1s autopkgtest [17:39:09]: starting date and time: 2025-03-15 17:39:09+0000 1s autopkgtest [17:39:09]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 1s autopkgtest [17:39:09]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.aq6ymul9/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-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-s390x-22.secgroup --name adt-plucky-s390x-qtltools-20250315-173908-juju-7f2275-prod-proposed-migration-environment-2-77c03b9c-206c-46c5-95d8-5fa350f3ec39 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-s390x -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/ 130s autopkgtest [17:41:18]: testbed dpkg architecture: s390x 130s autopkgtest [17:41:18]: testbed apt version: 2.9.33 130s autopkgtest [17:41:18]: @@@@@@@@@@@@@@@@@@@@ test bed setup 130s autopkgtest [17:41:18]: testbed release detected to be: None 131s autopkgtest [17:41:19]: updating testbed package index (apt update) 132s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 132s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 132s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 132s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 132s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 132s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 132s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 132s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [113 kB] 132s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1824 B] 132s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 132s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [320 kB] 132s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [13.4 kB] 132s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3776 B] 132s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [240 B] 133s Fetched 1073 kB in 1s (1093 kB/s) 133s Reading package lists... 134s Reading package lists... 134s Building dependency tree... 134s Reading state information... 134s Calculating upgrade... 134s Calculating upgrade... 134s The following packages were automatically installed and are no longer required: 134s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 134s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 134s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 134s linux-tools-6.11.0-8-generic 134s Use 'sudo apt autoremove' to remove them. 134s The following packages will be upgraded: 134s pinentry-curses python3-jinja2 strace 134s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 134s Need to get 652 kB of archives. 134s After this operation, 27.6 kB of additional disk space will be used. 134s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB] 135s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pinentry-curses s390x 1.3.1-2ubuntu3 [42.9 kB] 135s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 135s Fetched 652 kB in 1s (978 kB/s) 135s (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 ... 81428 files and directories currently installed.) 135s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ... 135s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 135s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_s390x.deb ... 135s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 135s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 135s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 135s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 135s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 136s Setting up strace (6.13+ds-1ubuntu1) ... 136s Processing triggers for man-db (2.13.0-1) ... 136s Reading package lists... 136s Building dependency tree... 136s Reading state information... 137s Solving dependencies... 137s The following packages will be REMOVED: 137s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 137s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 137s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 137s linux-tools-6.11.0-8-generic* 137s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded. 137s After this operation, 167 MB disk space will be freed. 137s (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 ... 81428 files and directories currently installed.) 137s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 137s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 137s Removing libpython3.12t64:s390x (3.12.9-1) ... 137s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 137s Removing libnsl2:s390x (1.3.0-3build3) ... 137s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 137s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 137s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 138s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 138s Processing triggers for libc-bin (2.41-1ubuntu1) ... 138s (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 ... 56328 files and directories currently installed.) 138s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 138s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 138s autopkgtest [17:41:26]: upgrading testbed (apt dist-upgrade and autopurge) 139s Reading package lists... 139s Building dependency tree... 139s Reading state information... 139s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 139s Starting 2 pkgProblemResolver with broken count: 0 139s Done 139s Entering ResolveByKeep 139s 140s Calculating upgrade... 140s The following packages will be upgraded: 140s libc-bin libc-dev-bin libc6 libc6-dev locales 140s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 140s Need to get 9512 kB of archives. 140s After this operation, 8192 B of additional disk space will be used. 140s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB] 140s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB] 140s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB] 141s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB] 141s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB] 141s Preconfiguring packages ... 141s Fetched 9512 kB in 1s (8764 kB/s) 141s (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 ... 56326 files and directories currently installed.) 141s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ... 141s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 141s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ... 141s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 141s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ... 141s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 141s Setting up libc6:s390x (2.41-1ubuntu2) ... 141s (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 ... 56326 files and directories currently installed.) 141s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ... 141s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 142s Setting up libc-bin (2.41-1ubuntu2) ... 142s (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 ... 56326 files and directories currently installed.) 142s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 142s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 142s Setting up locales (2.41-1ubuntu2) ... 142s Generating locales (this might take a while)... 143s en_US.UTF-8... done 143s Generation complete. 143s Setting up libc-dev-bin (2.41-1ubuntu2) ... 143s Setting up libc6-dev:s390x (2.41-1ubuntu2) ... 143s Processing triggers for man-db (2.13.0-1) ... 144s Processing triggers for systemd (257.3-1ubuntu3) ... 145s Reading package lists... 145s Building dependency tree... 145s Reading state information... 145s Starting pkgProblemResolver with broken count: 0 145s Starting 2 pkgProblemResolver with broken count: 0 145s Done 145s Solving dependencies... 146s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 146s autopkgtest [17:41:34]: rebooting testbed after setup commands that affected boot 165s autopkgtest [17:41:53]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025 167s autopkgtest [17:41:55]: @@@@@@@@@@@@@@@@@@@@ apt-source qtltools 171s Get:1 http://ftpmaster.internal/ubuntu plucky/universe qtltools 1.3.1+dfsg-4build4 (dsc) [2293 B] 171s Get:2 http://ftpmaster.internal/ubuntu plucky/universe qtltools 1.3.1+dfsg-4build4 (tar) [141 kB] 171s Get:3 http://ftpmaster.internal/ubuntu plucky/universe qtltools 1.3.1+dfsg-4build4 (diff) [13.6 MB] 171s gpgv: Signature made Tue Jul 30 08:32:15 2024 UTC 171s gpgv: using RSA key 92978A6E195E4921825F7FF0F34F09744E9F5DD9 171s gpgv: Can't check signature: No public key 171s dpkg-source: warning: cannot verify inline signature for ./qtltools_1.3.1+dfsg-4build4.dsc: no acceptable signature found 172s autopkgtest [17:42:00]: testing package qtltools version 1.3.1+dfsg-4build4 175s autopkgtest [17:42:03]: build not needed 177s autopkgtest [17:42:05]: test run-sample-analysis: preparing testbed 177s Reading package lists... 177s Building dependency tree... 177s Reading state information... 177s Starting pkgProblemResolver with broken count: 0 177s Starting 2 pkgProblemResolver with broken count: 0 177s Done 177s The following NEW packages will be installed: 177s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 177s libboost-iostreams1.83.0 libboost-program-options1.83.0 libcairo2 libdatrie1 177s libdeflate0 libfontconfig1 libfreetype6 libgfortran5 libgomp1 libgraphite2-3 177s libgsl28 libgslcblas0 libharfbuzz0b libhts3t64 libhtscodecs2 libice6 177s libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 libpango-1.0-0 177s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 177s libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 177s libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 177s qtltools qtltools-example r-base-core r-mathlib unzip x11-common xdg-utils 177s zip 178s 0 upgraded, 53 newly installed, 0 to remove and 0 not upgraded. 178s Need to get 59.3 MB of archives. 178s After this operation, 110 MB of additional disk space will be used. 178s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libfreetype6 s390x 2.13.3+dfsg-1 [431 kB] 178s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 178s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 178s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig-config s390x 2.15.0-2ubuntu1 [37.5 kB] 178s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x libfontconfig1 s390x 2.15.0-2ubuntu1 [150 kB] 178s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig s390x 2.15.0-2ubuntu1 [191 kB] 178s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.1-2 [252 kB] 178s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libboost-iostreams1.83.0 s390x 1.83.0-4.1ubuntu2 [259 kB] 178s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libboost-program-options1.83.0 s390x 1.83.0-4.1ubuntu2 [326 kB] 178s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libpixman-1-0 s390x 0.44.0-3 [201 kB] 179s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-render0 s390x 1.17.0-2 [17.0 kB] 179s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-shm0 s390x 1.17.0-2 [5862 B] 179s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x libxrender1 s390x 1:0.9.10-1.1build1 [20.4 kB] 179s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x libcairo2 s390x 1.18.2-2 [580 kB] 179s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x libdatrie1 s390x 0.2.13-3build1 [20.6 kB] 179s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate0 s390x 1.23-1 [46.1 kB] 179s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 15-20250222-0ubuntu1 [620 kB] 179s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x libgomp1 s390x 15-20250222-0ubuntu1 [152 kB] 179s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x libgraphite2-3 s390x 1.3.14-2ubuntu1 [79.8 kB] 179s Get:20 http://ftpmaster.internal/ubuntu plucky/universe s390x libgslcblas0 s390x 2.8+dfsg-5 [153 kB] 179s Get:21 http://ftpmaster.internal/ubuntu plucky/universe s390x libgsl28 s390x 2.8+dfsg-5 [1126 kB] 179s Get:22 http://ftpmaster.internal/ubuntu plucky/main s390x libharfbuzz0b s390x 10.2.0-1 [538 kB] 179s Get:23 http://ftpmaster.internal/ubuntu plucky/universe s390x libhtscodecs2 s390x 1.6.1-2 [91.0 kB] 179s Get:24 http://ftpmaster.internal/ubuntu plucky/universe s390x libhts3t64 s390x 1.21+ds-1 [479 kB] 179s Get:25 http://ftpmaster.internal/ubuntu plucky/main s390x x11-common all 1:7.7+23ubuntu3 [21.7 kB] 179s Get:26 http://ftpmaster.internal/ubuntu plucky/main s390x libice6 s390x 2:1.1.1-1 [45.4 kB] 179s Get:27 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-turbo8 s390x 2.1.5-3ubuntu2 [147 kB] 179s Get:28 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 179s Get:29 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.1-2 [2971 kB] 179s Get:30 http://ftpmaster.internal/ubuntu plucky/main s390x libthai-data all 0.1.29-2build1 [158 kB] 179s Get:31 http://ftpmaster.internal/ubuntu plucky/main s390x libthai0 s390x 0.1.29-2build1 [20.7 kB] 179s Get:32 http://ftpmaster.internal/ubuntu plucky/main s390x libpango-1.0-0 s390x 1.56.2-1 [253 kB] 179s Get:33 http://ftpmaster.internal/ubuntu plucky/main s390x libpangoft2-1.0-0 s390x 1.56.2-1 [50.2 kB] 179s Get:34 http://ftpmaster.internal/ubuntu plucky/main s390x libpangocairo-1.0-0 s390x 1.56.2-1 [28.2 kB] 179s Get:35 http://ftpmaster.internal/ubuntu plucky/main s390x libpaper2 s390x 2.2.5-0.3 [17.2 kB] 179s Get:36 http://ftpmaster.internal/ubuntu plucky/main s390x libpaper-utils s390x 2.2.5-0.3 [15.3 kB] 179s Get:37 http://ftpmaster.internal/ubuntu plucky/main s390x libsharpyuv0 s390x 1.5.0-0.1 [16.7 kB] 179s Get:38 http://ftpmaster.internal/ubuntu plucky/main s390x libsm6 s390x 2:1.2.4-1 [18.4 kB] 179s Get:39 http://ftpmaster.internal/ubuntu plucky/main s390x libtcl8.6 s390x 8.6.16+dfsg-1 [1034 kB] 180s Get:40 http://ftpmaster.internal/ubuntu plucky/main s390x libjbig0 s390x 2.1-6.1ubuntu2 [33.1 kB] 180s Get:41 http://ftpmaster.internal/ubuntu plucky/main s390x libwebp7 s390x 1.5.0-0.1 [210 kB] 180s Get:42 http://ftpmaster.internal/ubuntu plucky/main s390x libtiff6 s390x 4.5.1+git230720-4ubuntu4 [217 kB] 180s Get:43 http://ftpmaster.internal/ubuntu plucky/main s390x libxft2 s390x 2.3.6-1build1 [49.6 kB] 180s Get:44 http://ftpmaster.internal/ubuntu plucky/main s390x libxss1 s390x 1:1.2.3-1build3 [7396 B] 180s Get:45 http://ftpmaster.internal/ubuntu plucky/main s390x libtk8.6 s390x 8.6.16-1 [830 kB] 180s Get:46 http://ftpmaster.internal/ubuntu plucky/main s390x libxt6t64 s390x 1:1.2.1-1.2build1 [184 kB] 180s Get:47 http://ftpmaster.internal/ubuntu plucky/universe s390x r-mathlib s390x 4.4.3-1 [2519 kB] 180s Get:48 http://ftpmaster.internal/ubuntu plucky/main s390x zip s390x 3.0-14ubuntu2 [187 kB] 180s Get:49 http://ftpmaster.internal/ubuntu plucky/main s390x unzip s390x 6.0-28ubuntu6 [186 kB] 180s Get:50 http://ftpmaster.internal/ubuntu plucky/main s390x xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 180s Get:51 http://ftpmaster.internal/ubuntu plucky/universe s390x r-base-core s390x 4.4.3-1 [28.6 MB] 184s Get:52 http://ftpmaster.internal/ubuntu plucky/universe s390x qtltools s390x 1.3.1+dfsg-4build4 [736 kB] 184s Get:53 http://ftpmaster.internal/ubuntu plucky/universe s390x qtltools-example all 1.3.1+dfsg-4build4 [13.6 MB] 186s Preconfiguring packages ... 187s Fetched 59.3 MB in 9s (6805 kB/s) 187s Selecting previously unselected package libfreetype6:s390x. 187s (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 ... 56326 files and directories currently installed.) 187s Preparing to unpack .../00-libfreetype6_2.13.3+dfsg-1_s390x.deb ... 187s Unpacking libfreetype6:s390x (2.13.3+dfsg-1) ... 187s Selecting previously unselected package fonts-dejavu-mono. 187s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 187s Unpacking fonts-dejavu-mono (2.37-8) ... 187s Selecting previously unselected package fonts-dejavu-core. 187s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 187s Unpacking fonts-dejavu-core (2.37-8) ... 187s Selecting previously unselected package fontconfig-config. 187s Preparing to unpack .../03-fontconfig-config_2.15.0-2ubuntu1_s390x.deb ... 187s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 187s Selecting previously unselected package libfontconfig1:s390x. 187s Preparing to unpack .../04-libfontconfig1_2.15.0-2ubuntu1_s390x.deb ... 187s Unpacking libfontconfig1:s390x (2.15.0-2ubuntu1) ... 187s Selecting previously unselected package fontconfig. 187s Preparing to unpack .../05-fontconfig_2.15.0-2ubuntu1_s390x.deb ... 187s Unpacking fontconfig (2.15.0-2ubuntu1) ... 187s Selecting previously unselected package libblas3:s390x. 187s Preparing to unpack .../06-libblas3_3.12.1-2_s390x.deb ... 187s Unpacking libblas3:s390x (3.12.1-2) ... 187s Selecting previously unselected package libboost-iostreams1.83.0:s390x. 187s Preparing to unpack .../07-libboost-iostreams1.83.0_1.83.0-4.1ubuntu2_s390x.deb ... 187s Unpacking libboost-iostreams1.83.0:s390x (1.83.0-4.1ubuntu2) ... 187s Selecting previously unselected package libboost-program-options1.83.0:s390x. 187s Preparing to unpack .../08-libboost-program-options1.83.0_1.83.0-4.1ubuntu2_s390x.deb ... 187s Unpacking libboost-program-options1.83.0:s390x (1.83.0-4.1ubuntu2) ... 187s Selecting previously unselected package libpixman-1-0:s390x. 187s Preparing to unpack .../09-libpixman-1-0_0.44.0-3_s390x.deb ... 187s Unpacking libpixman-1-0:s390x (0.44.0-3) ... 187s Selecting previously unselected package libxcb-render0:s390x. 187s Preparing to unpack .../10-libxcb-render0_1.17.0-2_s390x.deb ... 187s Unpacking libxcb-render0:s390x (1.17.0-2) ... 187s Selecting previously unselected package libxcb-shm0:s390x. 187s Preparing to unpack .../11-libxcb-shm0_1.17.0-2_s390x.deb ... 187s Unpacking libxcb-shm0:s390x (1.17.0-2) ... 187s Selecting previously unselected package libxrender1:s390x. 187s Preparing to unpack .../12-libxrender1_1%3a0.9.10-1.1build1_s390x.deb ... 187s Unpacking libxrender1:s390x (1:0.9.10-1.1build1) ... 187s Selecting previously unselected package libcairo2:s390x. 187s Preparing to unpack .../13-libcairo2_1.18.2-2_s390x.deb ... 187s Unpacking libcairo2:s390x (1.18.2-2) ... 187s Selecting previously unselected package libdatrie1:s390x. 187s Preparing to unpack .../14-libdatrie1_0.2.13-3build1_s390x.deb ... 187s Unpacking libdatrie1:s390x (0.2.13-3build1) ... 187s Selecting previously unselected package libdeflate0:s390x. 187s Preparing to unpack .../15-libdeflate0_1.23-1_s390x.deb ... 187s Unpacking libdeflate0:s390x (1.23-1) ... 187s Selecting previously unselected package libgfortran5:s390x. 187s Preparing to unpack .../16-libgfortran5_15-20250222-0ubuntu1_s390x.deb ... 187s Unpacking libgfortran5:s390x (15-20250222-0ubuntu1) ... 187s Selecting previously unselected package libgomp1:s390x. 187s Preparing to unpack .../17-libgomp1_15-20250222-0ubuntu1_s390x.deb ... 187s Unpacking libgomp1:s390x (15-20250222-0ubuntu1) ... 187s Selecting previously unselected package libgraphite2-3:s390x. 187s Preparing to unpack .../18-libgraphite2-3_1.3.14-2ubuntu1_s390x.deb ... 187s Unpacking libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 187s Selecting previously unselected package libgslcblas0:s390x. 187s Preparing to unpack .../19-libgslcblas0_2.8+dfsg-5_s390x.deb ... 187s Unpacking libgslcblas0:s390x (2.8+dfsg-5) ... 187s Selecting previously unselected package libgsl28:s390x. 187s Preparing to unpack .../20-libgsl28_2.8+dfsg-5_s390x.deb ... 187s Unpacking libgsl28:s390x (2.8+dfsg-5) ... 187s Selecting previously unselected package libharfbuzz0b:s390x. 187s Preparing to unpack .../21-libharfbuzz0b_10.2.0-1_s390x.deb ... 187s Unpacking libharfbuzz0b:s390x (10.2.0-1) ... 187s Selecting previously unselected package libhtscodecs2:s390x. 187s Preparing to unpack .../22-libhtscodecs2_1.6.1-2_s390x.deb ... 187s Unpacking libhtscodecs2:s390x (1.6.1-2) ... 187s Selecting previously unselected package libhts3t64:s390x. 187s Preparing to unpack .../23-libhts3t64_1.21+ds-1_s390x.deb ... 187s Unpacking libhts3t64:s390x (1.21+ds-1) ... 187s Selecting previously unselected package x11-common. 187s Preparing to unpack .../24-x11-common_1%3a7.7+23ubuntu3_all.deb ... 187s Unpacking x11-common (1:7.7+23ubuntu3) ... 187s Selecting previously unselected package libice6:s390x. 187s Preparing to unpack .../25-libice6_2%3a1.1.1-1_s390x.deb ... 187s Unpacking libice6:s390x (2:1.1.1-1) ... 187s Selecting previously unselected package libjpeg-turbo8:s390x. 187s Preparing to unpack .../26-libjpeg-turbo8_2.1.5-3ubuntu2_s390x.deb ... 187s Unpacking libjpeg-turbo8:s390x (2.1.5-3ubuntu2) ... 187s Selecting previously unselected package libjpeg8:s390x. 187s Preparing to unpack .../27-libjpeg8_8c-2ubuntu11_s390x.deb ... 187s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 187s Selecting previously unselected package liblapack3:s390x. 187s Preparing to unpack .../28-liblapack3_3.12.1-2_s390x.deb ... 187s Unpacking liblapack3:s390x (3.12.1-2) ... 187s Selecting previously unselected package libthai-data. 187s Preparing to unpack .../29-libthai-data_0.1.29-2build1_all.deb ... 187s Unpacking libthai-data (0.1.29-2build1) ... 187s Selecting previously unselected package libthai0:s390x. 187s Preparing to unpack .../30-libthai0_0.1.29-2build1_s390x.deb ... 187s Unpacking libthai0:s390x (0.1.29-2build1) ... 187s Selecting previously unselected package libpango-1.0-0:s390x. 187s Preparing to unpack .../31-libpango-1.0-0_1.56.2-1_s390x.deb ... 187s Unpacking libpango-1.0-0:s390x (1.56.2-1) ... 187s Selecting previously unselected package libpangoft2-1.0-0:s390x. 187s Preparing to unpack .../32-libpangoft2-1.0-0_1.56.2-1_s390x.deb ... 187s Unpacking libpangoft2-1.0-0:s390x (1.56.2-1) ... 187s Selecting previously unselected package libpangocairo-1.0-0:s390x. 187s Preparing to unpack .../33-libpangocairo-1.0-0_1.56.2-1_s390x.deb ... 187s Unpacking libpangocairo-1.0-0:s390x (1.56.2-1) ... 187s Selecting previously unselected package libpaper2:s390x. 187s Preparing to unpack .../34-libpaper2_2.2.5-0.3_s390x.deb ... 187s Unpacking libpaper2:s390x (2.2.5-0.3) ... 187s Selecting previously unselected package libpaper-utils. 187s Preparing to unpack .../35-libpaper-utils_2.2.5-0.3_s390x.deb ... 187s Unpacking libpaper-utils (2.2.5-0.3) ... 187s Selecting previously unselected package libsharpyuv0:s390x. 187s Preparing to unpack .../36-libsharpyuv0_1.5.0-0.1_s390x.deb ... 187s Unpacking libsharpyuv0:s390x (1.5.0-0.1) ... 187s Selecting previously unselected package libsm6:s390x. 187s Preparing to unpack .../37-libsm6_2%3a1.2.4-1_s390x.deb ... 187s Unpacking libsm6:s390x (2:1.2.4-1) ... 187s Selecting previously unselected package libtcl8.6:s390x. 187s Preparing to unpack .../38-libtcl8.6_8.6.16+dfsg-1_s390x.deb ... 187s Unpacking libtcl8.6:s390x (8.6.16+dfsg-1) ... 187s Selecting previously unselected package libjbig0:s390x. 187s Preparing to unpack .../39-libjbig0_2.1-6.1ubuntu2_s390x.deb ... 187s Unpacking libjbig0:s390x (2.1-6.1ubuntu2) ... 187s Selecting previously unselected package libwebp7:s390x. 187s Preparing to unpack .../40-libwebp7_1.5.0-0.1_s390x.deb ... 187s Unpacking libwebp7:s390x (1.5.0-0.1) ... 187s Selecting previously unselected package libtiff6:s390x. 187s Preparing to unpack .../41-libtiff6_4.5.1+git230720-4ubuntu4_s390x.deb ... 187s Unpacking libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 187s Selecting previously unselected package libxft2:s390x. 187s Preparing to unpack .../42-libxft2_2.3.6-1build1_s390x.deb ... 187s Unpacking libxft2:s390x (2.3.6-1build1) ... 187s Selecting previously unselected package libxss1:s390x. 187s Preparing to unpack .../43-libxss1_1%3a1.2.3-1build3_s390x.deb ... 187s Unpacking libxss1:s390x (1:1.2.3-1build3) ... 187s Selecting previously unselected package libtk8.6:s390x. 187s Preparing to unpack .../44-libtk8.6_8.6.16-1_s390x.deb ... 187s Unpacking libtk8.6:s390x (8.6.16-1) ... 187s Selecting previously unselected package libxt6t64:s390x. 187s Preparing to unpack .../45-libxt6t64_1%3a1.2.1-1.2build1_s390x.deb ... 187s Unpacking libxt6t64:s390x (1:1.2.1-1.2build1) ... 187s Selecting previously unselected package r-mathlib. 187s Preparing to unpack .../46-r-mathlib_4.4.3-1_s390x.deb ... 187s Unpacking r-mathlib (4.4.3-1) ... 188s Selecting previously unselected package zip. 188s Preparing to unpack .../47-zip_3.0-14ubuntu2_s390x.deb ... 188s Unpacking zip (3.0-14ubuntu2) ... 188s Selecting previously unselected package unzip. 188s Preparing to unpack .../48-unzip_6.0-28ubuntu6_s390x.deb ... 188s Unpacking unzip (6.0-28ubuntu6) ... 188s Selecting previously unselected package xdg-utils. 188s Preparing to unpack .../49-xdg-utils_1.2.1-2ubuntu1_all.deb ... 188s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 188s Selecting previously unselected package r-base-core. 188s Preparing to unpack .../50-r-base-core_4.4.3-1_s390x.deb ... 188s Unpacking r-base-core (4.4.3-1) ... 188s Selecting previously unselected package qtltools. 188s Preparing to unpack .../51-qtltools_1.3.1+dfsg-4build4_s390x.deb ... 188s Unpacking qtltools (1.3.1+dfsg-4build4) ... 188s Selecting previously unselected package qtltools-example. 188s Preparing to unpack .../52-qtltools-example_1.3.1+dfsg-4build4_all.deb ... 188s Unpacking qtltools-example (1.3.1+dfsg-4build4) ... 188s Setting up libhtscodecs2:s390x (1.6.1-2) ... 188s Setting up libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 188s Setting up qtltools-example (1.3.1+dfsg-4build4) ... 188s Setting up libboost-program-options1.83.0:s390x (1.83.0-4.1ubuntu2) ... 188s Setting up libpixman-1-0:s390x (0.44.0-3) ... 188s Setting up libsharpyuv0:s390x (1.5.0-0.1) ... 188s Setting up libxrender1:s390x (1:0.9.10-1.1build1) ... 188s Setting up libdatrie1:s390x (0.2.13-3build1) ... 188s Setting up libgslcblas0:s390x (2.8+dfsg-5) ... 188s Setting up libxcb-render0:s390x (1.17.0-2) ... 188s Setting up unzip (6.0-28ubuntu6) ... 188s Setting up x11-common (1:7.7+23ubuntu3) ... 188s Setting up libdeflate0:s390x (1.23-1) ... 188s Setting up libxcb-shm0:s390x (1.17.0-2) ... 188s Setting up libgomp1:s390x (15-20250222-0ubuntu1) ... 188s Setting up libjbig0:s390x (2.1-6.1ubuntu2) ... 188s Setting up zip (3.0-14ubuntu2) ... 188s Setting up libblas3:s390x (3.12.1-2) ... 188s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 188s Setting up libfreetype6:s390x (2.13.3+dfsg-1) ... 188s Setting up libboost-iostreams1.83.0:s390x (1.83.0-4.1ubuntu2) ... 188s Setting up fonts-dejavu-mono (2.37-8) ... 188s Setting up libtcl8.6:s390x (8.6.16+dfsg-1) ... 188s Setting up fonts-dejavu-core (2.37-8) ... 188s Setting up libjpeg-turbo8:s390x (2.1.5-3ubuntu2) ... 188s Setting up libgfortran5:s390x (15-20250222-0ubuntu1) ... 188s Setting up libwebp7:s390x (1.5.0-0.1) ... 188s Setting up r-mathlib (4.4.3-1) ... 188s Setting up libhts3t64:s390x (1.21+ds-1) ... 188s Setting up libharfbuzz0b:s390x (10.2.0-1) ... 188s Setting up libthai-data (0.1.29-2build1) ... 188s Setting up libxss1:s390x (1:1.2.3-1build3) ... 188s Setting up libpaper2:s390x (2.2.5-0.3) ... 188s Setting up libgsl28:s390x (2.8+dfsg-5) ... 188s Setting up xdg-utils (1.2.1-2ubuntu1) ... 188s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 188s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 188s Setting up libice6:s390x (2:1.1.1-1) ... 188s Setting up liblapack3:s390x (3.12.1-2) ... 188s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 188s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 188s Setting up libpaper-utils (2.2.5-0.3) ... 188s Setting up libthai0:s390x (0.1.29-2build1) ... 188s Setting up libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 188s Setting up libfontconfig1:s390x (2.15.0-2ubuntu1) ... 188s Setting up libsm6:s390x (2:1.2.4-1) ... 188s Setting up fontconfig (2.15.0-2ubuntu1) ... 190s Regenerating fonts cache... done. 190s Setting up libxft2:s390x (2.3.6-1build1) ... 190s Setting up libtk8.6:s390x (8.6.16-1) ... 190s Setting up libpango-1.0-0:s390x (1.56.2-1) ... 190s Setting up libcairo2:s390x (1.18.2-2) ... 190s Setting up libxt6t64:s390x (1:1.2.1-1.2build1) ... 190s Setting up libpangoft2-1.0-0:s390x (1.56.2-1) ... 190s Setting up libpangocairo-1.0-0:s390x (1.56.2-1) ... 190s Setting up r-base-core (4.4.3-1) ... 190s Creating config file /etc/R/Renviron with new version 191s Setting up qtltools (1.3.1+dfsg-4build4) ... 191s Processing triggers for man-db (2.13.0-1) ... 192s Processing triggers for install-info (7.1.1-1) ... 192s Processing triggers for libc-bin (2.41-1ubuntu2) ... 193s autopkgtest [17:42:21]: test run-sample-analysis: [----------------------- 193s ./genes.50percent.chr22.bed.gz 193s ./genes.50percent.chr22.bed.gz.tbi 193s ./genes.covariates.pc50.txt.gz 193s ./genes.simulated.chr22.bed.gz 193s ./genes.simulated.chr22.bed.gz.tbi 193s ./genotypes.chr22.vcf.gz 194s ./genotypes.chr22.vcf.gz.tbi 194s 194s QTLtools 194s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 194s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 194s * Webpage : https://qtltools.github.io/qtltools/ 194s * Version : 1.3.1 194s * Date : 15/03/2025 - 17:42:22 194s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 194s 194s CONDUCT PCA ON DATA 194s 194s Initialize random number generator 194s * Built-in seed is 15112011 194s * First Integer = 30553 194s * First Double = 0.0126695 194s 194s Reading sample list from [genes.50percent.chr22.bed.gz] 194s * #samples = 358 194s 194s Merging sample sets from all input files 194s * #files = 1 194s * #samples in all files = 358 194s 194s Reading phenotype data in [genes.50percent.chr22.bed.gz] 194s * 358 samples included 194s * 608 phenotypes included 194s 194s Calculating PCA with a matrix 358 x 608 194s * Calculated mean and sd 194s * 0 sd==0 columns removed 194s * Variables centered 194s * Variables scaled to unit variance 194s * Running SVD 195s * SVD complete 195s * Calculated sd and var for PCs 195s * Calculated cumulative var for PCs 195s * Done! 195s 195s Running time: 1 seconds 195s 195s QTLtools 195s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 195s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 195s * Webpage : https://qtltools.github.io/qtltools/ 195s * Version : 1.3.1 195s * Date : 15/03/2025 - 17:42:23 195s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 195s 195s MAPPING QTL IN CIS 195s * TASK: Report all nominal associations with p <= 0.01 195s * Linear model: Phe ~ Var + Cov 195s * Cis-window size is 1000000 bp 195s * Region = [chr22:17000000-18000000] 195s 195s Initialize random number generator 195s * Built-in seed is 15112011 195s * First Integer = 30553 195s * First Double = 0.0126695 195s 195s Reading sample list from [genes.50percent.chr22.bed.gz] 195s * #samples = 358 195s 195s Read sample list from [genotypes.chr22.vcf.gz] 195s * #samples = 358 195s 195s Reading sample list from [genes.covariates.pc50.txt.gz] 195s * #samples = 358 195s 195s Merging sample sets from all input files 195s * #files = 3 195s * #samples in all files = 358 195s 195s Reading phenotype data in [genes.50percent.chr22.bed.gz] 195s * target region [chr22:17000000-18000000] 195s * 8 phenotypes included 195s * 3 phenotypes are on the negative strand 195s 195s Reading genotype data in [genotypes.chr22.vcf.gz] 195s * File format detected: VCF 195s * target region [chr22:16000000-19000000] 195s * 6404 variants included 195s 195s Reading covariates in [genes.covariates.pc50.txt.gz] 195s * 53 covariates included 195s 195s Residualize phenotypes for covariates 195s * #covariates = 53 195s 195s Processing phenotype [ENSG00000237438.2] [1/8] 195s * #variants in cis = 5095 195s * Best hit: [id=22_17542810, d=25350, pv=1.1864e-25, s=-0.7518] 195s 195s Processing phenotype [ENSG00000273203.1] [2/8] 195s * #variants in cis = 5170 195s * Best hit: [id=22_17517388, d=-31323, pv=5.86611e-06, s=-0.1406] 195s 195s Processing phenotype [ENSG00000273442.1] [3/8] 195s * #variants in cis = 5188 195s * Best hit: [id=22_17553526, d=-8065, pv=0.000244522, s=0.1340] 195s 195s Processing phenotype [ENSG00000177663.9] [4/8] 195s * #variants in cis = 5193 195s * Best hit: [id=22_17513703, d=-52141, pv=8.03358e-14, s=-0.2096] 195s 195s Processing phenotype [ENSG00000183307.3] [5/8] 195s * #variants in cis = 5230 195s * Best hit: [id=22_17587975, d=14282, pv=1.56789e-07, s=-0.0078] 195s 195s Processing phenotype [ENSG00000069998.8] [6/8] 195s * #variants in cis = 5291 195s * Best hit: [id=22_17620429, d=25748, pv=1.37287e-14, s=-1.5147] 195s 195s Processing phenotype [ENSG00000093072.11] [7/8] 195s * #variants in cis = 5293 195s * Best hit: [id=22_17699630, d=3249, pv=0.000578649, s=0.6404] 195s 195s Processing phenotype [ENSG00000099954.14] [8/8] 195s * #variants in cis = 5435 195s * Best hit: [id=22_17175937, d=-664900, pv=0.000866455, s=0.0067] 195s 195s Running time: 0 seconds 195s 195s QTLtools 195s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 195s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 195s * Webpage : https://qtltools.github.io/qtltools/ 195s * Version : 1.3.1 195s * Date : 15/03/2025 - 17:42:23 195s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 195s 195s MAPPING QTL IN CIS 195s * TASK: Perform 1000 permutations 195s * Linear model: Phe ~ Var + Cov 195s * Cis-window size is 1000000 bp 195s * Region = [chr22:17000000-18000000] 195s 195s Initialize random number generator 195s * Built-in seed is 15112011 195s * First Integer = 30553 195s * First Double = 0.0126695 195s 195s Reading sample list from [genes.50percent.chr22.bed.gz] 195s * #samples = 358 195s 195s Read sample list from [genotypes.chr22.vcf.gz] 195s * #samples = 358 195s 195s Reading sample list from [genes.covariates.pc50.txt.gz] 195s * #samples = 358 195s 195s Merging sample sets from all input files 195s * #files = 3 195s * #samples in all files = 358 195s 195s Reading phenotype data in [genes.50percent.chr22.bed.gz] 195s * target region [chr22:17000000-18000000] 195s * 8 phenotypes included 195s * 3 phenotypes are on the negative strand 195s 195s Reading genotype data in [genotypes.chr22.vcf.gz] 195s * File format detected: VCF 195s * target region [chr22:16000000-19000000] 195s * 6404 variants included 195s 195s Reading covariates in [genes.covariates.pc50.txt.gz] 195s * 53 covariates included 195s 195s Residualize phenotypes for covariates 195s * #covariates = 53 195s 195s Processing phenotype [ENSG00000237438.2] [1/8] 195s * #variants in cis = 5095 196s * Best hit: [id=22_17542810, d=25350, pv=1.1864e-25, s=-0.7518] 196s * Beta parameters: [s1=1.00995, s2=621.053] 196s * Adjusted p-values: [emp=0.000999001, beta=1.28062e-20] 196s 196s Processing phenotype [ENSG00000273203.1] [2/8] 196s * #variants in cis = 5170 197s * Best hit: [id=22_17517388, d=-31323, pv=5.86611e-06, s=-0.1406] 197s * Beta parameters: [s1=1.11817, s2=641.379] 197s * Adjusted p-values: [emp=0.00799201, beta=0.00751892] 197s 197s Processing phenotype [ENSG00000273442.1] [3/8] 197s * #variants in cis = 5188 198s * Best hit: [id=22_17553526, d=-8065, pv=0.000244522, s=0.1340] 198s * Beta parameters: [s1=1.08364, s2=467.63] 198s * Adjusted p-values: [emp=0.297702, beta=0.293948] 198s 198s Processing phenotype [ENSG00000177663.9] [4/8] 198s * #variants in cis = 5193 200s * Best hit: [id=22_17513703, d=-52141, pv=8.03358e-14, s=-0.2096] 200s * Beta parameters: [s1=0.989061, s2=704.553] 200s * Adjusted p-values: [emp=0.000999001, beta=7.91291e-10] 200s 200s Processing phenotype [ENSG00000183307.3] [5/8] 200s * #variants in cis = 5230 201s * Best hit: [id=22_17587975, d=14282, pv=1.56789e-07, s=-0.0078] 201s * Beta parameters: [s1=1.01322, s2=559.49] 201s * Adjusted p-values: [emp=0.000999001, beta=0.00050707] 201s 201s Processing phenotype [ENSG00000069998.8] [6/8] 201s * #variants in cis = 5291 202s * Best hit: [id=22_17620429, d=25748, pv=1.37287e-14, s=-1.5147] 202s * Beta parameters: [s1=1.02312, s2=563.339] 202s * Adjusted p-values: [emp=0.000999001, beta=2.56935e-10] 202s 202s Processing phenotype [ENSG00000093072.11] [7/8] 202s * #variants in cis = 5293 203s * Best hit: [id=22_17699630, d=3249, pv=0.000578649, s=0.6404] 203s * Beta parameters: [s1=0.957514, s2=559.397] 203s * Adjusted p-values: [emp=0.574426, beta=0.562826] 203s 203s Processing phenotype [ENSG00000099954.14] [8/8] 203s * #variants in cis = 5435 204s * Best hit: [id=22_17175937, d=-664900, pv=0.000866455, s=0.0067] 204s * Beta parameters: [s1=0.938041, s2=226.852] 204s * Adjusted p-values: [emp=0.842158, beta=0.84836] 204s 204s Running time: 8 seconds 204s 204s QTLtools 204s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 204s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 204s * Webpage : https://qtltools.github.io/qtltools/ 204s * Version : 1.3.1 204s * Date : 15/03/2025 - 17:42:32 204s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 204s 204s MAPPING QTL IN TRANS 204s * TASK: Perform a full nominal pass, do not adjust p-values 204s * Cis-window size is 5000000 bp 204s * #bins = 1000 204s * threshold = 1e-05 204s 204s Initialize random number generator 204s * Built-in seed is 15112011 204s * First Integer = 30553 204s * First Double = 0.0126695 204s 204s Read sample list from [genotypes.chr22.vcf.gz] 204s * #samples = 358 204s 204s Checking sample list in [genes.simulated.chr22.bed.gz] 204s * #samples = 358 204s 204s Reading phenotype data in [genes.simulated.chr22.bed.gz] from line 0 to 0 204s * 358 samples included 204s * 608 phenotypes included 204s * 275 phenotypes is on the negative strand 204s 204s Calculate correlation threshold 204s * thres = 1e-05 204s * corr = 0.2311 204s 204s Sweep through genotype data in [genotypes.chr22.vcf.gz] 204s * #variants=1950 #multi_allelic=0 #not_processed=0 #hits=101/1000000 speed=4.61MT/s 204s * #variants=4001 #multi_allelic=0 #not_processed=0 #hits=153/2000000 speed=4.57MT/s 205s * #variants=6187 #multi_allelic=0 #not_processed=0 #hits=244/3000000 speed=4.55MT/s 205s * #variants=8537 #multi_allelic=0 #not_processed=0 #hits=285/4000000 speed=4.44MT/s 205s * #variants=11025 #multi_allelic=0 #not_processed=0 #hits=312/5000000 speed=4.35MT/s 205s * #variants=13621 #multi_allelic=0 #not_processed=0 #hits=320/6000000 speed=3.73MT/s 206s * #variants=16217 #multi_allelic=0 #not_processed=0 #hits=342/7000000 speed=3.73MT/s 206s * #variants=18755 #multi_allelic=0 #not_processed=0 #hits=401/8000000 speed=3.80MT/s 206s * #variants=21237 #multi_allelic=0 #not_processed=0 #hits=402/9000000 speed=3.82MT/s 206s * #variants=23680 #multi_allelic=0 #not_processed=0 #hits=455/10000000 speed=4.24MT/s 207s * #variants=26171 #multi_allelic=0 #not_processed=0 #hits=463/11000000 speed=4.02MT/s 207s * #variants=28609 #multi_allelic=0 #not_processed=0 #hits=469/12000000 speed=3.57MT/s 207s * #variants=30861 #multi_allelic=0 #not_processed=0 #hits=973/13000000 speed=3.38MT/s 208s * #variants=32932 #multi_allelic=0 #not_processed=0 #hits=979/14000000 speed=3.68MT/s 208s * #variants=34974 #multi_allelic=0 #not_processed=0 #hits=1085/15000000 speed=3.94MT/s 208s * #variants=37021 #multi_allelic=0 #not_processed=0 #hits=1086/16000000 speed=3.94MT/s 208s * #variants=39122 #multi_allelic=0 #not_processed=0 #hits=1089/17000000 speed=3.77MT/s 209s * #variants=41334 #multi_allelic=0 #not_processed=0 #hits=1089/18000000 speed=3.91MT/s 209s * #variants=43627 #multi_allelic=0 #not_processed=0 #hits=1096/19000000 speed=3.80MT/s 209s * #variants=45897 #multi_allelic=0 #not_processed=0 #hits=1153/20000000 speed=3.94MT/s 209s * #variants=48114 #multi_allelic=0 #not_processed=0 #hits=1243/21000000 speed=3.97MT/s 210s * #variants=50410 #multi_allelic=0 #not_processed=0 #hits=1249/22000000 speed=3.89MT/s 210s * #variants=52820 #multi_allelic=0 #not_processed=0 #hits=1259/23000000 speed=3.58MT/s 210s * #variants=55279 #multi_allelic=0 #not_processed=0 #hits=1498/24000000 speed=3.85MT/s 210s * #variants=57789 #multi_allelic=0 #not_processed=0 #hits=1724/25000000 speed=3.53MT/s 211s * #variants=60201 #multi_allelic=0 #not_processed=0 #hits=2168/26000000 speed=3.79MT/s 211s * #variants=62476 #multi_allelic=0 #not_processed=0 #hits=2452/27000000 speed=3.80MT/s 211s * #variants=64608 #multi_allelic=0 #not_processed=0 #hits=2544/28000000 speed=3.86MT/s 211s * #variants=66709 #multi_allelic=0 #not_processed=0 #hits=2684/29000000 speed=3.70MT/s 212s * #variants=68871 #multi_allelic=0 #not_processed=0 #hits=2688/30000000 speed=3.83MT/s 212s * #variants=71070 #multi_allelic=0 #not_processed=0 #hits=2720/31000000 speed=3.97MT/s 212s * #variants=73151 #multi_allelic=0 #not_processed=0 #hits=2891/32000000 speed=4.00MT/s 212s * #variants=75122 #multi_allelic=0 #not_processed=0 #hits=3110/33000000 speed=3.75MT/s 213s * #variants=77058 #multi_allelic=0 #not_processed=0 #hits=3209/34000000 speed=3.79MT/s 213s * #variants=78989 #multi_allelic=0 #not_processed=0 #hits=3218/35000000 speed=3.56MT/s 213s * #variants=80903 #multi_allelic=0 #not_processed=0 #hits=3250/36000000 speed=4.15MT/s 214s * #variants=82811 #multi_allelic=0 #not_processed=0 #hits=3463/37000000 speed=4.13MT/s 214s * #variants=84694 #multi_allelic=0 #not_processed=0 #hits=4035/38000000 speed=4.20MT/s 214s * #variants=85485 #multi_allelic=0 #not_processed=0 #hits=4036/38425275 speed=4.01MT/s 214s 214s Running time: 9 seconds 214s 214s QTLtools 214s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 214s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 214s * Webpage : https://qtltools.github.io/qtltools/ 214s * Version : 1.3.1 214s * Date : 15/03/2025 - 17:42:42 214s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 214s 214s MAPPING QTL IN TRANS 214s * TASK: Permute randomly chosen phenotypes 1000 times and test 214s * Cis-window size is 5000000 bp 214s * #bins = 1000 214s * threshold = 1e-05 214s 214s Initialize random number generator 214s * Built-in seed is 15112011 214s * First Integer = 30553 214s * First Double = 0.0126695 214s 214s Read sample list from [genotypes.chr22.vcf.gz] 214s * #samples = 358 214s 214s Checking sample list in [genes.simulated.chr22.bed.gz] 214s * #samples = 358 214s 214s Reading phenotype data in [genes.simulated.chr22.bed.gz] from line 0 to 0 214s * 358 samples included 214s * 608 phenotypes included 214s * 275 phenotypes is on the negative strand 214s 214s Normal transform phenotypes 214s 214s Calculate correlation threshold 214s * thres = 1e-05 214s * corr = 0.2311 214s 214s Sweep through genotype data in [genotypes.chr22.vcf.gz] 214s * #variants=1177 #multi_allelic=0 #not_processed=0 #hits=28/1000000 speed=4.13MT/s 214s * #variants=2383 #multi_allelic=0 #not_processed=0 #hits=38/2000000 speed=4.35MT/s 215s * #variants=3633 #multi_allelic=0 #not_processed=0 #hits=53/3000000 speed=4.05MT/s 215s * #variants=4928 #multi_allelic=0 #not_processed=0 #hits=53/4000000 speed=4.31MT/s 215s * #variants=6269 #multi_allelic=0 #not_processed=0 #hits=71/5000000 speed=4.17MT/s 215s * #variants=7675 #multi_allelic=0 #not_processed=0 #hits=72/6000000 speed=4.03MT/s 216s * #variants=9151 #multi_allelic=0 #not_processed=0 #hits=88/7000000 speed=4.02MT/s 216s * #variants=10663 #multi_allelic=0 #not_processed=0 #hits=96/8000000 speed=3.91MT/s 216s * #variants=12202 #multi_allelic=0 #not_processed=0 #hits=96/9000000 speed=3.97MT/s 216s * #variants=13804 #multi_allelic=0 #not_processed=0 #hits=96/10000000 speed=3.98MT/s 217s * #variants=15381 #multi_allelic=0 #not_processed=0 #hits=120/11000000 speed=3.91MT/s 217s * #variants=16946 #multi_allelic=0 #not_processed=0 #hits=123/12000000 speed=4.07MT/s 217s * #variants=18483 #multi_allelic=0 #not_processed=0 #hits=129/13000000 speed=4.20MT/s 217s * #variants=19995 #multi_allelic=0 #not_processed=0 #hits=131/14000000 speed=3.86MT/s 218s * #variants=21489 #multi_allelic=0 #not_processed=0 #hits=132/15000000 speed=4.02MT/s 218s * #variants=22947 #multi_allelic=0 #not_processed=0 #hits=151/16000000 speed=4.67MT/s 218s * #variants=24445 #multi_allelic=0 #not_processed=0 #hits=168/17000000 speed=4.67MT/s 218s * #variants=25965 #multi_allelic=0 #not_processed=0 #hits=175/18000000 speed=4.65MT/s 219s * #variants=27472 #multi_allelic=0 #not_processed=0 #hits=179/19000000 speed=4.65MT/s 219s * #variants=28933 #multi_allelic=0 #not_processed=0 #hits=181/20000000 speed=4.69MT/s 219s * #variants=30325 #multi_allelic=0 #not_processed=0 #hits=181/21000000 speed=4.55MT/s 219s * #variants=31617 #multi_allelic=0 #not_processed=0 #hits=182/22000000 speed=3.94MT/s 220s * #variants=32875 #multi_allelic=0 #not_processed=0 #hits=190/23000000 speed=3.68MT/s 220s * #variants=34127 #multi_allelic=0 #not_processed=0 #hits=192/24000000 speed=4.50MT/s 220s * #variants=35392 #multi_allelic=0 #not_processed=0 #hits=206/25000000 speed=4.57MT/s 220s * #variants=36652 #multi_allelic=0 #not_processed=0 #hits=206/26000000 speed=4.39MT/s 220s * #variants=37940 #multi_allelic=0 #not_processed=0 #hits=213/27000000 speed=4.17MT/s 221s * #variants=39255 #multi_allelic=0 #not_processed=0 #hits=238/28000000 speed=3.94MT/s 221s * #variants=40602 #multi_allelic=0 #not_processed=0 #hits=239/29000000 speed=4.26MT/s 221s * #variants=41998 #multi_allelic=0 #not_processed=0 #hits=245/30000000 speed=4.69MT/s 221s * #variants=43398 #multi_allelic=0 #not_processed=0 #hits=245/31000000 speed=4.72MT/s 222s * #variants=44803 #multi_allelic=0 #not_processed=0 #hits=260/32000000 speed=4.69MT/s 222s * #variants=46187 #multi_allelic=0 #not_processed=0 #hits=261/33000000 speed=4.74MT/s 222s * #variants=47545 #multi_allelic=0 #not_processed=0 #hits=268/34000000 speed=4.69MT/s 222s * #variants=48904 #multi_allelic=0 #not_processed=0 #hits=280/35000000 speed=3.91MT/s 222s * #variants=50309 #multi_allelic=0 #not_processed=0 #hits=306/36000000 speed=3.92MT/s 223s * #variants=51731 #multi_allelic=0 #not_processed=0 #hits=314/37000000 speed=3.94MT/s 223s * #variants=53171 #multi_allelic=0 #not_processed=0 #hits=320/38000000 speed=4.27MT/s 223s * #variants=54621 #multi_allelic=0 #not_processed=0 #hits=323/39000000 speed=4.65MT/s 223s * #variants=56099 #multi_allelic=0 #not_processed=0 #hits=323/40000000 speed=4.57MT/s 224s * #variants=57584 #multi_allelic=0 #not_processed=0 #hits=340/41000000 speed=4.61MT/s 224s * #variants=59032 #multi_allelic=0 #not_processed=0 #hits=344/42000000 speed=4.63MT/s 224s * #variants=60437 #multi_allelic=0 #not_processed=0 #hits=345/43000000 speed=4.07MT/s 224s * #variants=61810 #multi_allelic=0 #not_processed=0 #hits=357/44000000 speed=3.91MT/s 225s * #variants=63129 #multi_allelic=0 #not_processed=0 #hits=384/45000000 speed=4.08MT/s 225s * #variants=64409 #multi_allelic=0 #not_processed=0 #hits=391/46000000 speed=4.03MT/s 225s * #variants=65679 #multi_allelic=0 #not_processed=0 #hits=430/47000000 speed=3.94MT/s 225s * #variants=66953 #multi_allelic=0 #not_processed=0 #hits=436/48000000 speed=4.20MT/s 226s * #variants=68247 #multi_allelic=0 #not_processed=0 #hits=446/49000000 speed=4.07MT/s 226s * #variants=69595 #multi_allelic=0 #not_processed=0 #hits=460/50000000 speed=3.58MT/s 226s * #variants=70918 #multi_allelic=0 #not_processed=0 #hits=481/51000000 speed=4.13MT/s 226s * #variants=72211 #multi_allelic=0 #not_processed=0 #hits=492/52000000 speed=4.02MT/s 227s * #variants=73449 #multi_allelic=0 #not_processed=0 #hits=492/53000000 speed=3.75MT/s 227s * #variants=74662 #multi_allelic=0 #not_processed=0 #hits=500/54000000 speed=4.10MT/s 227s * #variants=75863 #multi_allelic=0 #not_processed=0 #hits=506/55000000 speed=3.97MT/s 227s * #variants=77058 #multi_allelic=0 #not_processed=0 #hits=513/56000000 speed=3.77MT/s 228s * #variants=78253 #multi_allelic=0 #not_processed=0 #hits=515/57000000 speed=4.07MT/s 228s * #variants=79446 #multi_allelic=0 #not_processed=0 #hits=530/58000000 speed=3.72MT/s 228s * #variants=80634 #multi_allelic=0 #not_processed=0 #hits=581/59000000 speed=3.82MT/s 228s * #variants=81817 #multi_allelic=0 #not_processed=0 #hits=594/60000000 speed=4.27MT/s 229s * #variants=82993 #multi_allelic=0 #not_processed=0 #hits=598/61000000 speed=4.12MT/s 229s * #variants=84160 #multi_allelic=0 #not_processed=0 #hits=599/62000000 speed=4.39MT/s 229s * #variants=85304 #multi_allelic=0 #not_processed=0 #hits=609/63000000 speed=4.15MT/s 229s * #variants=85485 #multi_allelic=0 #not_processed=0 #hits=609/63157827 speed=4.15MT/s 229s 229s Running time: 15 seconds 229s autopkgtest [17:42:57]: test run-sample-analysis: -----------------------] 230s run-sample-analysis PASS 230s autopkgtest [17:42:58]: test run-sample-analysis: - - - - - - - - - - results - - - - - - - - - - 230s autopkgtest [17:42:58]: @@@@@@@@@@@@@@@@@@@@ summary 230s run-sample-analysis PASS 236s nova [W] Using flock in prodstack6-s390x 236s Creating nova instance adt-plucky-s390x-qtltools-20250315-173908-juju-7f2275-prod-proposed-migration-environment-2-77c03b9c-206c-46c5-95d8-5fa350f3ec39 from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 236s nova [W] Timed out waiting for caa057e3-6e0c-4d83-8bda-3248a7a5a6ee to get deleted.