.internal/ubuntu plucky/main ppc64el libheif-plugin-aomdec ppc64el 1.19.5-1build1 [11.7 kB]
 85s Get:45 http://ftpmaster.internal/ubuntu plucky/main ppc64el libde265-0 ppc64el 1.0.15-1build4 [284 kB]
 85s Get:46 http://ftpmaster.internal/ubuntu plucky/main ppc64el libheif-plugin-libde265 ppc64el 1.19.5-1build1 [9188 B]
 85s Get:47 http://ftpmaster.internal/ubuntu plucky/main ppc64el libheif1 ppc64el 1.19.5-1build1 [452 kB]
 85s Get:48 http://ftpmaster.internal/ubuntu plucky/main ppc64el libimagequant0 ppc64el 2.18.0-1build1 [43.2 kB]
 85s Get:49 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgraphite2-3 ppc64el 1.3.14-2ubuntu1 [84.6 kB]
 85s Get:50 http://ftpmaster.internal/ubuntu plucky/main ppc64el libharfbuzz0b ppc64el 10.2.0-1 [598 kB]
 85s Get:51 http://ftpmaster.internal/ubuntu plucky/main ppc64el libraqm0 ppc64el 0.10.2-1 [19.2 kB]
 85s Get:52 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdeflate0 ppc64el 1.23-1 [63.4 kB]
 85s Get:53 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu2 [35.9 kB]
 85s Get:54 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblerc4 ppc64el 4.0.0+ds-5ubuntu1 [298 kB]
 85s Get:55 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebp7 ppc64el 1.5.0-0.1 [315 kB]
 85s Get:56 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtiff6 ppc64el 4.5.1+git230720-4ubuntu4 [272 kB]
 85s Get:57 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxpm4 ppc64el 1:3.5.17-1build2 [49.9 kB]
 85s Get:58 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgd3 ppc64el 2.3.3-12ubuntu3 [165 kB]
 85s Get:59 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblua5.4-0 ppc64el 5.4.7-1 [211 kB]
 85s Get:60 http://ftpmaster.internal/ubuntu plucky/main ppc64el fontconfig ppc64el 2.15.0-1.1ubuntu2 [192 kB]
 85s Get:61 http://ftpmaster.internal/ubuntu plucky/main ppc64el libthai-data all 0.1.29-2build1 [158 kB]
 85s Get:62 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdatrie1 ppc64el 0.2.13-3build1 [22.7 kB]
 85s Get:63 http://ftpmaster.internal/ubuntu plucky/main ppc64el libthai0 ppc64el 0.1.29-2build1 [21.8 kB]
 85s Get:64 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpango-1.0-0 ppc64el 1.56.1-1 [277 kB]
 85s Get:65 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpangoft2-1.0-0 ppc64el 1.56.1-1 [58.6 kB]
 85s Get:66 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpangocairo-1.0-0 ppc64el 1.56.1-1 [30.6 kB]
 85s Get:67 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebpmux3 ppc64el 1.5.0-0.1 [31.1 kB]
 85s Get:68 http://ftpmaster.internal/ubuntu plucky/universe ppc64el gnuplot-nox ppc64el 6.0.0+dfsg1-1ubuntu3 [1225 kB]
 85s Get:69 http://ftpmaster.internal/ubuntu plucky/universe ppc64el canu ppc64el 2.2+dfsg-5 [1763 kB]
 86s Get:70 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhtscodecs2 ppc64el 1.6.1-1 [113 kB]
 86s Get:71 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhts3t64 ppc64el 1.21+ds-1 [585 kB]
 86s Get:72 http://ftpmaster.internal/ubuntu plucky/universe ppc64el samtools ppc64el 1.21-1 [690 kB]
 86s Get:73 http://ftpmaster.internal/ubuntu plucky/universe ppc64el fastaq all 3.17.0-9 [48.2 kB]
 86s Get:74 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-et-xmlfile all 2.0.0-1 [79.4 kB]
 86s Get:75 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxslt1.1 ppc64el 1.1.39-0exp1ubuntu2 [191 kB]
 86s Get:76 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-lxml ppc64el 5.3.1-1 [1752 kB]
 86s Get:77 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-openpyxl all 3.1.5+dfsg-1 [152 kB]
 86s Get:78 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-packaging all 24.2-1 [51.5 kB]
 86s Get:79 http://ftpmaster.internal/ubuntu plucky/universe ppc64el mummer ppc64el 3.23+dfsg-8 [714 kB]
 86s Get:80 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pymummer all 0.11.0-4 [17.1 kB]
 86s Get:81 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pysam ppc64el 0.23.0+ds-1 [4584 kB]
 86s Get:82 http://ftpmaster.internal/ubuntu plucky/universe ppc64el prodigal ppc64el 1:2.6.3-6 [1314 kB]
 86s Get:83 http://ftpmaster.internal/ubuntu plucky/universe ppc64el circlator all 1.5.6-12 [4617 kB]
 86s Get:84 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-all ppc64el 3.13.1-1~exp2 [896 B]
 86s Get:85 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-iniconfig all 1.1.1-2 [6024 B]
 86s Get:86 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pluggy all 1.5.0-1 [21.0 kB]
 86s Get:87 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pytest all 8.3.4-1 [252 kB]
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 95s Setting up libfilesys-df-perl (0.92-7build5) ...
 95s Setting up libdeflate0:ppc64el (1.23-1) ...
 95s Setting up python3-all (3.13.1-1~exp2) ...
 95s Setting up libxcb-shm0:ppc64el (1.17.0-2) ...
 95s Setting up libgomp1:ppc64el (15-20250213-1ubuntu1) ...
 95s Setting up libjbig0:ppc64el (2.1-6.1ubuntu2) ...
 95s Setting up libssw-java (1.1-15) ...
 95s Setting up libsnappy1v5:ppc64el (1.2.1-1) ...
 95s Setting up python3-packaging (24.2-1) ...
 95s Setting up aglfn (1.7+git20191031.4036a9c-2) ...
 95s Setting up libapache-pom-java (33-2) ...
 95s Setting up libatinject-jsr330-api-java (1.0+ds1-6) ...
 95s Setting up libimagequant0:ppc64el (2.18.0-1build1) ...
 95s Setting up fonts-dejavu-mono (2.37-8) ...
 95s Setting up binfmt-support (2.2.2-7) ...
 95s update-binfmts: warning: python3.13 already enabled in kernel.
 95s Created symlink '/etc/systemd/system/multi-user.target.wants/binfmt-support.service' → '/usr/lib/systemd/system/binfmt-support.service'.

 96s Setting up fonts-dejavu-core (2.37-8) ...
 96s Setting up libpcsclite1:ppc64el (2.3.1-1) ...
 96s Setting up libjpeg-turbo8:ppc64el (2.1.5-3ubuntu2) ...
 96s Setting up python3-pluggy (1.5.0-1) ...
 96s Setting up libwebp7:ppc64el (1.5.0-0.1) ...
 96s Setting up libxslt1.1:ppc64el (1.1.39-0exp1ubuntu2) ...
 96s Setting up mummer (3.23+dfsg-8) ...
 96s Setting up python3-et-xmlfile (2.0.0-1) ...
 97s Setting up libhts3t64:ppc64el (1.21+ds-1) ...
 97s Setting up liblua5.4-0:ppc64el (5.4.7-1) ...
 97s Setting up libharfbuzz0b:ppc64el (10.2.0-1) ...
 97s Setting up libthai-data (0.1.29-2build1) ...
 97s Setting up ca-certificates-java (20240118) ...
 97s No JRE found. Skipping Java certificates setup.
 97s Setting up libde265-0:ppc64el (1.0.15-1build4) ...
 97s Setting up libwebpmux3:ppc64el (1.5.0-0.1) ...
 97s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ...
 97s Setting up gnuplot-data (6.0.0+dfsg1-1ubuntu3) ...
 97s Setting up python3-pysam (0.23.0+ds-1) ...
 97s Setting up openjdk-21-jre-headless:ppc64el (21.0.6+7-1) ...
 97s update-alternatives: using /usr/lib/jvm/java-21-openjdk-ppc64el/bin/java to provide /usr/bin/java (java) in auto mode
 97s update-alternatives: using /usr/lib/jvm/java-21-openjdk-ppc64el/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode
 97s update-alternatives: using /usr/lib/jvm/java-21-openjdk-ppc64el/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
 97s update-alternatives: using /usr/lib/jvm/java-21-openjdk-ppc64el/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
 97s update-alternatives: using /usr/lib/jvm/java-21-openjdk-ppc64el/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
 97s Setting up jarwrapper (0.80) ...
 97s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ...
 97s Setting up python3-pytest (8.3.4-1) ...
 98s Setting up libcommons-parent-java (56-1) ...
 98s Setting up samtools (1.21-1) ...
 98s Setting up libthai0:ppc64el (0.1.29-2build1) ...
 98s Setting up libraqm0:ppc64el (0.10.2-1) ...
 98s Setting up python3-lxml:ppc64el (5.3.1-1) ...
 98s Setting up libtiff6:ppc64el (4.5.1+git230720-4ubuntu4) ...
 98s Setting up libfontconfig1:ppc64el (2.15.0-1.1ubuntu2) ...
 98s Setting up libcommons-codec-java (1.17.1-1) ...
 98s Setting up fontconfig (2.15.0-1.1ubuntu2) ...
100s Regenerating fonts cache... done.
100s Setting up libcommons-io-java (2.18.0-1) ...
100s Setting up fastaq (3.17.0-9) ...
101s Setting up libpango-1.0-0:ppc64el (1.56.1-1) ...
101s Setting up libcairo2:ppc64el (1.18.2-2) ...
101s Setting up python3-pymummer (0.11.0-4) ...
101s Setting up python3-openpyxl (3.1.5+dfsg-1) ...
102s Setting up libpangoft2-1.0-0:ppc64el (1.56.1-1) ...
102s Setting up libpangocairo-1.0-0:ppc64el (1.56.1-1) ...
102s Setting up libcommons-compress-java (1.27.1-2) ...
102s Setting up libheif-plugin-aomdec:ppc64el (1.19.5-1build1) ...
102s Setting up libheif-plugin-libde265:ppc64el (1.19.5-1build1) ...
102s Setting up liberror-prone-java (2.18.0-1) ...
102s Setting up libheif1:ppc64el (1.19.5-1build1) ...
102s Setting up libguava-java (32.0.1-1) ...
102s Setting up libgd3:ppc64el (2.3.3-12ubuntu3) ...
102s Setting up gnuplot-nox (6.0.0+dfsg1-1ubuntu3) ...
102s update-alternatives: using /usr/bin/gnuplot-nox to provide /usr/bin/gnuplot (gnuplot) in auto mode
102s Processing triggers for install-info (7.1.1-1) ...
102s Processing triggers for libc-bin (2.40-4ubuntu1) ...
102s Processing triggers for systemd (257.2-3ubuntu1) ...
102s Processing triggers for man-db (2.13.0-1) ...
105s Processing triggers for ca-certificates-java (20240118) ...
105s Adding debian:ACCVRAIZ1.pem
105s Adding debian:AC_RAIZ_FNMT-RCM.pem
105s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem
105s Adding debian:ANF_Secure_Server_Root_CA.pem
105s Adding debian:Actalis_Authentication_Root_CA.pem
105s Adding debian:AffirmTrust_Commercial.pem
105s Adding debian:AffirmTrust_Networking.pem
105s Adding debian:AffirmTrust_Premium.pem
106s Adding debian:AffirmTrust_Premium_ECC.pem
106s Adding debian:Amazon_Root_CA_1.pem
106s Adding debian:Amazon_Root_CA_2.pem
106s Adding debian:Amazon_Root_CA_3.pem
106s Adding debian:Amazon_Root_CA_4.pem
106s Adding debian:Atos_TrustedRoot_2011.pem
106s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem
106s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem
106s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
106s Adding debian:BJCA_Global_Root_CA1.pem
106s Adding debian:BJCA_Global_Root_CA2.pem
106s Adding debian:Baltimore_CyberTrust_Root.pem
106s Adding debian:Buypass_Class_2_Root_CA.pem
106s Adding debian:Buypass_Class_3_Root_CA.pem
106s Adding debian:CA_Disig_Root_R2.pem
106s Adding debian:CFCA_EV_ROOT.pem
106s Adding debian:COMODO_Certification_Authority.pem
106s Adding debian:COMODO_ECC_Certification_Authority.pem
106s Adding debian:COMODO_RSA_Certification_Authority.pem
106s Adding debian:Certainly_Root_E1.pem
106s Adding debian:Certainly_Root_R1.pem
106s Adding debian:Certigna.pem
106s Adding debian:Certigna_Root_CA.pem
106s Adding debian:Certum_EC-384_CA.pem
106s Adding debian:Certum_Trusted_Network_CA.pem
106s Adding debian:Certum_Trusted_Network_CA_2.pem
106s Adding debian:Certum_Trusted_Root_CA.pem
106s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem
106s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem
106s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem
106s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem
106s Adding debian:Comodo_AAA_Services_root.pem
106s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem
106s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem
106s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
106s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
106s Adding debian:DigiCert_Assured_ID_Root_CA.pem
106s Adding debian:DigiCert_Assured_ID_Root_G2.pem
106s Adding debian:DigiCert_Assured_ID_Root_G3.pem
106s Adding debian:DigiCert_Global_Root_CA.pem
106s Adding debian:DigiCert_Global_Root_G2.pem
106s Adding debian:DigiCert_Global_Root_G3.pem
106s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
106s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem
106s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem
106s Adding debian:DigiCert_Trusted_Root_G4.pem
106s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
106s Adding debian:Entrust_Root_Certification_Authority.pem
106s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
106s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
106s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem
106s Adding debian:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem
106s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem
106s Adding debian:GLOBALTRUST_2020.pem
106s Adding debian:GTS_Root_R1.pem
106s Adding debian:GTS_Root_R2.pem
106s Adding debian:GTS_Root_R3.pem
106s Adding debian:GTS_Root_R4.pem
106s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
106s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
106s Adding debian:GlobalSign_Root_CA.pem
106s Adding debian:GlobalSign_Root_CA_-_R3.pem
106s Adding debian:GlobalSign_Root_CA_-_R6.pem
106s Adding debian:GlobalSign_Root_E46.pem
106s Adding debian:GlobalSign_Root_R46.pem
106s Adding debian:Go_Daddy_Class_2_CA.pem
106s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
106s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem
106s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem
106s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem
106s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem
106s Adding debian:HiPKI_Root_CA_-_G1.pem
106s Adding debian:Hongkong_Post_Root_CA_3.pem
106s Adding debian:ISRG_Root_X1.pem
106s Adding debian:ISRG_Root_X2.pem
106s Adding debian:IdenTrust_Commercial_Root_CA_1.pem
106s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
106s Adding debian:Izenpe.com.pem
106s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
106s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem
106s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem
106s Adding debian:NAVER_Global_Root_Certification_Authority.pem
106s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
106s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
106s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem
106s Adding debian:QuoVadis_Root_CA_1_G3.pem
106s Adding debian:QuoVadis_Root_CA_2.pem
106s Adding debian:QuoVadis_Root_CA_2_G3.pem
106s Adding debian:QuoVadis_Root_CA_3.pem
106s Adding debian:QuoVadis_Root_CA_3_G3.pem
106s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem
106s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem
106s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem
106s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem
106s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem
106s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem
106s Adding debian:SZAFIR_ROOT_CA2.pem
106s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem
106s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem
106s Adding debian:SecureSign_RootCA11.pem
106s Adding debian:SecureSign_Root_CA12.pem
106s Adding debian:SecureSign_Root_CA14.pem
106s Adding debian:SecureSign_Root_CA15.pem
106s Adding debian:SecureTrust_CA.pem
106s Adding debian:Secure_Global_CA.pem
106s Adding debian:Security_Communication_ECC_RootCA1.pem
106s Adding debian:Security_Communication_RootCA2.pem
106s Adding debian:Security_Communication_RootCA3.pem
106s Adding debian:Starfield_Class_2_CA.pem
106s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
106s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
106s Adding debian:SwissSign_Gold_CA_-_G2.pem
106s Adding debian:SwissSign_Silver_CA_-_G2.pem
106s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
106s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
106s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
106s Adding debian:TWCA_CYBER_Root_CA.pem
106s Adding debian:TWCA_Global_Root_CA.pem
106s Adding debian:TWCA_Root_Certification_Authority.pem
106s Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem
106s Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem
106s Adding debian:TeliaSonera_Root_CA_v1.pem
106s Adding debian:Telia_Root_CA_v2.pem
106s Adding debian:TrustAsia_Global_Root_CA_G3.pem
106s Adding debian:TrustAsia_Global_Root_CA_G4.pem
106s Adding debian:Trustwave_Global_Certification_Authority.pem
106s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem
106s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem
106s Adding debian:TunTrust_Root_CA.pem
106s Adding debian:UCA_Extended_Validation_Root.pem
106s Adding debian:UCA_Global_G2_Root.pem
106s Adding debian:USERTrust_ECC_Certification_Authority.pem
106s Adding debian:USERTrust_RSA_Certification_Authority.pem
106s Adding debian:XRamp_Global_CA_Root.pem
106s Adding debian:certSIGN_ROOT_CA.pem
106s Adding debian:certSIGN_Root_CA_G2.pem
106s Adding debian:e-Szigno_Root_CA_2017.pem
106s Adding debian:ePKI_Root_Certification_Authority.pem
106s Adding debian:emSign_ECC_Root_CA_-_C3.pem
106s Adding debian:emSign_ECC_Root_CA_-_G3.pem
106s Adding debian:emSign_Root_CA_-_C1.pem
106s Adding debian:emSign_Root_CA_-_G1.pem
106s Adding debian:vTrus_ECC_Root_CA.pem
106s Adding debian:vTrus_Root_CA.pem
106s done.
106s Setting up default-jre-headless (2:1.21-76) ...
106s Setting up jaligner (1.0+dfsg-11) ...
106s Setting up mhap (2.1.3+dfsg-3) ...
106s Setting up canu (2.2+dfsg-5) ...
106s Setting up circlator (1.5.6-12) ...
108s autopkgtest [02:46:57]: test run-unit-test: [-----------------------
108s + pkg=circlator
108s + export LC_ALL=C.UTF-8
108s + LC_ALL=C.UTF-8
108s + '[' /tmp/autopkgtest.vFofwQ/autopkgtest_tmp = '' ']'
108s + cp -a /usr/share/doc/circlator/examples/assemble_test.py /usr/share/doc/circlator/examples/assembly_test.py /usr/share/doc/circlator/examples/bamfilter_test.py /usr/share/doc/circlator/examples/clean_test.py /usr/share/doc/circlator/examples/common_test.py /usr/share/doc/circlator/examples/data.tar.xz /usr/share/doc/circlator/examples/dnaa_test.py /usr/share/doc/circlator/examples/external_progs_test.py /usr/share/doc/circlator/examples/mapping_test.py /usr/share/doc/circlator/examples/merge_test.py /usr/share/doc/circlator/examples/minimus2_test.py /usr/share/doc/circlator/examples/start_fixer_test.py /tmp/autopkgtest.vFofwQ/autopkgtest_tmp
108s + cd /tmp/autopkgtest.vFofwQ/autopkgtest_tmp
108s + tar xaf data.tar.xz
108s + sed -i 's/data_dir = os.path.join(modules_dir, '\''tests'\'', '\''data'\'')/data_dir = os.path.join(os.getcwd(), '\''data'\'')/' ./assemble_test.py ./assembly_test.py ./bamfilter_test.py ./clean_test.py ./common_test.py ./dnaa_test.py ./external_progs_test.py ./mapping_test.py ./merge_test.py ./minimus2_test.py ./start_fixer_test.py
108s ++ py3versions --supported
108s + for py in $(py3versions --supported 2> /dev/null)
108s + eval dpkg-architecture --is amd64
108s ++ dpkg-architecture --is amd64
108s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation)
108s + python3.12 -m pytest -v -k 'not (test_build_spades_kmers or test_make_spades_command)'
109s ============================= test session starts ==============================
109s platform linux -- Python 3.12.9, pytest-8.3.4, pluggy-1.5.0 -- /usr/bin/python3.12
109s cachedir: .pytest_cache
109s rootdir: /tmp/autopkgtest.vFofwQ/autopkgtest_tmp
109s plugins: typeguard-4.4.1
109s collecting ... collected 115 items / 2 deselected / 113 selected
109s 
109s assemble_test.py::TestAssembleCanu::test_make_canu_command PASSED        [  0%]
109s assemble_test.py::TestAssembleCanu::test_rename_canu_contigs PASSED      [  1%]
109s assembly_test.py::TestAssembly::test_circular_contigs_from_canu_gfa PASSED [  2%]
109s assembly_test.py::TestAssembly::test_circular_contigs_from_spades_after_3_6_1 PASSED [  3%]
109s assembly_test.py::TestAssembly::test_circular_contigs_from_spades_before_3_6_1 PASSED [  4%]
109s assembly_test.py::TestAssembly::test_circular_contigs_just_fasta PASSED  [  5%]
109s assembly_test.py::TestAssembly::test_circular_contigs_spades_post_3_6_1 PASSED [  6%]
109s assembly_test.py::TestAssembly::test_circular_contigs_spades_pre_3_6_1 PASSED [  7%]
109s assembly_test.py::TestAssembly::test_circular_edges_to_edge_numbers_dict PASSED [  7%]
109s assembly_test.py::TestAssembly::test_get_contigs PASSED                  [  8%]
109s assembly_test.py::TestAssembly::test_init_file_not_dir PASSED            [  9%]
109s assembly_test.py::TestAssembly::test_init_post_3_6_1_ok PASSED           [ 10%]
109s assembly_test.py::TestAssembly::test_init_pre_3_6_1_ok PASSED            [ 11%]
109s assembly_test.py::TestAssembly::test_init_raises_error PASSED            [ 12%]
109s assembly_test.py::TestAssembly::test_spades_contigs_paths_to_dict PASSED [ 13%]
109s bamfilter_test.py::TestBamfilter::test_all_reads_from_contig PASSED      [ 14%]
109s bamfilter_test.py::TestBamfilter::test_break_reads PASSED                [ 15%]
109s bamfilter_test.py::TestBamfilter::test_check_contigs_to_use PASSED       [ 15%]
109s bamfilter_test.py::TestBamfilter::test_exclude_region PASSED             [ 16%]
109s bamfilter_test.py::TestBamfilter::test_get_all_unmapped_reads PASSED     [ 17%]
109s bamfilter_test.py::TestBamfilter::test_get_contigs_to_use PASSED         [ 18%]
109s bamfilter_test.py::TestBamfilter::test_get_ref_lengths PASSED            [ 19%]
109s bamfilter_test.py::TestBamfilter::test_get_region_end PASSED             [ 20%]
109s bamfilter_test.py::TestBamfilter::test_get_region_start PASSED           [ 21%]
109s bamfilter_test.py::TestBamfilter::test_run_discard_unmapped_no_quals PASSED [ 22%]
109s bamfilter_test.py::TestBamfilter::test_run_keep_unmapped_no_quals PASSED [ 23%]
109s bamfilter_test.py::TestBamfilter::test_run_keep_unmapped_with_quals PASSED [ 23%]
109s clean_test.py::TestClean::test_clean_contigs PASSED                      [ 24%]
109s clean_test.py::TestClean::test_collapse_list_of_sets PASSED              [ 25%]
109s clean_test.py::TestClean::test_containing_contigs PASSED                 [ 26%]
109s clean_test.py::TestClean::test_contains PASSED                           [ 27%]
109s clean_test.py::TestClean::test_expand_containing_using_transitivity PASSED [ 28%]
109s clean_test.py::TestClean::test_get_all_containing PASSED                 [ 29%]
109s clean_test.py::TestClean::test_get_containing_contigs PASSED             [ 30%]
109s clean_test.py::TestClean::test_get_contigs_to_keep PASSED                [ 30%]
109s clean_test.py::TestClean::test_get_identical_contigs PASSED              [ 31%]
109s clean_test.py::TestClean::test_infinite_recursion PASSED                 [ 32%]
109s clean_test.py::TestClean::test_load_nucmer_hits PASSED                   [ 33%]
109s clean_test.py::TestClean::test_longest_contig PASSED                     [ 34%]
109s clean_test.py::TestClean::test_remove_identical_contigs PASSED           [ 35%]
109s clean_test.py::TestClean::test_remove_small_contigs PASSED               [ 36%]
109s clean_test.py::TestClean::test_write_log PASSED                          [ 37%]
109s common_test.py::TestCommon::test_check_files_exist PASSED                [ 38%]
109s dnaa_test.py::TestDnaa::test_append_stop_to_seq PASSED                   [ 38%]
109s dnaa_test.py::TestDnaa::test_check_sequence PASSED                       [ 39%]
109s dnaa_test.py::TestDnaa::test_get_uniprot_url PASSED                      [ 40%]
109s dnaa_test.py::TestDnaa::test_header_matches_regex PASSED                 [ 41%]
109s dnaa_test.py::TestDnaa::test_header_to_genus_species PASSED              [ 42%]
109s dnaa_test.py::TestDnaa::test_reverse_translate PASSED                    [ 43%]
109s external_progs_test.py::TestExternalProgs::test_bwa_version PASSED       [ 44%]
109s external_progs_test.py::TestExternalProgs::test_canu_version PASSED      [ 45%]
109s external_progs_test.py::TestExternalProgs::test_nucmer_version PASSED    [ 46%]
109s external_progs_test.py::TestExternalProgs::test_prodigal_version PASSED  [ 46%]
109s external_progs_test.py::TestExternalProgs::test_samtools_original_version PASSED [ 47%]
109s external_progs_test.py::TestExternalProgs::test_samtools_version PASSED  [ 48%]
109s external_progs_test.py::TestExternalProgs::test_spades_version PASSED    [ 49%]
109s mapping_test.py::TestMapping::test_aligned_read_to_read PASSED           [ 50%]
110s mapping_test.py::TestMapping::test_bwa_index PASSED                      [ 51%]
110s mapping_test.py::TestMapping::test_bwa_index_clean PASSED                [ 52%]
110s mapping_test.py::TestMapping::test_bwa_mem PASSED                        [ 53%]
110s merge_test.py::TestMerge::test_can_circularise PASSED                    [ 53%]
110s merge_test.py::TestMerge::test_contigs_dict_to_file PASSED               [ 54%]
110s merge_test.py::TestMerge::test_filter_bridging_contigs PASSED            [ 55%]
110s merge_test.py::TestMerge::test_get_hit_nearest_ref_end PASSED            [ 56%]
110s merge_test.py::TestMerge::test_get_hit_nearest_ref_start PASSED          [ 57%]
110s merge_test.py::TestMerge::test_get_longest_hit_at_qry_end PASSED         [ 58%]
110s merge_test.py::TestMerge::test_get_longest_hit_at_qry_start PASSED       [ 59%]
110s merge_test.py::TestMerge::test_get_longest_hit_at_ref_end PASSED         [ 60%]
110s merge_test.py::TestMerge::test_get_longest_hit_at_ref_start PASSED       [ 61%]
110s merge_test.py::TestMerge::test_get_longest_hit_by_ref_length PASSED      [ 61%]
110s merge_test.py::TestMerge::test_get_possible_circular_ref_contigs PASSED  [ 62%]
110s merge_test.py::TestMerge::test_get_possible_circular_ref_contigs_same_best_hits PASSED [ 63%]
110s merge_test.py::TestMerge::test_get_possible_query_bridging_contigs PASSED [ 64%]
110s merge_test.py::TestMerge::test_get_spades_circular_nodes PASSED          [ 65%]
110s merge_test.py::TestMerge::test_has_qry_hit_longer_than PASSED            [ 66%]
110s merge_test.py::TestMerge::test_hits_hashed_by_query PASSED               [ 67%]
110s merge_test.py::TestMerge::test_hits_have_same_query PASSED               [ 68%]
110s merge_test.py::TestMerge::test_hits_have_same_reference PASSED           [ 69%]
110s merge_test.py::TestMerge::test_index_fasta PASSED                        [ 69%]
110s merge_test.py::TestMerge::test_is_at_qry_end PASSED                      [ 70%]
110s merge_test.py::TestMerge::test_is_at_qry_start PASSED                    [ 71%]
110s merge_test.py::TestMerge::test_is_at_ref_end PASSED                      [ 72%]
110s merge_test.py::TestMerge::test_is_at_ref_start PASSED                    [ 73%]
110s merge_test.py::TestMerge::test_load_nucmer_hits PASSED                   [ 74%]
110s merge_test.py::TestMerge::test_make_circularised_contig_1 PASSED         [ 75%]
110s merge_test.py::TestMerge::test_make_circularised_contig_2 PASSED         [ 76%]
110s merge_test.py::TestMerge::test_make_new_contig_from_nucmer_and_spades_not_hit PASSED [ 76%]
110s merge_test.py::TestMerge::test_make_new_contig_from_nucmer_and_spades_with_hit PASSED [ 77%]
110s merge_test.py::TestMerge::test_merge_bridged_contig_pair1 PASSED         [ 78%]
110s merge_test.py::TestMerge::test_merge_bridged_contig_pair2 PASSED         [ 79%]
110s merge_test.py::TestMerge::test_merge_bridged_contig_pair3 PASSED         [ 80%]
110s merge_test.py::TestMerge::test_merge_bridged_contig_pair4 PASSED         [ 81%]
110s merge_test.py::TestMerge::test_min_qry_hit_length PASSED                 [ 82%]
110s merge_test.py::TestMerge::test_orientation_ok_to_bridge_contigs PASSED   [ 83%]
110s merge_test.py::TestMerge::test_remove_keys_from_dict_with_nonunique_values PASSED [ 84%]
110s merge_test.py::TestMerge::test_write_act_files PASSED                    [ 84%]
110s minimus2_test.py::TestMinimus2::test_run_initial_merge SKIPPED (Amos...) [ 85%]
110s minimus2_test.py::TestMinimus2::test_run_minimus2 SKIPPED (Amos is n...) [ 86%]
110s minimus2_test.py::TestMinimus2::test_run_minimus2_on_each_contig SKIPPED [ 87%]
110s minimus2_test.py::TestMinimus2::test_run_minimus2_on_one_contig_will_not_work SKIPPED [ 88%]
110s minimus2_test.py::TestMinimus2::test_run_minimus2_on_one_contig_will_work SKIPPED [ 89%]
110s minimus2_test.py::TestMinimus2::test_write_split_contig SKIPPED (Amo...) [ 90%]
110s start_fixer_test.py::TestStartFixer::test_find_circular_using_prodigal PASSED [ 91%]
110s start_fixer_test.py::TestStartFixer::test_find_circular_using_promer PASSED [ 92%]
110s start_fixer_test.py::TestStartFixer::test_init PASSED                    [ 92%]
110s start_fixer_test.py::TestStartFixer::test_max_length_from_fasta_file PASSED [ 93%]
110s start_fixer_test.py::TestStartFixer::test_rearrange_contigs PASSED       [ 94%]
110s start_fixer_test.py::TestStartFixer::test_rename_contigs PASSED          [ 95%]
110s start_fixer_test.py::TestStartFixer::test_run_bit_of_everything PASSED   [ 96%]
110s start_fixer_test.py::TestStartFixer::test_run_ignore_all PASSED          [ 97%]
111s start_fixer_test.py::TestStartFixer::test_run_none_for_prodigal PASSED   [ 98%]
111s start_fixer_test.py::TestStartFixer::test_write_fasta_plus_circularized_ends PASSED [ 99%]
111s start_fixer_test.py::TestStartFixer::test_write_renamed_contigs PASSED   [100%]
111s 
111s =============================== warnings summary ===============================
111s ../../../usr/lib/python3/dist-packages/pyfastaq/__init__.py:3
111s   /usr/lib/python3/dist-packages/pyfastaq/__init__.py:3: DeprecationWarning: Unimplemented abstract methods {'locate_file', 'read_text'}
111s     __version__ = Distribution().from_name('pyfastaq').version
111s 
111s ../../../usr/lib/python3/dist-packages/circlator/__init__.py:1
111s   /usr/lib/python3/dist-packages/circlator/__init__.py:1: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
111s     from pkg_resources import get_distribution
111s 
111s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
111s =========== 107 passed, 6 skipped, 2 deselected, 2 warnings in 1.99s ===========
111s + for py in $(py3versions --supported 2> /dev/null)
111s + eval dpkg-architecture --is amd64
111s ++ dpkg-architecture --is amd64
111s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation)
111s + python3.13 -m pytest -v -k 'not (test_build_spades_kmers or test_make_spades_command)'
111s ============================= test session starts ==============================
111s platform linux -- Python 3.13.2, pytest-8.3.4, pluggy-1.5.0 -- /usr/bin/python3.13
111s cachedir: .pytest_cache
111s rootdir: /tmp/autopkgtest.vFofwQ/autopkgtest_tmp
111s plugins: typeguard-4.4.1
112s collecting ... collected 115 items / 2 deselected / 113 selected
112s 
112s assemble_test.py::TestAssembleCanu::test_make_canu_command PASSED        [  0%]
112s assemble_test.py::TestAssembleCanu::test_rename_canu_contigs PASSED      [  1%]
112s assembly_test.py::TestAssembly::test_circular_contigs_from_canu_gfa PASSED [  2%]
112s assembly_test.py::TestAssembly::test_circular_contigs_from_spades_after_3_6_1 PASSED [  3%]
112s assembly_test.py::TestAssembly::test_circular_contigs_from_spades_before_3_6_1 PASSED [  4%]
112s assembly_test.py::TestAssembly::test_circular_contigs_just_fasta PASSED  [  5%]
112s assembly_test.py::TestAssembly::test_circular_contigs_spades_post_3_6_1 PASSED [  6%]
112s assembly_test.py::TestAssembly::test_circular_contigs_spades_pre_3_6_1 PASSED [  7%]
112s assembly_test.py::TestAssembly::test_circular_edges_to_edge_numbers_dict PASSED [  7%]
112s assembly_test.py::TestAssembly::test_get_contigs PASSED                  [  8%]
112s assembly_test.py::TestAssembly::test_init_file_not_dir PASSED            [  9%]
112s assembly_test.py::TestAssembly::test_init_post_3_6_1_ok PASSED           [ 10%]
112s assembly_test.py::TestAssembly::test_init_pre_3_6_1_ok PASSED            [ 11%]
112s assembly_test.py::TestAssembly::test_init_raises_error PASSED            [ 12%]
112s assembly_test.py::TestAssembly::test_spades_contigs_paths_to_dict PASSED [ 13%]
112s bamfilter_test.py::TestBamfilter::test_all_reads_from_contig PASSED      [ 14%]
112s bamfilter_test.py::TestBamfilter::test_break_reads PASSED                [ 15%]
112s bamfilter_test.py::TestBamfilter::test_check_contigs_to_use PASSED       [ 15%]
112s bamfilter_test.py::TestBamfilter::test_exclude_region PASSED             [ 16%]
112s bamfilter_test.py::TestBamfilter::test_get_all_unmapped_reads PASSED     [ 17%]
112s bamfilter_test.py::TestBamfilter::test_get_contigs_to_use PASSED         [ 18%]
112s bamfilter_test.py::TestBamfilter::test_get_ref_lengths PASSED            [ 19%]
112s bamfilter_test.py::TestBamfilter::test_get_region_end PASSED             [ 20%]
112s bamfilter_test.py::TestBamfilter::test_get_region_start PASSED           [ 21%]
112s bamfilter_test.py::TestBamfilter::test_run_discard_unmapped_no_quals PASSED [ 22%]
112s bamfilter_test.py::TestBamfilter::test_run_keep_unmapped_no_quals PASSED [ 23%]
112s bamfilter_test.py::TestBamfilter::test_run_keep_unmapped_with_quals PASSED [ 23%]
112s clean_test.py::TestClean::test_clean_contigs PASSED                      [ 24%]
112s clean_test.py::TestClean::test_collapse_list_of_sets PASSED              [ 25%]
112s clean_test.py::TestClean::test_containing_contigs PASSED                 [ 26%]
112s clean_test.py::TestClean::test_contains PASSED                           [ 27%]
112s clean_test.py::TestClean::test_expand_containing_using_transitivity PASSED [ 28%]
112s clean_test.py::TestClean::test_get_all_containing PASSED                 [ 29%]
112s clean_test.py::TestClean::test_get_containing_contigs PASSED             [ 30%]
112s clean_test.py::TestClean::test_get_contigs_to_keep PASSED                [ 30%]
112s clean_test.py::TestClean::test_get_identical_contigs PASSED              [ 31%]
112s clean_test.py::TestClean::test_infinite_recursion PASSED                 [ 32%]
112s clean_test.py::TestClean::test_load_nucmer_hits PASSED                   [ 33%]
112s clean_test.py::TestClean::test_longest_contig PASSED                     [ 34%]
112s clean_test.py::TestClean::test_remove_identical_contigs PASSED           [ 35%]
112s clean_test.py::TestClean::test_remove_small_contigs PASSED               [ 36%]
112s clean_test.py::TestClean::test_write_log PASSED                          [ 37%]
112s common_test.py::TestCommon::test_check_files_exist PASSED                [ 38%]
112s dnaa_test.py::TestDnaa::test_append_stop_to_seq PASSED                   [ 38%]
112s dnaa_test.py::TestDnaa::test_check_sequence PASSED                       [ 39%]
112s dnaa_test.py::TestDnaa::test_get_uniprot_url PASSED                      [ 40%]
112s dnaa_test.py::TestDnaa::test_header_matches_regex PASSED                 [ 41%]
112s dnaa_test.py::TestDnaa::test_header_to_genus_species PASSED              [ 42%]
112s dnaa_test.py::TestDnaa::test_reverse_translate PASSED                    [ 43%]
112s external_progs_test.py::TestExternalProgs::test_bwa_version PASSED       [ 44%]
112s external_progs_test.py::TestExternalProgs::test_canu_version PASSED      [ 45%]
112s external_progs_test.py::TestExternalProgs::test_nucmer_version PASSED    [ 46%]
112s external_progs_test.py::TestExternalProgs::test_prodigal_version PASSED  [ 46%]
112s external_progs_test.py::TestExternalProgs::test_samtools_original_version PASSED [ 47%]
112s external_progs_test.py::TestExternalProgs::test_samtools_version PASSED  [ 48%]
112s external_progs_test.py::TestExternalProgs::test_spades_version PASSED    [ 49%]
112s mapping_test.py::TestMapping::test_aligned_read_to_read PASSED           [ 50%]
112s mapping_test.py::TestMapping::test_bwa_index PASSED                      [ 51%]
112s mapping_test.py::TestMapping::test_bwa_index_clean PASSED                [ 52%]
112s mapping_test.py::TestMapping::test_bwa_mem PASSED                        [ 53%]
112s merge_test.py::TestMerge::test_can_circularise PASSED                    [ 53%]
112s merge_test.py::TestMerge::test_contigs_dict_to_file PASSED               [ 54%]
112s merge_test.py::TestMerge::test_filter_bridging_contigs PASSED            [ 55%]
112s merge_test.py::TestMerge::test_get_hit_nearest_ref_end PASSED            [ 56%]
112s merge_test.py::TestMerge::test_get_hit_nearest_ref_start PASSED          [ 57%]
112s merge_test.py::TestMerge::test_get_longest_hit_at_qry_end PASSED         [ 58%]
112s merge_test.py::TestMerge::test_get_longest_hit_at_qry_start PASSED       [ 59%]
112s merge_test.py::TestMerge::test_get_longest_hit_at_ref_end PASSED         [ 60%]
112s merge_test.py::TestMerge::test_get_longest_hit_at_ref_start PASSED       [ 61%]
112s merge_test.py::TestMerge::test_get_longest_hit_by_ref_length PASSED      [ 61%]
112s merge_test.py::TestMerge::test_get_possible_circular_ref_contigs PASSED  [ 62%]
112s merge_test.py::TestMerge::test_get_possible_circular_ref_contigs_same_best_hits PASSED [ 63%]
112s merge_test.py::TestMerge::test_get_possible_query_bridging_contigs PASSED [ 64%]
112s merge_test.py::TestMerge::test_get_spades_circular_nodes PASSED          [ 65%]
112s merge_test.py::TestMerge::test_has_qry_hit_longer_than PASSED            [ 66%]
112s merge_test.py::TestMerge::test_hits_hashed_by_query PASSED               [ 67%]
112s merge_test.py::TestMerge::test_hits_have_same_query PASSED               [ 68%]
112s merge_test.py::TestMerge::test_hits_have_same_reference PASSED           [ 69%]
112s merge_test.py::TestMerge::test_index_fasta PASSED                        [ 69%]
112s merge_test.py::TestMerge::test_is_at_qry_end PASSED                      [ 70%]
112s merge_test.py::TestMerge::test_is_at_qry_start PASSED                    [ 71%]
112s merge_test.py::TestMerge::test_is_at_ref_end PASSED                      [ 72%]
112s merge_test.py::TestMerge::test_is_at_ref_start PASSED                    [ 73%]
112s merge_test.py::TestMerge::test_load_nucmer_hits PASSED                   [ 74%]
112s merge_test.py::TestMerge::test_make_circularised_contig_1 PASSED         [ 75%]
112s merge_test.py::TestMerge::test_make_circularised_contig_2 PASSED         [ 76%]
112s merge_test.py::TestMerge::test_make_new_contig_from_nucmer_and_spades_not_hit PASSED [ 76%]
112s merge_test.py::TestMerge::test_make_new_contig_from_nucmer_and_spades_with_hit PASSED [ 77%]
112s merge_test.py::TestMerge::test_merge_bridged_contig_pair1 PASSED         [ 78%]
112s merge_test.py::TestMerge::test_merge_bridged_contig_pair2 PASSED         [ 79%]
112s merge_test.py::TestMerge::test_merge_bridged_contig_pair3 PASSED         [ 80%]
112s merge_test.py::TestMerge::test_merge_bridged_contig_pair4 PASSED         [ 81%]
112s merge_test.py::TestMerge::test_min_qry_hit_length PASSED                 [ 82%]
112s merge_test.py::TestMerge::test_orientation_ok_to_bridge_contigs PASSED   [ 83%]
112s merge_test.py::TestMerge::test_remove_keys_from_dict_with_nonunique_values PASSED [ 84%]
112s merge_test.py::TestMerge::test_write_act_files PASSED                    [ 84%]
112s minimus2_test.py::TestMinimus2::test_run_initial_merge SKIPPED (Amos...) [ 85%]
112s minimus2_test.py::TestMinimus2::test_run_minimus2 SKIPPED (Amos is n...) [ 86%]
112s minimus2_test.py::TestMinimus2::test_run_minimus2_on_each_contig SKIPPED [ 87%]
112s minimus2_test.py::TestMinimus2::test_run_minimus2_on_one_contig_will_not_work SKIPPED [ 88%]
112s minimus2_test.py::TestMinimus2::test_run_minimus2_on_one_contig_will_work SKIPPED [ 89%]
112s minimus2_test.py::TestMinimus2::test_write_split_contig SKIPPED (Amo...) [ 90%]
112s start_fixer_test.py::TestStartFixer::test_find_circular_using_prodigal PASSED [ 91%]
112s start_fixer_test.py::TestStartFixer::test_find_circular_using_promer PASSED [ 92%]
112s start_fixer_test.py::TestStartFixer::test_init PASSED                    [ 92%]
112s start_fixer_test.py::TestStartFixer::test_max_length_from_fasta_file PASSED [ 93%]
113s start_fixer_test.py::TestStartFixer::test_rearrange_contigs PASSED       [ 94%]
113s start_fixer_test.py::TestStartFixer::test_rename_contigs PASSED          [ 95%]
113s start_fixer_test.py::TestStartFixer::test_run_bit_of_everything PASSED   [ 96%]
113s start_fixer_test.py::TestStartFixer::test_run_ignore_all PASSED          [ 97%]
113s start_fixer_test.py::TestStartFixer::test_run_none_for_prodigal PASSED   [ 98%]
113s start_fixer_test.py::TestStartFixer::test_write_fasta_plus_circularized_ends PASSED [ 99%]
113s start_fixer_test.py::TestStartFixer::test_write_renamed_contigs PASSED   [100%]
113s 
113s =============================== warnings summary ===============================
113s ../../../usr/lib/python3/dist-packages/pyfastaq/__init__.py:3
113s   /usr/lib/python3/dist-packages/pyfastaq/__init__.py:3: DeprecationWarning: Unimplemented abstract methods {'locate_file', 'read_text'}
113s     __version__ = Distribution().from_name('pyfastaq').version
113s 
113s ../../../usr/lib/python3/dist-packages/circlator/__init__.py:1
113s   /usr/lib/python3/dist-packages/circlator/__init__.py:1: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
113s     from pkg_resources import get_distribution
113s 
113s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
113s =========== 107 passed, 6 skipped, 2 deselected, 2 warnings in 1.86s ===========
113s autopkgtest [02:47:02]: test run-unit-test: -----------------------]
114s run-unit-test        PASS
114s autopkgtest [02:47:03]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
114s autopkgtest [02:47:03]: @@@@@@@@@@@@@@@@@@@@ summary
114s run-unit-test        PASS
119s nova [W] Using flock in prodstack6-ppc64el
119s Creating nova instance adt-plucky-ppc64el-circlator-20250217-024508-juju-7f2275-prod-proposed-migration-environment-15-9d1b909a-b15b-414f-b90f-ab440500ec45 from image adt/ubuntu-plucky-ppc64el-server-20250216.img (UUID 9f429617-9b5a-4215-a0f8-06b5a634d22b)...
119s nova [W] Timed out waiting for 09c3b70d-34b9-4755-bd75-ae5a577a359b to get deleted.