0s autopkgtest [17:56:18]: starting date and time: 2024-03-24 17:56:18+0000
  0s autopkgtest [17:56:18]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps
  0s autopkgtest [17:56:18]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.1dw2kmlv/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:samtools,src:curl,src:gnutls28,src:htslib,src:libpsl,src:nettle,src:openssl --apt-upgrade iva --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=samtools/1.19.2-1build1 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-arm64-17.secgroup --name adt-noble-arm64-iva-20240324-172719-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-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/
114s autopkgtest [17:58:12]: testbed dpkg architecture: arm64
114s autopkgtest [17:58:12]: testbed apt version: 2.7.12
114s autopkgtest [17:58:12]: @@@@@@@@@@@@@@@@@@@@ test bed setup
115s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
115s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB]
116s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3986 kB]
116s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB]
116s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B]
116s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [710 kB]
116s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B]
116s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB]
116s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B]
116s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4364 kB]
117s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B]
117s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [70.1 kB]
117s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B]
122s Fetched 9851 kB in 3s (3298 kB/s)
122s Reading package lists...
126s Reading package lists...
126s Building dependency tree...
126s Reading state information...
127s Calculating upgrade...
128s The following packages will be REMOVED:
128s   libssl3
128s The following NEW packages will be installed:
128s   libssl3t64
128s The following packages have been kept back:
128s   curl
128s The following packages will be upgraded:
128s   openssl
129s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded.
129s Need to get 2777 kB of archives.
129s After this operation, 139 kB of additional disk space will be used.
129s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu2 [985 kB]
129s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu2 [1793 kB]
130s Fetched 2777 kB in 1s (3638 kB/s)
130s (Reading database ... 
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(Reading database ... 75911 files and directories currently installed.)
130s Preparing to unpack .../openssl_3.0.13-0ubuntu2_arm64.deb ...
130s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ...
130s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested:
130s  wget depends on libssl3 (>= 3.0.0).
130s  u-boot-tools depends on libssl3 (>= 3.0.0).
130s  tnftp depends on libssl3 (>= 3.0.0).
130s  tcpdump depends on libssl3 (>= 3.0.0).
130s  systemd-resolved depends on libssl3 (>= 3.0.0).
130s  systemd depends on libssl3 (>= 3.0.0).
130s  sudo depends on libssl3 (>= 3.0.0).
130s  sbsigntool depends on libssl3 (>= 3.0.0).
130s  rsync depends on libssl3 (>= 3.0.0).
130s  python3-cryptography depends on libssl3 (>= 3.0.0).
130s  openssh-server depends on libssl3 (>= 3.0.10).
130s  openssh-client depends on libssl3 (>= 3.0.10).
130s  mtd-utils depends on libssl3 (>= 3.0.0).
130s  mokutil depends on libssl3 (>= 3.0.0).
130s  linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0).
130s  libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0).
130s  libssh-4:arm64 depends on libssl3 (>= 3.0.0).
130s  libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0).
130s  libsasl2-2:arm64 depends on libssl3 (>= 3.0.0).
130s  libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0).
130s  libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0).
130s  libnvme1 depends on libssl3 (>= 3.0.0).
130s  libkrb5-3:arm64 depends on libssl3 (>= 3.0.0).
130s  libkmod2:arm64 depends on libssl3 (>= 3.0.0).
130s  libfido2-1:arm64 depends on libssl3 (>= 3.0.0).
130s  libcurl4:arm64 depends on libssl3 (>= 3.0.0).
130s  libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0).
130s  kmod depends on libssl3 (>= 3.0.0).
130s  dhcpcd-base depends on libssl3 (>= 3.0.0).
130s  bind9-libs:arm64 depends on libssl3 (>= 3.0.0).
130s 
130s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 75911 files and directories currently installed.)
130s Removing libssl3:arm64 (3.0.10-1ubuntu4) ...
130s Selecting previously unselected package libssl3t64:arm64.
131s (Reading database ... 
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(Reading database ... 100%
(Reading database ... 75900 files and directories currently installed.)
131s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_arm64.deb ...
131s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu2) ...
131s Setting up libssl3t64:arm64 (3.0.13-0ubuntu2) ...
131s Setting up openssl (3.0.13-0ubuntu2) ...
131s Processing triggers for man-db (2.12.0-3) ...
132s Processing triggers for libc-bin (2.39-0ubuntu6) ...
132s Reading package lists...
132s Building dependency tree...
132s Reading state information...
134s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
135s sh: Attempting to set up Debian/Ubuntu apt sources automatically
135s sh: Distribution appears to be Ubuntu
136s Reading package lists...
137s Building dependency tree...
137s Reading state information...
138s eatmydata is already the newest version (131-1).
138s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
138s Reading package lists...
138s Building dependency tree...
138s Reading state information...
140s dbus is already the newest version (1.14.10-4ubuntu1).
140s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
140s Reading package lists...
140s Building dependency tree...
140s Reading state information...
141s rng-tools-debian is already the newest version (2.4).
141s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
141s Reading package lists...
142s Building dependency tree...
142s Reading state information...
143s The following packages will be REMOVED:
143s   cloud-init* python3-configobj* python3-debconf*
144s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded.
144s After this operation, 3256 kB disk space will be freed.
144s (Reading database ... 
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(Reading database ... 95%
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(Reading database ... 75913 files and directories currently installed.)
144s Removing cloud-init (24.1.2-0ubuntu1) ...
145s Removing python3-configobj (5.0.8-3) ...
145s Removing python3-debconf (1.5.86) ...
145s Processing triggers for man-db (2.12.0-3) ...
146s (Reading database ... 
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(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 75524 files and directories currently installed.)
146s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ...
147s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed
147s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ...
147s invoke-rc.d: policy-rc.d denied execution of try-restart.
147s Reading package lists...
148s Building dependency tree...
148s Reading state information...
149s linux-generic is already the newest version (6.8.0-11.11+1).
149s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
150s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
150s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
150s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
155s Reading package lists...
155s Reading package lists...
155s Building dependency tree...
155s Reading state information...
156s Calculating upgrade...
157s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
157s Reading package lists...
158s Building dependency tree...
158s Reading state information...
159s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
159s autopkgtest [17:58:57]: rebooting testbed after setup commands that affected boot
314s autopkgtest [18:01:31]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024
317s autopkgtest [18:01:35]: @@@@@@@@@@@@@@@@@@@@ apt-source iva
320s Get:1 http://ftpmaster.internal/ubuntu noble/universe iva 1.0.11+ds-5 (dsc) [2289 B]
320s Get:2 http://ftpmaster.internal/ubuntu noble/universe iva 1.0.11+ds-5 (tar) [8681 kB]
320s Get:3 http://ftpmaster.internal/ubuntu noble/universe iva 1.0.11+ds-5 (diff) [5992 B]
320s gpgv: Signature made Thu Feb  1 12:52:13 2024 UTC
320s gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
320s gpgv:                issuer "tille@debian.org"
320s gpgv: Can't check signature: No public key
320s dpkg-source: warning: cannot verify inline signature for ./iva_1.0.11+ds-5.dsc: no acceptable signature found
321s autopkgtest [18:01:39]: testing package iva version 1.0.11+ds-5
321s autopkgtest [18:01:39]: build not needed
322s autopkgtest [18:01:40]: test test-example: preparing testbed
331s Reading package lists...
331s Building dependency tree...
331s Reading state information...
332s Starting pkgProblemResolver with broken count: 0
332s Starting 2 pkgProblemResolver with broken count: 0
332s Done
333s The following additional packages will be installed:
333s   adwaita-icon-theme at-spi2-common ca-certificates-java default-jre
333s   default-jre-headless fastaq fontconfig fontconfig-config fonts-dejavu-core
333s   fonts-dejavu-mono gtk-update-icon-cache hicolor-icon-theme
333s   humanity-icon-theme iva java-common kmc libasound2 libasound2-data
333s   libatk1.0-0 libavahi-client3 libavahi-common-data libavahi-common3
333s   libbambamc0 libblas3 libcairo2 libcups2 libdatrie1 libdeflate0
333s   libdrm-amdgpu1 libdrm-nouveau2 libdrm-radeon1 libfontconfig1
333s   libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgif7 libgl1
333s   libgl1-mesa-dri libglapi-mesa libglvnd0 libglx-mesa0 libglx0 libgraphite2-3
333s   libgtk2.0-0 libgtk2.0-common libharfbuzz0b libhts3 libhtscodecs2 libjbig0
333s   libjbzip2-java libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4
333s   libllvm17 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpcsclite1
333s   libpixman-1-0 libsharpyuv0 libthai-data libthai0 libtiff6 libvulkan1
333s   libwebp7 libx11-xcb1 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0
333s   libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0
333s   libxcomposite1 libxcursor1 libxdamage1 libxfixes3 libxi6 libxinerama1
333s   libxrandr2 libxrender1 libxshmfence1 libxtst6 libxxf86vm1 mummer
333s   openjdk-21-jre openjdk-21-jre-headless python3-networkx python3-numpy
333s   python3-packaging python3-pysam samtools smalt trimmomatic ubuntu-mono
333s   x11-common
333s Suggested packages:
333s   libasound2-plugins alsa-utils cups-common gvfs liblcms2-utils pcscd
333s   libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho
333s   fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic python-networkx-doc
333s   python3-gdal python3-matplotlib python3-pydot python3-pygraphviz
333s   python3-scipy gcc gfortran python3-dev python3-pytest cwltool
333s Recommended packages:
333s   librsvg2-common r-base-core bioperl alsa-ucm-conf alsa-topology-conf
333s   libgdk-pixbuf2.0-bin libgl1-amber-dri libgail-common libgtk2.0-bin
333s   mesa-vulkan-drivers | vulkan-icd libatk-wrapper-java-jni fonts-dejavu-extra
333s The following NEW packages will be installed:
333s   adwaita-icon-theme at-spi2-common autopkgtest-satdep ca-certificates-java
333s   default-jre default-jre-headless fastaq fontconfig fontconfig-config
333s   fonts-dejavu-core fonts-dejavu-mono gtk-update-icon-cache hicolor-icon-theme
333s   humanity-icon-theme iva java-common kmc libasound2 libasound2-data
333s   libatk1.0-0 libavahi-client3 libavahi-common-data libavahi-common3
333s   libbambamc0 libblas3 libcairo2 libcups2 libdatrie1 libdeflate0
333s   libdrm-amdgpu1 libdrm-nouveau2 libdrm-radeon1 libfontconfig1
333s   libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgif7 libgl1
333s   libgl1-mesa-dri libglapi-mesa libglvnd0 libglx-mesa0 libglx0 libgraphite2-3
333s   libgtk2.0-0 libgtk2.0-common libharfbuzz0b libhts3 libhtscodecs2 libjbig0
333s   libjbzip2-java libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4
333s   libllvm17 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpcsclite1
333s   libpixman-1-0 libsharpyuv0 libthai-data libthai0 libtiff6 libvulkan1
333s   libwebp7 libx11-xcb1 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0
333s   libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0
333s   libxcomposite1 libxcursor1 libxdamage1 libxfixes3 libxi6 libxinerama1
333s   libxrandr2 libxrender1 libxshmfence1 libxtst6 libxxf86vm1 mummer
333s   openjdk-21-jre openjdk-21-jre-headless python3-networkx python3-numpy
333s   python3-packaging python3-pysam samtools smalt trimmomatic ubuntu-mono
333s   x11-common
333s 0 upgraded, 101 newly installed, 0 to remove and 0 not upgraded.
333s Need to get 116 MB/116 MB of archives.
333s After this operation, 529 MB of additional disk space will be used.
333s Get:1 /tmp/autopkgtest.jpRG9y/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [724 B]
334s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-3 [7624 B]
334s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB]
334s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B]
334s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB]
334s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB]
334s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB]
334s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB]
334s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB]
334s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB]
334s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libgdk-pixbuf-2.0-0 arm64 2.42.10+dfsg-3 [144 kB]
334s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 gtk-update-icon-cache arm64 3.24.40-2ubuntu1 [50.5 kB]
334s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 hicolor-icon-theme all 0.17-2 [9976 B]
334s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 humanity-icon-theme all 0.6.16 [1282 kB]
335s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-mono all 24.04-0ubuntu1 [151 kB]
335s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 adwaita-icon-theme all 46~rc-1 [723 kB]
335s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 at-spi2-common all 2.50.0-1 [7864 B]
335s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 ca-certificates-java all 20240118 [11.6 kB]
335s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 java-common all 0.75+exp1 [6798 B]
335s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libavahi-common-data arm64 0.8-13ubuntu2 [29.5 kB]
335s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libavahi-common3 arm64 0.8-13ubuntu2 [23.2 kB]
335s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libavahi-client3 arm64 0.8-13ubuntu2 [27.3 kB]
335s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libcups2 arm64 2.4.6-0ubuntu3 [270 kB]
335s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB]
335s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB]
335s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB]
336s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB]
336s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB]
336s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libasound2-data all 1.2.10-3build1 [20.7 kB]
336s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libasound2 arm64 1.2.10-3build1 [386 kB]
336s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB]
336s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB]
336s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libpcsclite1 arm64 2.0.0-1 [21.2 kB]
336s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 openjdk-21-jre-headless arm64 21.0.2+13-2 [45.8 MB]
339s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 default-jre-headless arm64 2:1.21-75+exp1 [3096 B]
339s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libgtk2.0-common all 2.24.33-2ubuntu2 [125 kB]
339s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libatk1.0-0 arm64 2.50.0-1 [53.8 kB]
339s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB]
339s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB]
339s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B]
339s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB]
339s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB]
339s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB]
339s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB]
339s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB]
339s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB]
339s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB]
339s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB]
339s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB]
339s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 libxcomposite1 arm64 1:0.4.5-1build2 [7080 B]
339s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 libxfixes3 arm64 1:6.0.0-2 [11.0 kB]
339s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 libxcursor1 arm64 1:1.2.1-1 [21.3 kB]
339s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 libxdamage1 arm64 1:1.1.6-1 [6032 B]
339s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 libxi6 arm64 2:1.8.1-1 [31.9 kB]
339s Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 libxinerama1 arm64 2:1.1.4-3 [7056 B]
339s Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 libxrandr2 arm64 2:1.5.2-2 [19.6 kB]
339s Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 libgtk2.0-0 arm64 2.24.33-2ubuntu2 [1981 kB]
339s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 libglvnd0 arm64 1.7.0-1 [60.0 kB]
339s Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 libglapi-mesa arm64 24.0.1-1ubuntu1 [57.8 kB]
339s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 libx11-xcb1 arm64 2:1.8.7-1 [7836 B]
339s Get:61 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-dri2-0 arm64 1.15-1 [7244 B]
339s Get:62 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-dri3-0 arm64 1.15-1 [7108 B]
339s Get:63 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-glx0 arm64 1.15-1 [25.2 kB]
339s Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-present0 arm64 1.15-1 [5732 B]
339s Get:65 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-randr0 arm64 1.15-1 [18.2 kB]
339s Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-sync1 arm64 1.15-1 [9412 B]
339s Get:67 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-xfixes0 arm64 1.15-1 [10.3 kB]
339s Get:68 http://ftpmaster.internal/ubuntu noble/main arm64 libxshmfence1 arm64 1.3-1build4 [5444 B]
339s Get:69 http://ftpmaster.internal/ubuntu noble/main arm64 libxxf86vm1 arm64 1:1.1.4-1build3 [10.3 kB]
339s Get:70 http://ftpmaster.internal/ubuntu noble/main arm64 libvulkan1 arm64 1.3.275.0-1 [150 kB]
339s Get:71 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-amdgpu1 arm64 2.4.120-2 [20.4 kB]
339s Get:72 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-nouveau2 arm64 2.4.120-2 [17.8 kB]
339s Get:73 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-radeon1 arm64 2.4.120-2 [20.9 kB]
339s Get:74 http://ftpmaster.internal/ubuntu noble/main arm64 libllvm17 arm64 1:17.0.6-5build1 [25.0 MB]
341s Get:75 http://ftpmaster.internal/ubuntu noble/main arm64 libgl1-mesa-dri arm64 24.0.1-1ubuntu1 [8226 kB]
341s Get:76 http://ftpmaster.internal/ubuntu noble/main arm64 libglx-mesa0 arm64 24.0.1-1ubuntu1 [166 kB]
341s Get:77 http://ftpmaster.internal/ubuntu noble/main arm64 libglx0 arm64 1.7.0-1 [32.4 kB]
341s Get:78 http://ftpmaster.internal/ubuntu noble/main arm64 libgl1 arm64 1.7.0-1 [107 kB]
341s Get:79 http://ftpmaster.internal/ubuntu noble/main arm64 libgif7 arm64 5.2.1-2.5 [34.2 kB]
341s Get:80 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB]
341s Get:81 http://ftpmaster.internal/ubuntu noble/main arm64 libxtst6 arm64 2:1.2.3-1.1 [13.7 kB]
341s Get:82 http://ftpmaster.internal/ubuntu noble/main arm64 openjdk-21-jre arm64 21.0.2+13-2 [226 kB]
341s Get:83 http://ftpmaster.internal/ubuntu noble/main arm64 default-jre arm64 2:1.21-75+exp1 [922 B]
341s Get:84 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB]
341s Get:85 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB]
341s Get:86 http://ftpmaster.internal/ubuntu noble/universe arm64 samtools arm64 1.19.2-1 [584 kB]
341s Get:87 http://ftpmaster.internal/ubuntu noble/universe arm64 fastaq all 3.17.0-6 [47.9 kB]
341s Get:88 http://ftpmaster.internal/ubuntu noble/main arm64 python3-networkx all 2.8.8-1ubuntu1 [1468 kB]
341s Get:89 http://ftpmaster.internal/ubuntu noble/main arm64 python3-packaging all 23.2-1 [40.6 kB]
341s Get:90 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pysam arm64 0.22.0+ds-1 [4399 kB]
341s Get:91 http://ftpmaster.internal/ubuntu noble/universe arm64 kmc arm64 3.2.4+dfsg-1 [951 kB]
341s Get:92 http://ftpmaster.internal/ubuntu noble/universe arm64 mummer arm64 3.23+dfsg-8 [673 kB]
341s Get:93 http://ftpmaster.internal/ubuntu noble/universe arm64 libbambamc0 arm64 0.0.50-6 [37.2 kB]
341s Get:94 http://ftpmaster.internal/ubuntu noble/universe arm64 smalt arm64 0.7.6-13 [95.2 kB]
341s Get:95 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB]
341s Get:96 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB]
341s Get:97 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB]
342s Get:98 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB]
342s Get:99 http://ftpmaster.internal/ubuntu noble/universe arm64 iva arm64 1.0.11+ds-5 [8582 kB]
342s Get:100 http://ftpmaster.internal/ubuntu noble/universe arm64 libjbzip2-java all 0.9.1-8 [42.4 kB]
342s Get:101 http://ftpmaster.internal/ubuntu noble/universe arm64 trimmomatic all 0.39+dfsg-2 [758 kB]
343s Fetched 116 MB in 9s (13.4 MB/s)
343s Selecting previously unselected package libgdk-pixbuf2.0-common.
343s (Reading database ... 
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(Reading database ... 75469 files and directories currently installed.)
343s Preparing to unpack .../000-libgdk-pixbuf2.0-common_2.42.10+dfsg-3_all.deb ...
343s Unpacking libgdk-pixbuf2.0-common (2.42.10+dfsg-3) ...
343s Selecting previously unselected package libjpeg-turbo8:arm64.
343s Preparing to unpack .../001-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ...
343s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ...
343s Selecting previously unselected package libjpeg8:arm64.
343s Preparing to unpack .../002-libjpeg8_8c-2ubuntu11_arm64.deb ...
343s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ...
343s Selecting previously unselected package libdeflate0:arm64.
343s Preparing to unpack .../003-libdeflate0_1.19-1_arm64.deb ...
343s Unpacking libdeflate0:arm64 (1.19-1) ...
343s Selecting previously unselected package libjbig0:arm64.
343s Preparing to unpack .../004-libjbig0_2.1-6.1ubuntu1_arm64.deb ...
343s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ...
344s Selecting previously unselected package liblerc4:arm64.
344s Preparing to unpack .../005-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ...
344s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ...
344s Selecting previously unselected package libsharpyuv0:arm64.
344s Preparing to unpack .../006-libsharpyuv0_1.3.2-0.4_arm64.deb ...
344s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ...
344s Selecting previously unselected package libwebp7:arm64.
344s Preparing to unpack .../007-libwebp7_1.3.2-0.4_arm64.deb ...
344s Unpacking libwebp7:arm64 (1.3.2-0.4) ...
344s Selecting previously unselected package libtiff6:arm64.
344s Preparing to unpack .../008-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ...
344s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ...
344s Selecting previously unselected package libgdk-pixbuf-2.0-0:arm64.
344s Preparing to unpack .../009-libgdk-pixbuf-2.0-0_2.42.10+dfsg-3_arm64.deb ...
344s Unpacking libgdk-pixbuf-2.0-0:arm64 (2.42.10+dfsg-3) ...
344s Selecting previously unselected package gtk-update-icon-cache.
344s Preparing to unpack .../010-gtk-update-icon-cache_3.24.40-2ubuntu1_arm64.deb ...
344s Unpacking gtk-update-icon-cache (3.24.40-2ubuntu1) ...
344s Selecting previously unselected package hicolor-icon-theme.
344s Preparing to unpack .../011-hicolor-icon-theme_0.17-2_all.deb ...
344s Unpacking hicolor-icon-theme (0.17-2) ...
344s Selecting previously unselected package humanity-icon-theme.
344s Preparing to unpack .../012-humanity-icon-theme_0.6.16_all.deb ...
344s Unpacking humanity-icon-theme (0.6.16) ...
346s Selecting previously unselected package ubuntu-mono.
346s Preparing to unpack .../013-ubuntu-mono_24.04-0ubuntu1_all.deb ...
346s Unpacking ubuntu-mono (24.04-0ubuntu1) ...
347s Selecting previously unselected package adwaita-icon-theme.
347s Preparing to unpack .../014-adwaita-icon-theme_46~rc-1_all.deb ...
347s Unpacking adwaita-icon-theme (46~rc-1) ...
347s Selecting previously unselected package at-spi2-common.
347s Preparing to unpack .../015-at-spi2-common_2.50.0-1_all.deb ...
347s Unpacking at-spi2-common (2.50.0-1) ...
347s Selecting previously unselected package ca-certificates-java.
347s Preparing to unpack .../016-ca-certificates-java_20240118_all.deb ...
347s Unpacking ca-certificates-java (20240118) ...
347s Selecting previously unselected package java-common.
347s Preparing to unpack .../017-java-common_0.75+exp1_all.deb ...
347s Unpacking java-common (0.75+exp1) ...
347s Selecting previously unselected package libavahi-common-data:arm64.
347s Preparing to unpack .../018-libavahi-common-data_0.8-13ubuntu2_arm64.deb ...
347s Unpacking libavahi-common-data:arm64 (0.8-13ubuntu2) ...
347s Selecting previously unselected package libavahi-common3:arm64.
347s Preparing to unpack .../019-libavahi-common3_0.8-13ubuntu2_arm64.deb ...
347s Unpacking libavahi-common3:arm64 (0.8-13ubuntu2) ...
347s Selecting previously unselected package libavahi-client3:arm64.
347s Preparing to unpack .../020-libavahi-client3_0.8-13ubuntu2_arm64.deb ...
347s Unpacking libavahi-client3:arm64 (0.8-13ubuntu2) ...
347s Selecting previously unselected package libcups2:arm64.
347s Preparing to unpack .../021-libcups2_2.4.6-0ubuntu3_arm64.deb ...
347s Unpacking libcups2:arm64 (2.4.6-0ubuntu3) ...
347s Selecting previously unselected package liblcms2-2:arm64.
347s Preparing to unpack .../022-liblcms2-2_2.14-2_arm64.deb ...
347s Unpacking liblcms2-2:arm64 (2.14-2) ...
347s Selecting previously unselected package fonts-dejavu-mono.
347s Preparing to unpack .../023-fonts-dejavu-mono_2.37-8_all.deb ...
347s Unpacking fonts-dejavu-mono (2.37-8) ...
347s Selecting previously unselected package fonts-dejavu-core.
347s Preparing to unpack .../024-fonts-dejavu-core_2.37-8_all.deb ...
347s Unpacking fonts-dejavu-core (2.37-8) ...
348s Selecting previously unselected package fontconfig-config.
348s Preparing to unpack .../025-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ...
348s Unpacking fontconfig-config (2.15.0-1ubuntu1) ...
348s Selecting previously unselected package libfontconfig1:arm64.
348s Preparing to unpack .../026-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ...
348s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ...
348s Selecting previously unselected package libasound2-data.
348s Preparing to unpack .../027-libasound2-data_1.2.10-3build1_all.deb ...
348s Unpacking libasound2-data (1.2.10-3build1) ...
348s Selecting previously unselected package libasound2:arm64.
348s Preparing to unpack .../028-libasound2_1.2.10-3build1_arm64.deb ...
348s Unpacking libasound2:arm64 (1.2.10-3build1) ...
348s Selecting previously unselected package libgraphite2-3:arm64.
348s Preparing to unpack .../029-libgraphite2-3_1.3.14-2_arm64.deb ...
348s Unpacking libgraphite2-3:arm64 (1.3.14-2) ...
348s Selecting previously unselected package libharfbuzz0b:arm64.
348s Preparing to unpack .../030-libharfbuzz0b_8.3.0-2_arm64.deb ...
348s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ...
348s Selecting previously unselected package libpcsclite1:arm64.
348s Preparing to unpack .../031-libpcsclite1_2.0.0-1_arm64.deb ...
348s Unpacking libpcsclite1:arm64 (2.0.0-1) ...
348s Selecting previously unselected package openjdk-21-jre-headless:arm64.
348s Preparing to unpack .../032-openjdk-21-jre-headless_21.0.2+13-2_arm64.deb ...
348s Unpacking openjdk-21-jre-headless:arm64 (21.0.2+13-2) ...
351s Selecting previously unselected package default-jre-headless.
351s Preparing to unpack .../033-default-jre-headless_2%3a1.21-75+exp1_arm64.deb ...
351s Unpacking default-jre-headless (2:1.21-75+exp1) ...
351s Selecting previously unselected package libgtk2.0-common.
351s Preparing to unpack .../034-libgtk2.0-common_2.24.33-2ubuntu2_all.deb ...
351s Unpacking libgtk2.0-common (2.24.33-2ubuntu2) ...
351s Selecting previously unselected package libatk1.0-0:arm64.
351s Preparing to unpack .../035-libatk1.0-0_2.50.0-1_arm64.deb ...
351s Unpacking libatk1.0-0:arm64 (2.50.0-1) ...
351s Selecting previously unselected package libpixman-1-0:arm64.
351s Preparing to unpack .../036-libpixman-1-0_0.42.2-1_arm64.deb ...
351s Unpacking libpixman-1-0:arm64 (0.42.2-1) ...
351s Selecting previously unselected package libxcb-render0:arm64.
351s Preparing to unpack .../037-libxcb-render0_1.15-1_arm64.deb ...
351s Unpacking libxcb-render0:arm64 (1.15-1) ...
351s Selecting previously unselected package libxcb-shm0:arm64.
351s Preparing to unpack .../038-libxcb-shm0_1.15-1_arm64.deb ...
351s Unpacking libxcb-shm0:arm64 (1.15-1) ...
351s Selecting previously unselected package libxrender1:arm64.
351s Preparing to unpack .../039-libxrender1_1%3a0.9.10-1.1_arm64.deb ...
351s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ...
351s Selecting previously unselected package libcairo2:arm64.
351s Preparing to unpack .../040-libcairo2_1.18.0-1_arm64.deb ...
351s Unpacking libcairo2:arm64 (1.18.0-1) ...
351s Selecting previously unselected package fontconfig.
351s Preparing to unpack .../041-fontconfig_2.15.0-1ubuntu1_arm64.deb ...
351s Unpacking fontconfig (2.15.0-1ubuntu1) ...
351s Selecting previously unselected package libthai-data.
351s Preparing to unpack .../042-libthai-data_0.1.29-2_all.deb ...
351s Unpacking libthai-data (0.1.29-2) ...
351s Selecting previously unselected package libdatrie1:arm64.
351s Preparing to unpack .../043-libdatrie1_0.2.13-3_arm64.deb ...
351s Unpacking libdatrie1:arm64 (0.2.13-3) ...
351s Selecting previously unselected package libthai0:arm64.
351s Preparing to unpack .../044-libthai0_0.1.29-2_arm64.deb ...
351s Unpacking libthai0:arm64 (0.1.29-2) ...
351s Selecting previously unselected package libpango-1.0-0:arm64.
351s Preparing to unpack .../045-libpango-1.0-0_1.51.0+ds-4_arm64.deb ...
351s Unpacking libpango-1.0-0:arm64 (1.51.0+ds-4) ...
351s Selecting previously unselected package libpangoft2-1.0-0:arm64.
351s Preparing to unpack .../046-libpangoft2-1.0-0_1.51.0+ds-4_arm64.deb ...
351s Unpacking libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ...
352s Selecting previously unselected package libpangocairo-1.0-0:arm64.
352s Preparing to unpack .../047-libpangocairo-1.0-0_1.51.0+ds-4_arm64.deb ...
352s Unpacking libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ...
352s Selecting previously unselected package libxcomposite1:arm64.
352s Preparing to unpack .../048-libxcomposite1_1%3a0.4.5-1build2_arm64.deb ...
352s Unpacking libxcomposite1:arm64 (1:0.4.5-1build2) ...
352s Selecting previously unselected package libxfixes3:arm64.
352s Preparing to unpack .../049-libxfixes3_1%3a6.0.0-2_arm64.deb ...
352s Unpacking libxfixes3:arm64 (1:6.0.0-2) ...
352s Selecting previously unselected package libxcursor1:arm64.
352s Preparing to unpack .../050-libxcursor1_1%3a1.2.1-1_arm64.deb ...
352s Unpacking libxcursor1:arm64 (1:1.2.1-1) ...
352s Selecting previously unselected package libxdamage1:arm64.
352s Preparing to unpack .../051-libxdamage1_1%3a1.1.6-1_arm64.deb ...
352s Unpacking libxdamage1:arm64 (1:1.1.6-1) ...
352s Selecting previously unselected package libxi6:arm64.
352s Preparing to unpack .../052-libxi6_2%3a1.8.1-1_arm64.deb ...
352s Unpacking libxi6:arm64 (2:1.8.1-1) ...
352s Selecting previously unselected package libxinerama1:arm64.
352s Preparing to unpack .../053-libxinerama1_2%3a1.1.4-3_arm64.deb ...
352s Unpacking libxinerama1:arm64 (2:1.1.4-3) ...
352s Selecting previously unselected package libxrandr2:arm64.
352s Preparing to unpack .../054-libxrandr2_2%3a1.5.2-2_arm64.deb ...
352s Unpacking libxrandr2:arm64 (2:1.5.2-2) ...
352s Selecting previously unselected package libgtk2.0-0:arm64.
352s Preparing to unpack .../055-libgtk2.0-0_2.24.33-2ubuntu2_arm64.deb ...
352s Unpacking libgtk2.0-0:arm64 (2.24.33-2ubuntu2) ...
352s Selecting previously unselected package libglvnd0:arm64.
352s Preparing to unpack .../056-libglvnd0_1.7.0-1_arm64.deb ...
352s Unpacking libglvnd0:arm64 (1.7.0-1) ...
352s Selecting previously unselected package libglapi-mesa:arm64.
352s Preparing to unpack .../057-libglapi-mesa_24.0.1-1ubuntu1_arm64.deb ...
352s Unpacking libglapi-mesa:arm64 (24.0.1-1ubuntu1) ...
352s Selecting previously unselected package libx11-xcb1:arm64.
352s Preparing to unpack .../058-libx11-xcb1_2%3a1.8.7-1_arm64.deb ...
352s Unpacking libx11-xcb1:arm64 (2:1.8.7-1) ...
352s Selecting previously unselected package libxcb-dri2-0:arm64.
352s Preparing to unpack .../059-libxcb-dri2-0_1.15-1_arm64.deb ...
352s Unpacking libxcb-dri2-0:arm64 (1.15-1) ...
352s Selecting previously unselected package libxcb-dri3-0:arm64.
352s Preparing to unpack .../060-libxcb-dri3-0_1.15-1_arm64.deb ...
352s Unpacking libxcb-dri3-0:arm64 (1.15-1) ...
352s Selecting previously unselected package libxcb-glx0:arm64.
352s Preparing to unpack .../061-libxcb-glx0_1.15-1_arm64.deb ...
352s Unpacking libxcb-glx0:arm64 (1.15-1) ...
352s Selecting previously unselected package libxcb-present0:arm64.
352s Preparing to unpack .../062-libxcb-present0_1.15-1_arm64.deb ...
352s Unpacking libxcb-present0:arm64 (1.15-1) ...
352s Selecting previously unselected package libxcb-randr0:arm64.
352s Preparing to unpack .../063-libxcb-randr0_1.15-1_arm64.deb ...
352s Unpacking libxcb-randr0:arm64 (1.15-1) ...
353s Selecting previously unselected package libxcb-sync1:arm64.
353s Preparing to unpack .../064-libxcb-sync1_1.15-1_arm64.deb ...
353s Unpacking libxcb-sync1:arm64 (1.15-1) ...
353s Selecting previously unselected package libxcb-xfixes0:arm64.
353s Preparing to unpack .../065-libxcb-xfixes0_1.15-1_arm64.deb ...
353s Unpacking libxcb-xfixes0:arm64 (1.15-1) ...
353s Selecting previously unselected package libxshmfence1:arm64.
353s Preparing to unpack .../066-libxshmfence1_1.3-1build4_arm64.deb ...
353s Unpacking libxshmfence1:arm64 (1.3-1build4) ...
353s Selecting previously unselected package libxxf86vm1:arm64.
353s Preparing to unpack .../067-libxxf86vm1_1%3a1.1.4-1build3_arm64.deb ...
353s Unpacking libxxf86vm1:arm64 (1:1.1.4-1build3) ...
353s Selecting previously unselected package libvulkan1:arm64.
353s Preparing to unpack .../068-libvulkan1_1.3.275.0-1_arm64.deb ...
353s Unpacking libvulkan1:arm64 (1.3.275.0-1) ...
353s Selecting previously unselected package libdrm-amdgpu1:arm64.
353s Preparing to unpack .../069-libdrm-amdgpu1_2.4.120-2_arm64.deb ...
353s Unpacking libdrm-amdgpu1:arm64 (2.4.120-2) ...
353s Selecting previously unselected package libdrm-nouveau2:arm64.
353s Preparing to unpack .../070-libdrm-nouveau2_2.4.120-2_arm64.deb ...
353s Unpacking libdrm-nouveau2:arm64 (2.4.120-2) ...
353s Selecting previously unselected package libdrm-radeon1:arm64.
353s Preparing to unpack .../071-libdrm-radeon1_2.4.120-2_arm64.deb ...
353s Unpacking libdrm-radeon1:arm64 (2.4.120-2) ...
353s Selecting previously unselected package libllvm17:arm64.
353s Preparing to unpack .../072-libllvm17_1%3a17.0.6-5build1_arm64.deb ...
353s Unpacking libllvm17:arm64 (1:17.0.6-5build1) ...
354s Selecting previously unselected package libgl1-mesa-dri:arm64.
354s Preparing to unpack .../073-libgl1-mesa-dri_24.0.1-1ubuntu1_arm64.deb ...
354s Unpacking libgl1-mesa-dri:arm64 (24.0.1-1ubuntu1) ...
355s Selecting previously unselected package libglx-mesa0:arm64.
355s Preparing to unpack .../074-libglx-mesa0_24.0.1-1ubuntu1_arm64.deb ...
355s Unpacking libglx-mesa0:arm64 (24.0.1-1ubuntu1) ...
355s Selecting previously unselected package libglx0:arm64.
355s Preparing to unpack .../075-libglx0_1.7.0-1_arm64.deb ...
355s Unpacking libglx0:arm64 (1.7.0-1) ...
355s Selecting previously unselected package libgl1:arm64.
355s Preparing to unpack .../076-libgl1_1.7.0-1_arm64.deb ...
355s Unpacking libgl1:arm64 (1.7.0-1) ...
355s Selecting previously unselected package libgif7:arm64.
355s Preparing to unpack .../077-libgif7_5.2.1-2.5_arm64.deb ...
355s Unpacking libgif7:arm64 (5.2.1-2.5) ...
355s Selecting previously unselected package x11-common.
355s Preparing to unpack .../078-x11-common_1%3a7.7+23ubuntu2_all.deb ...
355s Unpacking x11-common (1:7.7+23ubuntu2) ...
355s Selecting previously unselected package libxtst6:arm64.
355s Preparing to unpack .../079-libxtst6_2%3a1.2.3-1.1_arm64.deb ...
355s Unpacking libxtst6:arm64 (2:1.2.3-1.1) ...
355s Selecting previously unselected package openjdk-21-jre:arm64.
355s Preparing to unpack .../080-openjdk-21-jre_21.0.2+13-2_arm64.deb ...
355s Unpacking openjdk-21-jre:arm64 (21.0.2+13-2) ...
355s Selecting previously unselected package default-jre.
355s Preparing to unpack .../081-default-jre_2%3a1.21-75+exp1_arm64.deb ...
355s Unpacking default-jre (2:1.21-75+exp1) ...
355s Selecting previously unselected package libhtscodecs2:arm64.
355s Preparing to unpack .../082-libhtscodecs2_1.6.0-1_arm64.deb ...
355s Unpacking libhtscodecs2:arm64 (1.6.0-1) ...
355s Selecting previously unselected package libhts3:arm64.
355s Preparing to unpack .../083-libhts3_1.18+ds-1_arm64.deb ...
355s Unpacking libhts3:arm64 (1.18+ds-1) ...
355s Selecting previously unselected package samtools.
355s Preparing to unpack .../084-samtools_1.19.2-1_arm64.deb ...
355s Unpacking samtools (1.19.2-1) ...
355s Selecting previously unselected package fastaq.
356s Preparing to unpack .../085-fastaq_3.17.0-6_all.deb ...
356s Unpacking fastaq (3.17.0-6) ...
356s Selecting previously unselected package python3-networkx.
356s Preparing to unpack .../086-python3-networkx_2.8.8-1ubuntu1_all.deb ...
356s Unpacking python3-networkx (2.8.8-1ubuntu1) ...
356s Selecting previously unselected package python3-packaging.
356s Preparing to unpack .../087-python3-packaging_23.2-1_all.deb ...
356s Unpacking python3-packaging (23.2-1) ...
356s Selecting previously unselected package python3-pysam.
356s Preparing to unpack .../088-python3-pysam_0.22.0+ds-1_arm64.deb ...
356s Unpacking python3-pysam (0.22.0+ds-1) ...
357s Selecting previously unselected package kmc.
357s Preparing to unpack .../089-kmc_3.2.4+dfsg-1_arm64.deb ...
357s Unpacking kmc (3.2.4+dfsg-1) ...
357s Selecting previously unselected package mummer.
357s Preparing to unpack .../090-mummer_3.23+dfsg-8_arm64.deb ...
357s Unpacking mummer (3.23+dfsg-8) ...
357s Selecting previously unselected package libbambamc0:arm64.
357s Preparing to unpack .../091-libbambamc0_0.0.50-6_arm64.deb ...
357s Unpacking libbambamc0:arm64 (0.0.50-6) ...
357s Selecting previously unselected package smalt.
357s Preparing to unpack .../092-smalt_0.7.6-13_arm64.deb ...
357s Unpacking smalt (0.7.6-13) ...
357s Selecting previously unselected package libblas3:arm64.
357s Preparing to unpack .../093-libblas3_3.12.0-3_arm64.deb ...
357s Unpacking libblas3:arm64 (3.12.0-3) ...
357s Selecting previously unselected package libgfortran5:arm64.
357s Preparing to unpack .../094-libgfortran5_14-20240303-1ubuntu1_arm64.deb ...
357s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ...
357s Selecting previously unselected package liblapack3:arm64.
357s Preparing to unpack .../095-liblapack3_3.12.0-3_arm64.deb ...
357s Unpacking liblapack3:arm64 (3.12.0-3) ...
357s Selecting previously unselected package python3-numpy.
357s Preparing to unpack .../096-python3-numpy_1%3a1.24.2-2_arm64.deb ...
357s Unpacking python3-numpy (1:1.24.2-2) ...
358s Selecting previously unselected package iva.
358s Preparing to unpack .../097-iva_1.0.11+ds-5_arm64.deb ...
358s Unpacking iva (1.0.11+ds-5) ...
358s Selecting previously unselected package libjbzip2-java.
358s Preparing to unpack .../098-libjbzip2-java_0.9.1-8_all.deb ...
358s Unpacking libjbzip2-java (0.9.1-8) ...
358s Selecting previously unselected package trimmomatic.
358s Preparing to unpack .../099-trimmomatic_0.39+dfsg-2_all.deb ...
358s Unpacking trimmomatic (0.39+dfsg-2) ...
358s Selecting previously unselected package autopkgtest-satdep.
358s Preparing to unpack .../100-1-autopkgtest-satdep.deb ...
358s Unpacking autopkgtest-satdep (0) ...
358s Setting up libhtscodecs2:arm64 (1.6.0-1) ...
358s Setting up libgraphite2-3:arm64 (1.3.14-2) ...
358s Setting up libxcb-dri3-0:arm64 (1.15-1) ...
358s Setting up liblcms2-2:arm64 (2.14-2) ...
358s Setting up libpixman-1-0:arm64 (0.42.2-1) ...
358s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ...
358s Setting up libx11-xcb1:arm64 (2:1.8.7-1) ...
358s Setting up libdrm-nouveau2:arm64 (2.4.120-2) ...
358s Setting up libxdamage1:arm64 (1:1.1.6-1) ...
358s Setting up libxcb-xfixes0:arm64 (1.15-1) ...
358s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ...
358s Setting up hicolor-icon-theme (0.17-2) ...
358s Setting up libxi6:arm64 (2:1.8.1-1) ...
358s Setting up java-common (0.75+exp1) ...
358s Setting up libxrender1:arm64 (1:0.9.10-1.1) ...
358s Setting up libdatrie1:arm64 (0.2.13-3) ...
358s Setting up libxcb-render0:arm64 (1.15-1) ...
358s Setting up libdrm-radeon1:arm64 (2.4.120-2) ...
358s Setting up libglvnd0:arm64 (1.7.0-1) ...
358s Setting up libxcb-glx0:arm64 (1.15-1) ...
358s Setting up libgdk-pixbuf2.0-common (2.42.10+dfsg-3) ...
358s Setting up x11-common (1:7.7+23ubuntu2) ...
359s Setting up libdeflate0:arm64 (1.19-1) ...
359s Setting up libxcb-shm0:arm64 (1.15-1) ...
359s Setting up python3-networkx (2.8.8-1ubuntu1) ...
362s /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:556: SyntaxWarning: invalid octal escape sequence '\420'
362s   "graph [edge [ source u'u\4200' target u'u\4200' ] "
362s /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:557: SyntaxWarning: invalid octal escape sequence '\420'
362s   + "node [ id u'u\4200' label b ] ]"
362s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ...
362s Setting up libxxf86vm1:arm64 (1:1.1.4-1build3) ...
362s Setting up libxcb-present0:arm64 (1.15-1) ...
362s Setting up libasound2-data (1.2.10-3build1) ...
362s Setting up libblas3:arm64 (3.12.0-3) ...
362s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode
362s Setting up python3-packaging (23.2-1) ...
362s Setting up libxfixes3:arm64 (1:6.0.0-2) ...
362s Setting up libxcb-sync1:arm64 (1.15-1) ...
362s Setting up libavahi-common-data:arm64 (0.8-13ubuntu2) ...
362s Setting up libxinerama1:arm64 (2:1.1.4-3) ...
362s Setting up libbambamc0:arm64 (0.0.50-6) ...
362s Setting up fonts-dejavu-mono (2.37-8) ...
362s Setting up libxrandr2:arm64 (2:1.5.2-2) ...
362s Setting up fonts-dejavu-core (2.37-8) ...
362s Setting up libjbzip2-java (0.9.1-8) ...
362s Setting up libpcsclite1:arm64 (2.0.0-1) ...
362s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ...
362s Setting up libglapi-mesa:arm64 (24.0.1-1ubuntu1) ...
362s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ...
362s Setting up libvulkan1:arm64 (1.3.275.0-1) ...
362s Setting up libwebp7:arm64 (1.3.2-0.4) ...
362s Setting up libxcb-dri2-0:arm64 (1.15-1) ...
362s Setting up libgif7:arm64 (5.2.1-2.5) ...
362s Setting up libxshmfence1:arm64 (1.3-1build4) ...
362s Setting up at-spi2-common (2.50.0-1) ...
362s Setting up libxcb-randr0:arm64 (1.15-1) ...
362s Setting up libasound2:arm64 (1.2.10-3build1) ...
362s Setting up mummer (3.23+dfsg-8) ...
362s Setting up libharfbuzz0b:arm64 (8.3.0-2) ...
362s Setting up libthai-data (0.1.29-2) ...
362s Setting up libgtk2.0-common (2.24.33-2ubuntu2) ...
362s Setting up libatk1.0-0:arm64 (2.50.0-1) ...
362s Setting up ca-certificates-java (20240118) ...
362s No JRE found. Skipping Java certificates setup.
362s Setting up libllvm17:arm64 (1:17.0.6-5build1) ...
362s Setting up kmc (3.2.4+dfsg-1) ...
362s Setting up libxcomposite1:arm64 (1:0.4.5-1build2) ...
362s Setting up libdrm-amdgpu1:arm64 (2.4.120-2) ...
363s Setting up libjpeg8:arm64 (8c-2ubuntu11) ...
363s Setting up smalt (0.7.6-13) ...
363s Setting up liblapack3:arm64 (3.12.0-3) ...
363s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode
363s Setting up libhts3:arm64 (1.18+ds-1) ...
363s Setting up python3-pysam (0.22.0+ds-1) ...
363s Setting up fontconfig-config (2.15.0-1ubuntu1) ...
363s Setting up libxtst6:arm64 (2:1.2.3-1.1) ...
363s Setting up libxcursor1:arm64 (1:1.2.1-1) ...
363s Setting up libgl1-mesa-dri:arm64 (24.0.1-1ubuntu1) ...
363s Setting up libavahi-common3:arm64 (0.8-13ubuntu2) ...
363s Setting up samtools (1.19.2-1) ...
363s Setting up libthai0:arm64 (0.1.29-2) ...
363s Setting up python3-numpy (1:1.24.2-2) ...
367s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ...
367s Setting up libgdk-pixbuf-2.0-0:arm64 (2.42.10+dfsg-3) ...
368s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ...
368s Setting up libavahi-client3:arm64 (0.8-13ubuntu2) ...
368s Setting up gtk-update-icon-cache (3.24.40-2ubuntu1) ...
368s Setting up fontconfig (2.15.0-1ubuntu1) ...
370s Regenerating fonts cache... done.
370s Setting up libglx-mesa0:arm64 (24.0.1-1ubuntu1) ...
370s Setting up libglx0:arm64 (1.7.0-1) ...
370s Setting up fastaq (3.17.0-6) ...
370s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:37: SyntaxWarning: invalid escape sequence '\s'
370s   phylip_regex = re.compile('^\s*[0-9]+\s+[0-9]+$')
370s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:38: SyntaxWarning: invalid escape sequence '\s'
370s   gbk_regex = re.compile('^LOCUS\s+\S')
370s Setting up libpango-1.0-0:arm64 (1.51.0+ds-4) ...
370s Setting up libcairo2:arm64 (1.18.0-1) ...
370s Setting up libgl1:arm64 (1.7.0-1) ...
370s Setting up libcups2:arm64 (2.4.6-0ubuntu3) ...
370s Setting up libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ...
370s Setting up libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ...
370s Setting up openjdk-21-jre-headless:arm64 (21.0.2+13-2) ...
370s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode
370s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode
370s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
370s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
370s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
370s Setting up adwaita-icon-theme (46~rc-1) ...
370s update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode
370s Setting up libgtk2.0-0:arm64 (2.24.33-2ubuntu2) ...
370s Setting up humanity-icon-theme (0.6.16) ...
370s Setting up ubuntu-mono (24.04-0ubuntu1) ...
370s Processing triggers for man-db (2.12.0-3) ...
372s Processing triggers for libc-bin (2.39-0ubuntu6) ...
372s Processing triggers for ca-certificates-java (20240118) ...
373s Adding debian:ACCVRAIZ1.pem
373s Adding debian:AC_RAIZ_FNMT-RCM.pem
373s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem
373s Adding debian:ANF_Secure_Server_Root_CA.pem
373s Adding debian:Actalis_Authentication_Root_CA.pem
373s Adding debian:AffirmTrust_Commercial.pem
373s Adding debian:AffirmTrust_Networking.pem
373s Adding debian:AffirmTrust_Premium.pem
373s Adding debian:AffirmTrust_Premium_ECC.pem
373s Adding debian:Amazon_Root_CA_1.pem
373s Adding debian:Amazon_Root_CA_2.pem
373s Adding debian:Amazon_Root_CA_3.pem
373s Adding debian:Amazon_Root_CA_4.pem
373s Adding debian:Atos_TrustedRoot_2011.pem
373s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem
373s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem
373s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
373s Adding debian:BJCA_Global_Root_CA1.pem
373s Adding debian:BJCA_Global_Root_CA2.pem
373s Adding debian:Baltimore_CyberTrust_Root.pem
373s Adding debian:Buypass_Class_2_Root_CA.pem
373s Adding debian:Buypass_Class_3_Root_CA.pem
373s Adding debian:CA_Disig_Root_R2.pem
373s Adding debian:CFCA_EV_ROOT.pem
373s Adding debian:COMODO_Certification_Authority.pem
373s Adding debian:COMODO_ECC_Certification_Authority.pem
373s Adding debian:COMODO_RSA_Certification_Authority.pem
373s Adding debian:Certainly_Root_E1.pem
373s Adding debian:Certainly_Root_R1.pem
373s Adding debian:Certigna.pem
373s Adding debian:Certigna_Root_CA.pem
373s Adding debian:Certum_EC-384_CA.pem
373s Adding debian:Certum_Trusted_Network_CA.pem
373s Adding debian:Certum_Trusted_Network_CA_2.pem
373s Adding debian:Certum_Trusted_Root_CA.pem
373s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem
373s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem
373s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem
373s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem
373s Adding debian:Comodo_AAA_Services_root.pem
373s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem
373s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem
373s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
373s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
373s Adding debian:DigiCert_Assured_ID_Root_CA.pem
373s Adding debian:DigiCert_Assured_ID_Root_G2.pem
373s Adding debian:DigiCert_Assured_ID_Root_G3.pem
373s Adding debian:DigiCert_Global_Root_CA.pem
373s Adding debian:DigiCert_Global_Root_G2.pem
373s Adding debian:DigiCert_Global_Root_G3.pem
373s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
373s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem
373s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem
373s Adding debian:DigiCert_Trusted_Root_G4.pem
373s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
373s Adding debian:Entrust_Root_Certification_Authority.pem
373s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
373s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
373s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem
373s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem
373s Adding debian:GLOBALTRUST_2020.pem
373s Adding debian:GTS_Root_R1.pem
373s Adding debian:GTS_Root_R2.pem
373s Adding debian:GTS_Root_R3.pem
373s Adding debian:GTS_Root_R4.pem
373s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
373s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
373s Adding debian:GlobalSign_Root_CA.pem
373s Adding debian:GlobalSign_Root_CA_-_R3.pem
373s Adding debian:GlobalSign_Root_CA_-_R6.pem
373s Adding debian:GlobalSign_Root_E46.pem
373s Adding debian:GlobalSign_Root_R46.pem
373s Adding debian:Go_Daddy_Class_2_CA.pem
373s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
373s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem
373s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem
373s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem
373s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem
373s Adding debian:HiPKI_Root_CA_-_G1.pem
373s Adding debian:Hongkong_Post_Root_CA_3.pem
373s Adding debian:ISRG_Root_X1.pem
373s Adding debian:ISRG_Root_X2.pem
373s Adding debian:IdenTrust_Commercial_Root_CA_1.pem
373s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
373s Adding debian:Izenpe.com.pem
373s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
373s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem
373s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem
373s Adding debian:NAVER_Global_Root_Certification_Authority.pem
373s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
373s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
373s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem
373s Adding debian:QuoVadis_Root_CA_1_G3.pem
373s Adding debian:QuoVadis_Root_CA_2.pem
373s Adding debian:QuoVadis_Root_CA_2_G3.pem
373s Adding debian:QuoVadis_Root_CA_3.pem
373s Adding debian:QuoVadis_Root_CA_3_G3.pem
373s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem
373s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem
373s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem
373s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem
373s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem
373s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem
373s Adding debian:SZAFIR_ROOT_CA2.pem
373s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem
373s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem
373s Adding debian:SecureSign_RootCA11.pem
373s Adding debian:SecureTrust_CA.pem
373s Adding debian:Secure_Global_CA.pem
373s Adding debian:Security_Communication_ECC_RootCA1.pem
373s Adding debian:Security_Communication_RootCA2.pem
373s Adding debian:Security_Communication_RootCA3.pem
373s Adding debian:Security_Communication_Root_CA.pem
373s Adding debian:Starfield_Class_2_CA.pem
373s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
373s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
373s Adding debian:SwissSign_Gold_CA_-_G2.pem
373s Adding debian:SwissSign_Silver_CA_-_G2.pem
373s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
373s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
373s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
373s Adding debian:TWCA_Global_Root_CA.pem
374s Adding debian:TWCA_Root_Certification_Authority.pem
374s Adding debian:TeliaSonera_Root_CA_v1.pem
374s Adding debian:Telia_Root_CA_v2.pem
374s Adding debian:TrustAsia_Global_Root_CA_G3.pem
374s Adding debian:TrustAsia_Global_Root_CA_G4.pem
374s Adding debian:Trustwave_Global_Certification_Authority.pem
374s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem
374s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem
374s Adding debian:TunTrust_Root_CA.pem
374s Adding debian:UCA_Extended_Validation_Root.pem
374s Adding debian:UCA_Global_G2_Root.pem
374s Adding debian:USERTrust_ECC_Certification_Authority.pem
374s Adding debian:USERTrust_RSA_Certification_Authority.pem
374s Adding debian:XRamp_Global_CA_Root.pem
374s Adding debian:certSIGN_ROOT_CA.pem
374s Adding debian:certSIGN_Root_CA_G2.pem
374s Adding debian:e-Szigno_Root_CA_2017.pem
374s Adding debian:ePKI_Root_Certification_Authority.pem
374s Adding debian:emSign_ECC_Root_CA_-_C3.pem
374s Adding debian:emSign_ECC_Root_CA_-_G3.pem
374s Adding debian:emSign_Root_CA_-_C1.pem
374s Adding debian:emSign_Root_CA_-_G1.pem
374s Adding debian:vTrus_ECC_Root_CA.pem
374s Adding debian:vTrus_Root_CA.pem
374s done.
374s Setting up openjdk-21-jre:arm64 (21.0.2+13-2) ...
374s Setting up default-jre-headless (2:1.21-75+exp1) ...
374s Setting up iva (1.0.11+ds-5) ...
374s /usr/lib/python3/dist-packages/iva/external_progs.py:33: SyntaxWarning: invalid escape sequence '\('
374s   'kmc': ('kmc', re.compile('^K-Mer Counter \(KMC\) ver\. (.*) \(.*\)$')),
374s /usr/lib/python3/dist-packages/iva/external_progs.py:34: SyntaxWarning: invalid escape sequence '\('
374s   'kmc_dump': ('kmc_dump', re.compile('^KMC dump ver. (.*) \(.*\)$')),
374s /usr/lib/python3/dist-packages/iva/external_progs.py:37: SyntaxWarning: invalid escape sequence '\('
374s   'nucmer': ('nucmer --version', re.compile('^NUCmer \(NUCleotide MUMmer\) version (.*)$')),
374s /usr/lib/python3/dist-packages/iva/external_progs.py:38: SyntaxWarning: invalid escape sequence '\('
374s   'R': ('R --version', re.compile('^R version (.*) \(.*\) --')),
374s /usr/lib/python3/dist-packages/iva/external_progs.py:40: SyntaxWarning: invalid escape sequence '\d'
374s   'samtools': ('samtools', re.compile('(\d+\.\d+[\.\d]*)')),
374s /usr/lib/python3/dist-packages/iva/kraken.py:360: SyntaxWarning: invalid escape sequence '\.'
374s   self._genbank2embl(fname, re.sub('\.gbk$', '', fname) + '.embl')
374s /usr/lib/python3/dist-packages/iva/kraken.py:415: SyntaxWarning: invalid escape sequence '\W'
374s   return re.sub('\W', '_', s).strip('_')
374s /usr/lib/python3/dist-packages/iva/mapping.py:161: SyntaxWarning: invalid escape sequence '\^'
374s   s = re.sub('\^.', '', s)
374s Setting up default-jre (2:1.21-75+exp1) ...
374s Setting up trimmomatic (0.39+dfsg-2) ...
374s Setting up autopkgtest-satdep (0) ...
383s (Reading database ... 91862 files and directories currently installed.)
383s Removing autopkgtest-satdep (0) ...
385s autopkgtest [18:02:43]: test test-example: [-----------------------
446s Running iva in test mode...
446s Copied input test files into here: /tmp/tmp.8eAygXpGf6/test
446s Current working directory: /tmp/tmp.8eAygXpGf6/test
446s Running iva on the test data with the command:
446s /usr/bin/iva --threads 1 --trimmomatic /usr/share/java/trimmomatic.jar --pcr_primers hiv_pcr_primers.fa -f reads_1.fq.gz -r reads_2.fq.gz iva.out
446s The following command failed with exit code 1
446s /usr/bin/iva --threads 1 --trimmomatic /usr/share/java/trimmomatic.jar --pcr_primers hiv_pcr_primers.fa -f reads_1.fq.gz -r reads_2.fq.gz iva.out
446s 
446s The output was:
446s 
446s The following command failed with exit code 1
446s bash run_kmc.sh
446s 
446s The output was:
446s 
446s Error: std::bad_alloc
446s 
446s 
446s autopkgtest [18:03:44]: test test-example: -----------------------]
447s test-example         FAIL non-zero exit status 1
447s autopkgtest [18:03:45]: test test-example:  - - - - - - - - - - results - - - - - - - - - -
447s autopkgtest [18:03:45]: test test-example:  - - - - - - - - - - stderr - - - - - - - - - -
447s The following command failed with exit code 1
447s /usr/bin/iva --threads 1 --trimmomatic /usr/share/java/trimmomatic.jar --pcr_primers hiv_pcr_primers.fa -f reads_1.fq.gz -r reads_2.fq.gz iva.out
447s 
447s The output was:
447s 
447s The following command failed with exit code 1
447s bash run_kmc.sh
447s 
447s The output was:
447s 
447s Error: std::bad_alloc
447s 
447s 
447s autopkgtest [18:03:45]: @@@@@@@@@@@@@@@@@@@@ summary
447s test-example         FAIL non-zero exit status 1
462s Creating nova instance adt-noble-arm64-iva-20240324-172719-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240324.img (UUID 2df78aec-1bf7-4c70-8bf1-31fba04b7d21)...