0s autopkgtest [09:27:17]: starting date and time: 2025-04-14 09:27:17+0000 0s autopkgtest [09:27:17]: git checkout: 9986aa8c Merge branch 'skia/fix_network_interface' into 'ubuntu/production' 0s autopkgtest [09:27:17]: host juju-7f2275-prod-proposed-migration-environment-21; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.1vhsypds/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:spades --apt-upgrade unicycler --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=spades/4.0.0+dfsg1-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-21@bos03-5.secgroup --name adt-plucky-amd64-unicycler-20250414-092717-juju-7f2275-prod-proposed-migration-environment-21-566ef017-b2d1-47d1-965f-8c063d6d0ac6 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-21 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 50s autopkgtest [09:28:07]: testbed dpkg architecture: amd64 50s autopkgtest [09:28:07]: testbed apt version: 3.0.0 51s autopkgtest [09:28:08]: @@@@@@@@@@@@@@@@@@@@ test bed setup 51s autopkgtest [09:28:08]: testbed release detected to be: None 51s autopkgtest [09:28:08]: updating testbed package index (apt update) 52s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [265 kB] 52s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 52s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 52s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 52s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [9948 B] 52s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [204 kB] 52s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [5192 B] 52s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [3776 B] 52s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [2508 B] 52s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 c-n-f Metadata [288 B] 52s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 c-n-f Metadata [232 B] 52s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [61.6 kB] 52s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [130 kB] 52s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 c-n-f Metadata [9496 B] 52s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [2300 B] 52s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [6168 B] 52s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 c-n-f Metadata [440 B] 53s Fetched 701 kB in 1s (822 kB/s) 54s Reading package lists... 54s autopkgtest [09:28:11]: upgrading testbed (apt dist-upgrade and autopurge) 54s Reading package lists... 55s Building dependency tree... 55s Reading state information... 55s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 55s Starting 2 pkgProblemResolver with broken count: 0 55s Done 55s Entering ResolveByKeep 55s 56s Calculating upgrade... 56s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 56s Reading package lists... 56s Building dependency tree... 56s Reading state information... 56s Starting pkgProblemResolver with broken count: 0 56s Starting 2 pkgProblemResolver with broken count: 0 56s Done 57s Solving dependencies... 57s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 59s autopkgtest [09:28:16]: testbed running kernel: Linux 6.14.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Sun Apr 6 15:05:05 UTC 2025 59s autopkgtest [09:28:16]: @@@@@@@@@@@@@@@@@@@@ apt-source unicycler 68s Get:1 http://ftpmaster.internal/ubuntu plucky/universe unicycler 0.5.1+dfsg-3 (dsc) [2389 B] 68s Get:2 http://ftpmaster.internal/ubuntu plucky/universe unicycler 0.5.1+dfsg-3 (tar) [14.8 MB] 68s Get:3 http://ftpmaster.internal/ubuntu plucky/universe unicycler 0.5.1+dfsg-3 (diff) [12.9 kB] 69s gpgv: Signature made Wed Feb 5 20:29:48 2025 UTC 69s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 69s gpgv: issuer "tchet@debian.org" 69s gpgv: Can't check signature: No public key 69s dpkg-source: warning: cannot verify inline signature for ./unicycler_0.5.1+dfsg-3.dsc: no acceptable signature found 69s autopkgtest [09:28:26]: testing package unicycler version 0.5.1+dfsg-3 69s autopkgtest [09:28:26]: build not needed 72s autopkgtest [09:28:29]: test run-unit-test: preparing testbed 72s Reading package lists... 73s Building dependency tree... 73s Reading state information... 73s Starting pkgProblemResolver with broken count: 0 73s Starting 2 pkgProblemResolver with broken count: 0 73s Done 73s The following NEW packages will be installed: 73s adwaita-icon-theme at-spi2-common autoconf automake autopoint autotools-dev 73s bamtools bcftools bowtie2 build-essential bwa ca-certificates-java cpp 73s cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu dconf-gsettings-backend 73s dconf-service debhelper debugedit default-jdk default-jdk-headless 73s default-jre default-jre-headless dh-autoreconf dh-python 73s dh-strip-nondeterminism dwz fontconfig fontconfig-config fonts-dejavu-core 73s fonts-dejavu-mono g++ g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu 73s gcc gcc-14 gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gettext 73s gtk-update-icon-cache hicolor-icon-theme intltool-debian java-common 73s java-wrappers junit4 libapache-pom-java libarchive-zip-perl libasan8 73s libasound2-data libasound2t64 libatk-bridge2.0-0t64 libatk1.0-0t64 73s libatspi2.0-0t64 libavahi-client3 libavahi-common-data libavahi-common3 73s libbamtools2.5.2 libcairo-gobject2 libcairo2 libcc1-0 libcolord2 73s libcommons-beanutils-java libcommons-codec-java libcommons-collections3-java 73s libcommons-collections4-java libcommons-compress-java libcommons-io-java 73s libcommons-jexl2-java libcommons-lang-java libcommons-lang3-java 73s libcommons-logging-java libcommons-parent-java libcups2t64 libdatrie1 73s libdconf1 libdebhelper-perl libdeflate0 libdrm-intel1 libedlib1 libepoxy0 73s libezmorph-java libfile-stripnondeterminism-perl libfontconfig1 libgbm1 73s libgcc-14-dev libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgif7 libgl1 73s libgl1-mesa-dri libglvnd0 libglx-mesa0 libglx0 libgomp1 libgraphite2-3 73s libgtk-3-0t64 libgtk-3-common libhamcrest-java libharfbuzz0b libhts3t64 73s libhtscodecs2 libhtsjdk-java libhwasan0 libisl23 libitm1 libjaxen-java 73s libjbig0 libjpeg-turbo8 libjpeg8 libjson-java libjsoncpp26 liblcms2-2 73s liblerc4 liblsan0 libmbedcrypto16 libmbedtls21 libmbedx509-7 libmpc3 73s libncbi-ngs3 libncbi-vdb3 libngs-java libngs-jni libnlopt0 libpango-1.0-0 73s libpangocairo-1.0-0 libpangoft2-1.0-0 libpciaccess0 libpcsclite1 73s libpixman-1-0 libquadmath0 librhino-java libseqan2-dev libsharpyuv0 73s libslf4j-java libsnappy-java libsnappy-jni libsnappy1v5 libspoa7.0.0 libssw0 73s libstdc++-14-dev libthai-data libthai0 libtiff6 libtool libtsan2 libubsan1 73s libvulkan1 libwayland-client0 libwayland-cursor0 libwayland-egl1 73s libwayland-server0 libwebp7 libx11-xcb1 libxcb-dri3-0 libxcb-glx0 73s libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 73s libxcb-xfixes0 libxcomposite1 libxcursor1 libxdamage1 libxerces2-java 73s libxfixes3 libxi6 libxinerama1 libxml-commons-external-java 73s libxml-commons-resolver1.1-java libxom-java libxrandr2 libxrender1 73s libxshmfence1 libxtst6 libxxf86vm1 m4 mesa-libgallium miniasm ncbi-blast+ 73s ncbi-data ncbi-vdb-data openjdk-21-jdk openjdk-21-jdk-headless 73s openjdk-21-jre openjdk-21-jre-headless pilon po-debconf python3-all 73s python3-joblib python3-packaging racon samtools scala-library spades 73s unicycler unicycler-data unzip x11-common zlib1g-dev 74s 0 upgraded, 202 newly installed, 0 to remove and 0 not upgraded. 74s Need to get 302 MB of archives. 74s After this operation, 859 MB of additional disk space will be used. 74s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-2 [8004 B] 74s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 74s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 74s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB] 74s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 74s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 74s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 74s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 74s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 74s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-2 [161 kB] 74s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 gtk-update-icon-cache amd64 4.18.4+ds-1 [54.1 kB] 74s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 hicolor-icon-theme all 0.18-2 [13.3 kB] 74s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 adwaita-icon-theme all 48.0-1 [578 kB] 75s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 at-spi2-common all 2.56.1-1 [9142 B] 75s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 m4 amd64 1.4.19-7 [263 kB] 75s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 autoconf all 2.72-3ubuntu1 [383 kB] 75s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 autotools-dev all 20220109.1 [44.9 kB] 75s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 automake all 1:1.17-3ubuntu1 [572 kB] 75s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 autopoint all 0.23.1-1 [619 kB] 75s Get:20 http://ftpmaster.internal/ubuntu plucky/universe amd64 libbamtools2.5.2 amd64 2.5.2+dfsg-6build1 [144 kB] 75s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libjsoncpp26 amd64 1.9.6-3 [90.0 kB] 75s Get:22 http://ftpmaster.internal/ubuntu plucky/universe amd64 bamtools amd64 2.5.2+dfsg-6build1 [178 kB] 75s Get:23 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-2 [132 kB] 75s Get:24 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.21+ds-1 [514 kB] 75s Get:25 http://ftpmaster.internal/ubuntu plucky/universe amd64 bcftools amd64 1.21-1 [962 kB] 76s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB] 76s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 76s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-19ubuntu2 [11.9 MB] 77s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-19ubuntu2 [1030 B] 77s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [5586 B] 77s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.2.0-1ubuntu1 [22.4 kB] 77s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 15-20250404-0ubuntu1 [47.1 kB] 77s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250404-0ubuntu1 [151 kB] 77s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 15-20250404-0ubuntu1 [29.5 kB] 77s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 15-20250404-0ubuntu1 [3076 kB] 77s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 15-20250404-0ubuntu1 [1362 kB] 77s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 15-20250404-0ubuntu1 [2760 kB] 77s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 15-20250404-0ubuntu1 [1211 kB] 77s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 15-20250404-0ubuntu1 [1687 kB] 78s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 15-20250404-0ubuntu1 [153 kB] 78s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-19ubuntu2 [2815 kB] 78s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-19ubuntu2 [23.3 MB] 78s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-19ubuntu2 [540 kB] 78s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [1208 B] 78s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.2.0-1ubuntu1 [5004 B] 78s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-19ubuntu2 [2510 kB] 78s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-19ubuntu2 [13.4 MB] 79s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-19ubuntu2 [23.0 kB] 79s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [968 B] 79s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.2.0-1ubuntu1 [1100 B] 79s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.12ubuntu1 [5080 B] 79s Get:52 http://ftpmaster.internal/ubuntu plucky/universe amd64 bwa amd64 0.7.18-1 [204 kB] 79s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 ca-certificates-java all 20240118 [11.6 kB] 79s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libdconf1 amd64 0.40.0-5 [39.8 kB] 79s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 dconf-service amd64 0.40.0-5 [28.4 kB] 79s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 dconf-gsettings-backend amd64 0.40.0-5 [22.7 kB] 79s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebhelper-perl all 13.24.1ubuntu2 [95.4 kB] 79s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libtool all 2.5.4-4 [168 kB] 79s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-autoreconf all 20 [16.1 kB] 79s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] 79s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [20.3 kB] 79s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-strip-nondeterminism all 1.14.1-2 [5064 B] 79s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 debugedit amd64 1:5.1-2 [47.0 kB] 79s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 dwz amd64 0.15-1build6 [115 kB] 79s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 gettext amd64 0.23.1-1 [1086 kB] 79s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 79s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] 79s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 debhelper all 13.24.1ubuntu2 [895 kB] 79s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 java-common all 0.76 [6852 B] 79s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 79s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcsclite1 amd64 2.3.1-1 [26.6 kB] 79s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 openjdk-21-jre-headless amd64 21.0.7~8ea-1 [46.4 MB] 80s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 default-jre-headless amd64 2:1.21-76 [3178 B] 80s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libatk1.0-0t64 amd64 2.56.1-1 [55.4 kB] 80s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libxi6 amd64 2:1.8.2-1 [32.4 kB] 80s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libatspi2.0-0t64 amd64 2.56.1-1 [91.9 kB] 80s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 libatk-bridge2.0-0t64 amd64 2.56.1-1 [69.0 kB] 80s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 80s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 80s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-2.2ubuntu1 [37.8 kB] 80s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-2.2ubuntu1 [164 kB] 80s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 80s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 80s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 80s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 80s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.4-1 [662 kB] 80s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo-gobject2 amd64 1.18.4-1 [127 kB] 80s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 libcolord2 amd64 1.4.7-3 [155 kB] 80s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-common-data amd64 0.8-16ubuntu2 [31.0 kB] 80s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-common3 amd64 0.8-16ubuntu2 [23.6 kB] 80s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-client3 amd64 0.8-16ubuntu2 [27.5 kB] 80s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 libcups2t64 amd64 2.4.12-0ubuntu1 [292 kB] 80s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 libepoxy0 amd64 1.5.10-2 [218 kB] 81s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 81s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 81s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-2.2ubuntu1 [180 kB] 81s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 81s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB] 81s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 81s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.56.3-1 [256 kB] 81s Get:101 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.56.3-1 [52.9 kB] 81s Get:102 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.56.3-1 [29.1 kB] 81s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-client0 amd64 1.23.1-3 [29.7 kB] 81s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-cursor0 amd64 1.23.1-3 [10.9 kB] 81s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-egl1 amd64 1.23.1-3 [6168 B] 81s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcomposite1 amd64 1:0.4.6-1 [6642 B] 81s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 libxfixes3 amd64 1:6.0.0-2build1 [10.8 kB] 81s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcursor1 amd64 1:1.2.3-1 [23.1 kB] 81s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 libxdamage1 amd64 1:1.1.6-1build1 [6150 B] 81s Get:110 http://ftpmaster.internal/ubuntu plucky/main amd64 libxinerama1 amd64 2:1.1.4-3build1 [6396 B] 81s Get:111 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrandr2 amd64 2:1.5.4-1 [19.6 kB] 81s Get:112 http://ftpmaster.internal/ubuntu plucky/main amd64 libgtk-3-common all 3.24.49-2ubuntu1 [1424 kB] 81s Get:113 http://ftpmaster.internal/ubuntu plucky/main amd64 libgtk-3-0t64 amd64 3.24.49-2ubuntu1 [3172 kB] 81s Get:114 http://ftpmaster.internal/ubuntu plucky/main amd64 libglvnd0 amd64 1.7.0-1build1 [69.6 kB] 81s Get:115 http://ftpmaster.internal/ubuntu plucky/main amd64 libx11-xcb1 amd64 2:1.8.10-2 [7944 B] 81s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-dri3-0 amd64 1.17.0-2 [7508 B] 81s Get:117 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-glx0 amd64 1.17.0-2 [24.8 kB] 81s Get:118 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-present0 amd64 1.17.0-2 [6064 B] 81s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-xfixes0 amd64 1.17.0-2 [10.2 kB] 81s Get:120 http://ftpmaster.internal/ubuntu plucky/main amd64 libxxf86vm1 amd64 1:1.1.4-1build4 [9282 B] 81s Get:121 http://ftpmaster.internal/ubuntu plucky/main amd64 libpciaccess0 amd64 0.17-3build1 [18.6 kB] 81s Get:122 http://ftpmaster.internal/ubuntu plucky/main amd64 libdrm-intel1 amd64 2.4.124-2 [68.9 kB] 81s Get:123 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-randr0 amd64 1.17.0-2 [17.9 kB] 81s Get:124 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-sync1 amd64 1.17.0-2 [9312 B] 81s Get:125 http://ftpmaster.internal/ubuntu plucky/main amd64 libxshmfence1 amd64 1.3-1build5 [4764 B] 81s Get:126 http://ftpmaster.internal/ubuntu plucky/main amd64 mesa-libgallium amd64 25.0.3-1ubuntu2 [12.1 MB] 82s Get:127 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-server0 amd64 1.23.1-3 [37.2 kB] 82s Get:128 http://ftpmaster.internal/ubuntu plucky/main amd64 libgbm1 amd64 25.0.3-1ubuntu2 [33.4 kB] 82s Get:129 http://ftpmaster.internal/ubuntu plucky/main amd64 libvulkan1 amd64 1.4.304.0-1 [147 kB] 82s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 libgl1-mesa-dri amd64 25.0.3-1ubuntu2 [35.7 kB] 82s Get:131 http://ftpmaster.internal/ubuntu plucky/main amd64 libglx-mesa0 amd64 25.0.3-1ubuntu2 [146 kB] 82s Get:132 http://ftpmaster.internal/ubuntu plucky/main amd64 libglx0 amd64 1.7.0-1build1 [38.6 kB] 82s Get:133 http://ftpmaster.internal/ubuntu plucky/main amd64 libgl1 amd64 1.7.0-1build1 [102 kB] 82s Get:134 http://ftpmaster.internal/ubuntu plucky/main amd64 libasound2-data all 1.2.13-1build1 [21.1 kB] 82s Get:135 http://ftpmaster.internal/ubuntu plucky/main amd64 libasound2t64 amd64 1.2.13-1build1 [437 kB] 82s Get:136 http://ftpmaster.internal/ubuntu plucky/main amd64 libgif7 amd64 5.2.2-1ubuntu2 [36.0 kB] 82s Get:137 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu4 [21.8 kB] 82s Get:138 http://ftpmaster.internal/ubuntu plucky/main amd64 libxtst6 amd64 2:1.2.5-1 [13.0 kB] 82s Get:139 http://ftpmaster.internal/ubuntu plucky/main amd64 openjdk-21-jre amd64 21.0.7~8ea-1 [220 kB] 82s Get:140 http://ftpmaster.internal/ubuntu plucky/main amd64 default-jre amd64 2:1.21-76 [918 B] 82s Get:141 http://ftpmaster.internal/ubuntu plucky/main amd64 openjdk-21-jdk-headless amd64 21.0.7~8ea-1 [82.8 MB] 84s Get:142 http://ftpmaster.internal/ubuntu plucky/main amd64 default-jdk-headless amd64 2:1.21-76 [966 B] 84s Get:143 http://ftpmaster.internal/ubuntu plucky/main amd64 openjdk-21-jdk amd64 21.0.7~8ea-1 [3510 kB] 84s Get:144 http://ftpmaster.internal/ubuntu plucky/main amd64 default-jdk amd64 2:1.21-76 [922 B] 84s Get:145 http://ftpmaster.internal/ubuntu plucky/universe amd64 dh-python all 6.20250308 [118 kB] 84s Get:146 http://ftpmaster.internal/ubuntu plucky/main amd64 unzip amd64 6.0-28ubuntu6 [181 kB] 84s Get:147 http://ftpmaster.internal/ubuntu plucky/universe amd64 java-wrappers all 0.5 [9042 B] 84s Get:148 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhamcrest-java all 2.2-2 [117 kB] 84s Get:149 http://ftpmaster.internal/ubuntu plucky/universe amd64 junit4 all 4.13.2-5 [348 kB] 84s Get:150 http://ftpmaster.internal/ubuntu plucky/universe amd64 libapache-pom-java all 33-2 [5874 B] 84s Get:151 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-collections3-java all 3.2.2-3 [526 kB] 84s Get:152 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-parent-java all 56-1 [10.7 kB] 84s Get:153 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB] 84s Get:154 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-beanutils-java all 1.9.4-2 [228 kB] 84s Get:155 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-codec-java all 1.17.1-1 [302 kB] 84s Get:156 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-collections4-java all 4.4-2 [670 kB] 84s Get:157 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-io-java all 2.18.0-1 [477 kB] 84s Get:158 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-compress-java all 1.27.1-2 [610 kB] 84s Get:159 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-jexl2-java all 2.1.1-6 [250 kB] 84s Get:160 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-lang-java all 2.6-10 [270 kB] 84s Get:161 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-lang3-java all 3.17.0-1 [603 kB] 84s Get:162 http://ftpmaster.internal/ubuntu plucky/universe amd64 libedlib1 amd64 1.2.7-6build2 [18.7 kB] 84s Get:163 http://ftpmaster.internal/ubuntu plucky/universe amd64 libezmorph-java all 1.0.6-4 [76.0 kB] 84s Get:164 http://ftpmaster.internal/ubuntu plucky/universe amd64 libslf4j-java all 1.7.32-1 [141 kB] 84s Get:165 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjaxen-java all 1.1.6-5 [213 kB] 84s Get:166 http://ftpmaster.internal/ubuntu plucky/universe amd64 libxml-commons-external-java all 1.4.01-6 [240 kB] 84s Get:167 http://ftpmaster.internal/ubuntu plucky/universe amd64 libxml-commons-resolver1.1-java all 1.2-11 [97.6 kB] 84s Get:168 http://ftpmaster.internal/ubuntu plucky/universe amd64 libxerces2-java all 2.12.2-1 [1430 kB] 84s Get:169 http://ftpmaster.internal/ubuntu plucky/universe amd64 libxom-java all 1.3.9-1 [174 kB] 84s Get:170 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjson-java all 3.1.0+dfsg-2 [141 kB] 84s Get:171 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedcrypto16 amd64 3.6.2-3ubuntu1 [276 kB] 84s Get:172 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedx509-7 amd64 3.6.2-3ubuntu1 [37.1 kB] 84s Get:173 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedtls21 amd64 3.6.2-3ubuntu1 [126 kB] 84s Get:174 http://ftpmaster.internal/ubuntu plucky/universe amd64 ncbi-vdb-data all 3.2.1+dfsg-2 [81.3 kB] 85s Get:175 http://ftpmaster.internal/ubuntu plucky/universe amd64 libncbi-vdb3 amd64 3.2.1+dfsg-2 [1376 kB] 85s Get:176 http://ftpmaster.internal/ubuntu plucky/universe amd64 libncbi-ngs3 amd64 3.2.1+dfsg-3ubuntu1 [165 kB] 85s Get:177 http://ftpmaster.internal/ubuntu plucky/universe amd64 libngs-jni amd64 3.2.1+dfsg-3ubuntu1 [4808 B] 85s Get:178 http://ftpmaster.internal/ubuntu plucky/universe amd64 libngs-java amd64 3.2.1+dfsg-3ubuntu1 [91.1 kB] 85s Get:179 http://ftpmaster.internal/ubuntu plucky/universe amd64 librhino-java all 1.7.15-1 [1354 kB] 85s Get:180 http://ftpmaster.internal/ubuntu plucky/main amd64 libsnappy1v5 amd64 1.2.1-1 [30.4 kB] 85s Get:181 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsnappy-jni amd64 1.1.10.7-1 [6786 B] 85s Get:182 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsnappy-java all 1.1.10.7-1 [83.6 kB] 85s Get:183 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtsjdk-java all 4.1.3+dfsg-2 [1829 kB] 85s Get:184 http://ftpmaster.internal/ubuntu plucky/universe amd64 libseqan2-dev all 2.4.0+dfsg-16 [1206 kB] 85s Get:185 http://ftpmaster.internal/ubuntu plucky/universe amd64 libspoa7.0.0 amd64 4.1.4-2 [79.1 kB] 85s Get:186 http://ftpmaster.internal/ubuntu plucky/universe amd64 libssw0 amd64 1.1-15 [22.5 kB] 85s Get:187 http://ftpmaster.internal/ubuntu plucky/universe amd64 miniasm amd64 0.3+dfsg-4 [30.3 kB] 85s Get:188 http://ftpmaster.internal/ubuntu plucky/universe amd64 ncbi-data all 6.1.20170106+dfsg2-5 [3966 kB] 85s Get:189 http://ftpmaster.internal/ubuntu plucky/universe amd64 ncbi-blast+ amd64 2.16.0+ds-6build1 [15.8 MB] 85s Get:190 http://ftpmaster.internal/ubuntu plucky/universe amd64 scala-library all 2.11.12-6 [9545 kB] 86s Get:191 http://ftpmaster.internal/ubuntu plucky/universe amd64 pilon all 1.24-4 [495 kB] 86s Get:192 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all amd64 3.13.3-1 [882 B] 86s Get:193 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-joblib all 1.4.2-3 [205 kB] 86s Get:194 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.2-1 [51.5 kB] 86s Get:195 http://ftpmaster.internal/ubuntu plucky/universe amd64 racon amd64 1.5.0-3 [3113 kB] 86s Get:196 http://ftpmaster.internal/ubuntu plucky/universe amd64 samtools amd64 1.21-1 [655 kB] 86s Get:197 http://ftpmaster.internal/ubuntu plucky/universe amd64 libnlopt0 amd64 2.7.1-6ubuntu3 [251 kB] 86s Get:198 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 spades amd64 4.0.0+dfsg1-2 [8064 kB] 86s Get:199 http://ftpmaster.internal/ubuntu plucky/universe amd64 bowtie2 amd64 2.5.4-1 [1336 kB] 86s Get:200 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicycler amd64 0.5.1+dfsg-3 [910 kB] 86s Get:201 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicycler-data all 0.5.1+dfsg-3 [12.0 MB] 86s Get:202 http://ftpmaster.internal/ubuntu plucky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB] 87s Fetched 302 MB in 13s (23.6 MB/s) 87s Selecting previously unselected package libgdk-pixbuf2.0-common. 87s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 115893 files and directories currently installed.) 87s Preparing to unpack .../000-libgdk-pixbuf2.0-common_2.42.12+dfsg-2_all.deb ... 87s Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-2) ... 87s Selecting previously unselected package libjpeg-turbo8:amd64. 87s Preparing to unpack .../001-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ... 87s Unpacking libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 87s Selecting previously unselected package libjpeg8:amd64. 87s Preparing to unpack .../002-libjpeg8_8c-2ubuntu11_amd64.deb ... 87s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 87s Selecting previously unselected package libdeflate0:amd64. 87s Preparing to unpack .../003-libdeflate0_1.23-1_amd64.deb ... 87s Unpacking libdeflate0:amd64 (1.23-1) ... 87s Selecting previously unselected package libjbig0:amd64. 87s Preparing to unpack .../004-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 87s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 87s Selecting previously unselected package liblerc4:amd64. 87s Preparing to unpack .../005-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 87s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 87s Selecting previously unselected package libsharpyuv0:amd64. 87s Preparing to unpack .../006-libsharpyuv0_1.5.0-0.1_amd64.deb ... 87s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 87s Selecting previously unselected package libwebp7:amd64. 87s Preparing to unpack .../007-libwebp7_1.5.0-0.1_amd64.deb ... 87s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 87s Selecting previously unselected package libtiff6:amd64. 87s Preparing to unpack .../008-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 87s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 87s Selecting previously unselected package libgdk-pixbuf-2.0-0:amd64. 87s Preparing to unpack .../009-libgdk-pixbuf-2.0-0_2.42.12+dfsg-2_amd64.deb ... 87s Unpacking libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-2) ... 87s Selecting previously unselected package gtk-update-icon-cache. 87s Preparing to unpack .../010-gtk-update-icon-cache_4.18.4+ds-1_amd64.deb ... 87s No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed. 87s No diversion 'diversion of /usr/share/man/man8/update-icon-caches.8.gz to /usr/share/man/man8/update-icon-caches.gtk2.8.gz by libgtk-3-bin', none removed. 87s Unpacking gtk-update-icon-cache (4.18.4+ds-1) ... 87s Selecting previously unselected package hicolor-icon-theme. 87s Preparing to unpack .../011-hicolor-icon-theme_0.18-2_all.deb ... 87s Unpacking hicolor-icon-theme (0.18-2) ... 88s Selecting previously unselected package adwaita-icon-theme. 88s Preparing to unpack .../012-adwaita-icon-theme_48.0-1_all.deb ... 88s Unpacking adwaita-icon-theme (48.0-1) ... 88s Selecting previously unselected package at-spi2-common. 88s Preparing to unpack .../013-at-spi2-common_2.56.1-1_all.deb ... 88s Unpacking at-spi2-common (2.56.1-1) ... 88s Selecting previously unselected package m4. 88s Preparing to unpack .../014-m4_1.4.19-7_amd64.deb ... 88s Unpacking m4 (1.4.19-7) ... 88s Selecting previously unselected package autoconf. 88s Preparing to unpack .../015-autoconf_2.72-3ubuntu1_all.deb ... 88s Unpacking autoconf (2.72-3ubuntu1) ... 88s Selecting previously unselected package autotools-dev. 88s Preparing to unpack .../016-autotools-dev_20220109.1_all.deb ... 88s Unpacking autotools-dev (20220109.1) ... 88s Selecting previously unselected package automake. 88s Preparing to unpack .../017-automake_1%3a1.17-3ubuntu1_all.deb ... 88s Unpacking automake (1:1.17-3ubuntu1) ... 88s Selecting previously unselected package autopoint. 88s Preparing to unpack .../018-autopoint_0.23.1-1_all.deb ... 88s Unpacking autopoint (0.23.1-1) ... 88s Selecting previously unselected package libbamtools2.5.2:amd64. 88s Preparing to unpack .../019-libbamtools2.5.2_2.5.2+dfsg-6build1_amd64.deb ... 88s Unpacking libbamtools2.5.2:amd64 (2.5.2+dfsg-6build1) ... 88s Selecting previously unselected package libjsoncpp26:amd64. 88s Preparing to unpack .../020-libjsoncpp26_1.9.6-3_amd64.deb ... 88s Unpacking libjsoncpp26:amd64 (1.9.6-3) ... 88s Selecting previously unselected package bamtools. 88s Preparing to unpack .../021-bamtools_2.5.2+dfsg-6build1_amd64.deb ... 88s Unpacking bamtools (2.5.2+dfsg-6build1) ... 88s Selecting previously unselected package libhtscodecs2:amd64. 88s Preparing to unpack .../022-libhtscodecs2_1.6.1-2_amd64.deb ... 88s Unpacking libhtscodecs2:amd64 (1.6.1-2) ... 88s Selecting previously unselected package libhts3t64:amd64. 88s Preparing to unpack .../023-libhts3t64_1.21+ds-1_amd64.deb ... 88s Unpacking libhts3t64:amd64 (1.21+ds-1) ... 88s Selecting previously unselected package bcftools. 88s Preparing to unpack .../024-bcftools_1.21-1_amd64.deb ... 88s Unpacking bcftools (1.21-1) ... 88s Selecting previously unselected package libisl23:amd64. 88s Preparing to unpack .../025-libisl23_0.27-1_amd64.deb ... 88s Unpacking libisl23:amd64 (0.27-1) ... 88s Selecting previously unselected package libmpc3:amd64. 88s Preparing to unpack .../026-libmpc3_1.3.1-1build2_amd64.deb ... 88s Unpacking libmpc3:amd64 (1.3.1-1build2) ... 88s Selecting previously unselected package cpp-14-x86-64-linux-gnu. 88s Preparing to unpack .../027-cpp-14-x86-64-linux-gnu_14.2.0-19ubuntu2_amd64.deb ... 88s Unpacking cpp-14-x86-64-linux-gnu (14.2.0-19ubuntu2) ... 88s Selecting previously unselected package cpp-14. 88s Preparing to unpack .../028-cpp-14_14.2.0-19ubuntu2_amd64.deb ... 88s Unpacking cpp-14 (14.2.0-19ubuntu2) ... 88s Selecting previously unselected package cpp-x86-64-linux-gnu. 88s Preparing to unpack .../029-cpp-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 88s Unpacking cpp-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 88s Selecting previously unselected package cpp. 88s Preparing to unpack .../030-cpp_4%3a14.2.0-1ubuntu1_amd64.deb ... 88s Unpacking cpp (4:14.2.0-1ubuntu1) ... 89s Selecting previously unselected package libcc1-0:amd64. 89s Preparing to unpack .../031-libcc1-0_15-20250404-0ubuntu1_amd64.deb ... 89s Unpacking libcc1-0:amd64 (15-20250404-0ubuntu1) ... 89s Selecting previously unselected package libgomp1:amd64. 89s Preparing to unpack .../032-libgomp1_15-20250404-0ubuntu1_amd64.deb ... 89s Unpacking libgomp1:amd64 (15-20250404-0ubuntu1) ... 89s Selecting previously unselected package libitm1:amd64. 89s Preparing to unpack .../033-libitm1_15-20250404-0ubuntu1_amd64.deb ... 89s Unpacking libitm1:amd64 (15-20250404-0ubuntu1) ... 89s Selecting previously unselected package libasan8:amd64. 89s Preparing to unpack .../034-libasan8_15-20250404-0ubuntu1_amd64.deb ... 89s Unpacking libasan8:amd64 (15-20250404-0ubuntu1) ... 89s Selecting previously unselected package liblsan0:amd64. 89s Preparing to unpack .../035-liblsan0_15-20250404-0ubuntu1_amd64.deb ... 89s Unpacking liblsan0:amd64 (15-20250404-0ubuntu1) ... 89s Selecting previously unselected package libtsan2:amd64. 89s Preparing to unpack .../036-libtsan2_15-20250404-0ubuntu1_amd64.deb ... 89s Unpacking libtsan2:amd64 (15-20250404-0ubuntu1) ... 89s Selecting previously unselected package libubsan1:amd64. 89s Preparing to unpack .../037-libubsan1_15-20250404-0ubuntu1_amd64.deb ... 89s Unpacking libubsan1:amd64 (15-20250404-0ubuntu1) ... 89s Selecting previously unselected package libhwasan0:amd64. 89s Preparing to unpack .../038-libhwasan0_15-20250404-0ubuntu1_amd64.deb ... 89s Unpacking libhwasan0:amd64 (15-20250404-0ubuntu1) ... 89s Selecting previously unselected package libquadmath0:amd64. 89s Preparing to unpack .../039-libquadmath0_15-20250404-0ubuntu1_amd64.deb ... 89s Unpacking libquadmath0:amd64 (15-20250404-0ubuntu1) ... 89s Selecting previously unselected package libgcc-14-dev:amd64. 89s Preparing to unpack .../040-libgcc-14-dev_14.2.0-19ubuntu2_amd64.deb ... 89s Unpacking libgcc-14-dev:amd64 (14.2.0-19ubuntu2) ... 89s Selecting previously unselected package gcc-14-x86-64-linux-gnu. 89s Preparing to unpack .../041-gcc-14-x86-64-linux-gnu_14.2.0-19ubuntu2_amd64.deb ... 89s Unpacking gcc-14-x86-64-linux-gnu (14.2.0-19ubuntu2) ... 89s Selecting previously unselected package gcc-14. 89s Preparing to unpack .../042-gcc-14_14.2.0-19ubuntu2_amd64.deb ... 89s Unpacking gcc-14 (14.2.0-19ubuntu2) ... 89s Selecting previously unselected package gcc-x86-64-linux-gnu. 89s Preparing to unpack .../043-gcc-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 89s Unpacking gcc-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 89s Selecting previously unselected package gcc. 89s Preparing to unpack .../044-gcc_4%3a14.2.0-1ubuntu1_amd64.deb ... 89s Unpacking gcc (4:14.2.0-1ubuntu1) ... 89s Selecting previously unselected package libstdc++-14-dev:amd64. 89s Preparing to unpack .../045-libstdc++-14-dev_14.2.0-19ubuntu2_amd64.deb ... 89s Unpacking libstdc++-14-dev:amd64 (14.2.0-19ubuntu2) ... 90s Selecting previously unselected package g++-14-x86-64-linux-gnu. 90s Preparing to unpack .../046-g++-14-x86-64-linux-gnu_14.2.0-19ubuntu2_amd64.deb ... 90s Unpacking g++-14-x86-64-linux-gnu (14.2.0-19ubuntu2) ... 90s Selecting previously unselected package g++-14. 90s Preparing to unpack .../047-g++-14_14.2.0-19ubuntu2_amd64.deb ... 90s Unpacking g++-14 (14.2.0-19ubuntu2) ... 90s Selecting previously unselected package g++-x86-64-linux-gnu. 90s Preparing to unpack .../048-g++-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 90s Unpacking g++-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 90s Selecting previously unselected package g++. 90s Preparing to unpack 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previously unselected package po-debconf. 90s Preparing to unpack .../066-po-debconf_1.0.21+nmu1_all.deb ... 90s Unpacking po-debconf (1.0.21+nmu1) ... 90s Selecting previously unselected package debhelper. 90s Preparing to unpack .../067-debhelper_13.24.1ubuntu2_all.deb ... 90s Unpacking debhelper (13.24.1ubuntu2) ... 90s Selecting previously unselected package java-common. 91s Preparing to unpack .../068-java-common_0.76_all.deb ... 91s Unpacking java-common (0.76) ... 91s Selecting previously unselected package liblcms2-2:amd64. 91s Preparing to unpack .../069-liblcms2-2_2.16-2_amd64.deb ... 91s Unpacking liblcms2-2:amd64 (2.16-2) ... 91s Selecting previously unselected package libpcsclite1:amd64. 91s Preparing to unpack .../070-libpcsclite1_2.3.1-1_amd64.deb ... 91s Unpacking libpcsclite1:amd64 (2.3.1-1) ... 91s Selecting previously unselected package openjdk-21-jre-headless:amd64. 91s Preparing to unpack .../071-openjdk-21-jre-headless_21.0.7~8ea-1_amd64.deb ... 91s Unpacking openjdk-21-jre-headless:amd64 (21.0.7~8ea-1) ... 92s Selecting previously unselected package default-jre-headless. 92s Preparing to unpack .../072-default-jre-headless_2%3a1.21-76_amd64.deb ... 92s Unpacking default-jre-headless (2:1.21-76) ... 92s Selecting previously unselected package libatk1.0-0t64:amd64. 92s Preparing to unpack .../073-libatk1.0-0t64_2.56.1-1_amd64.deb ... 92s Unpacking libatk1.0-0t64:amd64 (2.56.1-1) ... 92s Selecting previously unselected package libxi6:amd64. 92s Preparing to unpack .../074-libxi6_2%3a1.8.2-1_amd64.deb ... 92s Unpacking libxi6:amd64 (2:1.8.2-1) ... 92s Selecting previously unselected package libatspi2.0-0t64:amd64. 92s Preparing to unpack .../075-libatspi2.0-0t64_2.56.1-1_amd64.deb ... 92s Unpacking libatspi2.0-0t64:amd64 (2.56.1-1) ... 92s Selecting previously unselected package libatk-bridge2.0-0t64:amd64. 92s Preparing to unpack .../076-libatk-bridge2.0-0t64_2.56.1-1_amd64.deb ... 92s Unpacking libatk-bridge2.0-0t64:amd64 (2.56.1-1) ... 92s Selecting previously unselected package fonts-dejavu-mono. 92s Preparing to unpack .../077-fonts-dejavu-mono_2.37-8_all.deb ... 92s Unpacking fonts-dejavu-mono (2.37-8) ... 92s Selecting previously unselected package fonts-dejavu-core. 92s Preparing to unpack .../078-fonts-dejavu-core_2.37-8_all.deb ... 92s Unpacking fonts-dejavu-core (2.37-8) ... 92s Selecting previously unselected package fontconfig-config. 92s Preparing to unpack .../079-fontconfig-config_2.15.0-2.2ubuntu1_amd64.deb ... 92s Unpacking fontconfig-config (2.15.0-2.2ubuntu1) ... 92s Selecting previously unselected package libfontconfig1:amd64. 92s Preparing to unpack .../080-libfontconfig1_2.15.0-2.2ubuntu1_amd64.deb ... 92s Unpacking libfontconfig1:amd64 (2.15.0-2.2ubuntu1) ... 92s Selecting previously unselected package libpixman-1-0:amd64. 92s Preparing to unpack .../081-libpixman-1-0_0.44.0-3_amd64.deb ... 92s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 92s Selecting previously unselected package 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previously unselected package libwayland-cursor0:amd64. 93s Preparing to unpack .../103-libwayland-cursor0_1.23.1-3_amd64.deb ... 93s Unpacking libwayland-cursor0:amd64 (1.23.1-3) ... 93s Selecting previously unselected package libwayland-egl1:amd64. 93s Preparing to unpack .../104-libwayland-egl1_1.23.1-3_amd64.deb ... 93s Unpacking libwayland-egl1:amd64 (1.23.1-3) ... 93s Selecting previously unselected package libxcomposite1:amd64. 93s Preparing to unpack .../105-libxcomposite1_1%3a0.4.6-1_amd64.deb ... 93s Unpacking libxcomposite1:amd64 (1:0.4.6-1) ... 93s Selecting previously unselected package libxfixes3:amd64. 93s Preparing to unpack .../106-libxfixes3_1%3a6.0.0-2build1_amd64.deb ... 93s Unpacking libxfixes3:amd64 (1:6.0.0-2build1) ... 93s Selecting previously unselected package libxcursor1:amd64. 93s Preparing to unpack .../107-libxcursor1_1%3a1.2.3-1_amd64.deb ... 93s Unpacking libxcursor1:amd64 (1:1.2.3-1) ... 93s Selecting previously unselected package libxdamage1:amd64. 93s 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(1.17.0-2) ... 93s Selecting previously unselected package libxxf86vm1:amd64. 93s Preparing to unpack .../119-libxxf86vm1_1%3a1.1.4-1build4_amd64.deb ... 93s Unpacking libxxf86vm1:amd64 (1:1.1.4-1build4) ... 93s Selecting previously unselected package libpciaccess0:amd64. 93s Preparing to unpack .../120-libpciaccess0_0.17-3build1_amd64.deb ... 93s Unpacking libpciaccess0:amd64 (0.17-3build1) ... 93s Selecting previously unselected package libdrm-intel1:amd64. 93s Preparing to unpack .../121-libdrm-intel1_2.4.124-2_amd64.deb ... 93s Unpacking libdrm-intel1:amd64 (2.4.124-2) ... 93s Selecting previously unselected package libxcb-randr0:amd64. 93s Preparing to unpack .../122-libxcb-randr0_1.17.0-2_amd64.deb ... 93s Unpacking libxcb-randr0:amd64 (1.17.0-2) ... 93s Selecting previously unselected package libxcb-sync1:amd64. 93s Preparing to unpack .../123-libxcb-sync1_1.17.0-2_amd64.deb ... 93s Unpacking libxcb-sync1:amd64 (1.17.0-2) ... 93s Selecting previously unselected package libxshmfence1:amd64. 93s Preparing to unpack .../124-libxshmfence1_1.3-1build5_amd64.deb ... 93s Unpacking libxshmfence1:amd64 (1.3-1build5) ... 93s Selecting previously unselected package mesa-libgallium:amd64. 93s Preparing to unpack .../125-mesa-libgallium_25.0.3-1ubuntu2_amd64.deb ... 93s Unpacking mesa-libgallium:amd64 (25.0.3-1ubuntu2) ... 94s Selecting previously unselected package libwayland-server0:amd64. 94s Preparing to unpack .../126-libwayland-server0_1.23.1-3_amd64.deb ... 94s Unpacking libwayland-server0:amd64 (1.23.1-3) ... 94s Selecting previously unselected package libgbm1:amd64. 94s Preparing to unpack .../127-libgbm1_25.0.3-1ubuntu2_amd64.deb ... 94s Unpacking libgbm1:amd64 (25.0.3-1ubuntu2) ... 94s Selecting previously unselected package libvulkan1:amd64. 94s Preparing to unpack .../128-libvulkan1_1.4.304.0-1_amd64.deb ... 94s Unpacking libvulkan1:amd64 (1.4.304.0-1) ... 94s Selecting previously unselected package libgl1-mesa-dri:amd64. 94s Preparing to unpack .../129-libgl1-mesa-dri_25.0.3-1ubuntu2_amd64.deb ... 94s Unpacking libgl1-mesa-dri:amd64 (25.0.3-1ubuntu2) ... 94s Selecting previously unselected package libglx-mesa0:amd64. 94s Preparing to unpack .../130-libglx-mesa0_25.0.3-1ubuntu2_amd64.deb ... 94s Unpacking libglx-mesa0:amd64 (25.0.3-1ubuntu2) ... 94s Selecting previously unselected package libglx0:amd64. 94s Preparing to unpack .../131-libglx0_1.7.0-1build1_amd64.deb ... 94s Unpacking libglx0:amd64 (1.7.0-1build1) ... 94s Selecting previously unselected package libgl1:amd64. 94s Preparing to unpack .../132-libgl1_1.7.0-1build1_amd64.deb ... 94s Unpacking libgl1:amd64 (1.7.0-1build1) ... 94s Selecting previously unselected package libasound2-data. 94s Preparing to unpack .../133-libasound2-data_1.2.13-1build1_all.deb ... 94s Unpacking libasound2-data (1.2.13-1build1) ... 94s Selecting previously unselected package libasound2t64:amd64. 94s Preparing to unpack .../134-libasound2t64_1.2.13-1build1_amd64.deb ... 94s Unpacking libasound2t64:amd64 (1.2.13-1build1) ... 94s Selecting previously unselected package libgif7:amd64. 94s Preparing to unpack .../135-libgif7_5.2.2-1ubuntu2_amd64.deb ... 94s Unpacking libgif7:amd64 (5.2.2-1ubuntu2) ... 94s Selecting previously unselected package x11-common. 94s Preparing to unpack .../136-x11-common_1%3a7.7+23ubuntu4_all.deb ... 94s Unpacking x11-common (1:7.7+23ubuntu4) ... 94s Selecting previously unselected package libxtst6:amd64. 94s Preparing to unpack .../137-libxtst6_2%3a1.2.5-1_amd64.deb ... 94s Unpacking libxtst6:amd64 (2:1.2.5-1) ... 94s Selecting previously unselected package openjdk-21-jre:amd64. 94s Preparing to unpack .../138-openjdk-21-jre_21.0.7~8ea-1_amd64.deb ... 94s Unpacking openjdk-21-jre:amd64 (21.0.7~8ea-1) ... 94s Selecting previously unselected package default-jre. 94s Preparing to unpack .../139-default-jre_2%3a1.21-76_amd64.deb ... 94s Unpacking default-jre (2:1.21-76) ... 94s Selecting previously unselected package openjdk-21-jdk-headless:amd64. 94s Preparing to unpack .../140-openjdk-21-jdk-headless_21.0.7~8ea-1_amd64.deb ... 94s Unpacking openjdk-21-jdk-headless:amd64 (21.0.7~8ea-1) ... 94s Selecting previously unselected package default-jdk-headless. 94s Preparing to unpack .../141-default-jdk-headless_2%3a1.21-76_amd64.deb ... 94s Unpacking default-jdk-headless (2:1.21-76) ... 94s Selecting previously unselected package openjdk-21-jdk:amd64. 94s Preparing to unpack .../142-openjdk-21-jdk_21.0.7~8ea-1_amd64.deb ... 94s Unpacking openjdk-21-jdk:amd64 (21.0.7~8ea-1) ... 94s Selecting previously unselected package default-jdk. 94s Preparing to unpack .../143-default-jdk_2%3a1.21-76_amd64.deb ... 94s Unpacking default-jdk (2:1.21-76) ... 94s Selecting previously unselected package dh-python. 94s Preparing to unpack .../144-dh-python_6.20250308_all.deb ... 94s Unpacking dh-python (6.20250308) ... 94s Selecting previously unselected package unzip. 94s Preparing to unpack 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libcommons-parent-java. 95s Preparing to unpack .../151-libcommons-parent-java_56-1_all.deb ... 95s Unpacking libcommons-parent-java (56-1) ... 95s Selecting previously unselected package libcommons-logging-java. 95s Preparing to unpack .../152-libcommons-logging-java_1.3.0-1ubuntu1_all.deb ... 95s Unpacking libcommons-logging-java (1.3.0-1ubuntu1) ... 95s Selecting previously unselected package libcommons-beanutils-java. 95s Preparing to unpack .../153-libcommons-beanutils-java_1.9.4-2_all.deb ... 95s Unpacking libcommons-beanutils-java (1.9.4-2) ... 95s Selecting previously unselected package libcommons-codec-java. 95s Preparing to unpack .../154-libcommons-codec-java_1.17.1-1_all.deb ... 95s Unpacking libcommons-codec-java (1.17.1-1) ... 95s Selecting previously unselected package libcommons-collections4-java. 95s Preparing to unpack .../155-libcommons-collections4-java_4.4-2_all.deb ... 95s Unpacking libcommons-collections4-java (4.4-2) ... 95s Selecting previously unselected package libcommons-io-java. 95s Preparing to unpack .../156-libcommons-io-java_2.18.0-1_all.deb ... 95s Unpacking libcommons-io-java (2.18.0-1) ... 95s Selecting previously unselected package libcommons-compress-java. 95s Preparing to unpack .../157-libcommons-compress-java_1.27.1-2_all.deb ... 95s Unpacking libcommons-compress-java (1.27.1-2) ... 95s Selecting previously unselected package libcommons-jexl2-java. 95s Preparing to unpack .../158-libcommons-jexl2-java_2.1.1-6_all.deb ... 95s Unpacking libcommons-jexl2-java (2.1.1-6) ... 95s Selecting previously unselected package libcommons-lang-java. 95s Preparing to unpack .../159-libcommons-lang-java_2.6-10_all.deb ... 95s Unpacking libcommons-lang-java (2.6-10) ... 95s Selecting previously unselected package libcommons-lang3-java. 95s Preparing to unpack .../160-libcommons-lang3-java_3.17.0-1_all.deb ... 95s Unpacking libcommons-lang3-java (3.17.0-1) ... 95s Selecting previously unselected package libedlib1:amd64. 95s Preparing to 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libmbedtls21:amd64. 95s Preparing to unpack .../172-libmbedtls21_3.6.2-3ubuntu1_amd64.deb ... 95s Unpacking libmbedtls21:amd64 (3.6.2-3ubuntu1) ... 95s Selecting previously unselected package ncbi-vdb-data. 95s Preparing to unpack .../173-ncbi-vdb-data_3.2.1+dfsg-2_all.deb ... 95s Unpacking ncbi-vdb-data (3.2.1+dfsg-2) ... 95s Selecting previously unselected package libncbi-vdb3:amd64. 96s Preparing to unpack .../174-libncbi-vdb3_3.2.1+dfsg-2_amd64.deb ... 96s Unpacking libncbi-vdb3:amd64 (3.2.1+dfsg-2) ... 96s Selecting previously unselected package libncbi-ngs3:amd64. 96s Preparing to unpack .../175-libncbi-ngs3_3.2.1+dfsg-3ubuntu1_amd64.deb ... 96s Unpacking libncbi-ngs3:amd64 (3.2.1+dfsg-3ubuntu1) ... 96s Selecting previously unselected package libngs-jni:amd64. 96s Preparing to unpack .../176-libngs-jni_3.2.1+dfsg-3ubuntu1_amd64.deb ... 96s Unpacking libngs-jni:amd64 (3.2.1+dfsg-3ubuntu1) ... 96s Selecting previously unselected package libngs-java:amd64. 96s Preparing to unpack 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Skipping Java certificates setup. 98s Setting up libxerces2-java (2.12.2-1) ... 98s Setting up libisl23:amd64 (0.27-1) ... 98s Setting up libsnappy-jni (1.1.10.7-1) ... 98s Setting up libezmorph-java (1.0.6-4) ... 98s Setting up libxcomposite1:amd64 (1:0.4.6-1) ... 98s Setting up libssw0:amd64 (1.1-15) ... 98s Setting up libcc1-0:amd64 (15-20250404-0ubuntu1) ... 98s Setting up liblsan0:amd64 (15-20250404-0ubuntu1) ... 98s Setting up libitm1:amd64 (15-20250404-0ubuntu1) ... 98s Setting up libwayland-client0:amd64 (1.23.1-3) ... 98s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 98s Setting up automake (1:1.17-3ubuntu1) ... 98s update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode 98s Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... 98s Setting up mesa-libgallium:amd64 (25.0.3-1ubuntu2) ... 98s Setting up gettext (0.23.1-1) ... 98s Setting up java-wrappers (0.5) ... 98s Setting up libatk1.0-0t64:amd64 (2.56.1-1) ... 98s Setting up openjdk-21-jre-headless:amd64 (21.0.7~8ea-1) ... 98s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode 98s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 98s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 98s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 98s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 98s Setting up libgbm1:amd64 (25.0.3-1ubuntu2) ... 98s Setting up fontconfig-config (2.15.0-2.2ubuntu1) ... 99s Setting up libxtst6:amd64 (2:1.2.5-1) ... 99s Setting up libxcursor1:amd64 (1:1.2.3-1) ... 99s Setting up libgl1-mesa-dri:amd64 (25.0.3-1ubuntu2) ... 99s Setting up bcftools (1.21-1) ... 99s Setting up libcommons-parent-java (56-1) ... 99s Setting up libavahi-common3:amd64 (0.8-16ubuntu2) ... 99s Setting up libcommons-logging-java (1.3.0-1ubuntu1) ... 99s Setting up dconf-service (0.40.0-5) ... 99s Setting up libxom-java (1.3.9-1) ... 99s Setting up libcommons-lang-java (2.6-10) ... 99s Setting up samtools (1.21-1) ... 99s Setting up intltool-debian (0.35.0+20060710.6) ... 99s Setting up libcommons-jexl2-java (2.1.1-6) ... 99s Setting up libthai0:amd64 (0.1.29-2build1) ... 99s Setting up libmbedx509-7:amd64 (3.6.2-3ubuntu1) ... 99s Setting up racon (1.5.0-3) ... 99s Setting up libcommons-collections4-java (4.4-2) ... 99s Setting up cpp-14-x86-64-linux-gnu (14.2.0-19ubuntu2) ... 99s Setting up libcommons-lang3-java (3.17.0-1) ... 99s Setting up cpp-14 (14.2.0-19ubuntu2) ... 99s Setting up libmbedtls21:amd64 (3.6.2-3ubuntu1) ... 99s Setting up dh-strip-nondeterminism (1.14.1-2) ... 99s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 99s Setting up libwayland-cursor0:amd64 (1.23.1-3) ... 99s Setting up libcommons-beanutils-java (1.9.4-2) ... 99s Setting up spades (4.0.0+dfsg1-2) ... 99s Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-2) ... 99s Setting up libsnappy-java (1.1.10.7-1) ... 99s Setting up libfontconfig1:amd64 (2.15.0-2.2ubuntu1) ... 99s Setting up libgcc-14-dev:amd64 (14.2.0-19ubuntu2) ... 99s Setting up libcommons-codec-java (1.17.1-1) ... 99s Setting up libstdc++-14-dev:amd64 (14.2.0-19ubuntu2) ... 99s Setting up libavahi-client3:amd64 (0.8-16ubuntu2) ... 99s Setting up cpp-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 99s Setting up libatk-bridge2.0-0t64:amd64 (2.56.1-1) ... 99s Setting up gtk-update-icon-cache (4.18.4+ds-1) ... 99s Setting up fontconfig (2.15.0-2.2ubuntu1) ... 101s Regenerating fonts cache... done. 101s Setting up libglx-mesa0:amd64 (25.0.3-1ubuntu2) ... 101s Setting up libglx0:amd64 (1.7.0-1build1) ... 101s Setting up dconf-gsettings-backend:amd64 (0.40.0-5) ... 101s Setting up libcommons-io-java (2.18.0-1) ... 101s Setting up po-debconf (1.0.21+nmu1) ... 101s Setting up libpango-1.0-0:amd64 (1.56.3-1) ... 101s Setting up libncbi-vdb3:amd64 (3.2.1+dfsg-2) ... 101s Setting up libcairo2:amd64 (1.18.4-1) ... 101s Setting up ncbi-blast+ (2.16.0+ds-6build1) ... 101s Setting up libgl1:amd64 (1.7.0-1build1) ... 101s Setting up adwaita-icon-theme (48.0-1) ... 101s update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode 101s Setting up cpp (4:14.2.0-1ubuntu1) ... 101s Setting up libcairo-gobject2:amd64 (1.18.4-1) ... 101s Setting up gcc-14-x86-64-linux-gnu (14.2.0-19ubuntu2) ... 101s Setting up libpangoft2-1.0-0:amd64 (1.56.3-1) ... 101s Setting up libcups2t64:amd64 (2.4.12-0ubuntu1) ... 101s Setting up libgtk-3-common (3.24.49-2ubuntu1) ... 101s Setting up libpangocairo-1.0-0:amd64 (1.56.3-1) ... 101s Setting up libncbi-ngs3:amd64 (3.2.1+dfsg-3ubuntu1) ... 101s Setting up libngs-jni:amd64 (3.2.1+dfsg-3ubuntu1) ... 101s Setting up gcc-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 101s Setting up libcommons-compress-java (1.27.1-2) ... 101s Setting up gcc-14 (14.2.0-19ubuntu2) ... 101s Setting up g++-14-x86-64-linux-gnu (14.2.0-19ubuntu2) ... 101s Setting up g++-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 101s Setting up g++-14 (14.2.0-19ubuntu2) ... 101s Setting up libngs-java:amd64 (3.2.1+dfsg-3ubuntu1) ... 101s Setting up libtool (2.5.4-4) ... 101s Setting up gcc (4:14.2.0-1ubuntu1) ... 101s Setting up dh-autoreconf (20) ... 101s Setting up g++ (4:14.2.0-1ubuntu1) ... 101s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 101s Setting up build-essential (12.12ubuntu1) ... 101s Setting up debhelper (13.24.1ubuntu2) ... 101s Processing triggers for man-db (2.13.0-1) ... 103s Processing triggers for libglib2.0-0t64:amd64 (2.84.1-1) ... 103s Setting up libgtk-3-0t64:amd64 (3.24.49-2ubuntu1) ... 103s Processing triggers for install-info (7.1.1-1) ... 103s Processing triggers for libc-bin (2.41-6ubuntu1) ... 103s Processing triggers for ca-certificates-java (20240118) ... 103s Adding debian:ACCVRAIZ1.pem 103s Adding debian:AC_RAIZ_FNMT-RCM.pem 103s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 103s Adding debian:ANF_Secure_Server_Root_CA.pem 103s Adding debian:Actalis_Authentication_Root_CA.pem 103s Adding debian:AffirmTrust_Commercial.pem 103s Adding debian:AffirmTrust_Networking.pem 103s Adding debian:AffirmTrust_Premium.pem 103s Adding debian:AffirmTrust_Premium_ECC.pem 103s Adding debian:Amazon_Root_CA_1.pem 103s Adding debian:Amazon_Root_CA_2.pem 103s Adding debian:Amazon_Root_CA_3.pem 103s Adding debian:Amazon_Root_CA_4.pem 103s Adding debian:Atos_TrustedRoot_2011.pem 103s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 103s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 103s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 103s Adding debian:BJCA_Global_Root_CA1.pem 103s Adding debian:BJCA_Global_Root_CA2.pem 103s Adding debian:Baltimore_CyberTrust_Root.pem 103s Adding debian:Buypass_Class_2_Root_CA.pem 103s Adding debian:Buypass_Class_3_Root_CA.pem 103s Adding debian:CA_Disig_Root_R2.pem 103s Adding debian:CFCA_EV_ROOT.pem 103s Adding debian:COMODO_Certification_Authority.pem 103s Adding debian:COMODO_ECC_Certification_Authority.pem 103s Adding debian:COMODO_RSA_Certification_Authority.pem 103s Adding debian:Certainly_Root_E1.pem 103s Adding debian:Certainly_Root_R1.pem 103s Adding debian:Certigna.pem 103s Adding debian:Certigna_Root_CA.pem 103s Adding debian:Certum_EC-384_CA.pem 103s Adding debian:Certum_Trusted_Network_CA.pem 103s Adding debian:Certum_Trusted_Network_CA_2.pem 103s Adding debian:Certum_Trusted_Root_CA.pem 103s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 103s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 103s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 103s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 103s Adding debian:Comodo_AAA_Services_root.pem 103s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 103s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 103s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 103s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 103s Adding debian:DigiCert_Assured_ID_Root_CA.pem 103s Adding debian:DigiCert_Assured_ID_Root_G2.pem 103s Adding debian:DigiCert_Assured_ID_Root_G3.pem 103s Adding debian:DigiCert_Global_Root_CA.pem 103s Adding debian:DigiCert_Global_Root_G2.pem 103s Adding debian:DigiCert_Global_Root_G3.pem 103s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 103s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 103s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 103s Adding debian:DigiCert_Trusted_Root_G4.pem 103s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 103s Adding debian:Entrust_Root_Certification_Authority.pem 103s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 103s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 103s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem 103s Adding debian:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem 103s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 103s Adding debian:GLOBALTRUST_2020.pem 103s Adding debian:GTS_Root_R1.pem 103s Adding debian:GTS_Root_R2.pem 103s Adding debian:GTS_Root_R3.pem 103s Adding debian:GTS_Root_R4.pem 103s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 103s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 103s Adding debian:GlobalSign_Root_CA.pem 103s Adding debian:GlobalSign_Root_CA_-_R3.pem 103s Adding debian:GlobalSign_Root_CA_-_R6.pem 103s Adding debian:GlobalSign_Root_E46.pem 103s Adding debian:GlobalSign_Root_R46.pem 103s Adding debian:Go_Daddy_Class_2_CA.pem 103s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 103s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 103s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 103s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 103s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 103s Adding debian:HiPKI_Root_CA_-_G1.pem 103s Adding debian:Hongkong_Post_Root_CA_3.pem 103s Adding debian:ISRG_Root_X1.pem 103s Adding debian:ISRG_Root_X2.pem 103s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 103s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 103s Adding debian:Izenpe.com.pem 103s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 103s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 103s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 103s Adding debian:NAVER_Global_Root_Certification_Authority.pem 103s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 103s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 103s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 103s Adding debian:QuoVadis_Root_CA_1_G3.pem 103s Adding debian:QuoVadis_Root_CA_2.pem 103s Adding debian:QuoVadis_Root_CA_2_G3.pem 103s Adding debian:QuoVadis_Root_CA_3.pem 103s Adding debian:QuoVadis_Root_CA_3_G3.pem 103s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 103s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 103s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 103s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 103s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 103s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 103s Adding debian:SZAFIR_ROOT_CA2.pem 103s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 103s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 103s Adding debian:SecureSign_RootCA11.pem 103s Adding debian:SecureSign_Root_CA12.pem 103s Adding debian:SecureSign_Root_CA14.pem 103s Adding debian:SecureSign_Root_CA15.pem 103s Adding debian:SecureTrust_CA.pem 103s Adding debian:Secure_Global_CA.pem 103s Adding debian:Security_Communication_ECC_RootCA1.pem 103s Adding debian:Security_Communication_RootCA2.pem 103s Adding debian:Security_Communication_RootCA3.pem 103s Adding debian:Starfield_Class_2_CA.pem 103s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 103s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 103s Adding debian:SwissSign_Gold_CA_-_G2.pem 103s Adding debian:SwissSign_Silver_CA_-_G2.pem 103s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 103s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 103s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 103s Adding debian:TWCA_CYBER_Root_CA.pem 103s Adding debian:TWCA_Global_Root_CA.pem 103s Adding debian:TWCA_Root_Certification_Authority.pem 103s Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem 103s Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem 103s Adding debian:TeliaSonera_Root_CA_v1.pem 103s Adding debian:Telia_Root_CA_v2.pem 103s Adding debian:TrustAsia_Global_Root_CA_G3.pem 103s Adding debian:TrustAsia_Global_Root_CA_G4.pem 103s Adding debian:Trustwave_Global_Certification_Authority.pem 103s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 103s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 103s Adding debian:TunTrust_Root_CA.pem 103s Adding debian:UCA_Extended_Validation_Root.pem 103s Adding debian:UCA_Global_G2_Root.pem 103s Adding debian:USERTrust_ECC_Certification_Authority.pem 103s Adding debian:USERTrust_RSA_Certification_Authority.pem 104s Adding debian:XRamp_Global_CA_Root.pem 104s Adding debian:certSIGN_ROOT_CA.pem 104s Adding debian:certSIGN_Root_CA_G2.pem 104s Adding debian:e-Szigno_Root_CA_2017.pem 104s Adding debian:ePKI_Root_Certification_Authority.pem 104s Adding debian:emSign_ECC_Root_CA_-_C3.pem 104s Adding debian:emSign_ECC_Root_CA_-_G3.pem 104s Adding debian:emSign_Root_CA_-_C1.pem 104s Adding debian:emSign_Root_CA_-_G1.pem 104s Adding debian:vTrus_ECC_Root_CA.pem 104s Adding debian:vTrus_Root_CA.pem 104s done. 104s Setting up openjdk-21-jre:amd64 (21.0.7~8ea-1) ... 104s Setting up junit4 (4.13.2-5) ... 104s Setting up openjdk-21-jdk-headless:amd64 (21.0.7~8ea-1) ... 104s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode 104s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode 104s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode 104s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode 104s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode 104s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode 104s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode 104s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode 104s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode 104s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode 104s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode 104s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode 104s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode 104s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode 104s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode 104s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode 104s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode 104s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode 104s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode 104s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode 104s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode 104s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jwebserver to provide /usr/bin/jwebserver (jwebserver) in auto mode 104s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode 104s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode 104s Setting up default-jre-headless (2:1.21-76) ... 104s Setting up default-jre (2:1.21-76) ... 104s Setting up openjdk-21-jdk:amd64 (21.0.7~8ea-1) ... 104s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode 104s Setting up default-jdk-headless (2:1.21-76) ... 104s Setting up libjson-java (3.1.0+dfsg-2) ... 104s Setting up libhtsjdk-java (4.1.3+dfsg-2) ... 104s Setting up default-jdk (2:1.21-76) ... 104s Setting up pilon (1.24-4) ... 104s Setting up unicycler (0.5.1+dfsg-3) ... 105s autopkgtest [09:29:02]: test run-unit-test: [----------------------- 105s 105s Starting Unicycler (2025-04-14 09:29:02) 105s Welcome to Unicycler, an assembly pipeline for bacterial genomes. Since you 105s provided only short reads, Unicycler will essentially function as a SPAdes- 105s optimiser. It will try many k-mer sizes, choose the best based on contig length 105s and graph connectivity, and scaffold the graph using SPAdes repeat resolution. 105s For more information, please see https://github.com/rrwick/Unicycler 105s 105s Command: /usr/bin/unicycler -1 short_reads_1.fastq.gz -2 short_reads_2.fastq.gz -o illumina_assembly 105s 105s Unicycler version: v0.5.1 105s Using 2 threads 105s 105s Making output directory: 105s /tmp/autopkgtest.nZCH4X/autopkgtest_tmp/illumina_assembly 105s 105s Dependencies: 105s Program Version Status  105s spades 4.0.0 good 105s racon not used 105s makeblastdb 2.16.0+ good 105s tblastn 2.16.0+ good 106s 106s 106s Choosing k-mer range for assembly (2025-04-14 09:29:03) 106s Unicycler chooses a k-mer range for SPAdes based on the length of the input 106s reads. It uses a wide range of many k-mer sizes to maximise the chance of 106s finding an ideal assembly. 106s 106s SPAdes maximum k-mer: 127 106s Median read length: 125 106s K-mer range: 25, 49, 67, 81, 93, 103, 111, 119 106s 106s 106s SPAdes assemblies (2025-04-14 09:29:03) 106s Unicycler now uses SPAdes to assemble the short reads. It scores the 106s assembly graph for each k-mer using the number of contigs (fewer is better) and 106s the number of dead ends (fewer is better). The score function is 1/(c*(d+2)), 106s where c is the contig count and d is the dead end count. 106s 106s spades -o /tmp/autopkgtest.nZCH4X/autopkgtest_tmp/illumina_assembly/spades_assembly -k 25 --threads 2 --gfa11 --isolate -1 /tmp/autopkgtest.nZCH4X/autopkgtest_tmp/short_reads_1.fastq.gz -2 /tmp/autopkgtest.nZCH4X/autopkgtest_tmp/short_reads_2.fastq.gz -m 1024 107s Error: SPAdes encountered an error: 107s 107s autopkgtest [09:29:04]: test run-unit-test: -----------------------] 107s run-unit-test FAIL non-zero exit status 1 107s autopkgtest [09:29:04]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 108s autopkgtest [09:29:05]: @@@@@@@@@@@@@@@@@@@@ summary 108s run-unit-test FAIL non-zero exit status 1 125s nova [W] Skipping flock for amd64 125s Creating nova instance adt-plucky-amd64-unicycler-20250414-092717-juju-7f2275-prod-proposed-migration-environment-21-566ef017-b2d1-47d1-965f-8c063d6d0ac6 from image adt/ubuntu-plucky-amd64-server-20250413.img (UUID ce7bceb9-7fec-43e7-b671-8afcf6291286)... 125s nova [W] Timed out waiting for 58fb7925-effd-488e-8575-f7abf68c0537 to get deleted.