0s autopkgtest [09:49:32]: starting date and time: 2026-01-24 09:49:32+0000 0s autopkgtest [09:49:32]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [09:49:32]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.9md41iy2/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade iva --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.14.2-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-2.secgroup --name adt-resolute-amd64-iva-20260124-094932-juju-7f2275-prod-proposed-migration-environment-2-fd9f77df-4019-4b52-9c75-335725636357 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-amd64-iva-20260124-094932-juju-7f2275-prod-proposed-migration-environment-2-fd9f77df-4019-4b52-9c75-335725636357 from image adt/ubuntu-resolute-amd64-server-20260124.img (UUID 46811f22-3700-43f4-953b-ee3c613d71bb)... 79s autopkgtest [09:50:51]: testbed dpkg architecture: amd64 79s autopkgtest [09:50:51]: testbed apt version: 3.1.13 79s autopkgtest [09:50:51]: @@@@@@@@@@@@@@@@@@@@ test bed setup 79s autopkgtest [09:50:51]: testbed release detected to be: None 80s autopkgtest [09:50:52]: updating testbed package index (apt update) 80s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 80s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 80s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 80s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 80s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [2820 B] 80s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [91.6 kB] 80s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [24.3 kB] 80s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1021 kB] 80s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [115 kB] 80s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [98.2 kB] 80s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [3776 B] 80s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3696 B] 80s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [12.3 kB] 80s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [336 B] 81s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [928 kB] 81s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [389 kB] 81s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [25.1 kB] 81s Get:18 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [12.4 kB] 81s Get:19 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [4704 B] 81s Get:20 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [824 B] 81s Fetched 2858 kB in 1s (3870 kB/s) 82s Reading package lists... 82s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 82s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 82s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 82s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 83s Reading package lists... 83s Reading package lists... 83s Building dependency tree... 83s Reading state information... 83s Calculating upgrade... 83s The following packages were automatically installed and are no longer required: 83s python3.13 python3.13-minimal 83s Use 'sudo apt autoremove' to remove them. 83s The following NEW packages will be installed: 83s libpython3.14-minimal libpython3.14-stdlib python3.14 python3.14-minimal 83s The following packages will be upgraded: 83s libpython3-stdlib python3 python3-gdbm python3-minimal rust-coreutils 83s 5 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 83s Need to get 10.4 MB of archives. 83s After this operation, 25.2 MB of additional disk space will be used. 83s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-minimal amd64 3.14.2-1 [920 kB] 84s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14-minimal amd64 3.14.2-1 [2563 kB] 84s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-minimal amd64 3.14.2-1 [28.2 kB] 84s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3 amd64 3.14.2-1 [22.9 kB] 84s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.2-1 [2398 kB] 84s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14 amd64 3.14.2-1 [816 kB] 84s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libpython3-stdlib amd64 3.14.2-1 [10.9 kB] 84s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 rust-coreutils amd64 0.5.0-0ubuntu1 [3628 kB] 84s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-gdbm amd64 3.14.2-1 [11.1 kB] 84s dpkg-preconfigure: unable to re-open stdin: No such file or directory 84s Fetched 10.4 MB in 1s (20.5 MB/s) 84s Selecting previously unselected package libpython3.14-minimal:amd64. 84s (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 ... 124177 files and directories currently installed.) 84s Preparing to unpack .../libpython3.14-minimal_3.14.2-1_amd64.deb ... 84s Unpacking libpython3.14-minimal:amd64 (3.14.2-1) ... 84s Selecting previously unselected package python3.14-minimal. 84s Preparing to unpack .../python3.14-minimal_3.14.2-1_amd64.deb ... 84s Unpacking python3.14-minimal (3.14.2-1) ... 84s Setting up libpython3.14-minimal:amd64 (3.14.2-1) ... 84s Setting up python3.14-minimal (3.14.2-1) ... 85s (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 ... 124519 files and directories currently installed.) 85s Preparing to unpack .../python3-minimal_3.14.2-1_amd64.deb ... 85s Unpacking python3-minimal (3.14.2-1) over (3.13.9-3) ... 85s Setting up python3-minimal (3.14.2-1) ... 85s (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 ... 124519 files and directories currently installed.) 85s Preparing to unpack .../python3_3.14.2-1_amd64.deb ... 85s running python pre-rtupdate hooks for python3.14... 85s Unpacking python3 (3.14.2-1) over (3.13.9-3) ... 85s Selecting previously unselected package libpython3.14-stdlib:amd64. 85s Preparing to unpack .../libpython3.14-stdlib_3.14.2-1_amd64.deb ... 85s Unpacking libpython3.14-stdlib:amd64 (3.14.2-1) ... 85s Selecting previously unselected package python3.14. 85s Preparing to unpack .../python3.14_3.14.2-1_amd64.deb ... 85s Unpacking python3.14 (3.14.2-1) ... 85s Preparing to unpack .../libpython3-stdlib_3.14.2-1_amd64.deb ... 85s Unpacking libpython3-stdlib:amd64 (3.14.2-1) over (3.13.9-3) ... 85s Preparing to unpack .../rust-coreutils_0.5.0-0ubuntu1_amd64.deb ... 85s Unpacking rust-coreutils (0.5.0-0ubuntu1) over (0.2.2-0ubuntu2) ... 85s Setting up rust-coreutils (0.5.0-0ubuntu1) ... 86s (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 ... 124980 files and directories currently installed.) 86s Preparing to unpack .../python3-gdbm_3.14.2-1_amd64.deb ... 86s Unpacking python3-gdbm (3.14.2-1) over (3.13.9-3) ... 86s Setting up libpython3.14-stdlib:amd64 (3.14.2-1) ... 86s Setting up python3.14 (3.14.2-1) ... 86s Setting up libpython3-stdlib:amd64 (3.14.2-1) ... 86s Setting up python3-gdbm (3.14.2-1) ... 86s Setting up python3 (3.14.2-1) ... 86s running python rtupdate hooks for python3.14... 86s running python post-rtupdate hooks for python3.14... 86s Processing triggers for man-db (2.13.1-1) ... 87s Processing triggers for systemd (259-1ubuntu2) ... 87s autopkgtest [09:50:59]: upgrading testbed (apt dist-upgrade and autopurge) 87s Reading package lists... 87s Building dependency tree... 87s Reading state information... 87s Calculating upgrade... 87s The following packages were automatically installed and are no longer required: 87s python3.13 python3.13-minimal 87s Use 'sudo apt autoremove' to remove them. 87s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 87s Reading package lists... 87s Building dependency tree... 87s Reading state information... 88s Solving dependencies... 88s The following packages will be REMOVED: 88s python3.13* python3.13-minimal* 88s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 88s After this operation, 7860 kB disk space will be freed. 88s (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 ... 124978 files and directories currently installed.) 88s Removing python3.13 (3.13.11-1) ... 88s Removing python3.13-minimal (3.13.11-1) ... 88s Processing triggers for man-db (2.13.1-1) ... 89s Processing triggers for systemd (259-1ubuntu2) ... 89s (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 ... 124951 files and directories currently installed.) 89s Purging configuration files for python3.13-minimal (3.13.11-1) ... 91s autopkgtest [09:51:03]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:49:02 UTC 2026 91s autopkgtest [09:51:03]: @@@@@@@@@@@@@@@@@@@@ apt-source iva 92s Get:1 http://ftpmaster.internal/ubuntu resolute/universe iva 1.0.11+ds-6build1 (dsc) [2288 B] 92s Get:2 http://ftpmaster.internal/ubuntu resolute/universe iva 1.0.11+ds-6build1 (tar) [8681 kB] 92s Get:3 http://ftpmaster.internal/ubuntu resolute/universe iva 1.0.11+ds-6build1 (diff) [7308 B] 92s gpgv: Signature made Wed Jan 21 19:54:50 2026 UTC 92s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 92s gpgv: Can't check signature: No public key 92s dpkg-source: warning: cannot verify inline signature for ./iva_1.0.11+ds-6build1.dsc: no acceptable signature found 93s autopkgtest [09:51:05]: testing package iva version 1.0.11+ds-6build1 93s autopkgtest [09:51:05]: build not needed 93s autopkgtest [09:51:05]: test test-example: preparing testbed 93s Reading package lists... 94s Building dependency tree... 94s Reading state information... 94s Solving dependencies... 94s The following NEW packages will be installed: 94s adwaita-icon-theme at-spi2-common ca-certificates-java 94s dconf-gsettings-backend dconf-service default-jre default-jre-headless 94s fastaq fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 94s gtk-update-icon-cache hicolor-icon-theme iva java-common kmc libasound2-data 94s libasound2t64 libatk-bridge2.0-0t64 libatk1.0-0t64 libatspi2.0-0t64 94s libavahi-client3 libavahi-common-data libavahi-common3 libbambamc0 libblas3 94s libcairo-gobject2 libcairo2 libcolord2 libcups2t64 libdatrie1 libdconf1 94s libdeflate0 libdrm-intel1 libepoxy0 libfontconfig1 libgbm1 94s libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgif7 libgl1 94s libgl1-mesa-dri libglvnd0 libglx-mesa0 libglx0 libgraphite2-3 libgtk-3-0t64 94s libgtk-3-common libharfbuzz0b libhts3t64 libhtscodecs2 libjbig0 94s libjbzip2-java libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4 94s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpciaccess0 94s libpcsclite1 libpixman-1-0 libsharpyuv0 libthai-data libthai0 libtiff6 94s libvulkan1 libwayland-client0 libwayland-cursor0 libwayland-egl1 libwebp7 94s libx11-xcb1 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 94s libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcomposite1 94s libxcursor1 libxdamage1 libxfixes3 libxi6 libxinerama1 libxrandr2 94s libxrender1 libxshmfence1 libxtst6 libxxf86vm1 mesa-libgallium mummer 94s openjdk-21-jre openjdk-21-jre-headless python3-networkx python3-numpy 94s python3-numpy-dev python3-pysam samtools smalt trimmomatic x11-common 94s 0 upgraded, 107 newly installed, 0 to remove and 0 not upgraded. 94s Need to get 112 MB of archives. 94s After this operation, 511 MB of additional disk space will be used. 94s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.3.5+ds-3 [147 kB] 94s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7ubuntu1 [260 kB] 94s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-11ubuntu1 [939 kB] 94s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7ubuntu1 [2739 kB] 94s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.3.5+ds-3 [8129 kB] 94s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdk-pixbuf2.0-common all 2.44.4+dfsg-1 [8584 B] 94s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu2 [152 kB] 94s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 94s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 94s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu3 [30.0 kB] 94s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu2 [207 kB] 94s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1build1 [17.6 kB] 94s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1build1 [264 kB] 94s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB] 94s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdk-pixbuf-2.0-0 amd64 2.44.4+dfsg-1 [153 kB] 94s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 gtk-update-icon-cache amd64 4.20.3+ds-3 [54.9 kB] 94s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 hicolor-icon-theme all 0.18-2build1 [13.2 kB] 94s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 adwaita-icon-theme all 49.0-1 [581 kB] 94s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 at-spi2-common all 2.59.0-1 [9774 B] 94s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 ca-certificates-java all 20240118build1 [11.7 kB] 94s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libdconf1 amd64 0.49.0-4 [40.5 kB] 94s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 dconf-service amd64 0.49.0-4 [27.7 kB] 94s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 dconf-gsettings-backend amd64 0.49.0-4 [22.2 kB] 94s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 java-common all 0.76build1 [6956 B] 94s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 liblcms2-2 amd64 2.17-1 [170 kB] 94s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcsclite1 amd64 2.4.0-2 [24.3 kB] 94s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 openjdk-21-jre-headless amd64 21.0.10~6ea-1 [46.5 MB] 95s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 default-jre-headless amd64 2:1.21-76build1 [3266 B] 95s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libatk1.0-0t64 amd64 2.59.0-1 [57.1 kB] 95s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 libxi6 amd64 2:1.8.2-2 [33.1 kB] 95s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libatspi2.0-0t64 amd64 2.59.0-1 [85.7 kB] 95s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libatk-bridge2.0-0t64 amd64 2.59.0-1 [67.6 kB] 95s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8build1 [502 kB] 95s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8build1 [834 kB] 95s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.15.0-2.4ubuntu1 [38.1 kB] 95s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.15.0-2.4ubuntu1 [143 kB] 95s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.46.4-1 [287 kB] 95s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2build1 [17.4 kB] 95s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2build1 [6120 B] 95s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB] 95s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-3 [579 kB] 95s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo-gobject2 amd64 1.18.4-3 [127 kB] 95s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 libcolord2 amd64 1.4.8-2build1 [149 kB] 95s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 libavahi-common-data amd64 0.8-17ubuntu2 [31.5 kB] 95s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libavahi-common3 amd64 0.8-17ubuntu2 [23.7 kB] 95s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libavahi-client3 amd64 0.8-17ubuntu2 [27.3 kB] 95s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libcups2t64 amd64 2.4.16-1ubuntu1 [273 kB] 95s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libepoxy0 amd64 1.5.10-2build1 [226 kB] 95s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-11ubuntu1 [73.7 kB] 95s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.3.0-4 [529 kB] 95s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig amd64 2.15.0-2.4ubuntu1 [178 kB] 95s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai-data all 0.1.30-1 [155 kB] 95s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libdatrie1 amd64 0.2.14-1 [19.8 kB] 95s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai0 amd64 0.1.30-1 [19.2 kB] 95s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libpango-1.0-0 amd64 1.56.4-1 [240 kB] 95s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangoft2-1.0-0 amd64 1.56.4-1 [53.2 kB] 95s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangocairo-1.0-0 amd64 1.56.4-1 [29.0 kB] 95s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 libwayland-client0 amd64 1.24.0-2 [28.5 kB] 95s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 libwayland-cursor0 amd64 1.24.0-2 [10.8 kB] 95s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 libwayland-egl1 amd64 1.24.0-2 [6248 B] 95s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcomposite1 amd64 1:0.4.6-1build1 [6664 B] 95s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 libxfixes3 amd64 1:6.0.0-2build2 [11.1 kB] 95s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcursor1 amd64 1:1.2.3-1build1 [22.1 kB] 95s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 libxdamage1 amd64 1:1.1.6-1build2 [6398 B] 95s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 libxinerama1 amd64 2:1.1.4-3build2 [6472 B] 95s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrandr2 amd64 2:1.5.4-1build1 [19.6 kB] 95s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 libgtk-3-common all 3.24.50-1ubuntu2 [1425 kB] 95s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 libgtk-3-0t64 amd64 3.24.50-1ubuntu2 [3263 kB] 95s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 libglvnd0 amd64 1.7.0-3 [64.1 kB] 95s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 libx11-xcb1 amd64 2:1.8.12-1build1 [8044 B] 95s Get:71 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-dri3-0 amd64 1.17.0-2build1 [8036 B] 95s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-glx0 amd64 1.17.0-2build1 [27.6 kB] 95s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-present0 amd64 1.17.0-2build1 [6446 B] 95s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-xfixes0 amd64 1.17.0-2build1 [11.1 kB] 95s Get:75 http://ftpmaster.internal/ubuntu resolute/main amd64 libxxf86vm1 amd64 1:1.1.4-2 [10.6 kB] 95s Get:76 http://ftpmaster.internal/ubuntu resolute/main amd64 libpciaccess0 amd64 0.18.1-1ubuntu2 [19.0 kB] 95s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-intel1 amd64 2.4.129-1 [66.7 kB] 95s Get:78 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-randr0 amd64 1.17.0-2build1 [19.7 kB] 95s Get:79 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-sync1 amd64 1.17.0-2build1 [10.1 kB] 95s Get:80 http://ftpmaster.internal/ubuntu resolute/main amd64 libxshmfence1 amd64 1.3.3-1 [5262 B] 95s Get:81 http://ftpmaster.internal/ubuntu resolute/main amd64 mesa-libgallium amd64 25.2.8-2ubuntu1 [11.1 MB] 95s Get:82 http://ftpmaster.internal/ubuntu resolute/main amd64 libgbm1 amd64 25.2.8-2ubuntu1 [34.0 kB] 95s Get:83 http://ftpmaster.internal/ubuntu resolute/main amd64 libvulkan1 amd64 1.4.335.0-1 [158 kB] 95s Get:84 http://ftpmaster.internal/ubuntu resolute/main amd64 libgl1-mesa-dri amd64 25.2.8-2ubuntu1 [36.9 kB] 95s Get:85 http://ftpmaster.internal/ubuntu resolute/main amd64 libglx-mesa0 amd64 25.2.8-2ubuntu1 [110 kB] 95s Get:86 http://ftpmaster.internal/ubuntu resolute/main amd64 libglx0 amd64 1.7.0-3 [38.9 kB] 95s Get:87 http://ftpmaster.internal/ubuntu resolute/main amd64 libgl1 amd64 1.7.0-3 [98.3 kB] 95s Get:88 http://ftpmaster.internal/ubuntu resolute/main amd64 libasound2-data all 1.2.15.1-1 [21.2 kB] 95s Get:89 http://ftpmaster.internal/ubuntu resolute/main amd64 libasound2t64 amd64 1.2.15.1-1 [418 kB] 95s Get:90 http://ftpmaster.internal/ubuntu resolute/main amd64 libgif7 amd64 5.2.2-1ubuntu3 [36.0 kB] 95s Get:91 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 95s Get:92 http://ftpmaster.internal/ubuntu resolute/main amd64 libxtst6 amd64 2:1.2.5-1build1 [13.1 kB] 95s Get:93 http://ftpmaster.internal/ubuntu resolute/main amd64 openjdk-21-jre amd64 21.0.10~6ea-1 [226 kB] 95s Get:94 http://ftpmaster.internal/ubuntu resolute/main amd64 default-jre amd64 2:1.21-76build1 [922 B] 95s Get:95 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhtscodecs2 amd64 1.6.1-2build1 [108 kB] 95s Get:96 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhts3t64 amd64 1.22.1+ds2-1 [461 kB] 95s Get:97 http://ftpmaster.internal/ubuntu resolute/universe amd64 samtools amd64 1.22.1-1 [645 kB] 95s Get:98 http://ftpmaster.internal/ubuntu resolute/universe amd64 fastaq all 3.17.0-9build1 [48.4 kB] 95s Get:99 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-networkx all 3.2.1-4ubuntu2 [11.8 MB] 96s Get:100 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pysam amd64 0.23.3+ds-2 [4536 kB] 96s Get:101 http://ftpmaster.internal/ubuntu resolute/universe amd64 kmc amd64 3.2.4+dfsg-1build1 [1131 kB] 96s Get:102 http://ftpmaster.internal/ubuntu resolute/universe amd64 mummer amd64 3.23+dfsg-8build1 [690 kB] 96s Get:103 http://ftpmaster.internal/ubuntu resolute/universe amd64 libbambamc0 amd64 0.0.50-7 [40.6 kB] 96s Get:104 http://ftpmaster.internal/ubuntu resolute/universe amd64 smalt amd64 0.7.6-13 [101 kB] 96s Get:105 http://ftpmaster.internal/ubuntu resolute/universe amd64 iva amd64 1.0.11+ds-6build1 [8583 kB] 96s Get:106 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjbzip2-java all 0.9.1-8 [42.4 kB] 96s Get:107 http://ftpmaster.internal/ubuntu resolute/universe amd64 trimmomatic all 0.39+dfsg-2build1 [754 kB] 97s Fetched 112 MB in 3s (43.5 MB/s) 97s Selecting previously unselected package python3-numpy-dev:amd64. 97s (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 ... 124953 files and directories currently installed.) 97s Preparing to unpack .../000-python3-numpy-dev_1%3a2.3.5+ds-3_amd64.deb ... 97s Unpacking python3-numpy-dev:amd64 (1:2.3.5+ds-3) ... 97s Selecting previously unselected package libblas3:amd64. 97s Preparing to unpack .../001-libblas3_3.12.1-7ubuntu1_amd64.deb ... 97s Unpacking libblas3:amd64 (3.12.1-7ubuntu1) ... 97s Selecting previously unselected package libgfortran5:amd64. 97s Preparing to unpack .../002-libgfortran5_15.2.0-11ubuntu1_amd64.deb ... 97s Unpacking libgfortran5:amd64 (15.2.0-11ubuntu1) ... 97s Selecting previously unselected package liblapack3:amd64. 97s Preparing to unpack .../003-liblapack3_3.12.1-7ubuntu1_amd64.deb ... 97s Unpacking liblapack3:amd64 (3.12.1-7ubuntu1) ... 97s Selecting previously unselected package python3-numpy. 97s Preparing to unpack .../004-python3-numpy_1%3a2.3.5+ds-3_amd64.deb ... 97s Unpacking python3-numpy (1:2.3.5+ds-3) ... 97s Selecting previously unselected package libgdk-pixbuf2.0-common. 97s Preparing to unpack .../005-libgdk-pixbuf2.0-common_2.44.4+dfsg-1_all.deb ... 97s Unpacking libgdk-pixbuf2.0-common (2.44.4+dfsg-1) ... 97s Selecting previously unselected package libjpeg-turbo8:amd64. 97s Preparing to unpack .../006-libjpeg-turbo8_2.1.5-4ubuntu2_amd64.deb ... 97s Unpacking libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 97s Selecting previously unselected package libjpeg8:amd64. 97s Preparing to unpack .../007-libjpeg8_8c-2ubuntu11_amd64.deb ... 97s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 97s Selecting previously unselected package libdeflate0:amd64. 97s Preparing to unpack .../008-libdeflate0_1.23-2_amd64.deb ... 97s Unpacking libdeflate0:amd64 (1.23-2) ... 97s Selecting previously unselected package libjbig0:amd64. 97s Preparing to unpack .../009-libjbig0_2.1-6.1ubuntu3_amd64.deb ... 97s Unpacking libjbig0:amd64 (2.1-6.1ubuntu3) ... 97s Selecting previously unselected package liblerc4:amd64. 97s Preparing to unpack .../010-liblerc4_4.0.0+ds-5ubuntu2_amd64.deb ... 97s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu2) ... 97s Selecting previously unselected package libsharpyuv0:amd64. 97s Preparing to unpack .../011-libsharpyuv0_1.5.0-0.1build1_amd64.deb ... 97s Unpacking libsharpyuv0:amd64 (1.5.0-0.1build1) ... 97s Selecting previously unselected package libwebp7:amd64. 97s Preparing to unpack .../012-libwebp7_1.5.0-0.1build1_amd64.deb ... 97s Unpacking libwebp7:amd64 (1.5.0-0.1build1) ... 97s Selecting previously unselected package libtiff6:amd64. 97s Preparing to unpack .../013-libtiff6_4.7.0-3ubuntu3_amd64.deb ... 97s Unpacking libtiff6:amd64 (4.7.0-3ubuntu3) ... 97s Selecting previously unselected package libgdk-pixbuf-2.0-0:amd64. 97s Preparing to unpack .../014-libgdk-pixbuf-2.0-0_2.44.4+dfsg-1_amd64.deb ... 97s Unpacking libgdk-pixbuf-2.0-0:amd64 (2.44.4+dfsg-1) ... 97s Selecting previously unselected package gtk-update-icon-cache. 97s Preparing to unpack .../015-gtk-update-icon-cache_4.20.3+ds-3_amd64.deb ... 97s No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed. 97s 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. 97s Unpacking gtk-update-icon-cache (4.20.3+ds-3) ... 97s Selecting previously unselected package hicolor-icon-theme. 97s Preparing to unpack .../016-hicolor-icon-theme_0.18-2build1_all.deb ... 97s Unpacking hicolor-icon-theme (0.18-2build1) ... 97s Selecting previously unselected package adwaita-icon-theme. 97s Preparing to unpack .../017-adwaita-icon-theme_49.0-1_all.deb ... 97s Unpacking adwaita-icon-theme (49.0-1) ... 97s Selecting previously unselected package at-spi2-common. 97s Preparing to unpack .../018-at-spi2-common_2.59.0-1_all.deb ... 97s Unpacking at-spi2-common (2.59.0-1) ... 97s Selecting previously unselected package ca-certificates-java. 97s Preparing to unpack .../019-ca-certificates-java_20240118build1_all.deb ... 97s Unpacking ca-certificates-java (20240118build1) ... 97s Selecting previously unselected package libdconf1:amd64. 97s Preparing to unpack .../020-libdconf1_0.49.0-4_amd64.deb ... 97s Unpacking libdconf1:amd64 (0.49.0-4) ... 97s Selecting previously unselected package dconf-service. 97s Preparing to unpack .../021-dconf-service_0.49.0-4_amd64.deb ... 97s Unpacking dconf-service (0.49.0-4) ... 97s Selecting previously unselected package dconf-gsettings-backend:amd64. 97s Preparing to unpack .../022-dconf-gsettings-backend_0.49.0-4_amd64.deb ... 97s Unpacking dconf-gsettings-backend:amd64 (0.49.0-4) ... 97s Selecting previously unselected package java-common. 97s Preparing to unpack .../023-java-common_0.76build1_all.deb ... 97s Unpacking java-common (0.76build1) ... 97s Selecting previously unselected package liblcms2-2:amd64. 97s Preparing to unpack .../024-liblcms2-2_2.17-1_amd64.deb ... 97s Unpacking liblcms2-2:amd64 (2.17-1) ... 97s Selecting previously unselected package libpcsclite1:amd64. 97s Preparing to unpack .../025-libpcsclite1_2.4.0-2_amd64.deb ... 97s Unpacking libpcsclite1:amd64 (2.4.0-2) ... 97s Selecting previously unselected package openjdk-21-jre-headless:amd64. 97s Preparing to unpack .../026-openjdk-21-jre-headless_21.0.10~6ea-1_amd64.deb ... 97s Unpacking openjdk-21-jre-headless:amd64 (21.0.10~6ea-1) ... 98s Selecting previously unselected package default-jre-headless. 98s Preparing to unpack .../027-default-jre-headless_2%3a1.21-76build1_amd64.deb ... 98s Unpacking default-jre-headless (2:1.21-76build1) ... 98s Selecting previously unselected package libatk1.0-0t64:amd64. 98s Preparing to unpack .../028-libatk1.0-0t64_2.59.0-1_amd64.deb ... 98s Unpacking libatk1.0-0t64:amd64 (2.59.0-1) ... 98s Selecting previously unselected package libxi6:amd64. 98s Preparing to unpack .../029-libxi6_2%3a1.8.2-2_amd64.deb ... 98s Unpacking libxi6:amd64 (2:1.8.2-2) ... 98s Selecting previously unselected package libatspi2.0-0t64:amd64. 98s Preparing to unpack .../030-libatspi2.0-0t64_2.59.0-1_amd64.deb ... 98s Unpacking libatspi2.0-0t64:amd64 (2.59.0-1) ... 98s Selecting previously unselected package libatk-bridge2.0-0t64:amd64. 98s Preparing to unpack .../031-libatk-bridge2.0-0t64_2.59.0-1_amd64.deb ... 98s Unpacking libatk-bridge2.0-0t64:amd64 (2.59.0-1) ... 98s Selecting previously unselected package fonts-dejavu-mono. 98s Preparing to unpack .../032-fonts-dejavu-mono_2.37-8build1_all.deb ... 98s Unpacking fonts-dejavu-mono (2.37-8build1) ... 98s Selecting previously unselected package fonts-dejavu-core. 98s Preparing to unpack .../033-fonts-dejavu-core_2.37-8build1_all.deb ... 98s Unpacking fonts-dejavu-core (2.37-8build1) ... 98s Selecting previously unselected package fontconfig-config. 98s Preparing to unpack .../034-fontconfig-config_2.15.0-2.4ubuntu1_amd64.deb ... 98s Unpacking fontconfig-config (2.15.0-2.4ubuntu1) ... 98s Selecting previously unselected package libfontconfig1:amd64. 98s Preparing to unpack .../035-libfontconfig1_2.15.0-2.4ubuntu1_amd64.deb ... 98s Unpacking libfontconfig1:amd64 (2.15.0-2.4ubuntu1) ... 98s Selecting previously unselected package libpixman-1-0:amd64. 98s Preparing to unpack .../036-libpixman-1-0_0.46.4-1_amd64.deb ... 98s Unpacking libpixman-1-0:amd64 (0.46.4-1) ... 98s Selecting previously unselected package libxcb-render0:amd64. 98s Preparing to unpack .../037-libxcb-render0_1.17.0-2build1_amd64.deb ... 98s Unpacking libxcb-render0:amd64 (1.17.0-2build1) ... 98s Selecting previously unselected package libxcb-shm0:amd64. 98s Preparing to unpack .../038-libxcb-shm0_1.17.0-2build1_amd64.deb ... 98s Unpacking libxcb-shm0:amd64 (1.17.0-2build1) ... 98s Selecting previously unselected package libxrender1:amd64. 98s Preparing to unpack .../039-libxrender1_1%3a0.9.12-1_amd64.deb ... 98s Unpacking libxrender1:amd64 (1:0.9.12-1) ... 98s Selecting previously unselected package libcairo2:amd64. 98s Preparing to unpack .../040-libcairo2_1.18.4-3_amd64.deb ... 98s Unpacking libcairo2:amd64 (1.18.4-3) ... 98s Selecting previously unselected package libcairo-gobject2:amd64. 98s Preparing to unpack .../041-libcairo-gobject2_1.18.4-3_amd64.deb ... 98s Unpacking libcairo-gobject2:amd64 (1.18.4-3) ... 98s Selecting previously unselected package libcolord2:amd64. 98s Preparing to unpack .../042-libcolord2_1.4.8-2build1_amd64.deb ... 98s Unpacking libcolord2:amd64 (1.4.8-2build1) ... 98s Selecting previously unselected package libavahi-common-data:amd64. 98s Preparing to unpack .../043-libavahi-common-data_0.8-17ubuntu2_amd64.deb ... 98s Unpacking libavahi-common-data:amd64 (0.8-17ubuntu2) ... 98s Selecting previously unselected package libavahi-common3:amd64. 98s Preparing to unpack .../044-libavahi-common3_0.8-17ubuntu2_amd64.deb ... 98s Unpacking libavahi-common3:amd64 (0.8-17ubuntu2) ... 98s Selecting previously unselected package libavahi-client3:amd64. 98s Preparing to unpack .../045-libavahi-client3_0.8-17ubuntu2_amd64.deb ... 98s Unpacking libavahi-client3:amd64 (0.8-17ubuntu2) ... 98s Selecting previously unselected package libcups2t64:amd64. 98s Preparing to unpack .../046-libcups2t64_2.4.16-1ubuntu1_amd64.deb ... 98s Unpacking libcups2t64:amd64 (2.4.16-1ubuntu1) ... 98s Selecting previously unselected package libepoxy0:amd64. 98s Preparing to unpack .../047-libepoxy0_1.5.10-2build1_amd64.deb ... 98s Unpacking libepoxy0:amd64 (1.5.10-2build1) ... 98s Selecting previously unselected package libgraphite2-3:amd64. 98s Preparing to unpack .../048-libgraphite2-3_1.3.14-11ubuntu1_amd64.deb ... 98s Unpacking libgraphite2-3:amd64 (1.3.14-11ubuntu1) ... 98s Selecting previously unselected package libharfbuzz0b:amd64. 98s Preparing to unpack .../049-libharfbuzz0b_12.3.0-4_amd64.deb ... 98s Unpacking libharfbuzz0b:amd64 (12.3.0-4) ... 98s Selecting previously unselected package fontconfig. 98s Preparing to unpack .../050-fontconfig_2.15.0-2.4ubuntu1_amd64.deb ... 98s Unpacking fontconfig (2.15.0-2.4ubuntu1) ... 98s Selecting previously unselected package libthai-data. 98s Preparing to unpack .../051-libthai-data_0.1.30-1_all.deb ... 98s Unpacking libthai-data (0.1.30-1) ... 98s Selecting previously unselected package libdatrie1:amd64. 98s Preparing to unpack .../052-libdatrie1_0.2.14-1_amd64.deb ... 98s Unpacking libdatrie1:amd64 (0.2.14-1) ... 98s Selecting previously unselected package libthai0:amd64. 98s Preparing to unpack .../053-libthai0_0.1.30-1_amd64.deb ... 98s Unpacking libthai0:amd64 (0.1.30-1) ... 98s Selecting previously unselected package libpango-1.0-0:amd64. 98s Preparing to unpack .../054-libpango-1.0-0_1.56.4-1_amd64.deb ... 98s Unpacking libpango-1.0-0:amd64 (1.56.4-1) ... 98s Selecting previously unselected package libpangoft2-1.0-0:amd64. 98s Preparing to unpack .../055-libpangoft2-1.0-0_1.56.4-1_amd64.deb ... 98s Unpacking libpangoft2-1.0-0:amd64 (1.56.4-1) ... 98s Selecting previously unselected package libpangocairo-1.0-0:amd64. 98s Preparing to unpack .../056-libpangocairo-1.0-0_1.56.4-1_amd64.deb ... 98s Unpacking libpangocairo-1.0-0:amd64 (1.56.4-1) ... 98s Selecting previously unselected package libwayland-client0:amd64. 98s Preparing to unpack .../057-libwayland-client0_1.24.0-2_amd64.deb ... 98s Unpacking libwayland-client0:amd64 (1.24.0-2) ... 98s Selecting previously unselected package libwayland-cursor0:amd64. 98s Preparing to unpack .../058-libwayland-cursor0_1.24.0-2_amd64.deb ... 98s Unpacking libwayland-cursor0:amd64 (1.24.0-2) ... 98s Selecting previously unselected package libwayland-egl1:amd64. 98s Preparing to unpack .../059-libwayland-egl1_1.24.0-2_amd64.deb ... 98s Unpacking libwayland-egl1:amd64 (1.24.0-2) ... 98s Selecting previously unselected package libxcomposite1:amd64. 98s Preparing to unpack .../060-libxcomposite1_1%3a0.4.6-1build1_amd64.deb ... 98s Unpacking libxcomposite1:amd64 (1:0.4.6-1build1) ... 98s Selecting previously unselected package libxfixes3:amd64. 98s Preparing to unpack .../061-libxfixes3_1%3a6.0.0-2build2_amd64.deb ... 98s Unpacking libxfixes3:amd64 (1:6.0.0-2build2) ... 98s Selecting previously unselected package libxcursor1:amd64. 98s Preparing to unpack .../062-libxcursor1_1%3a1.2.3-1build1_amd64.deb ... 98s Unpacking libxcursor1:amd64 (1:1.2.3-1build1) ... 98s Selecting previously unselected package libxdamage1:amd64. 98s Preparing to unpack .../063-libxdamage1_1%3a1.1.6-1build2_amd64.deb ... 98s Unpacking libxdamage1:amd64 (1:1.1.6-1build2) ... 98s Selecting previously unselected package libxinerama1:amd64. 98s Preparing to unpack .../064-libxinerama1_2%3a1.1.4-3build2_amd64.deb ... 98s Unpacking libxinerama1:amd64 (2:1.1.4-3build2) ... 98s Selecting previously unselected package libxrandr2:amd64. 98s Preparing to unpack .../065-libxrandr2_2%3a1.5.4-1build1_amd64.deb ... 98s Unpacking libxrandr2:amd64 (2:1.5.4-1build1) ... 98s Selecting previously unselected package libgtk-3-common. 98s Preparing to unpack .../066-libgtk-3-common_3.24.50-1ubuntu2_all.deb ... 98s Unpacking libgtk-3-common (3.24.50-1ubuntu2) ... 98s Selecting previously unselected package libgtk-3-0t64:amd64. 98s Preparing to unpack .../067-libgtk-3-0t64_3.24.50-1ubuntu2_amd64.deb ... 98s Unpacking libgtk-3-0t64:amd64 (3.24.50-1ubuntu2) ... 98s Selecting previously unselected package libglvnd0:amd64. 99s Preparing to unpack .../068-libglvnd0_1.7.0-3_amd64.deb ... 99s Unpacking libglvnd0:amd64 (1.7.0-3) ... 99s Selecting previously unselected package libx11-xcb1:amd64. 99s Preparing to unpack .../069-libx11-xcb1_2%3a1.8.12-1build1_amd64.deb ... 99s Unpacking libx11-xcb1:amd64 (2:1.8.12-1build1) ... 99s Selecting previously unselected package libxcb-dri3-0:amd64. 99s Preparing to unpack .../070-libxcb-dri3-0_1.17.0-2build1_amd64.deb ... 99s Unpacking libxcb-dri3-0:amd64 (1.17.0-2build1) ... 99s Selecting previously unselected package libxcb-glx0:amd64. 99s Preparing to unpack .../071-libxcb-glx0_1.17.0-2build1_amd64.deb ... 99s Unpacking libxcb-glx0:amd64 (1.17.0-2build1) ... 99s Selecting previously unselected package libxcb-present0:amd64. 99s Preparing to unpack .../072-libxcb-present0_1.17.0-2build1_amd64.deb ... 99s Unpacking libxcb-present0:amd64 (1.17.0-2build1) ... 99s Selecting previously unselected package libxcb-xfixes0:amd64. 99s Preparing to unpack .../073-libxcb-xfixes0_1.17.0-2build1_amd64.deb ... 99s Unpacking libxcb-xfixes0:amd64 (1.17.0-2build1) ... 99s Selecting previously unselected package libxxf86vm1:amd64. 99s Preparing to unpack .../074-libxxf86vm1_1%3a1.1.4-2_amd64.deb ... 99s Unpacking libxxf86vm1:amd64 (1:1.1.4-2) ... 99s Selecting previously unselected package libpciaccess0:amd64. 99s Preparing to unpack .../075-libpciaccess0_0.18.1-1ubuntu2_amd64.deb ... 99s Unpacking libpciaccess0:amd64 (0.18.1-1ubuntu2) ... 99s Selecting previously unselected package libdrm-intel1:amd64. 99s Preparing to unpack .../076-libdrm-intel1_2.4.129-1_amd64.deb ... 99s Unpacking libdrm-intel1:amd64 (2.4.129-1) ... 99s Selecting previously unselected package libxcb-randr0:amd64. 99s Preparing to unpack .../077-libxcb-randr0_1.17.0-2build1_amd64.deb ... 99s Unpacking libxcb-randr0:amd64 (1.17.0-2build1) ... 99s Selecting previously unselected package libxcb-sync1:amd64. 99s Preparing to unpack .../078-libxcb-sync1_1.17.0-2build1_amd64.deb ... 99s Unpacking libxcb-sync1:amd64 (1.17.0-2build1) ... 99s Selecting previously unselected package libxshmfence1:amd64. 99s Preparing to unpack .../079-libxshmfence1_1.3.3-1_amd64.deb ... 99s Unpacking libxshmfence1:amd64 (1.3.3-1) ... 99s Selecting previously unselected package mesa-libgallium:amd64. 99s Preparing to unpack .../080-mesa-libgallium_25.2.8-2ubuntu1_amd64.deb ... 99s Unpacking mesa-libgallium:amd64 (25.2.8-2ubuntu1) ... 99s Selecting previously unselected package libgbm1:amd64. 99s Preparing to unpack .../081-libgbm1_25.2.8-2ubuntu1_amd64.deb ... 99s Unpacking libgbm1:amd64 (25.2.8-2ubuntu1) ... 99s Selecting previously unselected package libvulkan1:amd64. 99s Preparing to unpack .../082-libvulkan1_1.4.335.0-1_amd64.deb ... 99s Unpacking libvulkan1:amd64 (1.4.335.0-1) ... 99s Selecting previously unselected package libgl1-mesa-dri:amd64. 99s Preparing to unpack .../083-libgl1-mesa-dri_25.2.8-2ubuntu1_amd64.deb ... 99s Unpacking libgl1-mesa-dri:amd64 (25.2.8-2ubuntu1) ... 99s Selecting previously unselected package libglx-mesa0:amd64. 99s Preparing to unpack .../084-libglx-mesa0_25.2.8-2ubuntu1_amd64.deb ... 99s Unpacking libglx-mesa0:amd64 (25.2.8-2ubuntu1) ... 99s Selecting previously unselected package libglx0:amd64. 99s Preparing to unpack .../085-libglx0_1.7.0-3_amd64.deb ... 99s Unpacking libglx0:amd64 (1.7.0-3) ... 99s Selecting previously unselected package libgl1:amd64. 99s Preparing to unpack .../086-libgl1_1.7.0-3_amd64.deb ... 99s Unpacking libgl1:amd64 (1.7.0-3) ... 99s Selecting previously unselected package libasound2-data. 99s Preparing to unpack .../087-libasound2-data_1.2.15.1-1_all.deb ... 99s Unpacking libasound2-data (1.2.15.1-1) ... 99s Selecting previously unselected package libasound2t64:amd64. 99s Preparing to unpack .../088-libasound2t64_1.2.15.1-1_amd64.deb ... 99s Unpacking libasound2t64:amd64 (1.2.15.1-1) ... 99s Selecting previously unselected package libgif7:amd64. 99s Preparing to unpack .../089-libgif7_5.2.2-1ubuntu3_amd64.deb ... 99s Unpacking libgif7:amd64 (5.2.2-1ubuntu3) ... 99s Selecting previously unselected package x11-common. 99s Preparing to unpack .../090-x11-common_1%3a7.7+24ubuntu1_all.deb ... 99s Unpacking x11-common (1:7.7+24ubuntu1) ... 99s Selecting previously unselected package libxtst6:amd64. 99s Preparing to unpack .../091-libxtst6_2%3a1.2.5-1build1_amd64.deb ... 99s Unpacking libxtst6:amd64 (2:1.2.5-1build1) ... 99s Selecting previously unselected package openjdk-21-jre:amd64. 99s Preparing to unpack .../092-openjdk-21-jre_21.0.10~6ea-1_amd64.deb ... 99s Unpacking openjdk-21-jre:amd64 (21.0.10~6ea-1) ... 99s Selecting previously unselected package default-jre. 99s Preparing to unpack .../093-default-jre_2%3a1.21-76build1_amd64.deb ... 99s Unpacking default-jre (2:1.21-76build1) ... 99s Selecting previously unselected package libhtscodecs2:amd64. 99s Preparing to unpack .../094-libhtscodecs2_1.6.1-2build1_amd64.deb ... 99s Unpacking libhtscodecs2:amd64 (1.6.1-2build1) ... 99s Selecting previously unselected package libhts3t64:amd64. 99s Preparing to unpack .../095-libhts3t64_1.22.1+ds2-1_amd64.deb ... 99s Unpacking libhts3t64:amd64 (1.22.1+ds2-1) ... 99s Selecting previously unselected package samtools. 99s Preparing to unpack .../096-samtools_1.22.1-1_amd64.deb ... 99s Unpacking samtools (1.22.1-1) ... 99s Selecting previously unselected package fastaq. 99s Preparing to unpack .../097-fastaq_3.17.0-9build1_all.deb ... 99s Unpacking fastaq (3.17.0-9build1) ... 99s Selecting previously unselected package python3-networkx. 99s Preparing to unpack .../098-python3-networkx_3.2.1-4ubuntu2_all.deb ... 99s Unpacking python3-networkx (3.2.1-4ubuntu2) ... 99s Selecting previously unselected package python3-pysam. 99s Preparing to unpack .../099-python3-pysam_0.23.3+ds-2_amd64.deb ... 99s Unpacking python3-pysam (0.23.3+ds-2) ... 99s Selecting previously unselected package kmc. 99s Preparing to unpack .../100-kmc_3.2.4+dfsg-1build1_amd64.deb ... 99s Unpacking kmc (3.2.4+dfsg-1build1) ... 99s Selecting previously unselected package mummer. 99s Preparing to unpack .../101-mummer_3.23+dfsg-8build1_amd64.deb ... 99s Unpacking mummer (3.23+dfsg-8build1) ... 100s Selecting previously unselected package libbambamc0:amd64. 100s Preparing to unpack .../102-libbambamc0_0.0.50-7_amd64.deb ... 100s Unpacking libbambamc0:amd64 (0.0.50-7) ... 100s Selecting previously unselected package smalt. 100s Preparing to unpack .../103-smalt_0.7.6-13_amd64.deb ... 100s Unpacking smalt (0.7.6-13) ... 100s Selecting previously unselected package iva. 100s Preparing to unpack .../104-iva_1.0.11+ds-6build1_amd64.deb ... 100s Unpacking iva (1.0.11+ds-6build1) ... 100s Selecting previously unselected package libjbzip2-java. 100s Preparing to unpack .../105-libjbzip2-java_0.9.1-8_all.deb ... 100s Unpacking libjbzip2-java (0.9.1-8) ... 100s Selecting previously unselected package trimmomatic. 100s Preparing to unpack .../106-trimmomatic_0.39+dfsg-2build1_all.deb ... 100s Unpacking trimmomatic (0.39+dfsg-2build1) ... 100s Setting up libhtscodecs2:amd64 (1.6.1-2build1) ... 100s Setting up libgraphite2-3:amd64 (1.3.14-11ubuntu1) ... 100s Setting up libxcb-dri3-0:amd64 (1.17.0-2build1) ... 100s Setting up liblcms2-2:amd64 (2.17-1) ... 100s Setting up libpixman-1-0:amd64 (0.46.4-1) ... 100s Setting up libsharpyuv0:amd64 (1.5.0-0.1build1) ... 100s Setting up libx11-xcb1:amd64 (2:1.8.12-1build1) ... 100s Setting up libpciaccess0:amd64 (0.18.1-1ubuntu2) ... 100s Setting up libxdamage1:amd64 (1:1.1.6-1build2) ... 100s Setting up libxcb-xfixes0:amd64 (1.17.0-2build1) ... 100s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu2) ... 100s Setting up hicolor-icon-theme (0.18-2build1) ... 100s Setting up libxi6:amd64 (2:1.8.2-2) ... 100s Setting up java-common (0.76build1) ... 100s Setting up libxrender1:amd64 (1:0.9.12-1) ... 100s Setting up libdatrie1:amd64 (0.2.14-1) ... 100s Setting up libxcb-render0:amd64 (1.17.0-2build1) ... 100s Setting up libglvnd0:amd64 (1.7.0-3) ... 100s Setting up libxcb-glx0:amd64 (1.17.0-2build1) ... 100s Setting up libdrm-intel1:amd64 (2.4.129-1) ... 100s Setting up libgdk-pixbuf2.0-common (2.44.4+dfsg-1) ... 100s Setting up x11-common (1:7.7+24ubuntu1) ... 100s Setting up libdeflate0:amd64 (1.23-2) ... 100s Setting up libxcb-shm0:amd64 (1.17.0-2build1) ... 100s Setting up python3-networkx (3.2.1-4ubuntu2) ... 101s Setting up libjbig0:amd64 (2.1-6.1ubuntu3) ... 101s Setting up libcolord2:amd64 (1.4.8-2build1) ... 101s Setting up libxxf86vm1:amd64 (1:1.1.4-2) ... 101s Setting up libxcb-present0:amd64 (1.17.0-2build1) ... 101s Setting up libdconf1:amd64 (0.49.0-4) ... 101s Setting up libasound2-data (1.2.15.1-1) ... 101s Setting up libblas3:amd64 (3.12.1-7ubuntu1) ... 101s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 101s Setting up libasound2t64:amd64 (1.2.15.1-1) ... 101s Setting up libepoxy0:amd64 (1.5.10-2build1) ... 101s Setting up libxfixes3:amd64 (1:6.0.0-2build2) ... 101s Setting up libxcb-sync1:amd64 (1.17.0-2build1) ... 101s Setting up libavahi-common-data:amd64 (0.8-17ubuntu2) ... 101s Setting up libatspi2.0-0t64:amd64 (2.59.0-1) ... 101s Setting up libxinerama1:amd64 (2:1.1.4-3build2) ... 101s Setting up libbambamc0:amd64 (0.0.50-7) ... 101s Setting up fonts-dejavu-mono (2.37-8build1) ... 101s Setting up python3-numpy-dev:amd64 (1:2.3.5+ds-3) ... 101s Setting up libxrandr2:amd64 (2:1.5.4-1build1) ... 101s Setting up fonts-dejavu-core (2.37-8build1) ... 101s Setting up libjbzip2-java (0.9.1-8) ... 101s Setting up libpcsclite1:amd64 (2.4.0-2) ... 101s Setting up libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 101s Setting up libgfortran5:amd64 (15.2.0-11ubuntu1) ... 101s Setting up libvulkan1:amd64 (1.4.335.0-1) ... 101s Setting up libwebp7:amd64 (1.5.0-0.1build1) ... 101s Setting up libgif7:amd64 (5.2.2-1ubuntu3) ... 101s Setting up libxshmfence1:amd64 (1.3.3-1) ... 101s Setting up at-spi2-common (2.59.0-1) ... 101s Setting up libxcb-randr0:amd64 (1.17.0-2build1) ... 101s Setting up mummer (3.23+dfsg-8build1) ... 101s Setting up libhts3t64:amd64 (1.22.1+ds2-1) ... 101s Setting up libharfbuzz0b:amd64 (12.3.0-4) ... 101s Setting up libthai-data (0.1.30-1) ... 101s Setting up libwayland-egl1:amd64 (1.24.0-2) ... 101s Setting up ca-certificates-java (20240118build1) ... 101s No JRE found. Skipping Java certificates setup. 101s Setting up kmc (3.2.4+dfsg-1build1) ... 101s Setting up libxcomposite1:amd64 (1:0.4.6-1build1) ... 101s Setting up libwayland-client0:amd64 (1.24.0-2) ... 101s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 101s Setting up smalt (0.7.6-13) ... 101s Setting up mesa-libgallium:amd64 (25.2.8-2ubuntu1) ... 101s Setting up liblapack3:amd64 (3.12.1-7ubuntu1) ... 101s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 101s Setting up python3-pysam (0.23.3+ds-2) ... 101s Setting up libatk1.0-0t64:amd64 (2.59.0-1) ... 101s Setting up openjdk-21-jre-headless:amd64 (21.0.10~6ea-1) ... 101s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode 101s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 101s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 101s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 101s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 101s Setting up libgbm1:amd64 (25.2.8-2ubuntu1) ... 101s Setting up fontconfig-config (2.15.0-2.4ubuntu1) ... 101s Setting up libxtst6:amd64 (2:1.2.5-1build1) ... 101s Setting up libxcursor1:amd64 (1:1.2.3-1build1) ... 101s Setting up libgl1-mesa-dri:amd64 (25.2.8-2ubuntu1) ... 101s Setting up libavahi-common3:amd64 (0.8-17ubuntu2) ... 101s Setting up dconf-service (0.49.0-4) ... 101s Setting up samtools (1.22.1-1) ... 101s Setting up libthai0:amd64 (0.1.30-1) ... 101s Setting up python3-numpy (1:2.3.5+ds-3) ... 102s Setting up libtiff6:amd64 (4.7.0-3ubuntu3) ... 102s Setting up libwayland-cursor0:amd64 (1.24.0-2) ... 102s Setting up libgdk-pixbuf-2.0-0:amd64 (2.44.4+dfsg-1) ... 102s Setting up libfontconfig1:amd64 (2.15.0-2.4ubuntu1) ... 102s Setting up libavahi-client3:amd64 (0.8-17ubuntu2) ... 102s Setting up libatk-bridge2.0-0t64:amd64 (2.59.0-1) ... 102s Setting up gtk-update-icon-cache (4.20.3+ds-3) ... 102s Setting up fontconfig (2.15.0-2.4ubuntu1) ... 104s Regenerating fonts cache... done. 104s Setting up libglx-mesa0:amd64 (25.2.8-2ubuntu1) ... 104s Setting up libglx0:amd64 (1.7.0-3) ... 104s Setting up dconf-gsettings-backend:amd64 (0.49.0-4) ... 104s Setting up fastaq (3.17.0-9build1) ... 104s Setting up libpango-1.0-0:amd64 (1.56.4-1) ... 104s Setting up libcairo2:amd64 (1.18.4-3) ... 104s Setting up libgl1:amd64 (1.7.0-3) ... 104s Setting up adwaita-icon-theme (49.0-1) ... 104s update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode 104s Setting up libcairo-gobject2:amd64 (1.18.4-3) ... 104s Setting up libpangoft2-1.0-0:amd64 (1.56.4-1) ... 104s Setting up libcups2t64:amd64 (2.4.16-1ubuntu1) ... 104s Setting up libgtk-3-common (3.24.50-1ubuntu2) ... 104s Setting up libpangocairo-1.0-0:amd64 (1.56.4-1) ... 104s Processing triggers for libc-bin (2.42-2ubuntu4) ... 104s Processing triggers for man-db (2.13.1-1) ... 105s Processing triggers for libglib2.0-0t64:amd64 (2.86.3-4) ... 105s Setting up libgtk-3-0t64:amd64 (3.24.50-1ubuntu2) ... 105s Processing triggers for ca-certificates-java (20240118build1) ... 105s Adding debian:ACCVRAIZ1.pem 105s Adding debian:AC_RAIZ_FNMT-RCM.pem 105s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 105s Adding debian:ANF_Secure_Server_Root_CA.pem 105s Adding debian:Actalis_Authentication_Root_CA.pem 105s Adding debian:AffirmTrust_Commercial.pem 105s Adding debian:AffirmTrust_Networking.pem 105s Adding debian:AffirmTrust_Premium.pem 105s Adding debian:AffirmTrust_Premium_ECC.pem 105s Adding debian:Amazon_Root_CA_1.pem 105s Adding debian:Amazon_Root_CA_2.pem 105s Adding debian:Amazon_Root_CA_3.pem 105s Adding debian:Amazon_Root_CA_4.pem 105s Adding debian:Atos_TrustedRoot_2011.pem 105s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 105s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 105s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 105s Adding debian:BJCA_Global_Root_CA1.pem 105s Adding debian:BJCA_Global_Root_CA2.pem 105s Adding debian:Baltimore_CyberTrust_Root.pem 105s Adding debian:Buypass_Class_2_Root_CA.pem 105s Adding debian:Buypass_Class_3_Root_CA.pem 105s Adding debian:CA_Disig_Root_R2.pem 105s Adding debian:CFCA_EV_ROOT.pem 105s Adding debian:COMODO_Certification_Authority.pem 105s Adding debian:COMODO_ECC_Certification_Authority.pem 105s Adding debian:COMODO_RSA_Certification_Authority.pem 105s Adding debian:Certainly_Root_E1.pem 105s Adding debian:Certainly_Root_R1.pem 105s Adding debian:Certigna.pem 105s Adding debian:Certigna_Root_CA.pem 105s Adding debian:Certum_EC-384_CA.pem 105s Adding debian:Certum_Trusted_Network_CA.pem 105s Adding debian:Certum_Trusted_Network_CA_2.pem 105s Adding debian:Certum_Trusted_Root_CA.pem 105s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 105s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 105s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 105s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 105s Adding debian:Comodo_AAA_Services_root.pem 105s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 105s Adding debian:D-TRUST_BR_Root_CA_2_2023.pem 105s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 105s Adding debian:D-TRUST_EV_Root_CA_2_2023.pem 105s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 105s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 105s Adding debian:DigiCert_Assured_ID_Root_CA.pem 105s Adding debian:DigiCert_Assured_ID_Root_G2.pem 105s Adding debian:DigiCert_Assured_ID_Root_G3.pem 105s Adding debian:DigiCert_Global_Root_CA.pem 105s Adding debian:DigiCert_Global_Root_G2.pem 105s Adding debian:DigiCert_Global_Root_G3.pem 105s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 105s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 105s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 105s Adding debian:DigiCert_Trusted_Root_G4.pem 105s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 105s Adding debian:Entrust_Root_Certification_Authority.pem 105s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 105s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 105s Adding debian:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem 105s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 105s Adding debian:GLOBALTRUST_2020.pem 105s Adding debian:GTS_Root_R1.pem 105s Adding debian:GTS_Root_R2.pem 105s Adding debian:GTS_Root_R3.pem 105s Adding debian:GTS_Root_R4.pem 105s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 105s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 105s Adding debian:GlobalSign_Root_CA.pem 105s Adding debian:GlobalSign_Root_CA_-_R3.pem 105s Adding debian:GlobalSign_Root_CA_-_R6.pem 105s Adding debian:GlobalSign_Root_E46.pem 105s Adding debian:GlobalSign_Root_R46.pem 105s Adding debian:Go_Daddy_Class_2_CA.pem 105s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 105s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 105s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 105s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 105s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 105s Adding debian:HiPKI_Root_CA_-_G1.pem 105s Adding debian:Hongkong_Post_Root_CA_3.pem 105s Adding debian:ISRG_Root_X1.pem 105s Adding debian:ISRG_Root_X2.pem 105s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 105s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 105s Adding debian:Izenpe.com.pem 105s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 105s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 105s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 105s Adding debian:NAVER_Global_Root_Certification_Authority.pem 105s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 105s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 105s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 105s Adding debian:QuoVadis_Root_CA_1_G3.pem 105s Adding debian:QuoVadis_Root_CA_2.pem 105s Adding debian:QuoVadis_Root_CA_2_G3.pem 105s Adding debian:QuoVadis_Root_CA_3.pem 105s Adding debian:QuoVadis_Root_CA_3_G3.pem 105s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 105s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 105s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 105s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 105s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 105s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 105s Adding debian:SZAFIR_ROOT_CA2.pem 105s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 105s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 105s Adding debian:SecureSign_Root_CA12.pem 105s Adding debian:SecureSign_Root_CA14.pem 105s Adding debian:SecureSign_Root_CA15.pem 105s Adding debian:SecureTrust_CA.pem 105s Adding debian:Secure_Global_CA.pem 105s Adding debian:Security_Communication_ECC_RootCA1.pem 105s Adding debian:Security_Communication_RootCA2.pem 105s Adding debian:Starfield_Class_2_CA.pem 105s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 105s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 105s Adding debian:SwissSign_Gold_CA_-_G2.pem 105s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 105s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 105s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 105s Adding debian:TWCA_CYBER_Root_CA.pem 105s Adding debian:TWCA_Global_Root_CA.pem 105s Adding debian:TWCA_Root_Certification_Authority.pem 105s Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem 105s Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem 105s Adding debian:TeliaSonera_Root_CA_v1.pem 105s Adding debian:Telia_Root_CA_v2.pem 105s Adding debian:TrustAsia_Global_Root_CA_G3.pem 105s Adding debian:TrustAsia_Global_Root_CA_G4.pem 105s Adding debian:Trustwave_Global_Certification_Authority.pem 105s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 105s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 105s Adding debian:TunTrust_Root_CA.pem 105s Adding debian:UCA_Extended_Validation_Root.pem 105s Adding debian:UCA_Global_G2_Root.pem 105s Adding debian:USERTrust_ECC_Certification_Authority.pem 105s Adding debian:USERTrust_RSA_Certification_Authority.pem 105s Adding debian:XRamp_Global_CA_Root.pem 105s Adding debian:certSIGN_ROOT_CA.pem 105s Adding debian:certSIGN_Root_CA_G2.pem 105s Adding debian:e-Szigno_Root_CA_2017.pem 105s Adding debian:ePKI_Root_Certification_Authority.pem 105s Adding debian:emSign_ECC_Root_CA_-_C3.pem 105s Adding debian:emSign_ECC_Root_CA_-_G3.pem 105s Adding debian:emSign_Root_CA_-_C1.pem 105s Adding debian:emSign_Root_CA_-_G1.pem 105s Adding debian:vTrus_ECC_Root_CA.pem 105s Adding debian:vTrus_Root_CA.pem 105s done. 105s Setting up default-jre-headless (2:1.21-76build1) ... 105s Setting up iva (1.0.11+ds-6build1) ... 105s Setting up openjdk-21-jre:amd64 (21.0.10~6ea-1) ... 105s Setting up default-jre (2:1.21-76build1) ... 105s Setting up trimmomatic (0.39+dfsg-2build1) ... 105s Processing triggers for libc-bin (2.42-2ubuntu4) ... 106s autopkgtest [09:51:18]: test test-example: [----------------------- 117s Running iva in test mode... 117s Copied input test files into here: /tmp/tmp.tJx6zYJkkw/test 117s Current working directory: /tmp/tmp.tJx6zYJkkw/test 117s Running iva on the test data with the command: 117s /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 117s The following command failed with exit code 1 117s /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 117s 117s The output was: 117s 117s usage: iva [options] {-f reads_fwd -r reads_rev | --fr reads} 117s iva: error: the following arguments are required: Output directory 117s Traceback (most recent call last): 117s File "/usr/bin/iva", line 184, in 117s p1.start() 117s ~~~~~~~~^^ 117s File "/usr/lib/python3.14/multiprocessing/process.py", line 121, in start 117s self._popen = self._Popen(self) 117s ~~~~~~~~~~~^^^^^^ 117s File "/usr/lib/python3.14/multiprocessing/context.py", line 224, in _Popen 117s return _default_context.get_context().Process._Popen(process_obj) 117s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^ 117s File "/usr/lib/python3.14/multiprocessing/context.py", line 300, in _Popen 117s return Popen(process_obj) 117s File "/usr/lib/python3.14/multiprocessing/popen_forkserver.py", line 35, in __init__ 117s super().__init__(process_obj) 117s ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^ 117s File "/usr/lib/python3.14/multiprocessing/popen_fork.py", line 20, in __init__ 117s self._launch(process_obj) 117s ~~~~~~~~~~~~^^^^^^^^^^^^^ 117s File "/usr/lib/python3.14/multiprocessing/popen_forkserver.py", line 51, in _launch 117s self.sentinel, w = forkserver.connect_to_new_process(self._fds) 117s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^ 117s File "/usr/lib/python3.14/multiprocessing/forkserver.py", line 106, in connect_to_new_process 117s connection.answer_challenge( 117s ~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 117s wrapped_client, self._forkserver_authkey) 117s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 117s File "/usr/lib/python3.14/multiprocessing/connection.py", line 970, in answer_challenge 117s message = connection.recv_bytes(256) # reject large message 117s File "/usr/lib/python3.14/multiprocessing/connection.py", line 222, in recv_bytes 117s buf = self._recv_bytes(maxlength) 117s File "/usr/lib/python3.14/multiprocessing/connection.py", line 447, in _recv_bytes 117s buf = self._recv(4) 117s File "/usr/lib/python3.14/multiprocessing/connection.py", line 412, in _recv 117s chunk = read(handle, to_read) 117s ConnectionResetError: [Errno 104] Connection reset by peer 117s 117s autopkgtest [09:51:29]: test test-example: -----------------------] 118s test-example FAIL non-zero exit status 1 118s autopkgtest [09:51:30]: test test-example: - - - - - - - - - - results - - - - - - - - - - 118s autopkgtest [09:51:30]: test test-example: - - - - - - - - - - stderr - - - - - - - - - - 118s The following command failed with exit code 1 118s /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 118s 118s The output was: 118s 118s usage: iva [options] {-f reads_fwd -r reads_rev | --fr reads} 118s iva: error: the following arguments are required: Output directory 118s Traceback (most recent call last): 118s File "/usr/bin/iva", line 184, in 118s p1.start() 118s ~~~~~~~~^^ 118s File "/usr/lib/python3.14/multiprocessing/process.py", line 121, in start 118s self._popen = self._Popen(self) 118s ~~~~~~~~~~~^^^^^^ 118s File "/usr/lib/python3.14/multiprocessing/context.py", line 224, in _Popen 118s return _default_context.get_context().Process._Popen(process_obj) 118s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^ 118s File "/usr/lib/python3.14/multiprocessing/context.py", line 300, in _Popen 118s return Popen(process_obj) 118s File "/usr/lib/python3.14/multiprocessing/popen_forkserver.py", line 35, in __init__ 118s super().__init__(process_obj) 118s ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^ 118s File "/usr/lib/python3.14/multiprocessing/popen_fork.py", line 20, in __init__ 118s self._launch(process_obj) 118s ~~~~~~~~~~~~^^^^^^^^^^^^^ 118s File "/usr/lib/python3.14/multiprocessing/popen_forkserver.py", line 51, in _launch 118s self.sentinel, w = forkserver.connect_to_new_process(self._fds) 118s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^ 118s File "/usr/lib/python3.14/multiprocessing/forkserver.py", line 106, in connect_to_new_process 118s connection.answer_challenge( 118s ~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 118s wrapped_client, self._forkserver_authkey) 118s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 118s File "/usr/lib/python3.14/multiprocessing/connection.py", line 970, in answer_challenge 118s message = connection.recv_bytes(256) # reject large message 118s File "/usr/lib/python3.14/multiprocessing/connection.py", line 222, in recv_bytes 118s buf = self._recv_bytes(maxlength) 118s File "/usr/lib/python3.14/multiprocessing/connection.py", line 447, in _recv_bytes 118s buf = self._recv(4) 118s File "/usr/lib/python3.14/multiprocessing/connection.py", line 412, in _recv 118s chunk = read(handle, to_read) 118s ConnectionResetError: [Errno 104] Connection reset by peer 118s 118s autopkgtest [09:51:30]: @@@@@@@@@@@@@@@@@@@@ summary 118s test-example FAIL non-zero exit status 1