0s autopkgtest [23:09:22]: starting date and time: 2025-03-15 23:09:22+0000 0s autopkgtest [23:09:22]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [23:09:22]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.r5uqnaus/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade shapeit4 --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@lcy02-71.secgroup --name adt-plucky-amd64-shapeit4-20250315-230922-juju-7f2275-prod-proposed-migration-environment-2-6bc67f96-e716-4c85-b102-002d9fb291f2 --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/ 44s autopkgtest [23:10:06]: testbed dpkg architecture: amd64 44s autopkgtest [23:10:06]: testbed apt version: 2.9.31ubuntu1 44s autopkgtest [23:10:06]: @@@@@@@@@@@@@@@@@@@@ test bed setup 45s autopkgtest [23:10:07]: testbed release detected to be: None 45s autopkgtest [23:10:07]: updating testbed package index (apt update) 45s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 45s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 45s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 45s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 45s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.5 kB] 45s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [369 kB] 45s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [44.1 kB] 45s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [85.7 kB] 45s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [67.4 kB] 45s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 c-n-f Metadata [1852 B] 45s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 c-n-f Metadata [116 B] 45s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [174 kB] 45s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [342 kB] 45s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 c-n-f Metadata [15.3 kB] 45s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [16.1 kB] 45s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [8544 B] 45s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 c-n-f Metadata [628 B] 46s Fetched 1265 kB in 0s (5034 kB/s) 47s Reading package lists... 47s Reading package lists... 47s Building dependency tree... 47s Reading state information... 48s Calculating upgrade... 48s Calculating upgrade... 48s The following package was automatically installed and is no longer required: 48s libnl-genl-3-200 48s Use 'sudo apt autoremove' to remove it. 48s The following NEW packages will be installed: 48s bpftool libdebuginfod-common libdebuginfod1t64 linux-headers-6.14.0-10 48s linux-headers-6.14.0-10-generic linux-image-6.14.0-10-generic 48s linux-modules-6.14.0-10-generic linux-modules-extra-6.14.0-10-generic 48s linux-perf linux-tools-6.14.0-10 linux-tools-6.14.0-10-generic pnp.ids 48s The following packages will be upgraded: 48s apparmor apt apt-utils binutils binutils-common binutils-x86-64-linux-gnu 48s cloud-init cloud-init-base curl dosfstools fwupd gir1.2-girepository-2.0 48s gir1.2-glib-2.0 htop hwdata libapparmor1 libapt-pkg7.0 libaudit-common 48s libaudit1 libbinutils libbrotli1 libcap-ng0 libctf-nobfd0 libctf0 48s libcurl3t64-gnutls libcurl4t64 libestr0 libfwupd3 libgirepository-1.0-1 48s libglib2.0-0t64 libglib2.0-data libgprofng0 libjemalloc2 liblz4-1 liblzma5 48s libmm-glib0 libncurses6 libncursesw6 libnl-3-200 libnl-genl-3-200 48s libnl-route-3-200 libpci3 libpython3-stdlib libpython3.13 48s libpython3.13-minimal libpython3.13-stdlib libselinux1 libsframe1 48s libsqlite3-0 libtinfo6 libxml2 linux-firmware linux-generic 48s linux-headers-generic linux-headers-virtual linux-image-generic 48s linux-image-virtual linux-libc-dev linux-tools-common linux-virtual 48s media-types ncurses-base ncurses-bin ncurses-term pci.ids pciutils 48s pinentry-curses python-apt-common python3 python3-apt python3-cffi-backend 48s python3-dbus python3-gi python3-jinja2 python3-lazr.uri python3-markupsafe 48s python3-minimal python3-systemd python3-yaml python3.13 python3.13-gdbm 48s python3.13-minimal rsync rsyslog strace xz-utils 48s 86 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 48s Need to get 807 MB of archives. 48s After this operation, 326 MB of additional disk space will be used. 48s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-bin amd64 6.5+20250216-2 [194 kB] 48s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-base all 6.5+20250216-2 [25.9 kB] 48s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-term all 6.5+20250216-2 [276 kB] 48s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 liblz4-1 amd64 1.10.0-4 [66.4 kB] 48s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma5 amd64 5.6.4-1 [157 kB] 48s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.33 [1138 kB] 48s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.33 [1439 kB] 49s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.33 [222 kB] 49s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-minimal amd64 3.13.2-2 [27.7 kB] 49s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 python3 amd64 3.13.2-2 [24.0 kB] 49s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13 amd64 3.13.2-2 [2341 kB] 49s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 media-types all 13.0.0 [29.9 kB] 49s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses6 amd64 6.5+20250216-2 [126 kB] 49s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libncursesw6 amd64 6.5+20250216-2 [165 kB] 49s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libtinfo6 amd64 6.5+20250216-2 [119 kB] 49s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libsqlite3-0 amd64 3.46.1-2 [715 kB] 49s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.2-2 [735 kB] 49s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.2-2 [2365 kB] 49s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.2-2 [883 kB] 49s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.2-2 [2066 kB] 49s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.4 kB] 49s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 rsync amd64 3.4.1+ds1-3 [482 kB] 49s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod-common all 0.192-4 [15.4 kB] 49s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu2 [6628 B] 49s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-4build1 [15.6 kB] 49s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu2 [54.0 kB] 49s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libselinux1 amd64 3.7-3ubuntu3 [87.3 kB] 49s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-girepository-2.0 amd64 1.83.4-1 [25.3 kB] 49s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-glib-2.0 amd64 2.84.0-1 [184 kB] 49s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-0t64 amd64 2.84.0-1 [1669 kB] 49s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libgirepository-1.0-1 amd64 1.83.4-1 [89.5 kB] 49s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libapparmor1 amd64 4.1.0~beta5-0ubuntu8 [55.0 kB] 49s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libestr0 amd64 0.1.11-2 [8340 B] 49s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-data all 2.84.0-1 [53.0 kB] 49s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2ubuntu5 [772 kB] 49s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 python-apt-common all 2.9.9build1 [21.3 kB] 49s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-apt amd64 2.9.9build1 [172 kB] 49s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cffi-backend amd64 1.17.1-2build2 [96.6 kB] 49s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dbus amd64 1.3.2-5build5 [102 kB] 49s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-gi amd64 3.50.0-4build1 [252 kB] 49s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-yaml amd64 6.0.2-1build2 [144 kB] 49s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu2 [555 kB] 49s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 apparmor amd64 4.1.0~beta5-0ubuntu8 [701 kB] 49s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 dosfstools amd64 4.2-1.2 [95.0 kB] 49s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-genl-3-200 amd64 3.7.0-1 [12.2 kB] 49s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-route-3-200 amd64 3.7.0-1 [191 kB] 49s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-3-200 amd64 3.7.0-1 [64.9 kB] 49s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 pci.ids all 0.0~2025.03.09-1 [285 kB] 49s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 pciutils amd64 1:3.13.0-2 [110 kB] 49s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libpci3 amd64 1:3.13.0-2 [39.8 kB] 49s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 strace amd64 6.13+ds-1ubuntu1 [622 kB] 49s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 xz-utils amd64 5.6.4-1 [278 kB] 49s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libgprofng0 amd64 2.44-3ubuntu1 [886 kB] 49s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf0 amd64 2.44-3ubuntu1 [96.5 kB] 49s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf-nobfd0 amd64 2.44-3ubuntu1 [98.9 kB] 49s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-x86-64-linux-gnu amd64 2.44-3ubuntu1 [1108 kB] 49s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libbinutils amd64 2.44-3ubuntu1 [585 kB] 49s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils amd64 2.44-3ubuntu1 [208 kB] 49s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-common amd64 2.44-3ubuntu1 [215 kB] 49s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libsframe1 amd64 2.44-3ubuntu1 [14.8 kB] 49s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 hwdata all 0.393-3 [1562 B] 49s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 pnp.ids all 0.393-3 [29.5 kB] 49s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-common all 6.14.0-10.10 [295 kB] 49s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 bpftool amd64 7.6.0+6.14.0-10.10 [1147 kB] 49s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build4 [13.4 kB] 49s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 49s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init-base all 25.1-0ubuntu3 [616 kB] 49s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli1 amd64 1.1.0-2build4 [365 kB] 49s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 curl amd64 8.12.1-3ubuntu1 [258 kB] 49s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4t64 amd64 8.12.1-3ubuntu1 [437 kB] 49s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl3t64-gnutls amd64 8.12.1-3ubuntu1 [432 kB] 49s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd amd64 2.0.6-4 [5408 kB] 49s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 libfwupd3 amd64 2.0.6-4 [136 kB] 49s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libmm-glib0 amd64 1.23.4-0ubuntu3 [251 kB] 49s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 htop amd64 3.4.0-2 [195 kB] 49s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod1t64 amd64 0.192-4 [21.0 kB] 49s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 libjemalloc2 amd64 5.3.0-3 [277 kB] 49s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-firmware amd64 20250310.git9e1370d3-0ubuntu1 [571 MB] 54s 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] 55s 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] 55s 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] 56s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-generic amd64 6.14.0-10.10 [1730 B] 56s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-generic amd64 6.14.0-10.10 [11.1 kB] 56s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-virtual amd64 6.14.0-10.10 [1722 B] 56s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-virtual amd64 6.14.0-10.10 [11.1 kB] 56s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-virtual amd64 6.14.0-10.10 [1642 B] 56s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10 all 6.14.0-10.10 [14.2 MB] 56s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10-generic amd64 6.14.0-10.10 [3915 kB] 56s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-generic amd64 6.14.0-10.10 [11.0 kB] 56s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-libc-dev amd64 6.14.0-10.10 [1723 kB] 56s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-perf amd64 6.14.0-10.10 [4122 kB] 56s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10 amd64 6.14.0-10.10 [1394 kB] 56s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10-generic amd64 6.14.0-10.10 [830 B] 56s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 pinentry-curses amd64 1.3.1-2ubuntu3 [42.3 kB] 56s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lazr.uri all 1.0.6-6 [13.7 kB] 56s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build6 [43.9 kB] 56s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.2-2 [31.9 kB] 56s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init all 25.1-0ubuntu3 [2100 B] 56s Preconfiguring packages ... 56s Fetched 807 MB in 8s (107 MB/s) 57s (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.) 57s Preparing to unpack .../ncurses-bin_6.5+20250216-2_amd64.deb ... 57s Unpacking ncurses-bin (6.5+20250216-2) over (6.5+20250216-1) ... 57s Setting up ncurses-bin (6.5+20250216-2) ... 57s (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.) 57s Preparing to unpack .../ncurses-base_6.5+20250216-2_all.deb ... 57s Unpacking ncurses-base (6.5+20250216-2) over (6.5+20250216-1) ... 57s Setting up ncurses-base (6.5+20250216-2) ... 57s (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.) 57s Preparing to unpack .../ncurses-term_6.5+20250216-2_all.deb ... 57s Unpacking ncurses-term (6.5+20250216-2) over (6.5+20250216-1) ... 58s Preparing to unpack .../liblz4-1_1.10.0-4_amd64.deb ... 58s Unpacking liblz4-1:amd64 (1.10.0-4) over (1.10.0-3) ... 58s Setting up liblz4-1:amd64 (1.10.0-4) ... 58s (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.) 58s Preparing to unpack .../liblzma5_5.6.4-1_amd64.deb ... 58s Unpacking liblzma5:amd64 (5.6.4-1) over (5.6.3-1) ... 58s Setting up liblzma5:amd64 (5.6.4-1) ... 58s (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.) 58s Preparing to unpack .../libapt-pkg7.0_2.9.33_amd64.deb ... 58s Unpacking libapt-pkg7.0:amd64 (2.9.33) over (2.9.31ubuntu1) ... 58s Setting up libapt-pkg7.0:amd64 (2.9.33) ... 58s (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.) 58s Preparing to unpack .../archives/apt_2.9.33_amd64.deb ... 58s Unpacking apt (2.9.33) over (2.9.31ubuntu1) ... 58s Setting up apt (2.9.33) ... 59s (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.) 59s Preparing to unpack .../apt-utils_2.9.33_amd64.deb ... 59s Unpacking apt-utils (2.9.33) over (2.9.31ubuntu1) ... 59s Preparing to unpack .../python3-minimal_3.13.2-2_amd64.deb ... 59s Unpacking python3-minimal (3.13.2-2) over (3.13.2-1) ... 59s Setting up python3-minimal (3.13.2-2) ... 59s (Reading database ... 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Preparing to unpack .../68-python3-systemd_235-1build6_amd64.deb ... 79s Unpacking python3-systemd (235-1build6) over (235-1build5) ... 79s Preparing to unpack .../69-python3.13-gdbm_3.13.2-2_amd64.deb ... 79s Unpacking python3.13-gdbm (3.13.2-2) over (3.13.2-1) ... 79s Preparing to unpack .../70-cloud-init_25.1-0ubuntu3_all.deb ... 79s Unpacking cloud-init (25.1-0ubuntu3) over (25.1-0ubuntu2) ... 79s Setting up linux-headers-6.14.0-10 (6.14.0-10.10) ... 79s Setting up media-types (13.0.0) ... 79s Installing new version of config file /etc/mime.types ... 79s Setting up linux-headers-6.14.0-10-generic (6.14.0-10.10) ... 79s Setting up libapparmor1:amd64 (4.1.0~beta5-0ubuntu8) ... 79s Setting up pci.ids (0.0~2025.03.09-1) ... 79s Setting up apt-utils (2.9.33) ... 79s Setting up libdebuginfod-common (0.192-4) ... 79s Setting up linux-firmware (20250310.git9e1370d3-0ubuntu1) ... 79s Setting up bpftool (7.6.0+6.14.0-10.10) ... 79s Setting up libestr0:amd64 (0.1.11-2) ... 79s Setting up libbrotli1:amd64 (1.1.0-2build4) ... 79s Setting up libsqlite3-0:amd64 (3.46.1-2) ... 79s Setting up dosfstools (4.2-1.2) ... 79s Setting up rsyslog (8.2412.0-2ubuntu2) ... 79s info: The user `syslog' is already a member of `adm'. 81s Setting up binutils-common:amd64 (2.44-3ubuntu1) ... 81s Setting up libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) ... 81s Setting up linux-libc-dev:amd64 (6.14.0-10.10) ... 81s Setting up libctf-nobfd0:amd64 (2.44-3ubuntu1) ... 81s Setting up linux-headers-generic (6.14.0-10.10) ... 81s Setting up libjemalloc2:amd64 (5.3.0-3) ... 81s Setting up libsframe1:amd64 (2.44-3ubuntu1) ... 81s Setting up libpython3.13-minimal:amd64 (3.13.2-2) ... 81s Setting up apparmor (4.1.0~beta5-0ubuntu8) ... 81s Installing new version of config file /etc/apparmor.d/openvpn ... 82s Reloading AppArmor profiles 84s Setting up libglib2.0-0t64:amd64 (2.84.0-1) ... 84s No schema files found: doing nothing. 84s Setting up libglib2.0-data (2.84.0-1) ... 84s Setting up libncurses6:amd64 (6.5+20250216-2) ... 84s Setting up strace (6.13+ds-1ubuntu1) ... 84s Setting up xz-utils (5.6.4-1) ... 84s Setting up gir1.2-glib-2.0:amd64 (2.84.0-1) ... 84s Setting up linux-modules-6.14.0-10-generic (6.14.0-10.10) ... 87s Setting up libncursesw6:amd64 (6.5+20250216-2) ... 87s Setting up libpci3:amd64 (1:3.13.0-2) ... 87s Setting up python-apt-common (2.9.9build1) ... 87s Setting up libmm-glib0:amd64 (1.23.4-0ubuntu3) ... 87s Setting up pnp.ids (0.393-3) ... 87s Setting up libnl-3-200:amd64 (3.7.0-1) ... 87s Setting up python3.13-minimal (3.13.2-2) ... 88s Setting up libgirepository-1.0-1:amd64 (1.83.4-1) ... 88s Setting up libbinutils:amd64 (2.44-3ubuntu1) ... 88s Setting up libpython3.13-stdlib:amd64 (3.13.2-2) ... 88s Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2ubuntu5) ... 88s Setting up rsync (3.4.1+ds1-3) ... 88s rsync.service is a disabled or a static unit not running, not starting it. 88s Setting up python3.13-gdbm (3.13.2-2) ... 88s Setting up libpython3-stdlib:amd64 (3.13.2-2) ... 88s Setting up ncurses-term (6.5+20250216-2) ... 88s Setting up libctf0:amd64 (2.44-3ubuntu1) ... 88s Setting up libpython3.13:amd64 (3.13.2-2) ... 88s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 88s Setting up libdebuginfod1t64:amd64 (0.192-4) ... 88s Setting up linux-headers-virtual (6.14.0-10.10) ... 88s Setting up libcurl4t64:amd64 (8.12.1-3ubuntu1) ... 88s Setting up python3.13 (3.13.2-2) ... 89s Setting up htop (3.4.0-2) ... 89s Setting up linux-image-6.14.0-10-generic (6.14.0-10.10) ... 92s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.12.0-16-generic 92s I: /boot/initrd.img.old is now a symlink to initrd.img-6.12.0-16-generic 92s I: /boot/vmlinuz is now a symlink to vmlinuz-6.14.0-10-generic 92s I: /boot/initrd.img is now a symlink to initrd.img-6.14.0-10-generic 92s Setting up libfwupd3:amd64 (2.0.6-4) ... 92s Setting up python3 (3.13.2-2) ... 92s Setting up python3-markupsafe (2.1.5-1build4) ... 92s Setting up linux-modules-extra-6.14.0-10-generic (6.14.0-10.10) ... 95s Setting up libnl-route-3-200:amd64 (3.7.0-1) ... 95s Setting up hwdata (0.393-3) ... 95s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 95s Setting up libgprofng0:amd64 (2.44-3ubuntu1) ... 95s Setting up linux-perf (6.14.0-10.10) ... 95s Setting up gir1.2-girepository-2.0:amd64 (1.83.4-1) ... 95s Setting up python3-gi (3.50.0-4build1) ... 95s Setting up pciutils (1:3.13.0-2) ... 95s Setting up libnl-genl-3-200:amd64 (3.7.0-1) ... 95s Setting up curl (8.12.1-3ubuntu1) ... 95s Setting up linux-image-virtual (6.14.0-10.10) ... 95s Setting up linux-tools-common (6.14.0-10.10) ... 95s Setting up fwupd (2.0.6-4) ... 96s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 96s fwupd.service is a disabled or a static unit not running, not starting it. 96s Setting up python3-systemd (235-1build6) ... 96s Setting up python3-cffi-backend:amd64 (1.17.1-2build2) ... 96s Setting up binutils-x86-64-linux-gnu (2.44-3ubuntu1) ... 96s Setting up linux-image-generic (6.14.0-10.10) ... 96s Setting up python3-dbus (1.3.2-5build5) ... 96s Setting up linux-tools-6.14.0-10 (6.14.0-10.10) ... 96s Setting up linux-generic (6.14.0-10.10) ... 96s Setting up python3-apt (2.9.9build1) ... 96s Setting up python3-yaml (6.0.2-1build2) ... 97s Setting up python3-lazr.uri (1.0.6-6) ... 97s Setting up binutils (2.44-3ubuntu1) ... 97s Setting up cloud-init-base (25.1-0ubuntu3) ... 99s Setting up linux-virtual (6.14.0-10.10) ... 99s Setting up linux-tools-6.14.0-10-generic (6.14.0-10.10) ... 99s Setting up cloud-init (25.1-0ubuntu3) ... 99s Processing triggers for systemd (257.3-1ubuntu3) ... 99s Processing triggers for man-db (2.13.0-1) ... 101s Processing triggers for dbus (1.16.2-1ubuntu1) ... 101s Processing triggers for libc-bin (2.41-1ubuntu1) ... 101s Processing triggers for initramfs-tools (0.146ubuntu1) ... 101s update-initramfs: Generating /boot/initrd.img-6.12.0-16-generic 101s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 115s Processing triggers for linux-image-6.14.0-10-generic (6.14.0-10.10) ... 115s /etc/kernel/postinst.d/initramfs-tools: 115s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 115s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 129s /etc/kernel/postinst.d/zz-update-grub: 129s Sourcing file `/etc/default/grub' 129s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 129s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 129s Generating grub configuration file ... 129s Found linux image: /boot/vmlinuz-6.14.0-10-generic 129s Found initrd image: /boot/initrd.img-6.14.0-10-generic 129s Found linux image: /boot/vmlinuz-6.12.0-16-generic 129s Found initrd image: /boot/initrd.img-6.12.0-16-generic 130s Found linux image: /boot/vmlinuz-6.11.0-8-generic 130s Found initrd image: /boot/initrd.img-6.11.0-8-generic 130s Warning: os-prober will not be executed to detect other bootable partitions. 130s Systems on them will not be added to the GRUB boot configuration. 130s Check GRUB_DISABLE_OS_PROBER documentation entry. 130s Adding boot menu entry for UEFI Firmware Settings ... 130s done 131s Reading package lists... 132s Building dependency tree... 132s Reading state information... 132s Solving dependencies... 132s The following packages will be REMOVED: 132s libnl-genl-3-200* libnsl2* libpython3.12-minimal* libpython3.12-stdlib* 132s libpython3.12t64* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 132s linux-headers-6.12.0-16* linux-headers-6.12.0-16-generic* 132s linux-image-6.11.0-8-generic* linux-image-6.12.0-16-generic* 132s linux-modules-6.11.0-8-generic* linux-modules-6.12.0-16-generic* 132s linux-modules-extra-6.12.0-16-generic* linux-tools-6.11.0-8* 132s linux-tools-6.11.0-8-generic* linux-tools-6.12.0-16* 132s linux-tools-6.12.0-16-generic* 133s 0 upgraded, 0 newly installed, 18 to remove and 5 not upgraded. 133s After this operation, 545 MB disk space will be freed. 133s (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.) 133s Removing libnl-genl-3-200:amd64 (3.7.0-1) ... 133s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 133s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 133s Removing libpython3.12t64:amd64 (3.12.9-1) ... 133s Removing libpython3.12-stdlib:amd64 (3.12.9-1) ... 133s Removing libnsl2:amd64 (1.3.0-3build3) ... 133s Removing libpython3.12-minimal:amd64 (3.12.9-1) ... 133s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 134s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 137s Removing linux-headers-6.12.0-16-generic (6.12.0-16.16) ... 138s Removing linux-headers-6.12.0-16 (6.12.0-16.16) ... 140s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 141s /etc/kernel/postrm.d/initramfs-tools: 141s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 141s /etc/kernel/postrm.d/zz-update-grub: 141s Sourcing file `/etc/default/grub' 141s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 141s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 141s Generating grub configuration file ... 141s Found linux image: /boot/vmlinuz-6.14.0-10-generic 141s Found initrd image: /boot/initrd.img-6.14.0-10-generic 141s Found linux image: /boot/vmlinuz-6.12.0-16-generic 141s Found initrd image: /boot/initrd.img-6.12.0-16-generic 142s Warning: os-prober will not be executed to detect other bootable partitions. 142s Systems on them will not be added to the GRUB boot configuration. 142s Check GRUB_DISABLE_OS_PROBER documentation entry. 142s Adding boot menu entry for UEFI Firmware Settings ... 142s done 142s Removing linux-image-6.12.0-16-generic (6.12.0-16.16) ... 142s W: Removing the running kernel 142s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 142s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 142s /etc/kernel/postrm.d/initramfs-tools: 142s update-initramfs: Deleting /boot/initrd.img-6.12.0-16-generic 142s /etc/kernel/postrm.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 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 Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 143s Removing linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 145s Removing linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 145s Removing linux-tools-6.12.0-16-generic (6.12.0-16.16) ... 145s Removing linux-tools-6.12.0-16 (6.12.0-16.16) ... 145s Processing triggers for libc-bin (2.41-1ubuntu1) ... 145s (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.) 145s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 145s Purging configuration files for libpython3.12-minimal:amd64 (3.12.9-1) ... 145s Purging configuration files for linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 145s Purging configuration files for linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 145s dpkg: warning: while removing linux-modules-6.12.0-16-generic, directory '/lib/modules/6.12.0-16-generic' not empty so not removed 145s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 145s Purging configuration files for linux-image-6.12.0-16-generic (6.12.0-16.16) ... 145s rmdir: failed to remove '/lib/modules/6.12.0-16-generic': Directory not empty 146s autopkgtest [23:11:48]: upgrading testbed (apt dist-upgrade and autopurge) 146s Reading package lists... 146s Building dependency tree... 146s Reading state information... 146s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 146s Starting 2 pkgProblemResolver with broken count: 0 146s Done 147s Entering ResolveByKeep 147s 147s Calculating upgrade... 148s The following packages will be upgraded: 148s libc-bin libc-dev-bin libc6 libc6-dev locales 148s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 148s Need to get 10.5 MB of archives. 148s After this operation, 1024 B of additional disk space will be used. 148s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6-dev amd64 2.41-1ubuntu2 [2183 kB] 148s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-dev-bin amd64 2.41-1ubuntu2 [24.7 kB] 148s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6 amd64 2.41-1ubuntu2 [3327 kB] 148s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-bin amd64 2.41-1ubuntu2 [700 kB] 148s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 locales all 2.41-1ubuntu2 [4246 kB] 149s Preconfiguring packages ... 149s Fetched 10.5 MB in 1s (19.1 MB/s) 149s (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.) 149s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_amd64.deb ... 149s Unpacking libc6-dev:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 149s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_amd64.deb ... 149s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 149s Preparing to unpack .../libc6_2.41-1ubuntu2_amd64.deb ... 150s Unpacking libc6:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 150s Setting up libc6:amd64 (2.41-1ubuntu2) ... 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 .../libc-bin_2.41-1ubuntu2_amd64.deb ... 150s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 150s Setting up libc-bin (2.41-1ubuntu2) ... 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 .../locales_2.41-1ubuntu2_all.deb ... 150s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 151s Setting up locales (2.41-1ubuntu2) ... 152s Generating locales (this might take a while)... 153s en_US.UTF-8... done 153s Generation complete. 153s Setting up libc-dev-bin (2.41-1ubuntu2) ... 153s Setting up libc6-dev:amd64 (2.41-1ubuntu2) ... 153s Processing triggers for man-db (2.13.0-1) ... 154s Processing triggers for systemd (257.3-1ubuntu3) ... 155s Reading package lists... 155s Building dependency tree... 155s Reading state information... 155s Starting pkgProblemResolver with broken count: 0 155s Starting 2 pkgProblemResolver with broken count: 0 155s Done 156s Solving dependencies... 156s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 156s autopkgtest [23:11:58]: rebooting testbed after setup commands that affected boot 160s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 172s autopkgtest [23:12:14]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 16:07:00 UTC 2025 173s autopkgtest [23:12:15]: @@@@@@@@@@@@@@@@@@@@ apt-source shapeit4 178s Get:1 http://ftpmaster.internal/ubuntu plucky/universe shapeit4 4.2.2+dfsg-1build3 (dsc) [2237 B] 178s Get:2 http://ftpmaster.internal/ubuntu plucky/universe shapeit4 4.2.2+dfsg-1build3 (tar) [59.0 MB] 178s Get:3 http://ftpmaster.internal/ubuntu plucky/universe shapeit4 4.2.2+dfsg-1build3 (diff) [5424 B] 178s gpgv: Signature made Mon Apr 1 08:00:11 2024 UTC 178s gpgv: using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984 178s gpgv: Can't check signature: No public key 178s dpkg-source: warning: cannot verify inline signature for ./shapeit4_4.2.2+dfsg-1build3.dsc: no acceptable signature found 180s autopkgtest [23:12:22]: testing package shapeit4 version 4.2.2+dfsg-1build3 180s autopkgtest [23:12:22]: build not needed 182s autopkgtest [23:12:24]: test run-sample-analysis: preparing testbed 182s Reading package lists... 182s Building dependency tree... 182s Reading state information... 182s Starting pkgProblemResolver with broken count: 0 182s Starting 2 pkgProblemResolver with broken count: 0 182s Done 183s The following NEW packages will be installed: 183s libboost-iostreams1.83.0 libboost-program-options1.83.0 libdeflate0 183s libhts3t64 libhtscodecs2 shapeit4 shapeit4-example 183s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 183s Need to get 53.7 MB of archives. 183s After this operation, 59.3 MB of additional disk space will be used. 183s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost-iostreams1.83.0 amd64 1.83.0-4.1ubuntu2 [260 kB] 183s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost-program-options1.83.0 amd64 1.83.0-4.1ubuntu2 [323 kB] 183s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB] 183s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-2 [132 kB] 183s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.21+ds-1 [514 kB] 183s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 shapeit4 amd64 4.2.2+dfsg-1build3 [179 kB] 183s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 shapeit4-example all 4.2.2+dfsg-1build3 [52.3 MB] 185s Fetched 53.7 MB in 1s (36.6 MB/s) 185s Selecting previously unselected package libboost-iostreams1.83.0:amd64. 185s (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.) 185s Preparing to unpack .../0-libboost-iostreams1.83.0_1.83.0-4.1ubuntu2_amd64.deb ... 185s Unpacking libboost-iostreams1.83.0:amd64 (1.83.0-4.1ubuntu2) ... 185s Selecting previously unselected package libboost-program-options1.83.0:amd64. 185s Preparing to unpack .../1-libboost-program-options1.83.0_1.83.0-4.1ubuntu2_amd64.deb ... 185s Unpacking libboost-program-options1.83.0:amd64 (1.83.0-4.1ubuntu2) ... 185s Selecting previously unselected package libdeflate0:amd64. 185s Preparing to unpack .../2-libdeflate0_1.23-1_amd64.deb ... 185s Unpacking libdeflate0:amd64 (1.23-1) ... 185s Selecting previously unselected package libhtscodecs2:amd64. 185s Preparing to unpack .../3-libhtscodecs2_1.6.1-2_amd64.deb ... 185s Unpacking libhtscodecs2:amd64 (1.6.1-2) ... 185s Selecting previously unselected package libhts3t64:amd64. 185s Preparing to unpack .../4-libhts3t64_1.21+ds-1_amd64.deb ... 185s Unpacking libhts3t64:amd64 (1.21+ds-1) ... 185s Selecting previously unselected package shapeit4. 185s Preparing to unpack .../5-shapeit4_4.2.2+dfsg-1build3_amd64.deb ... 185s Unpacking shapeit4 (4.2.2+dfsg-1build3) ... 185s Selecting previously unselected package shapeit4-example. 185s Preparing to unpack .../6-shapeit4-example_4.2.2+dfsg-1build3_all.deb ... 185s Unpacking shapeit4-example (4.2.2+dfsg-1build3) ... 186s Setting up libhtscodecs2:amd64 (1.6.1-2) ... 186s Setting up libboost-program-options1.83.0:amd64 (1.83.0-4.1ubuntu2) ... 186s Setting up libdeflate0:amd64 (1.23-1) ... 186s Setting up shapeit4-example (4.2.2+dfsg-1build3) ... 186s Setting up libboost-iostreams1.83.0:amd64 (1.83.0-4.1ubuntu2) ... 186s Setting up libhts3t64:amd64 (1.21+ds-1) ... 186s Setting up shapeit4 (4.2.2+dfsg-1build3) ... 186s Processing triggers for man-db (2.13.0-1) ... 187s Processing triggers for libc-bin (2.41-1ubuntu2) ... 188s autopkgtest [23:12:30]: test run-sample-analysis: [----------------------- 188s + shapeit4 --input unphased.vcf.gz --map chr20.b37.gmap.gz --region 20:2000000-3000000 --thread 4 --output phased.vcf.gz 188s 188s SHAPEIT 188s * Author : Olivier DELANEAU, University of Lausanne 188s * Contact : olivier.delaneau@gmail.com 188s * Version : 4.2.2 188s * Run date : 15/03/2025 - 23:12:30 188s 188s Files: 188s * Input VCF : [unphased.vcf.gz] 188s * Genetic Map : [chr20.b37.gmap.gz] 188s * Output VCF : [phased.vcf.gz] 188s 188s Parameters: 188s * Seed : 15052011 188s * Threads : 4 threads 188s * MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m] 188s * PBWT : Depth of PBWT neighbours to condition on: 4 188s * PBWT : Store indexes at variants [MAC>=2 / MDR<=0.5 / Dist=0.02 cM] 188s * HMM : K is variable / min W is 2.50cM / Ne is 15000 188s * HMM : Recombination rates given by genetic map 188s * HMM : AVX2 optimization inactive / Activating AVX2 substantially improves performance 188s 188s Initialization: 188s * VCF/BCF scanning ... * VCF/BCF scanning [N=203 / L=8651 / Reg=20:2000000-3000000] (0.07s) 188s * VCF/BCF parsing [0%] * VCF/BCF parsing [1%] * VCF/BCF parsing [2%] * VCF/BCF parsing [3%] * VCF/BCF parsing [4%] * VCF/BCF parsing [5%] * VCF/BCF parsing [6%] * VCF/BCF parsing [7%] * VCF/BCF parsing [8%] * VCF/BCF parsing [9%] * VCF/BCF parsing [10%] * VCF/BCF parsing [11%] * VCF/BCF parsing [12%] * VCF/BCF parsing [13%] * VCF/BCF parsing [14%] * VCF/BCF parsing [15%] * VCF/BCF parsing [16%] * VCF/BCF parsing [17%] * VCF/BCF 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[Hom=89.3% / Het=10.7% / Mis=0.0%] (0.08s) 188s * GMAP parsing [n=82962] (0.05s) 188s * cM interpolation [s=1236 / i=7415] (0.00s) 188s * Region length [999850 bp / 2.5 cM] 188s * HMM parameters [Ne=15000 / Error=0.0001 / #rare=2243] 188s * PBWT indexing [l=120] (0.00s) 188s * HAP update (0.02s) 188s * H2V transpose (0.00s) 188s * PBWT phase sweep [0%] * PBWT phase sweep [1%] * PBWT phase sweep [2%] * PBWT phase sweep [3%] * PBWT phase sweep [4%] * PBWT phase sweep [5%] * PBWT phase sweep [6%] * PBWT phase sweep [7%] * PBWT phase sweep [8%] * PBWT phase sweep [9%] * PBWT phase sweep [10%] * PBWT phase sweep [11%] * PBWT phase sweep [12%] * PBWT phase sweep [13%] * PBWT phase sweep [14%] * PBWT phase sweep [15%] * PBWT phase sweep [16%] * PBWT phase sweep [17%] * PBWT phase sweep [18%] * PBWT phase sweep [19%] * PBWT phase sweep [20%] * PBWT phase sweep [21%] * PBWT phase sweep [22%] * PBWT phase sweep [23%] * PBWT phase sweep [24%] * PBWT phase sweep [25%] * PBWT phase sweep [26%] * 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HAP update (0.01s) 227s * H2V transpose (0.00s) 227s 227s Main iteration [5/5] 227s * V2H transpose (0.00s) 227s * PBWT selection [0%] * PBWT selection [1%] * PBWT selection [2%] * PBWT selection [3%] * PBWT selection [4%] * PBWT selection [5%] * PBWT selection [6%] * PBWT selection [7%] * PBWT selection [8%] * PBWT selection [9%] * PBWT selection [10%] * PBWT selection [11%] * PBWT selection [12%] * PBWT selection [13%] * PBWT selection [14%] * PBWT selection [15%] * PBWT selection [16%] * PBWT selection [17%] * PBWT selection [18%] * PBWT selection [19%] * PBWT selection [20%] * PBWT selection [21%] * PBWT selection [22%] * PBWT selection [23%] * PBWT selection [24%] * PBWT selection [25%] * PBWT selection [26%] * PBWT selection [27%] * PBWT selection [28%] * PBWT selection [29%] * PBWT selection [30%] * PBWT selection [31%] * PBWT selection [32%] * PBWT selection [33%] * PBWT selection [34%] * PBWT selection [35%] * PBWT selection [36%] * PBWT selection [37%] * PBWT selection [38%] 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[100%] * HMM computations [K=208.394+/-17.250 / W=1.00Mb] (2.64s) 230s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 230s * HAP update (0.01s) 230s * H2V transpose (0.00s) 230s 230s Finalization: 230s * HAP solving (0.01s) 230s * HAP update (0.01s) 230s * H2V transpose (0.00s) 230s * VCF writing [0%] * VCF writing [1%] * VCF writing [2%] * VCF writing [3%] * VCF writing [4%] * VCF writing [5%] * VCF writing [6%] * VCF writing [7%] * VCF writing [8%] * VCF writing [9%] * VCF writing [10%] * VCF writing [11%] * VCF writing [12%] * VCF writing [13%] * VCF writing [14%] * VCF writing [15%] * VCF writing [16%] * VCF writing [17%] * VCF writing [18%] * VCF writing [19%] * VCF writing [20%] * VCF writing [21%] * VCF writing [22%] * VCF writing [23%] * VCF writing [24%] * VCF writing [25%] * VCF writing [26%] * VCF writing [27%] * VCF writing [28%] * VCF writing [29%] * VCF writing [30%] * VCF writing [31%] * VCF writing [32%] * VCF writing [33%] * VCF writing [34%] * VCF writing 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[85%] * VCF writing [86%] * VCF writing [87%] * VCF writing [88%] * VCF writing [89%] * VCF writing [90%] * VCF writing [91%] * VCF writing [92%] * VCF writing [93%] * VCF writing [94%] * VCF writing [95%] * VCF writing [96%] * VCF writing [97%] * VCF writing [98%] * VCF writing [99%] * VCF writing [100%] * VCF writing [Compressed / N=203 / L=8651] (0.11s) 230s * Total running time = 42 seconds 230s + shapeit4 --input unphased.bcf --map chr20.b37.gmap.gz --region 20 --reference reference.bcf --scaffold scaffold.bcf --use-PS 0.0001 --thread 4 --log phased.log --output phased.bcf 230s 230s SHAPEIT 230s * Author : Olivier DELANEAU, University of Lausanne 230s * Contact : olivier.delaneau@gmail.com 230s * Version : 4.2.2 230s * Run date : 15/03/2025 - 23:13:12 230s 230s Files: 230s * Input VCF : [unphased.bcf] 230s * Reference VCF : [reference.bcf] 230s * Scaffold VCF : [scaffold.bcf] 230s * Genetic Map : [chr20.b37.gmap.gz] 230s * Output VCF : [phased.bcf] 230s * Output LOG : [phased.log] 230s 230s Parameters: 230s * Seed : 15052011 230s * Threads : 4 threads 230s * MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m] 230s * PBWT : Depth of PBWT neighbours to condition on: 4 230s * PBWT : Store indexes at variants [MAC>=2 / MDR<=0.5 / Dist=0.02 cM] 230s * HMM : K is variable / min W is 2.50cM / Ne is 15000 230s * HMM : Recombination rates given by genetic map 230s * HMM : Inform phasing using VCF/PS field / Error rate of PS field is 0.0001 230s * HMM : AVX2 optimization inactive / Activating AVX2 substantially improves performance 230s 230s Initialization: 230s * VCF/BCF scanning ... * VCF/BCF scanning [Nm=203 / Nr=300 / L=24990 / Reg=20] (0.04s) 230s * VCF/BCF parsing [0%] * VCF/BCF parsing [1%] * VCF/BCF parsing [2%] * VCF/BCF parsing [3%] * VCF/BCF parsing [4%] * VCF/BCF parsing [5%] * VCF/BCF parsing [6%] * VCF/BCF parsing [7%] * VCF/BCF parsing [8%] * VCF/BCF parsing [9%] * VCF/BCF parsing [10%] * VCF/BCF parsing [11%] * VCF/BCF parsing [12%] * VCF/BCF parsing 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VCF/BCF parsing [97%] * VCF/BCF parsing [98%] * VCF/BCF parsing [99%] * VCF/BCF parsing [100%] * VCF/BCF parsing [Hom=90.0% / Het=10.0% / Pha=2.668% / Sca=0.778% / Mis=0.0%] (0.35s) 230s * GMAP parsing [n=82962] (0.05s) 230s * cM interpolation [s=3296 / i=21694] (0.00s) 230s * Region length [2999624 bp / 6.6 cM] 230s * HMM parameters [Ne=15000 / Error=0.0001 / #rare=9606] 230s * PBWT indexing [l=328] (0.00s) 230s * HAP update (0.07s) 230s * H2V transpose (0.02s) 231s * PBWT phase sweep [0%] * PBWT phase sweep [1%] * PBWT phase sweep [2%] * PBWT phase sweep [3%] * PBWT phase sweep [4%] * PBWT phase sweep [5%] * PBWT phase sweep [6%] * PBWT phase sweep [7%] * PBWT phase sweep [8%] * PBWT phase sweep [9%] * PBWT phase sweep [10%] * PBWT phase sweep [11%] * PBWT phase sweep [12%] * PBWT phase sweep [13%] * PBWT phase sweep [14%] * PBWT phase sweep [15%] * PBWT phase sweep [16%] * PBWT phase sweep [17%] * PBWT phase sweep [18%] * PBWT phase sweep [19%] * PBWT phase sweep [20%] * PBWT phase 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sweep (0.44s) 231s * Build genotype graphs [seg=164449] (0.04s) 231s 231s Burn-in iteration [1/5] 231s * V2H transpose (0.01s) 231s * PBWT selection [0%] * PBWT selection [1%] * PBWT selection [2%] * PBWT selection [3%] * PBWT selection [4%] * PBWT selection [5%] * PBWT selection [6%] * PBWT selection [7%] * PBWT selection [8%] * PBWT selection [9%] * PBWT selection [10%] * PBWT selection [11%] * PBWT selection [12%] * PBWT selection [13%] * PBWT selection [14%] * PBWT selection [15%] * PBWT selection [16%] * PBWT selection [17%] * PBWT selection [18%] * PBWT selection [19%] * PBWT selection [20%] * PBWT selection [21%] * PBWT selection [22%] * PBWT selection [23%] * PBWT selection [24%] * PBWT selection [25%] * PBWT selection [26%] * PBWT selection [27%] * PBWT selection [28%] * PBWT selection [29%] * PBWT selection [30%] * PBWT selection [31%] * PBWT selection [32%] * PBWT selection [33%] * PBWT selection [34%] * PBWT selection [35%] * PBWT selection [36%] * PBWT selection [37%] * 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computations [70%] * HMM computations [71%] * HMM computations [72%] * HMM computations [73%] * HMM computations [74%] * HMM computations [75%] * HMM computations [76%] * HMM computations [77%] * HMM computations [78%] * HMM computations [79%] * HMM computations [80%] * HMM computations [81%] * HMM computations [82%] * HMM computations [83%] * HMM computations [84%] * HMM computations [85%] * HMM computations [86%] * HMM computations [87%] * HMM computations [88%] * HMM computations [89%] * HMM computations [90%] * HMM computations [91%] * HMM computations [92%] * HMM computations [93%] * HMM computations [94%] * HMM computations [95%] * HMM computations [96%] * HMM computations [97%] * HMM computations [98%] * HMM computations [99%] * HMM computations [100%] * HMM computations [K=403.444+/-112.628 / W=2.26Mb] (16.46s) 329s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 329s * HAP update (0.02s) 329s * H2V transpose (0.01s) 329s * Trimming [pc=42.89%] 329s 329s Burn-in iteration [1/1] 329s * V2H transpose (0.01s) 330s * PBWT selection [0%] * PBWT selection [1%] * PBWT selection [2%] * PBWT selection [3%] * PBWT selection [4%] * PBWT selection [5%] * PBWT selection [6%] * PBWT selection [7%] * PBWT selection [8%] * PBWT selection [9%] * PBWT selection [10%] * PBWT selection [11%] * PBWT selection [12%] * PBWT selection [13%] * PBWT selection [14%] * PBWT selection [15%] * PBWT selection [16%] * PBWT selection [17%] * PBWT selection [18%] * PBWT selection [19%] * PBWT selection [20%] * PBWT selection [21%] * PBWT selection [22%] * PBWT selection [23%] * PBWT selection [24%] * PBWT selection [25%] * PBWT selection [26%] * PBWT selection [27%] * PBWT selection [28%] * PBWT selection [29%] * PBWT selection [30%] * PBWT selection [31%] * PBWT selection [32%] * PBWT selection [33%] * PBWT selection [34%] * PBWT selection [35%] * PBWT selection [36%] * PBWT selection [37%] * PBWT selection [38%] * PBWT selection [39%] * PBWT selection [40%] * PBWT selection 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(17.42s) 347s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 347s * HAP update (0.03s) 347s * H2V transpose (0.01s) 347s 347s Pruning iteration [1/1] 347s * V2H transpose (0.01s) 347s * PBWT selection [0%] * PBWT selection [1%] * PBWT selection [2%] * PBWT selection [3%] * PBWT selection [4%] * PBWT selection [5%] * PBWT selection [6%] * PBWT selection [7%] * PBWT selection [8%] * PBWT selection [9%] * PBWT selection [10%] * PBWT selection [11%] * PBWT selection [12%] * PBWT selection [13%] * PBWT selection [14%] * PBWT selection [15%] * PBWT selection [16%] * PBWT selection [17%] * PBWT selection [18%] * PBWT selection [19%] * PBWT selection [20%] * PBWT selection [21%] * PBWT selection [22%] * PBWT selection [23%] * PBWT selection [24%] * PBWT selection [25%] * PBWT selection [26%] * PBWT selection [27%] * PBWT selection [28%] * PBWT selection [29%] * PBWT selection [30%] * PBWT selection [31%] * PBWT selection [32%] * PBWT selection [33%] * PBWT selection [34%] * PBWT 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computations [84%] * HMM computations [85%] * HMM computations [86%] * HMM computations [87%] * HMM computations [88%] * HMM computations [89%] * HMM computations [90%] * HMM computations [91%] * HMM computations [92%] * HMM computations [93%] * HMM computations [94%] * HMM computations [95%] * HMM computations [96%] * HMM computations [97%] * HMM computations [98%] * HMM computations [99%] * HMM computations [100%] * HMM computations [K=390.465+/-113.036 / W=2.25Mb] (14.19s) 394s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 394s * HAP update (0.02s) 394s * H2V transpose (0.01s) 394s * Trimming [pc=78.64%] 394s 394s Main iteration [1/5] 394s * V2H transpose (0.01s) 394s * PBWT selection [0%] * PBWT selection [1%] * PBWT selection [2%] * PBWT selection [3%] * PBWT selection [4%] * PBWT selection [5%] * PBWT selection [6%] * PBWT selection [7%] * PBWT selection [8%] * PBWT selection [9%] * PBWT selection [10%] * PBWT selection [11%] * PBWT selection [12%] * PBWT selection 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PBWT selection [57%] * PBWT selection [58%] * PBWT selection [59%] * PBWT selection [60%] * PBWT selection [61%] * PBWT selection [62%] * PBWT selection [63%] * PBWT selection [64%] * PBWT selection [65%] * PBWT selection [66%] * PBWT selection [67%] * PBWT selection [68%] * PBWT selection [69%] * PBWT selection [70%] * PBWT selection [71%] * PBWT selection [72%] * PBWT selection [73%] * PBWT selection [74%] * PBWT selection [75%] * PBWT selection [76%] * PBWT selection [77%] * PBWT selection [78%] * PBWT selection [79%] * PBWT selection [80%] * PBWT selection [81%] * PBWT selection [82%] * PBWT selection [83%] * PBWT selection [84%] * PBWT selection [85%] * PBWT selection [86%] * PBWT selection [87%] * PBWT selection [88%] * PBWT selection [89%] * PBWT selection [90%] * PBWT selection [91%] * PBWT selection [92%] * PBWT selection [93%] * PBWT selection [94%] * PBWT selection [95%] * PBWT selection [96%] * PBWT selection [97%] * PBWT selection [98%] * PBWT selection [99%] * PBWT selection [100%] * PBWT selection (0.07s) 394s * C2H transpose (0.00s) 408s * HMM computations [0%] * HMM computations [1%] * HMM computations [2%] * HMM computations [3%] * HMM computations [4%] * HMM computations [5%] * HMM computations [6%] * HMM computations [7%] * HMM computations [8%] * HMM computations [9%] * HMM computations [10%] * HMM computations [11%] * HMM computations [12%] * HMM computations [13%] * HMM computations [14%] * HMM computations [15%] * HMM computations [16%] * HMM computations [17%] * HMM computations [18%] * HMM computations [19%] * HMM computations [20%] * HMM computations [21%] * HMM computations [22%] * HMM computations [23%] * HMM computations [24%] * HMM computations [25%] * HMM computations [26%] * HMM computations [27%] * HMM computations [28%] * HMM computations [29%] * HMM computations [30%] * HMM computations [31%] * HMM computations [32%] * HMM computations [33%] * HMM computations [34%] * HMM computations [35%] * HMM computations [36%] * HMM 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computations [77%] * HMM computations [78%] * HMM computations [79%] * HMM computations [80%] * HMM computations [81%] * HMM computations [82%] * HMM computations [83%] * HMM computations [84%] * HMM computations [85%] * HMM computations [86%] * HMM computations [87%] * HMM computations [88%] * HMM computations [89%] * HMM computations [90%] * HMM computations [91%] * HMM computations [92%] * HMM computations [93%] * HMM computations [94%] * HMM computations [95%] * HMM computations [96%] * HMM computations [97%] * HMM computations [98%] * HMM computations [99%] * HMM computations [100%] * HMM computations [K=393.004+/-111.143 / W=2.25Mb] (14.23s) 408s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 408s * HAP update (0.02s) 408s * H2V transpose (0.01s) 408s 408s Main iteration [2/5] 408s * V2H transpose (0.01s) 408s * PBWT selection [0%] * PBWT selection [1%] * PBWT selection [2%] * PBWT selection [3%] * PBWT selection [4%] * PBWT selection [5%] * PBWT selection [6%] * PBWT 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PBWT selection [94%] * PBWT selection [95%] * PBWT selection [96%] * PBWT selection [97%] * PBWT selection [98%] * PBWT selection [99%] * PBWT selection [100%] * PBWT selection (0.06s) 408s * C2H transpose (0.00s) 423s * HMM computations [0%] * HMM computations [1%] * HMM computations [2%] * HMM computations [3%] * HMM computations [4%] * HMM computations [5%] * HMM computations [6%] * HMM computations [7%] * HMM computations [8%] * HMM computations [9%] * HMM computations [10%] * HMM computations [11%] * HMM computations [12%] * HMM computations [13%] * HMM computations [14%] * HMM computations [15%] * HMM computations [16%] * HMM computations [17%] * HMM computations [18%] * HMM computations [19%] * HMM computations [20%] * HMM computations [21%] * HMM computations [22%] * HMM computations [23%] * HMM computations [24%] * HMM computations [25%] * HMM computations [26%] * HMM computations [27%] * HMM computations [28%] * HMM computations [29%] * HMM computations [30%] * HMM 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computations [71%] * HMM computations [72%] * HMM computations [73%] * HMM computations [74%] * HMM computations [75%] * HMM computations [76%] * HMM computations [77%] * HMM computations [78%] * HMM computations [79%] * HMM computations [80%] * HMM computations [81%] * HMM computations [82%] * HMM computations [83%] * HMM computations [84%] * HMM computations [85%] * HMM computations [86%] * HMM computations [87%] * HMM computations [88%] * HMM computations [89%] * HMM computations [90%] * HMM computations [91%] * HMM computations [92%] * HMM computations [93%] * HMM computations [94%] * HMM computations [95%] * HMM computations [96%] * HMM computations [97%] * HMM computations [98%] * HMM computations [99%] * HMM computations [100%] * HMM computations [K=393.945+/-110.406 / W=2.25Mb] (14.56s) 423s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 423s * HAP update (0.02s) 423s * H2V transpose (0.01s) 423s 423s Main iteration [3/5] 423s * V2H transpose (0.01s) 423s * PBWT 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computations [65%] * HMM computations [66%] * HMM computations [67%] * HMM computations [68%] * HMM computations [69%] * HMM computations [70%] * HMM computations [71%] * HMM computations [72%] * HMM computations [73%] * HMM computations [74%] * HMM computations [75%] * HMM computations [76%] * HMM computations [77%] * HMM computations [78%] * HMM computations [79%] * HMM computations [80%] * HMM computations [81%] * HMM computations [82%] * HMM computations [83%] * HMM computations [84%] * HMM computations [85%] * HMM computations [86%] * HMM computations [87%] * HMM computations [88%] * HMM computations [89%] * HMM computations [90%] * HMM computations [91%] * HMM computations [92%] * HMM computations [93%] * HMM computations [94%] * HMM computations [95%] * HMM computations [96%] * HMM computations [97%] * HMM computations [98%] * HMM computations [99%] * HMM computations [100%] * HMM computations [K=391.741+/-111.011 / W=2.26Mb] (13.38s) 436s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 436s * HAP update (0.02s) 436s * H2V transpose (0.01s) 436s 436s Main iteration [4/5] 436s * V2H transpose (0.01s) 436s * PBWT selection [0%] * PBWT selection [1%] * PBWT selection [2%] * PBWT selection [3%] * PBWT selection [4%] * PBWT selection [5%] * PBWT selection [6%] * PBWT selection [7%] * PBWT selection [8%] * PBWT selection [9%] * PBWT selection [10%] * PBWT selection [11%] * PBWT selection [12%] * PBWT selection [13%] * PBWT selection [14%] * PBWT selection [15%] * PBWT selection [16%] * PBWT selection [17%] * PBWT selection [18%] * PBWT selection [19%] * PBWT selection [20%] * PBWT selection [21%] * PBWT selection [22%] * PBWT selection [23%] * PBWT selection [24%] * PBWT selection [25%] * PBWT selection [26%] * PBWT selection [27%] * PBWT selection [28%] * PBWT selection [29%] * PBWT selection [30%] * PBWT selection [31%] * PBWT selection [32%] * PBWT selection [33%] * PBWT selection [34%] * PBWT selection [35%] * PBWT selection [36%] * PBWT 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computations [19%] * HMM computations [20%] * HMM computations [21%] * HMM computations [22%] * HMM computations [23%] * HMM computations [24%] * HMM computations [25%] * HMM computations [26%] * HMM computations [27%] * HMM computations [28%] * HMM computations [29%] * HMM computations [30%] * HMM computations [31%] * HMM computations [32%] * HMM computations [33%] * HMM computations [34%] * HMM computations [35%] * HMM computations [36%] * HMM computations [37%] * HMM computations [38%] * HMM computations [39%] * HMM computations [40%] * HMM computations [41%] * HMM computations [42%] * HMM computations [43%] * HMM computations [44%] * HMM computations [45%] * HMM computations [46%] * HMM computations [47%] * HMM computations [48%] * HMM computations [49%] * HMM computations [50%] * HMM computations [51%] * HMM computations [52%] * HMM computations [53%] * HMM computations [54%] * HMM computations [55%] * HMM computations [56%] * HMM computations [57%] * HMM computations [58%] * HMM computations [59%] * HMM computations [60%] * HMM computations [61%] * HMM computations [62%] * HMM computations [63%] * HMM computations [64%] * HMM computations [65%] * HMM computations [66%] * HMM computations [67%] * HMM computations [68%] * HMM computations [69%] * HMM computations [70%] * HMM computations [71%] * HMM computations [72%] * HMM computations [73%] * HMM computations [74%] * HMM computations [75%] * HMM computations [76%] * HMM computations [77%] * HMM computations [78%] * HMM computations [79%] * HMM computations [80%] * HMM computations [81%] * HMM computations [82%] * HMM computations [83%] * HMM computations [84%] * HMM computations [85%] * HMM computations [86%] * HMM computations [87%] * HMM computations [88%] * HMM computations [89%] * HMM computations [90%] * HMM computations [91%] * HMM computations [92%] * HMM computations [93%] * HMM computations [94%] * HMM computations [95%] * HMM computations [96%] * HMM computations [97%] * HMM computations [98%] * HMM computations [99%] * HMM computations [100%] * HMM computations [K=392.536+/-110.913 / W=2.28Mb] (14.15s) 451s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 451s * HAP update (0.02s) 451s * H2V transpose (0.01s) 451s 451s Main iteration [5/5] 451s * V2H transpose (0.01s) 451s * PBWT selection [0%] * PBWT selection [1%] * PBWT selection [2%] * PBWT selection [3%] * PBWT selection [4%] * PBWT selection [5%] * PBWT selection [6%] * PBWT selection [7%] * PBWT selection [8%] * PBWT selection [9%] * PBWT selection [10%] * PBWT selection [11%] * PBWT selection [12%] * PBWT selection [13%] * PBWT selection [14%] * PBWT selection [15%] * PBWT selection [16%] * PBWT selection [17%] * PBWT selection [18%] * PBWT selection [19%] * PBWT selection [20%] * PBWT selection [21%] * PBWT selection [22%] * PBWT selection [23%] * PBWT selection [24%] * PBWT selection [25%] * PBWT selection [26%] * PBWT selection [27%] * PBWT selection [28%] * PBWT selection [29%] * PBWT selection [30%] * PBWT 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[74%] * PBWT selection [75%] * PBWT selection [76%] * PBWT selection [77%] * PBWT selection [78%] * PBWT selection [79%] * PBWT selection [80%] * PBWT selection [81%] * PBWT selection [82%] * PBWT selection [83%] * PBWT selection [84%] * PBWT selection [85%] * PBWT selection [86%] * PBWT selection [87%] * PBWT selection [88%] * PBWT selection [89%] * PBWT selection [90%] * PBWT selection [91%] * PBWT selection [92%] * PBWT selection [93%] * PBWT selection [94%] * PBWT selection [95%] * PBWT selection [96%] * PBWT selection [97%] * PBWT selection [98%] * PBWT selection [99%] * PBWT selection [100%] * PBWT selection (0.05s) 451s * C2H transpose (0.00s) 464s * HMM computations [0%] * HMM computations [1%] * HMM computations [2%] * HMM computations [3%] * HMM computations [4%] * HMM computations [5%] * HMM computations [6%] * HMM computations [7%] * HMM computations [8%] * HMM computations [9%] * HMM computations [10%] * HMM computations [11%] * HMM computations [12%] * HMM computations 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[53%] * HMM computations [54%] * HMM computations [55%] * HMM computations [56%] * HMM computations [57%] * HMM computations [58%] * HMM computations [59%] * HMM computations [60%] * HMM computations [61%] * HMM computations [62%] * HMM computations [63%] * HMM computations [64%] * HMM computations [65%] * HMM computations [66%] * HMM computations [67%] * HMM computations [68%] * HMM computations [69%] * HMM computations [70%] * HMM computations [71%] * HMM computations [72%] * HMM computations [73%] * HMM computations [74%] * HMM computations [75%] * HMM computations [76%] * HMM computations [77%] * HMM computations [78%] * HMM computations [79%] * HMM computations [80%] * HMM computations [81%] * HMM computations [82%] * HMM computations [83%] * HMM computations [84%] * HMM computations [85%] * HMM computations [86%] * HMM computations [87%] * HMM computations [88%] * HMM computations [89%] * HMM computations [90%] * HMM computations [91%] * HMM computations [92%] * HMM computations [93%] * HMM computations [94%] * HMM computations [95%] * HMM computations [96%] * HMM computations [97%] * HMM computations [98%] * HMM computations [99%] * HMM computations [100%] * HMM computations [K=370.038+/-105.131 / W=2.09Mb] (12.99s) 464s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 464s * HAP update (0.02s) 464s * H2V transpose (0.01s) 464s 464s Finalization: 464s * HAP solving (0.03s) 464s * HAP update (0.02s) 464s * H2V transpose (0.01s) 464s * VCF writing [0%] * VCF writing [1%] * VCF writing [2%] * VCF writing [3%] * VCF writing [4%] * VCF writing [5%] * VCF writing [6%] * VCF writing [7%] * VCF writing [8%] * VCF writing [9%] * VCF writing [10%] * VCF writing [11%] * VCF writing [12%] * VCF writing [13%] * VCF writing [14%] * VCF writing [15%] * VCF writing [16%] * VCF writing [17%] * VCF writing [18%] * VCF writing [19%] * VCF writing [20%] * VCF writing [21%] * VCF writing [22%] * VCF writing [23%] * VCF writing [24%] * VCF writing [25%] * VCF writing [26%] * VCF writing [27%] * VCF writing [28%] * VCF writing [29%] * VCF writing [30%] * VCF writing [31%] * VCF writing [32%] * VCF writing [33%] * VCF writing [34%] * VCF writing [35%] * VCF writing [36%] * VCF writing [37%] * VCF writing [38%] * VCF writing [39%] * VCF writing [40%] * VCF writing [41%] * VCF writing [42%] * VCF writing [43%] * VCF writing [44%] * VCF writing [45%] * VCF writing [46%] * VCF writing [47%] * VCF writing [48%] * VCF writing [49%] * VCF writing [50%] * VCF writing [51%] * VCF writing [52%] * VCF writing [53%] * VCF writing [54%] * VCF writing [55%] * VCF writing [56%] * VCF writing [57%] * VCF writing [58%] * VCF writing [59%] * VCF writing [60%] * VCF writing [61%] * VCF writing [62%] * VCF writing [63%] * VCF writing [64%] * VCF writing [65%] * VCF writing [66%] * VCF writing [67%] * VCF writing [68%] * VCF writing [69%] * VCF writing [70%] * VCF writing [71%] * VCF writing [72%] * VCF writing [73%] * VCF writing [74%] * VCF writing [75%] * VCF writing [76%] * VCF writing [77%] * VCF writing [78%] * VCF writing [79%] * VCF writing [80%] * VCF writing [81%] * VCF writing [82%] * VCF writing [83%] * VCF writing [84%] * VCF writing [85%] * VCF writing [86%] * VCF writing [87%] * VCF writing [88%] * VCF writing [89%] * VCF writing [90%] * VCF writing [91%] * VCF writing [92%] * VCF writing [93%] * VCF writing [94%] * VCF writing [95%] * VCF writing [96%] * VCF writing [97%] * VCF writing [98%] * VCF writing [99%] * VCF writing [100%] * BCF writing [Compressed / N=203 / L=24990] (0.17s) 464s * Total running time = 233 seconds 464s autopkgtest [23:17:06]: test run-sample-analysis: -----------------------] 464s autopkgtest [23:17:06]: test run-sample-analysis: - - - - - - - - - - results - - - - - - - - - - 464s run-sample-analysis PASS 465s autopkgtest [23:17:07]: @@@@@@@@@@@@@@@@@@@@ summary 465s run-sample-analysis PASS 480s nova [W] Skipping flock for amd64 480s Creating nova instance adt-plucky-amd64-shapeit4-20250315-230922-juju-7f2275-prod-proposed-migration-environment-2-6bc67f96-e716-4c85-b102-002d9fb291f2 from image adt/ubuntu-plucky-amd64-server-20250306.img (UUID 60d877d7-b74c-4f24-920d-f4570db0a338)... 480s nova [W] Timed out waiting for 570981c6-a63b-47ca-9ecc-4b6c544f93b3 to get deleted.