0s autopkgtest [02:34:38]: starting date and time: 2025-02-17 02:34:38+0000
  0s autopkgtest [02:34:38]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production'
  0s autopkgtest [02:34:38]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.go0c0mmp/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-26.secgroup --name adt-plucky-arm64-circlator-20250217-023438-juju-7f2275-prod-proposed-migration-environment-15-3265e022-8a0e-4dce-8442-ae47eb77294c --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
259s autopkgtest [02:38:57]: testbed dpkg architecture: arm64
259s autopkgtest [02:38:57]: testbed apt version: 2.9.28
260s autopkgtest [02:38:58]: @@@@@@@@@@@@@@@@@@@@ test bed setup
260s autopkgtest [02:38:58]: testbed release detected to be: None
261s autopkgtest [02:38:59]: updating testbed package index (apt update)
261s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB]
261s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
261s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
261s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
262s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B]
262s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [698 kB]
262s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.9 kB]
262s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [61.5 kB]
262s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [74.9 kB]
262s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [7960 B]
262s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [611 kB]
262s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [10.0 kB]
262s Fetched 1592 kB in 1s (1665 kB/s)
263s Reading package lists...
263s + lsb_release --codename --short
263s + RELEASE=plucky
263s + cat
263s + [ plucky != trusty ]
263s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade
263s Reading package lists...
264s Building dependency tree...
264s Reading state information...
264s Calculating upgrade...
265s The following NEW packages will be installed:
265s   gcc-15-base
265s The following packages will be upgraded:
265s   libatomic1 libgcc-s1 libstdc++6 pci.ids
265s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
265s Need to get 1163 kB of archives.
265s After this operation, 186 kB of additional disk space will be used.
265s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-15-base arm64 15-20250213-1ubuntu1 [53.2 kB]
265s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-s1 arm64 15-20250213-1ubuntu1 [61.1 kB]
265s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++6 arm64 15-20250213-1ubuntu1 [754 kB]
265s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libatomic1 arm64 15-20250213-1ubuntu1 [11.2 kB]
265s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 pci.ids all 0.0~2025.02.12-1 [284 kB]
266s Fetched 1163 kB in 1s (1873 kB/s)
266s Selecting previously unselected package gcc-15-base:arm64.
267s (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 ... 116609 files and directories currently installed.)
267s Preparing to unpack .../gcc-15-base_15-20250213-1ubuntu1_arm64.deb ...
267s Unpacking gcc-15-base:arm64 (15-20250213-1ubuntu1) ...
267s Setting up gcc-15-base:arm64 (15-20250213-1ubuntu1) ...
268s (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 ... 116614 files and directories currently installed.)
268s Preparing to unpack .../libgcc-s1_15-20250213-1ubuntu1_arm64.deb ...
268s Unpacking libgcc-s1:arm64 (15-20250213-1ubuntu1) over (14.2.0-17ubuntu1) ...
268s Setting up libgcc-s1:arm64 (15-20250213-1ubuntu1) ...
268s (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 ... 116614 files and directories currently installed.)
268s Preparing to unpack .../libstdc++6_15-20250213-1ubuntu1_arm64.deb ...
268s Unpacking libstdc++6:arm64 (15-20250213-1ubuntu1) over (14.2.0-17ubuntu1) ...
268s Setting up libstdc++6:arm64 (15-20250213-1ubuntu1) ...
268s (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 ... 116614 files and directories currently installed.)
268s Preparing to unpack .../libatomic1_15-20250213-1ubuntu1_arm64.deb ...
268s Unpacking libatomic1:arm64 (15-20250213-1ubuntu1) over (14.2.0-17ubuntu1) ...
268s Preparing to unpack .../pci.ids_0.0~2025.02.12-1_all.deb ...
268s Unpacking pci.ids (0.0~2025.02.12-1) over (0.0~2025.02.05-1) ...
268s Setting up pci.ids (0.0~2025.02.12-1) ...
268s Setting up libatomic1:arm64 (15-20250213-1ubuntu1) ...
268s Processing triggers for libc-bin (2.40-4ubuntu1) ...
268s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref
268s + /usr/lib/apt/apt-helper analyze-pattern ?true
268s + uname -r
268s + sed s/\./\\./g
268s + running_kernel_pattern=^linux-.*6\.12\.0-15-generic.*
268s + apt list ?obsolete
268s + tail -n+2
268s + cut -d/ -f1
268s + grep -v ^linux-.*6\.12\.0-15-generic.*
269s + true
269s + obsolete_pkgs=
269s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove
269s Reading package lists...
269s Building dependency tree...
269s Reading state information...
270s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
270s + grep -q trusty /etc/lsb-release
270s + [ ! -d /usr/share/doc/unattended-upgrades ]
270s + [ ! -d /usr/share/doc/lxd ]
270s + [ ! -d /usr/share/doc/lxd-client ]
270s + [ ! -d /usr/share/doc/snapd ]
270s + type iptables
270s + cat
270s + chmod 755 /etc/rc.local
270s + . /etc/rc.local
270s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu
270s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP
270s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP
270s + uname -m
270s + [ aarch64 = ppc64le ]
270s + [ -d /run/systemd/system ]
270s + systemd-detect-virt --quiet --vm
270s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/
270s + cat
270s + grep -q lz4 /etc/initramfs-tools/initramfs.conf
270s + echo COMPRESS=lz4
270s autopkgtest [02:39:08]: upgrading testbed (apt dist-upgrade and autopurge)
270s Reading package lists...
270s Building dependency tree...
270s Reading state information...
271s Calculating upgrade...Starting pkgProblemResolver with broken count: 0
271s Starting 2 pkgProblemResolver with broken count: 0
271s Done
272s Entering ResolveByKeep
272s 
273s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
273s Reading package lists...
273s Building dependency tree...
273s Reading state information...
274s Starting pkgProblemResolver with broken count: 0
274s Starting 2 pkgProblemResolver with broken count: 0
274s Done
275s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
277s autopkgtest [02:39:15]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb  4 15:49:33 UTC 2025
278s autopkgtest [02:39:16]: @@@@@@@@@@@@@@@@@@@@ apt-source circlator
280s Get:1 http://ftpmaster.internal/ubuntu plucky/universe circlator 1.5.6-12 (dsc) [2302 B]
280s Get:2 http://ftpmaster.internal/ubuntu plucky/universe circlator 1.5.6-12 (tar) [5724 kB]
280s Get:3 http://ftpmaster.internal/ubuntu plucky/universe circlator 1.5.6-12 (diff) [6412 B]
281s gpgv: Signature made Fri Dec  6 09:53:32 2024 UTC
281s gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
281s gpgv:                issuer "tille@debian.org"
281s gpgv: Can't check signature: No public key
281s dpkg-source: warning: cannot verify inline signature for ./circlator_1.5.6-12.dsc: no acceptable signature found
281s autopkgtest [02:39:18]: testing package circlator version 1.5.6-12
281s autopkgtest [02:39:19]: build not needed
282s autopkgtest [02:39:20]: test run-unit-test: preparing testbed
282s Reading package lists...
282s Building dependency tree...
282s Reading state information...
283s Starting pkgProblemResolver with broken count: 0
283s Starting 2 pkgProblemResolver with broken count: 0
283s Done
284s The following NEW packages will be installed:
284s   aglfn binfmt-support bwa ca-certificates-java canu circlator
284s   default-jre-headless fastaq fastjar fontconfig fontconfig-config
284s   fonts-dejavu-core fonts-dejavu-mono gnuplot-data gnuplot-nox jaligner
284s   jarwrapper java-common libaom3 libapache-pom-java
284s   libatinject-jsr330-api-java libcairo2 libcommons-codec-java
284s   libcommons-compress-java libcommons-io-java libcommons-parent-java
284s   libdatrie1 libde265-0 libdeflate0 liberror-prone-java libfastutil-java
284s   libfilesys-df-perl libfontconfig1 libgd3 libgomp1 libgraphite2-3
284s   libguava-java libharfbuzz0b libheif-plugin-aomdec libheif-plugin-libde265
284s   libheif1 libhts3t64 libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8
284s   libjpeg8 libjsr305-java liblcms2-2 liblerc4 liblua5.4-0 libpango-1.0-0
284s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpcsclite1 libpixman-1-0 libraqm0
284s   libsharpyuv0 libsnappy1v5 libssw-java libthai-data libthai0 libtiff6
284s   libwebp7 libwebpmux3 libxcb-render0 libxcb-shm0 libxpm4 libxrender1
284s   libxslt1.1 mhap mummer openjdk-21-jre-headless prodigal python3-all
284s   python3-et-xmlfile python3-iniconfig python3-lxml python3-openpyxl
284s   python3-packaging python3-pluggy python3-pymummer python3-pysam
284s   python3-pytest python3.12 python3.12-minimal samtools
284s 0 upgraded, 87 newly installed, 0 to remove and 0 not upgraded.
284s Need to get 97.4 MB of archives.
284s After this operation, 367 MB of additional disk space will be used.
284s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-minimal arm64 3.12.9-1 [2236 kB]
285s Get:2 http://ftpmaster.internal/ubuntu plucky/universe arm64 binfmt-support arm64 2.2.2-7 [55.9 kB]
285s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12 arm64 3.12.9-1 [671 kB]
285s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 bwa arm64 0.7.18-1 [201 kB]
285s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 ca-certificates-java all 20240118 [11.6 kB]
285s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250213-1ubuntu1 [146 kB]
285s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libsnappy1v5 arm64 1.2.1-1 [30.4 kB]
285s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libfilesys-df-perl arm64 0.92-7build5 [11.0 kB]
285s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 java-common all 0.76 [6852 B]
285s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB]
285s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB]
285s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B]
285s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcsclite1 arm64 2.3.1-1 [25.0 kB]
285s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 openjdk-21-jre-headless arm64 21.0.6+7-1 [45.7 MB]
286s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 default-jre-headless arm64 2:1.21-76 [3176 B]
286s Get:16 http://ftpmaster.internal/ubuntu plucky/universe arm64 fastjar arm64 2:0.98-7 [61.9 kB]
286s Get:17 http://ftpmaster.internal/ubuntu plucky/universe arm64 jarwrapper all 0.80 [9800 B]
286s Get:18 http://ftpmaster.internal/ubuntu plucky/universe arm64 libapache-pom-java all 33-2 [5874 B]
286s Get:19 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcommons-parent-java all 56-1 [10.7 kB]
286s Get:20 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcommons-codec-java all 1.17.1-1 [302 kB]
286s Get:21 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcommons-io-java all 2.18.0-1 [477 kB]
286s Get:22 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcommons-compress-java all 1.27.1-2 [610 kB]
286s Get:23 http://ftpmaster.internal/ubuntu plucky/universe arm64 libfastutil-java all 8.5.15+dfsg-1 [20.2 MB]
286s Get:24 http://ftpmaster.internal/ubuntu plucky/universe arm64 libatinject-jsr330-api-java all 1.0+ds1-6 [5076 B]
286s Get:25 http://ftpmaster.internal/ubuntu plucky/universe arm64 liberror-prone-java all 2.18.0-1 [22.5 kB]
286s Get:26 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjsr305-java all 0.1~+svn49-12 [27.0 kB]
286s Get:27 http://ftpmaster.internal/ubuntu plucky/universe arm64 libguava-java all 32.0.1-1 [2692 kB]
287s Get:28 http://ftpmaster.internal/ubuntu plucky/universe arm64 jaligner all 1.0+dfsg-11 [136 kB]
287s Get:29 http://ftpmaster.internal/ubuntu plucky/universe arm64 libssw-java arm64 1.1-15 [18.6 kB]
287s Get:30 http://ftpmaster.internal/ubuntu plucky/universe arm64 mhap all 2.1.3+dfsg-3 [160 kB]
287s Get:31 http://ftpmaster.internal/ubuntu plucky/universe arm64 aglfn all 1.7+git20191031.4036a9c-2 [30.6 kB]
287s Get:32 http://ftpmaster.internal/ubuntu plucky/universe arm64 gnuplot-data all 6.0.0+dfsg1-1ubuntu3 [75.3 kB]
287s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB]
287s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB]
287s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB]
287s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB]
287s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB]
287s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB]
287s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B]
287s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB]
287s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB]
287s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB]
287s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libaom3 arm64 3.12.0-1 [1828 kB]
287s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libheif-plugin-aomdec arm64 1.19.5-1build1 [11.4 kB]
287s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libde265-0 arm64 1.0.15-1build4 [146 kB]
287s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libheif-plugin-libde265 arm64 1.19.5-1build1 [8902 B]
287s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libheif1 arm64 1.19.5-1build1 [369 kB]
287s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB]
287s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB]
287s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB]
287s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.2-1 [14.9 kB]
287s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB]
287s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB]
287s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB]
287s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB]
287s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB]
287s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 libxpm4 arm64 1:3.5.17-1build2 [35.1 kB]
287s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 libgd3 arm64 2.3.3-12ubuntu3 [122 kB]
287s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 liblua5.4-0 arm64 5.4.7-1 [158 kB]
287s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-1.1ubuntu2 [190 kB]
287s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB]
287s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB]
287s Get:63 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB]
287s Get:64 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.56.1-1 [238 kB]
287s Get:65 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.56.1-1 [49.6 kB]
287s Get:66 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.56.1-1 [27.6 kB]
287s Get:67 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.5.0-0.1 [25.4 kB]
287s Get:68 http://ftpmaster.internal/ubuntu plucky/universe arm64 gnuplot-nox arm64 6.0.0+dfsg1-1ubuntu3 [956 kB]
287s Get:69 http://ftpmaster.internal/ubuntu plucky/universe arm64 canu arm64 2.2+dfsg-5 [1500 kB]
287s Get:70 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.1-1 [82.5 kB]
287s Get:71 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts3t64 arm64 1.21+ds-1 [441 kB]
287s Get:72 http://ftpmaster.internal/ubuntu plucky/universe arm64 samtools arm64 1.21-1 [609 kB]
287s Get:73 http://ftpmaster.internal/ubuntu plucky/universe arm64 fastaq all 3.17.0-9 [48.2 kB]
287s Get:74 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-et-xmlfile all 2.0.0-1 [79.4 kB]
287s Get:75 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu2 [168 kB]
287s Get:76 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.1-1 [1600 kB]
287s Get:77 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-openpyxl all 3.1.5+dfsg-1 [152 kB]
287s Get:78 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.2-1 [51.5 kB]
287s Get:79 http://ftpmaster.internal/ubuntu plucky/universe arm64 mummer arm64 3.23+dfsg-8 [673 kB]
287s Get:80 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pymummer all 0.11.0-4 [17.1 kB]
287s Get:81 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pysam arm64 0.23.0+ds-1 [4080 kB]
287s Get:82 http://ftpmaster.internal/ubuntu plucky/universe arm64 prodigal arm64 1:2.6.3-6 [822 kB]
287s Get:83 http://ftpmaster.internal/ubuntu plucky/universe arm64 circlator all 1.5.6-12 [4617 kB]
288s Get:84 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.13.1-1~exp2 [894 B]
288s Get:85 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B]
288s Get:86 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB]
288s Get:87 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.4-1 [252 kB]
288s Fetched 97.4 MB in 4s (26.7 MB/s)
288s Selecting previously unselected package python3.12-minimal.
288s (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 ... 116614 files and directories currently installed.)
288s Preparing to unpack .../00-python3.12-minimal_3.12.9-1_arm64.deb ...
288s Unpacking python3.12-minimal (3.12.9-1) ...
288s Selecting previously unselected package binfmt-support.
288s Preparing to unpack .../01-binfmt-support_2.2.2-7_arm64.deb ...
288s Unpacking binfmt-support (2.2.2-7) ...
288s Selecting previously unselected package python3.12.
288s Preparing to unpack .../02-python3.12_3.12.9-1_arm64.deb ...
288s Unpacking python3.12 (3.12.9-1) ...
288s Selecting previously unselected package bwa.
289s Preparing to unpack .../03-bwa_0.7.18-1_arm64.deb ...
289s Unpacking bwa (0.7.18-1) ...
289s Selecting previously unselected package ca-certificates-java.
289s Preparing to unpack .../04-ca-certificates-java_20240118_all.deb ...
289s Unpacking ca-certificates-java (20240118) ...
289s Selecting previously unselected package libgomp1:arm64.
289s Preparing to unpack .../05-libgomp1_15-20250213-1ubuntu1_arm64.deb ...
289s Unpacking libgomp1:arm64 (15-20250213-1ubuntu1) ...
289s Selecting previously unselected package libsnappy1v5:arm64.
289s Preparing to unpack .../06-libsnappy1v5_1.2.1-1_arm64.deb ...
289s Unpacking libsnappy1v5:arm64 (1.2.1-1) ...
289s Selecting previously unselected package libfilesys-df-perl.
289s Preparing to unpack .../07-libfilesys-df-perl_0.92-7build5_arm64.deb ...
289s Unpacking libfilesys-df-perl (0.92-7build5) ...
289s Selecting previously unselected package java-common.
289s Preparing to unpack .../08-java-common_0.76_all.deb ...
289s Unpacking java-common (0.76) ...
289s Selecting previously unselected package liblcms2-2:arm64.
289s Preparing to unpack .../09-liblcms2-2_2.16-2_arm64.deb ...
289s Unpacking liblcms2-2:arm64 (2.16-2) ...
289s Selecting previously unselected package libjpeg-turbo8:arm64.
289s Preparing to unpack .../10-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ...
289s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ...
289s Selecting previously unselected package libjpeg8:arm64.
289s Preparing to unpack .../11-libjpeg8_8c-2ubuntu11_arm64.deb ...
289s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ...
289s Selecting previously unselected package libpcsclite1:arm64.
289s Preparing to unpack .../12-libpcsclite1_2.3.1-1_arm64.deb ...
289s Unpacking libpcsclite1:arm64 (2.3.1-1) ...
289s Selecting previously unselected package openjdk-21-jre-headless:arm64.
289s Preparing to unpack .../13-openjdk-21-jre-headless_21.0.6+7-1_arm64.deb ...
289s Unpacking openjdk-21-jre-headless:arm64 (21.0.6+7-1) ...
290s Selecting previously unselected package default-jre-headless.
290s Preparing to unpack .../14-default-jre-headless_2%3a1.21-76_arm64.deb ...
290s Unpacking default-jre-headless (2:1.21-76) ...
290s Selecting previously unselected package fastjar.
290s Preparing to unpack .../15-fastjar_2%3a0.98-7_arm64.deb ...
290s Unpacking fastjar (2:0.98-7) ...
290s Selecting previously unselected package jarwrapper.
290s Preparing to unpack .../16-jarwrapper_0.80_all.deb ...
290s Unpacking jarwrapper (0.80) ...
290s Selecting previously unselected package libapache-pom-java.
291s Preparing to unpack .../17-libapache-pom-java_33-2_all.deb ...
291s Unpacking libapache-pom-java (33-2) ...
291s Selecting previously unselected package libcommons-parent-java.
291s Preparing to unpack .../18-libcommons-parent-java_56-1_all.deb ...
291s Unpacking libcommons-parent-java (56-1) ...
291s Selecting previously unselected package libcommons-codec-java.
291s Preparing to unpack .../19-libcommons-codec-java_1.17.1-1_all.deb ...
291s Unpacking libcommons-codec-java (1.17.1-1) ...
291s Selecting previously unselected package libcommons-io-java.
291s Preparing to unpack .../20-libcommons-io-java_2.18.0-1_all.deb ...
291s Unpacking libcommons-io-java (2.18.0-1) ...
291s Selecting previously unselected package libcommons-compress-java.
291s Preparing to unpack .../21-libcommons-compress-java_1.27.1-2_all.deb ...
291s Unpacking libcommons-compress-java (1.27.1-2) ...
291s Selecting previously unselected package libfastutil-java.
291s Preparing to unpack .../22-libfastutil-java_8.5.15+dfsg-1_all.deb ...
291s Unpacking libfastutil-java (8.5.15+dfsg-1) ...
291s Selecting previously unselected package libatinject-jsr330-api-java.
291s Preparing to unpack .../23-libatinject-jsr330-api-java_1.0+ds1-6_all.deb ...
291s Unpacking libatinject-jsr330-api-java (1.0+ds1-6) ...
291s Selecting previously unselected package liberror-prone-java.
291s Preparing to unpack .../24-liberror-prone-java_2.18.0-1_all.deb ...
291s Unpacking liberror-prone-java (2.18.0-1) ...
291s Selecting previously unselected package libjsr305-java.
291s Preparing to unpack .../25-libjsr305-java_0.1~+svn49-12_all.deb ...
291s Unpacking libjsr305-java (0.1~+svn49-12) ...
291s Selecting previously unselected package libguava-java.
291s Preparing to unpack .../26-libguava-java_32.0.1-1_all.deb ...
291s Unpacking libguava-java (32.0.1-1) ...
291s Selecting previously unselected package jaligner.
291s Preparing to unpack .../27-jaligner_1.0+dfsg-11_all.deb ...
291s Unpacking jaligner (1.0+dfsg-11) ...
291s Selecting previously unselected package libssw-java.
291s Preparing to unpack .../28-libssw-java_1.1-15_arm64.deb ...
291s Unpacking libssw-java (1.1-15) ...
291s Selecting previously unselected package mhap.
291s Preparing to unpack .../29-mhap_2.1.3+dfsg-3_all.deb ...
291s Unpacking mhap (2.1.3+dfsg-3) ...
291s Selecting previously unselected package aglfn.
292s Preparing to unpack .../30-aglfn_1.7+git20191031.4036a9c-2_all.deb ...
292s Unpacking aglfn (1.7+git20191031.4036a9c-2) ...
292s Selecting previously unselected package gnuplot-data.
292s Preparing to unpack .../31-gnuplot-data_6.0.0+dfsg1-1ubuntu3_all.deb ...
292s Unpacking gnuplot-data (6.0.0+dfsg1-1ubuntu3) ...
292s Selecting previously unselected package fonts-dejavu-mono.
292s Preparing to unpack .../32-fonts-dejavu-mono_2.37-8_all.deb ...
292s Unpacking fonts-dejavu-mono (2.37-8) ...
292s Selecting previously unselected package fonts-dejavu-core.
292s Preparing to unpack .../33-fonts-dejavu-core_2.37-8_all.deb ...
292s Unpacking fonts-dejavu-core (2.37-8) ...
292s Selecting previously unselected package fontconfig-config.
292s Preparing to unpack .../34-fontconfig-config_2.15.0-1.1ubuntu2_arm64.deb ...
292s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ...
292s Selecting previously unselected package libfontconfig1:arm64.
292s Preparing to unpack .../35-libfontconfig1_2.15.0-1.1ubuntu2_arm64.deb ...
292s Unpacking libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ...
292s Selecting previously unselected package libpixman-1-0:arm64.
292s Preparing to unpack .../36-libpixman-1-0_0.44.0-3_arm64.deb ...
292s Unpacking libpixman-1-0:arm64 (0.44.0-3) ...
292s Selecting previously unselected package libxcb-render0:arm64.
292s Preparing to unpack .../37-libxcb-render0_1.17.0-2_arm64.deb ...
292s Unpacking libxcb-render0:arm64 (1.17.0-2) ...
292s Selecting previously unselected package libxcb-shm0:arm64.
292s Preparing to unpack .../38-libxcb-shm0_1.17.0-2_arm64.deb ...
292s Unpacking libxcb-shm0:arm64 (1.17.0-2) ...
292s Selecting previously unselected package libxrender1:arm64.
292s Preparing to unpack .../39-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ...
292s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ...
292s Selecting previously unselected package libcairo2:arm64.
293s Preparing to unpack .../40-libcairo2_1.18.2-2_arm64.deb ...
293s Unpacking libcairo2:arm64 (1.18.2-2) ...
293s Selecting previously unselected package libsharpyuv0:arm64.
293s Preparing to unpack .../41-libsharpyuv0_1.5.0-0.1_arm64.deb ...
293s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ...
293s Selecting previously unselected package libaom3:arm64.
293s Preparing to unpack .../42-libaom3_3.12.0-1_arm64.deb ...
293s Unpacking libaom3:arm64 (3.12.0-1) ...
293s Selecting previously unselected package libheif-plugin-aomdec:arm64.
293s Preparing to unpack .../43-libheif-plugin-aomdec_1.19.5-1build1_arm64.deb ...
293s Unpacking libheif-plugin-aomdec:arm64 (1.19.5-1build1) ...
293s Selecting previously unselected package libde265-0:arm64.
293s Preparing to unpack .../44-libde265-0_1.0.15-1build4_arm64.deb ...
293s Unpacking libde265-0:arm64 (1.0.15-1build4) ...
293s Selecting previously unselected package libheif-plugin-libde265:arm64.
293s Preparing to unpack .../45-libheif-plugin-libde265_1.19.5-1build1_arm64.deb ...
293s Unpacking libheif-plugin-libde265:arm64 (1.19.5-1build1) ...
293s Selecting previously unselected package libheif1:arm64.
293s Preparing to unpack .../46-libheif1_1.19.5-1build1_arm64.deb ...
293s Unpacking libheif1:arm64 (1.19.5-1build1) ...
293s Selecting previously unselected package libimagequant0:arm64.
293s Preparing to unpack .../47-libimagequant0_2.18.0-1build1_arm64.deb ...
293s Unpacking libimagequant0:arm64 (2.18.0-1build1) ...
293s Selecting previously unselected package libgraphite2-3:arm64.
293s Preparing to unpack .../48-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ...
293s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ...
293s Selecting previously unselected package libharfbuzz0b:arm64.
293s Preparing to unpack .../49-libharfbuzz0b_10.2.0-1_arm64.deb ...
293s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ...
293s Selecting previously unselected package libraqm0:arm64.
293s Preparing to unpack .../50-libraqm0_0.10.2-1_arm64.deb ...
293s Unpacking libraqm0:arm64 (0.10.2-1) ...
293s Selecting previously unselected package libdeflate0:arm64.
293s Preparing to unpack .../51-libdeflate0_1.23-1_arm64.deb ...
293s Unpacking libdeflate0:arm64 (1.23-1) ...
293s Selecting previously unselected package libjbig0:arm64.
293s Preparing to unpack .../52-libjbig0_2.1-6.1ubuntu2_arm64.deb ...
293s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ...
293s Selecting previously unselected package liblerc4:arm64.
294s Preparing to unpack .../53-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ...
294s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ...
294s Selecting previously unselected package libwebp7:arm64.
294s Preparing to unpack .../54-libwebp7_1.5.0-0.1_arm64.deb ...
294s Unpacking libwebp7:arm64 (1.5.0-0.1) ...
294s Selecting previously unselected package libtiff6:arm64.
294s Preparing to unpack .../55-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ...
294s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ...
294s Selecting previously unselected package libxpm4:arm64.
294s Preparing to unpack .../56-libxpm4_1%3a3.5.17-1build2_arm64.deb ...
294s Unpacking libxpm4:arm64 (1:3.5.17-1build2) ...
294s Selecting previously unselected package libgd3:arm64.
294s Preparing to unpack .../57-libgd3_2.3.3-12ubuntu3_arm64.deb ...
294s Unpacking libgd3:arm64 (2.3.3-12ubuntu3) ...
294s Selecting previously unselected package liblua5.4-0:arm64.
294s Preparing to unpack .../58-liblua5.4-0_5.4.7-1_arm64.deb ...
294s Unpacking liblua5.4-0:arm64 (5.4.7-1) ...
294s Selecting previously unselected package fontconfig.
294s Preparing to unpack .../59-fontconfig_2.15.0-1.1ubuntu2_arm64.deb ...
294s Unpacking fontconfig (2.15.0-1.1ubuntu2) ...
294s Selecting previously unselected package libthai-data.
294s Preparing to unpack .../60-libthai-data_0.1.29-2build1_all.deb ...
294s Unpacking libthai-data (0.1.29-2build1) ...
294s Selecting previously unselected package libdatrie1:arm64.
294s Preparing to unpack .../61-libdatrie1_0.2.13-3build1_arm64.deb ...
294s Unpacking libdatrie1:arm64 (0.2.13-3build1) ...
294s Selecting previously unselected package libthai0:arm64.
294s Preparing to unpack .../62-libthai0_0.1.29-2build1_arm64.deb ...
294s Unpacking libthai0:arm64 (0.1.29-2build1) ...
294s Selecting previously unselected package libpango-1.0-0:arm64.
294s Preparing to unpack .../63-libpango-1.0-0_1.56.1-1_arm64.deb ...
294s Unpacking libpango-1.0-0:arm64 (1.56.1-1) ...
294s Selecting previously unselected package libpangoft2-1.0-0:arm64.
294s Preparing to unpack .../64-libpangoft2-1.0-0_1.56.1-1_arm64.deb ...
294s Unpacking libpangoft2-1.0-0:arm64 (1.56.1-1) ...
294s Selecting previously unselected package libpangocairo-1.0-0:arm64.
295s Preparing to unpack .../65-libpangocairo-1.0-0_1.56.1-1_arm64.deb ...
295s Unpacking libpangocairo-1.0-0:arm64 (1.56.1-1) ...
295s Selecting previously unselected package libwebpmux3:arm64.
295s Preparing to unpack .../66-libwebpmux3_1.5.0-0.1_arm64.deb ...
295s Unpacking libwebpmux3:arm64 (1.5.0-0.1) ...
295s Selecting previously unselected package gnuplot-nox.
295s Preparing to unpack .../67-gnuplot-nox_6.0.0+dfsg1-1ubuntu3_arm64.deb ...
295s Unpacking gnuplot-nox (6.0.0+dfsg1-1ubuntu3) ...
295s Selecting previously unselected package canu.
295s Preparing to unpack .../68-canu_2.2+dfsg-5_arm64.deb ...
295s Unpacking canu (2.2+dfsg-5) ...
295s Selecting previously unselected package libhtscodecs2:arm64.
295s Preparing to unpack .../69-libhtscodecs2_1.6.1-1_arm64.deb ...
295s Unpacking libhtscodecs2:arm64 (1.6.1-1) ...
295s Selecting previously unselected package libhts3t64:arm64.
295s Preparing to unpack .../70-libhts3t64_1.21+ds-1_arm64.deb ...
295s Unpacking libhts3t64:arm64 (1.21+ds-1) ...
295s Selecting previously unselected package samtools.
295s Preparing to unpack .../71-samtools_1.21-1_arm64.deb ...
295s Unpacking samtools (1.21-1) ...
295s Selecting previously unselected package fastaq.
295s Preparing to unpack .../72-fastaq_3.17.0-9_all.deb ...
295s Unpacking fastaq (3.17.0-9) ...
295s Selecting previously unselected package python3-et-xmlfile.
295s Preparing to unpack .../73-python3-et-xmlfile_2.0.0-1_all.deb ...
295s Unpacking python3-et-xmlfile (2.0.0-1) ...
295s Selecting previously unselected package libxslt1.1:arm64.
295s Preparing to unpack .../74-libxslt1.1_1.1.39-0exp1ubuntu2_arm64.deb ...
295s Unpacking libxslt1.1:arm64 (1.1.39-0exp1ubuntu2) ...
295s Selecting previously unselected package python3-lxml:arm64.
295s Preparing to unpack .../75-python3-lxml_5.3.1-1_arm64.deb ...
295s Unpacking python3-lxml:arm64 (5.3.1-1) ...
295s Selecting previously unselected package python3-openpyxl.
296s Preparing to unpack .../76-python3-openpyxl_3.1.5+dfsg-1_all.deb ...
296s Unpacking python3-openpyxl (3.1.5+dfsg-1) ...
296s Selecting previously unselected package python3-packaging.
296s Preparing to unpack .../77-python3-packaging_24.2-1_all.deb ...
296s Unpacking python3-packaging (24.2-1) ...
296s Selecting previously unselected package mummer.
296s Preparing to unpack .../78-mummer_3.23+dfsg-8_arm64.deb ...
296s Unpacking mummer (3.23+dfsg-8) ...
296s Selecting previously unselected package python3-pymummer.
296s Preparing to unpack .../79-python3-pymummer_0.11.0-4_all.deb ...
296s Unpacking python3-pymummer (0.11.0-4) ...
296s Selecting previously unselected package python3-pysam.
296s Preparing to unpack .../80-python3-pysam_0.23.0+ds-1_arm64.deb ...
296s Unpacking python3-pysam (0.23.0+ds-1) ...
296s Selecting previously unselected package prodigal.
296s Preparing to unpack .../81-prodigal_1%3a2.6.3-6_arm64.deb ...
296s Unpacking prodigal (1:2.6.3-6) ...
296s Selecting previously unselected package circlator.
296s Preparing to unpack .../82-circlator_1.5.6-12_all.deb ...
296s Unpacking circlator (1.5.6-12) ...
296s Selecting previously unselected package python3-all.
296s Preparing to unpack .../83-python3-all_3.13.1-1~exp2_arm64.deb ...
296s Unpacking python3-all (3.13.1-1~exp2) ...
296s Selecting previously unselected package python3-iniconfig.
296s Preparing to unpack .../84-python3-iniconfig_1.1.1-2_all.deb ...
296s Unpacking python3-iniconfig (1.1.1-2) ...
296s Selecting previously unselected package python3-pluggy.
296s Preparing to unpack .../85-python3-pluggy_1.5.0-1_all.deb ...
296s Unpacking python3-pluggy (1.5.0-1) ...
296s Selecting previously unselected package python3-pytest.
297s Preparing to unpack .../86-python3-pytest_8.3.4-1_all.deb ...
297s Unpacking python3-pytest (8.3.4-1) ...
297s Setting up libhtscodecs2:arm64 (1.6.1-1) ...
297s Setting up fastjar (2:0.98-7) ...
297s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ...
297s Setting up liblcms2-2:arm64 (2.16-2) ...
297s Setting up python3-iniconfig (1.1.1-2) ...
297s Setting up libpixman-1-0:arm64 (0.44.0-3) ...
297s Setting up python3.12-minimal (3.12.9-1) ...
298s Setting up libfastutil-java (8.5.15+dfsg-1) ...
298s Setting up libsharpyuv0:arm64 (1.5.0-0.1) ...
298s Setting up libaom3:arm64 (3.12.0-1) ...
298s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu1) ...
298s Setting up libjsr305-java (0.1~+svn49-12) ...
298s Setting up libxpm4:arm64 (1:3.5.17-1build2) ...
298s Setting up java-common (0.76) ...
298s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ...
298s Setting up libdatrie1:arm64 (0.2.13-3build1) ...
298s Setting up libxcb-render0:arm64 (1.17.0-2) ...
298s Setting up prodigal (1:2.6.3-6) ...
298s Setting up bwa (0.7.18-1) ...
298s Setting up python3.12 (3.12.9-1) ...
300s Setting up libfilesys-df-perl (0.92-7build5) ...
300s Setting up libdeflate0:arm64 (1.23-1) ...
300s Setting up python3-all (3.13.1-1~exp2) ...
300s Setting up libxcb-shm0:arm64 (1.17.0-2) ...
300s Setting up libgomp1:arm64 (15-20250213-1ubuntu1) ...
300s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ...
300s Setting up libssw-java (1.1-15) ...
300s Setting up libsnappy1v5:arm64 (1.2.1-1) ...
300s Setting up python3-packaging (24.2-1) ...
300s Setting up aglfn (1.7+git20191031.4036a9c-2) ...
300s Setting up libapache-pom-java (33-2) ...
300s Setting up libatinject-jsr330-api-java (1.0+ds1-6) ...
300s Setting up libimagequant0:arm64 (2.18.0-1build1) ...
300s Setting up fonts-dejavu-mono (2.37-8) ...
300s Setting up binfmt-support (2.2.2-7) ...
300s update-binfmts: warning: python3.13 already enabled in kernel.
300s Created symlink '/etc/systemd/system/multi-user.target.wants/binfmt-support.service' → '/usr/lib/systemd/system/binfmt-support.service'.

301s Setting up fonts-dejavu-core (2.37-8) ...
301s Setting up libpcsclite1:arm64 (2.3.1-1) ...
301s Setting up libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ...
301s Setting up python3-pluggy (1.5.0-1) ...
301s Setting up libwebp7:arm64 (1.5.0-0.1) ...
301s Setting up libxslt1.1:arm64 (1.1.39-0exp1ubuntu2) ...
301s Setting up mummer (3.23+dfsg-8) ...
301s Setting up python3-et-xmlfile (2.0.0-1) ...
302s Setting up libhts3t64:arm64 (1.21+ds-1) ...
302s Setting up liblua5.4-0:arm64 (5.4.7-1) ...
302s Setting up libharfbuzz0b:arm64 (10.2.0-1) ...
302s Setting up libthai-data (0.1.29-2build1) ...
302s Setting up ca-certificates-java (20240118) ...
302s No JRE found. Skipping Java certificates setup.
302s Setting up libde265-0:arm64 (1.0.15-1build4) ...
302s Setting up libwebpmux3:arm64 (1.5.0-0.1) ...
302s Setting up libjpeg8:arm64 (8c-2ubuntu11) ...
302s Setting up gnuplot-data (6.0.0+dfsg1-1ubuntu3) ...
302s Setting up python3-pysam (0.23.0+ds-1) ...
302s Setting up openjdk-21-jre-headless:arm64 (21.0.6+7-1) ...
302s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode
302s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode
302s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
302s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
302s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
302s Setting up jarwrapper (0.80) ...
302s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ...
302s Setting up python3-pytest (8.3.4-1) ...
303s Setting up libcommons-parent-java (56-1) ...
303s Setting up samtools (1.21-1) ...
303s Setting up libthai0:arm64 (0.1.29-2build1) ...
303s Setting up libraqm0:arm64 (0.10.2-1) ...
303s Setting up python3-lxml:arm64 (5.3.1-1) ...
303s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ...
303s Setting up libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ...
303s Setting up libcommons-codec-java (1.17.1-1) ...
303s Setting up fontconfig (2.15.0-1.1ubuntu2) ...
305s Regenerating fonts cache... done.
305s Setting up libcommons-io-java (2.18.0-1) ...
305s Setting up fastaq (3.17.0-9) ...
306s Setting up libpango-1.0-0:arm64 (1.56.1-1) ...
306s Setting up libcairo2:arm64 (1.18.2-2) ...
306s Setting up python3-pymummer (0.11.0-4) ...
306s Setting up python3-openpyxl (3.1.5+dfsg-1) ...
306s Setting up libpangoft2-1.0-0:arm64 (1.56.1-1) ...
306s Setting up libpangocairo-1.0-0:arm64 (1.56.1-1) ...
306s Setting up libcommons-compress-java (1.27.1-2) ...
307s Setting up libheif-plugin-aomdec:arm64 (1.19.5-1build1) ...
307s Setting up libheif-plugin-libde265:arm64 (1.19.5-1build1) ...
307s Setting up liberror-prone-java (2.18.0-1) ...
307s Setting up libheif1:arm64 (1.19.5-1build1) ...
307s Setting up libguava-java (32.0.1-1) ...
307s Setting up libgd3:arm64 (2.3.3-12ubuntu3) ...
307s Setting up gnuplot-nox (6.0.0+dfsg1-1ubuntu3) ...
307s update-alternatives: using /usr/bin/gnuplot-nox to provide /usr/bin/gnuplot (gnuplot) in auto mode
307s Processing triggers for install-info (7.1.1-1) ...
307s Processing triggers for libc-bin (2.40-4ubuntu1) ...
307s Processing triggers for systemd (257.2-3ubuntu1) ...
307s Processing triggers for man-db (2.13.0-1) ...
309s Processing triggers for ca-certificates-java (20240118) ...
309s Adding debian:ACCVRAIZ1.pem
309s Adding debian:AC_RAIZ_FNMT-RCM.pem
309s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem
309s Adding debian:ANF_Secure_Server_Root_CA.pem
309s Adding debian:Actalis_Authentication_Root_CA.pem
309s Adding debian:AffirmTrust_Commercial.pem
309s Adding debian:AffirmTrust_Networking.pem
309s Adding debian:AffirmTrust_Premium.pem
309s Adding debian:AffirmTrust_Premium_ECC.pem
309s Adding debian:Amazon_Root_CA_1.pem
309s Adding debian:Amazon_Root_CA_2.pem
309s Adding debian:Amazon_Root_CA_3.pem
309s Adding debian:Amazon_Root_CA_4.pem
309s Adding debian:Atos_TrustedRoot_2011.pem
309s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem
309s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem
309s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
309s Adding debian:BJCA_Global_Root_CA1.pem
309s Adding debian:BJCA_Global_Root_CA2.pem
309s Adding debian:Baltimore_CyberTrust_Root.pem
309s Adding debian:Buypass_Class_2_Root_CA.pem
309s Adding debian:Buypass_Class_3_Root_CA.pem
309s Adding debian:CA_Disig_Root_R2.pem
309s Adding debian:CFCA_EV_ROOT.pem
309s Adding debian:COMODO_Certification_Authority.pem
309s Adding debian:COMODO_ECC_Certification_Authority.pem
309s Adding debian:COMODO_RSA_Certification_Authority.pem
309s Adding debian:Certainly_Root_E1.pem
309s Adding debian:Certainly_Root_R1.pem
309s Adding debian:Certigna.pem
309s Adding debian:Certigna_Root_CA.pem
309s Adding debian:Certum_EC-384_CA.pem
309s Adding debian:Certum_Trusted_Network_CA.pem
309s Adding debian:Certum_Trusted_Network_CA_2.pem
309s Adding debian:Certum_Trusted_Root_CA.pem
309s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem
309s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem
309s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem
309s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem
309s Adding debian:Comodo_AAA_Services_root.pem
309s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem
309s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem
309s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
309s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
309s Adding debian:DigiCert_Assured_ID_Root_CA.pem
309s Adding debian:DigiCert_Assured_ID_Root_G2.pem
309s Adding debian:DigiCert_Assured_ID_Root_G3.pem
309s Adding debian:DigiCert_Global_Root_CA.pem
309s Adding debian:DigiCert_Global_Root_G2.pem
309s Adding debian:DigiCert_Global_Root_G3.pem
309s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
309s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem
309s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem
309s Adding debian:DigiCert_Trusted_Root_G4.pem
309s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
309s Adding debian:Entrust_Root_Certification_Authority.pem
309s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
309s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
309s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem
309s Adding debian:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem
309s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem
309s Adding debian:GLOBALTRUST_2020.pem
309s Adding debian:GTS_Root_R1.pem
309s Adding debian:GTS_Root_R2.pem
309s Adding debian:GTS_Root_R3.pem
309s Adding debian:GTS_Root_R4.pem
309s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
309s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
309s Adding debian:GlobalSign_Root_CA.pem
309s Adding debian:GlobalSign_Root_CA_-_R3.pem
309s Adding debian:GlobalSign_Root_CA_-_R6.pem
309s Adding debian:GlobalSign_Root_E46.pem
309s Adding debian:GlobalSign_Root_R46.pem
309s Adding debian:Go_Daddy_Class_2_CA.pem
309s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
309s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem
309s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem
309s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem
309s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem
309s Adding debian:HiPKI_Root_CA_-_G1.pem
309s Adding debian:Hongkong_Post_Root_CA_3.pem
309s Adding debian:ISRG_Root_X1.pem
309s Adding debian:ISRG_Root_X2.pem
309s Adding debian:IdenTrust_Commercial_Root_CA_1.pem
309s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
309s Adding debian:Izenpe.com.pem
309s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
309s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem
309s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem
309s Adding debian:NAVER_Global_Root_Certification_Authority.pem
309s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
309s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
309s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem
309s Adding debian:QuoVadis_Root_CA_1_G3.pem
309s Adding debian:QuoVadis_Root_CA_2.pem
309s Adding debian:QuoVadis_Root_CA_2_G3.pem
309s Adding debian:QuoVadis_Root_CA_3.pem
310s Adding debian:QuoVadis_Root_CA_3_G3.pem
310s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem
310s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem
310s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem
310s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem
310s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem
310s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem
310s Adding debian:SZAFIR_ROOT_CA2.pem
310s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem
310s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem
310s Adding debian:SecureSign_RootCA11.pem
310s Adding debian:SecureSign_Root_CA12.pem
310s Adding debian:SecureSign_Root_CA14.pem
310s Adding debian:SecureSign_Root_CA15.pem
310s Adding debian:SecureTrust_CA.pem
310s Adding debian:Secure_Global_CA.pem
310s Adding debian:Security_Communication_ECC_RootCA1.pem
310s Adding debian:Security_Communication_RootCA2.pem
310s Adding debian:Security_Communication_RootCA3.pem
310s Adding debian:Starfield_Class_2_CA.pem
310s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
310s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
310s Adding debian:SwissSign_Gold_CA_-_G2.pem
310s Adding debian:SwissSign_Silver_CA_-_G2.pem
310s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
310s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
310s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
310s Adding debian:TWCA_CYBER_Root_CA.pem
310s Adding debian:TWCA_Global_Root_CA.pem
310s Adding debian:TWCA_Root_Certification_Authority.pem
310s Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem
310s Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem
310s Adding debian:TeliaSonera_Root_CA_v1.pem
310s Adding debian:Telia_Root_CA_v2.pem
310s Adding debian:TrustAsia_Global_Root_CA_G3.pem
310s Adding debian:TrustAsia_Global_Root_CA_G4.pem
310s Adding debian:Trustwave_Global_Certification_Authority.pem
310s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem
310s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem
310s Adding debian:TunTrust_Root_CA.pem
310s Adding debian:UCA_Extended_Validation_Root.pem
310s Adding debian:UCA_Global_G2_Root.pem
310s Adding debian:USERTrust_ECC_Certification_Authority.pem
310s Adding debian:USERTrust_RSA_Certification_Authority.pem
310s Adding debian:XRamp_Global_CA_Root.pem
310s Adding debian:certSIGN_ROOT_CA.pem
310s Adding debian:certSIGN_Root_CA_G2.pem
310s Adding debian:e-Szigno_Root_CA_2017.pem
310s Adding debian:ePKI_Root_Certification_Authority.pem
310s Adding debian:emSign_ECC_Root_CA_-_C3.pem
310s Adding debian:emSign_ECC_Root_CA_-_G3.pem
310s Adding debian:emSign_Root_CA_-_C1.pem
310s Adding debian:emSign_Root_CA_-_G1.pem
310s Adding debian:vTrus_ECC_Root_CA.pem
310s Adding debian:vTrus_Root_CA.pem
310s done.
310s Setting up default-jre-headless (2:1.21-76) ...
310s Setting up jaligner (1.0+dfsg-11) ...
310s Setting up mhap (2.1.3+dfsg-3) ...
310s Setting up canu (2.2+dfsg-5) ...
310s Setting up circlator (1.5.6-12) ...
311s autopkgtest [02:39:49]: test run-unit-test: [-----------------------
311s + pkg=circlator
311s + export LC_ALL=C.UTF-8
311s + LC_ALL=C.UTF-8
311s + '[' /tmp/autopkgtest.QtcAtU/autopkgtest_tmp = '' ']'
311s + 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.QtcAtU/autopkgtest_tmp
311s + cd /tmp/autopkgtest.QtcAtU/autopkgtest_tmp
311s + tar xaf data.tar.xz
311s + 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
311s ++ py3versions --supported
311s + for py in $(py3versions --supported 2> /dev/null)
311s + eval dpkg-architecture --is amd64
311s ++ dpkg-architecture --is amd64
311s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation)
311s + python3.12 -m pytest -v -k 'not (test_build_spades_kmers or test_make_spades_command)'
312s ============================= test session starts ==============================
312s platform linux -- Python 3.12.9, pytest-8.3.4, pluggy-1.5.0 -- /usr/bin/python3.12
312s cachedir: .pytest_cache
312s rootdir: /tmp/autopkgtest.QtcAtU/autopkgtest_tmp
312s plugins: typeguard-4.4.1
312s collecting ... collected 115 items / 2 deselected / 113 selected
312s 
312s assemble_test.py::TestAssembleCanu::test_make_canu_command PASSED        [  0%]
312s assemble_test.py::TestAssembleCanu::test_rename_canu_contigs PASSED      [  1%]
312s assembly_test.py::TestAssembly::test_circular_contigs_from_canu_gfa PASSED [  2%]
312s assembly_test.py::TestAssembly::test_circular_contigs_from_spades_after_3_6_1 PASSED [  3%]
312s assembly_test.py::TestAssembly::test_circular_contigs_from_spades_before_3_6_1 PASSED [  4%]
312s assembly_test.py::TestAssembly::test_circular_contigs_just_fasta PASSED  [  5%]
312s assembly_test.py::TestAssembly::test_circular_contigs_spades_post_3_6_1 PASSED [  6%]
312s assembly_test.py::TestAssembly::test_circular_contigs_spades_pre_3_6_1 PASSED [  7%]
312s assembly_test.py::TestAssembly::test_circular_edges_to_edge_numbers_dict PASSED [  7%]
312s assembly_test.py::TestAssembly::test_get_contigs PASSED                  [  8%]
312s assembly_test.py::TestAssembly::test_init_file_not_dir PASSED            [  9%]
312s assembly_test.py::TestAssembly::test_init_post_3_6_1_ok PASSED           [ 10%]
312s assembly_test.py::TestAssembly::test_init_pre_3_6_1_ok PASSED            [ 11%]
312s assembly_test.py::TestAssembly::test_init_raises_error PASSED            [ 12%]
312s assembly_test.py::TestAssembly::test_spades_contigs_paths_to_dict PASSED [ 13%]
312s bamfilter_test.py::TestBamfilter::test_all_reads_from_contig PASSED      [ 14%]
312s bamfilter_test.py::TestBamfilter::test_break_reads PASSED                [ 15%]
312s bamfilter_test.py::TestBamfilter::test_check_contigs_to_use PASSED       [ 15%]
312s bamfilter_test.py::TestBamfilter::test_exclude_region PASSED             [ 16%]
312s bamfilter_test.py::TestBamfilter::test_get_all_unmapped_reads PASSED     [ 17%]
312s bamfilter_test.py::TestBamfilter::test_get_contigs_to_use PASSED         [ 18%]
312s bamfilter_test.py::TestBamfilter::test_get_ref_lengths PASSED            [ 19%]
312s bamfilter_test.py::TestBamfilter::test_get_region_end PASSED             [ 20%]
312s bamfilter_test.py::TestBamfilter::test_get_region_start PASSED           [ 21%]
312s bamfilter_test.py::TestBamfilter::test_run_discard_unmapped_no_quals PASSED [ 22%]
312s bamfilter_test.py::TestBamfilter::test_run_keep_unmapped_no_quals PASSED [ 23%]
312s bamfilter_test.py::TestBamfilter::test_run_keep_unmapped_with_quals PASSED [ 23%]
312s clean_test.py::TestClean::test_clean_contigs PASSED                      [ 24%]
312s clean_test.py::TestClean::test_collapse_list_of_sets PASSED              [ 25%]
312s clean_test.py::TestClean::test_containing_contigs PASSED                 [ 26%]
312s clean_test.py::TestClean::test_contains PASSED                           [ 27%]
312s clean_test.py::TestClean::test_expand_containing_using_transitivity PASSED [ 28%]
312s clean_test.py::TestClean::test_get_all_containing PASSED                 [ 29%]
312s clean_test.py::TestClean::test_get_containing_contigs PASSED             [ 30%]
312s clean_test.py::TestClean::test_get_contigs_to_keep PASSED                [ 30%]
312s clean_test.py::TestClean::test_get_identical_contigs PASSED              [ 31%]
312s clean_test.py::TestClean::test_infinite_recursion PASSED                 [ 32%]
312s clean_test.py::TestClean::test_load_nucmer_hits PASSED                   [ 33%]
312s clean_test.py::TestClean::test_longest_contig PASSED                     [ 34%]
312s clean_test.py::TestClean::test_remove_identical_contigs PASSED           [ 35%]
312s clean_test.py::TestClean::test_remove_small_contigs PASSED               [ 36%]
312s clean_test.py::TestClean::test_write_log PASSED                          [ 37%]
312s common_test.py::TestCommon::test_check_files_exist PASSED                [ 38%]
312s dnaa_test.py::TestDnaa::test_append_stop_to_seq PASSED                   [ 38%]
312s dnaa_test.py::TestDnaa::test_check_sequence PASSED                       [ 39%]
312s dnaa_test.py::TestDnaa::test_get_uniprot_url PASSED                      [ 40%]
312s dnaa_test.py::TestDnaa::test_header_matches_regex PASSED                 [ 41%]
312s dnaa_test.py::TestDnaa::test_header_to_genus_species PASSED              [ 42%]
312s dnaa_test.py::TestDnaa::test_reverse_translate PASSED                    [ 43%]
312s external_progs_test.py::TestExternalProgs::test_bwa_version PASSED       [ 44%]
312s external_progs_test.py::TestExternalProgs::test_canu_version PASSED      [ 45%]
312s external_progs_test.py::TestExternalProgs::test_nucmer_version PASSED    [ 46%]
312s external_progs_test.py::TestExternalProgs::test_prodigal_version PASSED  [ 46%]
312s external_progs_test.py::TestExternalProgs::test_samtools_original_version PASSED [ 47%]
312s external_progs_test.py::TestExternalProgs::test_samtools_version PASSED  [ 48%]
312s external_progs_test.py::TestExternalProgs::test_spades_version PASSED    [ 49%]
312s mapping_test.py::TestMapping::test_aligned_read_to_read PASSED           [ 50%]
313s mapping_test.py::TestMapping::test_bwa_index PASSED                      [ 51%]
313s mapping_test.py::TestMapping::test_bwa_index_clean PASSED                [ 52%]
313s mapping_test.py::TestMapping::test_bwa_mem PASSED                        [ 53%]
313s merge_test.py::TestMerge::test_can_circularise PASSED                    [ 53%]
313s merge_test.py::TestMerge::test_contigs_dict_to_file PASSED               [ 54%]
313s merge_test.py::TestMerge::test_filter_bridging_contigs PASSED            [ 55%]
313s merge_test.py::TestMerge::test_get_hit_nearest_ref_end PASSED            [ 56%]
313s merge_test.py::TestMerge::test_get_hit_nearest_ref_start PASSED          [ 57%]
313s merge_test.py::TestMerge::test_get_longest_hit_at_qry_end PASSED         [ 58%]
313s merge_test.py::TestMerge::test_get_longest_hit_at_qry_start PASSED       [ 59%]
313s merge_test.py::TestMerge::test_get_longest_hit_at_ref_end PASSED         [ 60%]
313s merge_test.py::TestMerge::test_get_longest_hit_at_ref_start PASSED       [ 61%]
313s merge_test.py::TestMerge::test_get_longest_hit_by_ref_length PASSED      [ 61%]
313s merge_test.py::TestMerge::test_get_possible_circular_ref_contigs PASSED  [ 62%]
313s merge_test.py::TestMerge::test_get_possible_circular_ref_contigs_same_best_hits PASSED [ 63%]
313s merge_test.py::TestMerge::test_get_possible_query_bridging_contigs PASSED [ 64%]
313s merge_test.py::TestMerge::test_get_spades_circular_nodes PASSED          [ 65%]
313s merge_test.py::TestMerge::test_has_qry_hit_longer_than PASSED            [ 66%]
313s merge_test.py::TestMerge::test_hits_hashed_by_query PASSED               [ 67%]
313s merge_test.py::TestMerge::test_hits_have_same_query PASSED               [ 68%]
313s merge_test.py::TestMerge::test_hits_have_same_reference PASSED           [ 69%]
313s merge_test.py::TestMerge::test_index_fasta PASSED                        [ 69%]
313s merge_test.py::TestMerge::test_is_at_qry_end PASSED                      [ 70%]
313s merge_test.py::TestMerge::test_is_at_qry_start PASSED                    [ 71%]
313s merge_test.py::TestMerge::test_is_at_ref_end PASSED                      [ 72%]
313s merge_test.py::TestMerge::test_is_at_ref_start PASSED                    [ 73%]
313s merge_test.py::TestMerge::test_load_nucmer_hits PASSED                   [ 74%]
313s merge_test.py::TestMerge::test_make_circularised_contig_1 PASSED         [ 75%]
313s merge_test.py::TestMerge::test_make_circularised_contig_2 PASSED         [ 76%]
313s merge_test.py::TestMerge::test_make_new_contig_from_nucmer_and_spades_not_hit PASSED [ 76%]
313s merge_test.py::TestMerge::test_make_new_contig_from_nucmer_and_spades_with_hit PASSED [ 77%]
313s merge_test.py::TestMerge::test_merge_bridged_contig_pair1 PASSED         [ 78%]
313s merge_test.py::TestMerge::test_merge_bridged_contig_pair2 PASSED         [ 79%]
313s merge_test.py::TestMerge::test_merge_bridged_contig_pair3 PASSED         [ 80%]
313s merge_test.py::TestMerge::test_merge_bridged_contig_pair4 PASSED         [ 81%]
313s merge_test.py::TestMerge::test_min_qry_hit_length PASSED                 [ 82%]
313s merge_test.py::TestMerge::test_orientation_ok_to_bridge_contigs PASSED   [ 83%]
313s merge_test.py::TestMerge::test_remove_keys_from_dict_with_nonunique_values PASSED [ 84%]
313s merge_test.py::TestMerge::test_write_act_files PASSED                    [ 84%]
313s minimus2_test.py::TestMinimus2::test_run_initial_merge SKIPPED (Amos...) [ 85%]
313s minimus2_test.py::TestMinimus2::test_run_minimus2 SKIPPED (Amos is n...) [ 86%]
313s minimus2_test.py::TestMinimus2::test_run_minimus2_on_each_contig SKIPPED [ 87%]
313s minimus2_test.py::TestMinimus2::test_run_minimus2_on_one_contig_will_not_work SKIPPED [ 88%]
313s minimus2_test.py::TestMinimus2::test_run_minimus2_on_one_contig_will_work SKIPPED [ 89%]
313s minimus2_test.py::TestMinimus2::test_write_split_contig SKIPPED (Amo...) [ 90%]
313s start_fixer_test.py::TestStartFixer::test_find_circular_using_prodigal PASSED [ 91%]
313s start_fixer_test.py::TestStartFixer::test_find_circular_using_promer PASSED [ 92%]
313s start_fixer_test.py::TestStartFixer::test_init PASSED                    [ 92%]
313s start_fixer_test.py::TestStartFixer::test_max_length_from_fasta_file PASSED [ 93%]
313s start_fixer_test.py::TestStartFixer::test_rearrange_contigs PASSED       [ 94%]
313s start_fixer_test.py::TestStartFixer::test_rename_contigs PASSED          [ 95%]
314s start_fixer_test.py::TestStartFixer::test_run_bit_of_everything PASSED   [ 96%]
314s start_fixer_test.py::TestStartFixer::test_run_ignore_all PASSED          [ 97%]
314s start_fixer_test.py::TestStartFixer::test_run_none_for_prodigal PASSED   [ 98%]
314s start_fixer_test.py::TestStartFixer::test_write_fasta_plus_circularized_ends PASSED [ 99%]
314s start_fixer_test.py::TestStartFixer::test_write_renamed_contigs PASSED   [100%]
314s 
314s =============================== warnings summary ===============================
314s ../../../usr/lib/python3/dist-packages/pyfastaq/__init__.py:3
314s   /usr/lib/python3/dist-packages/pyfastaq/__init__.py:3: DeprecationWarning: Unimplemented abstract methods {'read_text', 'locate_file'}
314s     __version__ = Distribution().from_name('pyfastaq').version
314s 
314s ../../../usr/lib/python3/dist-packages/circlator/__init__.py:1
314s   /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
314s     from pkg_resources import get_distribution
314s 
314s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
314s =========== 107 passed, 6 skipped, 2 deselected, 2 warnings in 1.96s ===========
314s + for py in $(py3versions --supported 2> /dev/null)
314s + eval dpkg-architecture --is amd64
314s ++ dpkg-architecture --is amd64
314s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation)
314s + python3.13 -m pytest -v -k 'not (test_build_spades_kmers or test_make_spades_command)'
314s ============================= test session starts ==============================
314s platform linux -- Python 3.13.2, pytest-8.3.4, pluggy-1.5.0 -- /usr/bin/python3.13
314s cachedir: .pytest_cache
314s rootdir: /tmp/autopkgtest.QtcAtU/autopkgtest_tmp
314s plugins: typeguard-4.4.1
315s collecting ... collected 115 items / 2 deselected / 113 selected
315s 
315s assemble_test.py::TestAssembleCanu::test_make_canu_command PASSED        [  0%]
315s assemble_test.py::TestAssembleCanu::test_rename_canu_contigs PASSED      [  1%]
315s assembly_test.py::TestAssembly::test_circular_contigs_from_canu_gfa PASSED [  2%]
315s assembly_test.py::TestAssembly::test_circular_contigs_from_spades_after_3_6_1 PASSED [  3%]
315s assembly_test.py::TestAssembly::test_circular_contigs_from_spades_before_3_6_1 PASSED [  4%]
315s assembly_test.py::TestAssembly::test_circular_contigs_just_fasta PASSED  [  5%]
315s assembly_test.py::TestAssembly::test_circular_contigs_spades_post_3_6_1 PASSED [  6%]
315s assembly_test.py::TestAssembly::test_circular_contigs_spades_pre_3_6_1 PASSED [  7%]
315s assembly_test.py::TestAssembly::test_circular_edges_to_edge_numbers_dict PASSED [  7%]
315s assembly_test.py::TestAssembly::test_get_contigs PASSED                  [  8%]
315s assembly_test.py::TestAssembly::test_init_file_not_dir PASSED            [  9%]
315s assembly_test.py::TestAssembly::test_init_post_3_6_1_ok PASSED           [ 10%]
315s assembly_test.py::TestAssembly::test_init_pre_3_6_1_ok PASSED            [ 11%]
315s assembly_test.py::TestAssembly::test_init_raises_error PASSED            [ 12%]
315s assembly_test.py::TestAssembly::test_spades_contigs_paths_to_dict PASSED [ 13%]
315s bamfilter_test.py::TestBamfilter::test_all_reads_from_contig PASSED      [ 14%]
315s bamfilter_test.py::TestBamfilter::test_break_reads PASSED                [ 15%]
315s bamfilter_test.py::TestBamfilter::test_check_contigs_to_use PASSED       [ 15%]
315s bamfilter_test.py::TestBamfilter::test_exclude_region PASSED             [ 16%]
315s bamfilter_test.py::TestBamfilter::test_get_all_unmapped_reads PASSED     [ 17%]
315s bamfilter_test.py::TestBamfilter::test_get_contigs_to_use PASSED         [ 18%]
315s bamfilter_test.py::TestBamfilter::test_get_ref_lengths PASSED            [ 19%]
315s bamfilter_test.py::TestBamfilter::test_get_region_end PASSED             [ 20%]
315s bamfilter_test.py::TestBamfilter::test_get_region_start PASSED           [ 21%]
315s bamfilter_test.py::TestBamfilter::test_run_discard_unmapped_no_quals PASSED [ 22%]
315s bamfilter_test.py::TestBamfilter::test_run_keep_unmapped_no_quals PASSED [ 23%]
315s bamfilter_test.py::TestBamfilter::test_run_keep_unmapped_with_quals PASSED [ 23%]
315s clean_test.py::TestClean::test_clean_contigs PASSED                      [ 24%]
315s clean_test.py::TestClean::test_collapse_list_of_sets PASSED              [ 25%]
315s clean_test.py::TestClean::test_containing_contigs PASSED                 [ 26%]
315s clean_test.py::TestClean::test_contains PASSED                           [ 27%]
315s clean_test.py::TestClean::test_expand_containing_using_transitivity PASSED [ 28%]
315s clean_test.py::TestClean::test_get_all_containing PASSED                 [ 29%]
315s clean_test.py::TestClean::test_get_containing_contigs PASSED             [ 30%]
315s clean_test.py::TestClean::test_get_contigs_to_keep PASSED                [ 30%]
315s clean_test.py::TestClean::test_get_identical_contigs PASSED              [ 31%]
315s clean_test.py::TestClean::test_infinite_recursion PASSED                 [ 32%]
315s clean_test.py::TestClean::test_load_nucmer_hits PASSED                   [ 33%]
315s clean_test.py::TestClean::test_longest_contig PASSED                     [ 34%]
315s clean_test.py::TestClean::test_remove_identical_contigs PASSED           [ 35%]
315s clean_test.py::TestClean::test_remove_small_contigs PASSED               [ 36%]
315s clean_test.py::TestClean::test_write_log PASSED                          [ 37%]
315s common_test.py::TestCommon::test_check_files_exist PASSED                [ 38%]
315s dnaa_test.py::TestDnaa::test_append_stop_to_seq PASSED                   [ 38%]
315s dnaa_test.py::TestDnaa::test_check_sequence PASSED                       [ 39%]
315s dnaa_test.py::TestDnaa::test_get_uniprot_url PASSED                      [ 40%]
315s dnaa_test.py::TestDnaa::test_header_matches_regex PASSED                 [ 41%]
315s dnaa_test.py::TestDnaa::test_header_to_genus_species PASSED              [ 42%]
315s dnaa_test.py::TestDnaa::test_reverse_translate PASSED                    [ 43%]
315s external_progs_test.py::TestExternalProgs::test_bwa_version PASSED       [ 44%]
315s external_progs_test.py::TestExternalProgs::test_canu_version PASSED      [ 45%]
315s external_progs_test.py::TestExternalProgs::test_nucmer_version PASSED    [ 46%]
315s external_progs_test.py::TestExternalProgs::test_prodigal_version PASSED  [ 46%]
315s external_progs_test.py::TestExternalProgs::test_samtools_original_version PASSED [ 47%]
315s external_progs_test.py::TestExternalProgs::test_samtools_version PASSED  [ 48%]
315s external_progs_test.py::TestExternalProgs::test_spades_version PASSED    [ 49%]
315s mapping_test.py::TestMapping::test_aligned_read_to_read PASSED           [ 50%]
315s mapping_test.py::TestMapping::test_bwa_index PASSED                      [ 51%]
315s mapping_test.py::TestMapping::test_bwa_index_clean PASSED                [ 52%]
315s mapping_test.py::TestMapping::test_bwa_mem PASSED                        [ 53%]
315s merge_test.py::TestMerge::test_can_circularise PASSED                    [ 53%]
315s merge_test.py::TestMerge::test_contigs_dict_to_file PASSED               [ 54%]
315s merge_test.py::TestMerge::test_filter_bridging_contigs PASSED            [ 55%]
315s merge_test.py::TestMerge::test_get_hit_nearest_ref_end PASSED            [ 56%]
315s merge_test.py::TestMerge::test_get_hit_nearest_ref_start PASSED          [ 57%]
315s merge_test.py::TestMerge::test_get_longest_hit_at_qry_end PASSED         [ 58%]
315s merge_test.py::TestMerge::test_get_longest_hit_at_qry_start PASSED       [ 59%]
315s merge_test.py::TestMerge::test_get_longest_hit_at_ref_end PASSED         [ 60%]
315s merge_test.py::TestMerge::test_get_longest_hit_at_ref_start PASSED       [ 61%]
315s merge_test.py::TestMerge::test_get_longest_hit_by_ref_length PASSED      [ 61%]
315s merge_test.py::TestMerge::test_get_possible_circular_ref_contigs PASSED  [ 62%]
315s merge_test.py::TestMerge::test_get_possible_circular_ref_contigs_same_best_hits PASSED [ 63%]
315s merge_test.py::TestMerge::test_get_possible_query_bridging_contigs PASSED [ 64%]
315s merge_test.py::TestMerge::test_get_spades_circular_nodes PASSED          [ 65%]
315s merge_test.py::TestMerge::test_has_qry_hit_longer_than PASSED            [ 66%]
315s merge_test.py::TestMerge::test_hits_hashed_by_query PASSED               [ 67%]
315s merge_test.py::TestMerge::test_hits_have_same_query PASSED               [ 68%]
315s merge_test.py::TestMerge::test_hits_have_same_reference PASSED           [ 69%]
315s merge_test.py::TestMerge::test_index_fasta PASSED                        [ 69%]
315s merge_test.py::TestMerge::test_is_at_qry_end PASSED                      [ 70%]
315s merge_test.py::TestMerge::test_is_at_qry_start PASSED                    [ 71%]
315s merge_test.py::TestMerge::test_is_at_ref_end PASSED                      [ 72%]
315s merge_test.py::TestMerge::test_is_at_ref_start PASSED                    [ 73%]
315s merge_test.py::TestMerge::test_load_nucmer_hits PASSED                   [ 74%]
315s merge_test.py::TestMerge::test_make_circularised_contig_1 PASSED         [ 75%]
315s merge_test.py::TestMerge::test_make_circularised_contig_2 PASSED         [ 76%]
315s merge_test.py::TestMerge::test_make_new_contig_from_nucmer_and_spades_not_hit PASSED [ 76%]
315s merge_test.py::TestMerge::test_make_new_contig_from_nucmer_and_spades_with_hit PASSED [ 77%]
315s merge_test.py::TestMerge::test_merge_bridged_contig_pair1 PASSED         [ 78%]
315s merge_test.py::TestMerge::test_merge_bridged_contig_pair2 PASSED         [ 79%]
315s merge_test.py::TestMerge::test_merge_bridged_contig_pair3 PASSED         [ 80%]
315s merge_test.py::TestMerge::test_merge_bridged_contig_pair4 PASSED         [ 81%]
315s merge_test.py::TestMerge::test_min_qry_hit_length PASSED                 [ 82%]
315s merge_test.py::TestMerge::test_orientation_ok_to_bridge_contigs PASSED   [ 83%]
315s merge_test.py::TestMerge::test_remove_keys_from_dict_with_nonunique_values PASSED [ 84%]
315s merge_test.py::TestMerge::test_write_act_files PASSED                    [ 84%]
315s minimus2_test.py::TestMinimus2::test_run_initial_merge SKIPPED (Amos...) [ 85%]
315s minimus2_test.py::TestMinimus2::test_run_minimus2 SKIPPED (Amos is n...) [ 86%]
315s minimus2_test.py::TestMinimus2::test_run_minimus2_on_each_contig SKIPPED [ 87%]
315s minimus2_test.py::TestMinimus2::test_run_minimus2_on_one_contig_will_not_work SKIPPED [ 88%]
315s minimus2_test.py::TestMinimus2::test_run_minimus2_on_one_contig_will_work SKIPPED [ 89%]
315s minimus2_test.py::TestMinimus2::test_write_split_contig SKIPPED (Amo...) [ 90%]
315s start_fixer_test.py::TestStartFixer::test_find_circular_using_prodigal PASSED [ 91%]
315s start_fixer_test.py::TestStartFixer::test_find_circular_using_promer PASSED [ 92%]
315s start_fixer_test.py::TestStartFixer::test_init PASSED                    [ 92%]
315s start_fixer_test.py::TestStartFixer::test_max_length_from_fasta_file PASSED [ 93%]
315s start_fixer_test.py::TestStartFixer::test_rearrange_contigs PASSED       [ 94%]
315s start_fixer_test.py::TestStartFixer::test_rename_contigs PASSED          [ 95%]
316s start_fixer_test.py::TestStartFixer::test_run_bit_of_everything PASSED   [ 96%]
316s start_fixer_test.py::TestStartFixer::test_run_ignore_all PASSED          [ 97%]
316s start_fixer_test.py::TestStartFixer::test_run_none_for_prodigal PASSED   [ 98%]
316s start_fixer_test.py::TestStartFixer::test_write_fasta_plus_circularized_ends PASSED [ 99%]
316s start_fixer_test.py::TestStartFixer::test_write_renamed_contigs PASSED   [100%]
316s 
316s =============================== warnings summary ===============================
316s ../../../usr/lib/python3/dist-packages/pyfastaq/__init__.py:3
316s   /usr/lib/python3/dist-packages/pyfastaq/__init__.py:3: DeprecationWarning: Unimplemented abstract methods {'read_text', 'locate_file'}
316s     __version__ = Distribution().from_name('pyfastaq').version
316s 
316s ../../../usr/lib/python3/dist-packages/circlator/__init__.py:1
316s   /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
316s     from pkg_resources import get_distribution
316s 
316s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
316s =========== 107 passed, 6 skipped, 2 deselected, 2 warnings in 1.42s ===========
316s autopkgtest [02:39:54]: test run-unit-test: -----------------------]
317s run-unit-test        PASS
317s autopkgtest [02:39:55]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
317s autopkgtest [02:39:55]: @@@@@@@@@@@@@@@@@@@@ summary
317s run-unit-test        PASS
346s nova [W] Using flock in prodstack6-arm64
346s Creating nova instance adt-plucky-arm64-circlator-20250217-023438-juju-7f2275-prod-proposed-migration-environment-15-3265e022-8a0e-4dce-8442-ae47eb77294c from image adt/ubuntu-plucky-arm64-server-20250216.img (UUID a098a761-c895-418e-827f-00d410a1ece9)...
346s nova [W] Timed out waiting for 8b3d02c1-2b19-4f85-aeb0-9538526538b7 to get deleted.