0s autopkgtest [10:07:06]: starting date and time: 2026-02-05 10:07:06+0000 0s autopkgtest [10:07:06]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [10:07:06]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.6fp_t_aq/out --timeout-copy=6000 --needs-internet=try --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/2.42-2ubuntu5 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-ppc64el-25.secgroup --name adt-resolute-ppc64el-qtltools-20260205-100706-juju-7f2275-prod-proposed-migration-environment-2-02ce1123-34e0-483d-a3a4-c86a8032ea7a --image adt/ubuntu-resolute-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-ppc64el -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-ppc64el-qtltools-20260205-100706-juju-7f2275-prod-proposed-migration-environment-2-02ce1123-34e0-483d-a3a4-c86a8032ea7a from image adt/ubuntu-resolute-ppc64el-server-20260205.img (UUID f866c950-0b62-4023-bac6-0f13279e15ed)... 84s autopkgtest [10:08:30]: testbed dpkg architecture: ppc64el 84s autopkgtest [10:08:30]: testbed apt version: 3.1.14 85s autopkgtest [10:08:31]: @@@@@@@@@@@@@@@@@@@@ test bed setup 85s autopkgtest [10:08:31]: testbed release detected to be: None 86s autopkgtest [10:08:32]: updating testbed package index (apt update) 86s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 86s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 86s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 86s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 86s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [227 kB] 86s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5260 B] 86s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1696 kB] 86s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [35.4 kB] 86s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el Packages [261 kB] 86s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el Packages [1492 kB] 86s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse ppc64el Packages [21.9 kB] 87s Fetched 3863 kB in 1s (4840 kB/s) 88s Reading package lists... 88s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 88s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 88s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 88s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 89s Reading package lists... 89s Reading package lists... 89s Building dependency tree... 89s Reading state information... 89s Calculating upgrade... 89s The following packages will be upgraded: 89s libc-bin libc-gconv-modules-extra libc6 locales pollinate 89s python3-referencing sed 89s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 89s Need to get 8612 kB of archives. 89s After this operation, 0 B of additional disk space will be used. 89s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el sed ppc64el 4.9-2build3 [211 kB] 90s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el libc-gconv-modules-extra ppc64el 2.42-2ubuntu5 [1448 kB] 90s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el libc6 ppc64el 2.42-2ubuntu5 [1913 kB] 90s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el libc-bin ppc64el 2.42-2ubuntu5 [748 kB] 90s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el locales all 2.42-2ubuntu5 [4255 kB] 90s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el pollinate all 4.33-4ubuntu5 [14.0 kB] 90s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-referencing all 0.36.2-1ubuntu2 [22.2 kB] 90s dpkg-preconfigure: unable to re-open stdin: No such file or directory 90s Fetched 8612 kB in 0s (23.1 MB/s) 90s (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 ... 82008 files and directories currently installed.) 90s Preparing to unpack .../sed_4.9-2build3_ppc64el.deb ... 90s Unpacking sed (4.9-2build3) over (4.9-2build2) ... 90s Setting up sed (4.9-2build3) ... 91s (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 ... 82008 files and directories currently installed.) 91s Preparing to unpack .../libc-gconv-modules-extra_2.42-2ubuntu5_ppc64el.deb ... 91s Unpacking libc-gconv-modules-extra:ppc64el (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 91s Setting up libc-gconv-modules-extra:ppc64el (2.42-2ubuntu5) ... 91s (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 ... 82008 files and directories currently installed.) 91s Preparing to unpack .../libc6_2.42-2ubuntu5_ppc64el.deb ... 92s Unpacking libc6:ppc64el (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 92s Setting up libc6:ppc64el (2.42-2ubuntu5) ... 92s (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 ... 82008 files and directories currently installed.) 92s Preparing to unpack .../libc-bin_2.42-2ubuntu5_ppc64el.deb ... 92s Unpacking libc-bin (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 92s Setting up libc-bin (2.42-2ubuntu5) ... 92s (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 ... 82008 files and directories currently installed.) 92s Preparing to unpack .../locales_2.42-2ubuntu5_all.deb ... 92s Unpacking locales (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 93s Preparing to unpack .../pollinate_4.33-4ubuntu5_all.deb ... 93s Unpacking pollinate (4.33-4ubuntu5) over (4.33-4ubuntu4) ... 93s Preparing to unpack .../python3-referencing_0.36.2-1ubuntu2_all.deb ... 93s Unpacking python3-referencing (0.36.2-1ubuntu2) over (0.36.2-1ubuntu1) ... 93s Setting up locales (2.42-2ubuntu5) ... 93s Generating locales (this might take a while)... 95s en_US.UTF-8... done 95s Generation complete. 95s Setting up pollinate (4.33-4ubuntu5) ... 105s Setting up python3-referencing (0.36.2-1ubuntu2) ... 105s Processing triggers for man-db (2.13.1-1) ... 107s Processing triggers for install-info (7.2-5) ... 107s Processing triggers for systemd (259-1ubuntu3) ... 108s autopkgtest [10:08:54]: upgrading testbed (apt dist-upgrade and autopurge) 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 108s Calculating upgrade... 109s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 109s Reading package lists... 109s Building dependency tree... 109s Reading state information... 109s Solving dependencies... 109s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 109s autopkgtest [10:08:55]: rebooting testbed after setup commands that affected boot 147s autopkgtest [10:09:33]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:45:54 UTC 2026 150s autopkgtest [10:09:36]: @@@@@@@@@@@@@@@@@@@@ apt-source qtltools 155s Get:1 http://ftpmaster.internal/ubuntu resolute/universe qtltools 1.3.1+dfsg-4build6 (dsc) [2293 B] 155s Get:2 http://ftpmaster.internal/ubuntu resolute/universe qtltools 1.3.1+dfsg-4build6 (tar) [141 kB] 155s Get:3 http://ftpmaster.internal/ubuntu resolute/universe qtltools 1.3.1+dfsg-4build6 (diff) [13.6 MB] 155s gpgv: Signature made Wed Aug 6 15:09:47 2025 UTC 155s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 155s gpgv: Can't check signature: No public key 155s dpkg-source: warning: cannot verify inline signature for ./qtltools_1.3.1+dfsg-4build6.dsc: no acceptable signature found 156s autopkgtest [10:09:42]: testing package qtltools version 1.3.1+dfsg-4build6 158s autopkgtest [10:09:44]: build not needed 158s autopkgtest [10:09:44]: test run-sample-analysis: preparing testbed 158s Reading package lists... 159s Building dependency tree... 159s Reading state information... 159s Solving dependencies... 159s The following NEW packages will be installed: 159s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 159s libboost-iostreams1.88.0 libboost-program-options1.88.0 libcairo2 libdatrie1 159s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 libgsl28 159s libgslcblas0 libharfbuzz0b libhts3t64 libhtscodecs2 libice6 libjbig0 159s libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0 159s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 159s libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 159s libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 159s qtltools qtltools-example r-base-core r-mathlib unzip x11-common xdg-utils 159s zip 159s 0 upgraded, 53 newly installed, 0 to remove and 0 not upgraded. 159s Need to get 62.1 MB of archives. 159s After this operation, 123 MB of additional disk space will be used. 159s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-dejavu-mono all 2.37-8build1 [502 kB] 159s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-dejavu-core all 2.37-8build1 [834 kB] 159s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el fontconfig-config ppc64el 2.17.1-3ubuntu1 [38.5 kB] 159s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el libfontconfig1 ppc64el 2.17.1-3ubuntu1 [193 kB] 159s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el fontconfig ppc64el 2.17.1-3ubuntu1 [182 kB] 159s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el libblas3 ppc64el 3.12.1-7ubuntu1 [291 kB] 159s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el libboost-iostreams1.88.0 ppc64el 1.88.0-1.4ubuntu3 [262 kB] 159s Get:8 http://ftpmaster.internal/ubuntu resolute/main ppc64el libboost-program-options1.88.0 ppc64el 1.88.0-1.4ubuntu3 [334 kB] 159s Get:9 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpixman-1-0 ppc64el 0.46.4-1 [347 kB] 159s Get:10 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxcb-render0 ppc64el 1.17.0-2ubuntu1 [17.4 kB] 159s Get:11 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxcb-shm0 ppc64el 1.17.0-2ubuntu1 [6072 B] 159s Get:12 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxrender1 ppc64el 1:0.9.12-1 [23.0 kB] 159s Get:13 http://ftpmaster.internal/ubuntu resolute/main ppc64el libcairo2 ppc64el 1.18.4-3 [759 kB] 159s Get:14 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdatrie1 ppc64el 0.2.14-1 [22.7 kB] 159s Get:15 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdeflate0 ppc64el 1.23-2 [63.3 kB] 159s Get:16 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgfortran5 ppc64el 15.2.0-12ubuntu1 [620 kB] 159s Get:17 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgomp1 ppc64el 15.2.0-12ubuntu1 [169 kB] 159s Get:18 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgraphite2-3 ppc64el 1.3.14-11ubuntu1 [85.3 kB] 159s Get:19 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libgslcblas0 ppc64el 2.8+dfsg-6 [283 kB] 159s Get:20 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libgsl28 ppc64el 2.8+dfsg-6 [1411 kB] 159s Get:21 http://ftpmaster.internal/ubuntu resolute/main ppc64el libharfbuzz0b ppc64el 12.3.2-1 [663 kB] 159s Get:22 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhtscodecs2 ppc64el 1.6.1-2build1 [119 kB] 159s Get:23 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhts3t64 ppc64el 1.22.1+ds2-1 [617 kB] 159s Get:24 http://ftpmaster.internal/ubuntu resolute/main ppc64el x11-common all 1:7.7+24ubuntu1 [22.4 kB] 159s Get:25 http://ftpmaster.internal/ubuntu resolute/main ppc64el libice6 ppc64el 2:1.1.1-1build1 [51.9 kB] 159s Get:26 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-4ubuntu2 [215 kB] 159s Get:27 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 159s Get:28 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblapack3 ppc64el 3.12.1-7ubuntu1 [2960 kB] 160s Get:29 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblerc4 ppc64el 4.0.0+ds-5ubuntu2 [315 kB] 160s Get:30 http://ftpmaster.internal/ubuntu resolute/main ppc64el libthai-data all 0.1.30-1 [155 kB] 160s Get:31 http://ftpmaster.internal/ubuntu resolute/main ppc64el libthai0 ppc64el 0.1.30-1 [22.5 kB] 160s Get:32 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpango-1.0-0 ppc64el 1.57.0-1 [283 kB] 160s Get:33 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpangoft2-1.0-0 ppc64el 1.57.0-1 [61.2 kB] 160s Get:34 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpangocairo-1.0-0 ppc64el 1.57.0-1 [31.0 kB] 160s Get:35 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpaper2 ppc64el 2.2.5-0.3build1 [18.1 kB] 160s Get:36 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpaper-utils ppc64el 2.2.5-0.3build1 [15.7 kB] 160s Get:37 http://ftpmaster.internal/ubuntu resolute/main ppc64el libsharpyuv0 ppc64el 1.5.0-0.1build1 [24.7 kB] 160s Get:38 http://ftpmaster.internal/ubuntu resolute/main ppc64el libsm6 ppc64el 2:1.2.6-1 [18.6 kB] 160s Get:39 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtcl8.6 ppc64el 8.6.17+dfsg-1build1 [1239 kB] 160s Get:40 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu3 [37.1 kB] 160s Get:41 http://ftpmaster.internal/ubuntu resolute/main ppc64el libwebp7 ppc64el 1.5.0-0.1build1 [330 kB] 160s Get:42 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtiff6 ppc64el 4.7.0-3ubuntu3 [307 kB] 160s Get:43 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxft2 ppc64el 2.3.6-1build2 [61.6 kB] 160s Get:44 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxss1 ppc64el 1:1.2.3-1build4 [7470 B] 160s Get:45 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtk8.6 ppc64el 8.6.17-1 [968 kB] 160s Get:46 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxt6t64 ppc64el 1:1.2.1-1.3 [203 kB] 160s Get:47 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-mathlib ppc64el 4.5.2-1ubuntu2 [2665 kB] 160s Get:48 http://ftpmaster.internal/ubuntu resolute/main ppc64el zip ppc64el 3.0-15ubuntu2 [198 kB] 160s Get:49 http://ftpmaster.internal/ubuntu resolute/main ppc64el unzip ppc64el 6.0-29ubuntu1 [200 kB] 160s Get:50 http://ftpmaster.internal/ubuntu resolute/main ppc64el xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 160s Get:51 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-base-core ppc64el 4.5.2-1ubuntu2 [29.3 MB] 161s Get:52 http://ftpmaster.internal/ubuntu resolute/universe ppc64el qtltools ppc64el 1.3.1+dfsg-4build6 [885 kB] 161s Get:53 http://ftpmaster.internal/ubuntu resolute/universe ppc64el qtltools-example all 1.3.1+dfsg-4build6 [13.6 MB] 161s Preconfiguring packages ... 161s Fetched 62.1 MB in 2s (28.2 MB/s) 161s Selecting previously unselected package fonts-dejavu-mono. 162s (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 ... 82008 files and directories currently installed.) 162s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8build1_all.deb ... 162s Unpacking fonts-dejavu-mono (2.37-8build1) ... 162s Selecting previously unselected package fonts-dejavu-core. 162s Preparing to unpack .../01-fonts-dejavu-core_2.37-8build1_all.deb ... 162s Unpacking fonts-dejavu-core (2.37-8build1) ... 162s Selecting previously unselected package fontconfig-config. 162s Preparing to unpack .../02-fontconfig-config_2.17.1-3ubuntu1_ppc64el.deb ... 162s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 162s Selecting previously unselected package libfontconfig1:ppc64el. 162s Preparing to unpack .../03-libfontconfig1_2.17.1-3ubuntu1_ppc64el.deb ... 162s Unpacking libfontconfig1:ppc64el (2.17.1-3ubuntu1) ... 162s Selecting previously unselected package fontconfig. 162s Preparing to unpack .../04-fontconfig_2.17.1-3ubuntu1_ppc64el.deb ... 162s Unpacking fontconfig (2.17.1-3ubuntu1) ... 162s Selecting previously unselected package libblas3:ppc64el. 162s Preparing to unpack .../05-libblas3_3.12.1-7ubuntu1_ppc64el.deb ... 162s Unpacking libblas3:ppc64el (3.12.1-7ubuntu1) ... 162s Selecting previously unselected package libboost-iostreams1.88.0:ppc64el. 162s Preparing to unpack .../06-libboost-iostreams1.88.0_1.88.0-1.4ubuntu3_ppc64el.deb ... 162s Unpacking libboost-iostreams1.88.0:ppc64el (1.88.0-1.4ubuntu3) ... 162s Selecting previously unselected package libboost-program-options1.88.0:ppc64el. 162s Preparing to unpack .../07-libboost-program-options1.88.0_1.88.0-1.4ubuntu3_ppc64el.deb ... 162s Unpacking libboost-program-options1.88.0:ppc64el (1.88.0-1.4ubuntu3) ... 162s Selecting previously unselected package libpixman-1-0:ppc64el. 162s Preparing to unpack .../08-libpixman-1-0_0.46.4-1_ppc64el.deb ... 162s Unpacking libpixman-1-0:ppc64el (0.46.4-1) ... 162s Selecting previously unselected package libxcb-render0:ppc64el. 162s Preparing to unpack .../09-libxcb-render0_1.17.0-2ubuntu1_ppc64el.deb ... 162s Unpacking libxcb-render0:ppc64el (1.17.0-2ubuntu1) ... 162s Selecting previously unselected package libxcb-shm0:ppc64el. 162s Preparing to unpack .../10-libxcb-shm0_1.17.0-2ubuntu1_ppc64el.deb ... 162s Unpacking libxcb-shm0:ppc64el (1.17.0-2ubuntu1) ... 162s Selecting previously unselected package libxrender1:ppc64el. 162s Preparing to unpack .../11-libxrender1_1%3a0.9.12-1_ppc64el.deb ... 162s Unpacking libxrender1:ppc64el (1:0.9.12-1) ... 162s Selecting previously unselected package libcairo2:ppc64el. 162s Preparing to unpack .../12-libcairo2_1.18.4-3_ppc64el.deb ... 162s Unpacking libcairo2:ppc64el (1.18.4-3) ... 162s Selecting previously unselected package libdatrie1:ppc64el. 162s Preparing to unpack .../13-libdatrie1_0.2.14-1_ppc64el.deb ... 162s Unpacking libdatrie1:ppc64el (0.2.14-1) ... 162s Selecting previously unselected package libdeflate0:ppc64el. 162s Preparing to unpack .../14-libdeflate0_1.23-2_ppc64el.deb ... 162s Unpacking libdeflate0:ppc64el (1.23-2) ... 162s Selecting previously unselected package libgfortran5:ppc64el. 162s Preparing to unpack .../15-libgfortran5_15.2.0-12ubuntu1_ppc64el.deb ... 162s Unpacking libgfortran5:ppc64el (15.2.0-12ubuntu1) ... 162s Selecting previously unselected package libgomp1:ppc64el. 162s Preparing to unpack .../16-libgomp1_15.2.0-12ubuntu1_ppc64el.deb ... 162s Unpacking libgomp1:ppc64el (15.2.0-12ubuntu1) ... 162s Selecting previously unselected package libgraphite2-3:ppc64el. 162s Preparing to unpack .../17-libgraphite2-3_1.3.14-11ubuntu1_ppc64el.deb ... 162s Unpacking libgraphite2-3:ppc64el (1.3.14-11ubuntu1) ... 162s Selecting previously unselected package libgslcblas0:ppc64el. 162s Preparing to unpack .../18-libgslcblas0_2.8+dfsg-6_ppc64el.deb ... 162s Unpacking libgslcblas0:ppc64el (2.8+dfsg-6) ... 162s Selecting previously unselected package libgsl28:ppc64el. 162s Preparing to unpack .../19-libgsl28_2.8+dfsg-6_ppc64el.deb ... 162s Unpacking libgsl28:ppc64el (2.8+dfsg-6) ... 162s Selecting previously unselected package libharfbuzz0b:ppc64el. 162s Preparing to unpack .../20-libharfbuzz0b_12.3.2-1_ppc64el.deb ... 162s Unpacking libharfbuzz0b:ppc64el (12.3.2-1) ... 162s Selecting previously unselected package libhtscodecs2:ppc64el. 162s Preparing to unpack .../21-libhtscodecs2_1.6.1-2build1_ppc64el.deb ... 162s Unpacking libhtscodecs2:ppc64el (1.6.1-2build1) ... 162s Selecting previously unselected package libhts3t64:ppc64el. 162s Preparing to unpack .../22-libhts3t64_1.22.1+ds2-1_ppc64el.deb ... 162s Unpacking libhts3t64:ppc64el (1.22.1+ds2-1) ... 162s Selecting previously unselected package x11-common. 162s Preparing to unpack .../23-x11-common_1%3a7.7+24ubuntu1_all.deb ... 162s Unpacking x11-common (1:7.7+24ubuntu1) ... 162s Selecting previously unselected package libice6:ppc64el. 162s Preparing to unpack .../24-libice6_2%3a1.1.1-1build1_ppc64el.deb ... 162s Unpacking libice6:ppc64el (2:1.1.1-1build1) ... 162s Selecting previously unselected package libjpeg-turbo8:ppc64el. 162s Preparing to unpack .../25-libjpeg-turbo8_2.1.5-4ubuntu2_ppc64el.deb ... 162s Unpacking libjpeg-turbo8:ppc64el (2.1.5-4ubuntu2) ... 162s Selecting previously unselected package libjpeg8:ppc64el. 162s Preparing to unpack .../26-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 162s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 162s Selecting previously unselected package liblapack3:ppc64el. 162s Preparing to unpack .../27-liblapack3_3.12.1-7ubuntu1_ppc64el.deb ... 162s Unpacking liblapack3:ppc64el (3.12.1-7ubuntu1) ... 162s Selecting previously unselected package liblerc4:ppc64el. 162s Preparing to unpack .../28-liblerc4_4.0.0+ds-5ubuntu2_ppc64el.deb ... 162s Unpacking liblerc4:ppc64el (4.0.0+ds-5ubuntu2) ... 162s Selecting previously unselected package libthai-data. 162s Preparing to unpack .../29-libthai-data_0.1.30-1_all.deb ... 162s Unpacking libthai-data (0.1.30-1) ... 163s Selecting previously unselected package libthai0:ppc64el. 163s Preparing to unpack .../30-libthai0_0.1.30-1_ppc64el.deb ... 163s Unpacking libthai0:ppc64el (0.1.30-1) ... 163s Selecting previously unselected package libpango-1.0-0:ppc64el. 163s Preparing to unpack .../31-libpango-1.0-0_1.57.0-1_ppc64el.deb ... 163s Unpacking libpango-1.0-0:ppc64el (1.57.0-1) ... 163s Selecting previously unselected package libpangoft2-1.0-0:ppc64el. 163s Preparing to unpack .../32-libpangoft2-1.0-0_1.57.0-1_ppc64el.deb ... 163s Unpacking libpangoft2-1.0-0:ppc64el (1.57.0-1) ... 163s Selecting previously unselected package libpangocairo-1.0-0:ppc64el. 163s Preparing to unpack .../33-libpangocairo-1.0-0_1.57.0-1_ppc64el.deb ... 163s Unpacking libpangocairo-1.0-0:ppc64el (1.57.0-1) ... 163s Selecting previously unselected package libpaper2:ppc64el. 163s Preparing to unpack .../34-libpaper2_2.2.5-0.3build1_ppc64el.deb ... 163s Unpacking libpaper2:ppc64el (2.2.5-0.3build1) ... 163s Selecting previously unselected package libpaper-utils. 163s Preparing to unpack .../35-libpaper-utils_2.2.5-0.3build1_ppc64el.deb ... 163s Unpacking libpaper-utils (2.2.5-0.3build1) ... 163s Selecting previously unselected package libsharpyuv0:ppc64el. 163s Preparing to unpack .../36-libsharpyuv0_1.5.0-0.1build1_ppc64el.deb ... 163s Unpacking libsharpyuv0:ppc64el (1.5.0-0.1build1) ... 163s Selecting previously unselected package libsm6:ppc64el. 163s Preparing to unpack .../37-libsm6_2%3a1.2.6-1_ppc64el.deb ... 163s Unpacking libsm6:ppc64el (2:1.2.6-1) ... 163s Selecting previously unselected package libtcl8.6:ppc64el. 163s Preparing to unpack .../38-libtcl8.6_8.6.17+dfsg-1build1_ppc64el.deb ... 163s Unpacking libtcl8.6:ppc64el (8.6.17+dfsg-1build1) ... 163s Selecting previously unselected package libjbig0:ppc64el. 163s Preparing to unpack .../39-libjbig0_2.1-6.1ubuntu3_ppc64el.deb ... 163s Unpacking libjbig0:ppc64el (2.1-6.1ubuntu3) ... 163s Selecting previously unselected package libwebp7:ppc64el. 163s Preparing to unpack .../40-libwebp7_1.5.0-0.1build1_ppc64el.deb ... 163s Unpacking libwebp7:ppc64el (1.5.0-0.1build1) ... 163s Selecting previously unselected package libtiff6:ppc64el. 163s Preparing to unpack .../41-libtiff6_4.7.0-3ubuntu3_ppc64el.deb ... 163s Unpacking libtiff6:ppc64el (4.7.0-3ubuntu3) ... 163s Selecting previously unselected package libxft2:ppc64el. 163s Preparing to unpack .../42-libxft2_2.3.6-1build2_ppc64el.deb ... 163s Unpacking libxft2:ppc64el (2.3.6-1build2) ... 163s Selecting previously unselected package libxss1:ppc64el. 163s Preparing to unpack .../43-libxss1_1%3a1.2.3-1build4_ppc64el.deb ... 163s Unpacking libxss1:ppc64el (1:1.2.3-1build4) ... 163s Selecting previously unselected package libtk8.6:ppc64el. 163s Preparing to unpack .../44-libtk8.6_8.6.17-1_ppc64el.deb ... 163s Unpacking libtk8.6:ppc64el (8.6.17-1) ... 163s Selecting previously unselected package libxt6t64:ppc64el. 163s Preparing to unpack .../45-libxt6t64_1%3a1.2.1-1.3_ppc64el.deb ... 163s Unpacking libxt6t64:ppc64el (1:1.2.1-1.3) ... 163s Selecting previously unselected package r-mathlib. 163s Preparing to unpack .../46-r-mathlib_4.5.2-1ubuntu2_ppc64el.deb ... 163s Unpacking r-mathlib (4.5.2-1ubuntu2) ... 163s Selecting previously unselected package zip. 163s Preparing to unpack .../47-zip_3.0-15ubuntu2_ppc64el.deb ... 163s Unpacking zip (3.0-15ubuntu2) ... 163s Selecting previously unselected package unzip. 163s Preparing to unpack .../48-unzip_6.0-29ubuntu1_ppc64el.deb ... 163s Unpacking unzip (6.0-29ubuntu1) ... 163s Selecting previously unselected package xdg-utils. 163s Preparing to unpack .../49-xdg-utils_1.2.1-2ubuntu2_all.deb ... 163s Unpacking xdg-utils (1.2.1-2ubuntu2) ... 163s Selecting previously unselected package r-base-core. 163s Preparing to unpack .../50-r-base-core_4.5.2-1ubuntu2_ppc64el.deb ... 163s Unpacking r-base-core (4.5.2-1ubuntu2) ... 163s Selecting previously unselected package qtltools. 163s Preparing to unpack .../51-qtltools_1.3.1+dfsg-4build6_ppc64el.deb ... 163s Unpacking qtltools (1.3.1+dfsg-4build6) ... 163s Selecting previously unselected package qtltools-example. 163s Preparing to unpack .../52-qtltools-example_1.3.1+dfsg-4build6_all.deb ... 163s Unpacking qtltools-example (1.3.1+dfsg-4build6) ... 163s Setting up libhtscodecs2:ppc64el (1.6.1-2build1) ... 163s Setting up libboost-program-options1.88.0:ppc64el (1.88.0-1.4ubuntu3) ... 163s Setting up libgraphite2-3:ppc64el (1.3.14-11ubuntu1) ... 163s Setting up qtltools-example (1.3.1+dfsg-4build6) ... 163s Setting up libpixman-1-0:ppc64el (0.46.4-1) ... 163s Setting up libsharpyuv0:ppc64el (1.5.0-0.1build1) ... 163s Setting up liblerc4:ppc64el (4.0.0+ds-5ubuntu2) ... 163s Setting up libxrender1:ppc64el (1:0.9.12-1) ... 163s Setting up libdatrie1:ppc64el (0.2.14-1) ... 163s Setting up libgslcblas0:ppc64el (2.8+dfsg-6) ... 163s Setting up libxcb-render0:ppc64el (1.17.0-2ubuntu1) ... 163s Setting up unzip (6.0-29ubuntu1) ... 163s Setting up x11-common (1:7.7+24ubuntu1) ... 164s Setting up libdeflate0:ppc64el (1.23-2) ... 164s Setting up libxcb-shm0:ppc64el (1.17.0-2ubuntu1) ... 164s Setting up libboost-iostreams1.88.0:ppc64el (1.88.0-1.4ubuntu3) ... 164s Setting up libgomp1:ppc64el (15.2.0-12ubuntu1) ... 164s Setting up libjbig0:ppc64el (2.1-6.1ubuntu3) ... 164s Setting up zip (3.0-15ubuntu2) ... 164s Setting up libblas3:ppc64el (3.12.1-7ubuntu1) ... 164s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 164s Setting up fonts-dejavu-mono (2.37-8build1) ... 164s Setting up libtcl8.6:ppc64el (8.6.17+dfsg-1build1) ... 164s Setting up fonts-dejavu-core (2.37-8build1) ... 164s Setting up libjpeg-turbo8:ppc64el (2.1.5-4ubuntu2) ... 164s Setting up libgfortran5:ppc64el (15.2.0-12ubuntu1) ... 164s Setting up libwebp7:ppc64el (1.5.0-0.1build1) ... 164s Setting up r-mathlib (4.5.2-1ubuntu2) ... 164s Setting up libhts3t64:ppc64el (1.22.1+ds2-1) ... 164s Setting up libharfbuzz0b:ppc64el (12.3.2-1) ... 164s Setting up libthai-data (0.1.30-1) ... 164s Setting up libxss1:ppc64el (1:1.2.3-1build4) ... 164s Setting up libpaper2:ppc64el (2.2.5-0.3build1) ... 164s Setting up libgsl28:ppc64el (2.8+dfsg-6) ... 164s Setting up xdg-utils (1.2.1-2ubuntu2) ... 164s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 164s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 164s Setting up libice6:ppc64el (2:1.1.1-1build1) ... 164s Setting up liblapack3:ppc64el (3.12.1-7ubuntu1) ... 164s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 164s Setting up fontconfig-config (2.17.1-3ubuntu1) ... 164s Setting up libpaper-utils (2.2.5-0.3build1) ... 164s Setting up libthai0:ppc64el (0.1.30-1) ... 164s Setting up libtiff6:ppc64el (4.7.0-3ubuntu3) ... 164s Setting up libfontconfig1:ppc64el (2.17.1-3ubuntu1) ... 164s Setting up libsm6:ppc64el (2:1.2.6-1) ... 164s Setting up fontconfig (2.17.1-3ubuntu1) ... 166s Regenerating fonts cache... done. 166s Setting up libxft2:ppc64el (2.3.6-1build2) ... 166s Setting up libtk8.6:ppc64el (8.6.17-1) ... 166s Setting up libpango-1.0-0:ppc64el (1.57.0-1) ... 166s Setting up libcairo2:ppc64el (1.18.4-3) ... 166s Setting up libxt6t64:ppc64el (1:1.2.1-1.3) ... 166s Setting up libpangoft2-1.0-0:ppc64el (1.57.0-1) ... 166s Setting up libpangocairo-1.0-0:ppc64el (1.57.0-1) ... 166s Setting up r-base-core (4.5.2-1ubuntu2) ... 166s Creating config file /etc/R/Renviron with new version 167s Setting up qtltools (1.3.1+dfsg-4build6) ... 167s Processing triggers for man-db (2.13.1-1) ... 168s Processing triggers for install-info (7.2-5) ... 168s Processing triggers for libc-bin (2.42-2ubuntu5) ... 169s autopkgtest [10:09:55]: test run-sample-analysis: [----------------------- 169s ./genes.50percent.chr22.bed.gz 169s ./genes.50percent.chr22.bed.gz.tbi 169s ./genes.covariates.pc50.txt.gz 169s ./genes.simulated.chr22.bed.gz 169s ./genes.simulated.chr22.bed.gz.tbi 169s ./genotypes.chr22.vcf.gz 170s ./genotypes.chr22.vcf.gz.tbi 170s 170s QTLtools 170s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 170s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 170s * Webpage : https://qtltools.github.io/qtltools/ 170s * Version : 1.3.1 170s * Date : 05/02/2026 - 10:09:55 170s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 170s 170s CONDUCT PCA ON DATA 170s 170s Initialize random number generator 170s * Built-in seed is 15112011 170s * First Integer = 30553 170s * First Double = 0.0126695 170s 170s Reading sample list from [genes.50percent.chr22.bed.gz] 170s * #samples = 358 170s 170s Merging sample sets from all input files 170s * #files = 1 170s * #samples in all files = 358 170s 170s Reading phenotype data in [genes.50percent.chr22.bed.gz] 170s * 358 samples included 170s * 608 phenotypes included 170s 170s Calculating PCA with a matrix 358 x 608 170s * Calculated mean and sd 170s * 0 sd==0 columns removed 170s * Variables centered 170s * Variables scaled to unit variance 170s * Running SVD 170s * SVD complete 170s * Calculated sd and var for PCs 170s * Calculated cumulative var for PCs 170s * Done! 170s 170s Running time: 0 seconds 171s 171s QTLtools 171s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 171s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 171s * Webpage : https://qtltools.github.io/qtltools/ 171s * Version : 1.3.1 171s * Date : 05/02/2026 - 10:09:56 171s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 171s 171s MAPPING QTL IN CIS 171s * TASK: Report all nominal associations with p <= 0.01 171s * Linear model: Phe ~ Var + Cov 171s * Cis-window size is 1000000 bp 171s * Region = [chr22:17000000-18000000] 171s 171s Initialize random number generator 171s * Built-in seed is 15112011 171s * First Integer = 30553 171s * First Double = 0.0126695 171s 171s Reading sample list from [genes.50percent.chr22.bed.gz] 171s * #samples = 358 171s 171s Read sample list from [genotypes.chr22.vcf.gz] 171s * #samples = 358 171s 171s Reading sample list from [genes.covariates.pc50.txt.gz] 171s * #samples = 358 171s 171s Merging sample sets from all input files 171s * #files = 3 171s * #samples in all files = 358 171s 171s Reading phenotype data in [genes.50percent.chr22.bed.gz] 171s * target region [chr22:17000000-18000000] 171s * 8 phenotypes included 171s * 3 phenotypes are on the negative strand 171s 171s Reading genotype data in [genotypes.chr22.vcf.gz] 171s * File format detected: VCF 171s * target region [chr22:16000000-19000000] 171s * 6404 variants included 171s 171s Reading covariates in [genes.covariates.pc50.txt.gz] 171s * 53 covariates included 171s 171s Residualize phenotypes for covariates 171s * #covariates = 53 171s 171s Processing phenotype [ENSG00000237438.2] [1/8] 171s * #variants in cis = 5095 171s * Best hit: [id=22_17542810, d=25350, pv=1.1864e-25, s=-0.7518] 171s 171s Processing phenotype [ENSG00000273203.1] [2/8] 171s * #variants in cis = 5170 171s * Best hit: [id=22_17517388, d=-31323, pv=5.86611e-06, s=-0.1406] 171s 171s Processing phenotype [ENSG00000273442.1] [3/8] 171s * #variants in cis = 5188 171s * Best hit: [id=22_17553526, d=-8065, pv=0.000244522, s=0.1340] 171s 171s Processing phenotype [ENSG00000177663.9] [4/8] 171s * #variants in cis = 5193 171s * Best hit: [id=22_17513703, d=-52141, pv=8.03358e-14, s=-0.2096] 171s 171s Processing phenotype [ENSG00000183307.3] [5/8] 171s * #variants in cis = 5230 171s * Best hit: [id=22_17587975, d=14282, pv=1.56789e-07, s=-0.0078] 171s 171s Processing phenotype [ENSG00000069998.8] [6/8] 171s * #variants in cis = 5291 171s * Best hit: [id=22_17620429, d=25748, pv=1.37287e-14, s=-1.5147] 171s 171s Processing phenotype [ENSG00000093072.11] [7/8] 171s * #variants in cis = 5293 171s * Best hit: [id=22_17699630, d=3249, pv=0.000578649, s=0.6404] 171s 171s Processing phenotype [ENSG00000099954.14] [8/8] 171s * #variants in cis = 5435 171s * Best hit: [id=22_17175937, d=-664900, pv=0.000866455, s=0.0067] 171s 171s Running time: 0 seconds 171s 171s QTLtools 171s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 171s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 171s * Webpage : https://qtltools.github.io/qtltools/ 171s * Version : 1.3.1 171s * Date : 05/02/2026 - 10:09:56 171s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 171s 171s MAPPING QTL IN CIS 171s * TASK: Perform 1000 permutations 171s * Linear model: Phe ~ Var + Cov 171s * Cis-window size is 1000000 bp 171s * Region = [chr22:17000000-18000000] 171s 171s Initialize random number generator 171s * Built-in seed is 15112011 171s * First Integer = 30553 171s * First Double = 0.0126695 171s 171s Reading sample list from [genes.50percent.chr22.bed.gz] 171s * #samples = 358 171s 171s Read sample list from [genotypes.chr22.vcf.gz] 171s * #samples = 358 171s 171s Reading sample list from [genes.covariates.pc50.txt.gz] 171s * #samples = 358 171s 171s Merging sample sets from all input files 171s * #files = 3 171s * #samples in all files = 358 171s 171s Reading phenotype data in [genes.50percent.chr22.bed.gz] 171s * target region [chr22:17000000-18000000] 171s * 8 phenotypes included 171s * 3 phenotypes are on the negative strand 171s 171s Reading genotype data in [genotypes.chr22.vcf.gz] 171s * File format detected: VCF 171s * target region [chr22:16000000-19000000] 171s * 6404 variants included 171s 171s Reading covariates in [genes.covariates.pc50.txt.gz] 171s * 53 covariates included 171s 171s Residualize phenotypes for covariates 171s * #covariates = 53 171s 171s Processing phenotype [ENSG00000237438.2] [1/8] 171s * #variants in cis = 5095 172s * Best hit: [id=22_17542810, d=25350, pv=1.1864e-25, s=-0.7518] 172s * Beta parameters: [s1=1.00995, s2=621.053] 172s * Adjusted p-values: [emp=0.000999001, beta=1.28062e-20] 172s 172s Processing phenotype [ENSG00000273203.1] [2/8] 172s * #variants in cis = 5170 173s * Best hit: [id=22_17517388, d=-31323, pv=5.86611e-06, s=-0.1406] 173s * Beta parameters: [s1=1.11817, s2=641.379] 173s * Adjusted p-values: [emp=0.00799201, beta=0.00751892] 173s 173s Processing phenotype [ENSG00000273442.1] [3/8] 173s * #variants in cis = 5188 174s * Best hit: [id=22_17553526, d=-8065, pv=0.000244522, s=0.1340] 174s * Beta parameters: [s1=1.08364, s2=467.63] 174s * Adjusted p-values: [emp=0.297702, beta=0.293948] 174s 174s Processing phenotype [ENSG00000177663.9] [4/8] 174s * #variants in cis = 5193 175s * Best hit: [id=22_17513703, d=-52141, pv=8.03358e-14, s=-0.2096] 175s * Beta parameters: [s1=0.989061, s2=704.553] 175s * Adjusted p-values: [emp=0.000999001, beta=7.91291e-10] 175s 175s Processing phenotype [ENSG00000183307.3] [5/8] 175s * #variants in cis = 5230 176s * Best hit: [id=22_17587975, d=14282, pv=1.56789e-07, s=-0.0078] 176s * Beta parameters: [s1=1.01322, s2=559.49] 176s * Adjusted p-values: [emp=0.000999001, beta=0.00050707] 176s 176s Processing phenotype [ENSG00000069998.8] [6/8] 176s * #variants in cis = 5291 177s * Best hit: [id=22_17620429, d=25748, pv=1.37287e-14, s=-1.5147] 177s * Beta parameters: [s1=1.02312, s2=563.339] 177s * Adjusted p-values: [emp=0.000999001, beta=2.56935e-10] 177s 177s Processing phenotype [ENSG00000093072.11] [7/8] 177s * #variants in cis = 5293 179s * Best hit: [id=22_17699630, d=3249, pv=0.000578649, s=0.6404] 179s * Beta parameters: [s1=0.957514, s2=559.397] 179s * Adjusted p-values: [emp=0.574426, beta=0.562826] 179s 179s Processing phenotype [ENSG00000099954.14] [8/8] 179s * #variants in cis = 5435 180s * Best hit: [id=22_17175937, d=-664900, pv=0.000866455, s=0.0067] 180s * Beta parameters: [s1=0.938041, s2=226.852] 180s * Adjusted p-values: [emp=0.842158, beta=0.84836] 180s 180s Running time: 8 seconds 180s 180s QTLtools 180s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 180s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 180s * Webpage : https://qtltools.github.io/qtltools/ 180s * Version : 1.3.1 180s * Date : 05/02/2026 - 10:10:05 180s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 180s 180s MAPPING QTL IN TRANS 180s * TASK: Perform a full nominal pass, do not adjust p-values 180s * Cis-window size is 5000000 bp 180s * #bins = 1000 180s * threshold = 1e-05 180s 180s Initialize random number generator 180s * Built-in seed is 15112011 180s * First Integer = 30553 180s * First Double = 0.0126695 180s 180s Read sample list from [genotypes.chr22.vcf.gz] 180s * #samples = 358 180s 180s Checking sample list in [genes.simulated.chr22.bed.gz] 180s * #samples = 358 180s 180s Reading phenotype data in [genes.simulated.chr22.bed.gz] from line 0 to 0 180s * 358 samples included 180s * 608 phenotypes included 180s * 275 phenotypes is on the negative strand 180s 180s Calculate correlation threshold 180s * thres = 1e-05 180s * corr = 0.2311 180s 180s Sweep through genotype data in [genotypes.chr22.vcf.gz] 180s * #variants=1950 #multi_allelic=0 #not_processed=0 #hits=101/1000000 speed=3.89MT/s 180s * #variants=4001 #multi_allelic=0 #not_processed=0 #hits=153/2000000 speed=3.83MT/s 181s * #variants=6187 #multi_allelic=0 #not_processed=0 #hits=244/3000000 speed=3.83MT/s 181s * #variants=8537 #multi_allelic=0 #not_processed=0 #hits=285/4000000 speed=3.80MT/s 181s * #variants=11025 #multi_allelic=0 #not_processed=0 #hits=312/5000000 speed=3.76MT/s 181s * #variants=13621 #multi_allelic=0 #not_processed=0 #hits=320/6000000 speed=3.73MT/s 182s * #variants=16217 #multi_allelic=0 #not_processed=0 #hits=342/7000000 speed=3.73MT/s 182s * #variants=18755 #multi_allelic=0 #not_processed=0 #hits=401/8000000 speed=3.75MT/s 182s * #variants=21237 #multi_allelic=0 #not_processed=0 #hits=402/9000000 speed=3.76MT/s 182s * #variants=23680 #multi_allelic=0 #not_processed=0 #hits=455/10000000 speed=3.76MT/s 183s * #variants=26171 #multi_allelic=0 #not_processed=0 #hits=463/11000000 speed=3.75MT/s 183s * #variants=28609 #multi_allelic=0 #not_processed=0 #hits=469/12000000 speed=3.77MT/s 183s * #variants=30861 #multi_allelic=0 #not_processed=0 #hits=973/13000000 speed=3.77MT/s 183s * #variants=32932 #multi_allelic=0 #not_processed=0 #hits=979/14000000 speed=3.86MT/s 184s * #variants=34974 #multi_allelic=0 #not_processed=0 #hits=1085/15000000 speed=3.86MT/s 184s * #variants=37021 #multi_allelic=0 #not_processed=0 #hits=1086/16000000 speed=3.88MT/s 184s * #variants=39122 #multi_allelic=0 #not_processed=0 #hits=1089/17000000 speed=3.86MT/s 185s * #variants=41334 #multi_allelic=0 #not_processed=0 #hits=1089/18000000 speed=3.82MT/s 185s * #variants=43627 #multi_allelic=0 #not_processed=0 #hits=1096/19000000 speed=3.82MT/s 185s * #variants=45897 #multi_allelic=0 #not_processed=0 #hits=1153/20000000 speed=3.82MT/s 185s * #variants=48114 #multi_allelic=0 #not_processed=0 #hits=1243/21000000 speed=3.82MT/s 186s * #variants=50410 #multi_allelic=0 #not_processed=0 #hits=1249/22000000 speed=3.80MT/s 186s * #variants=52820 #multi_allelic=0 #not_processed=0 #hits=1259/23000000 speed=3.75MT/s 186s * #variants=55279 #multi_allelic=0 #not_processed=0 #hits=1498/24000000 speed=3.69MT/s 186s * #variants=57789 #multi_allelic=0 #not_processed=0 #hits=1724/25000000 speed=3.73MT/s 187s * #variants=60201 #multi_allelic=0 #not_processed=0 #hits=2168/26000000 speed=3.72MT/s 187s * #variants=62476 #multi_allelic=0 #not_processed=0 #hits=2452/27000000 speed=3.79MT/s 187s * #variants=64608 #multi_allelic=0 #not_processed=0 #hits=2544/28000000 speed=3.85MT/s 187s * #variants=66709 #multi_allelic=0 #not_processed=0 #hits=2684/29000000 speed=3.85MT/s 188s * #variants=68871 #multi_allelic=0 #not_processed=0 #hits=2688/30000000 speed=3.82MT/s 188s * #variants=71070 #multi_allelic=0 #not_processed=0 #hits=2720/31000000 speed=3.83MT/s 188s * #variants=73151 #multi_allelic=0 #not_processed=0 #hits=2891/32000000 speed=3.85MT/s 188s * #variants=75122 #multi_allelic=0 #not_processed=0 #hits=3110/33000000 speed=3.85MT/s 189s * #variants=77058 #multi_allelic=0 #not_processed=0 #hits=3209/34000000 speed=3.83MT/s 189s * #variants=78989 #multi_allelic=0 #not_processed=0 #hits=3218/35000000 speed=3.85MT/s 189s * #variants=80903 #multi_allelic=0 #not_processed=0 #hits=3250/36000000 speed=3.89MT/s 190s * #variants=82811 #multi_allelic=0 #not_processed=0 #hits=3463/37000000 speed=3.91MT/s 190s * #variants=84694 #multi_allelic=0 #not_processed=0 #hits=4035/38000000 speed=3.88MT/s 190s * #variants=85485 #multi_allelic=0 #not_processed=0 #hits=4036/38425275 speed=3.94MT/s 190s 190s Running time: 10 seconds 190s 190s QTLtools 190s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 190s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 190s * Webpage : https://qtltools.github.io/qtltools/ 190s * Version : 1.3.1 190s * Date : 05/02/2026 - 10:10:15 190s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 190s 190s MAPPING QTL IN TRANS 190s * TASK: Permute randomly chosen phenotypes 1000 times and test 190s * Cis-window size is 5000000 bp 190s * #bins = 1000 190s * threshold = 1e-05 190s 190s Initialize random number generator 190s * Built-in seed is 15112011 190s * First Integer = 30553 190s * First Double = 0.0126695 190s 190s Read sample list from [genotypes.chr22.vcf.gz] 190s * #samples = 358 190s 190s Checking sample list in [genes.simulated.chr22.bed.gz] 190s * #samples = 358 190s 190s Reading phenotype data in [genes.simulated.chr22.bed.gz] from line 0 to 0 190s * 358 samples included 190s * 608 phenotypes included 190s * 275 phenotypes is on the negative strand 190s 190s Normal transform phenotypes 190s 190s Calculate correlation threshold 190s * thres = 1e-05 190s * corr = 0.2311 190s 190s Sweep through genotype data in [genotypes.chr22.vcf.gz] 190s * #variants=1177 #multi_allelic=0 #not_processed=0 #hits=28/1000000 speed=4.07MT/s 190s * #variants=2383 #multi_allelic=0 #not_processed=0 #hits=38/2000000 speed=4.05MT/s 191s * #variants=3633 #multi_allelic=0 #not_processed=0 #hits=53/3000000 speed=4.02MT/s 191s * #variants=4928 #multi_allelic=0 #not_processed=0 #hits=53/4000000 speed=3.97MT/s 191s * #variants=6269 #multi_allelic=0 #not_processed=0 #hits=71/5000000 speed=3.88MT/s 192s * #variants=7675 #multi_allelic=0 #not_processed=0 #hits=72/6000000 speed=3.92MT/s 192s * #variants=9151 #multi_allelic=0 #not_processed=0 #hits=88/7000000 speed=3.88MT/s 192s * #variants=10663 #multi_allelic=0 #not_processed=0 #hits=96/8000000 speed=3.83MT/s 192s * #variants=12202 #multi_allelic=0 #not_processed=0 #hits=96/9000000 speed=3.83MT/s 193s * #variants=13804 #multi_allelic=0 #not_processed=0 #hits=96/10000000 speed=3.79MT/s 193s * #variants=15381 #multi_allelic=0 #not_processed=0 #hits=120/11000000 speed=3.80MT/s 193s * #variants=16946 #multi_allelic=0 #not_processed=0 #hits=123/12000000 speed=3.82MT/s 193s * #variants=18483 #multi_allelic=0 #not_processed=0 #hits=129/13000000 speed=3.83MT/s 194s * #variants=19995 #multi_allelic=0 #not_processed=0 #hits=131/14000000 speed=3.85MT/s 194s * #variants=21489 #multi_allelic=0 #not_processed=0 #hits=132/15000000 speed=3.86MT/s 194s * #variants=22947 #multi_allelic=0 #not_processed=0 #hits=151/16000000 speed=3.88MT/s 194s * #variants=24445 #multi_allelic=0 #not_processed=0 #hits=168/17000000 speed=3.79MT/s 195s * #variants=25965 #multi_allelic=0 #not_processed=0 #hits=175/18000000 speed=3.80MT/s 195s * #variants=27472 #multi_allelic=0 #not_processed=0 #hits=179/19000000 speed=3.82MT/s 195s * #variants=28933 #multi_allelic=0 #not_processed=0 #hits=181/20000000 speed=3.85MT/s 195s * #variants=30325 #multi_allelic=0 #not_processed=0 #hits=181/21000000 speed=3.89MT/s 196s * #variants=31617 #multi_allelic=0 #not_processed=0 #hits=182/22000000 speed=3.98MT/s 196s * #variants=32875 #multi_allelic=0 #not_processed=0 #hits=190/23000000 speed=4.00MT/s 196s * #variants=34127 #multi_allelic=0 #not_processed=0 #hits=192/24000000 speed=4.00MT/s 196s * #variants=35392 #multi_allelic=0 #not_processed=0 #hits=206/25000000 speed=3.73MT/s 197s * #variants=36652 #multi_allelic=0 #not_processed=0 #hits=206/26000000 speed=3.82MT/s 197s * #variants=37940 #multi_allelic=0 #not_processed=0 #hits=213/27000000 speed=3.92MT/s 197s * #variants=39255 #multi_allelic=0 #not_processed=0 #hits=238/28000000 speed=3.98MT/s 197s * #variants=40602 #multi_allelic=0 #not_processed=0 #hits=239/29000000 speed=3.95MT/s 198s * #variants=41998 #multi_allelic=0 #not_processed=0 #hits=245/30000000 speed=3.91MT/s 198s * #variants=43398 #multi_allelic=0 #not_processed=0 #hits=245/31000000 speed=3.91MT/s 198s * #variants=44803 #multi_allelic=0 #not_processed=0 #hits=260/32000000 speed=3.91MT/s 199s * #variants=46187 #multi_allelic=0 #not_processed=0 #hits=261/33000000 speed=3.92MT/s 199s * #variants=47545 #multi_allelic=0 #not_processed=0 #hits=268/34000000 speed=3.95MT/s 199s * #variants=48904 #multi_allelic=0 #not_processed=0 #hits=280/35000000 speed=3.95MT/s 199s * #variants=50309 #multi_allelic=0 #not_processed=0 #hits=306/36000000 speed=3.92MT/s 200s * #variants=51731 #multi_allelic=0 #not_processed=0 #hits=314/37000000 speed=3.91MT/s 200s * #variants=53171 #multi_allelic=0 #not_processed=0 #hits=320/38000000 speed=3.89MT/s 200s * #variants=54621 #multi_allelic=0 #not_processed=0 #hits=323/39000000 speed=3.89MT/s 200s * #variants=56099 #multi_allelic=0 #not_processed=0 #hits=323/40000000 speed=3.88MT/s 201s * #variants=57584 #multi_allelic=0 #not_processed=0 #hits=340/41000000 speed=3.86MT/s 201s * #variants=59032 #multi_allelic=0 #not_processed=0 #hits=344/42000000 speed=3.89MT/s 201s * #variants=60437 #multi_allelic=0 #not_processed=0 #hits=345/43000000 speed=3.91MT/s 201s * #variants=61810 #multi_allelic=0 #not_processed=0 #hits=357/44000000 speed=3.92MT/s 202s * #variants=63129 #multi_allelic=0 #not_processed=0 #hits=384/45000000 speed=3.95MT/s 202s * #variants=64409 #multi_allelic=0 #not_processed=0 #hits=391/46000000 speed=3.94MT/s 202s * #variants=65679 #multi_allelic=0 #not_processed=0 #hits=430/47000000 speed=3.92MT/s 202s * #variants=66953 #multi_allelic=0 #not_processed=0 #hits=436/48000000 speed=4.00MT/s 203s * #variants=68247 #multi_allelic=0 #not_processed=0 #hits=446/49000000 speed=3.98MT/s 203s * #variants=69595 #multi_allelic=0 #not_processed=0 #hits=460/50000000 speed=3.94MT/s 203s * #variants=70918 #multi_allelic=0 #not_processed=0 #hits=481/51000000 speed=3.95MT/s 203s * #variants=72211 #multi_allelic=0 #not_processed=0 #hits=492/52000000 speed=3.98MT/s 204s * #variants=73449 #multi_allelic=0 #not_processed=0 #hits=492/53000000 speed=4.02MT/s 204s * #variants=74662 #multi_allelic=0 #not_processed=0 #hits=500/54000000 speed=4.03MT/s 204s * #variants=75863 #multi_allelic=0 #not_processed=0 #hits=506/55000000 speed=4.05MT/s 204s * #variants=77058 #multi_allelic=0 #not_processed=0 #hits=513/56000000 speed=4.03MT/s 205s * #variants=78253 #multi_allelic=0 #not_processed=0 #hits=515/57000000 speed=4.07MT/s 205s * #variants=79446 #multi_allelic=0 #not_processed=0 #hits=530/58000000 speed=4.07MT/s 205s * #variants=80634 #multi_allelic=0 #not_processed=0 #hits=581/59000000 speed=4.07MT/s 205s * #variants=81817 #multi_allelic=0 #not_processed=0 #hits=594/60000000 speed=4.08MT/s 206s * #variants=82993 #multi_allelic=0 #not_processed=0 #hits=598/61000000 speed=4.08MT/s 206s * #variants=84160 #multi_allelic=0 #not_processed=0 #hits=599/62000000 speed=4.10MT/s 206s * #variants=85304 #multi_allelic=0 #not_processed=0 #hits=609/63000000 speed=4.10MT/s 206s * #variants=85485 #multi_allelic=0 #not_processed=0 #hits=609/63157827 speed=4.15MT/s 206s 206s Running time: 16 seconds 206s autopkgtest [10:10:32]: test run-sample-analysis: -----------------------] 207s run-sample-analysis PASS 207s autopkgtest [10:10:33]: test run-sample-analysis: - - - - - - - - - - results - - - - - - - - - - 207s autopkgtest [10:10:33]: @@@@@@@@@@@@@@@@@@@@ summary 207s run-sample-analysis PASS