0s autopkgtest [15:56:04]: starting date and time: 2025-03-15 15:56:04+0000 0s autopkgtest [15:56:04]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [15:56:04]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.0ngoznb7/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --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 -- lxd -r lxd-armhf-10.145.243.85 lxd-armhf-10.145.243.85:autopkgtest/ubuntu/plucky/armhf 27s autopkgtest [15:56:31]: testbed dpkg architecture: armhf 29s autopkgtest [15:56:33]: testbed apt version: 2.9.33 33s autopkgtest [15:56:37]: @@@@@@@@@@@@@@@@@@@@ test bed setup 35s autopkgtest [15:56:39]: testbed release detected to be: None 42s autopkgtest [15:56:46]: updating testbed package index (apt update) 44s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 44s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 45s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 45s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 45s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 45s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 46s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 46s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [114 kB] 46s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1832 B] 46s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 46s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [312 kB] 46s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [11.1 kB] 46s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 46s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [240 B] 46s Get:15 http://ftpmaster.internal/ubuntu plucky/main Sources [1394 kB] 48s Get:16 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 48s Get:17 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 72s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 74s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 74s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 74s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 90s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 92s Fetched 41.0 MB in 48s (861 kB/s) 93s Reading package lists... 99s autopkgtest [15:57:43]: upgrading testbed (apt dist-upgrade and autopurge) 101s Reading package lists... 101s Building dependency tree... 101s Reading state information... 102s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 102s Starting 2 pkgProblemResolver with broken count: 0 102s Done 103s Entering ResolveByKeep 104s 104s Calculating upgrade... 104s The following packages will be upgraded: 104s libc-bin libc6 locales pinentry-curses python3-jinja2 sos strace 105s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 105s Need to get 8683 kB of archives. 105s After this operation, 23.6 kB of additional disk space will be used. 105s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 109s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 110s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 114s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 114s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf pinentry-curses armhf 1.3.1-2ubuntu3 [40.6 kB] 114s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 114s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 115s Preconfiguring packages ... 115s Fetched 8683 kB in 10s (853 kB/s) 116s (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 ... 64655 files and directories currently installed.) 116s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 116s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 116s Setting up libc6:armhf (2.41-1ubuntu2) ... 116s (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 ... 64655 files and directories currently installed.) 116s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 116s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 116s Setting up libc-bin (2.41-1ubuntu2) ... 117s (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 ... 64655 files and directories currently installed.) 117s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 117s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 117s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 117s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 117s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_armhf.deb ... 117s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 117s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 117s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 117s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 118s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 118s Setting up sos (4.9.0-5) ... 119s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 119s Setting up locales (2.41-1ubuntu2) ... 120s Generating locales (this might take a while)... 122s en_US.UTF-8... done 122s Generation complete. 122s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 122s Setting up strace (6.13+ds-1ubuntu1) ... 122s Processing triggers for man-db (2.13.0-1) ... 124s Processing triggers for systemd (257.3-1ubuntu3) ... 127s Reading package lists... 127s Building dependency tree... 127s Reading state information... 127s Starting pkgProblemResolver with broken count: 0 127s Starting 2 pkgProblemResolver with broken count: 0 127s Done 128s Solving dependencies... 128s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 130s autopkgtest [15:58:14]: rebooting testbed after setup commands that affected boot 170s autopkgtest [15:58:54]: testbed running kernel: Linux 6.8.0-52-generic #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 18:10:51 UTC 2 195s autopkgtest [15:59:19]: @@@@@@@@@@@@@@@@@@@@ apt-source qtltools 223s Get:1 http://ftpmaster.internal/ubuntu plucky/universe qtltools 1.3.1+dfsg-4build4 (dsc) [2293 B] 223s Get:2 http://ftpmaster.internal/ubuntu plucky/universe qtltools 1.3.1+dfsg-4build4 (tar) [141 kB] 223s Get:3 http://ftpmaster.internal/ubuntu plucky/universe qtltools 1.3.1+dfsg-4build4 (diff) [13.6 MB] 223s gpgv: Signature made Tue Jul 30 08:32:15 2024 UTC 223s gpgv: using RSA key 92978A6E195E4921825F7FF0F34F09744E9F5DD9 223s gpgv: Can't check signature: No public key 223s dpkg-source: warning: cannot verify inline signature for ./qtltools_1.3.1+dfsg-4build4.dsc: no acceptable signature found 224s autopkgtest [15:59:48]: testing package qtltools version 1.3.1+dfsg-4build4 227s autopkgtest [15:59:51]: build not needed 230s autopkgtest [15:59:54]: test run-sample-analysis: preparing testbed 231s Reading package lists... 232s Building dependency tree... 232s Reading state information... 232s Starting pkgProblemResolver with broken count: 0 232s Starting 2 pkgProblemResolver with broken count: 0 232s Done 234s The following NEW packages will be installed: 234s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 234s libboost-iostreams1.83.0 libboost-program-options1.83.0 libcairo2 libdatrie1 234s libdeflate0 libfontconfig1 libfreetype6 libgfortran5 libgomp1 libgraphite2-3 234s libgsl28 libgslcblas0 libharfbuzz0b libhts3t64 libhtscodecs2 libice6 234s libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0 234s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 234s libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 234s libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 234s qtltools qtltools-example r-base-core r-mathlib unzip x11-common xdg-utils 234s zip 234s 0 upgraded, 54 newly installed, 0 to remove and 0 not upgraded. 234s Need to get 56.6 MB of archives. 234s After this operation, 97.2 MB of additional disk space will be used. 234s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 234s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 235s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 236s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig-config armhf 2.15.0-2ubuntu1 [37.5 kB] 237s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf libfontconfig1 armhf 2.15.0-2ubuntu1 [114 kB] 237s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig armhf 2.15.0-2ubuntu1 [190 kB] 237s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.1-2 [132 kB] 237s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf libboost-iostreams1.83.0 armhf 1.83.0-4.1ubuntu2 [258 kB] 237s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf libboost-program-options1.83.0 armhf 1.83.0-4.1ubuntu2 [345 kB] 238s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 238s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 238s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 238s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 238s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf libcairo2 armhf 1.18.2-2 [484 kB] 239s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf libdatrie1 armhf 0.2.13-3build1 [15.7 kB] 239s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.23-1 [38.5 kB] 239s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 15-20250222-0ubuntu1 [330 kB] 239s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 15-20250222-0ubuntu1 [128 kB] 240s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 240s Get:20 http://ftpmaster.internal/ubuntu plucky/universe armhf libgslcblas0 armhf 2.8+dfsg-5 [84.1 kB] 240s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf libgsl28 armhf 2.8+dfsg-5 [876 kB] 241s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf libharfbuzz0b armhf 10.2.0-1 [464 kB] 241s Get:23 http://ftpmaster.internal/ubuntu plucky/universe armhf libhtscodecs2 armhf 1.6.1-2 [67.5 kB] 241s Get:24 http://ftpmaster.internal/ubuntu plucky/universe armhf libhts3t64 armhf 1.21+ds-1 [399 kB] 242s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf x11-common all 1:7.7+23ubuntu3 [21.7 kB] 242s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf libice6 armhf 2:1.1.1-1 [36.5 kB] 242s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8 armhf 2.1.5-3ubuntu2 [127 kB] 242s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 242s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.1-2 [2091 kB] 244s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu1 [160 kB] 244s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf libthai-data all 0.1.29-2build1 [158 kB] 244s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf libthai0 armhf 0.1.29-2build1 [15.2 kB] 244s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf libpango-1.0-0 armhf 1.56.2-1 [216 kB] 245s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf libpangoft2-1.0-0 armhf 1.56.2-1 [43.6 kB] 245s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf libpangocairo-1.0-0 armhf 1.56.2-1 [25.1 kB] 245s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libpaper2 armhf 2.2.5-0.3 [16.3 kB] 245s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libpaper-utils armhf 2.2.5-0.3 [14.2 kB] 245s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libsharpyuv0 armhf 1.5.0-0.1 [16.4 kB] 245s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf libsm6 armhf 2:1.2.4-1 [15.1 kB] 245s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf libtcl8.6 armhf 8.6.16+dfsg-1 [909 kB] 246s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 246s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf libwebp7 armhf 1.5.0-0.1 [188 kB] 246s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu4 [179 kB] 247s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf libxft2 armhf 2.3.6-1build1 [37.4 kB] 247s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf libxss1 armhf 1:1.2.3-1build3 [6500 B] 247s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf libtk8.6 armhf 8.6.16-1 [686 kB] 248s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf libxt6t64 armhf 1:1.2.1-1.2build1 [145 kB] 248s Get:48 http://ftpmaster.internal/ubuntu plucky/universe armhf r-mathlib armhf 4.4.3-1 [2498 kB] 251s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf zip armhf 3.0-14ubuntu2 [164 kB] 251s Get:50 http://ftpmaster.internal/ubuntu plucky/main armhf unzip armhf 6.0-28ubuntu6 [167 kB] 251s Get:51 http://ftpmaster.internal/ubuntu plucky/main armhf xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 251s Get:52 http://ftpmaster.internal/ubuntu plucky/universe armhf r-base-core armhf 4.4.3-1 [28.2 MB] 285s Get:53 http://ftpmaster.internal/ubuntu plucky/universe armhf qtltools armhf 1.3.1+dfsg-4build4 [979 kB] 287s Get:54 http://ftpmaster.internal/ubuntu plucky/universe armhf qtltools-example all 1.3.1+dfsg-4build4 [13.6 MB] 309s Preconfiguring packages ... 309s Fetched 56.6 MB in 1min 14s (761 kB/s) 309s Selecting previously unselected package libfreetype6:armhf. 309s (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 ... 64655 files and directories currently installed.) 309s Preparing to unpack .../00-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 309s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 309s Selecting previously unselected package fonts-dejavu-mono. 309s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 309s Unpacking fonts-dejavu-mono (2.37-8) ... 309s Selecting previously unselected package fonts-dejavu-core. 309s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 309s Unpacking fonts-dejavu-core (2.37-8) ... 309s Selecting previously unselected package fontconfig-config. 309s Preparing to unpack .../03-fontconfig-config_2.15.0-2ubuntu1_armhf.deb ... 310s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 310s Selecting previously unselected package libfontconfig1:armhf. 310s Preparing to unpack .../04-libfontconfig1_2.15.0-2ubuntu1_armhf.deb ... 310s Unpacking libfontconfig1:armhf (2.15.0-2ubuntu1) ... 310s Selecting previously unselected package fontconfig. 310s Preparing to unpack .../05-fontconfig_2.15.0-2ubuntu1_armhf.deb ... 310s Unpacking fontconfig (2.15.0-2ubuntu1) ... 310s Selecting previously unselected package libblas3:armhf. 310s Preparing to unpack .../06-libblas3_3.12.1-2_armhf.deb ... 310s Unpacking libblas3:armhf (3.12.1-2) ... 310s Selecting previously unselected package libboost-iostreams1.83.0:armhf. 310s Preparing to unpack .../07-libboost-iostreams1.83.0_1.83.0-4.1ubuntu2_armhf.deb ... 310s Unpacking libboost-iostreams1.83.0:armhf (1.83.0-4.1ubuntu2) ... 310s Selecting previously unselected package libboost-program-options1.83.0:armhf. 310s Preparing to unpack .../08-libboost-program-options1.83.0_1.83.0-4.1ubuntu2_armhf.deb ... 310s Unpacking libboost-program-options1.83.0:armhf (1.83.0-4.1ubuntu2) ... 310s Selecting previously unselected package libpixman-1-0:armhf. 310s Preparing to unpack .../09-libpixman-1-0_0.44.0-3_armhf.deb ... 310s Unpacking libpixman-1-0:armhf (0.44.0-3) ... 310s Selecting previously unselected package libxcb-render0:armhf. 310s Preparing to unpack .../10-libxcb-render0_1.17.0-2_armhf.deb ... 310s Unpacking libxcb-render0:armhf (1.17.0-2) ... 310s Selecting previously unselected package libxcb-shm0:armhf. 310s Preparing to unpack .../11-libxcb-shm0_1.17.0-2_armhf.deb ... 310s Unpacking libxcb-shm0:armhf (1.17.0-2) ... 310s Selecting previously unselected package libxrender1:armhf. 310s Preparing to unpack .../12-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ... 310s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ... 310s Selecting previously unselected package libcairo2:armhf. 310s Preparing to unpack .../13-libcairo2_1.18.2-2_armhf.deb ... 310s Unpacking libcairo2:armhf (1.18.2-2) ... 310s Selecting previously unselected package libdatrie1:armhf. 310s Preparing to unpack .../14-libdatrie1_0.2.13-3build1_armhf.deb ... 310s Unpacking libdatrie1:armhf (0.2.13-3build1) ... 310s Selecting previously unselected package libdeflate0:armhf. 311s Preparing to unpack .../15-libdeflate0_1.23-1_armhf.deb ... 311s Unpacking libdeflate0:armhf (1.23-1) ... 311s Selecting previously unselected package libgfortran5:armhf. 311s Preparing to unpack .../16-libgfortran5_15-20250222-0ubuntu1_armhf.deb ... 311s Unpacking libgfortran5:armhf (15-20250222-0ubuntu1) ... 311s Selecting previously unselected package libgomp1:armhf. 311s Preparing to unpack .../17-libgomp1_15-20250222-0ubuntu1_armhf.deb ... 311s Unpacking libgomp1:armhf (15-20250222-0ubuntu1) ... 311s Selecting previously unselected package libgraphite2-3:armhf. 311s Preparing to unpack .../18-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 311s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 311s Selecting previously unselected package libgslcblas0:armhf. 311s Preparing to unpack .../19-libgslcblas0_2.8+dfsg-5_armhf.deb ... 311s Unpacking libgslcblas0:armhf (2.8+dfsg-5) ... 311s Selecting previously unselected package libgsl28:armhf. 311s Preparing to unpack .../20-libgsl28_2.8+dfsg-5_armhf.deb ... 311s Unpacking libgsl28:armhf (2.8+dfsg-5) ... 311s Selecting previously unselected package libharfbuzz0b:armhf. 311s Preparing to unpack .../21-libharfbuzz0b_10.2.0-1_armhf.deb ... 311s Unpacking libharfbuzz0b:armhf (10.2.0-1) ... 311s Selecting previously unselected package libhtscodecs2:armhf. 311s Preparing to unpack .../22-libhtscodecs2_1.6.1-2_armhf.deb ... 311s Unpacking libhtscodecs2:armhf (1.6.1-2) ... 311s Selecting previously unselected package libhts3t64:armhf. 311s Preparing to unpack .../23-libhts3t64_1.21+ds-1_armhf.deb ... 311s Unpacking libhts3t64:armhf (1.21+ds-1) ... 311s Selecting previously unselected package x11-common. 311s Preparing to unpack .../24-x11-common_1%3a7.7+23ubuntu3_all.deb ... 311s Unpacking x11-common (1:7.7+23ubuntu3) ... 311s Selecting previously unselected package libice6:armhf. 311s Preparing to unpack .../25-libice6_2%3a1.1.1-1_armhf.deb ... 311s Unpacking libice6:armhf (2:1.1.1-1) ... 311s Selecting previously unselected package libjpeg-turbo8:armhf. 311s Preparing to unpack .../26-libjpeg-turbo8_2.1.5-3ubuntu2_armhf.deb ... 311s Unpacking libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 311s Selecting previously unselected package libjpeg8:armhf. 311s Preparing to unpack .../27-libjpeg8_8c-2ubuntu11_armhf.deb ... 311s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 311s Selecting previously unselected package liblapack3:armhf. 311s Preparing to unpack .../28-liblapack3_3.12.1-2_armhf.deb ... 311s Unpacking liblapack3:armhf (3.12.1-2) ... 311s Selecting previously unselected package liblerc4:armhf. 311s Preparing to unpack .../29-liblerc4_4.0.0+ds-5ubuntu1_armhf.deb ... 311s Unpacking liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 311s Selecting previously unselected package libthai-data. 311s Preparing to unpack .../30-libthai-data_0.1.29-2build1_all.deb ... 311s Unpacking libthai-data (0.1.29-2build1) ... 312s Selecting previously unselected package libthai0:armhf. 312s Preparing to unpack .../31-libthai0_0.1.29-2build1_armhf.deb ... 312s Unpacking libthai0:armhf (0.1.29-2build1) ... 312s Selecting previously unselected package libpango-1.0-0:armhf. 312s Preparing to unpack .../32-libpango-1.0-0_1.56.2-1_armhf.deb ... 312s Unpacking libpango-1.0-0:armhf (1.56.2-1) ... 312s Selecting previously unselected package libpangoft2-1.0-0:armhf. 312s Preparing to unpack .../33-libpangoft2-1.0-0_1.56.2-1_armhf.deb ... 312s Unpacking libpangoft2-1.0-0:armhf (1.56.2-1) ... 312s Selecting previously unselected package libpangocairo-1.0-0:armhf. 312s Preparing to unpack .../34-libpangocairo-1.0-0_1.56.2-1_armhf.deb ... 312s Unpacking libpangocairo-1.0-0:armhf (1.56.2-1) ... 312s Selecting previously unselected package libpaper2:armhf. 312s Preparing to unpack .../35-libpaper2_2.2.5-0.3_armhf.deb ... 312s Unpacking libpaper2:armhf (2.2.5-0.3) ... 312s Selecting previously unselected package libpaper-utils. 312s Preparing to unpack .../36-libpaper-utils_2.2.5-0.3_armhf.deb ... 312s Unpacking libpaper-utils (2.2.5-0.3) ... 312s Selecting previously unselected package libsharpyuv0:armhf. 312s Preparing to unpack .../37-libsharpyuv0_1.5.0-0.1_armhf.deb ... 312s Unpacking libsharpyuv0:armhf (1.5.0-0.1) ... 312s Selecting previously unselected package libsm6:armhf. 312s Preparing to unpack .../38-libsm6_2%3a1.2.4-1_armhf.deb ... 312s Unpacking libsm6:armhf (2:1.2.4-1) ... 312s Selecting previously unselected package libtcl8.6:armhf. 312s Preparing to unpack .../39-libtcl8.6_8.6.16+dfsg-1_armhf.deb ... 312s Unpacking libtcl8.6:armhf (8.6.16+dfsg-1) ... 312s Selecting previously unselected package libjbig0:armhf. 312s Preparing to unpack .../40-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 312s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ... 312s Selecting previously unselected package libwebp7:armhf. 312s Preparing to unpack .../41-libwebp7_1.5.0-0.1_armhf.deb ... 312s Unpacking libwebp7:armhf (1.5.0-0.1) ... 312s Selecting previously unselected package libtiff6:armhf. 312s Preparing to unpack .../42-libtiff6_4.5.1+git230720-4ubuntu4_armhf.deb ... 312s Unpacking libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 312s Selecting previously unselected package libxft2:armhf. 312s Preparing to unpack .../43-libxft2_2.3.6-1build1_armhf.deb ... 312s Unpacking libxft2:armhf (2.3.6-1build1) ... 312s Selecting previously unselected package libxss1:armhf. 312s Preparing to unpack .../44-libxss1_1%3a1.2.3-1build3_armhf.deb ... 312s Unpacking libxss1:armhf (1:1.2.3-1build3) ... 312s Selecting previously unselected package libtk8.6:armhf. 312s Preparing to unpack .../45-libtk8.6_8.6.16-1_armhf.deb ... 312s Unpacking libtk8.6:armhf (8.6.16-1) ... 313s Selecting previously unselected package libxt6t64:armhf. 313s Preparing to unpack .../46-libxt6t64_1%3a1.2.1-1.2build1_armhf.deb ... 313s Unpacking libxt6t64:armhf (1:1.2.1-1.2build1) ... 313s Selecting previously unselected package r-mathlib. 313s Preparing to unpack .../47-r-mathlib_4.4.3-1_armhf.deb ... 313s Unpacking r-mathlib (4.4.3-1) ... 313s Selecting previously unselected package zip. 313s Preparing to unpack .../48-zip_3.0-14ubuntu2_armhf.deb ... 313s Unpacking zip (3.0-14ubuntu2) ... 313s Selecting previously unselected package unzip. 313s Preparing to unpack .../49-unzip_6.0-28ubuntu6_armhf.deb ... 313s Unpacking unzip (6.0-28ubuntu6) ... 313s Selecting previously unselected package xdg-utils. 313s Preparing to unpack .../50-xdg-utils_1.2.1-2ubuntu1_all.deb ... 313s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 313s Selecting previously unselected package r-base-core. 313s Preparing to unpack .../51-r-base-core_4.4.3-1_armhf.deb ... 313s Unpacking r-base-core (4.4.3-1) ... 314s Selecting previously unselected package qtltools. 314s Preparing to unpack .../52-qtltools_1.3.1+dfsg-4build4_armhf.deb ... 314s Unpacking qtltools (1.3.1+dfsg-4build4) ... 314s Selecting previously unselected package qtltools-example. 314s Preparing to unpack .../53-qtltools-example_1.3.1+dfsg-4build4_all.deb ... 314s Unpacking qtltools-example (1.3.1+dfsg-4build4) ... 314s Setting up libhtscodecs2:armhf (1.6.1-2) ... 314s Setting up libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 314s Setting up qtltools-example (1.3.1+dfsg-4build4) ... 314s Setting up libboost-program-options1.83.0:armhf (1.83.0-4.1ubuntu2) ... 314s Setting up libpixman-1-0:armhf (0.44.0-3) ... 314s Setting up libsharpyuv0:armhf (1.5.0-0.1) ... 314s Setting up liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 314s Setting up libxrender1:armhf (1:0.9.10-1.1build1) ... 314s Setting up libdatrie1:armhf (0.2.13-3build1) ... 314s Setting up libgslcblas0:armhf (2.8+dfsg-5) ... 314s Setting up libxcb-render0:armhf (1.17.0-2) ... 314s Setting up unzip (6.0-28ubuntu6) ... 314s Setting up x11-common (1:7.7+23ubuntu3) ... 314s Setting up libdeflate0:armhf (1.23-1) ... 314s Setting up libxcb-shm0:armhf (1.17.0-2) ... 314s Setting up libgomp1:armhf (15-20250222-0ubuntu1) ... 314s Setting up libjbig0:armhf (2.1-6.1ubuntu2) ... 314s Setting up zip (3.0-14ubuntu2) ... 314s Setting up libblas3:armhf (3.12.1-2) ... 314s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 314s Setting up libfreetype6:armhf (2.13.3+dfsg-1) ... 314s Setting up libboost-iostreams1.83.0:armhf (1.83.0-4.1ubuntu2) ... 314s Setting up fonts-dejavu-mono (2.37-8) ... 314s Setting up libtcl8.6:armhf (8.6.16+dfsg-1) ... 314s Setting up fonts-dejavu-core (2.37-8) ... 314s Setting up libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 314s Setting up libgfortran5:armhf (15-20250222-0ubuntu1) ... 314s Setting up libwebp7:armhf (1.5.0-0.1) ... 314s Setting up r-mathlib (4.4.3-1) ... 315s Setting up libhts3t64:armhf (1.21+ds-1) ... 315s Setting up libharfbuzz0b:armhf (10.2.0-1) ... 315s Setting up libthai-data (0.1.29-2build1) ... 315s Setting up libxss1:armhf (1:1.2.3-1build3) ... 315s Setting up libpaper2:armhf (2.2.5-0.3) ... 315s Setting up libgsl28:armhf (2.8+dfsg-5) ... 315s Setting up xdg-utils (1.2.1-2ubuntu1) ... 315s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 315s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 315s Setting up libice6:armhf (2:1.1.1-1) ... 315s Setting up liblapack3:armhf (3.12.1-2) ... 315s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 315s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 315s Setting up libpaper-utils (2.2.5-0.3) ... 315s Setting up libthai0:armhf (0.1.29-2build1) ... 315s Setting up libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 315s Setting up libfontconfig1:armhf (2.15.0-2ubuntu1) ... 315s Setting up libsm6:armhf (2:1.2.4-1) ... 315s Setting up fontconfig (2.15.0-2ubuntu1) ... 317s Regenerating fonts cache... done. 317s Setting up libxft2:armhf (2.3.6-1build1) ... 317s Setting up libtk8.6:armhf (8.6.16-1) ... 317s Setting up libpango-1.0-0:armhf (1.56.2-1) ... 317s Setting up libcairo2:armhf (1.18.2-2) ... 317s Setting up libxt6t64:armhf (1:1.2.1-1.2build1) ... 317s Setting up libpangoft2-1.0-0:armhf (1.56.2-1) ... 317s Setting up libpangocairo-1.0-0:armhf (1.56.2-1) ... 317s Setting up r-base-core (4.4.3-1) ... 318s Creating config file /etc/R/Renviron with new version 318s Setting up qtltools (1.3.1+dfsg-4build4) ... 318s Processing triggers for man-db (2.13.0-1) ... 319s Processing triggers for install-info (7.1.1-1) ... 319s Processing triggers for libc-bin (2.41-1ubuntu2) ... 328s autopkgtest [16:01:32]: test run-sample-analysis: [----------------------- 331s ./genes.50percent.chr22.bed.gz 331s ./genes.50percent.chr22.bed.gz.tbi 331s ./genes.covariates.pc50.txt.gz 331s ./genes.simulated.chr22.bed.gz 331s ./genes.simulated.chr22.bed.gz.tbi 331s ./genotypes.chr22.vcf.gz 331s ./genotypes.chr22.vcf.gz.tbi 331s 331s QTLtools 331s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 331s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 331s * Webpage : https://qtltools.github.io/qtltools/ 331s * Version : 1.3.1 331s * Date : 15/03/2025 - 16:01:35 331s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 331s 331s CONDUCT PCA ON DATA 331s 331s Initialize random number generator 331s * Built-in seed is 15112011 331s * First Integer = 30553 331s * First Double = 0.0126695 331s 331s Reading sample list from [genes.50percent.chr22.bed.gz] 331s * #samples = 358 331s 331s Merging sample sets from all input files 331s * #files = 1 331s * #samples in all files = 358 331s 331s Reading phenotype data in [genes.50percent.chr22.bed.gz] 331s * 358 samples included 331s * 608 phenotypes included 331s 331s Calculating PCA with a matrix 358 x 608 331s * Calculated mean and sd 331s * 0 sd==0 columns removed 331s * Variables centered 331s * Variables scaled to unit variance 331s * Running SVD 332s * SVD complete 332s * Calculated sd and var for PCs 332s * Calculated cumulative var for PCs 333s * Done! 333s 333s Running time: 1 seconds 333s 333s QTLtools 333s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 333s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 333s * Webpage : https://qtltools.github.io/qtltools/ 333s * Version : 1.3.1 333s * Date : 15/03/2025 - 16:01:37 333s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 333s 333s MAPPING QTL IN CIS 333s * TASK: Report all nominal associations with p <= 0.01 333s * Linear model: Phe ~ Var + Cov 333s * Cis-window size is 1000000 bp 333s * Region = [chr22:17000000-18000000] 333s 333s Initialize random number generator 333s * Built-in seed is 15112011 333s * First Integer = 30553 333s * First Double = 0.0126695 333s 333s Reading sample list from [genes.50percent.chr22.bed.gz] 333s * #samples = 358 333s 333s Read sample list from [genotypes.chr22.vcf.gz] 333s * #samples = 358 333s 333s Reading sample list from [genes.covariates.pc50.txt.gz] 333s * #samples = 358 333s 333s Merging sample sets from all input files 333s * #files = 3 333s * #samples in all files = 358 333s 333s Reading phenotype data in [genes.50percent.chr22.bed.gz] 333s * target region [chr22:17000000-18000000] 333s * 8 phenotypes included 333s * 3 phenotypes are on the negative strand 333s 333s Reading genotype data in [genotypes.chr22.vcf.gz] 333s * File format detected: VCF 333s * target region [chr22:16000000-19000000] 333s * 6404 variants included 333s 333s Reading covariates in [genes.covariates.pc50.txt.gz] 333s * 53 covariates included 333s 333s Residualize phenotypes for covariates 333s * #covariates = 53 333s 333s Processing phenotype [ENSG00000237438.2] [1/8] 333s * #variants in cis = 5095 333s * Best hit: [id=22_17542810, d=25350, pv=1.1864e-25, s=-0.7518] 333s 333s Processing phenotype [ENSG00000273203.1] [2/8] 333s * #variants in cis = 5170 333s * Best hit: [id=22_17517388, d=-31323, pv=5.86611e-06, s=-0.1406] 333s 333s Processing phenotype [ENSG00000273442.1] [3/8] 333s * #variants in cis = 5188 333s * Best hit: [id=22_17553526, d=-8065, pv=0.000244522, s=0.1340] 333s 333s Processing phenotype [ENSG00000177663.9] [4/8] 333s * #variants in cis = 5193 333s * Best hit: [id=22_17513703, d=-52141, pv=8.03358e-14, s=-0.2096] 333s 333s Processing phenotype [ENSG00000183307.3] [5/8] 333s * #variants in cis = 5230 333s * Best hit: [id=22_17587975, d=14282, pv=1.56789e-07, s=-0.0078] 333s 333s Processing phenotype [ENSG00000069998.8] [6/8] 333s * #variants in cis = 5291 333s * Best hit: [id=22_17620429, d=25748, pv=1.37287e-14, s=-1.5147] 333s 333s Processing phenotype [ENSG00000093072.11] [7/8] 333s * #variants in cis = 5293 333s * Best hit: [id=22_17699630, d=3249, pv=0.000578649, s=0.6404] 333s 333s Processing phenotype [ENSG00000099954.14] [8/8] 333s * #variants in cis = 5435 333s * Best hit: [id=22_17175937, d=-664900, pv=0.000866455, s=0.0067] 333s 333s Running time: 0 seconds 333s 333s QTLtools 333s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 333s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 333s * Webpage : https://qtltools.github.io/qtltools/ 333s * Version : 1.3.1 333s * Date : 15/03/2025 - 16:01:37 333s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 333s 333s MAPPING QTL IN CIS 333s * TASK: Perform 1000 permutations 333s * Linear model: Phe ~ Var + Cov 333s * Cis-window size is 1000000 bp 333s * Region = [chr22:17000000-18000000] 333s 333s Initialize random number generator 333s * Built-in seed is 15112011 333s * First Integer = 30553 333s * First Double = 0.0126695 333s 333s Reading sample list from [genes.50percent.chr22.bed.gz] 333s * #samples = 358 333s 333s Read sample list from [genotypes.chr22.vcf.gz] 333s * #samples = 358 333s 333s Reading sample list from [genes.covariates.pc50.txt.gz] 333s * #samples = 358 333s 333s Merging sample sets from all input files 333s * #files = 3 333s * #samples in all files = 358 333s 333s Reading phenotype data in [genes.50percent.chr22.bed.gz] 333s * target region [chr22:17000000-18000000] 333s * 8 phenotypes included 333s * 3 phenotypes are on the negative strand 333s 333s Reading genotype data in [genotypes.chr22.vcf.gz] 333s * File format detected: VCF 333s * target region [chr22:16000000-19000000] 333s * 6404 variants included 333s 333s Reading covariates in [genes.covariates.pc50.txt.gz] 333s * 53 covariates included 333s 333s Residualize phenotypes for covariates 333s * #covariates = 53 333s 333s Processing phenotype [ENSG00000237438.2] [1/8] 333s * #variants in cis = 5095 335s * Best hit: [id=22_17542810, d=25350, pv=1.1864e-25, s=-0.7518] 335s * Beta parameters: [s1=1.00995, s2=621.053] 335s * Adjusted p-values: [emp=0.000999001, beta=1.28062e-20] 335s 335s Processing phenotype [ENSG00000273203.1] [2/8] 335s * #variants in cis = 5170 336s * Best hit: [id=22_17517388, d=-31323, pv=5.86611e-06, s=-0.1406] 336s * Beta parameters: [s1=1.11817, s2=641.379] 336s * Adjusted p-values: [emp=0.00799201, beta=0.00751892] 336s 336s Processing phenotype [ENSG00000273442.1] [3/8] 336s * #variants in cis = 5188 338s * Best hit: [id=22_17553526, d=-8065, pv=0.000244522, s=0.1340] 338s * Beta parameters: [s1=1.08364, s2=467.63] 338s * Adjusted p-values: [emp=0.297702, beta=0.293948] 338s 338s Processing phenotype [ENSG00000177663.9] [4/8] 338s * #variants in cis = 5193 340s * Best hit: [id=22_17513703, d=-52141, pv=8.03358e-14, s=-0.2096] 340s * Beta parameters: [s1=0.989061, s2=704.553] 340s * Adjusted p-values: [emp=0.000999001, beta=7.91291e-10] 340s 340s Processing phenotype [ENSG00000183307.3] [5/8] 340s * #variants in cis = 5230 341s * Best hit: [id=22_17587975, d=14282, pv=1.56789e-07, s=-0.0078] 341s * Beta parameters: [s1=1.01322, s2=559.49] 341s * Adjusted p-values: [emp=0.000999001, beta=0.00050707] 341s 341s Processing phenotype [ENSG00000069998.8] [6/8] 341s * #variants in cis = 5291 343s * Best hit: [id=22_17620429, d=25748, pv=1.37287e-14, s=-1.5147] 343s * Beta parameters: [s1=1.02312, s2=563.339] 343s * Adjusted p-values: [emp=0.000999001, beta=2.56935e-10] 343s 343s Processing phenotype [ENSG00000093072.11] [7/8] 343s * #variants in cis = 5293 345s * Best hit: [id=22_17699630, d=3249, pv=0.000578649, s=0.6404] 345s * Beta parameters: [s1=0.957514, s2=559.397] 345s * Adjusted p-values: [emp=0.574426, beta=0.562826] 345s 345s Processing phenotype [ENSG00000099954.14] [8/8] 345s * #variants in cis = 5435 346s * Best hit: [id=22_17175937, d=-664900, pv=0.000866455, s=0.0067] 346s * Beta parameters: [s1=0.938041, s2=226.852] 346s * Adjusted p-values: [emp=0.842158, beta=0.84836] 346s 346s Running time: 13 seconds 346s 346s QTLtools 346s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 346s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 346s * Webpage : https://qtltools.github.io/qtltools/ 346s * Version : 1.3.1 346s * Date : 15/03/2025 - 16:01:50 346s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 346s 346s MAPPING QTL IN TRANS 346s * TASK: Perform a full nominal pass, do not adjust p-values 346s * Cis-window size is 5000000 bp 346s * #bins = 1000 346s * threshold = 1e-05 346s 346s Initialize random number generator 346s * Built-in seed is 15112011 346s * First Integer = 30553 346s * First Double = 0.0126695 346s 346s Read sample list from [genotypes.chr22.vcf.gz] 346s * #samples = 358 346s 346s Checking sample list in [genes.simulated.chr22.bed.gz] 346s * #samples = 358 346s 346s Reading phenotype data in [genes.simulated.chr22.bed.gz] from line 0 to 0 346s * 358 samples included 347s * 608 phenotypes included 347s * 275 phenotypes is on the negative strand 347s 347s Calculate correlation threshold 347s * thres = 1e-05 347s * corr = 0.2311 347s 347s Sweep through genotype data in [genotypes.chr22.vcf.gz] 347s * #variants=1950 #multi_allelic=0 #not_processed=0 #hits=101/1000000 speed=2.69MT/s 347s * #variants=4001 #multi_allelic=0 #not_processed=0 #hits=153/2000000 speed=2.69MT/s 348s * #variants=6187 #multi_allelic=0 #not_processed=0 #hits=244/3000000 speed=2.63MT/s 348s * #variants=8537 #multi_allelic=0 #not_processed=0 #hits=285/4000000 speed=2.61MT/s 348s * #variants=11025 #multi_allelic=0 #not_processed=0 #hits=312/5000000 speed=2.62MT/s 349s * #variants=13621 #multi_allelic=0 #not_processed=0 #hits=320/6000000 speed=2.65MT/s 349s * #variants=16217 #multi_allelic=0 #not_processed=0 #hits=342/7000000 speed=2.62MT/s 350s * #variants=18755 #multi_allelic=0 #not_processed=0 #hits=401/8000000 speed=2.63MT/s 350s * #variants=21237 #multi_allelic=0 #not_processed=0 #hits=402/9000000 speed=2.64MT/s 350s * #variants=23680 #multi_allelic=0 #not_processed=0 #hits=455/10000000 speed=2.62MT/s 351s * #variants=26171 #multi_allelic=0 #not_processed=0 #hits=463/11000000 speed=2.62MT/s 351s * #variants=28609 #multi_allelic=0 #not_processed=0 #hits=469/12000000 speed=2.65MT/s 351s * #variants=30861 #multi_allelic=0 #not_processed=0 #hits=973/13000000 speed=2.56MT/s 352s * #variants=32932 #multi_allelic=0 #not_processed=0 #hits=979/14000000 speed=2.72MT/s 352s * #variants=34974 #multi_allelic=0 #not_processed=0 #hits=1085/15000000 speed=2.70MT/s 353s * #variants=37021 #multi_allelic=0 #not_processed=0 #hits=1086/16000000 speed=2.73MT/s 353s * #variants=39122 #multi_allelic=0 #not_processed=0 #hits=1089/17000000 speed=2.72MT/s 353s * #variants=41334 #multi_allelic=0 #not_processed=0 #hits=1089/18000000 speed=2.70MT/s 354s * #variants=43627 #multi_allelic=0 #not_processed=0 #hits=1096/19000000 speed=2.67MT/s 354s * #variants=45897 #multi_allelic=0 #not_processed=0 #hits=1153/20000000 speed=2.64MT/s 354s * #variants=48114 #multi_allelic=0 #not_processed=0 #hits=1243/21000000 speed=2.62MT/s 355s * #variants=50410 #multi_allelic=0 #not_processed=0 #hits=1249/22000000 speed=2.65MT/s 355s * #variants=52820 #multi_allelic=0 #not_processed=0 #hits=1259/23000000 speed=2.65MT/s 356s * #variants=55279 #multi_allelic=0 #not_processed=0 #hits=1498/24000000 speed=2.62MT/s 356s * #variants=57789 #multi_allelic=0 #not_processed=0 #hits=1724/25000000 speed=2.62MT/s 356s * #variants=60201 #multi_allelic=0 #not_processed=0 #hits=2168/26000000 speed=2.62MT/s 357s * #variants=62476 #multi_allelic=0 #not_processed=0 #hits=2452/27000000 speed=2.64MT/s 357s * #variants=64608 #multi_allelic=0 #not_processed=0 #hits=2544/28000000 speed=2.73MT/s 357s * #variants=66709 #multi_allelic=0 #not_processed=0 #hits=2684/29000000 speed=2.72MT/s 358s * #variants=68871 #multi_allelic=0 #not_processed=0 #hits=2688/30000000 speed=2.72MT/s 358s * #variants=71070 #multi_allelic=0 #not_processed=0 #hits=2720/31000000 speed=2.70MT/s 359s * #variants=73151 #multi_allelic=0 #not_processed=0 #hits=2891/32000000 speed=2.70MT/s 359s * #variants=75122 #multi_allelic=0 #not_processed=0 #hits=3110/33000000 speed=2.72MT/s 359s * #variants=77058 #multi_allelic=0 #not_processed=0 #hits=3209/34000000 speed=2.74MT/s 360s * #variants=78989 #multi_allelic=0 #not_processed=0 #hits=3218/35000000 speed=2.75MT/s 360s * #variants=80903 #multi_allelic=0 #not_processed=0 #hits=3250/36000000 speed=2.77MT/s 360s * #variants=82811 #multi_allelic=0 #not_processed=0 #hits=3463/37000000 speed=2.74MT/s 361s * #variants=84694 #multi_allelic=0 #not_processed=0 #hits=4035/38000000 speed=2.68MT/s 361s * #variants=85485 #multi_allelic=0 #not_processed=0 #hits=4036/38425275 speed=2.80MT/s 361s 361s Running time: 14 seconds 361s 361s QTLtools 361s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 361s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 361s * Webpage : https://qtltools.github.io/qtltools/ 361s * Version : 1.3.1 361s * Date : 15/03/2025 - 16:02:05 361s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 361s 361s MAPPING QTL IN TRANS 361s * TASK: Permute randomly chosen phenotypes 1000 times and test 361s * Cis-window size is 5000000 bp 361s * #bins = 1000 361s * threshold = 1e-05 361s 361s Initialize random number generator 361s * Built-in seed is 15112011 361s * First Integer = 30553 361s * First Double = 0.0126695 361s 361s Read sample list from [genotypes.chr22.vcf.gz] 361s * #samples = 358 361s 361s Checking sample list in [genes.simulated.chr22.bed.gz] 361s * #samples = 358 361s 361s Reading phenotype data in [genes.simulated.chr22.bed.gz] from line 0 to 0 361s * 358 samples included 361s * 608 phenotypes included 361s * 275 phenotypes is on the negative strand 361s 361s Normal transform phenotypes 361s 361s Calculate correlation threshold 361s * thres = 1e-05 361s * corr = 0.2311 361s 361s Sweep through genotype data in [genotypes.chr22.vcf.gz] 361s * #variants=1177 #multi_allelic=0 #not_processed=0 #hits=28/1000000 speed=2.67MT/s 362s * #variants=2383 #multi_allelic=0 #not_processed=0 #hits=38/2000000 speed=2.64MT/s 362s * #variants=3633 #multi_allelic=0 #not_processed=0 #hits=53/3000000 speed=2.61MT/s 363s * #variants=4928 #multi_allelic=0 #not_processed=0 #hits=53/4000000 speed=2.61MT/s 363s * #variants=6269 #multi_allelic=0 #not_processed=0 #hits=71/5000000 speed=2.55MT/s 363s * #variants=7675 #multi_allelic=0 #not_processed=0 #hits=72/6000000 speed=2.48MT/s 364s * #variants=9151 #multi_allelic=0 #not_processed=0 #hits=88/7000000 speed=2.42MT/s 364s * #variants=10663 #multi_allelic=0 #not_processed=0 #hits=96/8000000 speed=2.42MT/s 365s * #variants=12202 #multi_allelic=0 #not_processed=0 #hits=96/9000000 speed=2.40MT/s 365s * #variants=13804 #multi_allelic=0 #not_processed=0 #hits=96/10000000 speed=2.39MT/s 365s * #variants=15381 #multi_allelic=0 #not_processed=0 #hits=120/11000000 speed=2.38MT/s 366s * #variants=16946 #multi_allelic=0 #not_processed=0 #hits=123/12000000 speed=2.39MT/s 366s * #variants=18483 #multi_allelic=0 #not_processed=0 #hits=129/13000000 speed=2.39MT/s 367s * #variants=19995 #multi_allelic=0 #not_processed=0 #hits=131/14000000 speed=2.45MT/s 367s * #variants=21489 #multi_allelic=0 #not_processed=0 #hits=132/15000000 speed=2.44MT/s 368s * #variants=22947 #multi_allelic=0 #not_processed=0 #hits=151/16000000 speed=2.43MT/s 368s * #variants=24445 #multi_allelic=0 #not_processed=0 #hits=168/17000000 speed=2.39MT/s 368s * #variants=25965 #multi_allelic=0 #not_processed=0 #hits=175/18000000 speed=2.41MT/s 369s * #variants=27472 #multi_allelic=0 #not_processed=0 #hits=179/19000000 speed=2.40MT/s 369s * #variants=28933 #multi_allelic=0 #not_processed=0 #hits=181/20000000 speed=2.46MT/s 370s * #variants=30325 #multi_allelic=0 #not_processed=0 #hits=181/21000000 speed=2.48MT/s 370s * #variants=31617 #multi_allelic=0 #not_processed=0 #hits=182/22000000 speed=2.57MT/s 370s * #variants=32875 #multi_allelic=0 #not_processed=0 #hits=190/23000000 speed=2.60MT/s 371s * #variants=34127 #multi_allelic=0 #not_processed=0 #hits=192/24000000 speed=2.59MT/s 371s * #variants=35392 #multi_allelic=0 #not_processed=0 #hits=206/25000000 speed=2.55MT/s 372s * #variants=36652 #multi_allelic=0 #not_processed=0 #hits=206/26000000 speed=2.60MT/s 372s * #variants=37940 #multi_allelic=0 #not_processed=0 #hits=213/27000000 speed=2.54MT/s 372s * #variants=39255 #multi_allelic=0 #not_processed=0 #hits=238/28000000 speed=2.49MT/s 373s * #variants=40602 #multi_allelic=0 #not_processed=0 #hits=239/29000000 speed=2.49MT/s 373s * #variants=41998 #multi_allelic=0 #not_processed=0 #hits=245/30000000 speed=2.48MT/s 374s * #variants=43398 #multi_allelic=0 #not_processed=0 #hits=245/31000000 speed=2.50MT/s 374s * #variants=44803 #multi_allelic=0 #not_processed=0 #hits=260/32000000 speed=2.46MT/s 374s * #variants=46187 #multi_allelic=0 #not_processed=0 #hits=261/33000000 speed=2.51MT/s 375s * #variants=47545 #multi_allelic=0 #not_processed=0 #hits=268/34000000 speed=2.50MT/s 375s * #variants=48904 #multi_allelic=0 #not_processed=0 #hits=280/35000000 speed=2.49MT/s 376s * #variants=50309 #multi_allelic=0 #not_processed=0 #hits=306/36000000 speed=2.48MT/s 376s * #variants=51731 #multi_allelic=0 #not_processed=0 #hits=314/37000000 speed=2.48MT/s 376s * #variants=53171 #multi_allelic=0 #not_processed=0 #hits=320/38000000 speed=2.48MT/s 377s * #variants=54621 #multi_allelic=0 #not_processed=0 #hits=323/39000000 speed=2.49MT/s 379s * #variants=56099 #multi_allelic=0 #not_processed=0 #hits=323/40000000 speed=2.46MT/s 379s * #variants=57584 #multi_allelic=0 #not_processed=0 #hits=340/41000000 speed=2.43MT/s 379s * #variants=59032 #multi_allelic=0 #not_processed=0 #hits=344/42000000 speed=2.49MT/s 379s * #variants=60437 #multi_allelic=0 #not_processed=0 #hits=345/43000000 speed=2.49MT/s 379s * #variants=61810 #multi_allelic=0 #not_processed=0 #hits=357/44000000 speed=2.52MT/s 379s * #variants=63129 #multi_allelic=0 #not_processed=0 #hits=384/45000000 speed=2.53MT/s 380s * #variants=64409 #multi_allelic=0 #not_processed=0 #hits=391/46000000 speed=2.56MT/s 380s * #variants=65679 #multi_allelic=0 #not_processed=0 #hits=430/47000000 speed=2.59MT/s 380s * #variants=66953 #multi_allelic=0 #not_processed=0 #hits=436/48000000 speed=2.55MT/s 381s * #variants=68247 #multi_allelic=0 #not_processed=0 #hits=446/49000000 speed=2.53MT/s 381s * #variants=69595 #multi_allelic=0 #not_processed=0 #hits=460/50000000 speed=2.48MT/s 382s * #variants=70918 #multi_allelic=0 #not_processed=0 #hits=481/51000000 speed=2.45MT/s 382s * #variants=72211 #multi_allelic=0 #not_processed=0 #hits=492/52000000 speed=2.48MT/s 382s * #variants=73449 #multi_allelic=0 #not_processed=0 #hits=492/53000000 speed=2.57MT/s 383s * #variants=74662 #multi_allelic=0 #not_processed=0 #hits=500/54000000 speed=2.56MT/s 383s * #variants=75863 #multi_allelic=0 #not_processed=0 #hits=506/55000000 speed=2.57MT/s 384s * #variants=77058 #multi_allelic=0 #not_processed=0 #hits=513/56000000 speed=2.57MT/s 384s * #variants=78253 #multi_allelic=0 #not_processed=0 #hits=515/57000000 speed=2.56MT/s 384s * #variants=79446 #multi_allelic=0 #not_processed=0 #hits=530/58000000 speed=2.58MT/s 385s * #variants=80634 #multi_allelic=0 #not_processed=0 #hits=581/59000000 speed=2.56MT/s 385s * #variants=81817 #multi_allelic=0 #not_processed=0 #hits=594/60000000 speed=2.58MT/s 385s * #variants=82993 #multi_allelic=0 #not_processed=0 #hits=598/61000000 speed=2.61MT/s 386s * #variants=84160 #multi_allelic=0 #not_processed=0 #hits=599/62000000 speed=2.61MT/s 386s * #variants=85304 #multi_allelic=0 #not_processed=0 #hits=609/63000000 speed=2.66MT/s 386s * #variants=85485 #multi_allelic=0 #not_processed=0 #hits=609/63157827 speed=2.68MT/s 386s 386s Running time: 25 seconds 387s autopkgtest [16:02:31]: test run-sample-analysis: -----------------------] 391s run-sample-analysis PASS 391s autopkgtest [16:02:35]: test run-sample-analysis: - - - - - - - - - - results - - - - - - - - - - 394s autopkgtest [16:02:38]: @@@@@@@@@@@@@@@@@@@@ summary 394s run-sample-analysis PASS