0s autopkgtest [16:48:17]: starting date and time: 2024-03-24 16:48:17+0000
  0s autopkgtest [16:48:17]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps
  0s autopkgtest [16:48:17]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.kf4_oj4v/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:python-pysam,src:curl,src:gnutls28,src:htslib,src:libpsl,src:nettle,src:openssl --apt-upgrade circlator --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python-pysam/0.22.0+ds-1build1 curl/8.5.0-2ubuntu7 gnutls28/3.8.3-1.1ubuntu2 htslib/1.19+ds-1.1build2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos03-arm64-12.secgroup --name adt-noble-arm64-circlator-20240324-164817-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
 74s autopkgtest [16:49:31]: testbed dpkg architecture: arm64
 74s autopkgtest [16:49:31]: testbed apt version: 2.7.12
 74s autopkgtest [16:49:31]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 75s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
 75s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B]
 75s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3984 kB]
 76s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB]
 76s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [495 kB]
 76s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [708 kB]
 76s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B]
 76s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB]
 76s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B]
 76s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4363 kB]
 76s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B]
 76s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [70.1 kB]
 76s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B]
 79s Fetched 9847 kB in 2s (5223 kB/s)
 79s Reading package lists...
 81s Reading package lists...
 81s Building dependency tree...
 81s Reading state information...
 82s Calculating upgrade...
 82s The following packages will be REMOVED:
 82s   libssl3
 82s The following NEW packages will be installed:
 82s   libssl3t64
 82s The following packages have been kept back:
 82s   curl
 82s The following packages will be upgraded:
 82s   openssl
 82s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded.
 82s Need to get 2777 kB of archives.
 82s After this operation, 139 kB of additional disk space will be used.
 82s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu2 [985 kB]
 82s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu2 [1793 kB]
 83s Fetched 2777 kB in 1s (4170 kB/s)
 83s (Reading database ... 
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(Reading database ... 100%
(Reading database ... 74819 files and directories currently installed.)
 83s Preparing to unpack .../openssl_3.0.13-0ubuntu2_arm64.deb ...
 83s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ...
 83s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested:
 83s  wget depends on libssl3 (>= 3.0.0).
 83s  u-boot-tools depends on libssl3 (>= 3.0.0).
 83s  tnftp depends on libssl3 (>= 3.0.0).
 83s  tcpdump depends on libssl3 (>= 3.0.0).
 83s  systemd-resolved depends on libssl3 (>= 3.0.0).
 83s  systemd depends on libssl3 (>= 3.0.0).
 83s  sudo depends on libssl3 (>= 3.0.0).
 83s  sbsigntool depends on libssl3 (>= 3.0.0).
 83s  rsync depends on libssl3 (>= 3.0.0).
 83s  python3-cryptography depends on libssl3 (>= 3.0.0).
 83s  openssh-server depends on libssl3 (>= 3.0.10).
 83s  openssh-client depends on libssl3 (>= 3.0.10).
 83s  mtd-utils depends on libssl3 (>= 3.0.0).
 83s  mokutil depends on libssl3 (>= 3.0.0).
 83s  linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0).
 83s  libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0).
 83s  libssh-4:arm64 depends on libssl3 (>= 3.0.0).
 83s  libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0).
 83s  libsasl2-2:arm64 depends on libssl3 (>= 3.0.0).
 83s  libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0).
 83s  libnvme1 depends on libssl3 (>= 3.0.0).
 83s  libkrb5-3:arm64 depends on libssl3 (>= 3.0.0).
 83s  libkmod2:arm64 depends on libssl3 (>= 3.0.0).
 83s  libfido2-1:arm64 depends on libssl3 (>= 3.0.0).
 83s  libcurl4:arm64 depends on libssl3 (>= 3.0.0).
 83s  libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0).
 83s  kmod depends on libssl3 (>= 3.0.0).
 83s  dhcpcd-base depends on libssl3 (>= 3.0.0).
 83s  bind9-libs:arm64 depends on libssl3 (>= 3.0.0).
 83s 
 83s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 74819 files and directories currently installed.)
 83s Removing libssl3:arm64 (3.0.10-1ubuntu4) ...
 83s Selecting previously unselected package libssl3t64:arm64.
 83s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 74808 files and directories currently installed.)
 83s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_arm64.deb ...
 83s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu2) ...
 84s Setting up libssl3t64:arm64 (3.0.13-0ubuntu2) ...
 84s Setting up openssl (3.0.13-0ubuntu2) ...
 84s Processing triggers for man-db (2.12.0-3) ...
 84s Processing triggers for libc-bin (2.39-0ubuntu6) ...
 84s Reading package lists...
 85s Building dependency tree...
 85s Reading state information...
 85s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
 86s sh: Attempting to set up Debian/Ubuntu apt sources automatically
 86s sh: Distribution appears to be Ubuntu
 87s Reading package lists...
 87s Building dependency tree...
 87s Reading state information...
 87s eatmydata is already the newest version (131-1).
 87s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 87s Reading package lists...
 88s Building dependency tree...
 88s Reading state information...
 88s dbus is already the newest version (1.14.10-4ubuntu1).
 88s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 88s Reading package lists...
 88s Building dependency tree...
 88s Reading state information...
 89s rng-tools-debian is already the newest version (2.4).
 89s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 89s Reading package lists...
 89s Building dependency tree...
 89s Reading state information...
 89s The following packages will be REMOVED:
 89s   cloud-init* python3-configobj* python3-debconf*
 90s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded.
 90s After this operation, 3256 kB disk space will be freed.
 90s (Reading database ... 
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(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 74821 files and directories currently installed.)
 90s Removing cloud-init (24.1.2-0ubuntu1) ...
 90s Removing python3-configobj (5.0.8-3) ...
 90s Removing python3-debconf (1.5.86) ...
 90s Processing triggers for man-db (2.12.0-3) ...
 91s (Reading database ... 
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(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 ... 74432 files and directories currently installed.)
 91s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ...
 92s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed
 92s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ...
 92s invoke-rc.d: policy-rc.d denied execution of try-restart.
 92s Reading package lists...
 92s Building dependency tree...
 92s Reading state information...
 92s linux-generic is already the newest version (6.8.0-11.11+1).
 92s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 93s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
 93s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
 93s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
 95s Reading package lists...
 95s Reading package lists...
 95s Building dependency tree...
 95s Reading state information...
 95s Calculating upgrade...
 96s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 96s Reading package lists...
 96s Building dependency tree...
 96s Reading state information...
 96s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 96s autopkgtest [16:49:53]: rebooting testbed after setup commands that affected boot
123s autopkgtest [16:50:20]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024
126s autopkgtest [16:50:23]: @@@@@@@@@@@@@@@@@@@@ apt-source circlator
128s Get:1 http://ftpmaster.internal/ubuntu noble/universe circlator 1.5.6-11 (dsc) [1672 B]
128s Get:2 http://ftpmaster.internal/ubuntu noble/universe circlator 1.5.6-11 (tar) [5724 kB]
128s Get:3 http://ftpmaster.internal/ubuntu noble/universe circlator 1.5.6-11 (diff) [6152 B]
128s gpgv: Signature made Sat Dec  2 21:39:17 2023 UTC
128s gpgv:                using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA
128s gpgv: Can't check signature: No public key
128s dpkg-source: warning: cannot verify inline signature for ./circlator_1.5.6-11.dsc: no acceptable signature found
129s autopkgtest [16:50:26]: testing package circlator version 1.5.6-11
129s autopkgtest [16:50:26]: build not needed
130s autopkgtest [16:50:27]: test run-unit-test: preparing testbed
134s Reading package lists...
134s Building dependency tree...
134s Reading state information...
134s Starting pkgProblemResolver with broken count: 0
134s Starting 2 pkgProblemResolver with broken count: 0
134s Done
135s The following additional packages will be installed:
135s   aglfn binfmt-support bwa ca-certificates-java canu circlator
135s   default-jre-headless fastaq fastjar fontconfig fontconfig-config
135s   fonts-dejavu-core fonts-dejavu-mono gnuplot-data gnuplot-nox jaligner
135s   jarwrapper java-common libapache-pom-java libasound2 libasound2-data
135s   libatinject-jsr330-api-java libavahi-client3 libavahi-common-data
135s   libavahi-common3 libcairo2 libcommons-compress-java libcommons-parent-java
135s   libcups2 libdatrie1 libdeflate0 liberror-prone-java libfastutil-java
135s   libfilesys-df-perl libfontconfig1 libgd3 libgomp1 libgraphite2-3
135s   libguava-java libharfbuzz0b libhts3 libhtscodecs2 libjbig0 libjpeg-turbo8
135s   libjpeg8 libjsr305-java liblcms2-2 liblerc4 liblua5.4-0 libpango-1.0-0
135s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpcsclite1 libpixman-1-0
135s   libsharpyuv0 libsnappy1v5 libssw-java libthai-data libthai0 libtiff6
135s   libwebp7 libxcb-render0 libxcb-shm0 libxpm4 libxrender1 libxslt1.1 mhap
135s   mummer openjdk-21-jre-headless prodigal python3-all python3-distutils
135s   python3-et-xmlfile python3-iniconfig python3-lib2to3 python3-lxml
135s   python3-openpyxl python3-packaging python3-pluggy python3-pymummer
135s   python3-pysam python3-pytest samtools
135s Suggested packages:
135s   nanopolish default-jre gnuplot-doc libasound2-plugins alsa-utils
135s   libatinject-jsr330-api-java-doc libasm-java libxz-java cups-common
135s   libgd-tools libjsr305-java-doc liblcms2-utils pcscd libnss-mdns
135s   fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho
135s   fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic python-lxml-doc
135s   python-openpyxl-doc cwltool
135s Recommended packages:
135s   spades fonts-liberation groff alsa-ucm-conf alsa-topology-conf python3-bs4
135s   python3-cssselect python3-html5lib python3-pil
135s The following NEW packages will be installed:
135s   aglfn autopkgtest-satdep binfmt-support bwa ca-certificates-java canu
135s   circlator default-jre-headless fastaq fastjar fontconfig fontconfig-config
135s   fonts-dejavu-core fonts-dejavu-mono gnuplot-data gnuplot-nox jaligner
135s   jarwrapper java-common libapache-pom-java libasound2 libasound2-data
135s   libatinject-jsr330-api-java libavahi-client3 libavahi-common-data
135s   libavahi-common3 libcairo2 libcommons-compress-java libcommons-parent-java
135s   libcups2 libdatrie1 libdeflate0 liberror-prone-java libfastutil-java
135s   libfilesys-df-perl libfontconfig1 libgd3 libgomp1 libgraphite2-3
135s   libguava-java libharfbuzz0b libhts3 libhtscodecs2 libjbig0 libjpeg-turbo8
135s   libjpeg8 libjsr305-java liblcms2-2 liblerc4 liblua5.4-0 libpango-1.0-0
135s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpcsclite1 libpixman-1-0
135s   libsharpyuv0 libsnappy1v5 libssw-java libthai-data libthai0 libtiff6
135s   libwebp7 libxcb-render0 libxcb-shm0 libxpm4 libxrender1 libxslt1.1 mhap
135s   mummer openjdk-21-jre-headless prodigal python3-all python3-distutils
135s   python3-et-xmlfile python3-iniconfig python3-lib2to3 python3-lxml
135s   python3-openpyxl python3-packaging python3-pluggy python3-pymummer
135s   python3-pysam python3-pytest samtools
135s 0 upgraded, 84 newly installed, 0 to remove and 0 not upgraded.
135s Need to get 92.5 MB/92.5 MB of archives.
135s After this operation, 351 MB of additional disk space will be used.
135s Get:1 /tmp/autopkgtest.kg4JTk/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [716 B]
135s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 binfmt-support arm64 2.2.2-6 [55.7 kB]
135s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 bwa arm64 0.7.17-7 [192 kB]
135s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 ca-certificates-java all 20240118 [11.6 kB]
135s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB]
135s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libsnappy1v5 arm64 1.1.10-1 [28.2 kB]
135s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libfilesys-df-perl arm64 0.92-7build2 [11.0 kB]
135s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 java-common all 0.75+exp1 [6798 B]
135s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libavahi-common-data arm64 0.8-13ubuntu2 [29.5 kB]
135s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libavahi-common3 arm64 0.8-13ubuntu2 [23.2 kB]
135s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libavahi-client3 arm64 0.8-13ubuntu2 [27.3 kB]
135s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libcups2 arm64 2.4.6-0ubuntu3 [270 kB]
135s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB]
135s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB]
135s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B]
135s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB]
135s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB]
135s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB]
135s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB]
135s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libasound2-data all 1.2.10-3build1 [20.7 kB]
135s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libasound2 arm64 1.2.10-3build1 [386 kB]
135s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB]
135s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB]
135s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libpcsclite1 arm64 2.0.0-1 [21.2 kB]
135s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 openjdk-21-jre-headless arm64 21.0.2+13-2 [45.8 MB]
138s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 default-jre-headless arm64 2:1.21-75+exp1 [3096 B]
138s Get:27 http://ftpmaster.internal/ubuntu noble/universe arm64 fastjar arm64 2:0.98-7 [61.9 kB]
138s Get:28 http://ftpmaster.internal/ubuntu noble/universe arm64 jarwrapper all 0.79 [10.3 kB]
138s Get:29 http://ftpmaster.internal/ubuntu noble/universe arm64 libapache-pom-java all 29-2 [5284 B]
138s Get:30 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-parent-java all 56-1 [10.7 kB]
138s Get:31 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-compress-java all 1.25.0-1 [612 kB]
138s Get:32 http://ftpmaster.internal/ubuntu noble/universe arm64 libfastutil-java all 8.5.12+dfsg-1 [19.8 MB]
138s Get:33 http://ftpmaster.internal/ubuntu noble/universe arm64 libatinject-jsr330-api-java all 1.0+ds1-5 [5348 B]
138s Get:34 http://ftpmaster.internal/ubuntu noble/universe arm64 liberror-prone-java all 2.18.0-1 [22.5 kB]
138s Get:35 http://ftpmaster.internal/ubuntu noble/universe arm64 libjsr305-java all 0.1~+svn49-11 [27.0 kB]
138s Get:36 http://ftpmaster.internal/ubuntu noble/universe arm64 libguava-java all 32.0.1-1 [2692 kB]
138s Get:37 http://ftpmaster.internal/ubuntu noble/universe arm64 jaligner all 1.0+dfsg-11 [136 kB]
138s Get:38 http://ftpmaster.internal/ubuntu noble/universe arm64 libssw-java arm64 1.1-14 [18.0 kB]
138s Get:39 http://ftpmaster.internal/ubuntu noble/universe arm64 mhap all 2.1.3+dfsg-3 [160 kB]
138s Get:40 http://ftpmaster.internal/ubuntu noble/universe arm64 aglfn all 1.7+git20191031.4036a9c-2 [30.6 kB]
138s Get:41 http://ftpmaster.internal/ubuntu noble/universe arm64 gnuplot-data all 5.4.4+dfsg1-2build1 [74.6 kB]
138s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB]
138s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB]
138s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B]
138s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB]
138s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB]
138s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB]
138s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB]
138s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB]
138s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB]
138s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB]
138s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB]
138s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 libxpm4 arm64 1:3.5.17-1 [34.5 kB]
138s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 libgd3 arm64 2.3.3-9ubuntu1 [119 kB]
138s Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 liblua5.4-0 arm64 5.4.6-3 [158 kB]
138s Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB]
138s Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB]
138s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB]
138s Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB]
138s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB]
138s Get:61 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB]
138s Get:62 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB]
138s Get:63 http://ftpmaster.internal/ubuntu noble/universe arm64 gnuplot-nox arm64 5.4.4+dfsg1-2build1 [879 kB]
138s Get:64 http://ftpmaster.internal/ubuntu noble/universe arm64 canu arm64 2.2+dfsg-5 [1500 kB]
138s Get:65 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB]
138s Get:66 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB]
138s Get:67 http://ftpmaster.internal/ubuntu noble/universe arm64 samtools arm64 1.19.2-1 [584 kB]
138s Get:68 http://ftpmaster.internal/ubuntu noble/universe arm64 fastaq all 3.17.0-6 [47.9 kB]
138s Get:69 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-et-xmlfile all 1.0.1-2.1 [9224 B]
138s Get:70 http://ftpmaster.internal/ubuntu noble/main arm64 libxslt1.1 arm64 1.1.39-0exp1 [166 kB]
138s Get:71 http://ftpmaster.internal/ubuntu noble/main arm64 python3-lxml arm64 5.1.0-1 [2042 kB]
138s Get:72 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-openpyxl all 3.1.2+dfsg-6 [152 kB]
138s Get:73 http://ftpmaster.internal/ubuntu noble/main arm64 python3-packaging all 23.2-1 [40.6 kB]
138s Get:74 http://ftpmaster.internal/ubuntu noble/universe arm64 mummer arm64 3.23+dfsg-8 [673 kB]
138s Get:75 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pymummer all 0.11.0-4 [17.1 kB]
138s Get:76 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pysam arm64 0.22.0+ds-1 [4399 kB]
138s Get:77 http://ftpmaster.internal/ubuntu noble/universe arm64 prodigal arm64 1:2.6.3-6 [822 kB]
138s Get:78 http://ftpmaster.internal/ubuntu noble/universe arm64 circlator all 1.5.6-11 [4618 kB]
138s Get:79 http://ftpmaster.internal/ubuntu noble/main arm64 python3-lib2to3 all 3.11.5-1 [79.0 kB]
138s Get:80 http://ftpmaster.internal/ubuntu noble/main arm64 python3-distutils all 3.11.5-1 [131 kB]
138s Get:81 http://ftpmaster.internal/ubuntu noble/main arm64 python3-all arm64 3.12.1-0ubuntu2 [906 B]
138s Get:82 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B]
138s Get:83 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pluggy all 1.4.0-1 [20.4 kB]
138s Get:84 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pytest all 7.4.4-1 [305 kB]
139s Fetched 92.5 MB in 3s (29.4 MB/s)
139s Selecting previously unselected package binfmt-support.
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139s Preparing to unpack .../00-binfmt-support_2.2.2-6_arm64.deb ...
139s Unpacking binfmt-support (2.2.2-6) ...
139s Selecting previously unselected package bwa.
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139s Unpacking bwa (0.7.17-7) ...
139s Selecting previously unselected package ca-certificates-java.
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139s Selecting previously unselected package libgomp1:arm64.
139s Preparing to unpack .../03-libgomp1_14-20240303-1ubuntu1_arm64.deb ...
139s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ...
139s Selecting previously unselected package libsnappy1v5:arm64.
139s Preparing to unpack .../04-libsnappy1v5_1.1.10-1_arm64.deb ...
139s Unpacking libsnappy1v5:arm64 (1.1.10-1) ...
139s Selecting previously unselected package libfilesys-df-perl.
139s Preparing to unpack .../05-libfilesys-df-perl_0.92-7build2_arm64.deb ...
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139s Selecting previously unselected package java-common.
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139s Selecting previously unselected package libavahi-common-data:arm64.
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139s Selecting previously unselected package libavahi-common3:arm64.
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139s Selecting previously unselected package libavahi-client3:arm64.
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139s Selecting previously unselected package libcups2:arm64.
139s Preparing to unpack .../10-libcups2_2.4.6-0ubuntu3_arm64.deb ...
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139s Selecting previously unselected package liblcms2-2:arm64.
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139s Selecting previously unselected package libjpeg-turbo8:arm64.
139s Preparing to unpack .../12-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ...
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139s Selecting previously unselected package libjpeg8:arm64.
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139s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ...
139s Selecting previously unselected package fonts-dejavu-mono.
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139s Selecting previously unselected package fonts-dejavu-core.
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139s Selecting previously unselected package fontconfig-config.
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140s Unpacking fontconfig-config (2.15.0-1ubuntu1) ...
140s Selecting previously unselected package libfontconfig1:arm64.
140s Preparing to unpack .../17-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ...
140s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ...
140s Selecting previously unselected package libasound2-data.
140s Preparing to unpack .../18-libasound2-data_1.2.10-3build1_all.deb ...
140s Unpacking libasound2-data (1.2.10-3build1) ...
140s Selecting previously unselected package libasound2:arm64.
140s Preparing to unpack .../19-libasound2_1.2.10-3build1_arm64.deb ...
140s Unpacking libasound2:arm64 (1.2.10-3build1) ...
140s Selecting previously unselected package libgraphite2-3:arm64.
140s Preparing to unpack .../20-libgraphite2-3_1.3.14-2_arm64.deb ...
140s Unpacking libgraphite2-3:arm64 (1.3.14-2) ...
140s Selecting previously unselected package libharfbuzz0b:arm64.
140s Preparing to unpack .../21-libharfbuzz0b_8.3.0-2_arm64.deb ...
140s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ...
140s Selecting previously unselected package libpcsclite1:arm64.
140s Preparing to unpack .../22-libpcsclite1_2.0.0-1_arm64.deb ...
140s Unpacking libpcsclite1:arm64 (2.0.0-1) ...
140s Selecting previously unselected package openjdk-21-jre-headless:arm64.
140s Preparing to unpack .../23-openjdk-21-jre-headless_21.0.2+13-2_arm64.deb ...
140s Unpacking openjdk-21-jre-headless:arm64 (21.0.2+13-2) ...
141s Selecting previously unselected package default-jre-headless.
141s Preparing to unpack .../24-default-jre-headless_2%3a1.21-75+exp1_arm64.deb ...
141s Unpacking default-jre-headless (2:1.21-75+exp1) ...
141s Selecting previously unselected package fastjar.
141s Preparing to unpack .../25-fastjar_2%3a0.98-7_arm64.deb ...
141s Unpacking fastjar (2:0.98-7) ...
141s Selecting previously unselected package jarwrapper.
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141s Unpacking jarwrapper (0.79) ...
141s Selecting previously unselected package libapache-pom-java.
141s Preparing to unpack .../27-libapache-pom-java_29-2_all.deb ...
141s Unpacking libapache-pom-java (29-2) ...
141s Selecting previously unselected package libcommons-parent-java.
141s Preparing to unpack .../28-libcommons-parent-java_56-1_all.deb ...
141s Unpacking libcommons-parent-java (56-1) ...
141s Selecting previously unselected package libcommons-compress-java.
141s Preparing to unpack .../29-libcommons-compress-java_1.25.0-1_all.deb ...
141s Unpacking libcommons-compress-java (1.25.0-1) ...
141s Selecting previously unselected package libfastutil-java.
141s Preparing to unpack .../30-libfastutil-java_8.5.12+dfsg-1_all.deb ...
141s Unpacking libfastutil-java (8.5.12+dfsg-1) ...
141s Selecting previously unselected package libatinject-jsr330-api-java.
141s Preparing to unpack .../31-libatinject-jsr330-api-java_1.0+ds1-5_all.deb ...
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141s Selecting previously unselected package liberror-prone-java.
141s Preparing to unpack .../32-liberror-prone-java_2.18.0-1_all.deb ...
141s Unpacking liberror-prone-java (2.18.0-1) ...
141s Selecting previously unselected package libjsr305-java.
141s Preparing to unpack .../33-libjsr305-java_0.1~+svn49-11_all.deb ...
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141s Selecting previously unselected package libguava-java.
142s Preparing to unpack .../34-libguava-java_32.0.1-1_all.deb ...
142s Unpacking libguava-java (32.0.1-1) ...
142s Selecting previously unselected package jaligner.
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142s Unpacking jaligner (1.0+dfsg-11) ...
142s Selecting previously unselected package libssw-java.
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142s Selecting previously unselected package mhap.
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142s Selecting previously unselected package aglfn.
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142s Unpacking aglfn (1.7+git20191031.4036a9c-2) ...
142s Selecting previously unselected package gnuplot-data.
142s Preparing to unpack .../39-gnuplot-data_5.4.4+dfsg1-2build1_all.deb ...
142s Unpacking gnuplot-data (5.4.4+dfsg1-2build1) ...
142s Selecting previously unselected package libpixman-1-0:arm64.
142s Preparing to unpack .../40-libpixman-1-0_0.42.2-1_arm64.deb ...
142s Unpacking libpixman-1-0:arm64 (0.42.2-1) ...
142s Selecting previously unselected package libxcb-render0:arm64.
142s Preparing to unpack .../41-libxcb-render0_1.15-1_arm64.deb ...
142s Unpacking libxcb-render0:arm64 (1.15-1) ...
142s Selecting previously unselected package libxcb-shm0:arm64.
142s Preparing to unpack .../42-libxcb-shm0_1.15-1_arm64.deb ...
142s Unpacking libxcb-shm0:arm64 (1.15-1) ...
142s Selecting previously unselected package libxrender1:arm64.
142s Preparing to unpack .../43-libxrender1_1%3a0.9.10-1.1_arm64.deb ...
142s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ...
142s Selecting previously unselected package libcairo2:arm64.
142s Preparing to unpack .../44-libcairo2_1.18.0-1_arm64.deb ...
142s Unpacking libcairo2:arm64 (1.18.0-1) ...
142s Selecting previously unselected package libdeflate0:arm64.
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142s Unpacking libdeflate0:arm64 (1.19-1) ...
142s Selecting previously unselected package libjbig0:arm64.
142s Preparing to unpack .../46-libjbig0_2.1-6.1ubuntu1_arm64.deb ...
142s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ...
142s Selecting previously unselected package liblerc4:arm64.
142s Preparing to unpack .../47-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ...
142s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ...
142s Selecting previously unselected package libsharpyuv0:arm64.
142s Preparing to unpack .../48-libsharpyuv0_1.3.2-0.4_arm64.deb ...
142s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ...
142s Selecting previously unselected package libwebp7:arm64.
142s Preparing to unpack .../49-libwebp7_1.3.2-0.4_arm64.deb ...
142s Unpacking libwebp7:arm64 (1.3.2-0.4) ...
142s Selecting previously unselected package libtiff6:arm64.
142s Preparing to unpack .../50-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ...
142s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ...
142s Selecting previously unselected package libxpm4:arm64.
142s Preparing to unpack .../51-libxpm4_1%3a3.5.17-1_arm64.deb ...
142s Unpacking libxpm4:arm64 (1:3.5.17-1) ...
142s Selecting previously unselected package libgd3:arm64.
142s Preparing to unpack .../52-libgd3_2.3.3-9ubuntu1_arm64.deb ...
142s Unpacking libgd3:arm64 (2.3.3-9ubuntu1) ...
142s Selecting previously unselected package liblua5.4-0:arm64.
142s Preparing to unpack .../53-liblua5.4-0_5.4.6-3_arm64.deb ...
142s Unpacking liblua5.4-0:arm64 (5.4.6-3) ...
142s Selecting previously unselected package fontconfig.
142s Preparing to unpack .../54-fontconfig_2.15.0-1ubuntu1_arm64.deb ...
142s Unpacking fontconfig (2.15.0-1ubuntu1) ...
142s Selecting previously unselected package libthai-data.
142s Preparing to unpack .../55-libthai-data_0.1.29-2_all.deb ...
142s Unpacking libthai-data (0.1.29-2) ...
142s Selecting previously unselected package libdatrie1:arm64.
142s Preparing to unpack .../56-libdatrie1_0.2.13-3_arm64.deb ...
142s Unpacking libdatrie1:arm64 (0.2.13-3) ...
142s Selecting previously unselected package libthai0:arm64.
142s Preparing to unpack .../57-libthai0_0.1.29-2_arm64.deb ...
142s Unpacking libthai0:arm64 (0.1.29-2) ...
142s Selecting previously unselected package libpango-1.0-0:arm64.
142s Preparing to unpack .../58-libpango-1.0-0_1.51.0+ds-4_arm64.deb ...
142s Unpacking libpango-1.0-0:arm64 (1.51.0+ds-4) ...
142s Selecting previously unselected package libpangoft2-1.0-0:arm64.
142s Preparing to unpack .../59-libpangoft2-1.0-0_1.51.0+ds-4_arm64.deb ...
142s Unpacking libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ...
142s Selecting previously unselected package libpangocairo-1.0-0:arm64.
142s Preparing to unpack .../60-libpangocairo-1.0-0_1.51.0+ds-4_arm64.deb ...
142s Unpacking libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ...
142s Selecting previously unselected package gnuplot-nox.
142s Preparing to unpack .../61-gnuplot-nox_5.4.4+dfsg1-2build1_arm64.deb ...
142s Unpacking gnuplot-nox (5.4.4+dfsg1-2build1) ...
142s Selecting previously unselected package canu.
142s Preparing to unpack .../62-canu_2.2+dfsg-5_arm64.deb ...
142s Unpacking canu (2.2+dfsg-5) ...
142s Selecting previously unselected package libhtscodecs2:arm64.
142s Preparing to unpack .../63-libhtscodecs2_1.6.0-1_arm64.deb ...
142s Unpacking libhtscodecs2:arm64 (1.6.0-1) ...
142s Selecting previously unselected package libhts3:arm64.
142s Preparing to unpack .../64-libhts3_1.18+ds-1_arm64.deb ...
142s Unpacking libhts3:arm64 (1.18+ds-1) ...
142s Selecting previously unselected package samtools.
142s Preparing to unpack .../65-samtools_1.19.2-1_arm64.deb ...
142s Unpacking samtools (1.19.2-1) ...
143s Selecting previously unselected package fastaq.
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143s Unpacking fastaq (3.17.0-6) ...
143s Selecting previously unselected package python3-et-xmlfile.
143s Preparing to unpack .../67-python3-et-xmlfile_1.0.1-2.1_all.deb ...
143s Unpacking python3-et-xmlfile (1.0.1-2.1) ...
143s Selecting previously unselected package libxslt1.1:arm64.
143s Preparing to unpack .../68-libxslt1.1_1.1.39-0exp1_arm64.deb ...
143s Unpacking libxslt1.1:arm64 (1.1.39-0exp1) ...
143s Selecting previously unselected package python3-lxml:arm64.
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143s Unpacking python3-lxml:arm64 (5.1.0-1) ...
143s Selecting previously unselected package python3-openpyxl.
143s Preparing to unpack .../70-python3-openpyxl_3.1.2+dfsg-6_all.deb ...
143s Unpacking python3-openpyxl (3.1.2+dfsg-6) ...
143s Selecting previously unselected package python3-packaging.
143s Preparing to unpack .../71-python3-packaging_23.2-1_all.deb ...
143s Unpacking python3-packaging (23.2-1) ...
143s Selecting previously unselected package mummer.
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143s Unpacking mummer (3.23+dfsg-8) ...
143s Selecting previously unselected package python3-pymummer.
143s Preparing to unpack .../73-python3-pymummer_0.11.0-4_all.deb ...
143s Unpacking python3-pymummer (0.11.0-4) ...
143s Selecting previously unselected package python3-pysam.
143s Preparing to unpack .../74-python3-pysam_0.22.0+ds-1_arm64.deb ...
143s Unpacking python3-pysam (0.22.0+ds-1) ...
143s Selecting previously unselected package prodigal.
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143s Unpacking prodigal (1:2.6.3-6) ...
143s Selecting previously unselected package circlator.
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143s Unpacking circlator (1.5.6-11) ...
143s Selecting previously unselected package python3-lib2to3.
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143s Unpacking python3-lib2to3 (3.11.5-1) ...
143s Selecting previously unselected package python3-distutils.
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143s Unpacking python3-distutils (3.11.5-1) ...
143s Selecting previously unselected package python3-all.
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143s Unpacking python3-all (3.12.1-0ubuntu2) ...
143s Selecting previously unselected package python3-iniconfig.
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143s Unpacking python3-iniconfig (1.1.1-2) ...
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143s Unpacking python3-pluggy (1.4.0-1) ...
143s Selecting previously unselected package python3-pytest.
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143s Unpacking python3-pytest (7.4.4-1) ...
143s Selecting previously unselected package autopkgtest-satdep.
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143s Unpacking autopkgtest-satdep (0) ...
143s Setting up libhtscodecs2:arm64 (1.6.0-1) ...
143s Setting up fastjar (2:0.98-7) ...
143s Setting up libgraphite2-3:arm64 (1.3.14-2) ...
143s Setting up liblcms2-2:arm64 (2.14-2) ...
143s Setting up python3-iniconfig (1.1.1-2) ...
144s Setting up libpixman-1-0:arm64 (0.42.2-1) ...
144s Setting up libfastutil-java (8.5.12+dfsg-1) ...
144s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ...
144s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ...
144s Setting up libjsr305-java (0.1~+svn49-11) ...
144s Setting up libxpm4:arm64 (1:3.5.17-1) ...
144s Setting up java-common (0.75+exp1) ...
144s Setting up libxrender1:arm64 (1:0.9.10-1.1) ...
144s Setting up libdatrie1:arm64 (0.2.13-3) ...
144s Setting up libxcb-render0:arm64 (1.15-1) ...
144s Setting up prodigal (1:2.6.3-6) ...
144s Setting up bwa (0.7.17-7) ...
144s Setting up libfilesys-df-perl (0.92-7build2) ...
144s Setting up libdeflate0:arm64 (1.19-1) ...
144s Setting up libxcb-shm0:arm64 (1.15-1) ...
144s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ...
144s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ...
144s Setting up libssw-java (1.1-14) ...
144s Setting up libsnappy1v5:arm64 (1.1.10-1) ...
144s Setting up libasound2-data (1.2.10-3build1) ...
144s Setting up python3-packaging (23.2-1) ...
144s Setting up aglfn (1.7+git20191031.4036a9c-2) ...
144s Setting up libapache-pom-java (29-2) ...
144s Setting up libavahi-common-data:arm64 (0.8-13ubuntu2) ...
144s Setting up libatinject-jsr330-api-java (1.0+ds1-5) ...
144s Setting up fonts-dejavu-mono (2.37-8) ...
144s Setting up binfmt-support (2.2.2-6) ...
144s update-binfmts: warning: python3.12 already enabled in kernel.
144s Created symlink /etc/systemd/system/multi-user.target.wants/binfmt-support.service → /usr/lib/systemd/system/binfmt-support.service.

144s Setting up fonts-dejavu-core (2.37-8) ...
145s Setting up libpcsclite1:arm64 (2.0.0-1) ...
145s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ...
145s Setting up python3-pluggy (1.4.0-1) ...
145s Setting up libwebp7:arm64 (1.3.2-0.4) ...
145s Setting up libasound2:arm64 (1.2.10-3build1) ...
145s Setting up libxslt1.1:arm64 (1.1.39-0exp1) ...
145s Setting up mummer (3.23+dfsg-8) ...
145s Setting up python3-et-xmlfile (1.0.1-2.1) ...
145s Setting up liblua5.4-0:arm64 (5.4.6-3) ...
145s Setting up libharfbuzz0b:arm64 (8.3.0-2) ...
145s Setting up libthai-data (0.1.29-2) ...
145s Setting up ca-certificates-java (20240118) ...
145s No JRE found. Skipping Java certificates setup.
145s Setting up python3-lib2to3 (3.11.5-1) ...
145s Setting up libjpeg8:arm64 (8c-2ubuntu11) ...
145s Setting up python3-distutils (3.11.5-1) ...
145s python3.12: can't get files for byte-compilation
145s Setting up gnuplot-data (5.4.4+dfsg1-2build1) ...
145s Setting up libhts3:arm64 (1.18+ds-1) ...
145s Setting up python3-pysam (0.22.0+ds-1) ...
145s Setting up jarwrapper (0.79) ...
145s Setting up fontconfig-config (2.15.0-1ubuntu1) ...
146s Setting up python3-pytest (7.4.4-1) ...
146s Setting up libcommons-parent-java (56-1) ...
146s Setting up libavahi-common3:arm64 (0.8-13ubuntu2) ...
146s Setting up python3-all (3.12.1-0ubuntu2) ...
146s Setting up samtools (1.19.2-1) ...
146s Setting up libthai0:arm64 (0.1.29-2) ...
146s Setting up python3-lxml:arm64 (5.1.0-1) ...
146s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ...
146s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ...
146s Setting up libavahi-client3:arm64 (0.8-13ubuntu2) ...
146s Setting up fontconfig (2.15.0-1ubuntu1) ...
148s Regenerating fonts cache... done.
148s Setting up libcommons-compress-java (1.25.0-1) ...
148s Setting up fastaq (3.17.0-6) ...
148s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:37: SyntaxWarning: invalid escape sequence '\s'
148s   phylip_regex = re.compile('^\s*[0-9]+\s+[0-9]+$')
148s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:38: SyntaxWarning: invalid escape sequence '\s'
148s   gbk_regex = re.compile('^LOCUS\s+\S')
148s Setting up libpango-1.0-0:arm64 (1.51.0+ds-4) ...
148s Setting up libcairo2:arm64 (1.18.0-1) ...
148s Setting up python3-pymummer (0.11.0-4) ...
148s Setting up python3-openpyxl (3.1.2+dfsg-6) ...
148s Setting up libgd3:arm64 (2.3.3-9ubuntu1) ...
148s Setting up libcups2:arm64 (2.4.6-0ubuntu3) ...
148s Setting up libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ...
148s Setting up libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ...
148s Setting up openjdk-21-jre-headless:arm64 (21.0.2+13-2) ...
148s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode
148s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode
148s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
148s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
148s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
148s Setting up gnuplot-nox (5.4.4+dfsg1-2build1) ...
148s update-alternatives: using /usr/bin/gnuplot-nox to provide /usr/bin/gnuplot (gnuplot) in auto mode
148s Setting up libguava-java (32.0.1-1) ...
148s Setting up liberror-prone-java (2.18.0-1) ...
148s Processing triggers for libc-bin (2.39-0ubuntu6) ...
148s Processing triggers for man-db (2.12.0-3) ...
149s Processing triggers for install-info (7.1-3) ...
149s Processing triggers for ca-certificates-java (20240118) ...
150s Adding debian:ACCVRAIZ1.pem
150s Adding debian:AC_RAIZ_FNMT-RCM.pem
150s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem
150s Adding debian:ANF_Secure_Server_Root_CA.pem
150s Adding debian:Actalis_Authentication_Root_CA.pem
150s Adding debian:AffirmTrust_Commercial.pem
150s Adding debian:AffirmTrust_Networking.pem
150s Adding debian:AffirmTrust_Premium.pem
150s Adding debian:AffirmTrust_Premium_ECC.pem
150s Adding debian:Amazon_Root_CA_1.pem
150s Adding debian:Amazon_Root_CA_2.pem
150s Adding debian:Amazon_Root_CA_3.pem
150s Adding debian:Amazon_Root_CA_4.pem
150s Adding debian:Atos_TrustedRoot_2011.pem
150s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem
150s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem
150s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
150s Adding debian:BJCA_Global_Root_CA1.pem
150s Adding debian:BJCA_Global_Root_CA2.pem
150s Adding debian:Baltimore_CyberTrust_Root.pem
150s Adding debian:Buypass_Class_2_Root_CA.pem
150s Adding debian:Buypass_Class_3_Root_CA.pem
150s Adding debian:CA_Disig_Root_R2.pem
150s Adding debian:CFCA_EV_ROOT.pem
150s Adding debian:COMODO_Certification_Authority.pem
150s Adding debian:COMODO_ECC_Certification_Authority.pem
150s Adding debian:COMODO_RSA_Certification_Authority.pem
150s Adding debian:Certainly_Root_E1.pem
150s Adding debian:Certainly_Root_R1.pem
150s Adding debian:Certigna.pem
150s Adding debian:Certigna_Root_CA.pem
150s Adding debian:Certum_EC-384_CA.pem
150s Adding debian:Certum_Trusted_Network_CA.pem
150s Adding debian:Certum_Trusted_Network_CA_2.pem
150s Adding debian:Certum_Trusted_Root_CA.pem
150s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem
150s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem
150s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem
150s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem
150s Adding debian:Comodo_AAA_Services_root.pem
150s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem
150s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem
150s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
150s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
150s Adding debian:DigiCert_Assured_ID_Root_CA.pem
150s Adding debian:DigiCert_Assured_ID_Root_G2.pem
150s Adding debian:DigiCert_Assured_ID_Root_G3.pem
150s Adding debian:DigiCert_Global_Root_CA.pem
150s Adding debian:DigiCert_Global_Root_G2.pem
150s Adding debian:DigiCert_Global_Root_G3.pem
150s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
150s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem
150s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem
150s Adding debian:DigiCert_Trusted_Root_G4.pem
150s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
150s Adding debian:Entrust_Root_Certification_Authority.pem
150s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
150s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
150s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem
150s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem
150s Adding debian:GLOBALTRUST_2020.pem
150s Adding debian:GTS_Root_R1.pem
150s Adding debian:GTS_Root_R2.pem
150s Adding debian:GTS_Root_R3.pem
150s Adding debian:GTS_Root_R4.pem
150s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
150s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
150s Adding debian:GlobalSign_Root_CA.pem
150s Adding debian:GlobalSign_Root_CA_-_R3.pem
150s Adding debian:GlobalSign_Root_CA_-_R6.pem
150s Adding debian:GlobalSign_Root_E46.pem
150s Adding debian:GlobalSign_Root_R46.pem
150s Adding debian:Go_Daddy_Class_2_CA.pem
150s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
150s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem
150s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem
150s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem
150s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem
150s Adding debian:HiPKI_Root_CA_-_G1.pem
150s Adding debian:Hongkong_Post_Root_CA_3.pem
150s Adding debian:ISRG_Root_X1.pem
150s Adding debian:ISRG_Root_X2.pem
150s Adding debian:IdenTrust_Commercial_Root_CA_1.pem
150s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
150s Adding debian:Izenpe.com.pem
150s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
150s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem
150s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem
150s Adding debian:NAVER_Global_Root_Certification_Authority.pem
150s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
150s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
150s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem
150s Adding debian:QuoVadis_Root_CA_1_G3.pem
150s Adding debian:QuoVadis_Root_CA_2.pem
150s Adding debian:QuoVadis_Root_CA_2_G3.pem
150s Adding debian:QuoVadis_Root_CA_3.pem
150s Adding debian:QuoVadis_Root_CA_3_G3.pem
150s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem
150s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem
150s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem
150s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem
150s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem
150s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem
150s Adding debian:SZAFIR_ROOT_CA2.pem
150s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem
150s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem
150s Adding debian:SecureSign_RootCA11.pem
150s Adding debian:SecureTrust_CA.pem
150s Adding debian:Secure_Global_CA.pem
150s Adding debian:Security_Communication_ECC_RootCA1.pem
150s Adding debian:Security_Communication_RootCA2.pem
150s Adding debian:Security_Communication_RootCA3.pem
150s Adding debian:Security_Communication_Root_CA.pem
150s Adding debian:Starfield_Class_2_CA.pem
150s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
150s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
150s Adding debian:SwissSign_Gold_CA_-_G2.pem
150s Adding debian:SwissSign_Silver_CA_-_G2.pem
150s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
150s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
150s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
150s Adding debian:TWCA_Global_Root_CA.pem
150s Adding debian:TWCA_Root_Certification_Authority.pem
150s Adding debian:TeliaSonera_Root_CA_v1.pem
150s Adding debian:Telia_Root_CA_v2.pem
150s Adding debian:TrustAsia_Global_Root_CA_G3.pem
150s Adding debian:TrustAsia_Global_Root_CA_G4.pem
150s Adding debian:Trustwave_Global_Certification_Authority.pem
150s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem
150s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem
150s Adding debian:TunTrust_Root_CA.pem
150s Adding debian:UCA_Extended_Validation_Root.pem
150s Adding debian:UCA_Global_G2_Root.pem
150s Adding debian:USERTrust_ECC_Certification_Authority.pem
150s Adding debian:USERTrust_RSA_Certification_Authority.pem
150s Adding debian:XRamp_Global_CA_Root.pem
150s Adding debian:certSIGN_ROOT_CA.pem
150s Adding debian:certSIGN_Root_CA_G2.pem
150s Adding debian:e-Szigno_Root_CA_2017.pem
150s Adding debian:ePKI_Root_Certification_Authority.pem
150s Adding debian:emSign_ECC_Root_CA_-_C3.pem
150s Adding debian:emSign_ECC_Root_CA_-_G3.pem
150s Adding debian:emSign_Root_CA_-_C1.pem
150s Adding debian:emSign_Root_CA_-_G1.pem
150s Adding debian:vTrus_ECC_Root_CA.pem
150s Adding debian:vTrus_Root_CA.pem
150s done.
150s Setting up default-jre-headless (2:1.21-75+exp1) ...
150s Setting up jaligner (1.0+dfsg-11) ...
150s Setting up mhap (2.1.3+dfsg-3) ...
150s Setting up canu (2.2+dfsg-5) ...
150s Setting up circlator (1.5.6-11) ...
150s /usr/lib/python3/dist-packages/circlator/dnaa.py:18: SyntaxWarning: invalid escape sequence '\s'
150s   self.uniprot_search = re.sub('\s+', '+', uniprot_search.strip())
150s Setting up autopkgtest-satdep (0) ...
154s (Reading database ... 77388 files and directories currently installed.)
154s Removing autopkgtest-satdep (0) ...
155s autopkgtest [16:50:52]: test run-unit-test: [-----------------------
155s + pkg=circlator
155s + export LC_ALL=C.UTF-8
155s + LC_ALL=C.UTF-8
155s + '[' /tmp/autopkgtest.kg4JTk/autopkgtest_tmp = '' ']'
155s + 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.kg4JTk/autopkgtest_tmp
155s + cd /tmp/autopkgtest.kg4JTk/autopkgtest_tmp
155s + tar xaf data.tar.xz
155s + 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
155s ++ py3versions --supported
155s + for py in $(py3versions --supported 2> /dev/null)
155s + eval dpkg-architecture --is amd64
155s ++ dpkg-architecture --is amd64
155s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation)
155s + python3.12 -m pytest -v -k 'not (test_build_spades_kmers or test_make_spades_command)'
156s ============================= test session starts ==============================
156s platform linux -- Python 3.12.2, pytest-7.4.4, pluggy-1.4.0 -- /usr/bin/python3.12
156s cachedir: .pytest_cache
156s rootdir: /tmp/autopkgtest.kg4JTk/autopkgtest_tmp
156s collecting ... collected 115 items / 2 deselected / 113 selected
156s 
156s assemble_test.py::TestAssembleCanu::test_make_canu_command PASSED        [  0%]
156s assemble_test.py::TestAssembleCanu::test_rename_canu_contigs PASSED      [  1%]
156s assembly_test.py::TestAssembly::test_circular_contigs_from_canu_gfa PASSED [  2%]
156s assembly_test.py::TestAssembly::test_circular_contigs_from_spades_after_3_6_1 PASSED [  3%]
156s assembly_test.py::TestAssembly::test_circular_contigs_from_spades_before_3_6_1 PASSED [  4%]
156s assembly_test.py::TestAssembly::test_circular_contigs_just_fasta PASSED  [  5%]
156s assembly_test.py::TestAssembly::test_circular_contigs_spades_post_3_6_1 PASSED [  6%]
156s assembly_test.py::TestAssembly::test_circular_contigs_spades_pre_3_6_1 PASSED [  7%]
156s assembly_test.py::TestAssembly::test_circular_edges_to_edge_numbers_dict PASSED [  7%]
156s assembly_test.py::TestAssembly::test_get_contigs PASSED                  [  8%]
156s assembly_test.py::TestAssembly::test_init_file_not_dir PASSED            [  9%]
156s assembly_test.py::TestAssembly::test_init_post_3_6_1_ok PASSED           [ 10%]
156s assembly_test.py::TestAssembly::test_init_pre_3_6_1_ok PASSED            [ 11%]
156s assembly_test.py::TestAssembly::test_init_raises_error PASSED            [ 12%]
156s assembly_test.py::TestAssembly::test_spades_contigs_paths_to_dict PASSED [ 13%]
156s bamfilter_test.py::TestBamfilter::test_all_reads_from_contig PASSED      [ 14%]
156s bamfilter_test.py::TestBamfilter::test_break_reads PASSED                [ 15%]
156s bamfilter_test.py::TestBamfilter::test_check_contigs_to_use PASSED       [ 15%]
156s bamfilter_test.py::TestBamfilter::test_exclude_region PASSED             [ 16%]
156s bamfilter_test.py::TestBamfilter::test_get_all_unmapped_reads PASSED     [ 17%]
156s bamfilter_test.py::TestBamfilter::test_get_contigs_to_use PASSED         [ 18%]
156s bamfilter_test.py::TestBamfilter::test_get_ref_lengths PASSED            [ 19%]
156s bamfilter_test.py::TestBamfilter::test_get_region_end PASSED             [ 20%]
156s bamfilter_test.py::TestBamfilter::test_get_region_start PASSED           [ 21%]
156s bamfilter_test.py::TestBamfilter::test_run_discard_unmapped_no_quals PASSED [ 22%]
156s bamfilter_test.py::TestBamfilter::test_run_keep_unmapped_no_quals PASSED [ 23%]
156s bamfilter_test.py::TestBamfilter::test_run_keep_unmapped_with_quals PASSED [ 23%]
156s clean_test.py::TestClean::test_clean_contigs PASSED                      [ 24%]
156s clean_test.py::TestClean::test_collapse_list_of_sets PASSED              [ 25%]
156s clean_test.py::TestClean::test_containing_contigs PASSED                 [ 26%]
156s clean_test.py::TestClean::test_contains PASSED                           [ 27%]
156s clean_test.py::TestClean::test_expand_containing_using_transitivity PASSED [ 28%]
156s clean_test.py::TestClean::test_get_all_containing PASSED                 [ 29%]
156s clean_test.py::TestClean::test_get_containing_contigs PASSED             [ 30%]
156s clean_test.py::TestClean::test_get_contigs_to_keep PASSED                [ 30%]
156s clean_test.py::TestClean::test_get_identical_contigs PASSED              [ 31%]
156s clean_test.py::TestClean::test_infinite_recursion PASSED                 [ 32%]
156s clean_test.py::TestClean::test_load_nucmer_hits PASSED                   [ 33%]
156s clean_test.py::TestClean::test_longest_contig PASSED                     [ 34%]
156s clean_test.py::TestClean::test_remove_identical_contigs PASSED           [ 35%]
156s clean_test.py::TestClean::test_remove_small_contigs PASSED               [ 36%]
156s clean_test.py::TestClean::test_write_log PASSED                          [ 37%]
156s common_test.py::TestCommon::test_check_files_exist PASSED                [ 38%]
156s dnaa_test.py::TestDnaa::test_append_stop_to_seq PASSED                   [ 38%]
156s dnaa_test.py::TestDnaa::test_check_sequence PASSED                       [ 39%]
156s dnaa_test.py::TestDnaa::test_get_uniprot_url PASSED                      [ 40%]
156s dnaa_test.py::TestDnaa::test_header_matches_regex PASSED                 [ 41%]
156s dnaa_test.py::TestDnaa::test_header_to_genus_species PASSED              [ 42%]
156s dnaa_test.py::TestDnaa::test_reverse_translate PASSED                    [ 43%]
156s external_progs_test.py::TestExternalProgs::test_bwa_version PASSED       [ 44%]
156s external_progs_test.py::TestExternalProgs::test_canu_version PASSED      [ 45%]
156s external_progs_test.py::TestExternalProgs::test_nucmer_version PASSED    [ 46%]
156s external_progs_test.py::TestExternalProgs::test_prodigal_version PASSED  [ 46%]
156s external_progs_test.py::TestExternalProgs::test_samtools_original_version PASSED [ 47%]
156s external_progs_test.py::TestExternalProgs::test_samtools_version PASSED  [ 48%]
156s external_progs_test.py::TestExternalProgs::test_spades_version PASSED    [ 49%]
156s mapping_test.py::TestMapping::test_aligned_read_to_read PASSED           [ 50%]
156s mapping_test.py::TestMapping::test_bwa_index PASSED                      [ 51%]
156s mapping_test.py::TestMapping::test_bwa_index_clean PASSED                [ 52%]
156s mapping_test.py::TestMapping::test_bwa_mem PASSED                        [ 53%]
156s merge_test.py::TestMerge::test_can_circularise PASSED                    [ 53%]
156s merge_test.py::TestMerge::test_contigs_dict_to_file PASSED               [ 54%]
156s merge_test.py::TestMerge::test_filter_bridging_contigs PASSED            [ 55%]
156s merge_test.py::TestMerge::test_get_hit_nearest_ref_end PASSED            [ 56%]
156s merge_test.py::TestMerge::test_get_hit_nearest_ref_start PASSED          [ 57%]
156s merge_test.py::TestMerge::test_get_longest_hit_at_qry_end PASSED         [ 58%]
156s merge_test.py::TestMerge::test_get_longest_hit_at_qry_start PASSED       [ 59%]
156s merge_test.py::TestMerge::test_get_longest_hit_at_ref_end PASSED         [ 60%]
156s merge_test.py::TestMerge::test_get_longest_hit_at_ref_start PASSED       [ 61%]
156s merge_test.py::TestMerge::test_get_longest_hit_by_ref_length PASSED      [ 61%]
156s merge_test.py::TestMerge::test_get_possible_circular_ref_contigs PASSED  [ 62%]
156s merge_test.py::TestMerge::test_get_possible_circular_ref_contigs_same_best_hits PASSED [ 63%]
156s merge_test.py::TestMerge::test_get_possible_query_bridging_contigs PASSED [ 64%]
156s merge_test.py::TestMerge::test_get_spades_circular_nodes PASSED          [ 65%]
156s merge_test.py::TestMerge::test_has_qry_hit_longer_than PASSED            [ 66%]
156s merge_test.py::TestMerge::test_hits_hashed_by_query PASSED               [ 67%]
156s merge_test.py::TestMerge::test_hits_have_same_query PASSED               [ 68%]
156s merge_test.py::TestMerge::test_hits_have_same_reference PASSED           [ 69%]
156s merge_test.py::TestMerge::test_index_fasta PASSED                        [ 69%]
156s merge_test.py::TestMerge::test_is_at_qry_end PASSED                      [ 70%]
156s merge_test.py::TestMerge::test_is_at_qry_start PASSED                    [ 71%]
156s merge_test.py::TestMerge::test_is_at_ref_end PASSED                      [ 72%]
156s merge_test.py::TestMerge::test_is_at_ref_start PASSED                    [ 73%]
156s merge_test.py::TestMerge::test_load_nucmer_hits PASSED                   [ 74%]
156s merge_test.py::TestMerge::test_make_circularised_contig_1 PASSED         [ 75%]
156s merge_test.py::TestMerge::test_make_circularised_contig_2 PASSED         [ 76%]
156s merge_test.py::TestMerge::test_make_new_contig_from_nucmer_and_spades_not_hit PASSED [ 76%]
156s merge_test.py::TestMerge::test_make_new_contig_from_nucmer_and_spades_with_hit PASSED [ 77%]
156s merge_test.py::TestMerge::test_merge_bridged_contig_pair1 PASSED         [ 78%]
156s merge_test.py::TestMerge::test_merge_bridged_contig_pair2 PASSED         [ 79%]
157s merge_test.py::TestMerge::test_merge_bridged_contig_pair3 PASSED         [ 80%]
157s merge_test.py::TestMerge::test_merge_bridged_contig_pair4 PASSED         [ 81%]
157s merge_test.py::TestMerge::test_min_qry_hit_length PASSED                 [ 82%]
157s merge_test.py::TestMerge::test_orientation_ok_to_bridge_contigs PASSED   [ 83%]
157s merge_test.py::TestMerge::test_remove_keys_from_dict_with_nonunique_values PASSED [ 84%]
157s merge_test.py::TestMerge::test_write_act_files PASSED                    [ 84%]
157s minimus2_test.py::TestMinimus2::test_run_initial_merge SKIPPED (Amos...) [ 85%]
157s minimus2_test.py::TestMinimus2::test_run_minimus2 SKIPPED (Amos is n...) [ 86%]
157s minimus2_test.py::TestMinimus2::test_run_minimus2_on_each_contig SKIPPED [ 87%]
157s minimus2_test.py::TestMinimus2::test_run_minimus2_on_one_contig_will_not_work SKIPPED [ 88%]
157s minimus2_test.py::TestMinimus2::test_run_minimus2_on_one_contig_will_work SKIPPED [ 89%]
157s minimus2_test.py::TestMinimus2::test_write_split_contig SKIPPED (Amo...) [ 90%]
157s start_fixer_test.py::TestStartFixer::test_find_circular_using_prodigal PASSED [ 91%]
157s start_fixer_test.py::TestStartFixer::test_find_circular_using_promer PASSED [ 92%]
157s start_fixer_test.py::TestStartFixer::test_init PASSED                    [ 92%]
157s start_fixer_test.py::TestStartFixer::test_max_length_from_fasta_file PASSED [ 93%]
157s start_fixer_test.py::TestStartFixer::test_rearrange_contigs PASSED       [ 94%]
157s start_fixer_test.py::TestStartFixer::test_rename_contigs PASSED          [ 95%]
157s start_fixer_test.py::TestStartFixer::test_run_bit_of_everything PASSED   [ 96%]
157s start_fixer_test.py::TestStartFixer::test_run_ignore_all PASSED          [ 97%]
157s start_fixer_test.py::TestStartFixer::test_run_none_for_prodigal PASSED   [ 98%]
157s start_fixer_test.py::TestStartFixer::test_write_fasta_plus_circularized_ends PASSED [ 99%]
157s start_fixer_test.py::TestStartFixer::test_write_renamed_contigs PASSED   [100%]
157s 
157s =============================== warnings summary ===============================
157s ../../../usr/lib/python3/dist-packages/pyfastaq/__init__.py:1
157s   /usr/lib/python3/dist-packages/pyfastaq/__init__.py:1: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
157s     from pkg_resources import get_distribution
157s 
157s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
157s =========== 107 passed, 6 skipped, 2 deselected, 1 warning in 1.44s ============
157s autopkgtest [16:50:54]: test run-unit-test: -----------------------]
158s autopkgtest [16:50:55]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
158s run-unit-test        PASS
158s autopkgtest [16:50:55]: @@@@@@@@@@@@@@@@@@@@ summary
158s run-unit-test        PASS
162s Creating nova instance adt-noble-arm64-circlator-20240324-164817-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240324.img (UUID 943dd583-2042-4622-b4ce-bdf10ad153ac)...