0s autopkgtest [15:03:05]: starting date and time: 2025-03-15 15:03:05+0000 0s autopkgtest [15:03:05]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [15:03:05]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.aiyv61u6/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade qtltools --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-15@bos03-arm64-43.secgroup --name adt-plucky-arm64-qtltools-20250315-150305-juju-7f2275-prod-proposed-migration-environment-15-30b27a1f-ef10-4de2-8773-d81509b53501 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --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/ 163s autopkgtest [15:05:48]: testbed dpkg architecture: arm64 164s autopkgtest [15:05:49]: testbed apt version: 2.9.33 164s autopkgtest [15:05:49]: @@@@@@@@@@@@@@@@@@@@ test bed setup 164s autopkgtest [15:05:49]: testbed release detected to be: None 165s autopkgtest [15:05:50]: updating testbed package index (apt update) 165s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 166s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 166s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 166s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 166s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 166s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 166s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 167s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [78.2 kB] 167s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1976 B] 167s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 167s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [346 kB] 167s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [15.8 kB] 167s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 167s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [572 B] 167s Fetched 1094 kB in 2s (550 kB/s) 168s Reading package lists... 169s + lsb_release --codename --short 169s + RELEASE=plucky 169s + cat 169s + [ plucky != trusty ] 169s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 169s Reading package lists... 169s Building dependency tree... 169s Reading state information... 170s Calculating upgrade... 170s Calculating upgrade... 170s The following packages will be upgraded: 170s python3-jinja2 strace 170s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 170s Need to get 608 kB of archives. 170s After this operation, 11.3 kB of additional disk space will be used. 170s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 171s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 172s Fetched 608 kB in 1s (573 kB/s) 172s (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 ... 117701 files and directories currently installed.) 172s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 172s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 172s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 172s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 172s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 172s Setting up strace (6.13+ds-1ubuntu1) ... 172s Processing triggers for man-db (2.13.0-1) ... 173s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 173s + /usr/lib/apt/apt-helper analyze-pattern ?true 173s + uname -r 173s + sed s/\./\\./g 173s + running_kernel_pattern=^linux-.*6\.14\.0-10-generic.* 173s + apt list ?obsolete+ + 173s tail -n+2 173s grep -v+ ^linux-.*6\.14\.0-10-generic.*cut -d/ -f1 173s 173s + obsolete_pkgs=linux-headers-6.11.0-8-generic 173s linux-headers-6.11.0-8 173s linux-image-6.11.0-8-generic 173s linux-modules-6.11.0-8-generic 173s linux-tools-6.11.0-8-generic 173s linux-tools-6.11.0-8 173s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove linux-headers-6.11.0-8-generic linux-headers-6.11.0-8 linux-image-6.11.0-8-generic linux-modules-6.11.0-8-generic linux-tools-6.11.0-8-generic linux-tools-6.11.0-8 173s Reading package lists... 174s Building dependency tree... 174s Reading state information... 174s Solving dependencies... 174s The following packages will be REMOVED: 174s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 174s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 174s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 174s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 175s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 175s After this operation, 267 MB disk space will be freed. 175s (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 ... 117701 files and directories currently installed.) 175s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 175s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 175s Removing libpython3.12t64:arm64 (3.12.9-1) ... 175s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 175s Removing libnsl2:arm64 (1.3.0-3build3) ... 175s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 175s Removing libunwind8:arm64 (1.6.2-3.1) ... 175s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 176s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 177s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 177s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 177s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 177s /etc/kernel/postrm.d/initramfs-tools: 177s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 177s /etc/kernel/postrm.d/zz-flash-kernel: 177s flash-kernel: Kernel 6.11.0-8-generic has been removed. 177s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 178s /etc/kernel/postrm.d/zz-update-grub: 178s Sourcing file `/etc/default/grub' 178s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 178s Generating grub configuration file ... 178s Found linux image: /boot/vmlinuz-6.14.0-10-generic 178s Found initrd image: /boot/initrd.img-6.14.0-10-generic 178s Warning: os-prober will not be executed to detect other bootable partitions. 178s Systems on them will not be added to the GRUB boot configuration. 178s Check GRUB_DISABLE_OS_PROBER documentation entry. 178s Adding boot menu entry for UEFI Firmware Settings ... 178s done 178s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 179s Processing triggers for libc-bin (2.41-1ubuntu1) ... 179s (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 ... 81650 files and directories currently installed.) 179s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 179s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 179s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 179s + grep -q trusty /etc/lsb-release 179s + [ ! -d /usr/share/doc/unattended-upgrades ] 179s + [ ! -d /usr/share/doc/lxd ] 179s + [ ! -d /usr/share/doc/lxd-client ] 179s + [ ! -d /usr/share/doc/snapd ] 179s + type iptables 179s + cat 179s + chmod 755 /etc/rc.local 179s + . /etc/rc.local 179s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 179s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 179s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 179s + uname -m 179s + [ aarch64 = ppc64le ] 179s + [ -d /run/systemd/system ] 179s + systemd-detect-virt --quiet --vm 179s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 179s + cat 179s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 179s + echo COMPRESS=lz4 179s autopkgtest [15:06:04]: upgrading testbed (apt dist-upgrade and autopurge) 179s Reading package lists... 179s Building dependency tree... 179s Reading state information... 180s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 180s Starting 2 pkgProblemResolver with broken count: 0 180s Done 181s Entering ResolveByKeep 181s 181s Calculating upgrade... 182s The following packages will be upgraded: 182s libc-bin libc-dev-bin libc6 libc6-dev locales 182s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 182s Need to get 9530 kB of archives. 182s After this operation, 0 B of additional disk space will be used. 182s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 184s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 184s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 188s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 189s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 194s Preconfiguring packages ... 195s Fetched 9530 kB in 12s (781 kB/s) 195s (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 ... 81647 files and directories currently installed.) 195s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 195s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 195s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 195s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 195s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 195s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 195s Setting up libc6:arm64 (2.41-1ubuntu2) ... 196s (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 ... 81647 files and directories currently installed.) 196s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 196s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 196s Setting up libc-bin (2.41-1ubuntu2) ... 196s (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 ... 81647 files and directories currently installed.) 196s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 196s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 196s Setting up locales (2.41-1ubuntu2) ... 197s Generating locales (this might take a while)... 198s en_US.UTF-8... done 198s Generation complete. 198s Setting up libc-dev-bin (2.41-1ubuntu2) ... 198s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 198s Processing triggers for man-db (2.13.0-1) ... 199s Processing triggers for systemd (257.3-1ubuntu3) ... 200s Reading package lists... 201s Building dependency tree... 201s Reading state information... 201s Starting pkgProblemResolver with broken count: 0 201s Starting 2 pkgProblemResolver with broken count: 0 201s Done 201s Solving dependencies... 202s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 202s autopkgtest [15:06:27]: rebooting testbed after setup commands that affected boot 225s autopkgtest [15:06:50]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 228s autopkgtest [15:06:53]: @@@@@@@@@@@@@@@@@@@@ apt-source qtltools 251s Get:1 http://ftpmaster.internal/ubuntu plucky/universe qtltools 1.3.1+dfsg-4build4 (dsc) [2293 B] 251s Get:2 http://ftpmaster.internal/ubuntu plucky/universe qtltools 1.3.1+dfsg-4build4 (tar) [141 kB] 251s Get:3 http://ftpmaster.internal/ubuntu plucky/universe qtltools 1.3.1+dfsg-4build4 (diff) [13.6 MB] 252s gpgv: Signature made Tue Jul 30 08:32:15 2024 UTC 252s gpgv: using RSA key 92978A6E195E4921825F7FF0F34F09744E9F5DD9 252s gpgv: Can't check signature: No public key 252s dpkg-source: warning: cannot verify inline signature for ./qtltools_1.3.1+dfsg-4build4.dsc: no acceptable signature found 252s autopkgtest [15:07:17]: testing package qtltools version 1.3.1+dfsg-4build4 253s autopkgtest [15:07:18]: build not needed 256s autopkgtest [15:07:21]: test run-sample-analysis: preparing testbed 256s Reading package lists... 257s Building dependency tree... 257s Reading state information... 257s Starting pkgProblemResolver with broken count: 0 257s Starting 2 pkgProblemResolver with broken count: 0 257s Done 258s The following NEW packages will be installed: 258s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 258s libboost-iostreams1.83.0 libboost-program-options1.83.0 libcairo2 libdatrie1 258s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 libgsl28 258s libgslcblas0 libharfbuzz0b libhts3t64 libhtscodecs2 libice6 libjbig0 258s libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0 258s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 258s libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 258s libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 258s qtltools qtltools-example r-base-core r-mathlib unzip x11-common xdg-utils 258s zip 258s 0 upgraded, 53 newly installed, 0 to remove and 0 not upgraded. 258s Need to get 57.3 MB of archives. 258s After this operation, 108 MB of additional disk space will be used. 258s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 259s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 260s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2ubuntu1 [37.5 kB] 260s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2ubuntu1 [144 kB] 260s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-2ubuntu1 [191 kB] 260s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 260s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libboost-iostreams1.83.0 arm64 1.83.0-4.1ubuntu2 [259 kB] 260s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libboost-program-options1.83.0 arm64 1.83.0-4.1ubuntu2 [319 kB] 261s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 261s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 261s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 261s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 261s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 262s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB] 262s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 262s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB] 262s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB] 262s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 262s Get:19 http://ftpmaster.internal/ubuntu plucky/universe arm64 libgslcblas0 arm64 2.8+dfsg-5 [87.3 kB] 262s Get:20 http://ftpmaster.internal/ubuntu plucky/universe arm64 libgsl28 arm64 2.8+dfsg-5 [983 kB] 263s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 264s Get:22 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.1-2 [82.7 kB] 264s Get:23 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts3t64 arm64 1.21+ds-1 [441 kB] 264s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 265s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB] 265s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 265s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 265s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 267s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 268s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB] 268s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB] 268s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.56.2-1 [237 kB] 268s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.56.2-1 [49.5 kB] 268s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.56.2-1 [27.6 kB] 268s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper2 arm64 2.2.5-0.3 [17.3 kB] 268s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper-utils arm64 2.2.5-0.3 [15.4 kB] 268s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 268s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB] 268s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 269s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 269s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 270s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 270s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 270s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 270s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 271s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB] 271s Get:47 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-mathlib arm64 4.4.3-1 [2537 kB] 273s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 zip arm64 3.0-14ubuntu2 [173 kB] 273s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 unzip arm64 6.0-28ubuntu6 [178 kB] 274s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 274s Get:51 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-core arm64 4.4.3-1 [28.4 MB] 303s Get:52 http://ftpmaster.internal/ubuntu plucky/universe arm64 qtltools arm64 1.3.1+dfsg-4build4 [673 kB] 304s Get:53 http://ftpmaster.internal/ubuntu plucky/universe arm64 qtltools-example all 1.3.1+dfsg-4build4 [13.6 MB] 318s Preconfiguring packages ... 318s Fetched 57.3 MB in 60s (953 kB/s) 318s Selecting previously unselected package fonts-dejavu-mono. 319s (Reading database ... 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libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 322s Setting up libsm6:arm64 (2:1.2.4-1) ... 322s Setting up fontconfig (2.15.0-2ubuntu1) ... 324s Regenerating fonts cache... done. 324s Setting up libxft2:arm64 (2.3.6-1build1) ... 324s Setting up libtk8.6:arm64 (8.6.16-1) ... 324s Setting up libpango-1.0-0:arm64 (1.56.2-1) ... 324s Setting up libcairo2:arm64 (1.18.2-2) ... 324s Setting up libxt6t64:arm64 (1:1.2.1-1.2build1) ... 324s Setting up libpangoft2-1.0-0:arm64 (1.56.2-1) ... 324s Setting up libpangocairo-1.0-0:arm64 (1.56.2-1) ... 324s Setting up r-base-core (4.4.3-1) ... 324s Creating config file /etc/R/Renviron with new version 325s Setting up qtltools (1.3.1+dfsg-4build4) ... 325s Processing triggers for man-db (2.13.0-1) ... 326s Processing triggers for install-info (7.1.1-1) ... 326s Processing triggers for libc-bin (2.41-1ubuntu2) ... 327s autopkgtest [15:08:32]: test run-sample-analysis: [----------------------- 327s ./genes.50percent.chr22.bed.gz 328s ./genes.50percent.chr22.bed.gz.tbi 328s ./genes.covariates.pc50.txt.gz 328s ./genes.simulated.chr22.bed.gz 328s ./genes.simulated.chr22.bed.gz.tbi 328s ./genotypes.chr22.vcf.gz 328s ./genotypes.chr22.vcf.gz.tbi 328s 328s QTLtools 328s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 328s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 328s * Webpage : https://qtltools.github.io/qtltools/ 328s * Version : 1.3.1 328s * Date : 15/03/2025 - 15:08:33 328s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 328s 328s CONDUCT PCA ON DATA 328s 328s Initialize random number generator 328s * Built-in seed is 15112011 328s * First Integer = 30553 328s * First Double = 0.0126695 328s 328s Reading sample list from [genes.50percent.chr22.bed.gz] 328s * #samples = 358 328s 328s Merging sample sets from all input files 328s * #files = 1 328s * #samples in all files = 358 328s 328s Reading phenotype data in [genes.50percent.chr22.bed.gz] 328s * 358 samples included 328s * 608 phenotypes included 328s 328s Calculating PCA with a matrix 358 x 608 328s * Calculated mean and sd 328s * 0 sd==0 columns removed 328s * Variables centered 328s * Variables scaled to unit variance 328s * Running SVD 329s * SVD complete 329s * Calculated sd and var for PCs 329s * Calculated cumulative var for PCs 329s * Done! 329s 329s Running time: 0 seconds 329s 329s QTLtools 329s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 329s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 329s * Webpage : https://qtltools.github.io/qtltools/ 329s * Version : 1.3.1 329s * Date : 15/03/2025 - 15:08:34 329s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 329s 329s MAPPING QTL IN CIS 329s * TASK: Report all nominal associations with p <= 0.01 329s * Linear model: Phe ~ Var + Cov 329s * Cis-window size is 1000000 bp 329s * Region = [chr22:17000000-18000000] 329s 329s Initialize random number generator 329s * Built-in seed is 15112011 329s * First Integer = 30553 329s * First Double = 0.0126695 329s 329s Reading sample list from [genes.50percent.chr22.bed.gz] 329s * #samples = 358 329s 329s Read sample list from [genotypes.chr22.vcf.gz] 329s * #samples = 358 329s 329s Reading sample list from [genes.covariates.pc50.txt.gz] 329s * #samples = 358 329s 329s Merging sample sets from all input files 329s * #files = 3 329s * #samples in all files = 358 329s 329s Reading phenotype data in [genes.50percent.chr22.bed.gz] 329s * target region [chr22:17000000-18000000] 329s * 8 phenotypes included 329s * 3 phenotypes are on the negative strand 329s 329s Reading genotype data in [genotypes.chr22.vcf.gz] 329s * File format detected: VCF 329s * target region [chr22:16000000-19000000] 329s * 6404 variants included 329s 329s Reading covariates in [genes.covariates.pc50.txt.gz] 329s * 53 covariates included 329s 329s Residualize phenotypes for covariates 329s * #covariates = 53 329s 329s Processing phenotype [ENSG00000237438.2] [1/8] 329s * #variants in cis = 5095 329s * Best hit: [id=22_17542810, d=25350, pv=1.1864e-25, s=-0.7518] 329s 329s Processing phenotype [ENSG00000273203.1] [2/8] 329s * #variants in cis = 5170 329s * Best hit: [id=22_17517388, d=-31323, pv=5.86611e-06, s=-0.1406] 329s 329s Processing phenotype [ENSG00000273442.1] [3/8] 329s * #variants in cis = 5188 329s * Best hit: [id=22_17553526, d=-8065, pv=0.000244522, s=0.1340] 329s 329s Processing phenotype [ENSG00000177663.9] [4/8] 329s * #variants in cis = 5193 329s * Best hit: [id=22_17513703, d=-52141, pv=8.03358e-14, s=-0.2096] 329s 329s Processing phenotype [ENSG00000183307.3] [5/8] 329s * #variants in cis = 5230 329s * Best hit: [id=22_17587975, d=14282, pv=1.56789e-07, s=-0.0078] 329s 329s Processing phenotype [ENSG00000069998.8] [6/8] 329s * #variants in cis = 5291 329s * Best hit: [id=22_17620429, d=25748, pv=1.37287e-14, s=-1.5147] 329s 329s Processing phenotype [ENSG00000093072.11] [7/8] 329s * #variants in cis = 5293 329s * Best hit: [id=22_17699630, d=3249, pv=0.000578649, s=0.6404] 329s 329s Processing phenotype [ENSG00000099954.14] [8/8] 329s * #variants in cis = 5435 329s * Best hit: [id=22_17175937, d=-664900, pv=0.000866455, s=0.0067] 329s 329s Running time: 0 seconds 329s 329s QTLtools 329s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 329s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 329s * Webpage : https://qtltools.github.io/qtltools/ 329s * Version : 1.3.1 329s * Date : 15/03/2025 - 15:08:34 329s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 329s 329s MAPPING QTL IN CIS 329s * TASK: Perform 1000 permutations 329s * Linear model: Phe ~ Var + Cov 329s * Cis-window size is 1000000 bp 329s * Region = [chr22:17000000-18000000] 329s 329s Initialize random number generator 329s * Built-in seed is 15112011 329s * First Integer = 30553 329s * First Double = 0.0126695 329s 329s Reading sample list from [genes.50percent.chr22.bed.gz] 329s * #samples = 358 329s 329s Read sample list from [genotypes.chr22.vcf.gz] 329s * #samples = 358 329s 329s Reading sample list from [genes.covariates.pc50.txt.gz] 329s * #samples = 358 329s 329s Merging sample sets from all input files 329s * #files = 3 329s * #samples in all files = 358 329s 329s Reading phenotype data in [genes.50percent.chr22.bed.gz] 329s * target region [chr22:17000000-18000000] 329s * 8 phenotypes included 329s * 3 phenotypes are on the negative strand 329s 329s Reading genotype data in [genotypes.chr22.vcf.gz] 329s * File format detected: VCF 329s * target region [chr22:16000000-19000000] 329s * 6404 variants included 329s 329s Reading covariates in [genes.covariates.pc50.txt.gz] 329s * 53 covariates included 329s 329s Residualize phenotypes for covariates 329s * #covariates = 53 329s 329s Processing phenotype [ENSG00000237438.2] [1/8] 329s * #variants in cis = 5095 330s * Best hit: [id=22_17542810, d=25350, pv=1.1864e-25, s=-0.7518] 330s * Beta parameters: [s1=1.00995, s2=621.053] 330s * Adjusted p-values: [emp=0.000999001, beta=1.28062e-20] 330s 330s Processing phenotype [ENSG00000273203.1] [2/8] 330s * #variants in cis = 5170 330s * Best hit: [id=22_17517388, d=-31323, pv=5.86611e-06, s=-0.1406] 330s * Beta parameters: [s1=1.11817, s2=641.379] 330s * Adjusted p-values: [emp=0.00799201, beta=0.00751892] 330s 330s Processing phenotype [ENSG00000273442.1] [3/8] 330s * #variants in cis = 5188 331s * Best hit: [id=22_17553526, d=-8065, pv=0.000244522, s=0.1340] 331s * Beta parameters: [s1=1.08364, s2=467.63] 331s * Adjusted p-values: [emp=0.297702, beta=0.293948] 331s 331s Processing phenotype [ENSG00000177663.9] [4/8] 331s * #variants in cis = 5193 332s * Best hit: [id=22_17513703, d=-52141, pv=8.03358e-14, s=-0.2096] 332s * Beta parameters: [s1=0.989061, s2=704.553] 332s * Adjusted p-values: [emp=0.000999001, beta=7.91291e-10] 332s 332s Processing phenotype [ENSG00000183307.3] [5/8] 332s * #variants in cis = 5230 332s * Best hit: [id=22_17587975, d=14282, pv=1.56789e-07, s=-0.0078] 332s * Beta parameters: [s1=1.01322, s2=559.49] 332s * Adjusted p-values: [emp=0.000999001, beta=0.00050707] 332s 332s Processing phenotype [ENSG00000069998.8] [6/8] 332s * #variants in cis = 5291 333s * Best hit: [id=22_17620429, d=25748, pv=1.37287e-14, s=-1.5147] 333s * Beta parameters: [s1=1.02312, s2=563.339] 333s * Adjusted p-values: [emp=0.000999001, beta=2.56935e-10] 333s 333s Processing phenotype [ENSG00000093072.11] [7/8] 333s * #variants in cis = 5293 334s * Best hit: [id=22_17699630, d=3249, pv=0.000578649, s=0.6404] 334s * Beta parameters: [s1=0.957514, s2=559.397] 334s * Adjusted p-values: [emp=0.574426, beta=0.562826] 334s 334s Processing phenotype [ENSG00000099954.14] [8/8] 334s * #variants in cis = 5435 334s * Best hit: [id=22_17175937, d=-664900, pv=0.000866455, s=0.0067] 334s * Beta parameters: [s1=0.938041, s2=226.852] 334s * Adjusted p-values: [emp=0.842158, beta=0.84836] 334s 334s Running time: 5 seconds 334s 334s QTLtools 334s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 334s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 334s * Webpage : https://qtltools.github.io/qtltools/ 334s * Version : 1.3.1 334s * Date : 15/03/2025 - 15:08:39 334s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 334s 334s MAPPING QTL IN TRANS 334s * TASK: Perform a full nominal pass, do not adjust p-values 334s * Cis-window size is 5000000 bp 334s * #bins = 1000 334s * threshold = 1e-05 334s 334s Initialize random number generator 334s * Built-in seed is 15112011 334s * First Integer = 30553 334s * First Double = 0.0126695 334s 334s Read sample list from [genotypes.chr22.vcf.gz] 334s * #samples = 358 334s 334s Checking sample list in [genes.simulated.chr22.bed.gz] 334s * #samples = 358 334s 334s Reading phenotype data in [genes.simulated.chr22.bed.gz] from line 0 to 0 334s * 358 samples included 334s * 608 phenotypes included 334s * 275 phenotypes is on the negative strand 334s 334s Calculate correlation threshold 334s * thres = 1e-05 334s * corr = 0.2311 334s 334s Sweep through genotype data in [genotypes.chr22.vcf.gz] 335s * #variants=1950 #multi_allelic=0 #not_processed=0 #hits=101/1000000 speed=6.45MT/s 335s * #variants=4001 #multi_allelic=0 #not_processed=0 #hits=153/2000000 speed=6.41MT/s 335s * #variants=6187 #multi_allelic=0 #not_processed=0 #hits=244/3000000 speed=6.29MT/s 335s * #variants=8537 #multi_allelic=0 #not_processed=0 #hits=285/4000000 speed=6.21MT/s 335s * #variants=11025 #multi_allelic=0 #not_processed=0 #hits=312/5000000 speed=6.13MT/s 336s * #variants=13621 #multi_allelic=0 #not_processed=0 #hits=320/6000000 speed=6.17MT/s 336s * #variants=16217 #multi_allelic=0 #not_processed=0 #hits=342/7000000 speed=6.17MT/s 336s * #variants=18755 #multi_allelic=0 #not_processed=0 #hits=401/8000000 speed=6.13MT/s 336s * #variants=21237 #multi_allelic=0 #not_processed=0 #hits=402/9000000 speed=6.21MT/s 336s * #variants=23680 #multi_allelic=0 #not_processed=0 #hits=455/10000000 speed=6.13MT/s 336s * #variants=26171 #multi_allelic=0 #not_processed=0 #hits=463/11000000 speed=6.17MT/s 336s * #variants=28609 #multi_allelic=0 #not_processed=0 #hits=469/12000000 speed=6.17MT/s 337s * #variants=30861 #multi_allelic=0 #not_processed=0 #hits=973/13000000 speed=6.06MT/s 337s * #variants=32932 #multi_allelic=0 #not_processed=0 #hits=979/14000000 speed=6.45MT/s 337s * #variants=34974 #multi_allelic=0 #not_processed=0 #hits=1085/15000000 speed=6.41MT/s 337s * #variants=37021 #multi_allelic=0 #not_processed=0 #hits=1086/16000000 speed=6.49MT/s 337s * #variants=39122 #multi_allelic=0 #not_processed=0 #hits=1089/17000000 speed=6.41MT/s 337s * #variants=41334 #multi_allelic=0 #not_processed=0 #hits=1089/18000000 speed=6.33MT/s 338s * #variants=43627 #multi_allelic=0 #not_processed=0 #hits=1096/19000000 speed=6.29MT/s 338s * #variants=45897 #multi_allelic=0 #not_processed=0 #hits=1153/20000000 speed=6.25MT/s 338s * #variants=48114 #multi_allelic=0 #not_processed=0 #hits=1243/21000000 speed=6.21MT/s 338s * #variants=50410 #multi_allelic=0 #not_processed=0 #hits=1249/22000000 speed=6.17MT/s 338s * #variants=52820 #multi_allelic=0 #not_processed=0 #hits=1259/23000000 speed=6.06MT/s 338s * #variants=55279 #multi_allelic=0 #not_processed=0 #hits=1498/24000000 speed=5.92MT/s 339s * #variants=57789 #multi_allelic=0 #not_processed=0 #hits=1724/25000000 speed=5.85MT/s 339s * #variants=60201 #multi_allelic=0 #not_processed=0 #hits=2168/26000000 speed=5.92MT/s 339s * #variants=62476 #multi_allelic=0 #not_processed=0 #hits=2452/27000000 speed=6.10MT/s 339s * #variants=64608 #multi_allelic=0 #not_processed=0 #hits=2544/28000000 speed=6.29MT/s 339s * #variants=66709 #multi_allelic=0 #not_processed=0 #hits=2684/29000000 speed=5.95MT/s 339s * #variants=68871 #multi_allelic=0 #not_processed=0 #hits=2688/30000000 speed=6.29MT/s 339s * #variants=71070 #multi_allelic=0 #not_processed=0 #hits=2720/31000000 speed=6.21MT/s 340s * #variants=73151 #multi_allelic=0 #not_processed=0 #hits=2891/32000000 speed=5.92MT/s 340s * #variants=75122 #multi_allelic=0 #not_processed=0 #hits=3110/33000000 speed=6.33MT/s 340s * #variants=77058 #multi_allelic=0 #not_processed=0 #hits=3209/34000000 speed=6.45MT/s 340s * #variants=78989 #multi_allelic=0 #not_processed=0 #hits=3218/35000000 speed=6.17MT/s 340s * #variants=80903 #multi_allelic=0 #not_processed=0 #hits=3250/36000000 speed=6.49MT/s 340s * #variants=82811 #multi_allelic=0 #not_processed=0 #hits=3463/37000000 speed=6.17MT/s 341s * #variants=84694 #multi_allelic=0 #not_processed=0 #hits=4035/38000000 speed=6.29MT/s 341s * #variants=85485 #multi_allelic=0 #not_processed=0 #hits=4036/38425275 speed=6.64MT/s 341s 341s Running time: 6 seconds 341s 341s QTLtools 341s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 341s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 341s * Webpage : https://qtltools.github.io/qtltools/ 341s * Version : 1.3.1 341s * Date : 15/03/2025 - 15:08:46 341s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 341s 341s MAPPING QTL IN TRANS 341s * TASK: Permute randomly chosen phenotypes 1000 times and test 341s * Cis-window size is 5000000 bp 341s * #bins = 1000 341s * threshold = 1e-05 341s 341s Initialize random number generator 341s * Built-in seed is 15112011 341s * First Integer = 30553 341s * First Double = 0.0126695 341s 341s Read sample list from [genotypes.chr22.vcf.gz] 341s * #samples = 358 341s 341s Checking sample list in [genes.simulated.chr22.bed.gz] 341s * #samples = 358 341s 341s Reading phenotype data in [genes.simulated.chr22.bed.gz] from line 0 to 0 341s * 358 samples included 341s * 608 phenotypes included 341s * 275 phenotypes is on the negative strand 341s 341s Normal transform phenotypes 341s 341s Calculate correlation threshold 341s * thres = 1e-05 341s * corr = 0.2311 341s 341s Sweep through genotype data in [genotypes.chr22.vcf.gz] 341s * #variants=1177 #multi_allelic=0 #not_processed=0 #hits=28/1000000 speed=6.71MT/s 341s * #variants=2383 #multi_allelic=0 #not_processed=0 #hits=38/2000000 speed=6.71MT/s 341s * #variants=3633 #multi_allelic=0 #not_processed=0 #hits=53/3000000 speed=6.58MT/s 341s * #variants=4928 #multi_allelic=0 #not_processed=0 #hits=53/4000000 speed=6.54MT/s 342s * #variants=6269 #multi_allelic=0 #not_processed=0 #hits=71/5000000 speed=6.41MT/s 342s * #variants=7675 #multi_allelic=0 #not_processed=0 #hits=72/6000000 speed=6.33MT/s 342s * #variants=9151 #multi_allelic=0 #not_processed=0 #hits=88/7000000 speed=6.10MT/s 342s * #variants=10663 #multi_allelic=0 #not_processed=0 #hits=96/8000000 speed=6.06MT/s 342s * #variants=12202 #multi_allelic=0 #not_processed=0 #hits=96/9000000 speed=6.06MT/s 342s * #variants=13804 #multi_allelic=0 #not_processed=0 #hits=96/10000000 speed=5.99MT/s 343s * #variants=15381 #multi_allelic=0 #not_processed=0 #hits=120/11000000 speed=5.95MT/s 343s * #variants=16946 #multi_allelic=0 #not_processed=0 #hits=123/12000000 speed=5.99MT/s 343s * #variants=18483 #multi_allelic=0 #not_processed=0 #hits=129/13000000 speed=6.06MT/s 343s * #variants=19995 #multi_allelic=0 #not_processed=0 #hits=131/14000000 speed=6.10MT/s 343s * #variants=21489 #multi_allelic=0 #not_processed=0 #hits=132/15000000 speed=6.10MT/s 343s * #variants=22947 #multi_allelic=0 #not_processed=0 #hits=151/16000000 speed=6.17MT/s 344s * #variants=24445 #multi_allelic=0 #not_processed=0 #hits=168/17000000 speed=6.02MT/s 344s * #variants=25965 #multi_allelic=0 #not_processed=0 #hits=175/18000000 speed=6.13MT/s 344s * #variants=27472 #multi_allelic=0 #not_processed=0 #hits=179/19000000 speed=6.17MT/s 344s * #variants=28933 #multi_allelic=0 #not_processed=0 #hits=181/20000000 speed=6.21MT/s 344s * #variants=30325 #multi_allelic=0 #not_processed=0 #hits=181/21000000 speed=6.33MT/s 344s * #variants=31617 #multi_allelic=0 #not_processed=0 #hits=182/22000000 speed=6.58MT/s 344s * #variants=32875 #multi_allelic=0 #not_processed=0 #hits=190/23000000 speed=6.67MT/s 345s * #variants=34127 #multi_allelic=0 #not_processed=0 #hits=192/24000000 speed=6.67MT/s 345s * #variants=35392 #multi_allelic=0 #not_processed=0 #hits=206/25000000 speed=6.58MT/s 345s * #variants=36652 #multi_allelic=0 #not_processed=0 #hits=206/26000000 speed=6.67MT/s 345s * #variants=37940 #multi_allelic=0 #not_processed=0 #hits=213/27000000 speed=6.58MT/s 345s * #variants=39255 #multi_allelic=0 #not_processed=0 #hits=238/28000000 speed=6.49MT/s 345s * #variants=40602 #multi_allelic=0 #not_processed=0 #hits=239/29000000 speed=6.49MT/s 346s * #variants=41998 #multi_allelic=0 #not_processed=0 #hits=245/30000000 speed=6.41MT/s 346s * #variants=43398 #multi_allelic=0 #not_processed=0 #hits=245/31000000 speed=6.45MT/s 346s * #variants=44803 #multi_allelic=0 #not_processed=0 #hits=260/32000000 speed=6.33MT/s 346s * #variants=46187 #multi_allelic=0 #not_processed=0 #hits=261/33000000 speed=6.41MT/s 346s * #variants=47545 #multi_allelic=0 #not_processed=0 #hits=268/34000000 speed=5.88MT/s 346s * #variants=48904 #multi_allelic=0 #not_processed=0 #hits=280/35000000 speed=6.41MT/s 347s * #variants=50309 #multi_allelic=0 #not_processed=0 #hits=306/36000000 speed=6.06MT/s 347s * #variants=51731 #multi_allelic=0 #not_processed=0 #hits=314/37000000 speed=5.99MT/s 347s * #variants=53171 #multi_allelic=0 #not_processed=0 #hits=320/38000000 speed=6.02MT/s 347s * #variants=54621 #multi_allelic=0 #not_processed=0 #hits=323/39000000 speed=6.02MT/s 347s * #variants=56099 #multi_allelic=0 #not_processed=0 #hits=323/40000000 speed=5.99MT/s 347s * #variants=57584 #multi_allelic=0 #not_processed=0 #hits=340/41000000 speed=5.99MT/s 348s * #variants=59032 #multi_allelic=0 #not_processed=0 #hits=344/42000000 speed=6.02MT/s 348s * #variants=60437 #multi_allelic=0 #not_processed=0 #hits=345/43000000 speed=6.21MT/s 348s * #variants=61810 #multi_allelic=0 #not_processed=0 #hits=357/44000000 speed=6.29MT/s 348s * #variants=63129 #multi_allelic=0 #not_processed=0 #hits=384/45000000 speed=6.41MT/s 348s * #variants=64409 #multi_allelic=0 #not_processed=0 #hits=391/46000000 speed=6.49MT/s 348s * #variants=65679 #multi_allelic=0 #not_processed=0 #hits=430/47000000 speed=6.41MT/s 348s * #variants=66953 #multi_allelic=0 #not_processed=0 #hits=436/48000000 speed=6.49MT/s 349s * #variants=68247 #multi_allelic=0 #not_processed=0 #hits=446/49000000 speed=6.45MT/s 349s * #variants=69595 #multi_allelic=0 #not_processed=0 #hits=460/50000000 speed=6.33MT/s 349s * #variants=70918 #multi_allelic=0 #not_processed=0 #hits=481/51000000 speed=6.37MT/s 349s * #variants=72211 #multi_allelic=0 #not_processed=0 #hits=492/52000000 speed=6.41MT/s 349s * #variants=73449 #multi_allelic=0 #not_processed=0 #hits=492/53000000 speed=6.54MT/s 349s * #variants=74662 #multi_allelic=0 #not_processed=0 #hits=500/54000000 speed=6.62MT/s 350s * #variants=75863 #multi_allelic=0 #not_processed=0 #hits=506/55000000 speed=6.62MT/s 350s * #variants=77058 #multi_allelic=0 #not_processed=0 #hits=513/56000000 speed=6.67MT/s 350s * #variants=78253 #multi_allelic=0 #not_processed=0 #hits=515/57000000 speed=6.67MT/s 350s * #variants=79446 #multi_allelic=0 #not_processed=0 #hits=530/58000000 speed=6.62MT/s 350s * #variants=80634 #multi_allelic=0 #not_processed=0 #hits=581/59000000 speed=6.67MT/s 350s * #variants=81817 #multi_allelic=0 #not_processed=0 #hits=594/60000000 speed=6.71MT/s 350s * #variants=82993 #multi_allelic=0 #not_processed=0 #hits=598/61000000 speed=6.71MT/s 351s * #variants=84160 #multi_allelic=0 #not_processed=0 #hits=599/62000000 speed=6.76MT/s 351s * #variants=85304 #multi_allelic=0 #not_processed=0 #hits=609/63000000 speed=6.80MT/s 351s * #variants=85485 #multi_allelic=0 #not_processed=0 #hits=609/63157827 speed=6.86MT/s 351s 351s Running time: 10 seconds 351s autopkgtest [15:08:56]: test run-sample-analysis: -----------------------] 352s run-sample-analysis PASS 352s autopkgtest [15:08:57]: test run-sample-analysis: - - - - - - - - - - results - - - - - - - - - - 352s autopkgtest [15:08:57]: @@@@@@@@@@@@@@@@@@@@ summary 352s run-sample-analysis PASS 357s nova [W] Using flock in prodstack6-arm64 357s flock: timeout while waiting to get lock 357s Creating nova instance adt-plucky-arm64-qtltools-20250315-150305-juju-7f2275-prod-proposed-migration-environment-15-30b27a1f-ef10-4de2-8773-d81509b53501 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 357s nova [W] Timed out waiting for c6ea3b95-0350-4f71-bd06-2fb2d3d1c599 to get deleted.