0s autopkgtest [02:43:59]: starting date and time: 2024-11-15 02:43:59+0000 0s autopkgtest [02:43:59]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [02:43:59]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.xzqwjoqu/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade unicycler --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-16.secgroup --name adt-plucky-amd64-unicycler-20241115-024359-juju-7f2275-prod-proposed-migration-environment-20-8199251d-1989-4bbc-976e-71f1c0887328 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 49s autopkgtest [02:44:48]: testbed dpkg architecture: amd64 49s autopkgtest [02:44:48]: testbed apt version: 2.9.8 49s autopkgtest [02:44:48]: @@@@@@@@@@@@@@@@@@@@ test bed setup 50s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 50s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 50s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 50s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1030 kB] 51s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.5 kB] 51s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [166 kB] 51s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [101 kB] 51s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 51s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [800 kB] 51s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [293 kB] 51s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [740 B] 51s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [9128 B] 51s Fetched 2631 kB in 1s (3080 kB/s) 51s Reading package lists... 53s Reading package lists... 53s Building dependency tree... 53s Reading state information... 54s Calculating upgrade... 54s The following NEW packages will be installed: 54s python3.13-gdbm 54s The following packages will be upgraded: 54s firmware-sof-signed libcap-ng0 libexpat1 libpython3-stdlib lxd-installer 54s man-db pastebinit python3 python3-gdbm python3-minimal python3-systemd 54s xfsprogs 54s 12 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 54s Need to get 9638 kB of archives. 54s After this operation, 542 kB of additional disk space will be used. 54s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 54s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 54s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 54s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 firmware-sof-signed all 2024.06-1ubuntu2 [7083 kB] 55s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-3build1 [15.6 kB] 55s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libexpat1 amd64 2.6.4-1 [94.9 kB] 55s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 man-db amd64 2.13.0-1 [1352 kB] 55s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 55s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 55s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 lxd-installer all 9 [5084 B] 55s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 pastebinit all 1.7.1-1 [14.9 kB] 55s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build5 [45.7 kB] 55s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 xfsprogs amd64 6.8.0-2.2ubuntu2 [926 kB] 55s Preconfiguring packages ... 55s Fetched 9638 kB in 1s (10.7 MB/s) 55s (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 ... 75542 files and directories currently installed.) 55s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 55s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 55s Setting up python3-minimal (3.12.7-1) ... 55s (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 ... 75542 files and directories currently installed.) 55s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 56s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 56s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 56s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 56s Preparing to unpack .../firmware-sof-signed_2024.06-1ubuntu2_all.deb ... 56s Unpacking firmware-sof-signed (2024.06-1ubuntu2) over (2024.06-1ubuntu1) ... 56s Preparing to unpack .../libcap-ng0_0.8.5-3build1_amd64.deb ... 56s Unpacking libcap-ng0:amd64 (0.8.5-3build1) over (0.8.5-1) ... 56s Setting up libcap-ng0:amd64 (0.8.5-3build1) ... 56s (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 ... 75568 files and directories currently installed.) 56s Preparing to unpack .../0-libexpat1_2.6.4-1_amd64.deb ... 56s Unpacking libexpat1:amd64 (2.6.4-1) over (2.6.2-2) ... 56s Preparing to unpack .../1-man-db_2.13.0-1_amd64.deb ... 56s Unpacking man-db (2.13.0-1) over (2.12.1-3) ... 56s Selecting previously unselected package python3.13-gdbm. 56s Preparing to unpack .../2-python3.13-gdbm_3.13.0-2_amd64.deb ... 56s Unpacking python3.13-gdbm (3.13.0-2) ... 56s Preparing to unpack .../3-python3-gdbm_3.12.7-1_amd64.deb ... 56s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 56s Preparing to unpack .../4-lxd-installer_9_all.deb ... 56s Unpacking lxd-installer (9) over (8) ... 56s Preparing to unpack .../5-pastebinit_1.7.1-1_all.deb ... 56s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 56s Preparing to unpack .../6-python3-systemd_235-1build5_amd64.deb ... 56s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 56s Preparing to unpack .../7-xfsprogs_6.8.0-2.2ubuntu2_amd64.deb ... 56s Unpacking xfsprogs (6.8.0-2.2ubuntu2) over (6.8.0-2.2ubuntu1) ... 56s Setting up libexpat1:amd64 (2.6.4-1) ... 56s Setting up firmware-sof-signed (2024.06-1ubuntu2) ... 56s Setting up man-db (2.13.0-1) ... 56s Updating database of manual pages ... 58s man-db.service is a disabled or a static unit not running, not starting it. 58s Setting up lxd-installer (9) ... 59s Setting up python3.13-gdbm (3.13.0-2) ... 59s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 59s Setting up python3 (3.12.7-1) ... 59s Setting up xfsprogs (6.8.0-2.2ubuntu2) ... 59s update-initramfs: deferring update (trigger activated) 59s Setting up python3-systemd (235-1build5) ... 59s Setting up python3-gdbm:amd64 (3.12.7-1) ... 59s Setting up pastebinit (1.7.1-1) ... 59s Processing triggers for libc-bin (2.40-1ubuntu3) ... 59s Processing triggers for initramfs-tools (0.142ubuntu34) ... 59s update-initramfs: Generating /boot/initrd.img-6.11.0-8-generic 59s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 67s Reading package lists... 67s Building dependency tree... 67s Reading state information... 68s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 68s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 68s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 68s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 68s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 69s Reading package lists... 69s Reading package lists... 69s Building dependency tree... 69s Reading state information... 69s Calculating upgrade... 70s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 70s Reading package lists... 70s Building dependency tree... 70s Reading state information... 70s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 70s autopkgtest [02:45:09]: rebooting testbed after setup commands that affected boot 88s autopkgtest [02:45:27]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 91s autopkgtest [02:45:30]: @@@@@@@@@@@@@@@@@@@@ apt-source unicycler 94s Get:1 http://ftpmaster.internal/ubuntu plucky/universe unicycler 0.5.0+dfsg-1 (dsc) [2379 B] 94s Get:2 http://ftpmaster.internal/ubuntu plucky/universe unicycler 0.5.0+dfsg-1 (tar) [14.8 MB] 94s Get:3 http://ftpmaster.internal/ubuntu plucky/universe unicycler 0.5.0+dfsg-1 (diff) [11.9 kB] 94s gpgv: Signature made Tue Dec 6 15:30:28 2022 UTC 94s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 94s gpgv: issuer "tille@debian.org" 94s gpgv: Can't check signature: No public key 94s dpkg-source: warning: cannot verify inline signature for ./unicycler_0.5.0+dfsg-1.dsc: no acceptable signature found 95s autopkgtest [02:45:34]: testing package unicycler version 0.5.0+dfsg-1 95s autopkgtest [02:45:34]: build not needed 96s autopkgtest [02:45:35]: test run-unit-test: preparing testbed 100s Reading package lists... 100s Building dependency tree... 100s Reading state information... 100s Starting pkgProblemResolver with broken count: 0 100s Starting 2 pkgProblemResolver with broken count: 0 100s Done 100s The following additional packages will be installed: 100s adwaita-icon-theme at-spi2-common autoconf automake autopoint autotools-dev 100s bamtools bcftools bowtie2 build-essential bwa ca-certificates-java cpp 100s cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu dconf-gsettings-backend 100s dconf-service debhelper debugedit default-jdk default-jdk-headless 100s default-jre default-jre-headless dh-autoreconf dh-python 100s dh-strip-nondeterminism dwz fontconfig fontconfig-config fonts-dejavu-core 100s fonts-dejavu-mono g++ g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu 100s gcc gcc-14 gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gettext 100s gtk-update-icon-cache hicolor-icon-theme humanity-icon-theme intltool-debian 100s java-common java-wrappers libapache-pom-java libarchive-zip-perl libasan8 100s libasound2-data libasound2t64 libatk-bridge2.0-0t64 libatk1.0-0t64 100s libatspi2.0-0t64 libavahi-client3 libavahi-common-data libavahi-common3 100s libbamtools2.5.2 libcairo-gobject2 libcairo2 libcc1-0 libcolord2 100s libcommons-codec-java libcommons-compress-java libcommons-io-java 100s libcommons-jexl2-java libcommons-lang-java libcommons-logging-java 100s libcommons-parent-java libcups2t64 libdatrie1 libdconf1 libdebhelper-perl 100s libdeflate0 libdrm-amdgpu1 libdrm-intel1 libdrm-radeon1 libedlib1 libepoxy0 100s libfile-stripnondeterminism-perl libfontconfig1 libgbm1 libgcc-14-dev 101s libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgif7 libgl1 libgl1-mesa-dri 101s libglapi-mesa libglvnd0 libglx-mesa0 libglx0 libgomp1 libgraphite2-3 101s libgtk-3-0t64 libgtk-3-common libharfbuzz0b libhts3t64 libhtscodecs2 101s libhtsjdk-java libhwasan0 libisl23 libitm1 libjbig0 libjpeg-turbo8 libjpeg8 101s libjsoncpp26 liblcms2-2 liblerc4 liblsan0 libmbedcrypto16 libmbedcrypto7t64 101s libmbedtls14t64 libmbedtls21 libmbedx509-1t64 libmbedx509-7 libmjson-java 101s libmpc3 libncbi-ngs3 libncbi-vdb3 libngs-java libngs-jni libnlopt0 101s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpciaccess0 101s libpcsclite1 libpixman-1-0 libpython3.13-minimal libpython3.13-stdlib 101s libquadmath0 librhino-java libseqan2-dev libsharpyuv0 libsnappy-java 101s libsnappy-jni libsnappy1v5 libspoa7.0.0 libssw0 libstdc++-14-dev 101s libthai-data libthai0 libtiff6 libtool libtsan2 libubsan1 libvulkan1 101s libwayland-client0 libwayland-cursor0 libwayland-egl1 libwayland-server0 101s libwebp7 libx11-xcb1 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 101s libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 101s libxcomposite1 libxcursor1 libxdamage1 libxfixes3 libxi6 libxinerama1 101s libxrandr2 libxrender1 libxshmfence1 libxtst6 libxxf86vm1 m4 mesa-libgallium 101s miniasm ncbi-blast+ ncbi-data ncbi-vdb-data openjdk-21-jdk 101s openjdk-21-jdk-headless openjdk-21-jre openjdk-21-jre-headless pilon 101s po-debconf python3-all python3-joblib python3-packaging python3.13 101s python3.13-minimal racon samtools scala-library spades ubuntu-mono unicycler 101s unicycler-data unzip x11-common zlib1g-dev 101s Suggested packages: 101s adwaita-icon-theme-legacy autoconf-archive gnu-standards autoconf-doc 101s python3-numpy texlive-latex-recommended bowtie2-examples cpp-doc 101s gcc-14-locales cpp-14-doc dh-make flit python3-build python3-installer 101s python3-wheel g++-multilib g++-14-multilib gcc-14-doc gcc-multilib 101s manpages-dev flex bison gdb gcc-doc gcc-14-multilib gdb-x86-64-linux-gnu 101s gettext-doc libasprintf-dev libgettextpo-dev alsa-utils libasound2-plugins 101s colord libasm-java libxz-java libcommons-lang-java-doc 101s libavalon-framework-java libexcalibur-logkit-java liblog4j1.2-java 101s cups-common gvfs picard-tools liblcms2-utils libngs-java-doc pcscd rhino 101s libstdc++-14-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc 101s openjdk-21-demo openjdk-21-source visualvm libnss-mdns fonts-dejavu-extra 101s fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei 101s | fonts-wqy-zenhei fonts-indic libmail-box-perl python-joblib-doc 101s python3.13-venv python3.13-doc binfmt-support cwltool zip 101s Recommended packages: 101s librsvg2-common python3-gffutils python3-matplotlib alsa-ucm-conf 101s alsa-topology-conf at-spi2-core libarchive-cpio-perl libgdk-pixbuf2.0-bin 101s libgl1-amber-dri libgtk-3-bin libltdl-dev mesa-vulkan-drivers | vulkan-icd 101s minimap libxt-dev libatk-wrapper-java-jni fonts-dejavu-extra 101s libmail-sendmail-perl python3-numpy python3-pytest python3-simplejson 101s python3-psutil rampler 101s The following NEW packages will be installed: 101s adwaita-icon-theme at-spi2-common autoconf automake autopkgtest-satdep 101s autopoint autotools-dev bamtools bcftools bowtie2 build-essential bwa 101s ca-certificates-java cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu 101s dconf-gsettings-backend dconf-service debhelper debugedit default-jdk 101s default-jdk-headless default-jre default-jre-headless dh-autoreconf 101s dh-python dh-strip-nondeterminism dwz fontconfig fontconfig-config 101s fonts-dejavu-core fonts-dejavu-mono g++ g++-14 g++-14-x86-64-linux-gnu 101s g++-x86-64-linux-gnu gcc gcc-14 gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu 101s gettext gtk-update-icon-cache hicolor-icon-theme humanity-icon-theme 101s intltool-debian java-common java-wrappers libapache-pom-java 101s libarchive-zip-perl libasan8 libasound2-data libasound2t64 101s libatk-bridge2.0-0t64 libatk1.0-0t64 libatspi2.0-0t64 libavahi-client3 101s libavahi-common-data libavahi-common3 libbamtools2.5.2 libcairo-gobject2 101s libcairo2 libcc1-0 libcolord2 libcommons-codec-java libcommons-compress-java 101s libcommons-io-java libcommons-jexl2-java libcommons-lang-java 101s libcommons-logging-java libcommons-parent-java libcups2t64 libdatrie1 101s libdconf1 libdebhelper-perl libdeflate0 libdrm-amdgpu1 libdrm-intel1 101s libdrm-radeon1 libedlib1 libepoxy0 libfile-stripnondeterminism-perl 101s libfontconfig1 libgbm1 libgcc-14-dev libgdk-pixbuf-2.0-0 101s libgdk-pixbuf2.0-common libgif7 libgl1 libgl1-mesa-dri libglapi-mesa 101s libglvnd0 libglx-mesa0 libglx0 libgomp1 libgraphite2-3 libgtk-3-0t64 101s libgtk-3-common libharfbuzz0b libhts3t64 libhtscodecs2 libhtsjdk-java 101s libhwasan0 libisl23 libitm1 libjbig0 libjpeg-turbo8 libjpeg8 libjsoncpp26 101s liblcms2-2 liblerc4 liblsan0 libmbedcrypto16 libmbedcrypto7t64 101s libmbedtls14t64 libmbedtls21 libmbedx509-1t64 libmbedx509-7 libmjson-java 101s libmpc3 libncbi-ngs3 libncbi-vdb3 libngs-java libngs-jni libnlopt0 101s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpciaccess0 101s libpcsclite1 libpixman-1-0 libpython3.13-minimal libpython3.13-stdlib 101s libquadmath0 librhino-java libseqan2-dev libsharpyuv0 libsnappy-java 101s libsnappy-jni libsnappy1v5 libspoa7.0.0 libssw0 libstdc++-14-dev 101s libthai-data libthai0 libtiff6 libtool libtsan2 libubsan1 libvulkan1 101s libwayland-client0 libwayland-cursor0 libwayland-egl1 libwayland-server0 101s libwebp7 libx11-xcb1 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 101s libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 101s libxcomposite1 libxcursor1 libxdamage1 libxfixes3 libxi6 libxinerama1 101s libxrandr2 libxrender1 libxshmfence1 libxtst6 libxxf86vm1 m4 mesa-libgallium 101s miniasm ncbi-blast+ ncbi-data ncbi-vdb-data openjdk-21-jdk 101s openjdk-21-jdk-headless openjdk-21-jre openjdk-21-jre-headless pilon 101s po-debconf python3-all python3-joblib python3-packaging python3.13 101s python3.13-minimal racon samtools scala-library spades ubuntu-mono unicycler 101s unicycler-data unzip x11-common zlib1g-dev 101s 0 upgraded, 203 newly installed, 0 to remove and 0 not upgraded. 101s Need to get 302 MB/302 MB of archives. 101s After this operation, 878 MB of additional disk space will be used. 101s Get:1 /tmp/autopkgtest.veHd19/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [852 B] 101s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.0-2 [879 kB] 101s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.0-2 [2188 kB] 102s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-1 [7888 B] 102s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB] 102s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 102s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 102s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 102s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB] 102s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 102s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 102s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 102s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-1 [147 kB] 102s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 gtk-update-icon-cache amd64 4.16.5+ds-1 [52.4 kB] 102s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 hicolor-icon-theme all 0.18-1 [13.5 kB] 102s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 humanity-icon-theme all 0.6.16 [1282 kB] 102s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-mono all 24.04-0ubuntu1 [151 kB] 102s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 adwaita-icon-theme all 47.0-2 [525 kB] 102s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 at-spi2-common all 2.54.0-1 [8774 B] 102s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 m4 amd64 1.4.19-4build1 [244 kB] 102s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 autoconf all 2.72-3 [382 kB] 102s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 autotools-dev all 20220109.1 [44.9 kB] 102s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 automake all 1:1.16.5-1.3ubuntu1 [558 kB] 102s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 autopoint all 0.22.5-2 [616 kB] 102s Get:25 http://ftpmaster.internal/ubuntu plucky/universe amd64 libbamtools2.5.2 amd64 2.5.2+dfsg-6build1 [144 kB] 102s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libjsoncpp26 amd64 1.9.6-2 [89.9 kB] 102s Get:27 http://ftpmaster.internal/ubuntu plucky/universe amd64 bamtools amd64 2.5.2+dfsg-6build1 [178 kB] 102s Get:28 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-1 [132 kB] 102s Get:29 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.20+ds-1 [439 kB] 102s Get:30 http://ftpmaster.internal/ubuntu plucky/universe amd64 bcftools amd64 1.20-2 [810 kB] 102s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB] 102s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 102s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [11.9 MB] 103s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-8ubuntu1 [1030 B] 103s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [5452 B] 103s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.1.0-2ubuntu1 [22.4 kB] 103s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 14.2.0-8ubuntu1 [47.6 kB] 103s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 103s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 14.2.0-8ubuntu1 [29.1 kB] 103s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 14.2.0-8ubuntu1 [2998 kB] 103s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 14.2.0-8ubuntu1 [1317 kB] 103s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 14.2.0-8ubuntu1 [2732 kB] 103s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 14.2.0-8ubuntu1 [1177 kB] 103s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 14.2.0-8ubuntu1 [1634 kB] 103s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 14.2.0-8ubuntu1 [153 kB] 103s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-8ubuntu1 [2814 kB] 103s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [23.3 MB] 104s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-8ubuntu1 [528 kB] 104s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [1214 B] 104s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.1.0-2ubuntu1 [5000 B] 104s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-8ubuntu1 [2504 kB] 104s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [13.3 MB] 104s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-8ubuntu1 [19.9 kB] 104s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [966 B] 104s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.1.0-2ubuntu1 [1100 B] 104s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 104s Get:57 http://ftpmaster.internal/ubuntu plucky/universe amd64 bwa amd64 0.7.18-1 [204 kB] 104s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 ca-certificates-java all 20240118 [11.6 kB] 104s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libdconf1 amd64 0.40.0-4build2 [39.4 kB] 104s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 dconf-service amd64 0.40.0-4build2 [27.5 kB] 104s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 dconf-gsettings-backend amd64 0.40.0-4build2 [22.1 kB] 104s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebhelper-perl all 13.20ubuntu1 [94.2 kB] 104s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 libtool all 2.4.7-7build1 [166 kB] 104s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-autoreconf all 20 [16.1 kB] 104s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] 104s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] 104s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-strip-nondeterminism all 1.14.0-1 [5058 B] 104s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 debugedit amd64 1:5.1-1 [46.9 kB] 104s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 dwz amd64 0.15-1build6 [115 kB] 104s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 gettext amd64 0.22.5-2 [948 kB] 104s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 104s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] 104s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 debhelper all 13.20ubuntu1 [893 kB] 104s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 java-common all 0.76 [6852 B] 104s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 104s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcsclite1 amd64 2.3.0-3 [26.5 kB] 104s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 openjdk-21-jre-headless amd64 21.0.5+11-1 [46.4 MB] 106s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 default-jre-headless amd64 2:1.21-76 [3178 B] 106s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 libatk1.0-0t64 amd64 2.54.0-1 [55.1 kB] 106s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 libxi6 amd64 2:1.8.2-1 [32.4 kB] 106s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libatspi2.0-0t64 amd64 2.54.0-1 [79.6 kB] 106s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 libatk-bridge2.0-0t64 amd64 2.54.0-1 [66.3 kB] 106s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 106s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 106s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 106s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 106s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 106s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 106s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 106s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 106s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 106s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo-gobject2 amd64 1.18.2-2 [127 kB] 106s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 libcolord2 amd64 1.4.7-1build2 [149 kB] 106s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-common-data amd64 0.8-13ubuntu6 [29.7 kB] 106s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-common3 amd64 0.8-13ubuntu6 [23.3 kB] 106s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-client3 amd64 0.8-13ubuntu6 [26.8 kB] 106s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 libcups2t64 amd64 2.4.10-1ubuntu2 [271 kB] 106s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 libepoxy0 amd64 1.5.10-2 [218 kB] 106s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 106s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB] 106s Get:101 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-1.1ubuntu2 [180 kB] 106s Get:102 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 106s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB] 106s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 106s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.54.0+ds-3 [252 kB] 106s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-3 [51.6 kB] 106s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-3 [29.1 kB] 106s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-client0 amd64 1.23.0-1 [27.1 kB] 106s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-cursor0 amd64 1.23.0-1 [10.8 kB] 106s Get:110 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-egl1 amd64 1.23.0-1 [5662 B] 106s Get:111 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcomposite1 amd64 1:0.4.6-1 [6642 B] 106s Get:112 http://ftpmaster.internal/ubuntu plucky/main amd64 libxfixes3 amd64 1:6.0.0-2build1 [10.8 kB] 106s Get:113 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcursor1 amd64 1:1.2.2-1 [20.9 kB] 106s Get:114 http://ftpmaster.internal/ubuntu plucky/main amd64 libxdamage1 amd64 1:1.1.6-1build1 [6150 B] 106s Get:115 http://ftpmaster.internal/ubuntu plucky/main amd64 libxinerama1 amd64 2:1.1.4-3build1 [6396 B] 106s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrandr2 amd64 2:1.5.4-1 [19.6 kB] 106s Get:117 http://ftpmaster.internal/ubuntu plucky/main amd64 libgtk-3-common all 3.24.43-3ubuntu2 [1202 kB] 107s Get:118 http://ftpmaster.internal/ubuntu plucky/main amd64 libgtk-3-0t64 amd64 3.24.43-3ubuntu2 [2927 kB] 107s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 libglvnd0 amd64 1.7.0-1build1 [69.6 kB] 107s Get:120 http://ftpmaster.internal/ubuntu plucky/main amd64 libglapi-mesa amd64 24.2.3-1ubuntu1 [42.4 kB] 107s Get:121 http://ftpmaster.internal/ubuntu plucky/main amd64 libx11-xcb1 amd64 2:1.8.10-2 [7944 B] 107s Get:122 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-dri2-0 amd64 1.17.0-2 [7222 B] 107s Get:123 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-dri3-0 amd64 1.17.0-2 [7508 B] 107s Get:124 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-glx0 amd64 1.17.0-2 [24.8 kB] 107s Get:125 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-present0 amd64 1.17.0-2 [6064 B] 107s Get:126 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-randr0 amd64 1.17.0-2 [17.9 kB] 107s Get:127 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-sync1 amd64 1.17.0-2 [9312 B] 107s Get:128 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-xfixes0 amd64 1.17.0-2 [10.2 kB] 107s Get:129 http://ftpmaster.internal/ubuntu plucky/main amd64 libxshmfence1 amd64 1.3-1build5 [4764 B] 107s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 libxxf86vm1 amd64 1:1.1.4-1build4 [9282 B] 107s Get:131 http://ftpmaster.internal/ubuntu plucky/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [21.7 kB] 107s Get:132 http://ftpmaster.internal/ubuntu plucky/main amd64 libpciaccess0 amd64 0.17-3build1 [18.6 kB] 107s Get:133 http://ftpmaster.internal/ubuntu plucky/main amd64 libdrm-intel1 amd64 2.4.123-1 [68.8 kB] 107s Get:134 http://ftpmaster.internal/ubuntu plucky/main amd64 libdrm-radeon1 amd64 2.4.123-1 [25.3 kB] 107s Get:135 http://ftpmaster.internal/ubuntu plucky/main amd64 mesa-libgallium amd64 24.2.3-1ubuntu1 [9904 kB] 107s Get:136 http://ftpmaster.internal/ubuntu plucky/main amd64 libvulkan1 amd64 1.3.296.0-1 [143 kB] 107s Get:137 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-server0 amd64 1.23.0-1 [35.1 kB] 107s Get:138 http://ftpmaster.internal/ubuntu plucky/main amd64 libgbm1 amd64 24.2.3-1ubuntu1 [32.0 kB] 107s Get:139 http://ftpmaster.internal/ubuntu plucky/main amd64 libgl1-mesa-dri amd64 24.2.3-1ubuntu1 [34.4 kB] 107s Get:140 http://ftpmaster.internal/ubuntu plucky/main amd64 libglx-mesa0 amd64 24.2.3-1ubuntu1 [153 kB] 107s Get:141 http://ftpmaster.internal/ubuntu plucky/main amd64 libglx0 amd64 1.7.0-1build1 [38.6 kB] 107s Get:142 http://ftpmaster.internal/ubuntu plucky/main amd64 libgl1 amd64 1.7.0-1build1 [102 kB] 107s Get:143 http://ftpmaster.internal/ubuntu plucky/main amd64 libasound2-data all 1.2.12-1 [21.0 kB] 107s Get:144 http://ftpmaster.internal/ubuntu plucky/main amd64 libasound2t64 amd64 1.2.12-1 [394 kB] 107s Get:145 http://ftpmaster.internal/ubuntu plucky/main amd64 libgif7 amd64 5.2.2-1ubuntu1 [35.2 kB] 107s Get:146 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 107s Get:147 http://ftpmaster.internal/ubuntu plucky/main amd64 libxtst6 amd64 2:1.2.3-1.1build1 [12.6 kB] 107s Get:148 http://ftpmaster.internal/ubuntu plucky/main amd64 openjdk-21-jre amd64 21.0.5+11-1 [220 kB] 107s Get:149 http://ftpmaster.internal/ubuntu plucky/main amd64 default-jre amd64 2:1.21-76 [918 B] 107s Get:150 http://ftpmaster.internal/ubuntu plucky/main amd64 openjdk-21-jdk-headless amd64 21.0.5+11-1 [82.8 MB] 110s Get:151 http://ftpmaster.internal/ubuntu plucky/main amd64 default-jdk-headless amd64 2:1.21-76 [966 B] 110s Get:152 http://ftpmaster.internal/ubuntu plucky/main amd64 openjdk-21-jdk amd64 21.0.5+11-1 [3422 kB] 111s Get:153 http://ftpmaster.internal/ubuntu plucky/main amd64 default-jdk amd64 2:1.21-76 [922 B] 111s Get:154 http://ftpmaster.internal/ubuntu plucky/universe amd64 dh-python all 6.20241024 [112 kB] 111s Get:155 http://ftpmaster.internal/ubuntu plucky/main amd64 unzip amd64 6.0-28ubuntu6 [181 kB] 111s Get:156 http://ftpmaster.internal/ubuntu plucky/universe amd64 java-wrappers all 0.5 [9042 B] 111s Get:157 http://ftpmaster.internal/ubuntu plucky/universe amd64 libapache-pom-java all 33-2 [5874 B] 111s Get:158 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-parent-java all 56-1 [10.7 kB] 111s Get:159 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-codec-java all 1.17.1-1 [302 kB] 111s Get:160 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-io-java all 2.17.0-1 [457 kB] 111s Get:161 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-compress-java all 1.27.1-2 [610 kB] 111s Get:162 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB] 111s Get:163 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-jexl2-java all 2.1.1-6 [250 kB] 111s Get:164 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-lang-java all 2.6-10 [270 kB] 111s Get:165 http://ftpmaster.internal/ubuntu plucky/universe amd64 libedlib1 amd64 1.2.7-6 [18.3 kB] 111s Get:166 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmjson-java all 1.4.0-3 [60.4 kB] 111s Get:167 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedcrypto16 amd64 3.6.2-2ubuntu1 [275 kB] 111s Get:168 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedx509-7 amd64 3.6.2-2ubuntu1 [37.1 kB] 111s Get:169 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedtls21 amd64 3.6.2-2ubuntu1 [126 kB] 111s Get:170 http://ftpmaster.internal/ubuntu plucky/universe amd64 ncbi-vdb-data all 3.0.9+dfsg-2 [67.7 kB] 111s Get:171 http://ftpmaster.internal/ubuntu plucky/universe amd64 libncbi-vdb3 amd64 3.0.9+dfsg-2 [1409 kB] 111s Get:172 http://ftpmaster.internal/ubuntu plucky/universe amd64 libncbi-ngs3 amd64 3.0.3+dfsg-9ubuntu1 [149 kB] 111s Get:173 http://ftpmaster.internal/ubuntu plucky/universe amd64 libngs-jni amd64 3.0.3+dfsg-9ubuntu1 [4848 B] 111s Get:174 http://ftpmaster.internal/ubuntu plucky/universe amd64 libngs-java amd64 3.0.3+dfsg-9ubuntu1 [91.1 kB] 111s Get:175 http://ftpmaster.internal/ubuntu plucky/universe amd64 librhino-java all 1.7.14-2.1 [1330 kB] 111s Get:176 http://ftpmaster.internal/ubuntu plucky/main amd64 libsnappy1v5 amd64 1.2.1-1 [30.4 kB] 111s Get:177 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsnappy-jni amd64 1.1.10.5-2 [6622 B] 111s Get:178 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsnappy-java all 1.1.10.5-2 [83.7 kB] 111s Get:179 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtsjdk-java all 4.1.0+dfsg-2 [1823 kB] 111s Get:180 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedcrypto7t64 amd64 2.28.8-1 [209 kB] 111s Get:181 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedx509-1t64 amd64 2.28.8-1 [46.6 kB] 111s Get:182 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedtls14t64 amd64 2.28.8-1 [82.2 kB] 111s Get:183 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [2107 kB] 111s Get:184 http://ftpmaster.internal/ubuntu plucky/universe amd64 libseqan2-dev all 2.4.0+dfsg-16 [1206 kB] 111s Get:185 http://ftpmaster.internal/ubuntu plucky/universe amd64 libspoa7.0.0 amd64 4.1.4-2 [79.1 kB] 111s Get:186 http://ftpmaster.internal/ubuntu plucky/universe amd64 libssw0 amd64 1.1-15 [22.5 kB] 111s Get:187 http://ftpmaster.internal/ubuntu plucky/universe amd64 miniasm amd64 0.3+dfsg-4 [30.3 kB] 111s Get:188 http://ftpmaster.internal/ubuntu plucky/universe amd64 ncbi-data all 6.1.20170106+dfsg2-5 [3966 kB] 111s Get:189 http://ftpmaster.internal/ubuntu plucky/universe amd64 ncbi-blast+ amd64 2.16.0+ds-6 [15.2 MB] 112s Get:190 http://ftpmaster.internal/ubuntu plucky/universe amd64 scala-library all 2.11.12-5 [9586 kB] 112s Get:191 http://ftpmaster.internal/ubuntu plucky/universe amd64 pilon all 1.24-3 [495 kB] 112s Get:192 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.0-2 [719 kB] 112s Get:193 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all amd64 3.12.7-1 [890 B] 112s Get:194 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-joblib all 1.3.2-5 [206 kB] 112s Get:195 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 112s Get:196 http://ftpmaster.internal/ubuntu plucky/universe amd64 racon amd64 1.5.0-3 [3113 kB] 112s Get:197 http://ftpmaster.internal/ubuntu plucky/universe amd64 samtools amd64 1.20-3 [599 kB] 112s Get:198 http://ftpmaster.internal/ubuntu plucky/universe amd64 libnlopt0 amd64 2.7.1-5ubuntu1 [183 kB] 112s Get:199 http://ftpmaster.internal/ubuntu plucky/universe amd64 spades amd64 3.15.5+dfsg-7 [9133 kB] 113s Get:200 http://ftpmaster.internal/ubuntu plucky/universe amd64 bowtie2 amd64 2.5.4-1 [1336 kB] 113s Get:201 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicycler amd64 0.5.0+dfsg-1 [862 kB] 113s Get:202 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicycler-data all 0.5.0+dfsg-1 [12.0 MB] 113s Get:203 http://ftpmaster.internal/ubuntu plucky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB] 114s Fetched 302 MB in 13s (24.0 MB/s) 114s Selecting previously unselected package libpython3.13-minimal:amd64. 114s (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 ... 75581 files and directories currently installed.) 114s Preparing to unpack .../000-libpython3.13-minimal_3.13.0-2_amd64.deb ... 114s Unpacking libpython3.13-minimal:amd64 (3.13.0-2) ... 114s Selecting previously unselected package python3.13-minimal. 114s Preparing to unpack .../001-python3.13-minimal_3.13.0-2_amd64.deb ... 114s Unpacking python3.13-minimal (3.13.0-2) ... 114s Selecting previously unselected package libgdk-pixbuf2.0-common. 114s Preparing to unpack .../002-libgdk-pixbuf2.0-common_2.42.12+dfsg-1_all.deb ... 114s Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-1) ... 114s Selecting previously unselected package libjpeg-turbo8:amd64. 114s Preparing to unpack .../003-libjpeg-turbo8_2.1.5-2ubuntu2_amd64.deb ... 114s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 114s Selecting previously unselected package libjpeg8:amd64. 114s Preparing to unpack .../004-libjpeg8_8c-2ubuntu11_amd64.deb ... 114s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 114s Selecting previously unselected package libdeflate0:amd64. 114s Preparing to unpack .../005-libdeflate0_1.22-1_amd64.deb ... 114s Unpacking libdeflate0:amd64 (1.22-1) ... 114s Selecting previously unselected package libjbig0:amd64. 114s Preparing to unpack .../006-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 114s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 114s Selecting previously unselected package liblerc4:amd64. 114s Preparing to unpack .../007-liblerc4_4.0.0+ds-4ubuntu2_amd64.deb ... 114s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 114s Selecting previously unselected package libsharpyuv0:amd64. 114s Preparing to unpack .../008-libsharpyuv0_1.4.0-0.1_amd64.deb ... 114s Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ... 114s Selecting previously unselected package libwebp7:amd64. 114s Preparing to unpack .../009-libwebp7_1.4.0-0.1_amd64.deb ... 114s Unpacking libwebp7:amd64 (1.4.0-0.1) ... 114s Selecting previously unselected package libtiff6:amd64. 114s Preparing to unpack .../010-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 114s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 114s Selecting previously unselected package libgdk-pixbuf-2.0-0:amd64. 114s Preparing to unpack .../011-libgdk-pixbuf-2.0-0_2.42.12+dfsg-1_amd64.deb ... 114s Unpacking libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-1) ... 114s Selecting previously unselected package gtk-update-icon-cache. 114s Preparing to unpack .../012-gtk-update-icon-cache_4.16.5+ds-1_amd64.deb ... 114s No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed. 114s 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. 114s Unpacking gtk-update-icon-cache (4.16.5+ds-1) ... 114s Selecting previously unselected package hicolor-icon-theme. 114s Preparing to unpack .../013-hicolor-icon-theme_0.18-1_all.deb ... 114s Unpacking hicolor-icon-theme (0.18-1) ... 114s Selecting previously unselected package humanity-icon-theme. 114s Preparing to unpack .../014-humanity-icon-theme_0.6.16_all.deb ... 114s Unpacking humanity-icon-theme (0.6.16) ... 115s Selecting previously unselected package ubuntu-mono. 115s Preparing to unpack .../015-ubuntu-mono_24.04-0ubuntu1_all.deb ... 115s Unpacking ubuntu-mono (24.04-0ubuntu1) ... 115s Selecting previously unselected package adwaita-icon-theme. 115s Preparing to unpack .../016-adwaita-icon-theme_47.0-2_all.deb ... 115s Unpacking adwaita-icon-theme (47.0-2) ... 116s Selecting previously unselected package at-spi2-common. 116s Preparing to unpack .../017-at-spi2-common_2.54.0-1_all.deb ... 116s Unpacking at-spi2-common (2.54.0-1) ... 116s Selecting previously unselected package m4. 116s Preparing to unpack .../018-m4_1.4.19-4build1_amd64.deb ... 116s Unpacking m4 (1.4.19-4build1) ... 116s Selecting previously unselected package autoconf. 116s Preparing to unpack .../019-autoconf_2.72-3_all.deb ... 116s Unpacking autoconf (2.72-3) ... 116s Selecting previously unselected package autotools-dev. 116s Preparing to unpack .../020-autotools-dev_20220109.1_all.deb ... 116s Unpacking autotools-dev (20220109.1) ... 116s Selecting previously unselected package automake. 116s Preparing to unpack .../021-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 116s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 116s Selecting previously unselected package autopoint. 116s Preparing to unpack .../022-autopoint_0.22.5-2_all.deb ... 116s Unpacking autopoint (0.22.5-2) ... 116s Selecting previously unselected package libbamtools2.5.2:amd64. 116s Preparing to unpack .../023-libbamtools2.5.2_2.5.2+dfsg-6build1_amd64.deb ... 116s Unpacking libbamtools2.5.2:amd64 (2.5.2+dfsg-6build1) ... 116s Selecting previously unselected package libjsoncpp26:amd64. 116s Preparing to unpack .../024-libjsoncpp26_1.9.6-2_amd64.deb ... 116s Unpacking libjsoncpp26:amd64 (1.9.6-2) ... 116s Selecting previously unselected package bamtools. 116s Preparing to unpack .../025-bamtools_2.5.2+dfsg-6build1_amd64.deb ... 116s Unpacking bamtools (2.5.2+dfsg-6build1) ... 116s Selecting previously unselected package libhtscodecs2:amd64. 116s Preparing to unpack .../026-libhtscodecs2_1.6.1-1_amd64.deb ... 116s Unpacking libhtscodecs2:amd64 (1.6.1-1) ... 116s Selecting previously unselected package libhts3t64:amd64. 116s Preparing to unpack .../027-libhts3t64_1.20+ds-1_amd64.deb ... 116s Unpacking libhts3t64:amd64 (1.20+ds-1) ... 116s Selecting previously unselected package bcftools. 116s Preparing to unpack .../028-bcftools_1.20-2_amd64.deb ... 116s Unpacking bcftools (1.20-2) ... 116s Selecting previously unselected package libisl23:amd64. 116s Preparing to unpack .../029-libisl23_0.27-1_amd64.deb ... 116s Unpacking libisl23:amd64 (0.27-1) ... 116s Selecting previously unselected package libmpc3:amd64. 116s Preparing to unpack .../030-libmpc3_1.3.1-1build2_amd64.deb ... 116s Unpacking libmpc3:amd64 (1.3.1-1build2) ... 116s Selecting previously unselected package cpp-14-x86-64-linux-gnu. 116s Preparing to unpack .../031-cpp-14-x86-64-linux-gnu_14.2.0-8ubuntu1_amd64.deb ... 116s Unpacking cpp-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 116s Selecting previously unselected package cpp-14. 116s Preparing to unpack .../032-cpp-14_14.2.0-8ubuntu1_amd64.deb ... 116s Unpacking cpp-14 (14.2.0-8ubuntu1) ... 116s Selecting previously unselected package cpp-x86-64-linux-gnu. 116s Preparing to unpack .../033-cpp-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ... 116s Unpacking cpp-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 116s Selecting previously unselected package cpp. 116s Preparing to unpack .../034-cpp_4%3a14.1.0-2ubuntu1_amd64.deb ... 116s Unpacking cpp (4:14.1.0-2ubuntu1) ... 116s Selecting previously unselected package libcc1-0:amd64. 116s Preparing to unpack .../035-libcc1-0_14.2.0-8ubuntu1_amd64.deb ... 116s Unpacking libcc1-0:amd64 (14.2.0-8ubuntu1) ... 116s Selecting previously unselected package libgomp1:amd64. 116s Preparing to unpack .../036-libgomp1_14.2.0-8ubuntu1_amd64.deb ... 116s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ... 116s Selecting previously unselected package libitm1:amd64. 116s Preparing to unpack .../037-libitm1_14.2.0-8ubuntu1_amd64.deb ... 116s Unpacking libitm1:amd64 (14.2.0-8ubuntu1) ... 116s Selecting previously unselected package libasan8:amd64. 116s Preparing to unpack .../038-libasan8_14.2.0-8ubuntu1_amd64.deb ... 116s Unpacking libasan8:amd64 (14.2.0-8ubuntu1) ... 116s Selecting previously unselected package liblsan0:amd64. 116s Preparing to unpack .../039-liblsan0_14.2.0-8ubuntu1_amd64.deb ... 116s Unpacking liblsan0:amd64 (14.2.0-8ubuntu1) ... 116s Selecting previously unselected package libtsan2:amd64. 116s Preparing to unpack .../040-libtsan2_14.2.0-8ubuntu1_amd64.deb ... 116s Unpacking libtsan2:amd64 (14.2.0-8ubuntu1) ... 116s Selecting previously unselected package libubsan1:amd64. 117s Preparing to unpack .../041-libubsan1_14.2.0-8ubuntu1_amd64.deb ... 117s Unpacking libubsan1:amd64 (14.2.0-8ubuntu1) ... 117s Selecting previously unselected package libhwasan0:amd64. 117s Preparing to unpack .../042-libhwasan0_14.2.0-8ubuntu1_amd64.deb ... 117s Unpacking libhwasan0:amd64 (14.2.0-8ubuntu1) ... 117s Selecting previously unselected package libquadmath0:amd64. 117s Preparing to unpack .../043-libquadmath0_14.2.0-8ubuntu1_amd64.deb ... 117s Unpacking libquadmath0:amd64 (14.2.0-8ubuntu1) ... 117s Selecting previously unselected package libgcc-14-dev:amd64. 117s Preparing to unpack .../044-libgcc-14-dev_14.2.0-8ubuntu1_amd64.deb ... 117s Unpacking libgcc-14-dev:amd64 (14.2.0-8ubuntu1) ... 117s Selecting previously unselected package gcc-14-x86-64-linux-gnu. 117s Preparing to unpack .../045-gcc-14-x86-64-linux-gnu_14.2.0-8ubuntu1_amd64.deb ... 117s Unpacking gcc-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 117s Selecting previously unselected package gcc-14. 117s Preparing to unpack .../046-gcc-14_14.2.0-8ubuntu1_amd64.deb ... 117s Unpacking gcc-14 (14.2.0-8ubuntu1) ... 117s Selecting previously unselected package gcc-x86-64-linux-gnu. 117s Preparing to unpack .../047-gcc-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ... 117s Unpacking gcc-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 117s Selecting previously unselected package gcc. 117s Preparing to unpack .../048-gcc_4%3a14.1.0-2ubuntu1_amd64.deb ... 117s Unpacking gcc (4:14.1.0-2ubuntu1) ... 117s Selecting previously unselected package libstdc++-14-dev:amd64. 117s Preparing to unpack .../049-libstdc++-14-dev_14.2.0-8ubuntu1_amd64.deb ... 117s Unpacking libstdc++-14-dev:amd64 (14.2.0-8ubuntu1) ... 117s Selecting previously unselected package g++-14-x86-64-linux-gnu. 117s Preparing to unpack .../050-g++-14-x86-64-linux-gnu_14.2.0-8ubuntu1_amd64.deb ... 117s Unpacking g++-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 117s Selecting previously unselected package g++-14. 117s Preparing to unpack .../051-g++-14_14.2.0-8ubuntu1_amd64.deb ... 117s Unpacking g++-14 (14.2.0-8ubuntu1) ... 117s Selecting previously unselected package g++-x86-64-linux-gnu. 118s Preparing to unpack .../052-g++-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ... 118s Unpacking g++-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 118s Selecting previously unselected package g++. 118s Preparing to unpack .../053-g++_4%3a14.1.0-2ubuntu1_amd64.deb ... 118s Unpacking g++ (4:14.1.0-2ubuntu1) ... 118s Selecting previously unselected package build-essential. 118s Preparing to unpack .../054-build-essential_12.10ubuntu1_amd64.deb ... 118s Unpacking build-essential (12.10ubuntu1) ... 118s Selecting previously unselected package bwa. 118s Preparing to unpack .../055-bwa_0.7.18-1_amd64.deb ... 118s Unpacking bwa (0.7.18-1) ... 118s Selecting previously unselected package ca-certificates-java. 118s Preparing to unpack .../056-ca-certificates-java_20240118_all.deb ... 118s Unpacking ca-certificates-java (20240118) ... 118s Selecting previously unselected package libdconf1:amd64. 118s Preparing to unpack .../057-libdconf1_0.40.0-4build2_amd64.deb ... 118s Unpacking libdconf1:amd64 (0.40.0-4build2) ... 118s Selecting previously unselected package dconf-service. 118s Preparing to unpack .../058-dconf-service_0.40.0-4build2_amd64.deb ... 118s Unpacking dconf-service (0.40.0-4build2) ... 118s Selecting previously unselected package dconf-gsettings-backend:amd64. 118s Preparing to unpack .../059-dconf-gsettings-backend_0.40.0-4build2_amd64.deb ... 118s Unpacking dconf-gsettings-backend:amd64 (0.40.0-4build2) ... 118s Selecting previously unselected package libdebhelper-perl. 118s Preparing to unpack .../060-libdebhelper-perl_13.20ubuntu1_all.deb ... 118s Unpacking libdebhelper-perl (13.20ubuntu1) ... 118s Selecting previously unselected package libtool. 118s Preparing to unpack .../061-libtool_2.4.7-7build1_all.deb ... 118s Unpacking libtool (2.4.7-7build1) ... 118s Selecting previously unselected package dh-autoreconf. 118s Preparing to unpack .../062-dh-autoreconf_20_all.deb ... 118s Unpacking dh-autoreconf (20) ... 118s Selecting previously unselected package libarchive-zip-perl. 118s Preparing to unpack .../063-libarchive-zip-perl_1.68-1_all.deb ... 118s Unpacking libarchive-zip-perl (1.68-1) ... 118s Selecting previously unselected package libfile-stripnondeterminism-perl. 118s Preparing to unpack .../064-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... 118s Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... 118s Selecting previously unselected package dh-strip-nondeterminism. 118s Preparing to unpack .../065-dh-strip-nondeterminism_1.14.0-1_all.deb ... 118s Unpacking dh-strip-nondeterminism (1.14.0-1) ... 118s Selecting previously unselected package debugedit. 118s Preparing to unpack .../066-debugedit_1%3a5.1-1_amd64.deb ... 118s Unpacking debugedit (1:5.1-1) ... 118s Selecting previously unselected package dwz. 118s Preparing to unpack .../067-dwz_0.15-1build6_amd64.deb ... 118s Unpacking dwz (0.15-1build6) ... 118s Selecting previously unselected package gettext. 118s Preparing to unpack .../068-gettext_0.22.5-2_amd64.deb ... 118s Unpacking gettext (0.22.5-2) ... 118s Selecting previously unselected package intltool-debian. 118s Preparing to unpack .../069-intltool-debian_0.35.0+20060710.6_all.deb ... 118s Unpacking intltool-debian (0.35.0+20060710.6) ... 118s Selecting previously unselected package po-debconf. 118s Preparing to unpack .../070-po-debconf_1.0.21+nmu1_all.deb ... 118s Unpacking po-debconf (1.0.21+nmu1) ... 118s Selecting previously unselected package debhelper. 118s Preparing to unpack .../071-debhelper_13.20ubuntu1_all.deb ... 118s Unpacking debhelper (13.20ubuntu1) ... 118s Selecting previously unselected package java-common. 118s Preparing to unpack .../072-java-common_0.76_all.deb ... 118s Unpacking java-common (0.76) ... 118s Selecting previously unselected package liblcms2-2:amd64. 118s Preparing to unpack .../073-liblcms2-2_2.16-2_amd64.deb ... 118s Unpacking liblcms2-2:amd64 (2.16-2) ... 118s Selecting previously unselected package libpcsclite1:amd64. 118s Preparing to unpack .../074-libpcsclite1_2.3.0-3_amd64.deb ... 118s Unpacking libpcsclite1:amd64 (2.3.0-3) ... 118s Selecting previously unselected package openjdk-21-jre-headless:amd64. 118s Preparing to unpack .../075-openjdk-21-jre-headless_21.0.5+11-1_amd64.deb ... 118s Unpacking openjdk-21-jre-headless:amd64 (21.0.5+11-1) ... 119s Selecting previously unselected package default-jre-headless. 119s Preparing to unpack .../076-default-jre-headless_2%3a1.21-76_amd64.deb ... 119s Unpacking default-jre-headless (2:1.21-76) ... 119s Selecting previously unselected package libatk1.0-0t64:amd64. 119s Preparing to unpack .../077-libatk1.0-0t64_2.54.0-1_amd64.deb ... 119s Unpacking libatk1.0-0t64:amd64 (2.54.0-1) ... 119s Selecting previously unselected package libxi6:amd64. 119s Preparing to unpack .../078-libxi6_2%3a1.8.2-1_amd64.deb ... 119s Unpacking libxi6:amd64 (2:1.8.2-1) ... 119s Selecting previously unselected package libatspi2.0-0t64:amd64. 119s Preparing to unpack .../079-libatspi2.0-0t64_2.54.0-1_amd64.deb ... 119s Unpacking libatspi2.0-0t64:amd64 (2.54.0-1) ... 119s Selecting previously unselected package libatk-bridge2.0-0t64:amd64. 119s Preparing to unpack .../080-libatk-bridge2.0-0t64_2.54.0-1_amd64.deb ... 119s Unpacking libatk-bridge2.0-0t64:amd64 (2.54.0-1) ... 119s Selecting previously unselected package fonts-dejavu-mono. 119s Preparing to unpack .../081-fonts-dejavu-mono_2.37-8_all.deb ... 119s Unpacking fonts-dejavu-mono (2.37-8) ... 119s Selecting previously unselected package fonts-dejavu-core. 119s Preparing to unpack .../082-fonts-dejavu-core_2.37-8_all.deb ... 119s Unpacking fonts-dejavu-core (2.37-8) ... 119s Selecting previously unselected package fontconfig-config. 119s Preparing to unpack .../083-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 119s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 119s Selecting previously unselected package libfontconfig1:amd64. 119s Preparing to unpack .../084-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 119s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 119s Selecting previously unselected package libpixman-1-0:amd64. 119s Preparing to unpack .../085-libpixman-1-0_0.44.0-3_amd64.deb ... 119s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 120s Selecting previously unselected package libxcb-render0:amd64. 120s 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unpack .../096-libepoxy0_1.5.10-2_amd64.deb ... 120s Unpacking libepoxy0:amd64 (1.5.10-2) ... 120s Selecting previously unselected package libgraphite2-3:amd64. 120s Preparing to unpack .../097-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 120s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 120s Selecting previously unselected package libharfbuzz0b:amd64. 120s Preparing to unpack .../098-libharfbuzz0b_10.0.1-1_amd64.deb ... 120s Unpacking libharfbuzz0b:amd64 (10.0.1-1) ... 120s Selecting previously unselected package fontconfig. 120s Preparing to unpack .../099-fontconfig_2.15.0-1.1ubuntu2_amd64.deb ... 120s Unpacking fontconfig (2.15.0-1.1ubuntu2) ... 120s Selecting previously unselected package libthai-data. 120s Preparing to unpack .../100-libthai-data_0.1.29-2build1_all.deb ... 120s Unpacking libthai-data (0.1.29-2build1) ... 120s Selecting previously unselected package libdatrie1:amd64. 120s Preparing to unpack .../101-libdatrie1_0.2.13-3build1_amd64.deb ... 120s Unpacking libdatrie1:amd64 (0.2.13-3build1) ... 120s Selecting previously unselected package libthai0:amd64. 120s Preparing to unpack .../102-libthai0_0.1.29-2build1_amd64.deb ... 120s Unpacking libthai0:amd64 (0.1.29-2build1) ... 120s Selecting previously unselected package libpango-1.0-0:amd64. 120s Preparing to unpack .../103-libpango-1.0-0_1.54.0+ds-3_amd64.deb ... 120s Unpacking libpango-1.0-0:amd64 (1.54.0+ds-3) ... 120s Selecting previously unselected package libpangoft2-1.0-0:amd64. 120s Preparing to unpack .../104-libpangoft2-1.0-0_1.54.0+ds-3_amd64.deb ... 120s Unpacking libpangoft2-1.0-0:amd64 (1.54.0+ds-3) ... 120s Selecting previously unselected package libpangocairo-1.0-0:amd64. 120s Preparing to unpack .../105-libpangocairo-1.0-0_1.54.0+ds-3_amd64.deb ... 120s Unpacking libpangocairo-1.0-0:amd64 (1.54.0+ds-3) ... 120s Selecting previously unselected package libwayland-client0:amd64. 120s Preparing to unpack .../106-libwayland-client0_1.23.0-1_amd64.deb ... 120s Unpacking libwayland-client0:amd64 (1.23.0-1) ... 120s Selecting previously unselected package libwayland-cursor0:amd64. 120s Preparing to unpack .../107-libwayland-cursor0_1.23.0-1_amd64.deb ... 120s Unpacking libwayland-cursor0:amd64 (1.23.0-1) ... 120s Selecting previously unselected package libwayland-egl1:amd64. 120s Preparing to unpack .../108-libwayland-egl1_1.23.0-1_amd64.deb ... 120s Unpacking libwayland-egl1:amd64 (1.23.0-1) ... 120s Selecting previously unselected package libxcomposite1:amd64. 120s Preparing to unpack .../109-libxcomposite1_1%3a0.4.6-1_amd64.deb ... 120s Unpacking libxcomposite1:amd64 (1:0.4.6-1) ... 120s Selecting previously unselected package libxfixes3:amd64. 120s Preparing to unpack .../110-libxfixes3_1%3a6.0.0-2build1_amd64.deb ... 120s Unpacking libxfixes3:amd64 (1:6.0.0-2build1) ... 120s Selecting previously unselected package libxcursor1:amd64. 120s Preparing to unpack .../111-libxcursor1_1%3a1.2.2-1_amd64.deb ... 120s Unpacking libxcursor1:amd64 (1:1.2.2-1) ... 120s Selecting previously unselected package libxdamage1:amd64. 120s Preparing to unpack .../112-libxdamage1_1%3a1.1.6-1build1_amd64.deb ... 120s Unpacking libxdamage1:amd64 (1:1.1.6-1build1) ... 120s Selecting previously unselected package libxinerama1:amd64. 120s Preparing to unpack .../113-libxinerama1_2%3a1.1.4-3build1_amd64.deb ... 120s Unpacking libxinerama1:amd64 (2:1.1.4-3build1) ... 120s Selecting previously unselected package libxrandr2:amd64. 120s Preparing to unpack .../114-libxrandr2_2%3a1.5.4-1_amd64.deb ... 120s Unpacking libxrandr2:amd64 (2:1.5.4-1) ... 120s Selecting previously unselected package libgtk-3-common. 120s Preparing to unpack .../115-libgtk-3-common_3.24.43-3ubuntu2_all.deb ... 120s Unpacking libgtk-3-common (3.24.43-3ubuntu2) ... 120s Selecting previously unselected package libgtk-3-0t64:amd64. 120s Preparing to unpack .../116-libgtk-3-0t64_3.24.43-3ubuntu2_amd64.deb ... 120s Unpacking libgtk-3-0t64:amd64 (3.24.43-3ubuntu2) ... 120s Selecting previously unselected package libglvnd0:amd64. 120s Preparing to unpack .../117-libglvnd0_1.7.0-1build1_amd64.deb ... 120s Unpacking libglvnd0:amd64 (1.7.0-1build1) ... 120s Selecting previously unselected package libglapi-mesa:amd64. 120s Preparing to unpack .../118-libglapi-mesa_24.2.3-1ubuntu1_amd64.deb ... 120s Unpacking libglapi-mesa:amd64 (24.2.3-1ubuntu1) ... 120s Selecting previously unselected package libx11-xcb1:amd64. 120s Preparing to unpack .../119-libx11-xcb1_2%3a1.8.10-2_amd64.deb ... 120s Unpacking libx11-xcb1:amd64 (2:1.8.10-2) ... 120s Selecting previously unselected package libxcb-dri2-0:amd64. 120s Preparing to unpack .../120-libxcb-dri2-0_1.17.0-2_amd64.deb ... 120s Unpacking libxcb-dri2-0:amd64 (1.17.0-2) ... 120s Selecting previously unselected package libxcb-dri3-0:amd64. 120s Preparing to unpack .../121-libxcb-dri3-0_1.17.0-2_amd64.deb ... 120s Unpacking libxcb-dri3-0:amd64 (1.17.0-2) ... 120s Selecting previously unselected package libxcb-glx0:amd64. 120s 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121s Unpacking libxshmfence1:amd64 (1.3-1build5) ... 121s Selecting previously unselected package libxxf86vm1:amd64. 121s Preparing to unpack .../128-libxxf86vm1_1%3a1.1.4-1build4_amd64.deb ... 121s Unpacking libxxf86vm1:amd64 (1:1.1.4-1build4) ... 121s Selecting previously unselected package libdrm-amdgpu1:amd64. 121s Preparing to unpack .../129-libdrm-amdgpu1_2.4.123-1_amd64.deb ... 121s Unpacking libdrm-amdgpu1:amd64 (2.4.123-1) ... 121s Selecting previously unselected package libpciaccess0:amd64. 121s Preparing to unpack .../130-libpciaccess0_0.17-3build1_amd64.deb ... 121s Unpacking libpciaccess0:amd64 (0.17-3build1) ... 121s Selecting previously unselected package libdrm-intel1:amd64. 121s Preparing to unpack .../131-libdrm-intel1_2.4.123-1_amd64.deb ... 121s Unpacking libdrm-intel1:amd64 (2.4.123-1) ... 121s Selecting previously unselected package libdrm-radeon1:amd64. 121s Preparing to unpack .../132-libdrm-radeon1_2.4.123-1_amd64.deb ... 121s Unpacking libdrm-radeon1:amd64 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Selecting previously unselected package libglx-mesa0:amd64. 121s Preparing to unpack .../138-libglx-mesa0_24.2.3-1ubuntu1_amd64.deb ... 121s Unpacking libglx-mesa0:amd64 (24.2.3-1ubuntu1) ... 121s Selecting previously unselected package libglx0:amd64. 121s Preparing to unpack .../139-libglx0_1.7.0-1build1_amd64.deb ... 121s Unpacking libglx0:amd64 (1.7.0-1build1) ... 121s Selecting previously unselected package libgl1:amd64. 121s Preparing to unpack .../140-libgl1_1.7.0-1build1_amd64.deb ... 121s Unpacking libgl1:amd64 (1.7.0-1build1) ... 121s Selecting previously unselected package libasound2-data. 121s Preparing to unpack .../141-libasound2-data_1.2.12-1_all.deb ... 121s Unpacking libasound2-data (1.2.12-1) ... 121s Selecting previously unselected package libasound2t64:amd64. 121s Preparing to unpack .../142-libasound2t64_1.2.12-1_amd64.deb ... 121s Unpacking libasound2t64:amd64 (1.2.12-1) ... 121s Selecting previously unselected package libgif7:amd64. 121s Preparing to unpack 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Unpacking openjdk-21-jdk-headless:amd64 (21.0.5+11-1) ... 122s Selecting previously unselected package default-jdk-headless. 122s Preparing to unpack .../149-default-jdk-headless_2%3a1.21-76_amd64.deb ... 122s Unpacking default-jdk-headless (2:1.21-76) ... 122s Selecting previously unselected package openjdk-21-jdk:amd64. 122s Preparing to unpack .../150-openjdk-21-jdk_21.0.5+11-1_amd64.deb ... 122s Unpacking openjdk-21-jdk:amd64 (21.0.5+11-1) ... 122s Selecting previously unselected package default-jdk. 122s Preparing to unpack .../151-default-jdk_2%3a1.21-76_amd64.deb ... 122s Unpacking default-jdk (2:1.21-76) ... 122s Selecting previously unselected package dh-python. 122s Preparing to unpack .../152-dh-python_6.20241024_all.deb ... 122s Unpacking dh-python (6.20241024) ... 122s Selecting previously unselected package unzip. 122s Preparing to unpack .../153-unzip_6.0-28ubuntu6_amd64.deb ... 122s Unpacking unzip (6.0-28ubuntu6) ... 122s Selecting previously unselected package java-wrappers. 122s Preparing to unpack .../154-java-wrappers_0.5_all.deb ... 122s Unpacking java-wrappers (0.5) ... 122s Selecting previously unselected package libapache-pom-java. 122s Preparing to unpack .../155-libapache-pom-java_33-2_all.deb ... 122s Unpacking libapache-pom-java (33-2) ... 122s Selecting previously unselected package libcommons-parent-java. 122s Preparing to unpack .../156-libcommons-parent-java_56-1_all.deb ... 122s Unpacking libcommons-parent-java (56-1) ... 122s Selecting previously unselected package libcommons-codec-java. 122s Preparing to unpack .../157-libcommons-codec-java_1.17.1-1_all.deb ... 122s Unpacking libcommons-codec-java (1.17.1-1) ... 122s Selecting previously unselected package libcommons-io-java. 122s Preparing to unpack .../158-libcommons-io-java_2.17.0-1_all.deb ... 122s Unpacking libcommons-io-java (2.17.0-1) ... 122s Selecting previously unselected package libcommons-compress-java. 122s Preparing to unpack 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... 122s Unpacking libmjson-java (1.4.0-3) ... 122s Selecting previously unselected package libmbedcrypto16:amd64. 122s Preparing to unpack .../165-libmbedcrypto16_3.6.2-2ubuntu1_amd64.deb ... 122s Unpacking libmbedcrypto16:amd64 (3.6.2-2ubuntu1) ... 122s Selecting previously unselected package libmbedx509-7:amd64. 122s Preparing to unpack .../166-libmbedx509-7_3.6.2-2ubuntu1_amd64.deb ... 122s Unpacking libmbedx509-7:amd64 (3.6.2-2ubuntu1) ... 122s Selecting previously unselected package libmbedtls21:amd64. 122s Preparing to unpack .../167-libmbedtls21_3.6.2-2ubuntu1_amd64.deb ... 122s Unpacking libmbedtls21:amd64 (3.6.2-2ubuntu1) ... 122s Selecting previously unselected package ncbi-vdb-data. 122s Preparing to unpack .../168-ncbi-vdb-data_3.0.9+dfsg-2_all.deb ... 122s Unpacking ncbi-vdb-data (3.0.9+dfsg-2) ... 122s Selecting previously unselected package libncbi-vdb3:amd64. 122s Preparing to unpack .../169-libncbi-vdb3_3.0.9+dfsg-2_amd64.deb ... 122s Unpacking libncbi-vdb3:amd64 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previously unselected package libsnappy-jni. 122s Preparing to unpack .../175-libsnappy-jni_1.1.10.5-2_amd64.deb ... 122s Unpacking libsnappy-jni (1.1.10.5-2) ... 122s Selecting previously unselected package libsnappy-java. 122s Preparing to unpack .../176-libsnappy-java_1.1.10.5-2_all.deb ... 122s Unpacking libsnappy-java (1.1.10.5-2) ... 122s Selecting previously unselected package libhtsjdk-java. 122s Preparing to unpack .../177-libhtsjdk-java_4.1.0+dfsg-2_all.deb ... 122s Unpacking libhtsjdk-java (4.1.0+dfsg-2) ... 122s Selecting previously unselected package libmbedcrypto7t64:amd64. 122s Preparing to unpack .../178-libmbedcrypto7t64_2.28.8-1_amd64.deb ... 122s Unpacking libmbedcrypto7t64:amd64 (2.28.8-1) ... 122s Selecting previously unselected package libmbedx509-1t64:amd64. 122s Preparing to unpack .../179-libmbedx509-1t64_2.28.8-1_amd64.deb ... 122s Unpacking libmbedx509-1t64:amd64 (2.28.8-1) ... 122s Selecting previously unselected package libmbedtls14t64:amd64. 122s Preparing to unpack .../180-libmbedtls14t64_2.28.8-1_amd64.deb ... 122s Unpacking libmbedtls14t64:amd64 (2.28.8-1) ... 123s Selecting previously unselected package libpython3.13-stdlib:amd64. 123s Preparing to unpack .../181-libpython3.13-stdlib_3.13.0-2_amd64.deb ... 123s Unpacking libpython3.13-stdlib:amd64 (3.13.0-2) ... 123s Selecting previously unselected package libseqan2-dev. 123s Preparing to unpack .../182-libseqan2-dev_2.4.0+dfsg-16_all.deb ... 123s Unpacking libseqan2-dev (2.4.0+dfsg-16) ... 123s Selecting previously unselected package libspoa7.0.0:amd64. 123s Preparing to unpack .../183-libspoa7.0.0_4.1.4-2_amd64.deb ... 123s Unpacking libspoa7.0.0:amd64 (4.1.4-2) ... 123s Selecting previously unselected package libssw0:amd64. 123s Preparing to unpack .../184-libssw0_1.1-15_amd64.deb ... 123s Unpacking libssw0:amd64 (1.1-15) ... 123s Selecting previously unselected package miniasm. 123s Preparing to unpack .../185-miniasm_0.3+dfsg-4_amd64.deb ... 123s Unpacking miniasm (0.3+dfsg-4) ... 123s Selecting previously unselected package ncbi-data. 123s Preparing to unpack .../186-ncbi-data_6.1.20170106+dfsg2-5_all.deb ... 123s Unpacking ncbi-data (6.1.20170106+dfsg2-5) ... 123s Selecting previously unselected package ncbi-blast+. 123s Preparing to unpack .../187-ncbi-blast+_2.16.0+ds-6_amd64.deb ... 123s Unpacking ncbi-blast+ (2.16.0+ds-6) ... 123s Selecting previously unselected package scala-library. 123s Preparing to unpack .../188-scala-library_2.11.12-5_all.deb ... 123s Unpacking scala-library (2.11.12-5) ... 124s Selecting previously unselected package pilon. 124s Preparing to unpack .../189-pilon_1.24-3_all.deb ... 124s Unpacking pilon (1.24-3) ... 124s Selecting previously unselected package python3.13. 124s Preparing to unpack .../190-python3.13_3.13.0-2_amd64.deb ... 124s Unpacking python3.13 (3.13.0-2) ... 124s Selecting previously unselected package python3-all. 124s Preparing to unpack .../191-python3-all_3.12.7-1_amd64.deb ... 124s Unpacking python3-all (3.12.7-1) ... 124s Selecting previously unselected package python3-joblib. 124s Preparing to unpack .../192-python3-joblib_1.3.2-5_all.deb ... 124s Unpacking python3-joblib (1.3.2-5) ... 124s Selecting previously unselected package python3-packaging. 124s Preparing to unpack .../193-python3-packaging_24.1-1_all.deb ... 124s Unpacking python3-packaging (24.1-1) ... 124s Selecting previously unselected package racon. 124s Preparing to unpack .../194-racon_1.5.0-3_amd64.deb ... 124s Unpacking racon (1.5.0-3) ... 124s Selecting previously unselected package samtools. 124s Preparing to unpack .../195-samtools_1.20-3_amd64.deb ... 124s Unpacking samtools (1.20-3) ... 124s Selecting previously unselected package libnlopt0:amd64. 124s Preparing to unpack .../196-libnlopt0_2.7.1-5ubuntu1_amd64.deb ... 124s Unpacking libnlopt0:amd64 (2.7.1-5ubuntu1) ... 124s Selecting previously unselected package spades. 124s Preparing to unpack .../197-spades_3.15.5+dfsg-7_amd64.deb ... 124s Unpacking spades (3.15.5+dfsg-7) ... 124s Selecting previously unselected package bowtie2. 124s Preparing to unpack .../198-bowtie2_2.5.4-1_amd64.deb ... 124s Unpacking bowtie2 (2.5.4-1) ... 124s Selecting previously unselected package unicycler. 124s Preparing to unpack .../199-unicycler_0.5.0+dfsg-1_amd64.deb ... 124s Unpacking unicycler (0.5.0+dfsg-1) ... 124s Selecting previously unselected package unicycler-data. 124s Preparing to unpack .../200-unicycler-data_0.5.0+dfsg-1_all.deb ... 124s Unpacking unicycler-data (0.5.0+dfsg-1) ... 124s Selecting previously unselected package zlib1g-dev:amd64. 124s Preparing to unpack .../201-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_amd64.deb ... 124s Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 124s Selecting previously unselected package autopkgtest-satdep. 124s Preparing to unpack .../202-1-autopkgtest-satdep.deb ... 124s Unpacking autopkgtest-satdep (0) ... 124s Setting up libhtscodecs2:amd64 (1.6.1-1) ... 124s Setting up dh-python (6.20241024) ... 124s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 124s Setting up libxcb-dri3-0:amd64 (1.17.0-2) ... 124s Setting up liblcms2-2:amd64 (2.16-2) ... 124s Setting up ncbi-data (6.1.20170106+dfsg2-5) ... 124s Setting up libpixman-1-0:amd64 (0.44.0-3) ... 124s Setting up libsharpyuv0:amd64 (1.4.0-0.1) ... 124s Setting up libwayland-server0:amd64 (1.23.0-1) ... 124s Setting up libx11-xcb1:amd64 (2:1.8.10-2) ... 124s Setting up libpciaccess0:amd64 (0.17-3build1) ... 124s Setting up libxdamage1:amd64 (1:1.1.6-1build1) ... 124s Setting up libxcb-xfixes0:amd64 (1.17.0-2) ... 124s Setting up liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 124s Setting up hicolor-icon-theme (0.18-1) ... 124s Setting up libxi6:amd64 (2:1.8.2-1) ... 124s Setting up libmbedcrypto7t64:amd64 (2.28.8-1) ... 124s Setting up java-common (0.76) ... 124s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 124s Setting up libdatrie1:amd64 (0.2.13-3build1) ... 124s Setting up python3-joblib (1.3.2-5) ... 125s Setting up miniasm (0.3+dfsg-4) ... 125s Setting up libxcb-render0:amd64 (1.17.0-2) ... 125s Setting up libarchive-zip-perl (1.68-1) ... 125s Setting up libdrm-radeon1:amd64 (2.4.123-1) ... 125s Setting up bwa (0.7.18-1) ... 125s Setting up libglvnd0:amd64 (1.7.0-1build1) ... 125s Setting up unicycler-data (0.5.0+dfsg-1) ... 125s Setting up libmjson-java (1.4.0-3) ... 125s Setting up libxcb-glx0:amd64 (1.17.0-2) ... 125s Setting up unzip (6.0-28ubuntu6) ... 125s Setting up libdebhelper-perl (13.20ubuntu1) ... 125s Setting up libdrm-intel1:amd64 (2.4.123-1) ... 125s Setting up libgdk-pixbuf2.0-common (2.42.12+dfsg-1) ... 125s Setting up x11-common (1:7.7+23ubuntu3) ... 125s Setting up libdeflate0:amd64 (1.22-1) ... 125s Setting up m4 (1.4.19-4build1) ... 125s Setting up scala-library (2.11.12-5) ... 125s Setting up libnlopt0:amd64 (2.7.1-5ubuntu1) ... 125s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 125s Setting up libgomp1:amd64 (14.2.0-8ubuntu1) ... 125s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 125s Setting up libcolord2:amd64 (1.4.7-1build2) ... 125s Setting up libxxf86vm1:amd64 (1:1.1.4-1build4) ... 125s Setting up libsnappy1v5:amd64 (1.2.1-1) ... 125s Setting up bowtie2 (2.5.4-1) ... 125s Setting up libseqan2-dev (2.4.0+dfsg-16) ... 125s Setting up libxcb-present0:amd64 (1.17.0-2) ... 125s Setting up libdconf1:amd64 (0.40.0-4build2) ... 125s Setting up libpython3.13-minimal:amd64 (3.13.0-2) ... 125s Setting up libasound2-data (1.2.12-1) ... 125s Setting up librhino-java (1.7.14-2.1) ... 125s Setting up autotools-dev (20220109.1) ... 125s Setting up python3-packaging (24.1-1) ... 125s Setting up libasound2t64:amd64 (1.2.12-1) ... 125s Setting up libepoxy0:amd64 (1.5.10-2) ... 125s Setting up libxfixes3:amd64 (1:6.0.0-2build1) ... 125s Setting up libxcb-sync1:amd64 (1.17.0-2) ... 125s Setting up libjsoncpp26:amd64 (1.9.6-2) ... 125s Setting up libapache-pom-java (33-2) ... 125s Setting up libavahi-common-data:amd64 (0.8-13ubuntu6) ... 125s Setting up libatspi2.0-0t64:amd64 (2.54.0-1) ... 125s Setting up libquadmath0:amd64 (14.2.0-8ubuntu1) ... 125s Setting up libxinerama1:amd64 (2:1.1.4-3build1) ... 125s Setting up fonts-dejavu-mono (2.37-8) ... 125s Setting up libspoa7.0.0:amd64 (4.1.4-2) ... 125s Setting up libmpc3:amd64 (1.3.1-1build2) ... 125s Setting up libxrandr2:amd64 (2:1.5.4-1) ... 125s Setting up autopoint (0.22.5-2) ... 125s Setting up fonts-dejavu-core (2.37-8) ... 125s Setting up libpcsclite1:amd64 (2.3.0-3) ... 125s Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 125s Setting up libbamtools2.5.2:amd64 (2.5.2+dfsg-6build1) ... 125s Setting up libglapi-mesa:amd64 (24.2.3-1ubuntu1) ... 125s Setting up libvulkan1:amd64 (1.3.296.0-1) ... 125s Setting up autoconf (2.72-3) ... 125s Setting up libwebp7:amd64 (1.4.0-0.1) ... 125s Setting up libubsan1:amd64 (14.2.0-8ubuntu1) ... 125s Setting up libxcb-dri2-0:amd64 (1.17.0-2) ... 125s Setting up libgif7:amd64 (5.2.2-1ubuntu1) ... 125s Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 125s Setting up libedlib1:amd64 (1.2.7-6) ... 125s Setting up dwz (0.15-1build6) ... 125s Setting up libxshmfence1:amd64 (1.3-1build5) ... 125s Setting up libhwasan0:amd64 (14.2.0-8ubuntu1) ... 125s Setting up at-spi2-common (2.54.0-1) ... 125s Setting up bamtools (2.5.2+dfsg-6build1) ... 125s Setting up libxcb-randr0:amd64 (1.17.0-2) ... 125s Setting up libasan8:amd64 (14.2.0-8ubuntu1) ... 125s Setting up debugedit (1:5.1-1) ... 125s Setting up libhts3t64:amd64 (1.20+ds-1) ... 125s Setting up python3.13-minimal (3.13.0-2) ... 126s Setting up libharfbuzz0b:amd64 (10.0.1-1) ... 126s Setting up ncbi-vdb-data (3.0.9+dfsg-2) ... 126s Setting up libthai-data (0.1.29-2build1) ... 126s Setting up libwayland-egl1:amd64 (1.23.0-1) ... 126s Setting up libmbedcrypto16:amd64 (3.6.2-2ubuntu1) ... 126s Setting up libtsan2:amd64 (14.2.0-8ubuntu1) ... 126s Setting up ca-certificates-java (20240118) ... 126s No JRE found. Skipping Java certificates setup. 126s Setting up libisl23:amd64 (0.27-1) ... 126s Setting up libsnappy-jni (1.1.10.5-2) ... 126s Setting up libxcomposite1:amd64 (1:0.4.6-1) ... 126s Setting up libpython3.13-stdlib:amd64 (3.13.0-2) ... 126s Setting up libssw0:amd64 (1.1-15) ... 126s Setting up libcc1-0:amd64 (14.2.0-8ubuntu1) ... 126s Setting up liblsan0:amd64 (14.2.0-8ubuntu1) ... 126s Setting up libitm1:amd64 (14.2.0-8ubuntu1) ... 126s Setting up libdrm-amdgpu1:amd64 (2.4.123-1) ... 126s Setting up libwayland-client0:amd64 (1.23.0-1) ... 126s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 126s Setting up automake (1:1.16.5-1.3ubuntu1) ... 126s update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode 126s Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... 126s Setting up mesa-libgallium:amd64 (24.2.3-1ubuntu1) ... 126s Setting up gettext (0.22.5-2) ... 126s Setting up libmbedx509-1t64:amd64 (2.28.8-1) ... 126s Setting up java-wrappers (0.5) ... 126s Setting up libatk1.0-0t64:amd64 (2.54.0-1) ... 126s Setting up openjdk-21-jre-headless:amd64 (21.0.5+11-1) ... 126s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode 126s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 126s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 126s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 126s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 126s Setting up libgbm1:amd64 (24.2.3-1ubuntu1) ... 126s Setting up python3.13 (3.13.0-2) ... 127s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 127s Setting up libxtst6:amd64 (2:1.2.3-1.1build1) ... 127s Setting up libxcursor1:amd64 (1:1.2.2-1) ... 127s Setting up libgl1-mesa-dri:amd64 (24.2.3-1ubuntu1) ... 127s Setting up bcftools (1.20-2) ... 127s Setting up libcommons-parent-java (56-1) ... 127s Setting up libavahi-common3:amd64 (0.8-13ubuntu6) ... 127s Setting up libcommons-logging-java (1.3.0-1ubuntu1) ... 127s Setting up python3-all (3.12.7-1) ... 127s Setting up dconf-service (0.40.0-4build2) ... 127s Setting up libcommons-lang-java (2.6-10) ... 127s Setting up samtools (1.20-3) ... 127s Setting up intltool-debian (0.35.0+20060710.6) ... 127s Setting up libcommons-jexl2-java (2.1.1-6) ... 127s Setting up libthai0:amd64 (0.1.29-2build1) ... 127s Setting up libmbedx509-7:amd64 (3.6.2-2ubuntu1) ... 127s Setting up racon (1.5.0-3) ... 127s Setting up cpp-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 127s Setting up cpp-14 (14.2.0-8ubuntu1) ... 127s Setting up libmbedtls21:amd64 (3.6.2-2ubuntu1) ... 127s Setting up dh-strip-nondeterminism (1.14.0-1) ... 127s Setting up libmbedtls14t64:amd64 (2.28.8-1) ... 127s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 127s Setting up libwayland-cursor0:amd64 (1.23.0-1) ... 127s Setting up spades (3.15.5+dfsg-7) ... 127s /usr/share/spades/spades_pipeline/support.py:531: SyntaxWarning: invalid escape sequence '\d' 127s return [atoi(c) for c in re.split("(\d+)", text)] 127s Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-1) ... 127s Setting up libsnappy-java (1.1.10.5-2) ... 127s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 127s Setting up libgcc-14-dev:amd64 (14.2.0-8ubuntu1) ... 127s Setting up libcommons-codec-java (1.17.1-1) ... 127s Setting up libstdc++-14-dev:amd64 (14.2.0-8ubuntu1) ... 127s Setting up libavahi-client3:amd64 (0.8-13ubuntu6) ... 127s Setting up cpp-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 127s Setting up libatk-bridge2.0-0t64:amd64 (2.54.0-1) ... 127s Setting up gtk-update-icon-cache (4.16.5+ds-1) ... 127s Setting up fontconfig (2.15.0-1.1ubuntu2) ... 129s Regenerating fonts cache... done. 129s Setting up libglx-mesa0:amd64 (24.2.3-1ubuntu1) ... 129s Setting up libglx0:amd64 (1.7.0-1build1) ... 129s Setting up dconf-gsettings-backend:amd64 (0.40.0-4build2) ... 129s Setting up libcommons-io-java (2.17.0-1) ... 129s Setting up po-debconf (1.0.21+nmu1) ... 129s Setting up libpango-1.0-0:amd64 (1.54.0+ds-3) ... 129s Setting up libncbi-vdb3:amd64 (3.0.9+dfsg-2) ... 129s Setting up libcairo2:amd64 (1.18.2-2) ... 129s Setting up ncbi-blast+ (2.16.0+ds-6) ... 129s Setting up libgl1:amd64 (1.7.0-1build1) ... 129s Setting up cpp (4:14.1.0-2ubuntu1) ... 129s Setting up libcairo-gobject2:amd64 (1.18.2-2) ... 129s Setting up gcc-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 129s Setting up libpangoft2-1.0-0:amd64 (1.54.0+ds-3) ... 129s Setting up libcups2t64:amd64 (2.4.10-1ubuntu2) ... 129s Setting up libgtk-3-common (3.24.43-3ubuntu2) ... 129s Setting up libpangocairo-1.0-0:amd64 (1.54.0+ds-3) ... 129s Setting up libncbi-ngs3:amd64 (3.0.3+dfsg-9ubuntu1) ... 129s Setting up libngs-jni:amd64 (3.0.3+dfsg-9ubuntu1) ... 129s Setting up gcc-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 129s Setting up libcommons-compress-java (1.27.1-2) ... 129s Setting up gcc-14 (14.2.0-8ubuntu1) ... 129s Setting up g++-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 129s Setting up g++-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 129s Setting up g++-14 (14.2.0-8ubuntu1) ... 129s Setting up libngs-java:amd64 (3.0.3+dfsg-9ubuntu1) ... 129s Setting up libhtsjdk-java (4.1.0+dfsg-2) ... 129s Setting up libtool (2.4.7-7build1) ... 129s Setting up gcc (4:14.1.0-2ubuntu1) ... 129s Setting up dh-autoreconf (20) ... 129s Setting up g++ (4:14.1.0-2ubuntu1) ... 129s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 129s Setting up build-essential (12.10ubuntu1) ... 129s Setting up debhelper (13.20ubuntu1) ... 129s Setting up adwaita-icon-theme (47.0-2) ... 129s update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode 129s Setting up humanity-icon-theme (0.6.16) ... 129s Setting up ubuntu-mono (24.04-0ubuntu1) ... 129s Processing triggers for systemd (256.5-2ubuntu4) ... 130s Processing triggers for man-db (2.13.0-1) ... 131s Processing triggers for libglib2.0-0t64:amd64 (2.82.1-0ubuntu1) ... 131s Setting up libgtk-3-0t64:amd64 (3.24.43-3ubuntu2) ... 131s Processing triggers for install-info (7.1.1-1) ... 131s Processing triggers for libc-bin (2.40-1ubuntu3) ... 131s Processing triggers for ca-certificates-java (20240118) ... 132s Adding debian:ACCVRAIZ1.pem 132s Adding debian:AC_RAIZ_FNMT-RCM.pem 132s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 132s Adding debian:ANF_Secure_Server_Root_CA.pem 132s Adding debian:Actalis_Authentication_Root_CA.pem 132s Adding debian:AffirmTrust_Commercial.pem 132s Adding debian:AffirmTrust_Networking.pem 132s Adding debian:AffirmTrust_Premium.pem 132s Adding debian:AffirmTrust_Premium_ECC.pem 132s Adding debian:Amazon_Root_CA_1.pem 132s Adding debian:Amazon_Root_CA_2.pem 132s Adding debian:Amazon_Root_CA_3.pem 132s Adding debian:Amazon_Root_CA_4.pem 132s Adding debian:Atos_TrustedRoot_2011.pem 132s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 132s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 132s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 132s Adding debian:BJCA_Global_Root_CA1.pem 132s Adding debian:BJCA_Global_Root_CA2.pem 132s Adding debian:Baltimore_CyberTrust_Root.pem 132s Adding debian:Buypass_Class_2_Root_CA.pem 132s Adding debian:Buypass_Class_3_Root_CA.pem 132s Adding debian:CA_Disig_Root_R2.pem 132s Adding debian:CFCA_EV_ROOT.pem 132s Adding debian:COMODO_Certification_Authority.pem 132s Adding debian:COMODO_ECC_Certification_Authority.pem 132s Adding debian:COMODO_RSA_Certification_Authority.pem 132s Adding debian:Certainly_Root_E1.pem 132s Adding debian:Certainly_Root_R1.pem 132s Adding debian:Certigna.pem 132s Adding debian:Certigna_Root_CA.pem 132s Adding debian:Certum_EC-384_CA.pem 132s Adding debian:Certum_Trusted_Network_CA.pem 132s Adding debian:Certum_Trusted_Network_CA_2.pem 132s Adding debian:Certum_Trusted_Root_CA.pem 132s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 132s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 132s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 132s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 132s Adding debian:Comodo_AAA_Services_root.pem 132s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 132s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 132s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 132s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 132s Adding debian:DigiCert_Assured_ID_Root_CA.pem 132s Adding debian:DigiCert_Assured_ID_Root_G2.pem 132s Adding debian:DigiCert_Assured_ID_Root_G3.pem 132s Adding debian:DigiCert_Global_Root_CA.pem 132s Adding debian:DigiCert_Global_Root_G2.pem 132s Adding debian:DigiCert_Global_Root_G3.pem 132s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 132s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 132s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 132s Adding debian:DigiCert_Trusted_Root_G4.pem 132s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 132s Adding debian:Entrust_Root_Certification_Authority.pem 132s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 132s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 132s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem 132s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 132s Adding debian:GLOBALTRUST_2020.pem 132s Adding debian:GTS_Root_R1.pem 132s Adding debian:GTS_Root_R2.pem 132s Adding debian:GTS_Root_R3.pem 132s Adding debian:GTS_Root_R4.pem 132s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 132s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 132s Adding debian:GlobalSign_Root_CA.pem 132s Adding debian:GlobalSign_Root_CA_-_R3.pem 132s Adding debian:GlobalSign_Root_CA_-_R6.pem 132s Adding debian:GlobalSign_Root_E46.pem 132s Adding debian:GlobalSign_Root_R46.pem 132s Adding debian:Go_Daddy_Class_2_CA.pem 132s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 132s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 132s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 132s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 132s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 132s Adding debian:HiPKI_Root_CA_-_G1.pem 132s Adding debian:Hongkong_Post_Root_CA_3.pem 132s Adding debian:ISRG_Root_X1.pem 132s Adding debian:ISRG_Root_X2.pem 132s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 132s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 132s Adding debian:Izenpe.com.pem 132s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 132s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 132s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 132s Adding debian:NAVER_Global_Root_Certification_Authority.pem 132s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 132s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 132s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 132s Adding debian:QuoVadis_Root_CA_1_G3.pem 132s Adding debian:QuoVadis_Root_CA_2.pem 132s Adding debian:QuoVadis_Root_CA_2_G3.pem 132s Adding debian:QuoVadis_Root_CA_3.pem 132s Adding debian:QuoVadis_Root_CA_3_G3.pem 132s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 132s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 132s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 132s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 132s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 132s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 132s Adding debian:SZAFIR_ROOT_CA2.pem 132s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 132s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 132s Adding debian:SecureSign_RootCA11.pem 132s Adding debian:SecureTrust_CA.pem 132s Adding debian:Secure_Global_CA.pem 132s Adding debian:Security_Communication_ECC_RootCA1.pem 132s Adding debian:Security_Communication_RootCA2.pem 132s Adding debian:Security_Communication_RootCA3.pem 132s Adding debian:Security_Communication_Root_CA.pem 132s Adding debian:Starfield_Class_2_CA.pem 132s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 132s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 132s Adding debian:SwissSign_Gold_CA_-_G2.pem 132s Adding debian:SwissSign_Silver_CA_-_G2.pem 132s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 132s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 132s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 132s Adding debian:TWCA_Global_Root_CA.pem 132s Adding debian:TWCA_Root_Certification_Authority.pem 132s Adding debian:TeliaSonera_Root_CA_v1.pem 132s Adding debian:Telia_Root_CA_v2.pem 132s Adding debian:TrustAsia_Global_Root_CA_G3.pem 132s Adding debian:TrustAsia_Global_Root_CA_G4.pem 132s Adding debian:Trustwave_Global_Certification_Authority.pem 132s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 132s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 132s Adding debian:TunTrust_Root_CA.pem 132s Adding debian:UCA_Extended_Validation_Root.pem 132s Adding debian:UCA_Global_G2_Root.pem 132s Adding debian:USERTrust_ECC_Certification_Authority.pem 132s Adding debian:USERTrust_RSA_Certification_Authority.pem 132s Adding debian:XRamp_Global_CA_Root.pem 132s Adding debian:certSIGN_ROOT_CA.pem 132s Adding debian:certSIGN_Root_CA_G2.pem 132s Adding debian:e-Szigno_Root_CA_2017.pem 132s Adding debian:ePKI_Root_Certification_Authority.pem 132s Adding debian:emSign_ECC_Root_CA_-_C3.pem 132s Adding debian:emSign_ECC_Root_CA_-_G3.pem 132s Adding debian:emSign_Root_CA_-_C1.pem 132s Adding debian:emSign_Root_CA_-_G1.pem 132s Adding debian:vTrus_ECC_Root_CA.pem 132s Adding debian:vTrus_Root_CA.pem 132s done. 132s Setting up openjdk-21-jre:amd64 (21.0.5+11-1) ... 132s Setting up openjdk-21-jdk-headless:amd64 (21.0.5+11-1) ... 132s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode 132s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode 132s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode 132s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode 132s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode 132s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode 132s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode 132s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode 132s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode 132s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode 132s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode 132s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode 132s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode 132s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode 132s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode 132s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode 132s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode 132s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode 132s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode 132s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode 132s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode 132s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jwebserver to provide /usr/bin/jwebserver (jwebserver) in auto mode 132s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode 132s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode 132s Setting up default-jre-headless (2:1.21-76) ... 132s Setting up default-jre (2:1.21-76) ... 132s Setting up openjdk-21-jdk:amd64 (21.0.5+11-1) ... 132s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode 132s Setting up default-jdk-headless (2:1.21-76) ... 132s Setting up pilon (1.24-3) ... 132s Setting up unicycler (0.5.0+dfsg-1) ... 132s /usr/lib/python3/dist-packages/unicycler/bridge_common.py:43: SyntaxWarning: invalid escape sequence '\l' 132s """ 132s /usr/lib/python3/dist-packages/unicycler/bridge_long_read.py:619: SyntaxWarning: invalid escape sequence '\c' 132s """ 132s /usr/lib/python3/dist-packages/unicycler/log.py:194: SyntaxWarning: invalid escape sequence '\[' 132s return re.sub('\033\[2m', '', text) 132s /usr/lib/python3/dist-packages/unicycler/misc.py:641: SyntaxWarning: invalid escape sequence '\[' 132s row_str = re.sub('\033\[4m', '', row_str) 132s /usr/lib/python3/dist-packages/unicycler/misc.py:743: SyntaxWarning: invalid escape sequence '\ ' 132s bold_red(" \ \___\n") + 132s /usr/lib/python3/dist-packages/unicycler/misc.py:744: SyntaxWarning: invalid escape sequence '\ ' 132s bold_red(" \ ___\\\n") + 132s /usr/lib/python3/dist-packages/unicycler/misc.py:753: SyntaxWarning: invalid escape sequence '\ ' 132s bold_yellow("| | | || '_ \ | | / __|| | | | / __|| | / _ \| '__|\n") + 132s /usr/lib/python3/dist-packages/unicycler/misc.py:754: SyntaxWarning: invalid escape sequence '\_' 132s bold_red("\\\\ \_ // ") + 132s /usr/lib/python3/dist-packages/unicycler/misc.py:757: SyntaxWarning: invalid escape sequence '\_' 132s bold_yellow("\____/ |_| |_||_| \___| \__, | \___||_| \___||_|\n") + 132s /usr/lib/python3/dist-packages/unicycler/bridge_common.py:43: SyntaxWarning: invalid escape sequence '\l' 132s """ 132s /usr/lib/python3/dist-packages/unicycler/bridge_long_read.py:619: SyntaxWarning: invalid escape sequence '\c' 132s """ 132s /usr/lib/python3/dist-packages/unicycler/log.py:194: SyntaxWarning: invalid escape sequence '\[' 132s return re.sub('\033\[2m', '', text) 132s /usr/lib/python3/dist-packages/unicycler/misc.py:641: SyntaxWarning: invalid escape sequence '\[' 132s row_str = re.sub('\033\[4m', '', row_str) 132s /usr/lib/python3/dist-packages/unicycler/misc.py:743: SyntaxWarning: invalid escape sequence '\ ' 132s bold_red(" \ \___\n") + 132s /usr/lib/python3/dist-packages/unicycler/misc.py:744: SyntaxWarning: invalid escape sequence '\ ' 132s bold_red(" \ ___\\\n") + 132s /usr/lib/python3/dist-packages/unicycler/misc.py:753: SyntaxWarning: invalid escape sequence '\ ' 132s bold_yellow("| | | || '_ \ | | / __|| | | | / __|| | / _ \| '__|\n") + 132s /usr/lib/python3/dist-packages/unicycler/misc.py:754: SyntaxWarning: invalid escape sequence '\_' 132s bold_red("\\\\ \_ // ") + 132s /usr/lib/python3/dist-packages/unicycler/misc.py:757: SyntaxWarning: invalid escape sequence '\_' 132s bold_yellow("\____/ |_| |_||_| \___| \__, | \___||_| \___||_|\n") + 132s Setting up default-jdk (2:1.21-76) ... 132s Setting up autopkgtest-satdep (0) ... 138s (Reading database ... 95166 files and directories currently installed.) 138s Removing autopkgtest-satdep (0) ... 139s autopkgtest [02:46:18]: test run-unit-test: [----------------------- 139s 139s Starting Unicycler (2024-11-15 02:46:18) 139s Welcome to Unicycler, an assembly pipeline for bacterial genomes. Since you 139s provided only short reads, Unicycler will essentially function as a SPAdes- 139s optimiser. It will try many k-mer sizes, choose the best based on contig length 139s and graph connectivity, and scaffold the graph using SPAdes repeat resolution. 139s For more information, please see https://github.com/rrwick/Unicycler 139s 139s Command: /usr/bin/unicycler -1 short_reads_1.fastq.gz -2 short_reads_2.fastq.gz -o illumina_assembly 139s 139s Unicycler version: v0.5.0 139s Using 2 threads 139s 139s Making output directory: 139s /tmp/autopkgtest.veHd19/autopkgtest_tmp/illumina_assembly 139s 139s Dependencies: 139s Program Version Status  139s spades 3.15.5 good 139s racon not used 139s makeblastdb 2.16.0+ good 139s tblastn 2.16.0+ good 139s 139s 139s Choosing k-mer range for assembly (2024-11-15 02:46:18) 139s Unicycler chooses a k-mer range for SPAdes based on the length of the input 139s reads. It uses a wide range of many k-mer sizes to maximise the chance of 139s finding an ideal assembly. 139s 139s SPAdes maximum k-mer: 127 139s Median read length: 125 139s K-mer range: 25, 49, 67, 81, 93, 103, 111, 119 139s 139s 139s SPAdes assemblies (2024-11-15 02:46:18) 139s Unicycler now uses SPAdes to assemble the short reads. It scores the 139s assembly graph for each k-mer using the number of contigs (fewer is better) and 139s the number of dead ends (fewer is better). The score function is 1/(c*(d+2)), 139s where c is the contig count and d is the dead end count. 139s 139s spades -o /tmp/autopkgtest.veHd19/autopkgtest_tmp/illumina_assembly/spades_assembly -k 25 --threads 2 --isolate -1 /tmp/autopkgtest.veHd19/autopkgtest_tmp/short_reads_1.fastq.gz -2 /tmp/autopkgtest.veHd19/autopkgtest_tmp/short_reads_2.fastq.gz -m 1024 147s 147s spades -o /tmp/autopkgtest.veHd19/autopkgtest_tmp/illumina_assembly/spades_assembly -k 25,49 --threads 2 --restart-from k25 -m 1024 155s 155s spades -o /tmp/autopkgtest.veHd19/autopkgtest_tmp/illumina_assembly/spades_assembly -k 25,49,67 --threads 2 --restart-from k49 -m 1024 162s 162s spades -o /tmp/autopkgtest.veHd19/autopkgtest_tmp/illumina_assembly/spades_assembly -k 25,49,67,81 --threads 2 --restart-from k67 -m 1024 170s 170s spades -o /tmp/autopkgtest.veHd19/autopkgtest_tmp/illumina_assembly/spades_assembly -k 25,49,67,81,93 --threads 2 --restart-from k81 -m 1024 178s 178s spades -o /tmp/autopkgtest.veHd19/autopkgtest_tmp/illumina_assembly/spades_assembly -k 25,49,67,81,93,103 --threads 2 --restart-from k93 -m 1024 185s 185s spades -o /tmp/autopkgtest.veHd19/autopkgtest_tmp/illumina_assembly/spades_assembly -k 25,49,67,81,93,103,111 --threads 2 --restart-from k103 -m 1024 191s 191s spades -o /tmp/autopkgtest.veHd19/autopkgtest_tmp/illumina_assembly/spades_assembly -k 25,49,67,81,93,103,111,119 --threads 2 --restart-from k111 -m 1024 196s 196s K-mer Contigs Dead ends Score  196s 25 639 0 7.82e-04 196s 49 370 0 1.35e-03 196s 67 300 0 1.67e-03 196s 81 273 0 1.83e-03 196s  93 258 0 1.94e-03 ← best 196s 103 247 2 1.01e-03 196s 111 218 5 6.55e-04 196s 119 44 52 4.21e-04 196s 196s Read depth filter: removed 0 contigs totalling 0 bp 196s Deleting /tmp/autopkgtest.veHd19/autopkgtest_tmp/illumina_assembly/spades_assembly/ 196s 196s 196s Determining graph multiplicity (2024-11-15 02:47:15) 196s Multiplicity is the number of times a sequence occurs in the underlying 196s sequence. Single-copy contigs (those with a multiplicity of one, occurring only 196s once in the underlying sequence) are particularly useful. 196s 196s Saving /tmp/autopkgtest.veHd19/autopkgtest_tmp/illumina_assembly/002_depth_filter.gfa 196s 196s 196s Cleaning graph (2024-11-15 02:47:15) 196s Unicycler now performs various cleaning procedures on the graph to remove 196s overlaps and simplify the graph structure. The end result is a graph ready for 196s bridging. 196s 196s Graph overlaps removed 196s 196s Removed zero-length segments: 196s 155, 156, 160, 161, 162, 163, 165, 167, 168, 169, 172, 176, 182, 188, 193, 196s 196, 201, 202, 203, 204, 210, 212, 214, 230, 232, 237, 242 196s 196s Removed zero-length segments: 196s 164, 171, 173, 174 196s 196s Removed zero-length segments: 196s 254 196s 196s Merged small segments: 196s 238, 239, 240, 245, 246, 250, 252, 255 196s 196s Saving /tmp/autopkgtest.veHd19/autopkgtest_tmp/illumina_assembly/003_overlaps_removed.gfa 196s 196s Unicycler now selects a set of anchor contigs from the single-copy contigs. 196s These are the contigs which will be connected via bridges to form the final 196s assembly. 196s 196s 38 anchor segments (154,950 bp) out of 218 total segments (187,257 bp) 196s 196s 196s Creating SPAdes contig bridges (2024-11-15 02:47:15) 196s SPAdes uses paired-end information to perform repeat resolution (RR) and 196s produce contigs from the assembly graph. SPAdes saves the graph paths 196s corresponding to these contigs in the contigs.paths file. When one of these 196s paths contains two or more anchor contigs, Unicycler can create a bridge from 196s the path. 196s 196s Bridge 196s Start Path End quality 196s -18 -143 33 63.2 196s -11 119 32 57.1 196s 1 156 → 148 → -100 → 106 → -202 → 124 → 114 → -171 → 136 → 81 → -214 → 104 20 18.8 196s 7 182 → -116 → 175 → 123 23 63.0 196s 13 -116 → -176 → 123 → 54 → 90 -40 20.0 196s 17 119 24 51.9 196s 28 85 → -172 → 129 → -149 35 62.1 196s 31 -113 → -141 → -60 14 31.3 196s 196s 196s Creating loop unrolling bridges (2024-11-15 02:47:15) 196s When a SPAdes contig path connects an anchor contig with the middle contig 196s of a simple loop, Unicycler concludes that the sequences are contiguous (i.e. 196s the loop is not a separate piece of DNA). It then uses the read depth of the 196s middle and repeat contigs to guess the number of times to traverse the loop and 196s makes a bridge. 196s 196s No loop unrolling bridges made 196s 196s 196s Applying bridges (2024-11-15 02:47:15) 196s Unicycler now applies to the graph in decreasing order of quality. This 196s ensures that when multiple, contradictory bridges exist, the most supported 196s option is used. 196s 196s Bridge type Start → end Path Quality 196s SPAdes -18 → 33 -143 63.217 196s SPAdes 7 → 23 182, -116, 175, 123 62.992 196s SPAdes 28 → 35 85, -172, 129, -149 62.061 196s SPAdes -11 → 32 119 57.144 196s SPAdes 17 → 24 119 51.896 196s SPAdes 31 → 14 -113, -141, -60 31.266 196s SPAdes 13 → -40 -116, -176, 123, 54, 90 20.024 196s SPAdes 1 → 20 156, 148, -100, 106, -202, 124, 114, 18.783 196s -171, 136, 81, -214, 104 196s 196s Saving /tmp/autopkgtest.veHd19/autopkgtest_tmp/illumina_assembly/004_bridges_applied.gfa 196s 196s 196s Bridged assembly graph (2024-11-15 02:47:15) 196s The assembly is now mostly finished and no more structural changes will be 196s made. Ideally the assembly graph should now have one contig per replicon and no 196s erroneous contigs (i.e. a complete assembly). If there are more contigs, then 196s the assembly is not complete. 196s 196s Saving /tmp/autopkgtest.veHd19/autopkgtest_tmp/illumina_assembly/005_final_clean.gfa 196s 196s Component Segments Links Length N50 Longest segment Status  196s total 182 255 189,619 5,545 37,237 196s 1 181 254 184,466 5,678 37,237  incomplete 196s 2 1 1 5,153 5,153 5,153  complete 196s 196s 196s Rotating completed replicons (2024-11-15 02:47:15) 196s Any completed circular contigs (i.e. single contigs which have one link 196s connecting end to start) can have their start position changed without altering 196s the sequence. For consistency, Unicycler now searches for a starting gene (dnaA 196s or repA) in each such contig, and if one is found, the contig is rotated to 196s start with that gene on the forward strand. 196s 204s Segment Length Depth Starting gene Position Strand Identity Coverage 204s 11 5,153 4.16x none found 204s 204s 204s Assembly complete (2024-11-15 02:47:23) 204s Saving /tmp/autopkgtest.veHd19/autopkgtest_tmp/illumina_assembly/assembly.gfa 204s Saving /tmp/autopkgtest.veHd19/autopkgtest_tmp/illumina_assembly/assembly.fasta 204s 204s 204s Starting Unicycler (2024-11-15 02:47:23) 204s Welcome to Unicycler, an assembly pipeline for bacterial genomes. Since you 204s provided both short and long reads, Unicycler will perform a hybrid assembly. 204s It will first use SPAdes to make a short-read assembly graph, and then it will 204s use various methods to scaffold that graph with the long reads. 204s For more information, please see https://github.com/rrwick/Unicycler 204s 204s Command: /usr/bin/unicycler -1 short_reads_1.fastq.gz -2 short_reads_2.fastq.gz -l long_reads_low_depth.fastq.gz -o hybrid_assembly 204s 204s Unicycler version: v0.5.0 204s Using 2 threads 204s 204s Making output directory: 204s /tmp/autopkgtest.veHd19/autopkgtest_tmp/hybrid_assembly 204s 204s Dependencies: 204s Program Version Status 204s spades 3.15.5 good 204s racon 1.5.0 good 204s makeblastdb 2.16.0+ good 204s tblastn 2.16.0+ good 204s 204s 204s Choosing k-mer range for assembly (2024-11-15 02:47:23) 204s Unicycler chooses a k-mer range for SPAdes based on the length of the input 204s reads. It uses a wide range of many k-mer sizes to maximise the chance of 204s finding an ideal assembly. 204s 204s SPAdes maximum k-mer: 127 205s Median read length: 125 205s K-mer range: 25, 49, 67, 81, 93, 103, 111, 119 205s 205s 205s SPAdes assemblies (2024-11-15 02:47:23) 205s Unicycler now uses SPAdes to assemble the short reads. It scores the 205s assembly graph for each k-mer using the number of contigs (fewer is better) and 205s the number of dead ends (fewer is better). The score function is 1/(c*(d+2)), 205s where c is the contig count and d is the dead end count. 205s 205s spades -o /tmp/autopkgtest.veHd19/autopkgtest_tmp/hybrid_assembly/spades_assembly -k 25 --threads 2 --isolate -1 /tmp/autopkgtest.veHd19/autopkgtest_tmp/short_reads_1.fastq.gz -2 /tmp/autopkgtest.veHd19/autopkgtest_tmp/short_reads_2.fastq.gz -m 1024 211s 211s spades -o /tmp/autopkgtest.veHd19/autopkgtest_tmp/hybrid_assembly/spades_assembly -k 25,49 --threads 2 --restart-from k25 -m 1024 221s 221s spades -o /tmp/autopkgtest.veHd19/autopkgtest_tmp/hybrid_assembly/spades_assembly -k 25,49,67 --threads 2 --restart-from k49 -m 1024 228s 228s spades -o /tmp/autopkgtest.veHd19/autopkgtest_tmp/hybrid_assembly/spades_assembly -k 25,49,67,81 --threads 2 --restart-from k67 -m 1024 237s 237s spades -o /tmp/autopkgtest.veHd19/autopkgtest_tmp/hybrid_assembly/spades_assembly -k 25,49,67,81,93 --threads 2 --restart-from k81 -m 1024 245s 245s spades -o /tmp/autopkgtest.veHd19/autopkgtest_tmp/hybrid_assembly/spades_assembly -k 25,49,67,81,93,103 --threads 2 --restart-from k93 -m 1024 252s 252s spades -o /tmp/autopkgtest.veHd19/autopkgtest_tmp/hybrid_assembly/spades_assembly -k 25,49,67,81,93,103,111 --threads 2 --restart-from k103 -m 1024 257s 257s spades -o /tmp/autopkgtest.veHd19/autopkgtest_tmp/hybrid_assembly/spades_assembly -k 25,49,67,81,93,103,111,119 --threads 2 --restart-from k111 -m 1024 262s 263s K-mer Contigs Dead ends Score  263s 25 639 0 7.82e-04 263s 49 370 0 1.35e-03 263s 67 300 0 1.67e-03 263s 81 273 0 1.83e-03 263s  93 258 0 1.94e-03 ← best 263s 103 247 2 1.01e-03 263s 111 218 5 6.55e-04 263s 119 44 52 4.21e-04 263s 263s Read depth filter: removed 0 contigs totalling 0 bp 263s Deleting /tmp/autopkgtest.veHd19/autopkgtest_tmp/hybrid_assembly/spades_assembly/ 263s 263s 263s Determining graph multiplicity (2024-11-15 02:48:22) 263s Multiplicity is the number of times a sequence occurs in the underlying 263s sequence. Single-copy contigs (those with a multiplicity of one, occurring only 263s once in the underlying sequence) are particularly useful. 263s 263s Saving /tmp/autopkgtest.veHd19/autopkgtest_tmp/hybrid_assembly/002_depth_filter.gfa 263s 263s 263s Cleaning graph (2024-11-15 02:48:22) 263s Unicycler now performs various cleaning procedures on the graph to remove 263s overlaps and simplify the graph structure. The end result is a graph ready for 263s bridging. 263s 263s Graph overlaps removed 263s 263s Removed zero-length segments: 263s 155, 156, 160, 161, 162, 163, 165, 167, 168, 169, 172, 176, 182, 188, 193, 263s 196, 201, 202, 203, 204, 210, 212, 214, 230, 232, 237, 242 263s 263s Removed zero-length segments: 263s 164, 171, 173, 174 263s 263s Removed zero-length segments: 263s 254 263s 263s Merged small segments: 263s 238, 239, 240, 245, 246, 250, 252, 255 263s 263s Saving /tmp/autopkgtest.veHd19/autopkgtest_tmp/hybrid_assembly/003_overlaps_removed.gfa 263s 263s Unicycler now selects a set of anchor contigs from the single-copy contigs. 263s These are the contigs which will be connected via bridges to form the final 263s assembly. 263s 263s 38 anchor segments (154,950 bp) out of 218 total segments (187,257 bp) 263s 263s 263s Creating SPAdes contig bridges (2024-11-15 02:48:22) 263s SPAdes uses paired-end information to perform repeat resolution (RR) and 263s produce contigs from the assembly graph. SPAdes saves the graph paths 263s corresponding to these contigs in the contigs.paths file. When one of these 263s paths contains two or more anchor contigs, Unicycler can create a bridge from 263s the path. 263s 263s Bridge 263s Start Path End quality 263s -18 -143 33 63.2 263s -11 119 32 57.1 263s 1 156 → 148 → -100 → 106 → -202 → 124 → 114 → -171 → 136 → 81 → -214 → 104 20 18.8 263s 7 182 → -116 → 175 → 123 23 63.0 263s 13 -116 → -176 → 123 → 54 → 90 -40 20.0 263s 17 119 24 51.9 263s 28 85 → -172 → 129 → -149 35 62.1 263s 31 -113 → -141 → -60 14 31.3 263s 263s 263s Creating loop unrolling bridges (2024-11-15 02:48:22) 263s When a SPAdes contig path connects an anchor contig with the middle contig 263s of a simple loop, Unicycler concludes that the sequences are contiguous (i.e. 263s the loop is not a separate piece of DNA). It then uses the read depth of the 263s middle and repeat contigs to guess the number of times to traverse the loop and 263s makes a bridge. 263s 263s No loop unrolling bridges made 263s 263s 263s Loading reads (2024-11-15 02:48:22) 263s 0 / 30 (0.0%) 1 / 30 (3.3%) - 5,061 bp 2 / 30 (6.7%) - 10,708 bp 3 / 30 (10.0%) - 22,523 bp 4 / 30 (13.3%) - 32,729 bp 5 / 30 (16.7%) - 43,186 bp 6 / 30 (20.0%) - 47,888 bp 7 / 30 (23.3%) - 56,548 bp 8 / 30 (26.7%) - 66,110 bp 9 / 30 (30.0%) - 76,667 bp 10 / 30 (33.3%) - 88,423 bp 11 / 30 (36.7%) - 98,106 bp 12 / 30 (40.0%) - 109,164 bp 13 / 30 (43.3%) - 119,099 bp 14 / 30 (46.7%) - 125,265 bp 15 / 30 (50.0%) - 130,218 bp 16 / 30 (53.3%) - 142,080 bp 17 / 30 (56.7%) - 153,905 bp 18 / 30 (60.0%) - 159,478 bp 19 / 30 (63.3%) - 168,165 bp 20 / 30 (66.7%) - 181,501 bp 21 / 30 (70.0%) - 186,440 bp 22 / 30 (73.3%) - 197,478 bp 23 / 30 (76.7%) - 208,632 bp 24 / 30 (80.0%) - 218,337 bp 25 / 30 (83.3%) - 220,369 bp 26 / 30 (86.7%) - 221,834 bp 27 / 30 (90.0%) - 231,551 bp 28 / 30 (93.3%) - 242,619 bp 29 / 30 (96.7%) - 251,830 bp 30 / 30 (100.0%) - 261,649 bp 30 / 30 (100.0%) - 261,649 bp 263s 263s 263s Assembling contigs and long reads with miniasm (2024-11-15 02:48:22) 263s Unicycler uses miniasm to construct a string graph assembly using both the 263s short read contigs and the long reads. It will then use the resulting string 263s graph to produce bridges between contigs. This method requires decent coverage 263s of long reads and therefore may not be fruitful if long reads are sparse. 263s However, it does not rely on the short read assembly graph having good 263s connectivity and is able to bridge an assembly graph even when it contains many 263s dead ends. 263s Unicycler uses two types of "reads" as assembly input: anchor contigs from 263s the short-read assembly and actual long reads which overlap two or more of 263s these contigs. It then assembles them with miniasm. 263s 263s Aligning long reads to graph using minimap 263s 263s Saving to /tmp/autopkgtest.veHd19/autopkgtest_tmp/hybrid_assembly/miniasm_assembly/01_assembly_reads.fastq: 263s 37 short-read contigs 263s 28 long reads 263s 263s Finding overlaps with minimap... success 263s 63 overlaps 263s 263s Assembling reads with miniasm... empty result 263s 263s 263s Creating simple long read bridges (2024-11-15 02:48:22) 263s Unicycler uses long read alignments (from minimap) to resolve simple repeat 263s structures in the graph. This takes care of some "low-hanging fruit" of the 263s graph simplification. 263s 263s Aligning long reads to graph using minimap 263s 263s Two-way junctions are defined as cases where two graph contigs (A and B) 263s join together (C) and then split apart again (D and E). This usually represents 263s a simple 2-copy repeat, and there are two possible options for its resolution: 263s (A→C→D and B→C→E) or (A→C→E and B→C→D). Each read which spans such a junction 263s gets to "vote" for option 1, option 2 or neither. Unicycler creates a bridge at 263s each junction for the most voted for option. 263s 263s Op. 1 Op. 2 Neither Final Bridge 263s Junction Option 1 Option 2 votes votes votes op. quality 263s 119 -11 → 119 → 24, -11 → 119 → 32, 0 4 0 2 82.1 263s 17 → 119 → 32 17 → 119 → 24 263s 263s Simple loops are parts of the graph where two contigs (A and B) are 263s connected via a repeat (C) which loops back to itself (via D). It is possible 263s to traverse the loop zero times (A→C→B), one time (A→C→D→C→B), two times 263s (A→C→D→C→D→C→B), etc. Long reads which span the loop inform which is the 263s correct number of times through. In this step, such reads are found and each is 263s aligned against alternative loop counts. A reads casts its "vote" for the loop 263s count it agrees best with, and Unicycler creates a bridge using the most voted 263s for count. 263s 263s No suitable simple loops present 263s 263s 263s Determining low score threshold (2024-11-15 02:48:22) 263s Before conducting semi-global alignment of the long reads to the assembly 263s graph, Unicycler must determine a minimum alignment score threshold such that 263s nonsense alignments are excluded. To choose a threshold automatically, it 263s examines alignments between random sequences and selects a score a few standard 263s deviations above the mean. 263s 263s Automatically choosing a threshold using random alignment scores. 263s 263s Random alignment mean score: 61.66 263s standard deviation: 1.31 263s Low score threshold: 61.66 + (7 x 1.31) = 70.86 263s 263s 263s Aligning reads (2024-11-15 02:48:22) 265s 0 / 30 (0.0%) 1 / 30 (3.3%) 2 / 30 (6.7%) 3 / 30 (10.0%) 4 / 30 (13.3%) 5 / 30 (16.7%) 6 / 30 (20.0%) 7 / 30 (23.3%) 8 / 30 (26.7%) 9 / 30 (30.0%) 10 / 30 (33.3%) 11 / 30 (36.7%) 12 / 30 (40.0%) 13 / 30 (43.3%) 14 / 30 (46.7%) 15 / 30 (50.0%) 16 / 30 (53.3%) 17 / 30 (56.7%) 18 / 30 (60.0%) 19 / 30 (63.3%) 20 / 30 (66.7%) 21 / 30 (70.0%) 22 / 30 (73.3%) 23 / 30 (76.7%) 24 / 30 (80.0%) 25 / 30 (83.3%) 26 / 30 (86.7%) 27 / 30 (90.0%) 28 / 30 (93.3%) 29 / 30 (96.7%) 30 / 30 (100.0%) 30 / 30 (100.0%) 265s 265s 265s Read alignment summary (2024-11-15 02:48:24) 265s Total read count: 30 265s Fully aligned reads: 3 265s Partially aligned reads: 27 265s Unaligned reads: 0 265s Total bases aligned: 201,232 bp 265s Mean alignment identity: 84.6% 265s 265s Deleting /tmp/autopkgtest.veHd19/autopkgtest_tmp/hybrid_assembly/read_alignment/ 265s 265s 265s Building long read bridges (2024-11-15 02:48:24) 265s Unicycler uses the long read alignments to produce bridges between anchor 265s segments. These bridges can be formed using as few as one long read, giving 265s Unicycler the ability to bridge the graph even when long-read depth is low. 265s 265s  Start → end Best path Quality 266s 1/19 22 → -15 -152, -45, -158, 26, -121, -162, -107, 61.176 266s 46, -49, 107, -95, -96 266s 2/19 -22 → 28 -147, 44, -201, -56, -212, -87, -192, 66.625 266s 80, 118, -138, 53, -179, -99, 122, -102, 266s 66, 135 266s 3/19 28 → -24 85, -172, 129, -149, 35, -71, -198, 64, 41.651 266s 210, -48, 83, -157 267s 4/19 38 → -27 177, 84, -180, -135, -66, 102, -122, 99, 58.017 267s -178, -59, 105, 42, -130, -205, -161, 267s 110, -218, -79 267s 5/19 33 → 34 185, 105, 42, -130, -199, 174, 167, 110, 57.118 267s -218, -79, 39 267s 6/19 23 → -5 -75, 50, 207, -47, 194, 76, -73, 57, 181 63.939 267s 7/19 -2 → 29 177, 84, -59, 91, 165, 52, 187, -88, 58.973 267s -68, 160, -89, 85, -115, -149 267s 8/19 26 → -15 -121, -162, -107, 46, -49, 107, -95, -96 60.674 268s 9/19 18 → -2 142, -121, 153, 184, 93, -150, 154, 82, 72.146 268s -140, -127, 132, 156, 61, 114, 173, 136, 268s 63 268s 10/19 35 → -24 -71, -198, 64, 210, -48, 83, -157 47.909 268s 11/19 34 → 36 30 52.723 268s 12/19 -4 → 17 -57, -77, 133, 78 70.292 268s 13/19 37 → -29 168, 45, 152, 134 50.481 268s 14/19 22 → 26 -152, -45, -158 62.323 268s 15/19 28 → 35 85, -172, 129, -149 52.937 268s 16/19 17 → 24 119 48.379 268s 17/19 -11 → 32 119 49.059 268s 18/19 -18 → 33 -143 30.238 269s 19/19 -1 → 27 41, -139, -127, -131, 156, 148, -101, 64.846 269s 106, -202, 124, 114, -126, 81, 213, 104, 269s 67, 128, 70, -166, 125, -109, -117, -143 269s 269s 269s Applying bridges (2024-11-15 02:48:28) 269s Unicycler now applies to the graph in decreasing order of quality. This 269s ensures that when multiple, contradictory bridges exist, the most supported 269s option is used. 269s 269s Bridge type Start → end Path Quality 269s simple long read -11 → 32 119 90.353 269s simple long read 17 → 24 119 82.055 269s long read 18 → -2 142, -121, 153, 184, 93, -150, 154, 82, 72.146 269s -140, -127, 132, 156, 61, 114, 173, 136, 269s 63 269s long read -4 → 17 -57, -77, 133, 78 70.292 269s long read -22 → 28 -147, 44, -201, -56, -212, -87, -192, 66.625 269s 80, 118, -138, 53, -179, -99, 122, -102, 269s 66, 135 269s long read -1 → 27 41, -139, -127, -131, 156, 148, -101, 64.846 269s 106, -202, 124, 114, -126, 81, 213, 104, 269s 67, 128, 70, -166, 125, -109, -117, -143 269s long read 23 → -5 -75, 50, 207, -47, 194, 76, -73, 57, 181 63.939 269s long read 22 → 26 -152, -45, -158 62.323 269s long read 26 → -15 -121, -162, -107, 46, -49, 107, -95, -96 61.176 269s long read -2 → 29 177, 84, -59, 91, 165, 52, 187, -88, 58.973 269s -68, 160, -89, 85, -115, -149 269s long read 38 → -27 177, 84, -180, -135, -66, 102, -122, 99, 58.017 269s -178, -59, 105, 42, -130, -205, -161, 269s 110, -218, -79 269s long read 33 → 34 185, 105, 42, -130, -199, 174, 167, 110, 57.118 269s -218, -79, 39 269s long read 28 → 35 85, -172, 129, -149 52.937 269s long read 34 → 36 30 52.723 269s long read 37 → -29 168, 45, 152, 134 50.481 269s long read 35 → -24 -71, -198, 64, 210, -48, 83, -157 47.909 269s long read -18 → 33 -143 30.238 269s SPAdes 7 → 23 182, -116, 175, 123 62.992 269s SPAdes 31 → 14 -113, -141, -60 31.266 269s SPAdes 13 → -40 -116, -176, 123, 54, 90 20.024 269s SPAdes 1 → 20 156, 148, -100, 106, -202, 124, 114, 18.783 269s -171, 136, 81, -214, 104 269s 269s Saving /tmp/autopkgtest.veHd19/autopkgtest_tmp/hybrid_assembly/004_bridges_applied.gfa 269s 269s 269s Bridged assembly graph (2024-11-15 02:48:28) 269s The assembly is now mostly finished and no more structural changes will be 269s made. Ideally the assembly graph should now have one contig per replicon and no 269s erroneous contigs (i.e. a complete assembly). If there are more contigs, then 269s the assembly is not complete. 269s 269s Saving /tmp/autopkgtest.veHd19/autopkgtest_tmp/hybrid_assembly/005_final_clean.gfa 269s 269s Component Segments Links Length N50 Longest segment Status  269s total 106 130 212,820 30,934 47,202 269s 1 105 129 207,667 30,934 47,202  incomplete 269s 2 1 1 5,153 5,153 5,153  complete 269s 269s 269s Rotating completed replicons (2024-11-15 02:48:28) 269s Any completed circular contigs (i.e. single contigs which have one link 269s connecting end to start) can have their start position changed without altering 269s the sequence. For consistency, Unicycler now searches for a starting gene (dnaA 269s or repA) in each such contig, and if one is found, the contig is rotated to 269s start with that gene on the forward strand. 269s 277s Segment Length Depth Starting gene Position Strand Identity Coverage 277s 10 5,153 4.18x none found 277s 277s 277s Assembly complete (2024-11-15 02:48:36) 277s Saving /tmp/autopkgtest.veHd19/autopkgtest_tmp/hybrid_assembly/assembly.gfa 277s Saving /tmp/autopkgtest.veHd19/autopkgtest_tmp/hybrid_assembly/assembly.fasta 277s 277s autopkgtest [02:48:36]: test run-unit-test: -----------------------] 278s run-unit-test PASS 278s autopkgtest [02:48:37]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 278s autopkgtest [02:48:37]: @@@@@@@@@@@@@@@@@@@@ summary 278s run-unit-test PASS 291s nova [W] Skipping flock for amd64 291s Creating nova instance adt-plucky-amd64-unicycler-20241115-024359-juju-7f2275-prod-proposed-migration-environment-20-8199251d-1989-4bbc-976e-71f1c0887328 from image adt/ubuntu-plucky-amd64-server-20241114.img (UUID 79d80331-8736-463c-82c6-8c9e13c0a4ca)...