0s autopkgtest [23:19:13]: starting date and time: 2025-03-15 23:19:13+0000 0s autopkgtest [23:19:13]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [23:19:13]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.dm2di_a1/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade stacks --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 autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@lcy02-1.secgroup --name adt-plucky-amd64-stacks-20250315-231912-juju-7f2275-prod-proposed-migration-environment-2-a008bbd1-71ac-4bfc-ab9c-1f050a238202 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,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/ 41s autopkgtest [23:19:54]: testbed dpkg architecture: amd64 41s autopkgtest [23:19:54]: testbed apt version: 2.9.31ubuntu1 41s autopkgtest [23:19:54]: @@@@@@@@@@@@@@@@@@@@ test bed setup 42s autopkgtest [23:19:55]: testbed release detected to be: None 42s autopkgtest [23:19:55]: updating testbed package index (apt update) 42s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 42s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 42s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 42s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 42s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.5 kB] 42s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [369 kB] 42s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [44.1 kB] 42s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [67.4 kB] 42s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [85.7 kB] 42s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 c-n-f Metadata [1852 B] 42s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 c-n-f Metadata [116 B] 42s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [174 kB] 42s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [342 kB] 42s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 c-n-f Metadata [15.3 kB] 42s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [8544 B] 42s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [16.1 kB] 42s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 c-n-f Metadata [628 B] 42s Fetched 1265 kB in 0s (5402 kB/s) 43s Reading package lists... 44s Reading package lists... 44s Building dependency tree... 44s Reading state information... 44s Calculating upgrade... 44s Calculating upgrade... 44s The following package was automatically installed and is no longer required: 44s libnl-genl-3-200 44s Use 'sudo apt autoremove' to remove it. 45s The following NEW packages will be installed: 45s bpftool libdebuginfod-common libdebuginfod1t64 linux-headers-6.14.0-10 45s linux-headers-6.14.0-10-generic linux-image-6.14.0-10-generic 45s linux-modules-6.14.0-10-generic linux-modules-extra-6.14.0-10-generic 45s linux-perf linux-tools-6.14.0-10 linux-tools-6.14.0-10-generic pnp.ids 45s The following packages will be upgraded: 45s apparmor apt apt-utils binutils binutils-common binutils-x86-64-linux-gnu 45s cloud-init cloud-init-base curl dosfstools fwupd gir1.2-girepository-2.0 45s gir1.2-glib-2.0 htop hwdata libapparmor1 libapt-pkg7.0 libaudit-common 45s libaudit1 libbinutils libbrotli1 libcap-ng0 libctf-nobfd0 libctf0 45s libcurl3t64-gnutls libcurl4t64 libestr0 libfwupd3 libgirepository-1.0-1 45s libglib2.0-0t64 libglib2.0-data libgprofng0 libjemalloc2 liblz4-1 liblzma5 45s libmm-glib0 libncurses6 libncursesw6 libnl-3-200 libnl-genl-3-200 45s libnl-route-3-200 libpci3 libpython3-stdlib libpython3.13 45s libpython3.13-minimal libpython3.13-stdlib libselinux1 libsframe1 45s libsqlite3-0 libtinfo6 libxml2 linux-firmware linux-generic 45s linux-headers-generic linux-headers-virtual linux-image-generic 45s linux-image-virtual linux-libc-dev linux-tools-common linux-virtual 45s media-types ncurses-base ncurses-bin ncurses-term pci.ids pciutils 45s pinentry-curses python-apt-common python3 python3-apt python3-cffi-backend 45s python3-dbus python3-gi python3-jinja2 python3-lazr.uri python3-markupsafe 45s python3-minimal python3-systemd python3-yaml python3.13 python3.13-gdbm 45s python3.13-minimal rsync rsyslog strace xz-utils 45s 86 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 45s Need to get 807 MB of archives. 45s After this operation, 326 MB of additional disk space will be used. 45s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-bin amd64 6.5+20250216-2 [194 kB] 45s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-base all 6.5+20250216-2 [25.9 kB] 45s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-term all 6.5+20250216-2 [276 kB] 45s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 liblz4-1 amd64 1.10.0-4 [66.4 kB] 45s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma5 amd64 5.6.4-1 [157 kB] 45s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.33 [1138 kB] 45s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.33 [1439 kB] 45s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.33 [222 kB] 45s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-minimal amd64 3.13.2-2 [27.7 kB] 45s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 python3 amd64 3.13.2-2 [24.0 kB] 45s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13 amd64 3.13.2-2 [2341 kB] 45s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 media-types all 13.0.0 [29.9 kB] 45s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses6 amd64 6.5+20250216-2 [126 kB] 45s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libncursesw6 amd64 6.5+20250216-2 [165 kB] 45s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libtinfo6 amd64 6.5+20250216-2 [119 kB] 45s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libsqlite3-0 amd64 3.46.1-2 [715 kB] 45s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.2-2 [735 kB] 45s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.2-2 [2365 kB] 45s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.2-2 [883 kB] 45s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.2-2 [2066 kB] 45s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.4 kB] 45s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 rsync amd64 3.4.1+ds1-3 [482 kB] 45s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod-common all 0.192-4 [15.4 kB] 45s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu2 [6628 B] 45s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-4build1 [15.6 kB] 45s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu2 [54.0 kB] 45s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libselinux1 amd64 3.7-3ubuntu3 [87.3 kB] 45s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-girepository-2.0 amd64 1.83.4-1 [25.3 kB] 45s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-glib-2.0 amd64 2.84.0-1 [184 kB] 45s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-0t64 amd64 2.84.0-1 [1669 kB] 45s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libgirepository-1.0-1 amd64 1.83.4-1 [89.5 kB] 45s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libapparmor1 amd64 4.1.0~beta5-0ubuntu8 [55.0 kB] 45s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libestr0 amd64 0.1.11-2 [8340 B] 45s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-data all 2.84.0-1 [53.0 kB] 45s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2ubuntu5 [772 kB] 45s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 python-apt-common all 2.9.9build1 [21.3 kB] 45s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-apt amd64 2.9.9build1 [172 kB] 45s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cffi-backend amd64 1.17.1-2build2 [96.6 kB] 45s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dbus amd64 1.3.2-5build5 [102 kB] 45s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-gi amd64 3.50.0-4build1 [252 kB] 45s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-yaml amd64 6.0.2-1build2 [144 kB] 45s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu2 [555 kB] 45s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 apparmor amd64 4.1.0~beta5-0ubuntu8 [701 kB] 45s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 dosfstools amd64 4.2-1.2 [95.0 kB] 45s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-genl-3-200 amd64 3.7.0-1 [12.2 kB] 45s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-route-3-200 amd64 3.7.0-1 [191 kB] 45s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-3-200 amd64 3.7.0-1 [64.9 kB] 45s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 pci.ids all 0.0~2025.03.09-1 [285 kB] 45s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 pciutils amd64 1:3.13.0-2 [110 kB] 45s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libpci3 amd64 1:3.13.0-2 [39.8 kB] 45s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 strace amd64 6.13+ds-1ubuntu1 [622 kB] 45s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 xz-utils amd64 5.6.4-1 [278 kB] 45s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libgprofng0 amd64 2.44-3ubuntu1 [886 kB] 45s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf0 amd64 2.44-3ubuntu1 [96.5 kB] 45s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf-nobfd0 amd64 2.44-3ubuntu1 [98.9 kB] 45s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-x86-64-linux-gnu amd64 2.44-3ubuntu1 [1108 kB] 45s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libbinutils amd64 2.44-3ubuntu1 [585 kB] 45s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils amd64 2.44-3ubuntu1 [208 kB] 45s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-common amd64 2.44-3ubuntu1 [215 kB] 45s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libsframe1 amd64 2.44-3ubuntu1 [14.8 kB] 45s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 hwdata all 0.393-3 [1562 B] 45s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 pnp.ids all 0.393-3 [29.5 kB] 45s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-common all 6.14.0-10.10 [295 kB] 45s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 bpftool amd64 7.6.0+6.14.0-10.10 [1147 kB] 45s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build4 [13.4 kB] 45s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 45s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init-base all 25.1-0ubuntu3 [616 kB] 45s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli1 amd64 1.1.0-2build4 [365 kB] 45s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 curl amd64 8.12.1-3ubuntu1 [258 kB] 45s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4t64 amd64 8.12.1-3ubuntu1 [437 kB] 45s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl3t64-gnutls amd64 8.12.1-3ubuntu1 [432 kB] 45s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd amd64 2.0.6-4 [5408 kB] 45s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 libfwupd3 amd64 2.0.6-4 [136 kB] 45s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libmm-glib0 amd64 1.23.4-0ubuntu3 [251 kB] 45s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 htop amd64 3.4.0-2 [195 kB] 45s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod1t64 amd64 0.192-4 [21.0 kB] 45s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 libjemalloc2 amd64 5.3.0-3 [277 kB] 45s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-firmware amd64 20250310.git9e1370d3-0ubuntu1 [571 MB] 50s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-6.14.0-10-generic amd64 6.14.0-10.10 [41.2 MB] 50s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-6.14.0-10-generic amd64 6.14.0-10.10 [15.3 MB] 50s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-extra-6.14.0-10-generic amd64 6.14.0-10.10 [120 MB] 51s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-generic amd64 6.14.0-10.10 [1730 B] 51s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-generic amd64 6.14.0-10.10 [11.1 kB] 51s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-virtual amd64 6.14.0-10.10 [1722 B] 51s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-virtual amd64 6.14.0-10.10 [11.1 kB] 51s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-virtual amd64 6.14.0-10.10 [1642 B] 51s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10 all 6.14.0-10.10 [14.2 MB] 51s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10-generic amd64 6.14.0-10.10 [3915 kB] 51s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-generic amd64 6.14.0-10.10 [11.0 kB] 51s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-libc-dev amd64 6.14.0-10.10 [1723 kB] 51s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-perf amd64 6.14.0-10.10 [4122 kB] 51s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10 amd64 6.14.0-10.10 [1394 kB] 51s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10-generic amd64 6.14.0-10.10 [830 B] 51s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 pinentry-curses amd64 1.3.1-2ubuntu3 [42.3 kB] 51s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lazr.uri all 1.0.6-6 [13.7 kB] 51s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build6 [43.9 kB] 51s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.2-2 [31.9 kB] 51s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init all 25.1-0ubuntu3 [2100 B] 52s Preconfiguring packages ... 52s Fetched 807 MB in 7s (123 MB/s) 52s (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 ... 109138 files and directories currently installed.) 52s Preparing to unpack .../ncurses-bin_6.5+20250216-2_amd64.deb ... 52s Unpacking ncurses-bin (6.5+20250216-2) over (6.5+20250216-1) ... 52s Setting up ncurses-bin (6.5+20250216-2) ... 52s (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 ... 109138 files and directories currently installed.) 52s Preparing to unpack .../ncurses-base_6.5+20250216-2_all.deb ... 52s Unpacking ncurses-base (6.5+20250216-2) over (6.5+20250216-1) ... 52s Setting up ncurses-base (6.5+20250216-2) ... 52s (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 ... 109138 files and directories currently installed.) 52s Preparing to unpack .../ncurses-term_6.5+20250216-2_all.deb ... 52s Unpacking ncurses-term (6.5+20250216-2) over (6.5+20250216-1) ... 53s Preparing to unpack .../liblz4-1_1.10.0-4_amd64.deb ... 53s Unpacking liblz4-1:amd64 (1.10.0-4) over (1.10.0-3) ... 53s Setting up liblz4-1:amd64 (1.10.0-4) ... 53s (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 ... 109138 files and directories currently installed.) 53s Preparing to unpack .../liblzma5_5.6.4-1_amd64.deb ... 53s Unpacking liblzma5:amd64 (5.6.4-1) over (5.6.3-1) ... 53s Setting up liblzma5:amd64 (5.6.4-1) ... 53s (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 ... 109138 files and directories currently installed.) 53s Preparing to unpack .../libapt-pkg7.0_2.9.33_amd64.deb ... 53s Unpacking libapt-pkg7.0:amd64 (2.9.33) over (2.9.31ubuntu1) ... 53s Setting up libapt-pkg7.0:amd64 (2.9.33) ... 53s (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 ... 109138 files and directories currently installed.) 53s Preparing to unpack .../archives/apt_2.9.33_amd64.deb ... 53s Unpacking apt (2.9.33) over (2.9.31ubuntu1) ... 53s Setting up apt (2.9.33) ... 54s (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 ... 109138 files and directories currently installed.) 54s Preparing to unpack .../apt-utils_2.9.33_amd64.deb ... 54s Unpacking apt-utils (2.9.33) over (2.9.31ubuntu1) ... 54s Preparing to unpack .../python3-minimal_3.13.2-2_amd64.deb ... 54s Unpacking python3-minimal (3.13.2-2) over (3.13.2-1) ... 54s Setting up python3-minimal (3.13.2-2) ... 54s (Reading database ... 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Preparing to unpack .../68-python3-systemd_235-1build6_amd64.deb ... 70s Unpacking python3-systemd (235-1build6) over (235-1build5) ... 70s Preparing to unpack .../69-python3.13-gdbm_3.13.2-2_amd64.deb ... 70s Unpacking python3.13-gdbm (3.13.2-2) over (3.13.2-1) ... 70s Preparing to unpack .../70-cloud-init_25.1-0ubuntu3_all.deb ... 70s Unpacking cloud-init (25.1-0ubuntu3) over (25.1-0ubuntu2) ... 70s Setting up linux-headers-6.14.0-10 (6.14.0-10.10) ... 70s Setting up media-types (13.0.0) ... 70s Installing new version of config file /etc/mime.types ... 70s Setting up linux-headers-6.14.0-10-generic (6.14.0-10.10) ... 70s Setting up libapparmor1:amd64 (4.1.0~beta5-0ubuntu8) ... 70s Setting up pci.ids (0.0~2025.03.09-1) ... 70s Setting up apt-utils (2.9.33) ... 70s Setting up libdebuginfod-common (0.192-4) ... 70s Setting up linux-firmware (20250310.git9e1370d3-0ubuntu1) ... 70s Setting up bpftool (7.6.0+6.14.0-10.10) ... 70s Setting up libestr0:amd64 (0.1.11-2) ... 70s Setting up libbrotli1:amd64 (1.1.0-2build4) ... 70s Setting up libsqlite3-0:amd64 (3.46.1-2) ... 70s Setting up dosfstools (4.2-1.2) ... 70s Setting up rsyslog (8.2412.0-2ubuntu2) ... 70s info: The user `syslog' is already a member of `adm'. 71s Setting up binutils-common:amd64 (2.44-3ubuntu1) ... 71s Setting up libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) ... 71s Setting up linux-libc-dev:amd64 (6.14.0-10.10) ... 71s Setting up libctf-nobfd0:amd64 (2.44-3ubuntu1) ... 71s Setting up linux-headers-generic (6.14.0-10.10) ... 71s Setting up libjemalloc2:amd64 (5.3.0-3) ... 71s Setting up libsframe1:amd64 (2.44-3ubuntu1) ... 71s Setting up libpython3.13-minimal:amd64 (3.13.2-2) ... 71s Setting up apparmor (4.1.0~beta5-0ubuntu8) ... 71s Installing new version of config file /etc/apparmor.d/openvpn ... 72s Reloading AppArmor profiles 74s Setting up libglib2.0-0t64:amd64 (2.84.0-1) ... 74s No schema files found: doing nothing. 74s Setting up libglib2.0-data (2.84.0-1) ... 74s Setting up libncurses6:amd64 (6.5+20250216-2) ... 74s Setting up strace (6.13+ds-1ubuntu1) ... 74s Setting up xz-utils (5.6.4-1) ... 74s Setting up gir1.2-glib-2.0:amd64 (2.84.0-1) ... 74s Setting up linux-modules-6.14.0-10-generic (6.14.0-10.10) ... 76s Setting up libncursesw6:amd64 (6.5+20250216-2) ... 76s Setting up libpci3:amd64 (1:3.13.0-2) ... 76s Setting up python-apt-common (2.9.9build1) ... 76s Setting up libmm-glib0:amd64 (1.23.4-0ubuntu3) ... 76s Setting up pnp.ids (0.393-3) ... 76s Setting up libnl-3-200:amd64 (3.7.0-1) ... 76s Setting up python3.13-minimal (3.13.2-2) ... 76s Setting up libgirepository-1.0-1:amd64 (1.83.4-1) ... 76s Setting up libbinutils:amd64 (2.44-3ubuntu1) ... 76s Setting up libpython3.13-stdlib:amd64 (3.13.2-2) ... 76s Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2ubuntu5) ... 76s Setting up rsync (3.4.1+ds1-3) ... 77s rsync.service is a disabled or a static unit not running, not starting it. 77s Setting up python3.13-gdbm (3.13.2-2) ... 77s Setting up libpython3-stdlib:amd64 (3.13.2-2) ... 77s Setting up ncurses-term (6.5+20250216-2) ... 77s Setting up libctf0:amd64 (2.44-3ubuntu1) ... 77s Setting up libpython3.13:amd64 (3.13.2-2) ... 77s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 77s Setting up libdebuginfod1t64:amd64 (0.192-4) ... 77s Setting up linux-headers-virtual (6.14.0-10.10) ... 77s Setting up libcurl4t64:amd64 (8.12.1-3ubuntu1) ... 77s Setting up python3.13 (3.13.2-2) ... 78s Setting up htop (3.4.0-2) ... 78s Setting up linux-image-6.14.0-10-generic (6.14.0-10.10) ... 80s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.12.0-16-generic 80s I: /boot/initrd.img.old is now a symlink to initrd.img-6.12.0-16-generic 80s I: /boot/vmlinuz is now a symlink to vmlinuz-6.14.0-10-generic 80s I: /boot/initrd.img is now a symlink to initrd.img-6.14.0-10-generic 80s Setting up libfwupd3:amd64 (2.0.6-4) ... 80s Setting up python3 (3.13.2-2) ... 80s Setting up python3-markupsafe (2.1.5-1build4) ... 81s Setting up linux-modules-extra-6.14.0-10-generic (6.14.0-10.10) ... 83s Setting up libnl-route-3-200:amd64 (3.7.0-1) ... 83s Setting up hwdata (0.393-3) ... 83s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 83s Setting up libgprofng0:amd64 (2.44-3ubuntu1) ... 83s Setting up linux-perf (6.14.0-10.10) ... 83s Setting up gir1.2-girepository-2.0:amd64 (1.83.4-1) ... 83s Setting up python3-gi (3.50.0-4build1) ... 83s Setting up pciutils (1:3.13.0-2) ... 83s Setting up libnl-genl-3-200:amd64 (3.7.0-1) ... 83s Setting up curl (8.12.1-3ubuntu1) ... 83s Setting up linux-image-virtual (6.14.0-10.10) ... 83s Setting up linux-tools-common (6.14.0-10.10) ... 83s Setting up fwupd (2.0.6-4) ... 83s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 83s fwupd.service is a disabled or a static unit not running, not starting it. 84s Setting up python3-systemd (235-1build6) ... 84s Setting up python3-cffi-backend:amd64 (1.17.1-2build2) ... 84s Setting up binutils-x86-64-linux-gnu (2.44-3ubuntu1) ... 84s Setting up linux-image-generic (6.14.0-10.10) ... 84s Setting up python3-dbus (1.3.2-5build5) ... 84s Setting up linux-tools-6.14.0-10 (6.14.0-10.10) ... 84s Setting up linux-generic (6.14.0-10.10) ... 84s Setting up python3-apt (2.9.9build1) ... 84s Setting up python3-yaml (6.0.2-1build2) ... 84s Setting up python3-lazr.uri (1.0.6-6) ... 84s Setting up binutils (2.44-3ubuntu1) ... 84s Setting up cloud-init-base (25.1-0ubuntu3) ... 86s Setting up linux-virtual (6.14.0-10.10) ... 86s Setting up linux-tools-6.14.0-10-generic (6.14.0-10.10) ... 86s Setting up cloud-init (25.1-0ubuntu3) ... 86s Processing triggers for systemd (257.3-1ubuntu3) ... 86s Processing triggers for man-db (2.13.0-1) ... 88s Processing triggers for dbus (1.16.2-1ubuntu1) ... 88s Processing triggers for libc-bin (2.41-1ubuntu1) ... 88s Processing triggers for initramfs-tools (0.146ubuntu1) ... 88s update-initramfs: Generating /boot/initrd.img-6.12.0-16-generic 88s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 99s Processing triggers for linux-image-6.14.0-10-generic (6.14.0-10.10) ... 99s /etc/kernel/postinst.d/initramfs-tools: 99s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 99s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 109s /etc/kernel/postinst.d/zz-update-grub: 109s Sourcing file `/etc/default/grub' 109s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 109s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 109s Generating grub configuration file ... 109s Found linux image: /boot/vmlinuz-6.14.0-10-generic 109s Found initrd image: /boot/initrd.img-6.14.0-10-generic 109s Found linux image: /boot/vmlinuz-6.12.0-16-generic 109s Found initrd image: /boot/initrd.img-6.12.0-16-generic 109s Found linux image: /boot/vmlinuz-6.11.0-8-generic 109s Found initrd image: /boot/initrd.img-6.11.0-8-generic 110s Warning: os-prober will not be executed to detect other bootable partitions. 110s Systems on them will not be added to the GRUB boot configuration. 110s Check GRUB_DISABLE_OS_PROBER documentation entry. 110s Adding boot menu entry for UEFI Firmware Settings ... 110s done 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 112s Solving dependencies... 112s The following packages will be REMOVED: 112s libnl-genl-3-200* libnsl2* libpython3.12-minimal* libpython3.12-stdlib* 112s libpython3.12t64* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 112s linux-headers-6.12.0-16* linux-headers-6.12.0-16-generic* 112s linux-image-6.11.0-8-generic* linux-image-6.12.0-16-generic* 112s linux-modules-6.11.0-8-generic* linux-modules-6.12.0-16-generic* 112s linux-modules-extra-6.12.0-16-generic* linux-tools-6.11.0-8* 112s linux-tools-6.11.0-8-generic* linux-tools-6.12.0-16* 112s linux-tools-6.12.0-16-generic* 112s 0 upgraded, 0 newly installed, 18 to remove and 5 not upgraded. 112s After this operation, 545 MB disk space will be freed. 112s (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.) 112s Removing libnl-genl-3-200:amd64 (3.7.0-1) ... 112s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 112s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 112s Removing libpython3.12t64:amd64 (3.12.9-1) ... 112s Removing libpython3.12-stdlib:amd64 (3.12.9-1) ... 112s Removing libnsl2:amd64 (1.3.0-3build3) ... 112s Removing libpython3.12-minimal:amd64 (3.12.9-1) ... 113s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 113s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 115s Removing linux-headers-6.12.0-16-generic (6.12.0-16.16) ... 116s Removing linux-headers-6.12.0-16 (6.12.0-16.16) ... 118s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 118s /etc/kernel/postrm.d/initramfs-tools: 118s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 118s /etc/kernel/postrm.d/zz-update-grub: 118s Sourcing file `/etc/default/grub' 118s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 118s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 118s Generating grub configuration file ... 118s Found linux image: /boot/vmlinuz-6.14.0-10-generic 118s Found initrd image: /boot/initrd.img-6.14.0-10-generic 118s Found linux image: /boot/vmlinuz-6.12.0-16-generic 118s Found initrd image: /boot/initrd.img-6.12.0-16-generic 119s Warning: os-prober will not be executed to detect other bootable partitions. 119s Systems on them will not be added to the GRUB boot configuration. 119s Check GRUB_DISABLE_OS_PROBER documentation entry. 119s Adding boot menu entry for UEFI Firmware Settings ... 119s done 119s Removing linux-image-6.12.0-16-generic (6.12.0-16.16) ... 119s W: Removing the running kernel 119s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 119s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 119s /etc/kernel/postrm.d/initramfs-tools: 119s update-initramfs: Deleting /boot/initrd.img-6.12.0-16-generic 119s /etc/kernel/postrm.d/zz-update-grub: 119s Sourcing file `/etc/default/grub' 119s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 119s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 119s Generating grub configuration file ... 119s Found linux image: /boot/vmlinuz-6.14.0-10-generic 119s Found initrd image: /boot/initrd.img-6.14.0-10-generic 119s Warning: os-prober will not be executed to detect other bootable partitions. 119s Systems on them will not be added to the GRUB boot configuration. 119s Check GRUB_DISABLE_OS_PROBER documentation entry. 119s Adding boot menu entry for UEFI Firmware Settings ... 119s done 119s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 120s Removing linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 121s Removing linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 121s Removing linux-tools-6.12.0-16-generic (6.12.0-16.16) ... 121s Removing linux-tools-6.12.0-16 (6.12.0-16.16) ... 121s Processing triggers for libc-bin (2.41-1ubuntu1) ... 121s (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.) 121s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 121s Purging configuration files for libpython3.12-minimal:amd64 (3.12.9-1) ... 121s Purging configuration files for linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 121s Purging configuration files for linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 121s dpkg: warning: while removing linux-modules-6.12.0-16-generic, directory '/lib/modules/6.12.0-16-generic' not empty so not removed 121s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 121s Purging configuration files for linux-image-6.12.0-16-generic (6.12.0-16.16) ... 121s rmdir: failed to remove '/lib/modules/6.12.0-16-generic': Directory not empty 122s autopkgtest [23:21:15]: upgrading testbed (apt dist-upgrade and autopurge) 122s Reading package lists... 122s Building dependency tree... 122s Reading state information... 123s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 123s Starting 2 pkgProblemResolver with broken count: 0 123s Done 123s Entering ResolveByKeep 124s 124s Calculating upgrade... 124s The following packages will be upgraded: 124s libc-bin libc-dev-bin libc6 libc6-dev locales 124s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 124s Need to get 10.5 MB of archives. 124s After this operation, 1024 B of additional disk space will be used. 124s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6-dev amd64 2.41-1ubuntu2 [2183 kB] 124s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-dev-bin amd64 2.41-1ubuntu2 [24.7 kB] 124s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6 amd64 2.41-1ubuntu2 [3327 kB] 124s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-bin amd64 2.41-1ubuntu2 [700 kB] 124s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 locales all 2.41-1ubuntu2 [4246 kB] 124s Preconfiguring packages ... 124s Fetched 10.5 MB in 0s (43.1 MB/s) 125s (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.) 125s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_amd64.deb ... 125s Unpacking libc6-dev:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 125s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_amd64.deb ... 125s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 125s Preparing to unpack .../libc6_2.41-1ubuntu2_amd64.deb ... 125s Unpacking libc6:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 125s Setting up libc6:amd64 (2.41-1ubuntu2) ... 125s (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.) 125s Preparing to unpack .../libc-bin_2.41-1ubuntu2_amd64.deb ... 125s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 125s Setting up libc-bin (2.41-1ubuntu2) ... 125s (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.) 125s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 125s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 126s Setting up locales (2.41-1ubuntu2) ... 126s Generating locales (this might take a while)... 128s en_US.UTF-8... done 128s Generation complete. 128s Setting up libc-dev-bin (2.41-1ubuntu2) ... 128s Setting up libc6-dev:amd64 (2.41-1ubuntu2) ... 128s Processing triggers for man-db (2.13.0-1) ... 128s Processing triggers for systemd (257.3-1ubuntu3) ... 129s Reading package lists... 129s Building dependency tree... 129s Reading state information... 130s Starting pkgProblemResolver with broken count: 0 130s Starting 2 pkgProblemResolver with broken count: 0 130s Done 130s Solving dependencies... 130s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 130s autopkgtest [23:21:23]: rebooting testbed after setup commands that affected boot 134s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 146s autopkgtest [23:21:39]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 16:07:00 UTC 2025 147s autopkgtest [23:21:40]: @@@@@@@@@@@@@@@@@@@@ apt-source stacks 148s Get:1 http://ftpmaster.internal/ubuntu plucky/universe stacks 2.68+dfsg-2 (dsc) [2050 B] 148s Get:2 http://ftpmaster.internal/ubuntu plucky/universe stacks 2.68+dfsg-2 (tar) [371 kB] 148s Get:3 http://ftpmaster.internal/ubuntu plucky/universe stacks 2.68+dfsg-2 (diff) [12.5 kB] 148s gpgv: Signature made Sun Feb 16 10:21:57 2025 UTC 148s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 148s gpgv: issuer "emollier@debian.org" 148s gpgv: Can't check signature: No public key 148s dpkg-source: warning: cannot verify inline signature for ./stacks_2.68+dfsg-2.dsc: no acceptable signature found 148s autopkgtest [23:21:41]: testing package stacks version 2.68+dfsg-2 148s autopkgtest [23:21:41]: build not needed 148s autopkgtest [23:21:41]: test run-unit-test: preparing testbed 148s Reading package lists... 149s Building dependency tree... 149s Reading state information... 149s Starting pkgProblemResolver with broken count: 0 149s Starting 2 pkgProblemResolver with broken count: 0 149s Done 150s The following NEW packages will be installed: 150s libdbi-perl libdeflate0 libgomp1 libhts3t64 libhtscodecs2 samtools stacks 150s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 150s Need to get 3536 kB of archives. 150s After this operation, 10.4 MB of additional disk space will be used. 150s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libdbi-perl amd64 1.647-1 [832 kB] 150s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB] 150s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250222-0ubuntu1 [148 kB] 150s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-2 [132 kB] 150s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.21+ds-1 [514 kB] 150s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 samtools amd64 1.21-1 [655 kB] 150s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 stacks amd64 2.68+dfsg-2 [1190 kB] 150s Fetched 3536 kB in 0s (15.2 MB/s) 150s Selecting previously unselected package libdbi-perl:amd64. 150s (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.) 150s Preparing to unpack .../0-libdbi-perl_1.647-1_amd64.deb ... 150s Unpacking libdbi-perl:amd64 (1.647-1) ... 151s Selecting previously unselected package libdeflate0:amd64. 151s Preparing to unpack .../1-libdeflate0_1.23-1_amd64.deb ... 151s Unpacking libdeflate0:amd64 (1.23-1) ... 151s Selecting previously unselected package libgomp1:amd64. 151s Preparing to unpack .../2-libgomp1_15-20250222-0ubuntu1_amd64.deb ... 151s Unpacking libgomp1:amd64 (15-20250222-0ubuntu1) ... 151s Selecting previously unselected package libhtscodecs2:amd64. 151s Preparing to unpack .../3-libhtscodecs2_1.6.1-2_amd64.deb ... 151s Unpacking libhtscodecs2:amd64 (1.6.1-2) ... 151s Selecting previously unselected package libhts3t64:amd64. 151s Preparing to unpack .../4-libhts3t64_1.21+ds-1_amd64.deb ... 151s Unpacking libhts3t64:amd64 (1.21+ds-1) ... 151s Selecting previously unselected package samtools. 151s Preparing to unpack .../5-samtools_1.21-1_amd64.deb ... 151s Unpacking samtools (1.21-1) ... 151s Selecting previously unselected package stacks. 151s Preparing to unpack .../6-stacks_2.68+dfsg-2_amd64.deb ... 151s Unpacking stacks (2.68+dfsg-2) ... 151s Setting up libhtscodecs2:amd64 (1.6.1-2) ... 151s Setting up libdeflate0:amd64 (1.23-1) ... 151s Setting up libgomp1:amd64 (15-20250222-0ubuntu1) ... 151s Setting up libhts3t64:amd64 (1.21+ds-1) ... 151s Setting up libdbi-perl:amd64 (1.647-1) ... 151s Setting up samtools (1.21-1) ... 151s Setting up stacks (2.68+dfsg-2) ... 151s Processing triggers for man-db (2.13.0-1) ... 152s Processing triggers for libc-bin (2.41-1ubuntu2) ... 152s autopkgtest [23:21:45]: test run-unit-test: [----------------------- 152s Stacks - a pipeline for building loci from short-read sequences 152s v2.68+dfsg http://creskolab.uoregon.edu/stacks/ 152s 152s This is the Stacks wrapper script for Debian. Usage: 152s stacks 152s 152s Programs available are: 152s clone_filter ref_map 152s cstacks sstacks 152s denovo_map stacks-dist-extract 152s gstacks stacks-gdb 152s kmer_filter stacks-integrate-alignments 152s phasedstacks stacks-private-alleles 152s populations stacks-samtools-tview 152s process_radtags tsv2bam 152s process_shortreads ustacks 152s 152s Or else add /usr/libexec/stacks/bin to your $PATH to invoke the commands directly. 152s 152s clone_filter 2.68 152s clone_filter [-f in_file | -p in_dir [-P] [-I] | -1 pair_1 -2 pair_2] -o out_dir [-i type] [-y type] [-D] [-h] 152s f: path to the input file if processing single-end sequences. 152s p: path to a directory of files. 152s P: files contained within directory specified by '-p' are paired. 152s 1: first input file in a set of paired-end sequences. 152s 2: second input file in a set of paired-end sequences. 152s i: input file type, either 'bustard', 'fastq', 'fasta', 'gzfasta', or 'gzfastq' (default 'fastq'). 152s o: path to output the processed files. 152s y: output type, either 'fastq', 'fasta', 'gzfasta', or 'gzfastq' (default same as input type). 152s D: capture discarded reads to a file. 152s h: display this help message. 152s --oligo-len-1 len: length of the single-end oligo sequence in data set. 152s --oligo-len-2 len: length of the paired-end oligo sequence in data set. 152s --retain-oligo: do not trim off the random oligo sequence (if oligo is inline). 152s 152s Oligo sequence options: 152s --inline-null: random oligo is inline with sequence, occurs only on single-end read (default). 152s --null-inline: random oligo is inline with sequence, occurs only on the paired-end read. 152s --null-index: random oligo is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 152s --index-null: random oligo is provded in FASTQ header (Illumina i5 or i7 read). 152s --inline-inline: random oligo is inline with sequence, occurs on single and paired-end read. 152s --index-index: random oligo is provded in FASTQ header (Illumina i5 and i7 read). 152s --inline-index: random oligo is inline with sequence on single-end read and second oligo occurs in FASTQ header. 152s --index-inline: random oligo occurs in FASTQ header (Illumina i5 or i7 read) and is inline with sequence on single-end read (if single read data) or paired-end read (if paired data). 152s 152s cstacks 2.68 152s cstacks -P in_dir -M popmap [-n num_mismatches] [-t num_threads] 152s cstacks -s sample1_path [-s sample2_path ...] -o path [-n num_mismatches] [-t num_threads] 152s 152s -P,--in-path: path to the directory containing Stacks files. 152s -M,--popmap: path to a population map file. 152s -n: number of mismatches allowed between sample loci when build the catalog (default 1; suggested: set to ustacks -M). 152s -t,--threads: enable parallel execution with num_threads threads. 152s -s: sample prefix from which to load loci into the catalog. 152s -o,--outpath: output path to write results. 152s -c,--catalog : add to an existing catalog. 152s 152s Gapped assembly options: 152s --max-gaps: number of gaps allowed between stacks before merging (default: 2). 152s --min-aln-len: minimum length of aligned sequence in a gapped alignment (default: 0.80). 152s --disable-gapped: disable gapped alignments between stacks (default: use gapped alignments). 152s 152s Advanced options: 152s --k-len : specify k-mer size for matching between between catalog loci (automatically calculated by default). 152s --report-mmatches: report query loci that match more than one catalog locus. 152s denovo_map.pl 2.68 152s denovo_map.pl --samples dir --popmap path --out-path dir [--paired [--rm-pcr-duplicates]] (assembly options) (filtering options) [-X prog:"opts" ...] 152s 152s Input/Output files: 152s --samples: path to the directory containing the reads files for each sample. 152s --popmap: path to a population map file (format is " TAB ", one sample per line). 152s -o,--out-path: path to an output directory. 152s 152s General options: 152s -X: additional options for specific pipeline components, e.g. -X "populations: --min-maf 0.05". 152s -T, --threads: the number of threads/CPUs to use (default: 1). 152s --dry-run: dry run. Do not actually execute anything, just print the commands that would be executed. 152s --resume: resume executing the pipeline from a previous run. 152s 152s Stack assembly options: 152s -M: number of mismatches allowed between stacks within individuals (for ustacks). 152s -n: number of mismatches allowed between stacks between individuals (for cstacks; default: set to ustacks -M). 152s 152s SNP model options: 152s --var-alpha: significance level at which to call variant sites (for gstacks; default: 0.05). 152s --gt-alpha: significance level at which to call genotypes (for gstacks; default: 0.05). 152s 152s Paired-end options: 152s --paired: after assembling RAD loci, assemble mini-contigs with paired-end reads. 152s --rm-pcr-duplicates: remove all but one set of read pairs of the same sample that have 152s the same insert length. 152s 152s Population filtering options: 152s -r,--min-samples-per-pop: minimum percentage of individuals in a population required to process a locus for that population (for populations; default: 0) 152s -p,--min-populations: minimum number of populations a locus must be present in to process a locus (for populations; default: 1) 152s 152s For large datasets: 152s --catalog-popmap: path to a second population map file containing a subset of samples for use only in building the catalog. 152s 152s Miscellaneous: 152s --time-components (for benchmarking) 152s gstacks 2.68 152s 152s De novo mode: 152s gstacks -P stacks_dir -M popmap 152s 152s -P: input directory containing '*.matches.bam' files created by the 152s de novo Stacks pipeline, ustacks-cstacks-sstacks-tsv2bam 152s 152s Reference-based mode: 152s gstacks -I bam_dir -M popmap [-S suffix] -O out_dir 152s gstacks -B bam_file [-B ...] -O out_dir 152s 152s -I: input directory containing BAM files 152s -S: with -I/-M, suffix to use to build BAM file names: by default this 152s is just '.bam', i.e. the program expects 'SAMPLE_NAME.bam' 152s -B: input BAM file(s) 152s 152s The input BAM file(s) must be sorted by coordinate. 152s With -B, records must be assigned to samples using BAM "reads groups" 152s (gstacks uses the ID/identifier and SM/sample name fields). Read groups 152s must be consistent if repeated different files. Note that with -I, read 152s groups are unneeded and ignored. 152s 152s For both modes: 152s -M: path to a population map giving the list of samples 152s -O: output directory (default: none with -B; with -P same as the input 152s directory) 152s -t,--threads: number of threads to use (default: 1) 152s 152s SNP Model options: 152s --model: model to use to call variants and genotypes; one of 152s marukilow (default), marukihigh, or snp 152s --var-alpha: alpha threshold for discovering SNPs (default: 0.01 for marukilow) 152s --gt-alpha: alpha threshold for calling genotypes (default: 0.05) 152s 152s Paired-end options: 152s --rm-pcr-duplicates: remove all but one set ofread pairs of the same sample that 152s have the same insert length (implies --rm-unpaired-reads) 152s --rm-unpaired-reads: discard unpaired reads 152s --ignore-pe-reads: ignore paired-end reads even if present in the input 152s --unpaired: ignore read pairing (only for paired-end GBS; treat READ2's as if they were READ1's) 152s 152s Advanced options: 152s (De novo mode) 152s --kmer-length: kmer length for the de Bruijn graph (default: 31, max. 31) 152s --max-debruijn-reads: maximum number of reads to use in the de Bruijn graph (default: 1000) 152s --min-kmer-cov: minimum coverage to consider a kmer (default: 2) 152s --write-alignments: save read alignments (heavy BAM files) 152s 152s (Reference-based mode) 152s --methyl-status: assumes a methylation-aware molecular protocol used; calls methylated bases. 152s --min-mapq: minimum PHRED-scaled mapping quality to consider a read (default: 10) 152s --max-clipped: maximum soft-clipping level, in fraction of read length (default: 0.20) 152s --max-insert-len: maximum allowed sequencing insert length (default: 1000) 152s 152s --details: write a heavier output 152s --phasing-cooccurrences-thr-range: range of edge coverage thresholds to 152s iterate over when building the graph of allele cooccurrences for 152s SNP phasing (default: 1,2) 152s --phasing-dont-prune-hets: don't try to ignore dubious heterozygote 152s genotypes during phasing 152s 152s kmer_filter 2.68 152s kmer_filter [-f in_file_1 [-f in_file_2...] | -p in_dir] [-1 pair_1 -2 pair_2 [-1 pair_1...]] -o out_dir [-i type] [-y type] [-D] [-h] 152s f: path to the input file if processing single-end seqeunces. 152s i: input file type, either 'bustard' for the Illumina BUSTARD output files, 'fasta', 'fastq', 'gzfasta', or 'gzfastq' (default 'fastq'). 152s p: path to a directory of files (for single-end files only). 152s 1: specify the first in a pair of files to be processed together. 152s 2: specify the second in a pair of files to be processed together. 152s o: path to output the processed files. 152s y: output type, either 'fastq' or 'fasta' (default fastq). 152s D: capture discarded reads to a file. 152s h: display this help message. 152s 152s Filtering options: 152s --rare: turn on filtering based on rare k-mers. 152s --abundant: turn on filtering based on abundant k-mers. 152s --k-len : specify k-mer size (default 15). 152s 152s Advanced filtering options: 152s --max-k-freq : specify the number of times a kmer must occur to be considered abundant (default 20,000). 152s --min-lim : specify number of rare kmers occurring in a row required to discard a read (default 80% of the k-mer length). 152s --max-lim : specify number of abundant kmers required to discard a read (default 80% of the k-mers in a read). 152s 152s Normalize data: 152s --normalize : normalize read depth according to k-mer coverage. 152s 152s Characterizing K-mers: 152s --write-k-freq: write kmers along with their frequency of occurrence and exit. 152s --k-dist: print k-mer frequency distribution and exit. 152s 152s Advanced input options: 152s --read-k-freq : read a set of kmers along with their frequencies of occurrence instead of reading raw input files. 152s 152s phasedstacks 2.68 152s phasedstacks -b id -S path -P path -t file_type [-p threads] [-M popmap] [-v] [-h] 152s b: Stacks batch ID. 152s P: path to the phased output files. 152s S: path to the Stacks output files. 152s t: input file type. Supported types: fastphase, and beagle. 152s p: number of processes to run in parallel sections of code. 152s M: path to the population map, a tab separated file describing which individuals belong in which population. 152s v: print program version. 152s h: display this help message. 152s --haplotypes: data were phased as RAD locus haplotypes. 152s --dprime-bin-size: size of buckets for binning SNPs at a particular distance to calculate the mean D' value. 152s --dprime-threshold : if D' values fall above , set the D' to 1, otherwise set D' to 0. 152s 152s Filtering options: 152s --skip-zeros: do not include D' values of zero in the D' output. 152s --minor-allele-freq: specify a minimum minor allele frequency required to process a nucleotide site (0 < a < 0.5). 152s --min-inform-pairs: when building D' haplotype blocks, the minimum number of informative D' measures to combine two blocks (default 0.9). 152s 152s populations 2.68 152s Usage: 152s populations -P dir [-O dir] [-M popmap] (filters) [--fstats] [-k [--sigma=150000] [--bootstrap [-N 100]]] (output formats) 152s populations -V vcf -O dir [-M popmap] (filters) [--fstats] [-k [--sigma=150000] [--bootstrap [-N 100]]] (output formats) 152s 152s -P,--in-path: path to a directory containing Stacks output files. 152s -V,--in-vcf: path to a standalone input VCF file. 152s -O,--out-path: path to a directory where to write the output files. (Required by -V; otherwise defaults to value of -P.) 152s -M,--popmap: path to a population map. (Format is 'SAMPLE1 \t POP1 \n SAMPLE2 ...'.) 152s -t,--threads: number of threads to run in parallel sections of code. 152s --batch-size [int]: the number of loci to process in a batch (default: 10,000 in de novo mode; in reference mode, one chromosome 152s per batch). Increase to speed analysis, uses more memory, decrease to save memory). 152s 152s Data Filtering: 152s -p,--min-populations [int]: minimum number of populations a locus must be present in to process a locus. 152s -r,--min-samples-per-pop [float]: minimum percentage of individuals in a population required to process a locus for that population. 152s -R,--min-samples-overall [float]: minimum percentage of individuals across populations required to process a locus. 152s -H,--filter-haplotype-wise: apply the above filters haplotype wise 152s (unshared SNPs will be pruned to reduce haplotype-wise missing data). 152s --min-maf [float]: specify a minimum minor allele frequency required to process a SNP (0 < min_maf < 0.5; applied to the metapopulation). 152s --min-mac [int]: specify a minimum minor allele count required to process a SNP (applied to the metapopulation). 152s --max-obs-het [float]: specify a maximum observed heterozygosity required to process a SNP (applied ot the metapopulation). 152s --min-gt-depth [int]: specify a minimum number of reads to include a called SNP (otherwise marked as missing data). 152s 152s --write-single-snp: restrict data analysis to only the first SNP per locus (implies --no-haps). 152s --write-random-snp: restrict data analysis to one random SNP per locus (implies --no-haps). 152s -B,--blacklist: path to a file containing Blacklisted markers to be excluded from the export. 152s -W,--whitelist: path to a file containing Whitelisted markers to include in the export. 152s 152s Locus stats: 152s --hwe: calculate divergence from Hardy-Weinberg equilibrium for each locus. 152s 152s Fstats: 152s --fstats: enable SNP and haplotype-based F statistics. 152s --fst-correction: specify a p-value correction to be applied to Fst values based on a Fisher's exact test. Default: off. 152s --p-value-cutoff [float]: maximum p-value to keep an Fst measurement. Default: 0.05. 152s 152s Kernel-smoothing algorithm: 152s -k,--smooth: enable kernel-smoothed Pi, Fis, Fst, Fst', and Phi_st calculations. 152s --smooth-fstats: enable kernel-smoothed Fst, Fst', and Phi_st calculations. 152s --smooth-popstats: enable kernel-smoothed Pi and Fis calculations. 152s (Note: turning on smoothing implies --ordered-export.) 152s --sigma [int]: standard deviation of the kernel smoothing weight distribution. Sliding window size is defined as 3 x sigma; (default sigma = 150kbp). 152s --bootstrap-archive: archive statistical values for use in bootstrap resampling in a subsequent run, statistics must be enabled to be archived. 152s --bootstrap: turn on boostrap resampling for all kernel-smoothed statistics. 152s -N,--bootstrap-reps [int]: number of bootstrap resamplings to calculate (default 100). 152s --bootstrap-pifis: turn on boostrap resampling for smoothed SNP-based Pi and Fis calculations. 152s --bootstrap-fst: turn on boostrap resampling for smoothed Fst calculations based on pairwise population comparison of SNPs. 152s --bootstrap-div: turn on boostrap resampling for smoothed haplotype diveristy and gene diversity calculations based on haplotypes. 152s --bootstrap-phist: turn on boostrap resampling for smoothed Phi_st calculations based on haplotypes. 152s --bootstrap-wl [path]: only bootstrap loci contained in this whitelist. 152s 152s File output options: 152s --ordered-export: if data is reference aligned, exports will be ordered; only a single representative of each overlapping site. 152s --fasta-loci: output locus consensus sequences in FASTA format. 152s --fasta-samples: output the sequences of the two haplotypes of each (diploid) sample, for each locus, in FASTA format. 152s --vcf: output SNPs and haplotypes in Variant Call Format (VCF). 152s --vcf-all: output all sites in Variant Call Format (VCF). 152s --genepop: output SNPs and haplotypes in GenePop format. 152s --structure: output results in Structure format. 152s --radpainter: output results in fineRADstructure/RADpainter format. 152s --plink: output genotypes in PLINK format. 152s --hzar: output genotypes in Hybrid Zone Analysis using R (HZAR) format. 152s --phylip: output nucleotides that are fixed-within, and variant among populations in Phylip format for phylogenetic tree construction. 152s --phylip-var: include variable sites in the phylip output encoded using IUPAC notation. 152s --phylip-var-all: include all sequence as well as variable sites in the phylip output encoded using IUPAC notation. 152s --treemix: output SNPs in a format useable for the TreeMix program (Pickrell and Pritchard). 152s --gtf: output locus positions in a GTF annotation file. 152s --no-hap-exports: omit haplotype outputs. 152s --fasta-samples-raw: output all haplotypes observed in each sample, for each locus, in FASTA format. 152s 152s Genetic map output options (population map must specify a genetic cross): 152s --map-type: genetic map type to write. 'CP', 'DH', 'F2', and 'BC1' are the currently supported map types. 152s --map-format: mapping program format to write, 'joinmap', 'onemap', and 'rqtl' are currently supported. 152s 152s Additional options: 152s -h,--help: display this help message. 152s -v,--version: print program version. 152s --verbose: turn on additional logging. 152s --log-fst-comp: log components of Fst/Phi_st calculations to a file. 152s process_radtags 2.68 152s process_radtags -p in_dir [-P] [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 152s process_radtags -f in_file [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 152s process_radtags --in-path in_dir [--paired] [--barcodes barcode_file] --out-path out_dir --renz-1 enz [--renz-2 enz] [--threads num] [-c] [-q] [-r] [-t len] 152s process_radtags -1 pair_1 -2 pair_2 [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 152s 152s -p,--in-path: path to a directory of files. 152s -P,--paired: files contained within the directory are paired. 152s -I,--interleaved: specify that the paired-end reads are interleaved in single files. 152s -b,--barcodes: path to a file containing barcodes for this run, omit to ignore any barcoding or for already demultiplexed data. 152s -f: path to the input file if processing single-end sequences. 152s -1: first input file in a set of paired-end sequences. 152s -2: second input file in a set of paired-end sequences. 152s -o,--out-path: path to output the processed files. 152s --basename: specify the prefix of the output files when using -f or -1/-2. 152s 152s --threads: number of threads to run. 152s -c,--clean: clean data, remove any read with an uncalled base ('N'). 152s -q,--quality: discard reads with low quality (phred) scores. 152s -r,--rescue: rescue barcodes and RAD-Tag cut sites. 152s -t,--truncate: truncate final read length to this value. 152s -D,--discards: capture discarded reads to a file. 152s 152s Barcode options: 152s --inline-null: barcode is inline with sequence, occurs only on single-end read (default). 152s --index-null: barcode is provded in FASTQ header (Illumina i5 or i7 read). 152s --null-index: barcode is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 152s --inline-inline: barcode is inline with sequence, occurs on single and paired-end read. 152s --index-index: barcode is provded in FASTQ header (Illumina i5 and i7 reads). 152s --inline-index: barcode is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read). 152s --index-inline: barcode occurs in FASTQ header (Illumina i5 or i7 read) and is inline with single-end sequence (for single-end data) on paired-end read (for paired-end data). 152s 152s Restriction enzyme options: 152s -e [enz], --renz-1 [enz]: provide the restriction enzyme used (cut site occurs on single-end read) 152s --renz-2 [enz]: if a double digest was used, provide the second restriction enzyme used (cut site occurs on the paired-end read). 152s Currently supported enzymes include: 152s 'aciI', 'aclI', 'ageI', 'aluI', 'apaLI', 'apeKI', 'apoI', 'aseI', 152s 'bamHI', 'bbvCI', 'bfaI', 'bfuCI', 'bgIII', 'bsaHI', 'bspDI', 'bstYI', 152s 'btgI', 'cac8I', 'claI', 'csp6I', 'ddeI', 'dpnII', 'eaeI', 'ecoRI', 152s 'ecoRV', 'ecoT22I', 'haeII', 'haeIII', 'hhaI', 'hinP1I', 'hindIII', 'hpaII', 152s 'hpyCH4IV', 'kpnI', 'mluCI', 'mseI', 'mslI', 'mspI', 'ncoI', 'ndeI', 152s 'ngoMIV', 'nheI', 'nlaIII', 'notI', 'nsiI', 'nspI', 'pacI', 'pspXI', 152s 'pstI', 'pstIshi', 'rsaI', 'sacI', 'sau3AI', 'sbfI', 'sexAI', 'sgrAI', 152s 'speI', 'sphI', 'taqI', 'xbaI', or 'xhoI' 152s 152s Protocol-specific options: 152s --bestrad: library was generated using BestRAD, check for restriction enzyme on either read and potentially tranpose reads. 152s --methylrad: library was generated using enzymatic methyl-seq (EM-seq) or bisulphite sequencing. 152s 152s Adapter options: 152s --adapter-1 : provide adaptor sequence that may occur on the single-end read for filtering. 152s --adapter-2 : provide adaptor sequence that may occur on the paired-read for filtering. 152s --adapter-mm : number of mismatches allowed in the adapter sequence. 152s 152s Input/Output options: 152s --in-type: input file type, either 'fastq', 'gzfastq' (gzipped fastq), 'bam', or 'bustard' (default: guess, or gzfastq if unable to). 152s --out-type: output type, either 'fastq', 'gzfastq', 'fasta', or 'gzfasta' (default: match input type). 152s --retain-header: retain unmodified FASTQ headers in the output. 152s --merge: if no barcodes are specified, merge all input files into a single output file. 152s 152s Advanced options: 152s --filter-illumina: discard reads that have been marked by Illumina's chastity/purity filter as failing. 152s --disable-rad-check: disable checking if the RAD cut site is intact. 152s --force-poly-g-check: force a check for runs of poly-Gs (default: autodetect based on machine type in FASTQ header). 152s --disable-poly-g-check: disable checking for runs of poly-Gs (default: autodetect based on machine type in FASTQ header). 152s --encoding: specify how quality scores are encoded, 'phred33' (Illumina 1.8+/Sanger, default) or 'phred64' (Illumina 1.3-1.5). 152s --window-size: set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15). 152s --score-limit: set the phred score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10). 152s --len-limit : specify a minimum sequence length (useful if your data has already been trimmed). 152s --barcode-dist-1: the number of allowed mismatches when rescuing single-end barcodes (default 1). 152s --barcode-dist-2: the number of allowed mismatches when rescuing paired-end barcodes (defaults to --barcode-dist-1). 152s process_shortreads 2.68 152s process_shortreads [-f in_file | -p in_dir [-P] [-I] | -1 pair_1 -2 pair_2] -b barcode_file -o out_dir [-i type] [-y type] [-c] [-q] [-r] [-E encoding] [-t len] [-D] [-w size] [-s lim] [-h] 152s f: path to the input file if processing single-end seqeunces. 152s i: input file type, either 'bustard' for the Illumina BUSTARD format, 'bam', 'fastq' (default), or 'gzfastq' for gzipped FASTQ. 152s p: path to a directory of single-end Illumina files. 152s 1: first input file in a set of paired-end sequences. 152s 2: second input file in a set of paired-end sequences. 152s P: specify that input is paired (for use with '-p'). 152s I: specify that the paired-end reads are interleaved in single files. 152s o: path to output the processed files. 152s y: output type, either 'fastq' or 'fasta' (default gzfastq). 152s b: a list of barcodes for this run. 152s c: clean data, remove any read with an uncalled base. 152s q: discard reads with low quality scores. 152s r: rescue barcodes. 152s t: truncate final read length to this value. 152s E: specify how quality scores are encoded, 'phred33' (Illumina 1.8+/Sanger, default) or 'phred64' (Illumina 1.3-1.5). 152s D: capture discarded reads to a file. 152s w: set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15). 152s s: set the score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10). 152s h: display this help message. 152s 152s Barcode options: 152s --inline-null: barcode is inline with sequence, occurs only on single-end read (default). 152s --index-null: barcode is provded in FASTQ header (Illumina i5 or i7 read). 152s --null-index: barcode is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 152s --inline-inline: barcode is inline with sequence, occurs on single and paired-end read. 152s --index-index: barcode is provded in FASTQ header (Illumina i5 and i7 reads). 152s --inline-index: barcode is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read). 152s --index-inline: barcode occurs in FASTQ header (Illumina i5 or i7 read) and is inline with single-end sequence (for single-end data) on paired-end read (for paired-end data). 152s 152s Adapter options: 152s --adapter-1 : provide adaptor sequence that may occur on the first read for filtering. 152s --adapter-2 : provide adaptor sequence that may occur on the paired-read for filtering. 152s --adapter-mm : number of mismatches allowed in the adapter sequence. 152s 152s Output options: 152s --retain-header: retain unmodified FASTQ headers in the output. 152s --merge: if no barcodes are specified, merge all input files into a single output file (or single pair of files). 152s 152s Advanced options: 152s --no-read-trimming: do not trim low quality reads, just discard them. 152s --len-limit : when trimming sequences, specify the minimum length a sequence must be to keep it (default 31bp). 152s --filter-illumina: discard reads that have been marked by Illumina's chastity/purity filter as failing. 152s --barcode-dist: provide the distace between barcodes to allow for barcode rescue (default 2) 152s --mate-pair: raw reads are circularized mate-pair data, first read will be reverse complemented. 152s --no-overhang: data does not contain an overhang nucleotide between barcode and seqeunce. 152s ref_map.pl 2.68 152s ref_map.pl --samples path --popmap path [-s spacer] --out-path path [--rm-pcr-duplicates] [-X prog:"opts" ...] 152s 152s Input/Output files: 152s --samples: path to the directory containing the samples BAM (or SAM) alignment files. 152s --popmap: path to a population map file (format is " TAB ", one sample per line). 152s -s: spacer for file names: by default this is empty and the program looks for files 152s named 'SAMPLE_NAME.bam'; if this option is given the program looks for files 152s named 'SAMPLE_NAME.SPACER.bam'. 152s -o,--out-path: path to an output directory. 152s 152s General options: 152s -X: additional options for specific pipeline components, e.g. -X "populations: -p 3 -r 0.50" 152s -T: the number of threads/CPUs to use (default: 1). 152s -d: Dry run. Do not actually execute anything, just print the individual pipeline commands 152s that would be executed. 152s 152s SNP model options: 152s --var-alpha: significance level at which to call variant sites (for gstacks; default: 0.05). 152s --gt-alpha: significance level at which to call genotypes (for gstacks; default: 0.05). 152s 152s Paired-end options: 152s --rm-pcr-duplicates: remove all but one copy of read pairs of the same sample that have 152s the same insert length. 152s --ignore-pe-reads: ignore paired-end reads even if present in the input 152s --unpaired: ignore read pairing (for paired-end GBS; treat READ2's as if they were READ1's) 152s 152s Population filtering options: 152s -r,--min-samples-per-pop: minimum percentage of individuals in a population required to process a locus for that population (for populations; default: 0) 152s -p,--min-populations: minimum number of populations a locus must be present in to process a locus (for populations; default: 1) 152s 152s Miscellaneous: 152s --time-components (for benchmarking) 152s sstacks 2.68 152s sstacks -P dir -M popmap [-t n_threads] 152s sstacks -c catalog_path -s sample_path [-s sample_path ...] -o path [-t n_threads] 152s -P,--in-path: path to the directory containing Stacks files. 152s -M,--popmap: path to a population map file from which to take sample names. 152s -s,--sample: filename prefix from which to load sample loci. 152s -c,--catalog: path to the catalog. 152s -t,--threads: enable parallel execution with n_threads threads. 152s -o,--out-path: output path to write results. 152s -x: don't verify haplotype of matching locus. 152s 152s Gapped assembly options: 152s --disable-gapped: disable gapped alignments between stacks (default: enable gapped alignments). 153s usage: 153s stacks-dist-extract logfile [section] 153s stacks-dist-extract [--pretty] [--out-path path] logfile [section] 153s cat logfile | stacks-dist-extract [--pretty] [--section section] 153s 153s Export a paricular section of a Stacks log or distribs file. If you supply a 153s log path alone, stacks-dist-extract will print the available sections to 153s output. The log file can also be supplied via stdin. 153s 153s options: 153s -h, --help show this help message and exit 153s -p, --pretty Output data as a table with columns lined up. 153s -o, --out-path path Path to output file. 153s -s, --section section 153s Name of section to output from the log file. 153s Usage: 153s stacks-gdb PROGRAM ARGUMENTS 153s 153s e.g. 153s stacks-gdb populations -P . -p 3 -r 0.5 --vcf 153s 153s This utility will run the `PROGRAM ARGUMENTS` command as specified, but in 153s case of a crash it will print additional information, helping us in fixing the 153s crash. 153s 153s This utility requires GDB, the GNU Debugger, to be installed on the system where 153s Stacks is run. You can check whether this is the case by just typing: 153s 153s gdb --version 153s 153s at the command prompt. Note that you may need to load the corresponding module. 153s GDB is standard scientific software, but may not be installed on some systems. 153s For further information please contact the administrators of your system; 153s trying to install GDB without administrator priviledges is not recommended. 153s 153s For questions please contact us, e.g. at stacks-users@googlegroups.com 153s usage: stacks-integrate-alignments [-h] -P path -B path -O path [-q MIN_MAPQ] 153s [-a MIN_ALNCOV] [-p MIN_PCTID] [--verbose] 153s [--version] 153s 153s Extracts the coordinates of the RAD loci from the given BAM file into a 153s 'locus_coordinates.tsv' table, then rewrites the 'catalog.fa.gz' and 153s 'catalog.calls' files so that they include the genomic coordinates given in 153s the input BAM file. 153s 153s options: 153s -h, --help show this help message and exit 153s -P, --in-path path Path to a directory containing Stacks ouput files. 153s -B, --bam-path path Path to a SAM or BAM file containing alignment of de 153s novo catalog loci to a reference genome. 153s -O, --out-path path Path to write the integrated ouput files. 153s -q, --min_mapq MIN_MAPQ 153s Minimum mapping quality as listed in the BAM file 153s (default 20). 153s -a, --min_alncov MIN_ALNCOV 153s Minimum fraction of the de novo catalog locus that 153s must participate in the alignment (default 0.6). 153s -p, --min_pctid MIN_PCTID 153s Minimum BLAST-style percent identity of the largest 153s alignment fragment for a de novo catalog locus 153s (default 0.6). 153s --verbose Provide verbose output. 153s --version show program's version number and exit 153s usage: 153s stacks-samtools-tview -P gstacks_dir -c catalog_locus_id -s sample_name 153s 153s Displays the read alignments of the given sample for the given locus, in text 153s format, to the standard output. Requires gstacks to have been run with the 153s --write-alignments option. (This is a convenience wrapper around samtools-tview.) 153s tsv2bam 2.68 153s tsv2bam -P stacks_dir -M popmap [-R paired_reads_dir] 153s tsv2bam -P stacks_dir -s sample [-s sample ...] [-R paired_reads_dir] 153s 153s -P,--in-dir: input directory. 153s -M,--popmap: population map. 153s -s,--sample: name of one sample. 153s -R,--pe-reads-dir: directory where to find the paired-end reads files (in fastq/fasta/bam (gz) format). 153s -t: number of threads to use (default: 1). 153s 153s ustacks 2.68 153s ustacks -f in_path -o out_path [-M max_dist] [-m min_reads] [-t num_threads] 153s -f,--file: input file path. 153s -o,--out-path: output path to write results. 153s -M: Maximum distance (in nucleotides) allowed between stacks (default 2). 153s -m: Minimum number of reads to seed a new stack (default 3). 153s -N: Maximum distance allowed to align secondary reads to primary stacks (default: M + 2). 153s -t,--threads: enable parallel execution with num_threads threads. 153s -i,--in-type: input file type. Supported types: fasta, fastq, gzfasta, or gzfastq (default: guess). 153s -n,--name: a name for the sample (default: input file name minus the suffix). 153s -R: retain unused reads. 153s -H: disable calling haplotypes from secondary reads. 153s 153s Stack assembly options: 153s --force-diff-len: allow raw input reads of different lengths, e.g. after trimming (default: ustacks prefers raw input reads of uniform length). 153s --keep-high-cov: disable the algorithm that removes highly-repetitive stacks and nearby errors. 153s --high-cov-thres: highly-repetitive stacks threshold, in standard deviation units (default: 3.0). 153s --max-locus-stacks : maximum number of stacks at a single de novo locus (default 3). 153s --k-len : specify k-mer size for matching between alleles and loci (automatically calculated by default). 153s --deleverage: enable the Deleveraging algorithm, used for resolving over merged tags. 153s 153s Gapped assembly options: 153s --max-gaps: number of gaps allowed between stacks before merging (default: 2). 153s --min-aln-len: minimum length of aligned sequence in a gapped alignment (default: 0.80). 153s --disable-gapped: do not preform gapped alignments between stacks (default: gapped alignements enabled). 153s 153s Model options: 153s --model-type: either 'snp' (default), 'bounded', or 'fixed' 153s For the SNP or Bounded SNP model: 153s --alpha : chi square significance level required to call a heterozygote or homozygote, either 0.1, 0.05 (default), 0.01, or 0.001. 153s For the Bounded SNP model: 153s --bound-low : lower bound for epsilon, the error rate, between 0 and 1.0 (default 0). 153s --bound-high : upper bound for epsilon, the error rate, between 0 and 1.0 (default 1). 153s For the Fixed model: 153s --bc-err-freq : specify the barcode error frequency, between 0 and 1.0. 153s 153s h: display this help message. 153s autopkgtest [23:21:46]: test run-unit-test: -----------------------] 153s autopkgtest [23:21:46]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 153s run-unit-test PASS (superficial) 153s autopkgtest [23:21:46]: @@@@@@@@@@@@@@@@@@@@ summary 153s run-unit-test PASS (superficial) 169s nova [W] Skipping flock for amd64 169s Creating nova instance adt-plucky-amd64-stacks-20250315-231912-juju-7f2275-prod-proposed-migration-environment-2-a008bbd1-71ac-4bfc-ab9c-1f050a238202 from image adt/ubuntu-plucky-amd64-server-20250306.img (UUID 60d877d7-b74c-4f24-920d-f4570db0a338)... 169s nova [W] Timed out waiting for 52ba94a7-586c-4868-ab5e-7a78086b51f4 to get deleted.