0s autopkgtest [02:29:53]: starting date and time: 2025-02-17 02:29:53+0000
  0s autopkgtest [02:29:53]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production'
  0s autopkgtest [02:29:53]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work._3gzm_d4/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 builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-25.secgroup --name adt-plucky-amd64-circlator-20250217-022953-juju-7f2275-prod-proposed-migration-environment-15-fb1e1401-acc0-46a5-957b-861d355aa6a4 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
 67s autopkgtest [02:31:00]: testbed dpkg architecture: amd64
 68s autopkgtest [02:31:01]: testbed apt version: 2.9.28
 68s autopkgtest [02:31:01]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 68s autopkgtest [02:31:01]: testbed release detected to be: None
 69s autopkgtest [02:31:02]: updating testbed package index (apt update)
 69s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB]
 70s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
 70s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
 70s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
 70s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.9 kB]
 70s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B]
 70s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [698 kB]
 70s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [61.5 kB]
 70s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [80.7 kB]
 70s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [62.3 kB]
 70s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2412 B]
 70s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [7984 B]
 70s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [614 kB]
 70s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [233 kB]
 70s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [11.3 kB]
 70s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [3512 B]
 71s Fetched 1902 kB in 1s (1584 kB/s)
 72s Reading package lists...
 72s + lsb_release --codename --short
 72s + RELEASE=plucky
 72s + cat
 72s + [ plucky != trusty ]
 72s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade
 72s Reading package lists...
 73s Building dependency tree...
 73s Reading state information...
 73s Calculating upgrade...
 73s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 73s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref
 73s + /usr/lib/apt/apt-helper analyze-pattern ?true
 73s + + uname -r
 73s sed s/\./\\./g
 73s + running_kernel_pattern=^linux-.*6\.12\.0-15-generic.*
 73s + apt list ?obsolete
 73s + tail -n+2
 73s + cut -d/ -f1
 73s + grep -v ^linux-.*6\.12\.0-15-generic.*
 74s + true
 74s + obsolete_pkgs=
 74s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove
 74s Reading package lists...
 74s Building dependency tree...
 74s Reading state information...
 74s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 74s + grep -q trusty /etc/lsb-release
 74s + [ ! -d /usr/share/doc/unattended-upgrades ]
 74s + [ ! -d /usr/share/doc/lxd ]
 74s + [ ! -d /usr/share/doc/lxd-client ]
 74s + [ ! -d /usr/share/doc/snapd ]
 74s + type iptables
 74s + cat
 74s + chmod 755 /etc/rc.local
 74s + . /etc/rc.local
 74s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu
 74s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP
 74s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP
 74s + uname -m
 74s + [ x86_64 = ppc64le ]
 74s + [ -d /run/systemd/system ]
 74s + systemd-detect-virt --quiet --vm
 74s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/
 74s + cat
 74s + grep -q lz4 /etc/initramfs-tools/initramfs.conf
 74s + echo COMPRESS=lz4
 74s autopkgtest [02:31:07]: upgrading testbed (apt dist-upgrade and autopurge)
 74s Reading package lists...
 75s Building dependency tree...
 75s Reading state information...
 75s Calculating upgrade...Starting pkgProblemResolver with broken count: 0
 75s Starting 2 pkgProblemResolver with broken count: 0
 75s Done
 76s Entering ResolveByKeep
 76s 
 77s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 77s Reading package lists...
 77s Building dependency tree...
 77s Reading state information...
 78s Starting pkgProblemResolver with broken count: 0
 78s Starting 2 pkgProblemResolver with broken count: 0
 78s Done
 78s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 81s autopkgtest [02:31:14]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb  4 16:02:16 UTC 2025
 81s autopkgtest [02:31:14]: @@@@@@@@@@@@@@@@@@@@ apt-source circlator
 85s Get:1 http://ftpmaster.internal/ubuntu plucky/universe circlator 1.5.6-12 (dsc) [2302 B]
 85s Get:2 http://ftpmaster.internal/ubuntu plucky/universe circlator 1.5.6-12 (tar) [5724 kB]
 85s Get:3 http://ftpmaster.internal/ubuntu plucky/universe circlator 1.5.6-12 (diff) [6412 B]
 85s gpgv: Signature made Fri Dec  6 09:53:32 2024 UTC
 85s gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
 85s gpgv:                issuer "tille@debian.org"
 85s gpgv: Can't check signature: No public key
 85s dpkg-source: warning: cannot verify inline signature for ./circlator_1.5.6-12.dsc: no acceptable signature found
 85s autopkgtest [02:31:18]: testing package circlator version 1.5.6-12
 85s autopkgtest [02:31:18]: build not needed
 86s autopkgtest [02:31:19]: test run-unit-test: preparing testbed
 86s Reading package lists...
 87s Building dependency tree...
 87s Reading state information...
 87s Starting pkgProblemResolver with broken count: 0
 87s Starting 2 pkgProblemResolver with broken count: 0
 87s Done
 88s The following NEW packages will be installed:
 88s   aglfn bamtools binfmt-support bwa ca-certificates-java canu circlator
 88s   default-jre-headless fastaq fastjar fontconfig fontconfig-config
 88s   fonts-dejavu-core fonts-dejavu-mono gnuplot-data gnuplot-nox jaligner
 88s   jarwrapper java-common libaom3 libapache-pom-java
 88s   libatinject-jsr330-api-java libbamtools2.5.2 libcairo2 libcommons-codec-java
 88s   libcommons-compress-java libcommons-io-java libcommons-parent-java
 88s   libdatrie1 libde265-0 libdeflate0 liberror-prone-java libfastutil-java
 88s   libfilesys-df-perl libfontconfig1 libgd3 libgomp1 libgraphite2-3
 88s   libguava-java libharfbuzz0b libheif-plugin-aomdec libheif-plugin-libde265
 88s   libheif1 libhts3t64 libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8
 88s   libjpeg8 libjsoncpp26 libjsr305-java liblcms2-2 liblerc4 liblua5.4-0
 88s   libnlopt0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpcsclite1
 88s   libpixman-1-0 libraqm0 libsharpyuv0 libsnappy1v5 libspoa7.0.0 libssw-java
 88s   libssw0 libthai-data libthai0 libtiff6 libwebp7 libwebpmux3 libxcb-render0
 88s   libxcb-shm0 libxpm4 libxrender1 libxslt1.1 mhap mummer
 88s   openjdk-21-jre-headless prodigal python3-all python3-et-xmlfile
 88s   python3-iniconfig python3-joblib python3-lxml python3-openpyxl
 88s   python3-packaging python3-pluggy python3-pymummer python3-pysam
 88s   python3-pytest python3.12 python3.12-minimal samtools spades
 88s 0 upgraded, 95 newly installed, 0 to remove and 0 not upgraded.
 88s Need to get 110 MB of archives.
 88s After this operation, 424 MB of additional disk space will be used.
 88s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-minimal amd64 3.12.9-1 [2348 kB]
 89s Get:2 http://ftpmaster.internal/ubuntu plucky/universe amd64 binfmt-support amd64 2.2.2-7 [56.2 kB]
 89s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12 amd64 3.12.9-1 [671 kB]
 89s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 libbamtools2.5.2 amd64 2.5.2+dfsg-6build1 [144 kB]
 89s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libjsoncpp26 amd64 1.9.6-3 [90.0 kB]
 89s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 bamtools amd64 2.5.2+dfsg-6build1 [178 kB]
 90s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 bwa amd64 0.7.18-1 [204 kB]
 90s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 ca-certificates-java all 20240118 [11.6 kB]
 90s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250213-1ubuntu1 [148 kB]
 90s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libsnappy1v5 amd64 1.2.1-1 [30.4 kB]
 90s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libfilesys-df-perl amd64 0.92-7build5 [11.4 kB]
 90s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 java-common all 0.76 [6852 B]
 90s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB]
 90s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB]
 90s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B]
 90s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcsclite1 amd64 2.3.1-1 [26.6 kB]
 90s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 openjdk-21-jre-headless amd64 21.0.6+7-1 [46.4 MB]
110s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 default-jre-headless amd64 2:1.21-76 [3178 B]
110s Get:19 http://ftpmaster.internal/ubuntu plucky/universe amd64 fastjar amd64 2:0.98-7 [67.1 kB]
110s Get:20 http://ftpmaster.internal/ubuntu plucky/universe amd64 jarwrapper all 0.80 [9800 B]
110s Get:21 http://ftpmaster.internal/ubuntu plucky/universe amd64 libapache-pom-java all 33-2 [5874 B]
110s Get:22 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-parent-java all 56-1 [10.7 kB]
110s Get:23 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-codec-java all 1.17.1-1 [302 kB]
110s Get:24 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-io-java all 2.18.0-1 [477 kB]
110s Get:25 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-compress-java all 1.27.1-2 [610 kB]
110s Get:26 http://ftpmaster.internal/ubuntu plucky/universe amd64 libfastutil-java all 8.5.15+dfsg-1 [20.2 MB]
118s Get:27 http://ftpmaster.internal/ubuntu plucky/universe amd64 libatinject-jsr330-api-java all 1.0+ds1-6 [5076 B]
118s Get:28 http://ftpmaster.internal/ubuntu plucky/universe amd64 liberror-prone-java all 2.18.0-1 [22.5 kB]
118s Get:29 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjsr305-java all 0.1~+svn49-12 [27.0 kB]
118s Get:30 http://ftpmaster.internal/ubuntu plucky/universe amd64 libguava-java all 32.0.1-1 [2692 kB]
121s Get:31 http://ftpmaster.internal/ubuntu plucky/universe amd64 jaligner all 1.0+dfsg-11 [136 kB]
121s Get:32 http://ftpmaster.internal/ubuntu plucky/universe amd64 libssw-java amd64 1.1-15 [18.9 kB]
121s Get:33 http://ftpmaster.internal/ubuntu plucky/universe amd64 mhap all 2.1.3+dfsg-3 [160 kB]
121s Get:34 http://ftpmaster.internal/ubuntu plucky/universe amd64 aglfn all 1.7+git20191031.4036a9c-2 [30.6 kB]
121s Get:35 http://ftpmaster.internal/ubuntu plucky/universe amd64 gnuplot-data all 6.0.0+dfsg1-1ubuntu3 [75.3 kB]
121s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB]
122s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB]
122s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB]
123s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB]
123s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB]
123s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB]
123s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B]
123s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB]
123s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB]
124s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB]
124s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libaom3 amd64 3.12.0-1 [2742 kB]
126s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libheif-plugin-aomdec amd64 1.19.5-1build1 [11.6 kB]
126s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libde265-0 amd64 1.0.15-1build4 [168 kB]
126s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libheif-plugin-libde265 amd64 1.19.5-1build1 [9074 B]
126s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libheif1 amd64 1.19.5-1build1 [422 kB]
126s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB]
126s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB]
126s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB]
127s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.2-1 [17.2 kB]
127s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB]
127s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB]
127s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB]
127s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB]
128s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB]
128s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libxpm4 amd64 1:3.5.17-1build2 [36.5 kB]
128s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libgd3 amd64 2.3.3-12ubuntu3 [127 kB]
128s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 liblua5.4-0 amd64 5.4.7-1 [196 kB]
128s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-1.1ubuntu2 [180 kB]
129s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB]
129s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB]
129s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB]
129s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.56.1-1 [255 kB]
129s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.56.1-1 [52.6 kB]
129s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.56.1-1 [29.1 kB]
129s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB]
130s Get:71 http://ftpmaster.internal/ubuntu plucky/universe amd64 gnuplot-nox amd64 6.0.0+dfsg1-1ubuntu3 [989 kB]
131s Get:72 http://ftpmaster.internal/ubuntu plucky/universe amd64 canu amd64 2.2+dfsg-5 [1536 kB]
132s Get:73 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-1 [132 kB]
132s Get:74 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.21+ds-1 [514 kB]
133s Get:75 http://ftpmaster.internal/ubuntu plucky/universe amd64 samtools amd64 1.21-1 [655 kB]
133s Get:76 http://ftpmaster.internal/ubuntu plucky/universe amd64 fastaq all 3.17.0-9 [48.2 kB]
133s Get:77 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-et-xmlfile all 2.0.0-1 [79.4 kB]
134s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu2 [175 kB]
134s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.1-1 [1831 kB]
135s Get:80 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-openpyxl all 3.1.5+dfsg-1 [152 kB]
135s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.2-1 [51.5 kB]
136s Get:82 http://ftpmaster.internal/ubuntu plucky/universe amd64 mummer amd64 3.23+dfsg-8 [685 kB]
136s Get:83 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pymummer all 0.11.0-4 [17.1 kB]
136s Get:84 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pysam amd64 0.23.0+ds-1 [4558 kB]
140s Get:85 http://ftpmaster.internal/ubuntu plucky/universe amd64 prodigal amd64 1:2.6.3-6 [643 kB]
140s Get:86 http://ftpmaster.internal/ubuntu plucky/universe amd64 circlator all 1.5.6-12 [4617 kB]
144s Get:87 http://ftpmaster.internal/ubuntu plucky/universe amd64 libspoa7.0.0 amd64 4.1.4-2 [79.1 kB]
144s Get:88 http://ftpmaster.internal/ubuntu plucky/universe amd64 libssw0 amd64 1.1-15 [22.5 kB]
144s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all amd64 3.13.1-1~exp2 [894 B]
144s Get:90 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B]
144s Get:91 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-joblib all 1.4.2-2 [205 kB]
144s Get:92 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB]
144s Get:93 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.4-1 [252 kB]
145s Get:94 http://ftpmaster.internal/ubuntu plucky/universe amd64 libnlopt0 amd64 2.7.1-6ubuntu2 [251 kB]
145s Get:95 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 spades amd64 4.0.0+dfsg1-2 [8064 kB]
151s Fetched 110 MB in 1min 3s (1757 kB/s)
151s Selecting previously unselected package python3.12-minimal.
151s (Reading database ... 
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(Reading database ... 108919 files and directories currently installed.)
151s Preparing to unpack .../00-python3.12-minimal_3.12.9-1_amd64.deb ...
151s Unpacking python3.12-minimal (3.12.9-1) ...
151s Selecting previously unselected package binfmt-support.
151s Preparing to unpack .../01-binfmt-support_2.2.2-7_amd64.deb ...
151s Unpacking binfmt-support (2.2.2-7) ...
151s Selecting previously unselected package python3.12.
151s Preparing to unpack .../02-python3.12_3.12.9-1_amd64.deb ...
151s Unpacking python3.12 (3.12.9-1) ...
151s Selecting previously unselected package libbamtools2.5.2:amd64.
151s Preparing to unpack .../03-libbamtools2.5.2_2.5.2+dfsg-6build1_amd64.deb ...
151s Unpacking libbamtools2.5.2:amd64 (2.5.2+dfsg-6build1) ...
151s Selecting previously unselected package libjsoncpp26:amd64.
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151s Selecting previously unselected package bamtools.
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151s Selecting previously unselected package bwa.
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151s Selecting previously unselected package libfilesys-df-perl.
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151s Selecting previously unselected package libjpeg-turbo8:amd64.
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152s Selecting previously unselected package libpcsclite1:amd64.
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152s Unpacking libpcsclite1:amd64 (2.3.1-1) ...
152s Selecting previously unselected package openjdk-21-jre-headless:amd64.
152s Preparing to unpack .../16-openjdk-21-jre-headless_21.0.6+7-1_amd64.deb ...
152s Unpacking openjdk-21-jre-headless:amd64 (21.0.6+7-1) ...
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153s Selecting previously unselected package libatinject-jsr330-api-java.
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153s Selecting previously unselected package libjsr305-java.
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153s Selecting previously unselected package libguava-java.
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153s Selecting previously unselected package libssw-java.
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154s Selecting previously unselected package libfontconfig1:amd64.
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154s Selecting previously unselected package libpixman-1-0:amd64.
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154s Selecting previously unselected package libxcb-render0:amd64.
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154s Selecting previously unselected package libxcb-shm0:amd64.
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154s Selecting previously unselected package libxrender1:amd64.
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154s Selecting previously unselected package libcairo2:amd64.
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154s Unpacking libcairo2:amd64 (1.18.2-2) ...
154s Selecting previously unselected package libsharpyuv0:amd64.
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154s Selecting previously unselected package libaom3:amd64.
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154s Selecting previously unselected package libheif-plugin-aomdec:amd64.
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154s Selecting previously unselected package libheif-plugin-libde265:amd64.
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154s Selecting previously unselected package libheif1:amd64.
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154s Selecting previously unselected package libimagequant0:amd64.
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154s Selecting previously unselected package libgraphite2-3:amd64.
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154s Selecting previously unselected package libharfbuzz0b:amd64.
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154s Selecting previously unselected package libraqm0:amd64.
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154s Selecting previously unselected package libdeflate0:amd64.
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154s Selecting previously unselected package libjbig0:amd64.
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154s Selecting previously unselected package liblerc4:amd64.
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154s Selecting previously unselected package libwebp7:amd64.
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154s Selecting previously unselected package libtiff6:amd64.
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154s Selecting previously unselected package libxpm4:amd64.
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154s Selecting previously unselected package libgd3:amd64.
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154s Selecting previously unselected package liblua5.4-0:amd64.
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154s Selecting previously unselected package fontconfig.
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155s Selecting previously unselected package libthai-data.
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155s Selecting previously unselected package libdatrie1:amd64.
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155s Selecting previously unselected package libpango-1.0-0:amd64.
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155s Selecting previously unselected package libpangoft2-1.0-0:amd64.
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155s Selecting previously unselected package libpangocairo-1.0-0:amd64.
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155s Selecting previously unselected package libwebpmux3:amd64.
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156s Setting up libhtscodecs2:amd64 (1.6.1-1) ...
156s Setting up fastjar (2:0.98-7) ...
156s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ...
156s Setting up liblcms2-2:amd64 (2.16-2) ...
156s Setting up python3-iniconfig (1.1.1-2) ...
157s Setting up libpixman-1-0:amd64 (0.44.0-3) ...
157s Setting up python3.12-minimal (3.12.9-1) ...
158s Setting up libfastutil-java (8.5.15+dfsg-1) ...
158s Setting up libsharpyuv0:amd64 (1.5.0-0.1) ...
158s Setting up libaom3:amd64 (3.12.0-1) ...
158s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ...
158s Setting up libjsr305-java (0.1~+svn49-12) ...
158s Setting up libxpm4:amd64 (1:3.5.17-1build2) ...
158s Setting up java-common (0.76) ...
158s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ...
158s Setting up libdatrie1:amd64 (0.2.13-3build1) ...
158s Setting up python3-joblib (1.4.2-2) ...
158s Setting up libxcb-render0:amd64 (1.17.0-2) ...
158s Setting up prodigal (1:2.6.3-6) ...
158s Setting up bwa (0.7.18-1) ...
158s Setting up python3.12 (3.12.9-1) ...
159s Setting up libfilesys-df-perl (0.92-7build5) ...
159s Setting up libdeflate0:amd64 (1.23-1) ...
159s Setting up python3-all (3.13.1-1~exp2) ...
159s Setting up libnlopt0:amd64 (2.7.1-6ubuntu2) ...
159s Setting up libxcb-shm0:amd64 (1.17.0-2) ...
159s Setting up libgomp1:amd64 (15-20250213-1ubuntu1) ...
159s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ...
159s Setting up libssw-java (1.1-15) ...
159s Setting up libsnappy1v5:amd64 (1.2.1-1) ...
159s Setting up python3-packaging (24.2-1) ...
160s Setting up libjsoncpp26:amd64 (1.9.6-3) ...
160s Setting up aglfn (1.7+git20191031.4036a9c-2) ...
160s Setting up libapache-pom-java (33-2) ...
160s Setting up libatinject-jsr330-api-java (1.0+ds1-6) ...
160s Setting up libimagequant0:amd64 (2.18.0-1build1) ...
160s Setting up fonts-dejavu-mono (2.37-8) ...
160s Setting up libspoa7.0.0:amd64 (4.1.4-2) ...
160s Setting up binfmt-support (2.2.2-7) ...
160s update-binfmts: warning: python3.13 already enabled in kernel.
160s Created symlink '/etc/systemd/system/multi-user.target.wants/binfmt-support.service' → '/usr/lib/systemd/system/binfmt-support.service'.

161s Setting up fonts-dejavu-core (2.37-8) ...
161s Setting up libpcsclite1:amd64 (2.3.1-1) ...
161s Setting up libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ...
161s Setting up libbamtools2.5.2:amd64 (2.5.2+dfsg-6build1) ...
161s Setting up python3-pluggy (1.5.0-1) ...
161s Setting up libwebp7:amd64 (1.5.0-0.1) ...
161s Setting up bamtools (2.5.2+dfsg-6build1) ...
161s Setting up libxslt1.1:amd64 (1.1.39-0exp1ubuntu2) ...
161s Setting up mummer (3.23+dfsg-8) ...
161s Setting up python3-et-xmlfile (2.0.0-1) ...
162s Setting up libhts3t64:amd64 (1.21+ds-1) ...
162s Setting up liblua5.4-0:amd64 (5.4.7-1) ...
162s Setting up libharfbuzz0b:amd64 (10.2.0-1) ...
162s Setting up libthai-data (0.1.29-2build1) ...
162s Setting up ca-certificates-java (20240118) ...
162s No JRE found. Skipping Java certificates setup.
162s Setting up libde265-0:amd64 (1.0.15-1build4) ...
162s Setting up libwebpmux3:amd64 (1.5.0-0.1) ...
162s Setting up libssw0:amd64 (1.1-15) ...
162s Setting up libjpeg8:amd64 (8c-2ubuntu11) ...
162s Setting up gnuplot-data (6.0.0+dfsg1-1ubuntu3) ...
162s Setting up python3-pysam (0.23.0+ds-1) ...
162s Setting up openjdk-21-jre-headless:amd64 (21.0.6+7-1) ...
162s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode
162s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode
162s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
162s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
162s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
162s Setting up jarwrapper (0.80) ...
162s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ...
162s Setting up python3-pytest (8.3.4-1) ...
162s Setting up libcommons-parent-java (56-1) ...
162s Setting up samtools (1.21-1) ...
162s Setting up libthai0:amd64 (0.1.29-2build1) ...
162s Setting up libraqm0:amd64 (0.10.2-1) ...
162s Setting up python3-lxml:amd64 (5.3.1-1) ...
163s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ...
163s Setting up spades (4.0.0+dfsg1-2) ...
163s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ...
163s Setting up libcommons-codec-java (1.17.1-1) ...
163s Setting up fontconfig (2.15.0-1.1ubuntu2) ...
165s Regenerating fonts cache... done.
165s Setting up libcommons-io-java (2.18.0-1) ...
165s Setting up fastaq (3.17.0-9) ...
165s Setting up libpango-1.0-0:amd64 (1.56.1-1) ...
165s Setting up libcairo2:amd64 (1.18.2-2) ...
165s Setting up python3-pymummer (0.11.0-4) ...
165s Setting up python3-openpyxl (3.1.5+dfsg-1) ...
166s Setting up libpangoft2-1.0-0:amd64 (1.56.1-1) ...
166s Setting up libpangocairo-1.0-0:amd64 (1.56.1-1) ...
166s Setting up libcommons-compress-java (1.27.1-2) ...
166s Setting up libheif-plugin-aomdec:amd64 (1.19.5-1build1) ...
166s Setting up libheif-plugin-libde265:amd64 (1.19.5-1build1) ...
166s Setting up liberror-prone-java (2.18.0-1) ...
166s Setting up libheif1:amd64 (1.19.5-1build1) ...
166s Setting up libguava-java (32.0.1-1) ...
166s Setting up libgd3:amd64 (2.3.3-12ubuntu3) ...
166s Setting up gnuplot-nox (6.0.0+dfsg1-1ubuntu3) ...
166s update-alternatives: using /usr/bin/gnuplot-nox to provide /usr/bin/gnuplot (gnuplot) in auto mode
166s Processing triggers for install-info (7.1.1-1) ...
166s Processing triggers for libc-bin (2.40-4ubuntu1) ...
166s Processing triggers for systemd (257.2-3ubuntu1) ...
166s Processing triggers for man-db (2.13.0-1) ...
168s Processing triggers for ca-certificates-java (20240118) ...
168s Adding debian:ACCVRAIZ1.pem
168s Adding debian:AC_RAIZ_FNMT-RCM.pem
168s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem
168s Adding debian:ANF_Secure_Server_Root_CA.pem
168s Adding debian:Actalis_Authentication_Root_CA.pem
168s Adding debian:AffirmTrust_Commercial.pem
168s Adding debian:AffirmTrust_Networking.pem
168s Adding debian:AffirmTrust_Premium.pem
169s Adding debian:AffirmTrust_Premium_ECC.pem
169s Adding debian:Amazon_Root_CA_1.pem
169s Adding debian:Amazon_Root_CA_2.pem
169s Adding debian:Amazon_Root_CA_3.pem
169s Adding debian:Amazon_Root_CA_4.pem
169s Adding debian:Atos_TrustedRoot_2011.pem
169s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem
169s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem
169s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
169s Adding debian:BJCA_Global_Root_CA1.pem
169s Adding debian:BJCA_Global_Root_CA2.pem
169s Adding debian:Baltimore_CyberTrust_Root.pem
169s Adding debian:Buypass_Class_2_Root_CA.pem
169s Adding debian:Buypass_Class_3_Root_CA.pem
169s Adding debian:CA_Disig_Root_R2.pem
169s Adding debian:CFCA_EV_ROOT.pem
169s Adding debian:COMODO_Certification_Authority.pem
169s Adding debian:COMODO_ECC_Certification_Authority.pem
169s Adding debian:COMODO_RSA_Certification_Authority.pem
169s Adding debian:Certainly_Root_E1.pem
169s Adding debian:Certainly_Root_R1.pem
169s Adding debian:Certigna.pem
169s Adding debian:Certigna_Root_CA.pem
169s Adding debian:Certum_EC-384_CA.pem
169s Adding debian:Certum_Trusted_Network_CA.pem
169s Adding debian:Certum_Trusted_Network_CA_2.pem
169s Adding debian:Certum_Trusted_Root_CA.pem
169s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem
169s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem
169s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem
169s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem
169s Adding debian:Comodo_AAA_Services_root.pem
169s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem
169s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem
169s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
169s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
169s Adding debian:DigiCert_Assured_ID_Root_CA.pem
169s Adding debian:DigiCert_Assured_ID_Root_G2.pem
169s Adding debian:DigiCert_Assured_ID_Root_G3.pem
169s Adding debian:DigiCert_Global_Root_CA.pem
169s Adding debian:DigiCert_Global_Root_G2.pem
169s Adding debian:DigiCert_Global_Root_G3.pem
169s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
169s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem
169s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem
169s Adding debian:DigiCert_Trusted_Root_G4.pem
169s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
169s Adding debian:Entrust_Root_Certification_Authority.pem
169s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
169s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
169s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem
169s Adding debian:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem
169s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem
169s Adding debian:GLOBALTRUST_2020.pem
169s Adding debian:GTS_Root_R1.pem
169s Adding debian:GTS_Root_R2.pem
169s Adding debian:GTS_Root_R3.pem
169s Adding debian:GTS_Root_R4.pem
169s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
169s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
169s Adding debian:GlobalSign_Root_CA.pem
169s Adding debian:GlobalSign_Root_CA_-_R3.pem
169s Adding debian:GlobalSign_Root_CA_-_R6.pem
169s Adding debian:GlobalSign_Root_E46.pem
169s Adding debian:GlobalSign_Root_R46.pem
169s Adding debian:Go_Daddy_Class_2_CA.pem
169s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
169s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem
169s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem
169s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem
169s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem
169s Adding debian:HiPKI_Root_CA_-_G1.pem
169s Adding debian:Hongkong_Post_Root_CA_3.pem
169s Adding debian:ISRG_Root_X1.pem
169s Adding debian:ISRG_Root_X2.pem
169s Adding debian:IdenTrust_Commercial_Root_CA_1.pem
169s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
169s Adding debian:Izenpe.com.pem
169s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
169s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem
169s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem
169s Adding debian:NAVER_Global_Root_Certification_Authority.pem
169s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
169s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
169s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem
169s Adding debian:QuoVadis_Root_CA_1_G3.pem
169s Adding debian:QuoVadis_Root_CA_2.pem
169s Adding debian:QuoVadis_Root_CA_2_G3.pem
169s Adding debian:QuoVadis_Root_CA_3.pem
169s Adding debian:QuoVadis_Root_CA_3_G3.pem
169s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem
169s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem
169s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem
169s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem
169s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem
169s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem
169s Adding debian:SZAFIR_ROOT_CA2.pem
169s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem
169s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem
169s Adding debian:SecureSign_RootCA11.pem
169s Adding debian:SecureSign_Root_CA12.pem
169s Adding debian:SecureSign_Root_CA14.pem
169s Adding debian:SecureSign_Root_CA15.pem
169s Adding debian:SecureTrust_CA.pem
169s Adding debian:Secure_Global_CA.pem
169s Adding debian:Security_Communication_ECC_RootCA1.pem
169s Adding debian:Security_Communication_RootCA2.pem
169s Adding debian:Security_Communication_RootCA3.pem
169s Adding debian:Starfield_Class_2_CA.pem
169s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
169s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
169s Adding debian:SwissSign_Gold_CA_-_G2.pem
169s Adding debian:SwissSign_Silver_CA_-_G2.pem
169s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
169s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
169s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
169s Adding debian:TWCA_CYBER_Root_CA.pem
169s Adding debian:TWCA_Global_Root_CA.pem
169s Adding debian:TWCA_Root_Certification_Authority.pem
169s Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem
169s Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem
169s Adding debian:TeliaSonera_Root_CA_v1.pem
169s Adding debian:Telia_Root_CA_v2.pem
169s Adding debian:TrustAsia_Global_Root_CA_G3.pem
169s Adding debian:TrustAsia_Global_Root_CA_G4.pem
169s Adding debian:Trustwave_Global_Certification_Authority.pem
169s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem
169s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem
169s Adding debian:TunTrust_Root_CA.pem
169s Adding debian:UCA_Extended_Validation_Root.pem
169s Adding debian:UCA_Global_G2_Root.pem
169s Adding debian:USERTrust_ECC_Certification_Authority.pem
169s Adding debian:USERTrust_RSA_Certification_Authority.pem
169s Adding debian:XRamp_Global_CA_Root.pem
169s Adding debian:certSIGN_ROOT_CA.pem
169s Adding debian:certSIGN_Root_CA_G2.pem
169s Adding debian:e-Szigno_Root_CA_2017.pem
169s Adding debian:ePKI_Root_Certification_Authority.pem
169s Adding debian:emSign_ECC_Root_CA_-_C3.pem
169s Adding debian:emSign_ECC_Root_CA_-_G3.pem
169s Adding debian:emSign_Root_CA_-_C1.pem
169s Adding debian:emSign_Root_CA_-_G1.pem
169s Adding debian:vTrus_ECC_Root_CA.pem
169s Adding debian:vTrus_Root_CA.pem
169s done.
169s Setting up default-jre-headless (2:1.21-76) ...
169s Setting up jaligner (1.0+dfsg-11) ...
169s Setting up mhap (2.1.3+dfsg-3) ...
169s Setting up canu (2.2+dfsg-5) ...
169s Setting up circlator (1.5.6-12) ...
170s autopkgtest [02:32:43]: test run-unit-test: [-----------------------
170s + pkg=circlator
170s + export LC_ALL=C.UTF-8
170s + LC_ALL=C.UTF-8
170s + '[' /tmp/autopkgtest.dO1juT/autopkgtest_tmp = '' ']'
170s + 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.dO1juT/autopkgtest_tmp
170s + cd /tmp/autopkgtest.dO1juT/autopkgtest_tmp
170s + tar xaf data.tar.xz
170s + 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
170s ++ py3versions --supported
170s + for py in $(py3versions --supported 2> /dev/null)
170s + eval dpkg-architecture --is amd64
170s ++ dpkg-architecture --is amd64
170s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation)
170s + python3.12 -m pytest -v
171s ============================= test session starts ==============================
171s platform linux -- Python 3.12.9, pytest-8.3.4, pluggy-1.5.0 -- /usr/bin/python3.12
171s cachedir: .pytest_cache
171s rootdir: /tmp/autopkgtest.dO1juT/autopkgtest_tmp
171s plugins: typeguard-4.4.1
171s collecting ... collected 115 items
171s 
171s assemble_test.py::TestAssembleSpades::test_build_spades_kmers PASSED     [  0%]
171s assemble_test.py::TestAssembleSpades::test_make_spades_command PASSED    [  1%]
171s assemble_test.py::TestAssembleCanu::test_make_canu_command PASSED        [  2%]
171s assemble_test.py::TestAssembleCanu::test_rename_canu_contigs PASSED      [  3%]
171s assembly_test.py::TestAssembly::test_circular_contigs_from_canu_gfa PASSED [  4%]
171s assembly_test.py::TestAssembly::test_circular_contigs_from_spades_after_3_6_1 PASSED [  5%]
171s assembly_test.py::TestAssembly::test_circular_contigs_from_spades_before_3_6_1 PASSED [  6%]
171s assembly_test.py::TestAssembly::test_circular_contigs_just_fasta PASSED  [  6%]
171s assembly_test.py::TestAssembly::test_circular_contigs_spades_post_3_6_1 PASSED [  7%]
171s assembly_test.py::TestAssembly::test_circular_contigs_spades_pre_3_6_1 PASSED [  8%]
171s assembly_test.py::TestAssembly::test_circular_edges_to_edge_numbers_dict PASSED [  9%]
171s assembly_test.py::TestAssembly::test_get_contigs PASSED                  [ 10%]
171s assembly_test.py::TestAssembly::test_init_file_not_dir PASSED            [ 11%]
171s assembly_test.py::TestAssembly::test_init_post_3_6_1_ok PASSED           [ 12%]
171s assembly_test.py::TestAssembly::test_init_pre_3_6_1_ok PASSED            [ 13%]
171s assembly_test.py::TestAssembly::test_init_raises_error PASSED            [ 13%]
171s assembly_test.py::TestAssembly::test_spades_contigs_paths_to_dict PASSED [ 14%]
171s bamfilter_test.py::TestBamfilter::test_all_reads_from_contig PASSED      [ 15%]
171s bamfilter_test.py::TestBamfilter::test_break_reads PASSED                [ 16%]
171s bamfilter_test.py::TestBamfilter::test_check_contigs_to_use PASSED       [ 17%]
171s bamfilter_test.py::TestBamfilter::test_exclude_region PASSED             [ 18%]
171s bamfilter_test.py::TestBamfilter::test_get_all_unmapped_reads PASSED     [ 19%]
171s bamfilter_test.py::TestBamfilter::test_get_contigs_to_use PASSED         [ 20%]
171s bamfilter_test.py::TestBamfilter::test_get_ref_lengths PASSED            [ 20%]
171s bamfilter_test.py::TestBamfilter::test_get_region_end PASSED             [ 21%]
171s bamfilter_test.py::TestBamfilter::test_get_region_start PASSED           [ 22%]
171s bamfilter_test.py::TestBamfilter::test_run_discard_unmapped_no_quals PASSED [ 23%]
171s bamfilter_test.py::TestBamfilter::test_run_keep_unmapped_no_quals PASSED [ 24%]
171s bamfilter_test.py::TestBamfilter::test_run_keep_unmapped_with_quals PASSED [ 25%]
171s clean_test.py::TestClean::test_clean_contigs PASSED                      [ 26%]
171s clean_test.py::TestClean::test_collapse_list_of_sets PASSED              [ 26%]
171s clean_test.py::TestClean::test_containing_contigs PASSED                 [ 27%]
171s clean_test.py::TestClean::test_contains PASSED                           [ 28%]
171s clean_test.py::TestClean::test_expand_containing_using_transitivity PASSED [ 29%]
171s clean_test.py::TestClean::test_get_all_containing PASSED                 [ 30%]
171s clean_test.py::TestClean::test_get_containing_contigs PASSED             [ 31%]
171s clean_test.py::TestClean::test_get_contigs_to_keep PASSED                [ 32%]
171s clean_test.py::TestClean::test_get_identical_contigs PASSED              [ 33%]
171s clean_test.py::TestClean::test_infinite_recursion PASSED                 [ 33%]
171s clean_test.py::TestClean::test_load_nucmer_hits PASSED                   [ 34%]
171s clean_test.py::TestClean::test_longest_contig PASSED                     [ 35%]
171s clean_test.py::TestClean::test_remove_identical_contigs PASSED           [ 36%]
171s clean_test.py::TestClean::test_remove_small_contigs PASSED               [ 37%]
171s clean_test.py::TestClean::test_write_log PASSED                          [ 38%]
171s common_test.py::TestCommon::test_check_files_exist PASSED                [ 39%]
171s dnaa_test.py::TestDnaa::test_append_stop_to_seq PASSED                   [ 40%]
171s dnaa_test.py::TestDnaa::test_check_sequence PASSED                       [ 40%]
171s dnaa_test.py::TestDnaa::test_get_uniprot_url PASSED                      [ 41%]
171s dnaa_test.py::TestDnaa::test_header_matches_regex PASSED                 [ 42%]
171s dnaa_test.py::TestDnaa::test_header_to_genus_species PASSED              [ 43%]
171s dnaa_test.py::TestDnaa::test_reverse_translate PASSED                    [ 44%]
171s external_progs_test.py::TestExternalProgs::test_bwa_version PASSED       [ 45%]
171s external_progs_test.py::TestExternalProgs::test_canu_version PASSED      [ 46%]
171s external_progs_test.py::TestExternalProgs::test_nucmer_version PASSED    [ 46%]
171s external_progs_test.py::TestExternalProgs::test_prodigal_version PASSED  [ 47%]
171s external_progs_test.py::TestExternalProgs::test_samtools_original_version PASSED [ 48%]
171s external_progs_test.py::TestExternalProgs::test_samtools_version PASSED  [ 49%]
171s external_progs_test.py::TestExternalProgs::test_spades_version PASSED    [ 50%]
172s mapping_test.py::TestMapping::test_aligned_read_to_read PASSED           [ 51%]
172s mapping_test.py::TestMapping::test_bwa_index PASSED                      [ 52%]
172s mapping_test.py::TestMapping::test_bwa_index_clean PASSED                [ 53%]
172s mapping_test.py::TestMapping::test_bwa_mem PASSED                        [ 53%]
172s merge_test.py::TestMerge::test_can_circularise PASSED                    [ 54%]
172s merge_test.py::TestMerge::test_contigs_dict_to_file PASSED               [ 55%]
172s merge_test.py::TestMerge::test_filter_bridging_contigs PASSED            [ 56%]
172s merge_test.py::TestMerge::test_get_hit_nearest_ref_end PASSED            [ 57%]
172s merge_test.py::TestMerge::test_get_hit_nearest_ref_start PASSED          [ 58%]
172s merge_test.py::TestMerge::test_get_longest_hit_at_qry_end PASSED         [ 59%]
172s merge_test.py::TestMerge::test_get_longest_hit_at_qry_start PASSED       [ 60%]
172s merge_test.py::TestMerge::test_get_longest_hit_at_ref_end PASSED         [ 60%]
172s merge_test.py::TestMerge::test_get_longest_hit_at_ref_start PASSED       [ 61%]
172s merge_test.py::TestMerge::test_get_longest_hit_by_ref_length PASSED      [ 62%]
172s merge_test.py::TestMerge::test_get_possible_circular_ref_contigs PASSED  [ 63%]
172s merge_test.py::TestMerge::test_get_possible_circular_ref_contigs_same_best_hits PASSED [ 64%]
172s merge_test.py::TestMerge::test_get_possible_query_bridging_contigs PASSED [ 65%]
172s merge_test.py::TestMerge::test_get_spades_circular_nodes PASSED          [ 66%]
172s merge_test.py::TestMerge::test_has_qry_hit_longer_than PASSED            [ 66%]
172s merge_test.py::TestMerge::test_hits_hashed_by_query PASSED               [ 67%]
172s merge_test.py::TestMerge::test_hits_have_same_query PASSED               [ 68%]
172s merge_test.py::TestMerge::test_hits_have_same_reference PASSED           [ 69%]
172s merge_test.py::TestMerge::test_index_fasta PASSED                        [ 70%]
172s merge_test.py::TestMerge::test_is_at_qry_end PASSED                      [ 71%]
172s merge_test.py::TestMerge::test_is_at_qry_start PASSED                    [ 72%]
172s merge_test.py::TestMerge::test_is_at_ref_end PASSED                      [ 73%]
172s merge_test.py::TestMerge::test_is_at_ref_start PASSED                    [ 73%]
172s merge_test.py::TestMerge::test_load_nucmer_hits PASSED                   [ 74%]
172s merge_test.py::TestMerge::test_make_circularised_contig_1 PASSED         [ 75%]
172s merge_test.py::TestMerge::test_make_circularised_contig_2 PASSED         [ 76%]
172s merge_test.py::TestMerge::test_make_new_contig_from_nucmer_and_spades_not_hit PASSED [ 77%]
172s merge_test.py::TestMerge::test_make_new_contig_from_nucmer_and_spades_with_hit PASSED [ 78%]
172s merge_test.py::TestMerge::test_merge_bridged_contig_pair1 PASSED         [ 79%]
172s merge_test.py::TestMerge::test_merge_bridged_contig_pair2 PASSED         [ 80%]
172s merge_test.py::TestMerge::test_merge_bridged_contig_pair3 PASSED         [ 80%]
172s merge_test.py::TestMerge::test_merge_bridged_contig_pair4 PASSED         [ 81%]
172s merge_test.py::TestMerge::test_min_qry_hit_length PASSED                 [ 82%]
172s merge_test.py::TestMerge::test_orientation_ok_to_bridge_contigs PASSED   [ 83%]
172s merge_test.py::TestMerge::test_remove_keys_from_dict_with_nonunique_values PASSED [ 84%]
172s merge_test.py::TestMerge::test_write_act_files PASSED                    [ 85%]
172s minimus2_test.py::TestMinimus2::test_run_initial_merge SKIPPED (Amos...) [ 86%]
172s minimus2_test.py::TestMinimus2::test_run_minimus2 SKIPPED (Amos is n...) [ 86%]
172s minimus2_test.py::TestMinimus2::test_run_minimus2_on_each_contig SKIPPED [ 87%]
172s minimus2_test.py::TestMinimus2::test_run_minimus2_on_one_contig_will_not_work SKIPPED [ 88%]
172s minimus2_test.py::TestMinimus2::test_run_minimus2_on_one_contig_will_work SKIPPED [ 89%]
172s minimus2_test.py::TestMinimus2::test_write_split_contig SKIPPED (Amo...) [ 90%]
172s start_fixer_test.py::TestStartFixer::test_find_circular_using_prodigal PASSED [ 91%]
172s start_fixer_test.py::TestStartFixer::test_find_circular_using_promer PASSED [ 92%]
172s start_fixer_test.py::TestStartFixer::test_init PASSED                    [ 93%]
172s start_fixer_test.py::TestStartFixer::test_max_length_from_fasta_file PASSED [ 93%]
172s start_fixer_test.py::TestStartFixer::test_rearrange_contigs PASSED       [ 94%]
172s start_fixer_test.py::TestStartFixer::test_rename_contigs PASSED          [ 95%]
172s start_fixer_test.py::TestStartFixer::test_run_bit_of_everything PASSED   [ 96%]
172s start_fixer_test.py::TestStartFixer::test_run_ignore_all PASSED          [ 97%]
172s start_fixer_test.py::TestStartFixer::test_run_none_for_prodigal PASSED   [ 98%]
172s start_fixer_test.py::TestStartFixer::test_write_fasta_plus_circularized_ends PASSED [ 99%]
172s start_fixer_test.py::TestStartFixer::test_write_renamed_contigs PASSED   [100%]
172s 
172s =============================== warnings summary ===============================
172s ../../../usr/lib/python3/dist-packages/pyfastaq/__init__.py:3
172s   /usr/lib/python3/dist-packages/pyfastaq/__init__.py:3: DeprecationWarning: Unimplemented abstract methods {'locate_file', 'read_text'}
172s     __version__ = Distribution().from_name('pyfastaq').version
172s 
172s ../../../usr/lib/python3/dist-packages/circlator/__init__.py:1
172s   /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
172s     from pkg_resources import get_distribution
172s 
172s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
172s ================== 109 passed, 6 skipped, 2 warnings in 1.69s ==================
173s + for py in $(py3versions --supported 2> /dev/null)
173s + eval dpkg-architecture --is amd64
173s ++ dpkg-architecture --is amd64
173s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation)
173s + python3.13 -m pytest -v
173s ============================= test session starts ==============================
173s platform linux -- Python 3.13.2, pytest-8.3.4, pluggy-1.5.0 -- /usr/bin/python3.13
173s cachedir: .pytest_cache
173s rootdir: /tmp/autopkgtest.dO1juT/autopkgtest_tmp
173s plugins: typeguard-4.4.1
173s collecting ... collected 115 items
173s 
173s assemble_test.py::TestAssembleSpades::test_build_spades_kmers PASSED     [  0%]
173s assemble_test.py::TestAssembleSpades::test_make_spades_command PASSED    [  1%]
174s assemble_test.py::TestAssembleCanu::test_make_canu_command PASSED        [  2%]
174s assemble_test.py::TestAssembleCanu::test_rename_canu_contigs PASSED      [  3%]
174s assembly_test.py::TestAssembly::test_circular_contigs_from_canu_gfa PASSED [  4%]
174s assembly_test.py::TestAssembly::test_circular_contigs_from_spades_after_3_6_1 PASSED [  5%]
174s assembly_test.py::TestAssembly::test_circular_contigs_from_spades_before_3_6_1 PASSED [  6%]
174s assembly_test.py::TestAssembly::test_circular_contigs_just_fasta PASSED  [  6%]
174s assembly_test.py::TestAssembly::test_circular_contigs_spades_post_3_6_1 PASSED [  7%]
174s assembly_test.py::TestAssembly::test_circular_contigs_spades_pre_3_6_1 PASSED [  8%]
174s assembly_test.py::TestAssembly::test_circular_edges_to_edge_numbers_dict PASSED [  9%]
174s assembly_test.py::TestAssembly::test_get_contigs PASSED                  [ 10%]
174s assembly_test.py::TestAssembly::test_init_file_not_dir PASSED            [ 11%]
174s assembly_test.py::TestAssembly::test_init_post_3_6_1_ok PASSED           [ 12%]
174s assembly_test.py::TestAssembly::test_init_pre_3_6_1_ok PASSED            [ 13%]
174s assembly_test.py::TestAssembly::test_init_raises_error PASSED            [ 13%]
174s assembly_test.py::TestAssembly::test_spades_contigs_paths_to_dict PASSED [ 14%]
174s bamfilter_test.py::TestBamfilter::test_all_reads_from_contig PASSED      [ 15%]
174s bamfilter_test.py::TestBamfilter::test_break_reads PASSED                [ 16%]
174s bamfilter_test.py::TestBamfilter::test_check_contigs_to_use PASSED       [ 17%]
174s bamfilter_test.py::TestBamfilter::test_exclude_region PASSED             [ 18%]
174s bamfilter_test.py::TestBamfilter::test_get_all_unmapped_reads PASSED     [ 19%]
174s bamfilter_test.py::TestBamfilter::test_get_contigs_to_use PASSED         [ 20%]
174s bamfilter_test.py::TestBamfilter::test_get_ref_lengths PASSED            [ 20%]
174s bamfilter_test.py::TestBamfilter::test_get_region_end PASSED             [ 21%]
174s bamfilter_test.py::TestBamfilter::test_get_region_start PASSED           [ 22%]
174s bamfilter_test.py::TestBamfilter::test_run_discard_unmapped_no_quals PASSED [ 23%]
174s bamfilter_test.py::TestBamfilter::test_run_keep_unmapped_no_quals PASSED [ 24%]
174s bamfilter_test.py::TestBamfilter::test_run_keep_unmapped_with_quals PASSED [ 25%]
174s clean_test.py::TestClean::test_clean_contigs PASSED                      [ 26%]
174s clean_test.py::TestClean::test_collapse_list_of_sets PASSED              [ 26%]
174s clean_test.py::TestClean::test_containing_contigs PASSED                 [ 27%]
174s clean_test.py::TestClean::test_contains PASSED                           [ 28%]
174s clean_test.py::TestClean::test_expand_containing_using_transitivity PASSED [ 29%]
174s clean_test.py::TestClean::test_get_all_containing PASSED                 [ 30%]
174s clean_test.py::TestClean::test_get_containing_contigs PASSED             [ 31%]
174s clean_test.py::TestClean::test_get_contigs_to_keep PASSED                [ 32%]
174s clean_test.py::TestClean::test_get_identical_contigs PASSED              [ 33%]
174s clean_test.py::TestClean::test_infinite_recursion PASSED                 [ 33%]
174s clean_test.py::TestClean::test_load_nucmer_hits PASSED                   [ 34%]
174s clean_test.py::TestClean::test_longest_contig PASSED                     [ 35%]
174s clean_test.py::TestClean::test_remove_identical_contigs PASSED           [ 36%]
174s clean_test.py::TestClean::test_remove_small_contigs PASSED               [ 37%]
174s clean_test.py::TestClean::test_write_log PASSED                          [ 38%]
174s common_test.py::TestCommon::test_check_files_exist PASSED                [ 39%]
174s dnaa_test.py::TestDnaa::test_append_stop_to_seq PASSED                   [ 40%]
174s dnaa_test.py::TestDnaa::test_check_sequence PASSED                       [ 40%]
174s dnaa_test.py::TestDnaa::test_get_uniprot_url PASSED                      [ 41%]
174s dnaa_test.py::TestDnaa::test_header_matches_regex PASSED                 [ 42%]
174s dnaa_test.py::TestDnaa::test_header_to_genus_species PASSED              [ 43%]
174s dnaa_test.py::TestDnaa::test_reverse_translate PASSED                    [ 44%]
174s external_progs_test.py::TestExternalProgs::test_bwa_version PASSED       [ 45%]
174s external_progs_test.py::TestExternalProgs::test_canu_version PASSED      [ 46%]
174s external_progs_test.py::TestExternalProgs::test_nucmer_version PASSED    [ 46%]
174s external_progs_test.py::TestExternalProgs::test_prodigal_version PASSED  [ 47%]
174s external_progs_test.py::TestExternalProgs::test_samtools_original_version PASSED [ 48%]
174s external_progs_test.py::TestExternalProgs::test_samtools_version PASSED  [ 49%]
174s external_progs_test.py::TestExternalProgs::test_spades_version PASSED    [ 50%]
174s mapping_test.py::TestMapping::test_aligned_read_to_read PASSED           [ 51%]
174s mapping_test.py::TestMapping::test_bwa_index PASSED                      [ 52%]
174s mapping_test.py::TestMapping::test_bwa_index_clean PASSED                [ 53%]
174s mapping_test.py::TestMapping::test_bwa_mem PASSED                        [ 53%]
174s merge_test.py::TestMerge::test_can_circularise PASSED                    [ 54%]
174s merge_test.py::TestMerge::test_contigs_dict_to_file PASSED               [ 55%]
174s merge_test.py::TestMerge::test_filter_bridging_contigs PASSED            [ 56%]
174s merge_test.py::TestMerge::test_get_hit_nearest_ref_end PASSED            [ 57%]
174s merge_test.py::TestMerge::test_get_hit_nearest_ref_start PASSED          [ 58%]
174s merge_test.py::TestMerge::test_get_longest_hit_at_qry_end PASSED         [ 59%]
174s merge_test.py::TestMerge::test_get_longest_hit_at_qry_start PASSED       [ 60%]
174s merge_test.py::TestMerge::test_get_longest_hit_at_ref_end PASSED         [ 60%]
174s merge_test.py::TestMerge::test_get_longest_hit_at_ref_start PASSED       [ 61%]
174s merge_test.py::TestMerge::test_get_longest_hit_by_ref_length PASSED      [ 62%]
174s merge_test.py::TestMerge::test_get_possible_circular_ref_contigs PASSED  [ 63%]
174s merge_test.py::TestMerge::test_get_possible_circular_ref_contigs_same_best_hits PASSED [ 64%]
174s merge_test.py::TestMerge::test_get_possible_query_bridging_contigs PASSED [ 65%]
174s merge_test.py::TestMerge::test_get_spades_circular_nodes PASSED          [ 66%]
174s merge_test.py::TestMerge::test_has_qry_hit_longer_than PASSED            [ 66%]
174s merge_test.py::TestMerge::test_hits_hashed_by_query PASSED               [ 67%]
174s merge_test.py::TestMerge::test_hits_have_same_query PASSED               [ 68%]
174s merge_test.py::TestMerge::test_hits_have_same_reference PASSED           [ 69%]
174s merge_test.py::TestMerge::test_index_fasta PASSED                        [ 70%]
174s merge_test.py::TestMerge::test_is_at_qry_end PASSED                      [ 71%]
174s merge_test.py::TestMerge::test_is_at_qry_start PASSED                    [ 72%]
174s merge_test.py::TestMerge::test_is_at_ref_end PASSED                      [ 73%]
174s merge_test.py::TestMerge::test_is_at_ref_start PASSED                    [ 73%]
174s merge_test.py::TestMerge::test_load_nucmer_hits PASSED                   [ 74%]
174s merge_test.py::TestMerge::test_make_circularised_contig_1 PASSED         [ 75%]
174s merge_test.py::TestMerge::test_make_circularised_contig_2 PASSED         [ 76%]
174s merge_test.py::TestMerge::test_make_new_contig_from_nucmer_and_spades_not_hit PASSED [ 77%]
174s merge_test.py::TestMerge::test_make_new_contig_from_nucmer_and_spades_with_hit PASSED [ 78%]
174s merge_test.py::TestMerge::test_merge_bridged_contig_pair1 PASSED         [ 79%]
174s merge_test.py::TestMerge::test_merge_bridged_contig_pair2 PASSED         [ 80%]
174s merge_test.py::TestMerge::test_merge_bridged_contig_pair3 PASSED         [ 80%]
174s merge_test.py::TestMerge::test_merge_bridged_contig_pair4 PASSED         [ 81%]
174s merge_test.py::TestMerge::test_min_qry_hit_length PASSED                 [ 82%]
174s merge_test.py::TestMerge::test_orientation_ok_to_bridge_contigs PASSED   [ 83%]
174s merge_test.py::TestMerge::test_remove_keys_from_dict_with_nonunique_values PASSED [ 84%]
174s merge_test.py::TestMerge::test_write_act_files PASSED                    [ 85%]
174s minimus2_test.py::TestMinimus2::test_run_initial_merge SKIPPED (Amos...) [ 86%]
174s minimus2_test.py::TestMinimus2::test_run_minimus2 SKIPPED (Amos is n...) [ 86%]
174s minimus2_test.py::TestMinimus2::test_run_minimus2_on_each_contig SKIPPED [ 87%]
174s minimus2_test.py::TestMinimus2::test_run_minimus2_on_one_contig_will_not_work SKIPPED [ 88%]
174s minimus2_test.py::TestMinimus2::test_run_minimus2_on_one_contig_will_work SKIPPED [ 89%]
174s minimus2_test.py::TestMinimus2::test_write_split_contig SKIPPED (Amo...) [ 90%]
174s start_fixer_test.py::TestStartFixer::test_find_circular_using_prodigal PASSED [ 91%]
174s start_fixer_test.py::TestStartFixer::test_find_circular_using_promer PASSED [ 92%]
174s start_fixer_test.py::TestStartFixer::test_init PASSED                    [ 93%]
174s start_fixer_test.py::TestStartFixer::test_max_length_from_fasta_file PASSED [ 93%]
174s start_fixer_test.py::TestStartFixer::test_rearrange_contigs PASSED       [ 94%]
174s start_fixer_test.py::TestStartFixer::test_rename_contigs PASSED          [ 95%]
174s start_fixer_test.py::TestStartFixer::test_run_bit_of_everything PASSED   [ 96%]
174s start_fixer_test.py::TestStartFixer::test_run_ignore_all PASSED          [ 97%]
174s start_fixer_test.py::TestStartFixer::test_run_none_for_prodigal PASSED   [ 98%]
174s start_fixer_test.py::TestStartFixer::test_write_fasta_plus_circularized_ends PASSED [ 99%]
174s start_fixer_test.py::TestStartFixer::test_write_renamed_contigs PASSED   [100%]
174s 
174s =============================== warnings summary ===============================
174s ../../../usr/lib/python3/dist-packages/pyfastaq/__init__.py:3
174s   /usr/lib/python3/dist-packages/pyfastaq/__init__.py:3: DeprecationWarning: Unimplemented abstract methods {'locate_file', 'read_text'}
174s     __version__ = Distribution().from_name('pyfastaq').version
174s 
174s ../../../usr/lib/python3/dist-packages/circlator/__init__.py:1
174s   /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
174s     from pkg_resources import get_distribution
174s 
174s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
174s ================== 109 passed, 6 skipped, 2 warnings in 1.52s ==================
175s autopkgtest [02:32:48]: test run-unit-test: -----------------------]
175s run-unit-test        PASS
175s autopkgtest [02:32:48]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
176s autopkgtest [02:32:49]: @@@@@@@@@@@@@@@@@@@@ summary
176s run-unit-test        PASS
193s nova [W] Skipping flock for amd64
193s Creating nova instance adt-plucky-amd64-circlator-20250217-022953-juju-7f2275-prod-proposed-migration-environment-15-fb1e1401-acc0-46a5-957b-861d355aa6a4 from image adt/ubuntu-plucky-amd64-server-20250216.img (UUID e02231ec-e8e1-4cbd-bfb9-4b4d8900eab3)...
193s nova [W] Timed out waiting for 4ecc57bf-9f4f-4c9c-946b-1b92070751bc to get deleted.