0s autopkgtest [21:31:25]: starting date and time: 2025-03-15 21:31:25+0000 0s autopkgtest [21:31:25]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [21:31:25]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.dq496zgp/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade proteinortho --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-17.secgroup --name adt-plucky-amd64-proteinortho-20250315-213125-juju-7f2275-prod-proposed-migration-environment-2-5ce25858-3bf4-4bf4-be88-de5e4e41e2d5 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 50s autopkgtest [21:32:15]: testbed dpkg architecture: amd64 51s autopkgtest [21:32:16]: testbed apt version: 2.9.31ubuntu1 51s autopkgtest [21:32:16]: @@@@@@@@@@@@@@@@@@@@ test bed setup 51s autopkgtest [21:32:16]: testbed release detected to be: None 52s autopkgtest [21:32:17]: updating testbed package index (apt update) 52s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 53s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 53s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 53s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 53s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [369 kB] 53s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.5 kB] 53s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [44.1 kB] 53s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [85.7 kB] 53s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [67.4 kB] 53s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 c-n-f Metadata [1852 B] 53s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 c-n-f Metadata [116 B] 53s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [342 kB] 53s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [174 kB] 53s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 c-n-f Metadata [15.3 kB] 53s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [8544 B] 53s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [16.1 kB] 53s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 c-n-f Metadata [628 B] 53s Fetched 1265 kB in 1s (1507 kB/s) 54s Reading package lists... 55s Reading package lists... 55s Building dependency tree... 55s Reading state information... 55s Calculating upgrade... 56s Calculating upgrade... 56s The following package was automatically installed and is no longer required: 56s libnl-genl-3-200 56s Use 'sudo apt autoremove' to remove it. 56s The following NEW packages will be installed: 56s bpftool libdebuginfod-common libdebuginfod1t64 linux-headers-6.14.0-10 56s linux-headers-6.14.0-10-generic linux-image-6.14.0-10-generic 56s linux-modules-6.14.0-10-generic linux-modules-extra-6.14.0-10-generic 56s linux-perf linux-tools-6.14.0-10 linux-tools-6.14.0-10-generic pnp.ids 56s The following packages will be upgraded: 56s apparmor apt apt-utils binutils binutils-common binutils-x86-64-linux-gnu 56s cloud-init cloud-init-base curl dosfstools exfatprogs fwupd gcc-15-base 56s gir1.2-girepository-2.0 gir1.2-glib-2.0 htop hwdata initramfs-tools 56s initramfs-tools-bin initramfs-tools-core libapparmor1 libapt-pkg7.0 56s libassuan9 libatomic1 libaudit-common libaudit1 libbinutils libbrotli1 56s libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libctf-nobfd0 libctf0 56s libcurl3t64-gnutls libcurl4t64 libestr0 libftdi1-2 libfwupd3 libgcc-s1 56s libgirepository-1.0-1 libglib2.0-0t64 libglib2.0-data libgpgme11t64 56s libgprofng0 libjemalloc2 liblz4-1 liblzma5 libmm-glib0 libncurses6 56s libncursesw6 libnewt0.52 libnl-3-200 libnl-genl-3-200 libnl-route-3-200 56s libnss-systemd libpam-systemd libparted2t64 libpci3 libpython3-stdlib 56s libpython3.13 libpython3.13-minimal libpython3.13-stdlib libseccomp2 56s libselinux1 libsemanage-common libsemanage2 libsframe1 libsqlite3-0 56s libstdc++6 libsystemd-shared libsystemd0 libtinfo6 libudev1 libxml2 56s linux-firmware linux-generic linux-headers-generic linux-headers-virtual 56s linux-image-generic linux-image-virtual linux-libc-dev linux-tools-common 56s linux-virtual locales media-types ncurses-base ncurses-bin ncurses-term 56s parted pci.ids pciutils pinentry-curses python-apt-common python3 56s python3-apt python3-bcrypt python3-cffi-backend python3-dbus python3-gi 56s python3-jinja2 python3-lazr.uri python3-markupsafe python3-minimal 56s python3-newt python3-rpds-py python3-systemd python3-yaml python3.13 56s python3.13-gdbm python3.13-minimal rsync rsyslog strace systemd 56s systemd-cryptsetup systemd-resolved systemd-sysv systemd-timesyncd 56s ubuntu-kernel-accessories ubuntu-minimal ubuntu-standard udev whiptail 56s xz-utils 56s 126 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 56s Need to get 829 MB of archives. 56s After this operation, 325 MB of additional disk space will be used. 56s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-bin amd64 6.5+20250216-2 [194 kB] 56s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-dev-bin amd64 2.41-1ubuntu1 [24.7 kB] 56s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6-dev amd64 2.41-1ubuntu1 [2182 kB] 57s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 locales all 2.41-1ubuntu1 [4246 kB] 57s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6 amd64 2.41-1ubuntu1 [3327 kB] 57s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-bin amd64 2.41-1ubuntu1 [701 kB] 57s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-libc-dev amd64 6.14.0-10.10 [1723 kB] 57s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libatomic1 amd64 15-20250222-0ubuntu1 [10.4 kB] 57s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-15-base amd64 15-20250222-0ubuntu1 [53.4 kB] 57s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-s1 amd64 15-20250222-0ubuntu1 [77.8 kB] 57s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++6 amd64 15-20250222-0ubuntu1 [798 kB] 57s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-base all 6.5+20250216-2 [25.9 kB] 57s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-term all 6.5+20250216-2 [276 kB] 57s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 liblz4-1 amd64 1.10.0-4 [66.4 kB] 57s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma5 amd64 5.6.4-1 [157 kB] 57s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd0 amd64 257.3-1ubuntu3 [595 kB] 57s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libnss-systemd amd64 257.3-1ubuntu3 [199 kB] 57s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-sysv amd64 257.3-1ubuntu3 [11.9 kB] 57s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-resolved amd64 257.3-1ubuntu3 [345 kB] 57s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam-systemd amd64 257.3-1ubuntu3 [302 kB] 57s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd-shared amd64 257.3-1ubuntu3 [2371 kB] 57s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd amd64 257.3-1ubuntu3 [3052 kB] 57s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-timesyncd amd64 257.3-1ubuntu3 [42.1 kB] 57s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-cryptsetup amd64 257.3-1ubuntu3 [124 kB] 57s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 udev amd64 257.3-1ubuntu3 [1404 kB] 57s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libudev1 amd64 257.3-1ubuntu3 [215 kB] 57s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu2 [6628 B] 57s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-4build1 [15.6 kB] 57s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu2 [54.0 kB] 57s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libseccomp2 amd64 2.5.5-1ubuntu6 [53.5 kB] 57s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libselinux1 amd64 3.7-3ubuntu3 [87.3 kB] 57s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libapparmor1 amd64 4.1.0~beta5-0ubuntu8 [55.0 kB] 57s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.33 [1138 kB] 57s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.33 [1439 kB] 57s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.33 [222 kB] 57s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-minimal amd64 3.13.2-2 [27.7 kB] 57s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 python3 amd64 3.13.2-2 [24.0 kB] 57s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13 amd64 3.13.2-2 [2341 kB] 57s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 media-types all 13.0.0 [29.9 kB] 57s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses6 amd64 6.5+20250216-2 [126 kB] 57s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libncursesw6 amd64 6.5+20250216-2 [165 kB] 57s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libtinfo6 amd64 6.5+20250216-2 [119 kB] 58s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libsqlite3-0 amd64 3.46.1-2 [715 kB] 58s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.2-2 [735 kB] 58s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.2-2 [2365 kB] 58s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.2-2 [883 kB] 58s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.2-2 [2066 kB] 58s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.4 kB] 58s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 rsync amd64 3.4.1+ds1-3 [482 kB] 58s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod-common all 0.192-4 [15.4 kB] 58s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage-common all 3.7-2.1build1 [7268 B] 58s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage2 amd64 3.7-2.1build1 [106 kB] 58s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libassuan9 amd64 3.0.2-2 [43.1 kB] 58s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-girepository-2.0 amd64 1.83.4-1 [25.3 kB] 58s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-glib-2.0 amd64 2.84.0-1 [184 kB] 58s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-0t64 amd64 2.84.0-1 [1669 kB] 58s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libgirepository-1.0-1 amd64 1.83.4-1 [89.5 kB] 58s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libestr0 amd64 0.1.11-2 [8340 B] 58s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-data all 2.84.0-1 [53.0 kB] 58s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-newt amd64 0.52.24-4ubuntu2 [21.1 kB] 58s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libnewt0.52 amd64 0.52.24-4ubuntu2 [55.7 kB] 58s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2ubuntu5 [772 kB] 58s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 python-apt-common all 2.9.9build1 [21.3 kB] 58s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-apt amd64 2.9.9build1 [172 kB] 58s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cffi-backend amd64 1.17.1-2build2 [96.6 kB] 58s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dbus amd64 1.3.2-5build5 [102 kB] 58s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-gi amd64 3.50.0-4build1 [252 kB] 58s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-yaml amd64 6.0.2-1build2 [144 kB] 58s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu2 [555 kB] 58s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 whiptail amd64 0.52.24-4ubuntu2 [19.1 kB] 58s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-minimal amd64 1.549 [11.5 kB] 58s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 apparmor amd64 4.1.0~beta5-0ubuntu8 [701 kB] 58s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 dosfstools amd64 4.2-1.2 [95.0 kB] 58s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-genl-3-200 amd64 3.7.0-1 [12.2 kB] 58s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-route-3-200 amd64 3.7.0-1 [191 kB] 58s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-3-200 amd64 3.7.0-1 [64.9 kB] 58s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 parted amd64 3.6-5 [53.9 kB] 58s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libparted2t64 amd64 3.6-5 [158 kB] 58s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 pci.ids all 0.0~2025.03.09-1 [285 kB] 58s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 pciutils amd64 1:3.13.0-2 [110 kB] 58s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libpci3 amd64 1:3.13.0-2 [39.8 kB] 58s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 strace amd64 6.13+ds-1ubuntu1 [622 kB] 58s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 xz-utils amd64 5.6.4-1 [278 kB] 58s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-standard amd64 1.549 [11.5 kB] 58s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 libgprofng0 amd64 2.44-3ubuntu1 [886 kB] 58s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf0 amd64 2.44-3ubuntu1 [96.5 kB] 58s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf-nobfd0 amd64 2.44-3ubuntu1 [98.9 kB] 58s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-x86-64-linux-gnu amd64 2.44-3ubuntu1 [1108 kB] 58s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 libbinutils amd64 2.44-3ubuntu1 [585 kB] 58s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils amd64 2.44-3ubuntu1 [208 kB] 58s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-common amd64 2.44-3ubuntu1 [215 kB] 58s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 libsframe1 amd64 2.44-3ubuntu1 [14.8 kB] 58s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 hwdata all 0.393-3 [1562 B] 58s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 pnp.ids all 0.393-3 [29.5 kB] 58s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-common all 6.14.0-10.10 [295 kB] 58s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 bpftool amd64 7.6.0+6.14.0-10.10 [1147 kB] 58s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build4 [13.4 kB] 58s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 58s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init-base all 25.1-0ubuntu3 [616 kB] 58s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli1 amd64 1.1.0-2build4 [365 kB] 58s Get:101 http://ftpmaster.internal/ubuntu plucky/main amd64 curl amd64 8.12.1-3ubuntu1 [258 kB] 59s Get:102 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4t64 amd64 8.12.1-3ubuntu1 [437 kB] 59s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 exfatprogs amd64 1.2.8-1 [76.3 kB] 59s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl3t64-gnutls amd64 8.12.1-3ubuntu1 [432 kB] 59s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd amd64 2.0.6-4 [5408 kB] 59s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 libfwupd3 amd64 2.0.6-4 [136 kB] 59s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 libmm-glib0 amd64 1.23.4-0ubuntu3 [251 kB] 59s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 htop amd64 3.4.0-2 [195 kB] 59s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-firmware amd64 20250310.git9e1370d3-0ubuntu1 [571 MB] 79s Get:110 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools all 0.146ubuntu1 [7920 B] 79s Get:111 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-core all 0.146ubuntu1 [51.9 kB] 79s Get:112 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-bin amd64 0.146ubuntu1 [26.2 kB] 79s Get:113 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod1t64 amd64 0.192-4 [21.0 kB] 79s Get:114 http://ftpmaster.internal/ubuntu plucky/main amd64 libftdi1-2 amd64 1.5-8build1 [30.2 kB] 79s Get:115 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.24.2-1ubuntu2 [155 kB] 79s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 libjemalloc2 amd64 5.3.0-3 [277 kB] 79s Get:117 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-6.14.0-10-generic amd64 6.14.0-10.10 [41.2 MB] 80s Get:118 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-6.14.0-10-generic amd64 6.14.0-10.10 [15.3 MB] 81s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-extra-6.14.0-10-generic amd64 6.14.0-10.10 [120 MB] 85s Get:120 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-generic amd64 6.14.0-10.10 [1730 B] 85s Get:121 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-generic amd64 6.14.0-10.10 [11.1 kB] 85s Get:122 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-virtual amd64 6.14.0-10.10 [1722 B] 85s Get:123 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-virtual amd64 6.14.0-10.10 [11.1 kB] 85s Get:124 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-virtual amd64 6.14.0-10.10 [1642 B] 85s Get:125 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10 all 6.14.0-10.10 [14.2 MB] 85s Get:126 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10-generic amd64 6.14.0-10.10 [3915 kB] 86s Get:127 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-generic amd64 6.14.0-10.10 [11.0 kB] 86s Get:128 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-perf amd64 6.14.0-10.10 [4122 kB] 86s Get:129 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10 amd64 6.14.0-10.10 [1394 kB] 86s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10-generic amd64 6.14.0-10.10 [830 B] 86s Get:131 http://ftpmaster.internal/ubuntu plucky/main amd64 pinentry-curses amd64 1.3.1-2ubuntu3 [42.3 kB] 86s Get:132 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lazr.uri all 1.0.6-6 [13.7 kB] 86s Get:133 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-rpds-py amd64 0.21.0-2ubuntu2 [278 kB] 86s Get:134 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build6 [43.9 kB] 86s Get:135 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.2-2 [31.9 kB] 86s Get:136 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-kernel-accessories amd64 1.549 [11.2 kB] 86s Get:137 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init all 25.1-0ubuntu3 [2100 B] 86s Get:138 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-bcrypt amd64 4.2.0-2.1build1 [221 kB] 86s Preconfiguring packages ... 86s Fetched 829 MB in 30s (27.7 MB/s) 87s (Reading database ... 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(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 ... 109146 files and directories currently installed.) 90s Preparing to unpack .../systemd_257.3-1ubuntu3_amd64.deb ... 90s Unpacking systemd (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 90s Preparing to unpack .../systemd-timesyncd_257.3-1ubuntu3_amd64.deb ... 90s Unpacking systemd-timesyncd (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 90s Preparing to unpack .../systemd-cryptsetup_257.3-1ubuntu3_amd64.deb ... 90s Unpacking systemd-cryptsetup (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 90s Preparing to unpack .../udev_257.3-1ubuntu3_amd64.deb ... 90s Unpacking udev (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 90s Preparing to unpack .../libudev1_257.3-1ubuntu3_amd64.deb ... 90s Unpacking libudev1:amd64 (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 91s Setting up libudev1:amd64 (257.3-1ubuntu3) ... 91s (Reading database ... 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(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 ... 109146 files and directories currently installed.) 91s Preparing to unpack .../libaudit1_1%3a4.0.2-2ubuntu2_amd64.deb ... 91s Unpacking libaudit1:amd64 (1:4.0.2-2ubuntu2) over (1:4.0.2-2ubuntu1) ... 91s Setting up libaudit1:amd64 (1:4.0.2-2ubuntu2) ... 91s (Reading database ... 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(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 ... 109146 files and directories currently installed.) 92s Preparing to unpack .../apt-utils_2.9.33_amd64.deb ... 92s Unpacking apt-utils (2.9.33) over (2.9.31ubuntu1) ... 92s Preparing to unpack .../python3-minimal_3.13.2-2_amd64.deb ... 92s Unpacking python3-minimal (3.13.2-2) over (3.13.2-1) ... 92s Setting up python3-minimal (3.13.2-2) ... 92s (Reading database ... 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(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 ... 109146 files and directories currently installed.) 93s Preparing to unpack .../0-libsqlite3-0_3.46.1-2_amd64.deb ... 93s Unpacking libsqlite3-0:amd64 (3.46.1-2) over (3.46.1-1) ... 93s Preparing to unpack .../1-python3.13_3.13.2-2_amd64.deb ... 93s Unpacking python3.13 (3.13.2-2) over (3.13.2-1) ... 93s Preparing to unpack .../2-python3.13-minimal_3.13.2-2_amd64.deb ... 93s Unpacking python3.13-minimal (3.13.2-2) over (3.13.2-1) ... 93s Preparing to unpack .../3-libpython3.13-minimal_3.13.2-2_amd64.deb ... 93s Unpacking libpython3.13-minimal:amd64 (3.13.2-2) over (3.13.2-1) ... 93s Preparing to unpack .../4-libpython3.13-stdlib_3.13.2-2_amd64.deb ... 93s Unpacking libpython3.13-stdlib:amd64 (3.13.2-2) over (3.13.2-1) ... 93s Preparing to unpack .../5-libpython3-stdlib_3.13.2-2_amd64.deb ... 93s Unpacking libpython3-stdlib:amd64 (3.13.2-2) over (3.13.2-1) ... 93s Preparing to unpack .../6-rsync_3.4.1+ds1-3_amd64.deb ... 93s Unpacking rsync (3.4.1+ds1-3) over (3.4.1-0syncable1) ... 93s Selecting previously unselected package libdebuginfod-common. 93s Preparing to unpack .../7-libdebuginfod-common_0.192-4_all.deb ... 93s Unpacking libdebuginfod-common (0.192-4) ... 93s Preparing to unpack .../8-libsemanage-common_3.7-2.1build1_all.deb ... 93s Unpacking libsemanage-common (3.7-2.1build1) over (3.7-2.1) ... 94s Setting up libsemanage-common (3.7-2.1build1) ... 94s (Reading database ... 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unpack .../29-xz-utils_5.6.4-1_amd64.deb ... 97s Unpacking xz-utils (5.6.4-1) over (5.6.3-1) ... 97s Preparing to unpack .../30-ubuntu-standard_1.549_amd64.deb ... 97s Unpacking ubuntu-standard (1.549) over (1.548) ... 97s Preparing to unpack .../31-libgprofng0_2.44-3ubuntu1_amd64.deb ... 97s Unpacking libgprofng0:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 97s Preparing to unpack .../32-libctf0_2.44-3ubuntu1_amd64.deb ... 97s Unpacking libctf0:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 97s Preparing to unpack .../33-libctf-nobfd0_2.44-3ubuntu1_amd64.deb ... 97s Unpacking libctf-nobfd0:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 97s Preparing to unpack .../34-binutils-x86-64-linux-gnu_2.44-3ubuntu1_amd64.deb ... 97s Unpacking binutils-x86-64-linux-gnu (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 97s Preparing to unpack .../35-libbinutils_2.44-3ubuntu1_amd64.deb ... 97s Unpacking libbinutils:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 97s Preparing to unpack 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previously unselected package linux-perf. 107s Preparing to unpack .../74-linux-perf_6.14.0-10.10_amd64.deb ... 107s Unpacking linux-perf (6.14.0-10.10) ... 107s Selecting previously unselected package linux-tools-6.14.0-10. 107s Preparing to unpack .../75-linux-tools-6.14.0-10_6.14.0-10.10_amd64.deb ... 107s Unpacking linux-tools-6.14.0-10 (6.14.0-10.10) ... 107s Selecting previously unselected package linux-tools-6.14.0-10-generic. 107s Preparing to unpack .../76-linux-tools-6.14.0-10-generic_6.14.0-10.10_amd64.deb ... 107s Unpacking linux-tools-6.14.0-10-generic (6.14.0-10.10) ... 107s Preparing to unpack .../77-pinentry-curses_1.3.1-2ubuntu3_amd64.deb ... 107s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 108s Preparing to unpack .../78-python3-lazr.uri_1.0.6-6_all.deb ... 108s Unpacking python3-lazr.uri (1.0.6-6) over (1.0.6-5) ... 108s Preparing to unpack .../79-python3-rpds-py_0.21.0-2ubuntu2_amd64.deb ... 108s Unpacking python3-rpds-py (0.21.0-2ubuntu2) over (0.21.0-2ubuntu1) ... 108s Preparing to unpack .../80-python3-systemd_235-1build6_amd64.deb ... 108s Unpacking python3-systemd (235-1build6) over (235-1build5) ... 108s Preparing to unpack .../81-python3.13-gdbm_3.13.2-2_amd64.deb ... 108s Unpacking python3.13-gdbm (3.13.2-2) over (3.13.2-1) ... 108s Preparing to unpack .../82-ubuntu-kernel-accessories_1.549_amd64.deb ... 108s Unpacking ubuntu-kernel-accessories (1.549) over (1.548) ... 108s Preparing to unpack .../83-cloud-init_25.1-0ubuntu3_all.deb ... 108s Unpacking cloud-init (25.1-0ubuntu3) over (25.1-0ubuntu2) ... 108s Preparing to unpack .../84-python3-bcrypt_4.2.0-2.1build1_amd64.deb ... 108s Unpacking python3-bcrypt (4.2.0-2.1build1) over (4.2.0-2.1) ... 108s Setting up linux-headers-6.14.0-10 (6.14.0-10.10) ... 108s Setting up media-types (13.0.0) ... 108s Installing new version of config file /etc/mime.types ... 108s Setting up linux-headers-6.14.0-10-generic (6.14.0-10.10) ... 108s Setting up ubuntu-kernel-accessories (1.549) ... 108s Setting up libapparmor1:amd64 (4.1.0~beta5-0ubuntu8) ... 108s Setting up pci.ids (0.0~2025.03.09-1) ... 108s Setting up libnewt0.52:amd64 (0.52.24-4ubuntu2) ... 108s Setting up apt-utils (2.9.33) ... 108s Setting up libdebuginfod-common (0.192-4) ... 108s Setting up exfatprogs (1.2.8-1) ... 108s Setting up linux-firmware (20250310.git9e1370d3-0ubuntu1) ... 108s Setting up bpftool (7.6.0+6.14.0-10.10) ... 108s Setting up libestr0:amd64 (0.1.11-2) ... 108s Setting up libbrotli1:amd64 (1.1.0-2build4) ... 108s Setting up libsqlite3-0:amd64 (3.46.1-2) ... 108s Setting up dosfstools (4.2-1.2) ... 108s Setting up rsyslog (8.2412.0-2ubuntu2) ... 108s info: The user `syslog' is already a member of `adm'. 109s Setting up binutils-common:amd64 (2.44-3ubuntu1) ... 109s Setting up libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) ... 109s Setting up linux-libc-dev:amd64 (6.14.0-10.10) ... 109s Setting up libctf-nobfd0:amd64 (2.44-3ubuntu1) ... 109s Setting up systemd (257.3-1ubuntu3) ... 109s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 109s Created symlink '/run/systemd/system/tmp.mount' → '/dev/null'. 110s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 110s Setting up libparted2t64:amd64 (3.6-5) ... 110s Removing 'diversion of /lib/x86_64-linux-gnu/libparted.so.2 to /lib/x86_64-linux-gnu/libparted.so.2.usr-is-merged by libparted2t64' 110s Removing 'diversion of /lib/x86_64-linux-gnu/libparted.so.2.0.5 to /lib/x86_64-linux-gnu/libparted.so.2.0.5.usr-is-merged by libparted2t64' 110s Setting up linux-headers-generic (6.14.0-10.10) ... 110s Setting up libjemalloc2:amd64 (5.3.0-3) ... 110s Setting up locales (2.41-1ubuntu1) ... 110s Installing new version of config file /etc/locale.alias ... 111s Generating locales (this might take a while)... 112s en_US.UTF-8... done 112s Generation complete. 112s Setting up libsframe1:amd64 (2.44-3ubuntu1) ... 112s Setting up libpython3.13-minimal:amd64 (3.13.2-2) ... 112s Setting up apparmor (4.1.0~beta5-0ubuntu8) ... 112s Installing new version of config file /etc/apparmor.d/fusermount3 ... 112s Installing new version of config file /etc/apparmor.d/lsusb ... 112s Installing new version of config file /etc/apparmor.d/openvpn ... 113s Reloading AppArmor profiles 115s Setting up libftdi1-2:amd64 (1.5-8build1) ... 115s Setting up libglib2.0-data (2.84.0-1) ... 115s Setting up systemd-cryptsetup (257.3-1ubuntu3) ... 115s Setting up libncurses6:amd64 (6.5+20250216-2) ... 115s Setting up strace (6.13+ds-1ubuntu1) ... 115s Setting up xz-utils (5.6.4-1) ... 115s Setting up systemd-timesyncd (257.3-1ubuntu3) ... 115s systemd-time-wait-sync.service is a disabled or a static unit not running, not starting it. 116s Setting up libatomic1:amd64 (15-20250222-0ubuntu1) ... 116s Setting up udev (257.3-1ubuntu3) ... 116s Setting up linux-modules-6.14.0-10-generic (6.14.0-10.10) ... 118s Setting up libncursesw6:amd64 (6.5+20250216-2) ... 118s Setting up libpci3:amd64 (1:3.13.0-2) ... 118s Setting up whiptail (0.52.24-4ubuntu2) ... 118s Setting up python-apt-common (2.9.9build1) ... 118s Setting up pnp.ids (0.393-3) ... 118s Setting up libnl-3-200:amd64 (3.7.0-1) ... 118s Setting up python3.13-minimal (3.13.2-2) ... 119s Setting up libgpgme11t64:amd64 (1.24.2-1ubuntu2) ... 119s Setting up libbinutils:amd64 (2.44-3ubuntu1) ... 119s Setting up libc-dev-bin (2.41-1ubuntu1) ... 119s Setting up libpython3.13-stdlib:amd64 (3.13.2-2) ... 119s Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2ubuntu5) ... 119s Setting up rsync (3.4.1+ds1-3) ... 120s rsync.service is a disabled or a static unit not running, not starting it. 120s Setting up python3.13-gdbm (3.13.2-2) ... 120s Setting up libpython3-stdlib:amd64 (3.13.2-2) ... 120s Setting up systemd-resolved (257.3-1ubuntu3) ... 121s Setting up initramfs-tools-bin (0.146ubuntu1) ... 121s Setting up ncurses-term (6.5+20250216-2) ... 121s Setting up libctf0:amd64 (2.44-3ubuntu1) ... 121s Setting up libpython3.13:amd64 (3.13.2-2) ... 121s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 121s Setting up libdebuginfod1t64:amd64 (0.192-4) ... 121s Setting up systemd-sysv (257.3-1ubuntu3) ... 121s Setting up linux-headers-virtual (6.14.0-10.10) ... 121s Setting up libcurl4t64:amd64 (8.12.1-3ubuntu1) ... 121s Setting up python3.13 (3.13.2-2) ... 122s Setting up htop (3.4.0-2) ... 122s Setting up linux-image-6.14.0-10-generic (6.14.0-10.10) ... 124s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.12.0-16-generic 124s I: /boot/initrd.img.old is now a symlink to initrd.img-6.12.0-16-generic 124s I: /boot/vmlinuz is now a symlink to vmlinuz-6.14.0-10-generic 124s I: /boot/initrd.img is now a symlink to initrd.img-6.14.0-10-generic 124s Setting up parted (3.6-5) ... 124s Setting up libnss-systemd:amd64 (257.3-1ubuntu3) ... 124s Setting up python3 (3.13.2-2) ... 124s Setting up python3-newt:amd64 (0.52.24-4ubuntu2) ... 124s Setting up python3-markupsafe (2.1.5-1build4) ... 124s Setting up linux-modules-extra-6.14.0-10-generic (6.14.0-10.10) ... 126s Setting up libnl-route-3-200:amd64 (3.7.0-1) ... 126s Setting up hwdata (0.393-3) ... 126s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 126s Setting up libglib2.0-0t64:amd64 (2.84.0-1) ... 126s No schema files found: doing nothing. 126s Setting up libgprofng0:amd64 (2.44-3ubuntu1) ... 126s Setting up linux-perf (6.14.0-10.10) ... 126s Setting up gir1.2-glib-2.0:amd64 (2.84.0-1) ... 126s Setting up pciutils (1:3.13.0-2) ... 126s Setting up python3-rpds-py (0.21.0-2ubuntu2) ... 127s Setting up libmm-glib0:amd64 (1.23.4-0ubuntu3) ... 127s Setting up libnl-genl-3-200:amd64 (3.7.0-1) ... 127s Setting up libpam-systemd:amd64 (257.3-1ubuntu3) ... 127s Setting up libc6-dev:amd64 (2.41-1ubuntu1) ... 127s Setting up libgirepository-1.0-1:amd64 (1.83.4-1) ... 127s Setting up curl (8.12.1-3ubuntu1) ... 127s Setting up linux-image-virtual (6.14.0-10.10) ... 127s Setting up initramfs-tools-core (0.146ubuntu1) ... 127s Setting up linux-tools-common (6.14.0-10.10) ... 127s Setting up python3-systemd (235-1build6) ... 127s Setting up python3-cffi-backend:amd64 (1.17.1-2build2) ... 127s Setting up binutils-x86-64-linux-gnu (2.44-3ubuntu1) ... 127s Setting up linux-image-generic (6.14.0-10.10) ... 127s Setting up python3-dbus (1.3.2-5build5) ... 127s Setting up linux-tools-6.14.0-10 (6.14.0-10.10) ... 127s Setting up initramfs-tools (0.146ubuntu1) ... 127s Installing new version of config file /etc/kernel/postinst.d/initramfs-tools ... 127s Installing new version of config file /etc/kernel/postrm.d/initramfs-tools ... 127s update-initramfs: deferring update (trigger activated) 127s Setting up linux-generic (6.14.0-10.10) ... 127s Setting up ubuntu-minimal (1.549) ... 127s Setting up python3-apt (2.9.9build1) ... 127s Setting up python3-bcrypt (4.2.0-2.1build1) ... 127s Setting up python3-yaml (6.0.2-1build2) ... 127s Setting up libfwupd3:amd64 (2.0.6-4) ... 127s Setting up python3-lazr.uri (1.0.6-6) ... 128s Setting up binutils (2.44-3ubuntu1) ... 128s Setting up ubuntu-standard (1.549) ... 128s Setting up cloud-init-base (25.1-0ubuntu3) ... 129s Setting up linux-virtual (6.14.0-10.10) ... 129s Setting up gir1.2-girepository-2.0:amd64 (1.83.4-1) ... 129s Setting up python3-gi (3.50.0-4build1) ... 129s Setting up linux-tools-6.14.0-10-generic (6.14.0-10.10) ... 129s Setting up fwupd (2.0.6-4) ... 130s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 130s fwupd.service is a disabled or a static unit not running, not starting it. 130s Setting up cloud-init (25.1-0ubuntu3) ... 130s Processing triggers for man-db (2.13.0-1) ... 131s Processing triggers for dbus (1.16.2-1ubuntu1) ... 131s Processing triggers for shared-mime-info (2.4-5) ... 132s Warning: program compiled against libxml 212 using older 209 132s Processing triggers for libc-bin (2.41-1ubuntu1) ... 132s Processing triggers for linux-image-6.14.0-10-generic (6.14.0-10.10) ... 132s /etc/kernel/postinst.d/initramfs-tools: 132s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 132s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 142s /etc/kernel/postinst.d/zz-update-grub: 142s Sourcing file `/etc/default/grub' 142s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 142s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 142s Generating grub configuration file ... 142s Found linux image: /boot/vmlinuz-6.14.0-10-generic 142s Found initrd image: /boot/initrd.img-6.14.0-10-generic 143s Found linux image: /boot/vmlinuz-6.12.0-16-generic 143s Found initrd image: /boot/initrd.img-6.12.0-16-generic 143s Found linux image: /boot/vmlinuz-6.11.0-8-generic 143s Found initrd image: /boot/initrd.img-6.11.0-8-generic 143s Warning: os-prober will not be executed to detect other bootable partitions. 143s Systems on them will not be added to the GRUB boot configuration. 143s Check GRUB_DISABLE_OS_PROBER documentation entry. 143s Adding boot menu entry for UEFI Firmware Settings ... 143s done 143s Processing triggers for initramfs-tools (0.146ubuntu1) ... 143s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 143s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 154s Reading package lists... 155s Building dependency tree... 155s Reading state information... 155s Solving dependencies... 155s The following packages will be REMOVED: 155s libnl-genl-3-200* libnsl2* libpython3.12-minimal* libpython3.12-stdlib* 155s libpython3.12t64* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 155s linux-headers-6.12.0-16* linux-headers-6.12.0-16-generic* 155s linux-image-6.11.0-8-generic* linux-image-6.12.0-16-generic* 155s linux-modules-6.11.0-8-generic* linux-modules-6.12.0-16-generic* 155s linux-modules-extra-6.12.0-16-generic* linux-tools-6.11.0-8* 155s linux-tools-6.11.0-8-generic* linux-tools-6.12.0-16* 155s linux-tools-6.12.0-16-generic* 155s 0 upgraded, 0 newly installed, 18 to remove and 5 not upgraded. 155s After this operation, 545 MB disk space will be freed. 155s (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 ... 148643 files and directories currently installed.) 155s Removing libnl-genl-3-200:amd64 (3.7.0-1) ... 155s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 155s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 155s Removing libpython3.12t64:amd64 (3.12.9-1) ... 155s Removing libpython3.12-stdlib:amd64 (3.12.9-1) ... 155s Removing libnsl2:amd64 (1.3.0-3build3) ... 155s Removing libpython3.12-minimal:amd64 (3.12.9-1) ... 155s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 156s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 158s Removing linux-headers-6.12.0-16-generic (6.12.0-16.16) ... 159s Removing linux-headers-6.12.0-16 (6.12.0-16.16) ... 161s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 161s /etc/kernel/postrm.d/initramfs-tools: 161s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 161s /etc/kernel/postrm.d/zz-update-grub: 161s Sourcing file `/etc/default/grub' 161s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 161s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 161s Generating grub configuration file ... 161s Found linux image: /boot/vmlinuz-6.14.0-10-generic 161s Found initrd image: /boot/initrd.img-6.14.0-10-generic 161s Found linux image: /boot/vmlinuz-6.12.0-16-generic 161s Found initrd image: /boot/initrd.img-6.12.0-16-generic 162s Warning: os-prober will not be executed to detect other bootable partitions. 162s Systems on them will not be added to the GRUB boot configuration. 162s Check GRUB_DISABLE_OS_PROBER documentation entry. 162s Adding boot menu entry for UEFI Firmware Settings ... 162s done 162s Removing linux-image-6.12.0-16-generic (6.12.0-16.16) ... 162s W: Removing the running kernel 162s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 162s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 162s /etc/kernel/postrm.d/initramfs-tools: 162s update-initramfs: Deleting /boot/initrd.img-6.12.0-16-generic 162s /etc/kernel/postrm.d/zz-update-grub: 162s Sourcing file `/etc/default/grub' 162s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 162s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 162s Generating grub configuration file ... 162s Found linux image: /boot/vmlinuz-6.14.0-10-generic 162s Found initrd image: /boot/initrd.img-6.14.0-10-generic 162s Warning: os-prober will not be executed to detect other bootable partitions. 162s Systems on them will not be added to the GRUB boot configuration. 162s Check GRUB_DISABLE_OS_PROBER documentation entry. 162s Adding boot menu entry for UEFI Firmware Settings ... 162s done 162s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 163s Removing linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 164s Removing linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 164s Removing linux-tools-6.12.0-16-generic (6.12.0-16.16) ... 164s Removing linux-tools-6.12.0-16 (6.12.0-16.16) ... 164s Processing triggers for libc-bin (2.41-1ubuntu1) ... 164s (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 ... 76972 files and directories currently installed.) 164s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 164s Purging configuration files for libpython3.12-minimal:amd64 (3.12.9-1) ... 164s Purging configuration files for linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 164s Purging configuration files for linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 164s dpkg: warning: while removing linux-modules-6.12.0-16-generic, directory '/lib/modules/6.12.0-16-generic' not empty so not removed 165s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 165s Purging configuration files for linux-image-6.12.0-16-generic (6.12.0-16.16) ... 165s rmdir: failed to remove '/lib/modules/6.12.0-16-generic': Directory not empty 165s autopkgtest [21:34:10]: upgrading testbed (apt dist-upgrade and autopurge) 165s Reading package lists... 165s Building dependency tree... 165s Reading state information... 166s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 166s Starting 2 pkgProblemResolver with broken count: 0 166s Done 166s Entering ResolveByKeep 167s 167s Calculating upgrade... 167s The following packages will be upgraded: 167s libc-bin libc-dev-bin libc6 libc6-dev locales 167s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 167s Need to get 10.5 MB of archives. 167s After this operation, 1024 B of additional disk space will be used. 167s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6-dev amd64 2.41-1ubuntu2 [2183 kB] 168s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-dev-bin amd64 2.41-1ubuntu2 [24.7 kB] 168s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6 amd64 2.41-1ubuntu2 [3327 kB] 168s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-bin amd64 2.41-1ubuntu2 [700 kB] 168s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 locales all 2.41-1ubuntu2 [4246 kB] 168s Preconfiguring packages ... 168s Fetched 10.5 MB in 1s (11.7 MB/s) 168s (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 ... 76968 files and directories currently installed.) 168s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_amd64.deb ... 168s Unpacking libc6-dev:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 169s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_amd64.deb ... 169s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 169s Preparing to unpack .../libc6_2.41-1ubuntu2_amd64.deb ... 169s Unpacking libc6:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 169s Setting up libc6:amd64 (2.41-1ubuntu2) ... 169s (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 ... 76968 files and directories currently installed.) 169s Preparing to unpack .../libc-bin_2.41-1ubuntu2_amd64.deb ... 169s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 169s Setting up libc-bin (2.41-1ubuntu2) ... 169s (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 ... 76968 files and directories currently installed.) 169s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 169s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 170s Setting up locales (2.41-1ubuntu2) ... 170s Generating locales (this might take a while)... 172s en_US.UTF-8... done 172s Generation complete. 172s Setting up libc-dev-bin (2.41-1ubuntu2) ... 172s Setting up libc6-dev:amd64 (2.41-1ubuntu2) ... 172s Processing triggers for man-db (2.13.0-1) ... 172s Processing triggers for systemd (257.3-1ubuntu3) ... 173s Reading package lists... 174s Building dependency tree... 174s Reading state information... 174s Starting pkgProblemResolver with broken count: 0 174s Starting 2 pkgProblemResolver with broken count: 0 174s Done 174s Solving dependencies... 175s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 175s autopkgtest [21:34:20]: rebooting testbed after setup commands that affected boot 198s autopkgtest [21:34:43]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 16:07:00 UTC 2025 201s autopkgtest [21:34:46]: @@@@@@@@@@@@@@@@@@@@ apt-source proteinortho 203s Get:1 http://ftpmaster.internal/ubuntu plucky/universe proteinortho 6.3.1+dfsg-1 (dsc) [2161 B] 203s Get:2 http://ftpmaster.internal/ubuntu plucky/universe proteinortho 6.3.1+dfsg-1 (tar) [376 kB] 203s Get:3 http://ftpmaster.internal/ubuntu plucky/universe proteinortho 6.3.1+dfsg-1 (diff) [7248 B] 203s gpgv: Signature made Fri Jan 12 05:54:55 2024 UTC 203s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 203s gpgv: issuer "tille@debian.org" 203s gpgv: Can't check signature: No public key 203s dpkg-source: warning: cannot verify inline signature for ./proteinortho_6.3.1+dfsg-1.dsc: no acceptable signature found 203s autopkgtest [21:34:48]: testing package proteinortho version 6.3.1+dfsg-1 204s autopkgtest [21:34:49]: build not needed 204s autopkgtest [21:34:49]: test run-unit-test: preparing testbed 205s Reading package lists... 205s Building dependency tree... 205s Reading state information... 205s Starting pkgProblemResolver with broken count: 0 205s Starting 2 pkgProblemResolver with broken count: 0 205s Done 206s The following NEW packages will be installed: 206s diamond-aligner libblas3 libgfortran5 libgomp1 liblapack3 libmbedcrypto16 206s libmbedtls21 libmbedx509-7 ncbi-blast+ ncbi-data proteinortho 206s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. 206s Need to get 27.7 MB of archives. 206s After this operation, 113 MB of additional disk space will be used. 206s Get:1 http://ftpmaster.internal/ubuntu plucky/universe amd64 diamond-aligner amd64 2.1.11-2 [2572 kB] 207s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 207s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 15-20250222-0ubuntu1 [919 kB] 207s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250222-0ubuntu1 [148 kB] 207s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 208s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedcrypto16 amd64 3.6.2-3ubuntu1 [276 kB] 208s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedx509-7 amd64 3.6.2-3ubuntu1 [37.1 kB] 208s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedtls21 amd64 3.6.2-3ubuntu1 [126 kB] 208s Get:9 http://ftpmaster.internal/ubuntu plucky/universe amd64 ncbi-data all 6.1.20170106+dfsg2-5 [3966 kB] 209s Get:10 http://ftpmaster.internal/ubuntu plucky/universe amd64 ncbi-blast+ amd64 2.16.0+ds-6build1 [15.8 MB] 210s Get:11 http://ftpmaster.internal/ubuntu plucky/universe amd64 proteinortho amd64 6.3.1+dfsg-1 [358 kB] 210s Fetched 27.7 MB in 4s (6884 kB/s) 210s Selecting previously unselected package diamond-aligner. 210s (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 ... 76968 files and directories currently installed.) 210s Preparing to unpack .../00-diamond-aligner_2.1.11-2_amd64.deb ... 210s Unpacking diamond-aligner (2.1.11-2) ... 211s Selecting previously unselected package libblas3:amd64. 211s Preparing to unpack .../01-libblas3_3.12.1-2_amd64.deb ... 211s Unpacking libblas3:amd64 (3.12.1-2) ... 211s Selecting previously unselected package libgfortran5:amd64. 211s Preparing to unpack .../02-libgfortran5_15-20250222-0ubuntu1_amd64.deb ... 211s Unpacking libgfortran5:amd64 (15-20250222-0ubuntu1) ... 211s Selecting previously unselected package libgomp1:amd64. 211s Preparing to unpack .../03-libgomp1_15-20250222-0ubuntu1_amd64.deb ... 211s Unpacking libgomp1:amd64 (15-20250222-0ubuntu1) ... 211s Selecting previously unselected package liblapack3:amd64. 211s Preparing to unpack .../04-liblapack3_3.12.1-2_amd64.deb ... 211s Unpacking liblapack3:amd64 (3.12.1-2) ... 211s Selecting previously unselected package libmbedcrypto16:amd64. 211s Preparing to unpack .../05-libmbedcrypto16_3.6.2-3ubuntu1_amd64.deb ... 211s Unpacking libmbedcrypto16:amd64 (3.6.2-3ubuntu1) ... 211s Selecting previously unselected package libmbedx509-7:amd64. 211s Preparing to unpack .../06-libmbedx509-7_3.6.2-3ubuntu1_amd64.deb ... 211s Unpacking libmbedx509-7:amd64 (3.6.2-3ubuntu1) ... 211s Selecting previously unselected package libmbedtls21:amd64. 211s Preparing to unpack .../07-libmbedtls21_3.6.2-3ubuntu1_amd64.deb ... 211s Unpacking libmbedtls21:amd64 (3.6.2-3ubuntu1) ... 211s Selecting previously unselected package ncbi-data. 211s Preparing to unpack .../08-ncbi-data_6.1.20170106+dfsg2-5_all.deb ... 211s Unpacking ncbi-data (6.1.20170106+dfsg2-5) ... 211s Selecting previously unselected package ncbi-blast+. 211s Preparing to unpack .../09-ncbi-blast+_2.16.0+ds-6build1_amd64.deb ... 211s Unpacking ncbi-blast+ (2.16.0+ds-6build1) ... 211s Selecting previously unselected package proteinortho. 211s Preparing to unpack .../10-proteinortho_6.3.1+dfsg-1_amd64.deb ... 211s Unpacking proteinortho (6.3.1+dfsg-1) ... 211s Setting up ncbi-data (6.1.20170106+dfsg2-5) ... 211s Setting up libgomp1:amd64 (15-20250222-0ubuntu1) ... 211s Setting up diamond-aligner (2.1.11-2) ... 211s Setting up libblas3:amd64 (3.12.1-2) ... 211s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 211s Setting up libgfortran5:amd64 (15-20250222-0ubuntu1) ... 211s Setting up libmbedcrypto16:amd64 (3.6.2-3ubuntu1) ... 211s Setting up liblapack3:amd64 (3.12.1-2) ... 211s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 211s Setting up libmbedx509-7:amd64 (3.6.2-3ubuntu1) ... 211s Setting up libmbedtls21:amd64 (3.6.2-3ubuntu1) ... 211s Setting up ncbi-blast+ (2.16.0+ds-6build1) ... 211s Setting up proteinortho (6.3.1+dfsg-1) ... 212s Processing triggers for man-db (2.13.0-1) ... 212s Processing triggers for libc-bin (2.41-1ubuntu2) ... 213s autopkgtest [21:34:58]: test run-unit-test: [----------------------- 214s ***************************************************************** 214s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 214s ***************************************************************** 214s Detected 2 CPU threads (1 threads per processes each with 2 threads) adjust this with -cpus, Detected 'blastp+' version 2.16.0+ 214s Checking input files. 214s Checking input files. 214s Checking test/C_clean.faa... ok 214s Checking test/C2.faa... ok 214s Checking test/E.faa... ok 214s Checking test/L.faa... ok 214s Checking test/M.faa... ok 214s Checking test/C.faa... 214s  [WARNING] input 'test/C.faa' contains a gene-name with a comma, this causes problems with the proteinortho.tsv output, I will clean the file ('test/C_clean.faa') and restart the analysis !!! 214s The line is: 214s C_10,test 214s ok 214s Checking test/C_clean.faa... ok 214s Checking test/L.faa... ok 214s Checking test/C2.faa... ok 214s Checking test/E.faa... ok 214s 214s **Step 1** 214s Generating indices anyway (forced). 214s Building database for 'test/C2.faa' (4 sequences) 214s Generating indices anyway (forced). 214s Building database for 'test/E.faa' (144 sequences) 214s Generating indices anyway (forced). 214s Building database for 'test/C_clean.faa' (218 sequences) 214s Generating indices anyway (forced). 214s Building database for 'test/L.faa' (80 sequences) 214s Generating indices anyway (forced). 214s Building database for 'test/M.faa' (40 sequences) 214s 214s **Step 2** using blastp+ 218s Running blast analysis: 0% (0/10) Running blast analysis: 10% (1/10) Running blast analysis: 20% (2/10) Running blast analysis: 30% (3/10) Running blast analysis: 40% (4/10) Running blast analysis: 50% (5/10) Running blast analysis: 60% (6/10) Running blast analysis: 70% (7/10) Running blast analysis: 80% (8/10) Running blast analysis: 100% (10/10) Running blast analysis: 90% (9/10) Running blast analysis: 100% (10/10) 218s [OUTPUT] -> written to test_blastp.blast-graph 218s 218s **Step 3** 218s Clustering by similarity (Proteinortho mode) using 2 cpu core(s). Please wait... 218s Reading test_blastp.blast-graph 218s 5 species 218s 112 paired proteins 218s 149 bidirectional edges 219s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components 219s [OUTPUT] -> Orthologous groups are written to test_blastp.proteinortho.tsv 219s You can extract the fasta files of each orthology group with 219s proteinortho_grab_proteins.pl -tofiles test_blastp.proteinortho.tsv 'test/C2.faa' 'test/E.faa' 'test/C_clean.faa' 'test/L.faa' 'test/M.faa' 219s (Careful: This will generate a file foreach line in the file test_blastp.proteinortho.tsv). 219s [OUTPUT] -> Orthologous pairs are written to test_blastp.proteinortho-graph 219s # test_blastp.proteinortho.tsv statistics: 219s # number of groups that contains at least p% species: 219s # p species groups genes in groups 219s 0% 0 32 (100%) 112 (100%) 219s 20% 1 32 (100%) 112 (100%) 219s 40% 2 32 (100%) 112 (100%) 219s 60% 3 17 (53.12%) 74 (66.07%) 219s 80% 4 11 (34.37%) 51 (45.53%) 219s 100% 5 1 (3.12%) 5 (4.46%) 219s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 219s # number of groups for each input species: 219s L.faa 32 100% 219s M.faa 32 100% 219s E.faa 15 46.87% 219s C_clean.faa 13 40.62% 219s C2.faa 1 3.12% 219s 219s [OUTPUT] -> Summary is written to test_blastp.proteinortho-graph.summary 219s 219s [OUTPUT] -> Orthologous groups are written to test_blastp.proteinortho.html 219s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 219s proteinortho2xml.pl test_blastp.proteinortho.tsv >test_blastp.proteinortho.tsv.xml 219s 219s All finished. 219s ***************************************************************** 219s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 219s ***************************************************************** 219s Detected 2 CPU threads (1 threads per processes each with 2 threads) adjust this with -cpus, Detected 'blastp+' version 2.16.0+ 219s Checking input files. 219s Checking test/C_clean.faa... ok 219s Checking test/C2.faa... ok 219s Checking test/E.faa... ok 219s Checking test/L.faa... ok 219s Checking test/M.faa... ok 219s 219s **Step 1** 219s Generating indices anyway (forced). 219s Building database for 'test/C_clean.faa' (109 sequences) 219s Generating indices anyway (forced). 219s Building database for 'test/M.faa' (40 sequences) 219s Generating indices anyway (forced). 219s Building database for 'test/C2.faa' (2 sequences) 219s Generating indices anyway (forced). 219s Building database for 'test/E.faa' (72 sequences) 219s Generating indices anyway (forced). 219s Building database for 'test/L.faa' (40 sequences) 219s 219s **Step 2** using blastp+ with : synteny 224s Running blast analysis: 0% (0/10) Running blast analysis: 10% (1/10) Running blast analysis: 20% (2/10) Running blast analysis: 30% (3/10) Running blast analysis: 40% (4/10) Running blast analysis: 50% (5/10) Running blast analysis: 60% (6/10) Running blast analysis: 70% (7/10) Running blast analysis: 80% (8/10) Running blast analysis: 100% (10/10) Running blast analysis: 90% (9/10) Running blast analysis: 100% (10/10) 224s [OUTPUT] -> written to test_synteny.blast-graph 224s 224s **Step 3** 224s Clustering by similarity (Proteinortho mode) using 2 cpu core(s). Please wait... 224s Reading test_synteny.blast-graph 224s 5 species 224s 112 paired proteins 224s 147 bidirectional edges 225s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components 225s [OUTPUT] -> Orthologous groups are written to test_synteny.proteinortho.tsv 225s You can extract the fasta files of each orthology group with 225s proteinortho_grab_proteins.pl -tofiles test_synteny.proteinortho.tsv 'test/C_clean.faa' 'test/M.faa' 'test/C2.faa' 'test/E.faa' 'test/L.faa' 225s (Careful: This will generate a file foreach line in the file test_synteny.proteinortho.tsv). 225s Adding singles... 225s [OUTPUT] -> Orthologous pairs are written to test_synteny.proteinortho-graph 225s # test_synteny.proteinortho.tsv statistics: 225s # number of groups that contains at least p% species: 225s # p species groups genes in groups 225s 0% 0 182 (100%) 262 (100%) 225s 20% 1 182 (100%) 262 (100%) 225s 40% 2 32 (17.58%) 112 (42.74%) 225s 60% 3 17 (9.34%) 74 (28.24%) 225s 80% 4 11 (6.04%) 51 (19.46%) 225s 100% 5 1 (0.54%) 5 (1.9%) 225s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 225s # groups that contains only one species: 225s single 5 150 (82.41%) 150 (57.25%) 225s # number of groups for each input species: 225s L.faa 32 100% 225s M.faa 32 100% 225s E.faa 15 46.87% 225s C_clean.faa 13 40.62% 225s C2.faa 1 3.12% 225s 225s [OUTPUT] -> Summary is written to test_synteny.proteinortho-graph.summary 225s 225s [OUTPUT] -> Orthologous groups are written to test_synteny.proteinortho.html 225s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 225s proteinortho2xml.pl test_synteny.proteinortho.tsv >test_synteny.proteinortho.tsv.xml 225s 225s 225s Clustering by gene-order (POFF mode) 225s Reading test_synteny.ffadj-graph 225s 5 species 225s 105 paired proteins 225s 106 bidirectional edges 226s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (33@lapack* + 0@power) connected components Clustering: working on (32@lapack* + 0@power) connected components Clustering: working on (31@lapack* + 0@power) connected components Clustering: working on (32@lapack* + 0@power) connected components Clustering: working on (31@lapack* + 0@power) connected components Clustering: working on (30@lapack* + 0@power) connected components Clustering: working on (29@lapack* + 0@power) connected components Clustering: working on (28@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Reading test_synteny.ffadj-graph 226s 5 species 226s 105 paired proteins 226s 106 bidirectional edges 227s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (33@lapack* + 0@power) connected components Clustering: working on (32@lapack* + 0@power) connected components Clustering: working on (31@lapack* + 0@power) connected components Clustering: working on (30@lapack* + 0@power) connected components Clustering: working on (29@lapack* + 0@power) connected components Clustering: working on (30@lapack* + 0@power) connected components Clustering: working on (29@lapack* + 0@power) connected components Clustering: working on (28@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components 227s [OUTPUT] -> Orthologous groups are written to test_synteny.poff.tsv 227s You can extract the fasta files of each orthology group with 227s proteinortho_grab_proteins.pl -tofiles test_synteny.poff.tsv 'test/C_clean.faa' 'test/M.faa' 'test/C2.faa' 'test/E.faa' 'test/L.faa' 227s (Careful: This will generate a file foreach line in the file test_synteny.poff.tsv). 227s Adding singles... 227s [OUTPUT] -> Orthologous pairs written to test_synteny.poff-graph 227s # test_synteny.poff.tsv statistics: 227s # number of groups that contains at least p% species: 227s # p species groups genes in groups 227s 0% 0 195 (100%) 262 (100%) 227s 20% 1 195 (100%) 262 (100%) 227s 40% 2 37 (18.97%) 104 (39.69%) 227s 60% 3 17 (8.71%) 64 (24.42%) 227s 80% 4 10 (5.12%) 43 (16.41%) 227s 100% 5 1 (0.51%) 5 (1.9%) 227s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 227s # groups that contains only one species: 227s single 5 158 (81.02%) 158 (60.3%) 227s # number of groups for each input species: 227s L.faa 37 100% 227s M.faa 37 100% 227s E.faa 14 37.83% 227s C_clean.faa 13 35.13% 227s C2.faa 1 2.7% 227s 227s [OUTPUT] -> Summary is written to test_synteny.poff-graph.summary 227s 227s [OUTPUT] -> Orthologous groups are written to test_synteny.poff.html 227s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 227s proteinortho2xml.pl test_synteny.proteinortho.tsv >test_synteny.proteinortho.tsv.xml 227s 227s All finished. 227s ***************************************************************** 227s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 227s ***************************************************************** 227s Detected 2 CPU threads (1 threads per processes each with 2 threads) adjust this with -cpus, Detected 'diamond' version 2.1.11 227s Checking input files. 227s Checking test/C_clean.faa... ok 227s Checking test/C2.faa... ok 227s Checking test/E.faa... ok 227s Checking test/L.faa... ok 227s Checking test/M.faa... ok 227s 227s **Step 1** 227s Generating indices anyway (forced). 227s Building database for 'test/E.faa' (72 sequences) 227s Generating indices anyway (forced). 227s Building database for 'test/M.faa' (40 sequences) 227s Generating indices anyway (forced). 227s Building database for 'test/C2.faa' (2 sequences) 227s Generating indices anyway (forced). 227s Building database for 'test/L.faa' (40 sequences) 227s Generating indices anyway (forced). 227s Building database for 'test/C_clean.faa' (109 sequences) 227s 227s **Step 2** using diamond 231s Running blast analysis: 0% (0/10) Running blast analysis: 10% (1/10) Running blast analysis: 20% (2/10) Running blast analysis: 30% (3/10) Running blast analysis: 40% (4/10) Running blast analysis: 50% (5/10) Running blast analysis: 60% (6/10) Running blast analysis: 70% (7/10) Running blast analysis: 80% (8/10) Running blast analysis: 100% (10/10) Running blast analysis: 90% (9/10) Running blast analysis: 100% (10/10) 231s [OUTPUT] -> written to test_diamond.blast-graph 231s 231s **Step 3** 231s Clustering by similarity (Proteinortho mode) using 2 cpu core(s). Please wait... 231s Reading test_diamond.blast-graph 231s 5 species 231s 112 paired proteins 231s 145 bidirectional edges 232s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components 232s [OUTPUT] -> Orthologous groups are written to test_diamond.proteinortho.tsv 232s You can extract the fasta files of each orthology group with 232s proteinortho_grab_proteins.pl -tofiles test_diamond.proteinortho.tsv 'test/E.faa' 'test/M.faa' 'test/C2.faa' 'test/L.faa' 'test/C_clean.faa' 232s (Careful: This will generate a file foreach line in the file test_diamond.proteinortho.tsv). 232s [OUTPUT] -> Orthologous pairs are written to test_diamond.proteinortho-graph 232s # test_diamond.proteinortho.tsv statistics: 232s # number of groups that contains at least p% species: 232s # p species groups genes in groups 232s 0% 0 32 (100%) 111 (100%) 232s 20% 1 32 (100%) 111 (100%) 232s 40% 2 32 (100%) 111 (100%) 232s 60% 3 17 (53.12%) 75 (67.56%) 232s 80% 4 11 (34.37%) 52 (46.84%) 232s 100% 5 1 (3.12%) 5 (4.5%) 232s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 232s # number of groups for each input species: 232s L.faa 32 100% 232s M.faa 32 100% 232s E.faa 15 46.87% 232s C_clean.faa 13 40.62% 232s C2.faa 1 3.12% 232s 232s [OUTPUT] -> Summary is written to test_diamond.proteinortho-graph.summary 232s 232s [OUTPUT] -> Orthologous groups are written to test_diamond.proteinortho.html 232s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 232s proteinortho2xml.pl test_diamond.proteinortho.tsv >test_diamond.proteinortho.tsv.xml 232s 232s All finished. 232s ***************************************************************** 232s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 232s ***************************************************************** 232s Detected 2 CPU threads (1 threads per processes each with 2 threads) adjust this with -cpus, Detected 'diamond' version 2.1.11 232s Checking input files. 232s Checking test/C_clean.faa... ok 232s Checking test/C2.faa... ok 232s Checking test/E.faa... ok 232s Checking test/L.faa... ok 232s Checking test/M.faa... ok 232s 232s **Step 1** 232s Generating indices anyway (forced). 232s Building database for 'test/C_clean.faa' (109 sequences) 232s Generating indices anyway (forced). 232s Building database for 'test/L.faa' (40 sequences) 232s Generating indices anyway (forced). 232s Building database for 'test/C2.faa' (2 sequences) 232s Generating indices anyway (forced). 232s Building database for 'test/M.faa' (40 sequences) 232s Generating indices anyway (forced). 232s Building database for 'test/E.faa' (72 sequences) 232s 232s **Step 2** using diamond 236s Running blast analysis: 0% (0/10) Running blast analysis: 10% (1/10) Running blast analysis: 20% (2/10) Running blast analysis: 30% (3/10) Running blast analysis: 40% (4/10) Running blast analysis: 50% (5/10) Running blast analysis: 60% (6/10) Running blast analysis: 70% (7/10) Running blast analysis: 80% (8/10) Running blast analysis: 100% (10/10) Running blast analysis: 90% (9/10) Running blast analysis: 100% (10/10) 236s [OUTPUT] -> written to test_diamondmoresensitive.blast-graph 236s 236s **Step 3** 236s Clustering by similarity (Proteinortho mode) using 2 cpu core(s). Please wait... 236s Reading test_diamondmoresensitive.blast-graph 236s 5 species 236s 113 paired proteins 236s 147 bidirectional edges 237s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components 237s [OUTPUT] -> Orthologous groups are written to test_diamondmoresensitive.proteinortho.tsv 237s You can extract the fasta files of each orthology group with 237s proteinortho_grab_proteins.pl -tofiles test_diamondmoresensitive.proteinortho.tsv 'test/C_clean.faa' 'test/L.faa' 'test/C2.faa' 'test/M.faa' 'test/E.faa' 237s (Careful: This will generate a file foreach line in the file test_diamondmoresensitive.proteinortho.tsv). 237s [OUTPUT] -> Orthologous pairs are written to test_diamondmoresensitive.proteinortho-graph 237s # test_diamondmoresensitive.proteinortho.tsv statistics: 237s # number of groups that contains at least p% species: 237s # p species groups genes in groups 237s 0% 0 32 (100%) 112 (100%) 237s 20% 1 32 (100%) 112 (100%) 237s 40% 2 32 (100%) 112 (100%) 237s 60% 3 17 (53.12%) 76 (67.85%) 237s 80% 4 11 (34.37%) 53 (47.32%) 237s 100% 5 1 (3.12%) 5 (4.46%) 237s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 237s # number of groups for each input species: 237s L.faa 32 100% 237s M.faa 32 100% 237s E.faa 15 46.87% 237s C_clean.faa 13 40.62% 237s C2.faa 1 3.12% 237s 237s [OUTPUT] -> Summary is written to test_diamondmoresensitive.proteinortho-graph.summary 237s 237s [OUTPUT] -> Orthologous groups are written to test_diamondmoresensitive.proteinortho.html 237s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 237s proteinortho2xml.pl test_diamondmoresensitive.proteinortho.tsv >test_diamondmoresensitive.proteinortho.tsv.xml 237s 237s All finished. 237s ***************************************************************** 237s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 237s ***************************************************************** 237s Detected 2 CPU threads (1 threads per processes each with 2 threads) adjust this with -cpus, Detected 'blastp+' version 2.16.0+ 237s Checking input files. 237s Checking test/C_clean.faa... ok 237s Checking test/C2.faa... ok 237s Checking test/E.faa... ok 237s Checking test/L.faa... ok 237s Checking test/M.faa... ok 237s 237s **Step 1** 237s Generating indices anyway (forced). 237s Building database for 'test/C_clean.faa' (109 sequences) 237s Generating indices anyway (forced). 237s Building database for 'test/E.faa' (72 sequences) 237s Generating indices anyway (forced). 237s Building database for 'test/C2.faa' (2 sequences) 237s Generating indices anyway (forced). 237s Building database for 'test/M.faa' (40 sequences) 237s Generating indices anyway (forced). 237s Building database for 'test/L.faa' (40 sequences) 237s 237s **Step 2** using blastp+ 241s Running blast analysis: 0% (0/10) Running blast analysis: 10% (1/10) Running blast analysis: 20% (2/10) Running blast analysis: 30% (3/10) Running blast analysis: 40% (4/10) Running blast analysis: 50% (5/10) Running blast analysis: 60% (6/10) Running blast analysis: 70% (7/10) Running blast analysis: 80% (8/10) Running blast analysis: 100% (10/10) Running blast analysis: 90% (9/10) Running blast analysis: 100% (10/10) 241s [OUTPUT] -> written to test_blastall.blast-graph 241s 241s **Step 3** 241s Clustering by similarity (Proteinortho mode) using 2 cpu core(s). Please wait... 241s Reading test_blastall.blast-graph 241s 5 species 241s 112 paired proteins 241s 147 bidirectional edges 242s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components 242s [OUTPUT] -> Orthologous groups are written to test_blastall.proteinortho.tsv 242s You can extract the fasta files of each orthology group with 242s proteinortho_grab_proteins.pl -tofiles test_blastall.proteinortho.tsv 'test/C_clean.faa' 'test/E.faa' 'test/C2.faa' 'test/M.faa' 'test/L.faa' 242s (Careful: This will generate a file foreach line in the file test_blastall.proteinortho.tsv). 242s [OUTPUT] -> Orthologous pairs are written to test_blastall.proteinortho-graph 242s # test_blastall.proteinortho.tsv statistics: 242s # number of groups that contains at least p% species: 242s # p species groups genes in groups 242s 0% 0 32 (100%) 112 (100%) 242s 20% 1 32 (100%) 112 (100%) 242s 40% 2 32 (100%) 112 (100%) 242s 60% 3 17 (53.12%) 74 (66.07%) 242s 80% 4 11 (34.37%) 51 (45.53%) 242s 100% 5 1 (3.12%) 5 (4.46%) 242s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 242s # number of groups for each input species: 242s L.faa 32 100% 242s M.faa 32 100% 242s E.faa 15 46.87% 242s C_clean.faa 13 40.62% 242s C2.faa 1 3.12% 242s 242s [OUTPUT] -> Summary is written to test_blastall.proteinortho-graph.summary 242s 242s [OUTPUT] -> Orthologous groups are written to test_blastall.proteinortho.html 242s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 242s proteinortho2xml.pl test_blastall.proteinortho.tsv >test_blastall.proteinortho.tsv.xml 242s 242s All finished. 242s - test max_of_diag() : OK 242s - test generate_random_vector() : OK 242s - test get_new_x() : OK 242s - test makeOrthogonal() : OK 242s - test normalize() : OK 242s - test getY() : OK 242s - test lapack() : OK 242s - test power() : OK 242s - test smirnov-grubb() : OK 242s All test passed. 242s Reading test_blastp.blast-graph 242s 5 species 242s 112 paired proteins 242s 149 bidirectional edges 242s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components# Species Genes Alg.-Conn. C2.faa C_clean.faa E.faa L.faa M.faa 243s Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components 5 5 1 C_10 C_10;test E_10 L_10 M_10 243s 4 4 1 * C_11 E_11 L_11 M_11 243s 4 6 0.333 * C_12,C_21 E_313,E_315 L_313 M_313 243s 4 4 1 * C_14 E_14 L_14 M_14 243s 4 4 1 * C_15 E_15 L_15 M_15 243s 4 4 1 * C_16 E_16 L_16 M_16 243s 4 4 1 * C_17 E_17 L_17 M_17 243s 4 4 1 * C_64 E_18 L_18 M_18 243s 4 5 0.2 * C_63,C_22 E_19 L_19 M_19 243s 3 3 0.33 * * E_367 L_319 M_319 243s 3 3 0.33 * * E_432 L_328 M_328 243s 2 2 1 * * * L_619 M_619 243s 2 2 1 * * * L_617 M_617 243s 2 5 0.166 * * * L_641,L_643 M_642,M_640,M_649 243s 2 4 0.5 * * * L_645,L_647 M_644,M_646 243s 2 2 1 * * * L_333 M_333 243s 3 3 1 * C_20 * L_20 M_20 243s 3 6 0.333 * C_2,C_164,C_166,C_167 * L_2 M_2 243s 2 2 1 * * * L_3 M_3 243s 2 2 1 * * * L_4 M_4 243s 2 2 1 * * * L_5 M_5 243s 2 2 1 * * * L_6 M_6 243s 2 2 1 * * * L_8 M_8 243s 2 2 1 * * * L_9 M_9 243s 2 2 1 * * * L_623 M_623 243s 4 4 1 * C_13 E_13 L_621 M_621 243s 2 4 0.146 * * * L_637,L_639 M_636,M_638 243s 3 3 0.33 * * E_437 L_317 M_317 243s 2 3 0.33 * * * L_631,L_633 M_632 243s 4 7 0.119 * C_1 E_368,E_366 L_323,L_627,L_336 M_627 243s 2 2 1 * * * L_331 M_331 243s 3 5 0.2 * * E_317 L_635 M_336,M_323,M_634 243s Reading test_blastp.blast-graph 243s 5 species 243s 112 paired proteins 243s 149 bidirectional edges 243s Clustering: working on (2@lapack* + 0@power) connected components # Species Genes Alg.-Conn. C2.faa C_clean.faa E.faa L.faa M.faa 244s Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 1@power) connected components Clustering: working on (13@lapack* + 2@power) connected components Clustering: working on (12@lapack* + 3@power) connected components Clustering: working on (11@lapack* + 4@power) connected components Clustering: working on (10@lapack* + 5@power) connected components Clustering: working on (9@lapack* + 6@power) connected components Clustering: working on (8@lapack* + 7@power) connected components Clustering: working on (7@lapack* + 8@power) connected components Clustering: working on (6@lapack* + 9@power) connected components Clustering: working on (5@lapack* + 10@power) connected components Clustering: working on (4@lapack* + 11@power) connected components Clustering: working on (3@lapack* + 12@power) connected components Clustering: working on (2@lapack* + 13@power) connected components Clustering: working on (0@lapack + 15@power*) connected components Clustering: working on (0@lapack + 14@power*) connected components Clustering: working on (0@lapack + 13@power*) connected components Clustering: working on (0@lapack + 12@power*) connected components Clustering: working on (3@lapack* + 10@power) connected components Clustering: working on (2@lapack* + 10@power) connected components Clustering: working on (0@lapack + 12@power*) connected components Clustering: working on (0@lapack + 11@power*) connected components Clustering: working on (0@lapack + 10@power*) connected components Clustering: working on (0@lapack + 9@power*) connected components Clustering: working on (0@lapack + 8@power*) connected components Clustering: working on (0@lapack + 7@power*) connected components Clustering: working on (0@lapack + 6@power*) connected components Clustering: working on (4@lapack* + 4@power) connected components Clustering: working on (3@lapack* + 4@power) connected components Clustering: working on (2@lapack* + 5@power) connected components Clustering: working on (0@lapack + 7@power*) connected components Clustering: working on (0@lapack + 6@power*) connected components Clustering: working on (0@lapack + 5@power*) connected components Clustering: working on (0@lapack + 4@power*) connected components Clustering: working on (0@lapack + 3@power*) connected components Clustering: working on (0@lapack + 2@power*) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 1@power) connected components Clustering: working on (0@lapack + 3@power*) connected components Clustering: working on (3@lapack* + 1@power) connected components Clustering: working on (2@lapack* + 1@power) connected components Clustering: working on (0@lapack + 3@power*) connected components Clustering: working on (3@lapack* + 1@power) connected components Clustering: working on (2@lapack* + 1@power) connected components Clustering: working on (0@lapack + 3@power*) connected components Clustering: working on (0@lapack + 2@power*) connected components 3 3 0.33 * * E_367 L_319 M_319 244s 3 3 0.33 * * E_432 L_328 M_328 244s 2 2 1 * * * L_619 M_619 244s 2 2 1 * * * L_617 M_617 244s 2 2 1 * * * L_333 M_333 244s 3 3 1 * C_20 * L_20 M_20 244s 2 2 1 * * * L_3 M_3 244s 2 2 1 * * * L_4 M_4 244s 2 2 1 * * * L_5 M_5 244s 2 2 1 * * * L_6 M_6 244s 2 2 1 * * * L_8 M_8 244s 2 2 1 * * * L_9 M_9 244s 5 5 0.694 C_10 C_10;test E_10 L_10 M_10 244s 4 4 0.727 * C_11 E_11 L_11 M_11 244s 4 6 0.297 * C_12,C_21 E_313,E_315 L_313 M_313 244s 2 2 1 * * * L_623 M_623 244s 4 4 0.743 * C_14 E_14 L_14 M_14 244s 4 4 0.818 * C_15 E_15 L_15 M_15 244s 4 4 0.815 * C_16 E_16 L_16 M_16 244s 4 4 0.824 * C_17 E_17 L_17 M_17 244s 4 4 0.777 * C_64 E_18 L_18 M_18 244s 4 5 0.178 * C_63,C_22 E_19 L_19 M_19 244s 3 3 0.33 * * E_437 L_317 M_317 244s 2 5 0.16 * * * L_641,L_643 M_642,M_640,M_649 244s 2 4 0.478 * * * L_645,L_647 M_644,M_646 244s 3 6 0.314 * C_2,C_164,C_166,C_167 * L_2 M_2 244s 4 4 0.702 * C_13 E_13 L_621 M_621 244s 2 4 0.145 * * * L_637,L_639 M_636,M_638 244s 2 2 1 * * * L_331 M_331 244s 2 3 0.33 * * * L_631,L_633 M_632 244s 3 5 0.181 * * E_317 L_635 M_336,M_323,M_634 244s 4 7 0.108 * C_1 E_368,E_366 L_323,L_627,L_336 M_627 244s Test okay 245s autopkgtest [21:35:30]: test run-unit-test: -----------------------] 245s autopkgtest [21:35:30]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 245s run-unit-test PASS 245s autopkgtest [21:35:30]: @@@@@@@@@@@@@@@@@@@@ summary 245s run-unit-test PASS 263s nova [W] Skipping flock for amd64 263s Creating nova instance adt-plucky-amd64-proteinortho-20250315-213125-juju-7f2275-prod-proposed-migration-environment-2-5ce25858-3bf4-4bf4-be88-de5e4e41e2d5 from image adt/ubuntu-plucky-amd64-server-20250304.img (UUID 9c7d4da5-d95f-4c85-ac1f-51eb37e75c4c)... 263s nova [W] Timed out waiting for 6fa657b5-067c-41de-849d-9989983498ae to get deleted.