0s autopkgtest [15:29:22]: starting date and time: 2024-03-23 15:29:22+0000
  0s autopkgtest [15:29:22]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps
  0s autopkgtest [15:29:22]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ogbzuh6w/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-2@bos01-ppc64el-5.secgroup --name adt-noble-ppc64el-circlator-20240323-151747-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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://us.ports.ubuntu.com/ubuntu-ports/
131s autopkgtest [15:31:33]: testbed dpkg architecture: ppc64el
131s autopkgtest [15:31:33]: testbed apt version: 2.7.12
131s autopkgtest [15:31:33]: @@@@@@@@@@@@@@@@@@@@ test bed setup
132s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
132s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B]
132s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB]
132s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [493 kB]
132s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3969 kB]
133s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [659 kB]
133s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B]
133s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B]
133s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B]
133s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4248 kB]
133s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B]
133s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [60.8 kB]
133s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B]
136s Fetched 9623 kB in 2s (4056 kB/s)
136s Reading package lists...
139s Reading package lists...
139s Building dependency tree...
139s Reading state information...
140s Calculating upgrade...
140s The following packages will be REMOVED:
140s   libssl3
140s The following NEW packages will be installed:
140s   libssl3t64
140s The following packages have been kept back:
140s   curl
140s The following packages will be upgraded:
140s   cloud-init fonts-ubuntu-console libbsd0 libc-bin libc6 locales openssl
140s   python3-markupsafe
140s 8 upgraded, 1 newly installed, 1 to remove and 1 not upgraded.
140s Need to get 12.1 MB of archives.
140s After this operation, 10.2 kB of additional disk space will be used.
140s Get:1 http://ftpmaster.internal/ubuntu noble/main ppc64el libc6 ppc64el 2.39-0ubuntu6 [3274 kB]
140s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libc-bin ppc64el 2.39-0ubuntu6 [751 kB]
140s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu2 [1026 kB]
141s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu2 [2125 kB]
141s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el libbsd0 ppc64el 0.12.1-1 [56.9 kB]
141s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el locales all 2.39-0ubuntu6 [4232 kB]
141s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-ubuntu-console all 0.869+git20240321-0ubuntu1 [18.7 kB]
141s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-markupsafe ppc64el 2.1.5-1build1 [13.2 kB]
141s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el cloud-init all 24.1.2-0ubuntu1 [597 kB]
141s Preconfiguring packages ...
141s Fetched 12.1 MB in 1s (9470 kB/s)
141s (Reading database ... 
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(Reading database ... 70157 files and directories currently installed.)
141s Preparing to unpack .../libc6_2.39-0ubuntu6_ppc64el.deb ...
142s Unpacking libc6:ppc64el (2.39-0ubuntu6) over (2.39-0ubuntu2) ...
142s Setting up libc6:ppc64el (2.39-0ubuntu6) ...
142s (Reading database ... 
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142s Preparing to unpack .../libc-bin_2.39-0ubuntu6_ppc64el.deb ...
142s Unpacking libc-bin (2.39-0ubuntu6) over (2.39-0ubuntu2) ...
142s Setting up libc-bin (2.39-0ubuntu6) ...
142s (Reading database ... 
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(Reading database ... 70157 files and directories currently installed.)
142s Preparing to unpack .../openssl_3.0.13-0ubuntu2_ppc64el.deb ...
142s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ...
143s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested:
143s  wget depends on libssl3 (>= 3.0.0).
143s  tnftp depends on libssl3 (>= 3.0.0).
143s  tcpdump depends on libssl3 (>= 3.0.0).
143s  systemd-resolved depends on libssl3 (>= 3.0.0).
143s  systemd depends on libssl3 (>= 3.0.0).
143s  sudo depends on libssl3 (>= 3.0.0).
143s  rsync depends on libssl3 (>= 3.0.0).
143s  python3-cryptography depends on libssl3 (>= 3.0.0).
143s  openssh-server depends on libssl3 (>= 3.0.10).
143s  openssh-client depends on libssl3 (>= 3.0.10).
143s  linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0).
143s  libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0).
143s  libssh-4:ppc64el depends on libssl3 (>= 3.0.0).
143s  libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0).
143s  libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0).
143s  libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0).
143s  libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0).
143s  libnvme1 depends on libssl3 (>= 3.0.0).
143s  libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0).
143s  libkmod2:ppc64el depends on libssl3 (>= 3.0.0).
143s  libfido2-1:ppc64el depends on libssl3 (>= 3.0.0).
143s  libcurl4:ppc64el depends on libssl3 (>= 3.0.0).
143s  libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0).
143s  kmod depends on libssl3 (>= 3.0.0).
143s  dhcpcd-base depends on libssl3 (>= 3.0.0).
143s  bind9-libs:ppc64el depends on libssl3 (>= 3.0.0).
143s 
143s (Reading database ... 
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(Reading database ... 70157 files and directories currently installed.)
143s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ...
143s Selecting previously unselected package libssl3t64:ppc64el.
143s (Reading database ... 
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(Reading database ... 70146 files and directories currently installed.)
143s Preparing to unpack .../0-libssl3t64_3.0.13-0ubuntu2_ppc64el.deb ...
143s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu2) ...
143s Preparing to unpack .../1-libbsd0_0.12.1-1_ppc64el.deb ...
143s Unpacking libbsd0:ppc64el (0.12.1-1) over (0.11.8-1) ...
143s Preparing to unpack .../2-locales_2.39-0ubuntu6_all.deb ...
143s Unpacking locales (2.39-0ubuntu6) over (2.39-0ubuntu2) ...
143s Preparing to unpack .../3-fonts-ubuntu-console_0.869+git20240321-0ubuntu1_all.deb ...
143s Unpacking fonts-ubuntu-console (0.869+git20240321-0ubuntu1) over (0.869-0ubuntu1) ...
143s Preparing to unpack .../4-python3-markupsafe_2.1.5-1build1_ppc64el.deb ...
143s Unpacking python3-markupsafe (2.1.5-1build1) over (2.1.5-1) ...
143s Preparing to unpack .../5-cloud-init_24.1.2-0ubuntu1_all.deb ...
143s Unpacking cloud-init (24.1.2-0ubuntu1) over (24.1.1-0ubuntu1) ...
143s Setting up fonts-ubuntu-console (0.869+git20240321-0ubuntu1) ...
143s Setting up cloud-init (24.1.2-0ubuntu1) ...
145s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu2) ...
145s Setting up locales (2.39-0ubuntu6) ...
145s Generating locales (this might take a while)...
147s   en_US.UTF-8... done
147s Generation complete.
147s Setting up python3-markupsafe (2.1.5-1build1) ...
147s Setting up openssl (3.0.13-0ubuntu2) ...
147s Setting up libbsd0:ppc64el (0.12.1-1) ...
147s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ...
147s Processing triggers for man-db (2.12.0-3) ...
148s Processing triggers for libc-bin (2.39-0ubuntu6) ...
148s Reading package lists...
148s Building dependency tree...
148s Reading state information...
148s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
149s sh: Attempting to set up Debian/Ubuntu apt sources automatically
149s sh: Distribution appears to be Ubuntu
150s Reading package lists...
150s Building dependency tree...
150s Reading state information...
150s eatmydata is already the newest version (131-1).
150s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
150s Reading package lists...
150s Building dependency tree...
150s Reading state information...
151s dbus is already the newest version (1.14.10-4ubuntu1).
151s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
151s Reading package lists...
151s Building dependency tree...
151s Reading state information...
151s rng-tools-debian is already the newest version (2.4).
151s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
151s Reading package lists...
151s Building dependency tree...
151s Reading state information...
151s The following packages will be REMOVED:
151s   cloud-init* python3-configobj* python3-debconf*
152s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded.
152s After this operation, 3256 kB disk space will be freed.
152s (Reading database ... 
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(Reading database ... 70158 files and directories currently installed.)
152s Removing cloud-init (24.1.2-0ubuntu1) ...
152s Removing python3-configobj (5.0.8-3) ...
152s Removing python3-debconf (1.5.86) ...
152s Processing triggers for man-db (2.12.0-3) ...
153s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 69769 files and directories currently installed.)
153s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ...
153s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed
153s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ...
153s invoke-rc.d: policy-rc.d denied execution of try-restart.
153s Reading package lists...
153s Building dependency tree...
153s Reading state information...
154s linux-generic is already the newest version (6.8.0-11.11+1).
154s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
154s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
154s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
154s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
157s Reading package lists...
157s Reading package lists...
157s Building dependency tree...
157s Reading state information...
157s Calculating upgrade...
157s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
157s Reading package lists...
157s Building dependency tree...
157s Reading state information...
158s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
158s autopkgtest [15:32:00]: rebooting testbed after setup commands that affected boot
314s autopkgtest [15:34:36]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024
317s autopkgtest [15:34:39]: @@@@@@@@@@@@@@@@@@@@ apt-source circlator
319s Get:1 http://ftpmaster.internal/ubuntu noble/universe circlator 1.5.6-11 (dsc) [1672 B]
319s Get:2 http://ftpmaster.internal/ubuntu noble/universe circlator 1.5.6-11 (tar) [5724 kB]
319s Get:3 http://ftpmaster.internal/ubuntu noble/universe circlator 1.5.6-11 (diff) [6152 B]
319s gpgv: Signature made Sat Dec  2 21:39:17 2023 UTC
319s gpgv:                using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA
319s gpgv: Can't check signature: No public key
319s dpkg-source: warning: cannot verify inline signature for ./circlator_1.5.6-11.dsc: no acceptable signature found
319s autopkgtest [15:34:41]: testing package circlator version 1.5.6-11
320s autopkgtest [15:34:42]: build not needed
321s autopkgtest [15:34:43]: test run-unit-test: preparing testbed
322s Reading package lists...
322s Building dependency tree...
322s Reading state information...
322s Starting pkgProblemResolver with broken count: 0
322s Starting 2 pkgProblemResolver with broken count: 0
322s Done
323s The following additional packages will be installed:
323s   aglfn binfmt-support bwa ca-certificates-java canu circlator
323s   default-jre-headless fastaq fastjar fontconfig fontconfig-config
323s   fonts-dejavu-core fonts-dejavu-mono gnuplot-data gnuplot-nox jaligner
323s   jarwrapper java-common libapache-pom-java libasound2 libasound2-data
323s   libatinject-jsr330-api-java libavahi-client3 libavahi-common-data
323s   libavahi-common3 libcairo2 libcommons-compress-java libcommons-parent-java
323s   libcups2 libdatrie1 libdeflate0 liberror-prone-java libfastutil-java
323s   libfilesys-df-perl libfontconfig1 libgd3 libgomp1 libgraphite2-3
323s   libguava-java libharfbuzz0b libhts3 libhtscodecs2 libjbig0 libjpeg-turbo8
323s   libjpeg8 libjsr305-java liblcms2-2 liblerc4 liblua5.4-0 libpango-1.0-0
323s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpcsclite1 libpixman-1-0
323s   libsharpyuv0 libsnappy1v5 libssw-java libthai-data libthai0 libtiff6
323s   libwebp7 libxcb-render0 libxcb-shm0 libxpm4 libxrender1 libxslt1.1 mhap
323s   mummer openjdk-21-jre-headless prodigal python3-all python3-et-xmlfile
323s   python3-iniconfig python3-lxml python3-openpyxl python3-packaging
323s   python3-pluggy python3-pymummer python3-pysam python3-pytest samtools
323s Suggested packages:
323s   nanopolish default-jre gnuplot-doc libasound2-plugins alsa-utils
323s   libatinject-jsr330-api-java-doc libasm-java libxz-java cups-common
323s   libgd-tools libjsr305-java-doc liblcms2-utils pcscd libnss-mdns
323s   fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho
323s   fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic python-lxml-doc
323s   python-openpyxl-doc cwltool
323s Recommended packages:
323s   spades fonts-liberation groff alsa-ucm-conf alsa-topology-conf python3-bs4
323s   python3-cssselect python3-html5lib python3-pil
323s The following NEW packages will be installed:
323s   aglfn autopkgtest-satdep binfmt-support bwa ca-certificates-java canu
323s   circlator default-jre-headless fastaq fastjar fontconfig fontconfig-config
323s   fonts-dejavu-core fonts-dejavu-mono gnuplot-data gnuplot-nox jaligner
323s   jarwrapper java-common libapache-pom-java libasound2 libasound2-data
323s   libatinject-jsr330-api-java libavahi-client3 libavahi-common-data
323s   libavahi-common3 libcairo2 libcommons-compress-java libcommons-parent-java
323s   libcups2 libdatrie1 libdeflate0 liberror-prone-java libfastutil-java
323s   libfilesys-df-perl libfontconfig1 libgd3 libgomp1 libgraphite2-3
323s   libguava-java libharfbuzz0b libhts3 libhtscodecs2 libjbig0 libjpeg-turbo8
323s   libjpeg8 libjsr305-java liblcms2-2 liblerc4 liblua5.4-0 libpango-1.0-0
323s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpcsclite1 libpixman-1-0
323s   libsharpyuv0 libsnappy1v5 libssw-java libthai-data libthai0 libtiff6
323s   libwebp7 libxcb-render0 libxcb-shm0 libxpm4 libxrender1 libxslt1.1 mhap
323s   mummer openjdk-21-jre-headless prodigal python3-all python3-et-xmlfile
323s   python3-iniconfig python3-lxml python3-openpyxl python3-packaging
323s   python3-pluggy python3-pymummer python3-pysam python3-pytest samtools
323s 0 upgraded, 82 newly installed, 0 to remove and 0 not upgraded.
323s Need to get 95.8 MB/95.8 MB of archives.
323s After this operation, 368 MB of additional disk space will be used.
323s Get:1 /tmp/autopkgtest.c6zXij/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [724 B]
323s Get:2 http://ftpmaster.internal/ubuntu noble/universe ppc64el binfmt-support ppc64el 2.2.2-6 [66.7 kB]
323s Get:3 http://ftpmaster.internal/ubuntu noble/universe ppc64el bwa ppc64el 0.7.17-7 [214 kB]
323s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el ca-certificates-java all 20240118 [11.6 kB]
323s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240303-1ubuntu1 [161 kB]
323s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el libsnappy1v5 ppc64el 1.1.10-1 [30.5 kB]
323s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el libfilesys-df-perl ppc64el 0.92-7build2 [11.2 kB]
323s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el java-common all 0.75+exp1 [6798 B]
323s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el libavahi-common-data ppc64el 0.8-13ubuntu2 [29.5 kB]
323s Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el libavahi-common3 ppc64el 0.8-13ubuntu2 [25.8 kB]
323s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el libavahi-client3 ppc64el 0.8-13ubuntu2 [30.6 kB]
323s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el libcups2 ppc64el 2.4.6-0ubuntu3 [344 kB]
323s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el liblcms2-2 ppc64el 2.14-2 [243 kB]
323s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu1 [212 kB]
323s Get:15 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B]
323s Get:16 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB]
323s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB]
323s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el fontconfig-config ppc64el 2.15.0-1ubuntu1 [37.0 kB]
323s Get:19 http://ftpmaster.internal/ubuntu noble/main ppc64el libfontconfig1 ppc64el 2.15.0-1ubuntu1 [190 kB]
323s Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el libasound2-data all 1.2.10-3build1 [20.7 kB]
323s Get:21 http://ftpmaster.internal/ubuntu noble/main ppc64el libasound2 ppc64el 1.2.10-3build1 [496 kB]
323s Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el libgraphite2-3 ppc64el 1.3.14-2 [105 kB]
323s Get:23 http://ftpmaster.internal/ubuntu noble/main ppc64el libharfbuzz0b ppc64el 8.3.0-2 [576 kB]
323s Get:24 http://ftpmaster.internal/ubuntu noble/main ppc64el libpcsclite1 ppc64el 2.0.0-1 [27.9 kB]
323s Get:25 http://ftpmaster.internal/ubuntu noble/main ppc64el openjdk-21-jre-headless ppc64el 21.0.2+13-2 [45.8 MB]
325s Get:26 http://ftpmaster.internal/ubuntu noble/main ppc64el default-jre-headless ppc64el 2:1.21-75+exp1 [3102 B]
325s Get:27 http://ftpmaster.internal/ubuntu noble/universe ppc64el fastjar ppc64el 2:0.98-7 [79.7 kB]
325s Get:28 http://ftpmaster.internal/ubuntu noble/universe ppc64el jarwrapper all 0.79 [10.3 kB]
325s Get:29 http://ftpmaster.internal/ubuntu noble/universe ppc64el libapache-pom-java all 29-2 [5284 B]
325s Get:30 http://ftpmaster.internal/ubuntu noble/universe ppc64el libcommons-parent-java all 56-1 [10.7 kB]
325s Get:31 http://ftpmaster.internal/ubuntu noble/universe ppc64el libcommons-compress-java all 1.25.0-1 [612 kB]
325s Get:32 http://ftpmaster.internal/ubuntu noble/universe ppc64el libfastutil-java all 8.5.12+dfsg-1 [19.8 MB]
326s Get:33 http://ftpmaster.internal/ubuntu noble/universe ppc64el libatinject-jsr330-api-java all 1.0+ds1-5 [5348 B]
326s Get:34 http://ftpmaster.internal/ubuntu noble/universe ppc64el liberror-prone-java all 2.18.0-1 [22.5 kB]
326s Get:35 http://ftpmaster.internal/ubuntu noble/universe ppc64el libjsr305-java all 0.1~+svn49-11 [27.0 kB]
326s Get:36 http://ftpmaster.internal/ubuntu noble/universe ppc64el libguava-java all 32.0.1-1 [2692 kB]
326s Get:37 http://ftpmaster.internal/ubuntu noble/universe ppc64el jaligner all 1.0+dfsg-11 [136 kB]
326s Get:38 http://ftpmaster.internal/ubuntu noble/universe ppc64el libssw-java ppc64el 1.1-14 [20.3 kB]
326s Get:39 http://ftpmaster.internal/ubuntu noble/universe ppc64el mhap all 2.1.3+dfsg-3 [160 kB]
326s Get:40 http://ftpmaster.internal/ubuntu noble/universe ppc64el aglfn all 1.7+git20191031.4036a9c-2 [30.6 kB]
326s Get:41 http://ftpmaster.internal/ubuntu noble/universe ppc64el gnuplot-data all 5.4.4+dfsg1-2build1 [74.6 kB]
326s Get:42 http://ftpmaster.internal/ubuntu noble/main ppc64el libpixman-1-0 ppc64el 0.42.2-1 [300 kB]
326s Get:43 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-render0 ppc64el 1.15-1 [17.2 kB]
326s Get:44 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-shm0 ppc64el 1.15-1 [5896 B]
326s Get:45 http://ftpmaster.internal/ubuntu noble/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1 [23.3 kB]
326s Get:46 http://ftpmaster.internal/ubuntu noble/main ppc64el libcairo2 ppc64el 1.18.0-1 [735 kB]
326s Get:47 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB]
326s Get:48 http://ftpmaster.internal/ubuntu noble/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu1 [34.7 kB]
326s Get:49 http://ftpmaster.internal/ubuntu noble/main ppc64el liblerc4 ppc64el 4.0.0+ds-4ubuntu1 [266 kB]
326s Get:50 http://ftpmaster.internal/ubuntu noble/main ppc64el libsharpyuv0 ppc64el 1.3.2-0.4 [28.7 kB]
326s Get:51 http://ftpmaster.internal/ubuntu noble/main ppc64el libwebp7 ppc64el 1.3.2-0.4 [312 kB]
326s Get:52 http://ftpmaster.internal/ubuntu noble/main ppc64el libtiff6 ppc64el 4.5.1+git230720-3ubuntu1 [323 kB]
326s Get:53 http://ftpmaster.internal/ubuntu noble/main ppc64el libxpm4 ppc64el 1:3.5.17-1 [48.6 kB]
326s Get:54 http://ftpmaster.internal/ubuntu noble/main ppc64el libgd3 ppc64el 2.3.3-9ubuntu1 [155 kB]
326s Get:55 http://ftpmaster.internal/ubuntu noble/main ppc64el liblua5.4-0 ppc64el 5.4.6-3 [216 kB]
326s Get:56 http://ftpmaster.internal/ubuntu noble/main ppc64el fontconfig ppc64el 2.15.0-1ubuntu1 [192 kB]
326s Get:57 http://ftpmaster.internal/ubuntu noble/main ppc64el libthai-data all 0.1.29-2 [158 kB]
326s Get:58 http://ftpmaster.internal/ubuntu noble/main ppc64el libdatrie1 ppc64el 0.2.13-3 [25.1 kB]
326s Get:59 http://ftpmaster.internal/ubuntu noble/main ppc64el libthai0 ppc64el 0.1.29-2 [21.4 kB]
326s Get:60 http://ftpmaster.internal/ubuntu noble/main ppc64el libpango-1.0-0 ppc64el 1.51.0+ds-4 [266 kB]
326s Get:61 http://ftpmaster.internal/ubuntu noble/main ppc64el libpangoft2-1.0-0 ppc64el 1.51.0+ds-4 [49.5 kB]
326s Get:62 http://ftpmaster.internal/ubuntu noble/main ppc64el libpangocairo-1.0-0 ppc64el 1.51.0+ds-4 [31.2 kB]
326s Get:63 http://ftpmaster.internal/ubuntu noble/universe ppc64el gnuplot-nox ppc64el 5.4.4+dfsg1-2build1 [1103 kB]
326s Get:64 http://ftpmaster.internal/ubuntu noble/universe ppc64el canu ppc64el 2.2+dfsg-5 [1763 kB]
326s Get:65 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB]
326s Get:66 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB]
326s Get:67 http://ftpmaster.internal/ubuntu noble/universe ppc64el samtools ppc64el 1.19.2-1 [669 kB]
326s Get:68 http://ftpmaster.internal/ubuntu noble/universe ppc64el fastaq all 3.17.0-6 [47.9 kB]
326s Get:69 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-et-xmlfile all 1.0.1-2.1 [9224 B]
326s Get:70 http://ftpmaster.internal/ubuntu noble/main ppc64el libxslt1.1 ppc64el 1.1.39-0exp1 [192 kB]
326s Get:71 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-lxml ppc64el 5.1.0-1 [2191 kB]
326s Get:72 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-openpyxl all 3.1.2+dfsg-6 [152 kB]
326s Get:73 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-packaging all 23.2-1 [40.6 kB]
326s Get:74 http://ftpmaster.internal/ubuntu noble/universe ppc64el mummer ppc64el 3.23+dfsg-8 [714 kB]
326s Get:75 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pymummer all 0.11.0-4 [17.1 kB]
326s Get:76 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pysam ppc64el 0.22.0+ds-1 [5037 kB]
327s Get:77 http://ftpmaster.internal/ubuntu noble/universe ppc64el prodigal ppc64el 1:2.6.3-6 [1314 kB]
327s Get:78 http://ftpmaster.internal/ubuntu noble/universe ppc64el circlator all 1.5.6-11 [4618 kB]
327s Get:79 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-all ppc64el 3.12.1-0ubuntu2 [904 B]
327s Get:80 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-iniconfig all 1.1.1-2 [6024 B]
327s Get:81 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pluggy all 1.4.0-1 [20.4 kB]
327s Get:82 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pytest all 7.4.4-1 [305 kB]
327s Fetched 95.8 MB in 4s (23.3 MB/s)
327s Selecting previously unselected package binfmt-support.
327s (Reading database ... 
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(Reading database ... 69714 files and directories currently installed.)
327s Preparing to unpack .../00-binfmt-support_2.2.2-6_ppc64el.deb ...
327s Unpacking binfmt-support (2.2.2-6) ...
327s Selecting previously unselected package bwa.
327s Preparing to unpack .../01-bwa_0.7.17-7_ppc64el.deb ...
327s Unpacking bwa (0.7.17-7) ...
327s Selecting previously unselected package ca-certificates-java.
327s Preparing to unpack .../02-ca-certificates-java_20240118_all.deb ...
327s Unpacking ca-certificates-java (20240118) ...
327s Selecting previously unselected package libgomp1:ppc64el.
327s Preparing to unpack .../03-libgomp1_14-20240303-1ubuntu1_ppc64el.deb ...
327s Unpacking libgomp1:ppc64el (14-20240303-1ubuntu1) ...
327s Selecting previously unselected package libsnappy1v5:ppc64el.
327s Preparing to unpack .../04-libsnappy1v5_1.1.10-1_ppc64el.deb ...
327s Unpacking libsnappy1v5:ppc64el (1.1.10-1) ...
327s Selecting previously unselected package libfilesys-df-perl.
327s Preparing to unpack .../05-libfilesys-df-perl_0.92-7build2_ppc64el.deb ...
327s Unpacking libfilesys-df-perl (0.92-7build2) ...
327s Selecting previously unselected package java-common.
327s Preparing to unpack .../06-java-common_0.75+exp1_all.deb ...
327s Unpacking java-common (0.75+exp1) ...
327s Selecting previously unselected package libavahi-common-data:ppc64el.
327s Preparing to unpack .../07-libavahi-common-data_0.8-13ubuntu2_ppc64el.deb ...
327s Unpacking libavahi-common-data:ppc64el (0.8-13ubuntu2) ...
327s Selecting previously unselected package libavahi-common3:ppc64el.
327s Preparing to unpack .../08-libavahi-common3_0.8-13ubuntu2_ppc64el.deb ...
327s Unpacking libavahi-common3:ppc64el (0.8-13ubuntu2) ...
327s Selecting previously unselected package libavahi-client3:ppc64el.
327s Preparing to unpack .../09-libavahi-client3_0.8-13ubuntu2_ppc64el.deb ...
327s Unpacking libavahi-client3:ppc64el (0.8-13ubuntu2) ...
327s Selecting previously unselected package libcups2:ppc64el.
327s Preparing to unpack .../10-libcups2_2.4.6-0ubuntu3_ppc64el.deb ...
327s Unpacking libcups2:ppc64el (2.4.6-0ubuntu3) ...
327s Selecting previously unselected package liblcms2-2:ppc64el.
327s Preparing to unpack .../11-liblcms2-2_2.14-2_ppc64el.deb ...
327s Unpacking liblcms2-2:ppc64el (2.14-2) ...
327s Selecting previously unselected package libjpeg-turbo8:ppc64el.
327s Preparing to unpack .../12-libjpeg-turbo8_2.1.5-2ubuntu1_ppc64el.deb ...
327s Unpacking libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ...
327s Selecting previously unselected package libjpeg8:ppc64el.
327s Preparing to unpack .../13-libjpeg8_8c-2ubuntu11_ppc64el.deb ...
327s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ...
327s Selecting previously unselected package fonts-dejavu-mono.
327s Preparing to unpack .../14-fonts-dejavu-mono_2.37-8_all.deb ...
327s Unpacking fonts-dejavu-mono (2.37-8) ...
327s Selecting previously unselected package fonts-dejavu-core.
327s Preparing to unpack .../15-fonts-dejavu-core_2.37-8_all.deb ...
327s Unpacking fonts-dejavu-core (2.37-8) ...
327s Selecting previously unselected package fontconfig-config.
327s Preparing to unpack .../16-fontconfig-config_2.15.0-1ubuntu1_ppc64el.deb ...
328s Unpacking fontconfig-config (2.15.0-1ubuntu1) ...
328s Selecting previously unselected package libfontconfig1:ppc64el.
328s Preparing to unpack .../17-libfontconfig1_2.15.0-1ubuntu1_ppc64el.deb ...
328s Unpacking libfontconfig1:ppc64el (2.15.0-1ubuntu1) ...
328s Selecting previously unselected package libasound2-data.
328s Preparing to unpack .../18-libasound2-data_1.2.10-3build1_all.deb ...
328s Unpacking libasound2-data (1.2.10-3build1) ...
328s Selecting previously unselected package libasound2:ppc64el.
328s Preparing to unpack .../19-libasound2_1.2.10-3build1_ppc64el.deb ...
328s Unpacking libasound2:ppc64el (1.2.10-3build1) ...
328s Selecting previously unselected package libgraphite2-3:ppc64el.
328s Preparing to unpack .../20-libgraphite2-3_1.3.14-2_ppc64el.deb ...
328s Unpacking libgraphite2-3:ppc64el (1.3.14-2) ...
328s Selecting previously unselected package libharfbuzz0b:ppc64el.
328s Preparing to unpack .../21-libharfbuzz0b_8.3.0-2_ppc64el.deb ...
328s Unpacking libharfbuzz0b:ppc64el (8.3.0-2) ...
328s Selecting previously unselected package libpcsclite1:ppc64el.
328s Preparing to unpack .../22-libpcsclite1_2.0.0-1_ppc64el.deb ...
328s Unpacking libpcsclite1:ppc64el (2.0.0-1) ...
328s Selecting previously unselected package openjdk-21-jre-headless:ppc64el.
328s Preparing to unpack .../23-openjdk-21-jre-headless_21.0.2+13-2_ppc64el.deb ...
328s Unpacking openjdk-21-jre-headless:ppc64el (21.0.2+13-2) ...
329s Selecting previously unselected package default-jre-headless.
329s Preparing to unpack .../24-default-jre-headless_2%3a1.21-75+exp1_ppc64el.deb ...
329s Unpacking default-jre-headless (2:1.21-75+exp1) ...
329s Selecting previously unselected package fastjar.
329s Preparing to unpack .../25-fastjar_2%3a0.98-7_ppc64el.deb ...
329s Unpacking fastjar (2:0.98-7) ...
329s Selecting previously unselected package jarwrapper.
329s Preparing to unpack .../26-jarwrapper_0.79_all.deb ...
329s Unpacking jarwrapper (0.79) ...
329s Selecting previously unselected package libapache-pom-java.
329s Preparing to unpack .../27-libapache-pom-java_29-2_all.deb ...
329s Unpacking libapache-pom-java (29-2) ...
329s Selecting previously unselected package libcommons-parent-java.
329s Preparing to unpack .../28-libcommons-parent-java_56-1_all.deb ...
329s Unpacking libcommons-parent-java (56-1) ...
329s Selecting previously unselected package libcommons-compress-java.
329s Preparing to unpack .../29-libcommons-compress-java_1.25.0-1_all.deb ...
329s Unpacking libcommons-compress-java (1.25.0-1) ...
329s Selecting previously unselected package libfastutil-java.
329s Preparing to unpack .../30-libfastutil-java_8.5.12+dfsg-1_all.deb ...
329s Unpacking libfastutil-java (8.5.12+dfsg-1) ...
329s Selecting previously unselected package libatinject-jsr330-api-java.
329s Preparing to unpack .../31-libatinject-jsr330-api-java_1.0+ds1-5_all.deb ...
329s Unpacking libatinject-jsr330-api-java (1.0+ds1-5) ...
329s Selecting previously unselected package liberror-prone-java.
329s Preparing to unpack .../32-liberror-prone-java_2.18.0-1_all.deb ...
329s Unpacking liberror-prone-java (2.18.0-1) ...
329s Selecting previously unselected package libjsr305-java.
329s Preparing to unpack .../33-libjsr305-java_0.1~+svn49-11_all.deb ...
329s Unpacking libjsr305-java (0.1~+svn49-11) ...
329s Selecting previously unselected package libguava-java.
329s Preparing to unpack .../34-libguava-java_32.0.1-1_all.deb ...
329s Unpacking libguava-java (32.0.1-1) ...
329s Selecting previously unselected package jaligner.
329s Preparing to unpack .../35-jaligner_1.0+dfsg-11_all.deb ...
329s Unpacking jaligner (1.0+dfsg-11) ...
329s Selecting previously unselected package libssw-java.
329s Preparing to unpack .../36-libssw-java_1.1-14_ppc64el.deb ...
329s Unpacking libssw-java (1.1-14) ...
329s Selecting previously unselected package mhap.
329s Preparing to unpack .../37-mhap_2.1.3+dfsg-3_all.deb ...
329s Unpacking mhap (2.1.3+dfsg-3) ...
329s Selecting previously unselected package aglfn.
329s Preparing to unpack .../38-aglfn_1.7+git20191031.4036a9c-2_all.deb ...
329s Unpacking aglfn (1.7+git20191031.4036a9c-2) ...
329s Selecting previously unselected package gnuplot-data.
329s Preparing to unpack .../39-gnuplot-data_5.4.4+dfsg1-2build1_all.deb ...
329s Unpacking gnuplot-data (5.4.4+dfsg1-2build1) ...
329s Selecting previously unselected package libpixman-1-0:ppc64el.
329s Preparing to unpack .../40-libpixman-1-0_0.42.2-1_ppc64el.deb ...
329s Unpacking libpixman-1-0:ppc64el (0.42.2-1) ...
329s Selecting previously unselected package libxcb-render0:ppc64el.
329s Preparing to unpack .../41-libxcb-render0_1.15-1_ppc64el.deb ...
329s Unpacking libxcb-render0:ppc64el (1.15-1) ...
329s Selecting previously unselected package libxcb-shm0:ppc64el.
329s Preparing to unpack .../42-libxcb-shm0_1.15-1_ppc64el.deb ...
329s Unpacking libxcb-shm0:ppc64el (1.15-1) ...
330s Selecting previously unselected package libxrender1:ppc64el.
330s Preparing to unpack .../43-libxrender1_1%3a0.9.10-1.1_ppc64el.deb ...
330s Unpacking libxrender1:ppc64el (1:0.9.10-1.1) ...
330s Selecting previously unselected package libcairo2:ppc64el.
330s Preparing to unpack .../44-libcairo2_1.18.0-1_ppc64el.deb ...
330s Unpacking libcairo2:ppc64el (1.18.0-1) ...
330s Selecting previously unselected package libdeflate0:ppc64el.
330s Preparing to unpack .../45-libdeflate0_1.19-1_ppc64el.deb ...
330s Unpacking libdeflate0:ppc64el (1.19-1) ...
330s Selecting previously unselected package libjbig0:ppc64el.
330s Preparing to unpack .../46-libjbig0_2.1-6.1ubuntu1_ppc64el.deb ...
330s Unpacking libjbig0:ppc64el (2.1-6.1ubuntu1) ...
330s Selecting previously unselected package liblerc4:ppc64el.
330s Preparing to unpack .../47-liblerc4_4.0.0+ds-4ubuntu1_ppc64el.deb ...
330s Unpacking liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ...
330s Selecting previously unselected package libsharpyuv0:ppc64el.
330s Preparing to unpack .../48-libsharpyuv0_1.3.2-0.4_ppc64el.deb ...
330s Unpacking libsharpyuv0:ppc64el (1.3.2-0.4) ...
330s Selecting previously unselected package libwebp7:ppc64el.
330s Preparing to unpack .../49-libwebp7_1.3.2-0.4_ppc64el.deb ...
330s Unpacking libwebp7:ppc64el (1.3.2-0.4) ...
330s Selecting previously unselected package libtiff6:ppc64el.
330s Preparing to unpack .../50-libtiff6_4.5.1+git230720-3ubuntu1_ppc64el.deb ...
330s Unpacking libtiff6:ppc64el (4.5.1+git230720-3ubuntu1) ...
330s Selecting previously unselected package libxpm4:ppc64el.
330s Preparing to unpack .../51-libxpm4_1%3a3.5.17-1_ppc64el.deb ...
330s Unpacking libxpm4:ppc64el (1:3.5.17-1) ...
330s Selecting previously unselected package libgd3:ppc64el.
330s Preparing to unpack .../52-libgd3_2.3.3-9ubuntu1_ppc64el.deb ...
330s Unpacking libgd3:ppc64el (2.3.3-9ubuntu1) ...
330s Selecting previously unselected package liblua5.4-0:ppc64el.
330s Preparing to unpack .../53-liblua5.4-0_5.4.6-3_ppc64el.deb ...
330s Unpacking liblua5.4-0:ppc64el (5.4.6-3) ...
330s Selecting previously unselected package fontconfig.
330s Preparing to unpack .../54-fontconfig_2.15.0-1ubuntu1_ppc64el.deb ...
330s Unpacking fontconfig (2.15.0-1ubuntu1) ...
330s Selecting previously unselected package libthai-data.
330s Preparing to unpack .../55-libthai-data_0.1.29-2_all.deb ...
330s Unpacking libthai-data (0.1.29-2) ...
330s Selecting previously unselected package libdatrie1:ppc64el.
330s Preparing to unpack .../56-libdatrie1_0.2.13-3_ppc64el.deb ...
330s Unpacking libdatrie1:ppc64el (0.2.13-3) ...
330s Selecting previously unselected package libthai0:ppc64el.
330s Preparing to unpack .../57-libthai0_0.1.29-2_ppc64el.deb ...
330s Unpacking libthai0:ppc64el (0.1.29-2) ...
330s Selecting previously unselected package libpango-1.0-0:ppc64el.
330s Preparing to unpack .../58-libpango-1.0-0_1.51.0+ds-4_ppc64el.deb ...
330s Unpacking libpango-1.0-0:ppc64el (1.51.0+ds-4) ...
330s Selecting previously unselected package libpangoft2-1.0-0:ppc64el.
330s Preparing to unpack .../59-libpangoft2-1.0-0_1.51.0+ds-4_ppc64el.deb ...
330s Unpacking libpangoft2-1.0-0:ppc64el (1.51.0+ds-4) ...
330s Selecting previously unselected package libpangocairo-1.0-0:ppc64el.
330s Preparing to unpack .../60-libpangocairo-1.0-0_1.51.0+ds-4_ppc64el.deb ...
330s Unpacking libpangocairo-1.0-0:ppc64el (1.51.0+ds-4) ...
330s Selecting previously unselected package gnuplot-nox.
330s Preparing to unpack .../61-gnuplot-nox_5.4.4+dfsg1-2build1_ppc64el.deb ...
330s Unpacking gnuplot-nox (5.4.4+dfsg1-2build1) ...
330s Selecting previously unselected package canu.
330s Preparing to unpack .../62-canu_2.2+dfsg-5_ppc64el.deb ...
330s Unpacking canu (2.2+dfsg-5) ...
330s Selecting previously unselected package libhtscodecs2:ppc64el.
330s Preparing to unpack .../63-libhtscodecs2_1.6.0-1_ppc64el.deb ...
330s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ...
330s Selecting previously unselected package libhts3:ppc64el.
330s Preparing to unpack .../64-libhts3_1.18+ds-1_ppc64el.deb ...
330s Unpacking libhts3:ppc64el (1.18+ds-1) ...
330s Selecting previously unselected package samtools.
330s Preparing to unpack .../65-samtools_1.19.2-1_ppc64el.deb ...
330s Unpacking samtools (1.19.2-1) ...
330s Selecting previously unselected package fastaq.
330s Preparing to unpack .../66-fastaq_3.17.0-6_all.deb ...
330s Unpacking fastaq (3.17.0-6) ...
330s Selecting previously unselected package python3-et-xmlfile.
330s Preparing to unpack .../67-python3-et-xmlfile_1.0.1-2.1_all.deb ...
330s Unpacking python3-et-xmlfile (1.0.1-2.1) ...
330s Selecting previously unselected package libxslt1.1:ppc64el.
330s Preparing to unpack .../68-libxslt1.1_1.1.39-0exp1_ppc64el.deb ...
330s Unpacking libxslt1.1:ppc64el (1.1.39-0exp1) ...
330s Selecting previously unselected package python3-lxml:ppc64el.
330s Preparing to unpack .../69-python3-lxml_5.1.0-1_ppc64el.deb ...
330s Unpacking python3-lxml:ppc64el (5.1.0-1) ...
330s Selecting previously unselected package python3-openpyxl.
330s Preparing to unpack .../70-python3-openpyxl_3.1.2+dfsg-6_all.deb ...
330s Unpacking python3-openpyxl (3.1.2+dfsg-6) ...
330s Selecting previously unselected package python3-packaging.
330s Preparing to unpack .../71-python3-packaging_23.2-1_all.deb ...
330s Unpacking python3-packaging (23.2-1) ...
330s Selecting previously unselected package mummer.
330s Preparing to unpack .../72-mummer_3.23+dfsg-8_ppc64el.deb ...
330s Unpacking mummer (3.23+dfsg-8) ...
330s Selecting previously unselected package python3-pymummer.
330s Preparing to unpack .../73-python3-pymummer_0.11.0-4_all.deb ...
330s Unpacking python3-pymummer (0.11.0-4) ...
330s Selecting previously unselected package python3-pysam.
330s Preparing to unpack .../74-python3-pysam_0.22.0+ds-1_ppc64el.deb ...
330s Unpacking python3-pysam (0.22.0+ds-1) ...
331s Selecting previously unselected package prodigal.
331s Preparing to unpack .../75-prodigal_1%3a2.6.3-6_ppc64el.deb ...
331s Unpacking prodigal (1:2.6.3-6) ...
331s Selecting previously unselected package circlator.
331s Preparing to unpack .../76-circlator_1.5.6-11_all.deb ...
331s Unpacking circlator (1.5.6-11) ...
331s Selecting previously unselected package python3-all.
331s Preparing to unpack .../77-python3-all_3.12.1-0ubuntu2_ppc64el.deb ...
331s Unpacking python3-all (3.12.1-0ubuntu2) ...
331s Selecting previously unselected package python3-iniconfig.
331s Preparing to unpack .../78-python3-iniconfig_1.1.1-2_all.deb ...
331s Unpacking python3-iniconfig (1.1.1-2) ...
331s Selecting previously unselected package python3-pluggy.
331s Preparing to unpack .../79-python3-pluggy_1.4.0-1_all.deb ...
331s Unpacking python3-pluggy (1.4.0-1) ...
331s Selecting previously unselected package python3-pytest.
331s Preparing to unpack .../80-python3-pytest_7.4.4-1_all.deb ...
331s Unpacking python3-pytest (7.4.4-1) ...
331s Selecting previously unselected package autopkgtest-satdep.
331s Preparing to unpack .../81-1-autopkgtest-satdep.deb ...
331s Unpacking autopkgtest-satdep (0) ...
331s Setting up libhtscodecs2:ppc64el (1.6.0-1) ...
331s Setting up fastjar (2:0.98-7) ...
331s Setting up libgraphite2-3:ppc64el (1.3.14-2) ...
331s Setting up liblcms2-2:ppc64el (2.14-2) ...
331s Setting up python3-iniconfig (1.1.1-2) ...
331s Setting up libpixman-1-0:ppc64el (0.42.2-1) ...
331s Setting up libfastutil-java (8.5.12+dfsg-1) ...
331s Setting up libsharpyuv0:ppc64el (1.3.2-0.4) ...
331s Setting up liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ...
331s Setting up libjsr305-java (0.1~+svn49-11) ...
331s Setting up libxpm4:ppc64el (1:3.5.17-1) ...
331s Setting up java-common (0.75+exp1) ...
331s Setting up libxrender1:ppc64el (1:0.9.10-1.1) ...
331s Setting up libdatrie1:ppc64el (0.2.13-3) ...
331s Setting up libxcb-render0:ppc64el (1.15-1) ...
331s Setting up prodigal (1:2.6.3-6) ...
331s Setting up bwa (0.7.17-7) ...
331s Setting up libfilesys-df-perl (0.92-7build2) ...
331s Setting up libdeflate0:ppc64el (1.19-1) ...
331s Setting up python3-all (3.12.1-0ubuntu2) ...
331s Setting up libxcb-shm0:ppc64el (1.15-1) ...
331s Setting up libgomp1:ppc64el (14-20240303-1ubuntu1) ...
331s Setting up libjbig0:ppc64el (2.1-6.1ubuntu1) ...
331s Setting up libssw-java (1.1-14) ...
331s Setting up libsnappy1v5:ppc64el (1.1.10-1) ...
331s Setting up libasound2-data (1.2.10-3build1) ...
331s Setting up python3-packaging (23.2-1) ...
331s Setting up aglfn (1.7+git20191031.4036a9c-2) ...
331s Setting up libapache-pom-java (29-2) ...
331s Setting up libavahi-common-data:ppc64el (0.8-13ubuntu2) ...
331s Setting up libatinject-jsr330-api-java (1.0+ds1-5) ...
331s Setting up fonts-dejavu-mono (2.37-8) ...
331s Setting up binfmt-support (2.2.2-6) ...
331s update-binfmts: warning: python3.11 already enabled in kernel.
331s update-binfmts: warning: python3.12 already enabled in kernel.
332s Created symlink /etc/systemd/system/multi-user.target.wants/binfmt-support.service → /usr/lib/systemd/system/binfmt-support.service.

332s Setting up fonts-dejavu-core (2.37-8) ...
332s Setting up libpcsclite1:ppc64el (2.0.0-1) ...
332s Setting up libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ...
332s Setting up python3-pluggy (1.4.0-1) ...
332s Setting up libwebp7:ppc64el (1.3.2-0.4) ...
332s Setting up libasound2:ppc64el (1.2.10-3build1) ...
332s Setting up libxslt1.1:ppc64el (1.1.39-0exp1) ...
332s Setting up mummer (3.23+dfsg-8) ...
332s Setting up python3-et-xmlfile (1.0.1-2.1) ...
332s Setting up liblua5.4-0:ppc64el (5.4.6-3) ...
332s Setting up libharfbuzz0b:ppc64el (8.3.0-2) ...
332s Setting up libthai-data (0.1.29-2) ...
332s Setting up ca-certificates-java (20240118) ...
332s No JRE found. Skipping Java certificates setup.
332s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ...
332s Setting up gnuplot-data (5.4.4+dfsg1-2build1) ...
332s Setting up libhts3:ppc64el (1.18+ds-1) ...
332s Setting up python3-pysam (0.22.0+ds-1) ...
333s Setting up jarwrapper (0.79) ...
333s Setting up fontconfig-config (2.15.0-1ubuntu1) ...
333s Setting up python3-pytest (7.4.4-1) ...
333s Setting up libcommons-parent-java (56-1) ...
333s Setting up libavahi-common3:ppc64el (0.8-13ubuntu2) ...
333s Setting up samtools (1.19.2-1) ...
333s Setting up libthai0:ppc64el (0.1.29-2) ...
333s Setting up python3-lxml:ppc64el (5.1.0-1) ...
333s Setting up libtiff6:ppc64el (4.5.1+git230720-3ubuntu1) ...
333s Setting up libfontconfig1:ppc64el (2.15.0-1ubuntu1) ...
333s Setting up libavahi-client3:ppc64el (0.8-13ubuntu2) ...
333s Setting up fontconfig (2.15.0-1ubuntu1) ...
335s Regenerating fonts cache... done.
335s Setting up libcommons-compress-java (1.25.0-1) ...
335s Setting up fastaq (3.17.0-6) ...
335s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:37: SyntaxWarning: invalid escape sequence '\s'
335s   phylip_regex = re.compile('^\s*[0-9]+\s+[0-9]+$')
335s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:38: SyntaxWarning: invalid escape sequence '\s'
335s   gbk_regex = re.compile('^LOCUS\s+\S')
335s Setting up libpango-1.0-0:ppc64el (1.51.0+ds-4) ...
335s Setting up libcairo2:ppc64el (1.18.0-1) ...
335s Setting up python3-pymummer (0.11.0-4) ...
335s Setting up python3-openpyxl (3.1.2+dfsg-6) ...
336s Setting up libgd3:ppc64el (2.3.3-9ubuntu1) ...
336s Setting up libcups2:ppc64el (2.4.6-0ubuntu3) ...
336s Setting up libpangoft2-1.0-0:ppc64el (1.51.0+ds-4) ...
336s Setting up libpangocairo-1.0-0:ppc64el (1.51.0+ds-4) ...
336s Setting up openjdk-21-jre-headless:ppc64el (21.0.2+13-2) ...
336s update-alternatives: using /usr/lib/jvm/java-21-openjdk-ppc64el/bin/java to provide /usr/bin/java (java) in auto mode
336s update-alternatives: using /usr/lib/jvm/java-21-openjdk-ppc64el/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode
336s update-alternatives: using /usr/lib/jvm/java-21-openjdk-ppc64el/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
336s update-alternatives: using /usr/lib/jvm/java-21-openjdk-ppc64el/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
336s update-alternatives: using /usr/lib/jvm/java-21-openjdk-ppc64el/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
336s Setting up gnuplot-nox (5.4.4+dfsg1-2build1) ...
336s update-alternatives: using /usr/bin/gnuplot-nox to provide /usr/bin/gnuplot (gnuplot) in auto mode
336s Setting up libguava-java (32.0.1-1) ...
336s Setting up liberror-prone-java (2.18.0-1) ...
336s Processing triggers for libc-bin (2.39-0ubuntu6) ...
336s Processing triggers for man-db (2.12.0-3) ...
337s Processing triggers for install-info (7.1-3) ...
337s Processing triggers for ca-certificates-java (20240118) ...
337s Adding debian:ACCVRAIZ1.pem
337s Adding debian:AC_RAIZ_FNMT-RCM.pem
337s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem
337s Adding debian:ANF_Secure_Server_Root_CA.pem
337s Adding debian:Actalis_Authentication_Root_CA.pem
337s Adding debian:AffirmTrust_Commercial.pem
337s Adding debian:AffirmTrust_Networking.pem
337s Adding debian:AffirmTrust_Premium.pem
337s Adding debian:AffirmTrust_Premium_ECC.pem
337s Adding debian:Amazon_Root_CA_1.pem
337s Adding debian:Amazon_Root_CA_2.pem
337s Adding debian:Amazon_Root_CA_3.pem
337s Adding debian:Amazon_Root_CA_4.pem
337s Adding debian:Atos_TrustedRoot_2011.pem
337s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem
337s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem
337s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
337s Adding debian:BJCA_Global_Root_CA1.pem
337s Adding debian:BJCA_Global_Root_CA2.pem
337s Adding debian:Baltimore_CyberTrust_Root.pem
337s Adding debian:Buypass_Class_2_Root_CA.pem
337s Adding debian:Buypass_Class_3_Root_CA.pem
337s Adding debian:CA_Disig_Root_R2.pem
337s Adding debian:CFCA_EV_ROOT.pem
337s Adding debian:COMODO_Certification_Authority.pem
337s Adding debian:COMODO_ECC_Certification_Authority.pem
337s Adding debian:COMODO_RSA_Certification_Authority.pem
337s Adding debian:Certainly_Root_E1.pem
337s Adding debian:Certainly_Root_R1.pem
337s Adding debian:Certigna.pem
337s Adding debian:Certigna_Root_CA.pem
337s Adding debian:Certum_EC-384_CA.pem
337s Adding debian:Certum_Trusted_Network_CA.pem
337s Adding debian:Certum_Trusted_Network_CA_2.pem
337s Adding debian:Certum_Trusted_Root_CA.pem
337s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem
337s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem
337s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem
337s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem
337s Adding debian:Comodo_AAA_Services_root.pem
337s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem
337s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem
337s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
337s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
337s Adding debian:DigiCert_Assured_ID_Root_CA.pem
337s Adding debian:DigiCert_Assured_ID_Root_G2.pem
337s Adding debian:DigiCert_Assured_ID_Root_G3.pem
337s Adding debian:DigiCert_Global_Root_CA.pem
337s Adding debian:DigiCert_Global_Root_G2.pem
337s Adding debian:DigiCert_Global_Root_G3.pem
337s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
337s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem
337s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem
337s Adding debian:DigiCert_Trusted_Root_G4.pem
337s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
337s Adding debian:Entrust_Root_Certification_Authority.pem
337s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
337s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
337s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem
337s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem
337s Adding debian:GLOBALTRUST_2020.pem
337s Adding debian:GTS_Root_R1.pem
337s Adding debian:GTS_Root_R2.pem
337s Adding debian:GTS_Root_R3.pem
337s Adding debian:GTS_Root_R4.pem
337s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
337s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
337s Adding debian:GlobalSign_Root_CA.pem
337s Adding debian:GlobalSign_Root_CA_-_R3.pem
337s Adding debian:GlobalSign_Root_CA_-_R6.pem
337s Adding debian:GlobalSign_Root_E46.pem
337s Adding debian:GlobalSign_Root_R46.pem
337s Adding debian:Go_Daddy_Class_2_CA.pem
337s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
337s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem
337s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem
337s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem
338s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem
338s Adding debian:HiPKI_Root_CA_-_G1.pem
338s Adding debian:Hongkong_Post_Root_CA_3.pem
338s Adding debian:ISRG_Root_X1.pem
338s Adding debian:ISRG_Root_X2.pem
338s Adding debian:IdenTrust_Commercial_Root_CA_1.pem
338s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
338s Adding debian:Izenpe.com.pem
338s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
338s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem
338s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem
338s Adding debian:NAVER_Global_Root_Certification_Authority.pem
338s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
338s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
338s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem
338s Adding debian:QuoVadis_Root_CA_1_G3.pem
338s Adding debian:QuoVadis_Root_CA_2.pem
338s Adding debian:QuoVadis_Root_CA_2_G3.pem
338s Adding debian:QuoVadis_Root_CA_3.pem
338s Adding debian:QuoVadis_Root_CA_3_G3.pem
338s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem
338s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem
338s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem
338s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem
338s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem
338s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem
338s Adding debian:SZAFIR_ROOT_CA2.pem
338s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem
338s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem
338s Adding debian:SecureSign_RootCA11.pem
338s Adding debian:SecureTrust_CA.pem
338s Adding debian:Secure_Global_CA.pem
338s Adding debian:Security_Communication_ECC_RootCA1.pem
338s Adding debian:Security_Communication_RootCA2.pem
338s Adding debian:Security_Communication_RootCA3.pem
338s Adding debian:Security_Communication_Root_CA.pem
338s Adding debian:Starfield_Class_2_CA.pem
338s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
338s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
338s Adding debian:SwissSign_Gold_CA_-_G2.pem
338s Adding debian:SwissSign_Silver_CA_-_G2.pem
338s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
338s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
338s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
338s Adding debian:TWCA_Global_Root_CA.pem
338s Adding debian:TWCA_Root_Certification_Authority.pem
338s Adding debian:TeliaSonera_Root_CA_v1.pem
338s Adding debian:Telia_Root_CA_v2.pem
338s Adding debian:TrustAsia_Global_Root_CA_G3.pem
338s Adding debian:TrustAsia_Global_Root_CA_G4.pem
338s Adding debian:Trustwave_Global_Certification_Authority.pem
338s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem
338s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem
338s Adding debian:TunTrust_Root_CA.pem
338s Adding debian:UCA_Extended_Validation_Root.pem
338s Adding debian:UCA_Global_G2_Root.pem
338s Adding debian:USERTrust_ECC_Certification_Authority.pem
338s Adding debian:USERTrust_RSA_Certification_Authority.pem
338s Adding debian:XRamp_Global_CA_Root.pem
338s Adding debian:certSIGN_ROOT_CA.pem
338s Adding debian:certSIGN_Root_CA_G2.pem
338s Adding debian:e-Szigno_Root_CA_2017.pem
338s Adding debian:ePKI_Root_Certification_Authority.pem
338s Adding debian:emSign_ECC_Root_CA_-_C3.pem
338s Adding debian:emSign_ECC_Root_CA_-_G3.pem
338s Adding debian:emSign_Root_CA_-_C1.pem
338s Adding debian:emSign_Root_CA_-_G1.pem
338s Adding debian:vTrus_ECC_Root_CA.pem
338s Adding debian:vTrus_Root_CA.pem
338s done.
338s Setting up default-jre-headless (2:1.21-75+exp1) ...
338s Setting up jaligner (1.0+dfsg-11) ...
338s Setting up mhap (2.1.3+dfsg-3) ...
338s Setting up canu (2.2+dfsg-5) ...
338s Setting up circlator (1.5.6-11) ...
338s /usr/lib/python3/dist-packages/circlator/dnaa.py:18: SyntaxWarning: invalid escape sequence '\s'
338s   self.uniprot_search = re.sub('\s+', '+', uniprot_search.strip())
338s Setting up autopkgtest-satdep (0) ...
341s (Reading database ... 72503 files and directories currently installed.)
341s Removing autopkgtest-satdep (0) ...
342s autopkgtest [15:35:04]: test run-unit-test: [-----------------------
342s + pkg=circlator
342s + export LC_ALL=C.UTF-8
342s + LC_ALL=C.UTF-8
342s + '[' /tmp/autopkgtest.c6zXij/autopkgtest_tmp = '' ']'
342s + 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.c6zXij/autopkgtest_tmp
342s + cd /tmp/autopkgtest.c6zXij/autopkgtest_tmp
342s + tar xaf data.tar.xz
342s + 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
342s ++ py3versions --supported
342s + for py in $(py3versions --supported 2> /dev/null)
342s + eval dpkg-architecture --is amd64
342s ++ dpkg-architecture --is amd64
342s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation)
342s + python3.12 -m pytest -v -k 'not (test_build_spades_kmers or test_make_spades_command)'
342s ============================= test session starts ==============================
342s platform linux -- Python 3.12.2, pytest-7.4.4, pluggy-1.4.0 -- /usr/bin/python3.12
342s cachedir: .pytest_cache
342s rootdir: /tmp/autopkgtest.c6zXij/autopkgtest_tmp
343s collecting ... collected 115 items / 2 deselected / 113 selected
343s 
343s assemble_test.py::TestAssembleCanu::test_make_canu_command PASSED        [  0%]
343s assemble_test.py::TestAssembleCanu::test_rename_canu_contigs PASSED      [  1%]
343s assembly_test.py::TestAssembly::test_circular_contigs_from_canu_gfa PASSED [  2%]
343s assembly_test.py::TestAssembly::test_circular_contigs_from_spades_after_3_6_1 PASSED [  3%]
343s assembly_test.py::TestAssembly::test_circular_contigs_from_spades_before_3_6_1 PASSED [  4%]
343s assembly_test.py::TestAssembly::test_circular_contigs_just_fasta PASSED  [  5%]
343s assembly_test.py::TestAssembly::test_circular_contigs_spades_post_3_6_1 PASSED [  6%]
343s assembly_test.py::TestAssembly::test_circular_contigs_spades_pre_3_6_1 PASSED [  7%]
343s assembly_test.py::TestAssembly::test_circular_edges_to_edge_numbers_dict PASSED [  7%]
343s assembly_test.py::TestAssembly::test_get_contigs PASSED                  [  8%]
343s assembly_test.py::TestAssembly::test_init_file_not_dir PASSED            [  9%]
343s assembly_test.py::TestAssembly::test_init_post_3_6_1_ok PASSED           [ 10%]
343s assembly_test.py::TestAssembly::test_init_pre_3_6_1_ok PASSED            [ 11%]
343s assembly_test.py::TestAssembly::test_init_raises_error PASSED            [ 12%]
343s assembly_test.py::TestAssembly::test_spades_contigs_paths_to_dict PASSED [ 13%]
343s bamfilter_test.py::TestBamfilter::test_all_reads_from_contig PASSED      [ 14%]
343s bamfilter_test.py::TestBamfilter::test_break_reads PASSED                [ 15%]
343s bamfilter_test.py::TestBamfilter::test_check_contigs_to_use PASSED       [ 15%]
343s bamfilter_test.py::TestBamfilter::test_exclude_region PASSED             [ 16%]
343s bamfilter_test.py::TestBamfilter::test_get_all_unmapped_reads PASSED     [ 17%]
343s bamfilter_test.py::TestBamfilter::test_get_contigs_to_use PASSED         [ 18%]
343s bamfilter_test.py::TestBamfilter::test_get_ref_lengths PASSED            [ 19%]
343s bamfilter_test.py::TestBamfilter::test_get_region_end PASSED             [ 20%]
343s bamfilter_test.py::TestBamfilter::test_get_region_start PASSED           [ 21%]
343s bamfilter_test.py::TestBamfilter::test_run_discard_unmapped_no_quals PASSED [ 22%]
343s bamfilter_test.py::TestBamfilter::test_run_keep_unmapped_no_quals PASSED [ 23%]
343s bamfilter_test.py::TestBamfilter::test_run_keep_unmapped_with_quals PASSED [ 23%]
343s clean_test.py::TestClean::test_clean_contigs PASSED                      [ 24%]
343s clean_test.py::TestClean::test_collapse_list_of_sets PASSED              [ 25%]
343s clean_test.py::TestClean::test_containing_contigs PASSED                 [ 26%]
343s clean_test.py::TestClean::test_contains PASSED                           [ 27%]
343s clean_test.py::TestClean::test_expand_containing_using_transitivity PASSED [ 28%]
343s clean_test.py::TestClean::test_get_all_containing PASSED                 [ 29%]
343s clean_test.py::TestClean::test_get_containing_contigs PASSED             [ 30%]
343s clean_test.py::TestClean::test_get_contigs_to_keep PASSED                [ 30%]
343s clean_test.py::TestClean::test_get_identical_contigs PASSED              [ 31%]
343s clean_test.py::TestClean::test_infinite_recursion PASSED                 [ 32%]
343s clean_test.py::TestClean::test_load_nucmer_hits PASSED                   [ 33%]
343s clean_test.py::TestClean::test_longest_contig PASSED                     [ 34%]
343s clean_test.py::TestClean::test_remove_identical_contigs PASSED           [ 35%]
343s clean_test.py::TestClean::test_remove_small_contigs PASSED               [ 36%]
343s clean_test.py::TestClean::test_write_log PASSED                          [ 37%]
343s common_test.py::TestCommon::test_check_files_exist PASSED                [ 38%]
343s dnaa_test.py::TestDnaa::test_append_stop_to_seq PASSED                   [ 38%]
343s dnaa_test.py::TestDnaa::test_check_sequence PASSED                       [ 39%]
343s dnaa_test.py::TestDnaa::test_get_uniprot_url PASSED                      [ 40%]
343s dnaa_test.py::TestDnaa::test_header_matches_regex PASSED                 [ 41%]
343s dnaa_test.py::TestDnaa::test_header_to_genus_species PASSED              [ 42%]
343s dnaa_test.py::TestDnaa::test_reverse_translate PASSED                    [ 43%]
343s external_progs_test.py::TestExternalProgs::test_bwa_version PASSED       [ 44%]
343s external_progs_test.py::TestExternalProgs::test_canu_version PASSED      [ 45%]
343s external_progs_test.py::TestExternalProgs::test_nucmer_version PASSED    [ 46%]
343s external_progs_test.py::TestExternalProgs::test_prodigal_version PASSED  [ 46%]
343s external_progs_test.py::TestExternalProgs::test_samtools_original_version PASSED [ 47%]
343s external_progs_test.py::TestExternalProgs::test_samtools_version PASSED  [ 48%]
343s external_progs_test.py::TestExternalProgs::test_spades_version PASSED    [ 49%]
343s mapping_test.py::TestMapping::test_aligned_read_to_read PASSED           [ 50%]
343s mapping_test.py::TestMapping::test_bwa_index PASSED                      [ 51%]
343s mapping_test.py::TestMapping::test_bwa_index_clean PASSED                [ 52%]
343s mapping_test.py::TestMapping::test_bwa_mem PASSED                        [ 53%]
343s merge_test.py::TestMerge::test_can_circularise PASSED                    [ 53%]
343s merge_test.py::TestMerge::test_contigs_dict_to_file PASSED               [ 54%]
343s merge_test.py::TestMerge::test_filter_bridging_contigs PASSED            [ 55%]
343s merge_test.py::TestMerge::test_get_hit_nearest_ref_end PASSED            [ 56%]
343s merge_test.py::TestMerge::test_get_hit_nearest_ref_start PASSED          [ 57%]
343s merge_test.py::TestMerge::test_get_longest_hit_at_qry_end PASSED         [ 58%]
343s merge_test.py::TestMerge::test_get_longest_hit_at_qry_start PASSED       [ 59%]
343s merge_test.py::TestMerge::test_get_longest_hit_at_ref_end PASSED         [ 60%]
343s merge_test.py::TestMerge::test_get_longest_hit_at_ref_start PASSED       [ 61%]
343s merge_test.py::TestMerge::test_get_longest_hit_by_ref_length PASSED      [ 61%]
343s merge_test.py::TestMerge::test_get_possible_circular_ref_contigs PASSED  [ 62%]
343s merge_test.py::TestMerge::test_get_possible_circular_ref_contigs_same_best_hits PASSED [ 63%]
343s merge_test.py::TestMerge::test_get_possible_query_bridging_contigs PASSED [ 64%]
343s merge_test.py::TestMerge::test_get_spades_circular_nodes PASSED          [ 65%]
343s merge_test.py::TestMerge::test_has_qry_hit_longer_than PASSED            [ 66%]
343s merge_test.py::TestMerge::test_hits_hashed_by_query PASSED               [ 67%]
343s merge_test.py::TestMerge::test_hits_have_same_query PASSED               [ 68%]
343s merge_test.py::TestMerge::test_hits_have_same_reference PASSED           [ 69%]
343s merge_test.py::TestMerge::test_index_fasta PASSED                        [ 69%]
343s merge_test.py::TestMerge::test_is_at_qry_end PASSED                      [ 70%]
343s merge_test.py::TestMerge::test_is_at_qry_start PASSED                    [ 71%]
343s merge_test.py::TestMerge::test_is_at_ref_end PASSED                      [ 72%]
343s merge_test.py::TestMerge::test_is_at_ref_start PASSED                    [ 73%]
343s merge_test.py::TestMerge::test_load_nucmer_hits PASSED                   [ 74%]
343s merge_test.py::TestMerge::test_make_circularised_contig_1 PASSED         [ 75%]
343s merge_test.py::TestMerge::test_make_circularised_contig_2 PASSED         [ 76%]
343s merge_test.py::TestMerge::test_make_new_contig_from_nucmer_and_spades_not_hit PASSED [ 76%]
343s merge_test.py::TestMerge::test_make_new_contig_from_nucmer_and_spades_with_hit PASSED [ 77%]
343s merge_test.py::TestMerge::test_merge_bridged_contig_pair1 PASSED         [ 78%]
343s merge_test.py::TestMerge::test_merge_bridged_contig_pair2 PASSED         [ 79%]
343s merge_test.py::TestMerge::test_merge_bridged_contig_pair3 PASSED         [ 80%]
343s merge_test.py::TestMerge::test_merge_bridged_contig_pair4 PASSED         [ 81%]
343s merge_test.py::TestMerge::test_min_qry_hit_length PASSED                 [ 82%]
343s merge_test.py::TestMerge::test_orientation_ok_to_bridge_contigs PASSED   [ 83%]
343s merge_test.py::TestMerge::test_remove_keys_from_dict_with_nonunique_values PASSED [ 84%]
343s merge_test.py::TestMerge::test_write_act_files PASSED                    [ 84%]
343s minimus2_test.py::TestMinimus2::test_run_initial_merge SKIPPED (Amos...) [ 85%]
343s minimus2_test.py::TestMinimus2::test_run_minimus2 SKIPPED (Amos is n...) [ 86%]
343s minimus2_test.py::TestMinimus2::test_run_minimus2_on_each_contig SKIPPED [ 87%]
343s minimus2_test.py::TestMinimus2::test_run_minimus2_on_one_contig_will_not_work SKIPPED [ 88%]
343s minimus2_test.py::TestMinimus2::test_run_minimus2_on_one_contig_will_work SKIPPED [ 89%]
343s minimus2_test.py::TestMinimus2::test_write_split_contig SKIPPED (Amo...) [ 90%]
343s start_fixer_test.py::TestStartFixer::test_find_circular_using_prodigal PASSED [ 91%]
343s start_fixer_test.py::TestStartFixer::test_find_circular_using_promer PASSED [ 92%]
343s start_fixer_test.py::TestStartFixer::test_init PASSED                    [ 92%]
343s start_fixer_test.py::TestStartFixer::test_max_length_from_fasta_file PASSED [ 93%]
343s start_fixer_test.py::TestStartFixer::test_rearrange_contigs PASSED       [ 94%]
343s start_fixer_test.py::TestStartFixer::test_rename_contigs PASSED          [ 95%]
343s start_fixer_test.py::TestStartFixer::test_run_bit_of_everything PASSED   [ 96%]
343s start_fixer_test.py::TestStartFixer::test_run_ignore_all PASSED          [ 97%]
343s start_fixer_test.py::TestStartFixer::test_run_none_for_prodigal PASSED   [ 98%]
343s start_fixer_test.py::TestStartFixer::test_write_fasta_plus_circularized_ends PASSED [ 99%]
343s start_fixer_test.py::TestStartFixer::test_write_renamed_contigs PASSED   [100%]
343s 
343s =============================== warnings summary ===============================
343s ../../../usr/lib/python3/dist-packages/pyfastaq/__init__.py:1
343s   /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
343s     from pkg_resources import get_distribution
343s 
343s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
343s =========== 107 passed, 6 skipped, 2 deselected, 1 warning in 1.27s ============
344s autopkgtest [15:35:06]: test run-unit-test: -----------------------]
344s autopkgtest [15:35:06]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
344s run-unit-test        PASS
344s autopkgtest [15:35:06]: @@@@@@@@@@@@@@@@@@@@ summary
344s run-unit-test        PASS
359s Creating nova instance adt-noble-ppc64el-circlator-20240323-151747-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240321.img (UUID 024d6af5-fcba-4a84-85f9-01f41e1878d6)...