0s autopkgtest [00:14:22]: starting date and time: 2024-08-13 00:14:22+0000 0s autopkgtest [00:14:22]: git checkout: fd3bed09 nova: allow more retries for quota issues 0s autopkgtest [00:14:22]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.2t3n1lbb/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade qtltools --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.39-0ubuntu8.3 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-ppc64el-31.secgroup --name adt-noble-ppc64el-qtltools-20240813-001421-juju-7f2275-prod-proposed-migration-environment-2-39bbe0a2-a0e1-4d9e-9f42-e11a29e740cc --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-ppc64el -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 113s autopkgtest [00:16:15]: testbed dpkg architecture: ppc64el 113s autopkgtest [00:16:15]: testbed apt version: 2.7.14build2 113s autopkgtest [00:16:15]: @@@@@@@@@@@@@@@@@@@@ test bed setup 114s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [265 kB] 115s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6660 B] 115s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [2280 B] 115s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [27.0 kB] 115s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [60.8 kB] 115s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [101 kB] 115s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [5180 B] 115s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1548 B] 115s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 115s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [61.0 kB] 115s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [2560 B] 115s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 117s Fetched 533 kB in 1s (735 kB/s) 117s Reading package lists... 120s Reading package lists... 120s Building dependency tree... 120s Reading state information... 120s Calculating upgrade... 120s The following packages will be upgraded: 120s libc-bin libc-dev-bin libc-devtools libc6 libc6-dev locales 120s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 120s Need to get 10.5 MB of archives. 120s After this operation, 1239 kB disk space will be freed. 120s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libc-devtools ppc64el 2.39-0ubuntu8.3 [69.8 kB] 121s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libc6-dev ppc64el 2.39-0ubuntu8.3 [2131 kB] 121s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libc-dev-bin ppc64el 2.39-0ubuntu8.3 [61.3 kB] 121s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libc6 ppc64el 2.39-0ubuntu8.3 [3258 kB] 121s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libc-bin ppc64el 2.39-0ubuntu8.3 [786 kB] 121s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el locales all 2.39-0ubuntu8.3 [4231 kB] 122s Preconfiguring packages ... 122s Fetched 10.5 MB in 1s (7769 kB/s) 122s (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 ... 72211 files and directories currently installed.) 122s Preparing to unpack .../libc-devtools_2.39-0ubuntu8.3_ppc64el.deb ... 122s Unpacking libc-devtools (2.39-0ubuntu8.3) over (2.39-0ubuntu8.2) ... 122s Preparing to unpack .../libc6-dev_2.39-0ubuntu8.3_ppc64el.deb ... 122s Unpacking libc6-dev:ppc64el (2.39-0ubuntu8.3) over (2.39-0ubuntu8.2) ... 122s Preparing to unpack .../libc-dev-bin_2.39-0ubuntu8.3_ppc64el.deb ... 122s Unpacking libc-dev-bin (2.39-0ubuntu8.3) over (2.39-0ubuntu8.2) ... 122s Preparing to unpack .../libc6_2.39-0ubuntu8.3_ppc64el.deb ... 122s Unpacking libc6:ppc64el (2.39-0ubuntu8.3) over (2.39-0ubuntu8.2) ... 123s Setting up libc6:ppc64el (2.39-0ubuntu8.3) ... 123s (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 ... 72215 files and directories currently installed.) 123s Preparing to unpack .../libc-bin_2.39-0ubuntu8.3_ppc64el.deb ... 123s Unpacking libc-bin (2.39-0ubuntu8.3) over (2.39-0ubuntu8.2) ... 123s Setting up libc-bin (2.39-0ubuntu8.3) ... 123s (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 ... 72216 files and directories currently installed.) 123s Preparing to unpack .../locales_2.39-0ubuntu8.3_all.deb ... 123s Unpacking locales (2.39-0ubuntu8.3) over (2.39-0ubuntu8.2) ... 123s Setting up locales (2.39-0ubuntu8.3) ... 124s Generating locales (this might take a while)... 125s en_US.UTF-8... done 125s Generation complete. 125s Setting up libc-dev-bin (2.39-0ubuntu8.3) ... 125s Setting up libc-devtools (2.39-0ubuntu8.3) ... 125s Setting up libc6-dev:ppc64el (2.39-0ubuntu8.3) ... 125s Processing triggers for man-db (2.12.0-4build2) ... 127s Reading package lists... 127s Building dependency tree... 127s Reading state information... 127s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 128s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 128s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 128s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 128s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 129s Reading package lists... 129s Reading package lists... 129s Building dependency tree... 129s Reading state information... 129s Calculating upgrade... 129s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 129s Reading package lists... 129s Building dependency tree... 129s Reading state information... 130s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 133s autopkgtest [00:16:35]: testbed running kernel: Linux 6.8.0-40-generic #40-Ubuntu SMP Fri Jul 5 10:50:38 UTC 2024 133s autopkgtest [00:16:35]: @@@@@@@@@@@@@@@@@@@@ apt-source qtltools 136s Get:1 http://ftpmaster.internal/ubuntu noble/universe qtltools 1.3.1+dfsg-4build3 (dsc) [2293 B] 136s Get:2 http://ftpmaster.internal/ubuntu noble/universe qtltools 1.3.1+dfsg-4build3 (tar) [141 kB] 136s Get:3 http://ftpmaster.internal/ubuntu noble/universe qtltools 1.3.1+dfsg-4build3 (diff) [13.6 MB] 136s gpgv: Signature made Mon Apr 1 07:33:53 2024 UTC 136s gpgv: using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984 136s gpgv: Can't check signature: No public key 136s dpkg-source: warning: cannot verify inline signature for ./qtltools_1.3.1+dfsg-4build3.dsc: no acceptable signature found 137s autopkgtest [00:16:39]: testing package qtltools version 1.3.1+dfsg-4build3 139s autopkgtest [00:16:41]: build not needed 139s autopkgtest [00:16:41]: test run-sample-analysis: preparing testbed 141s Reading package lists... 141s Building dependency tree... 141s Reading state information... 141s Starting pkgProblemResolver with broken count: 0 141s Starting 2 pkgProblemResolver with broken count: 0 141s Done 141s The following additional packages will be installed: 141s fontconfig libblas3 libboost-iostreams1.83.0 libboost-program-options1.83.0 141s libcairo2 libdatrie1 libgfortran5 libgomp1 libgraphite2-3 libgsl27 141s libgslcblas0 libharfbuzz0b libhts3t64 libhtscodecs2 libice6 liblapack3 141s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 141s libpaper1 libpixman-1-0 libsm6 libtcl8.6 libthai-data libthai0 libtk8.6 141s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 qtltools 141s qtltools-example r-base-core r-mathlib unzip x11-common xdg-utils zip 141s Suggested packages: 141s gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html tcl8.6 tk8.6 141s elpa-ess r-doc-info | r-doc-pdf r-base-html 141s Recommended packages: 141s r-bioc-qvalue r-recommended r-base-dev r-doc-html libfile-mimeinfo-perl 141s libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils 141s The following NEW packages will be installed: 141s autopkgtest-satdep fontconfig libblas3 libboost-iostreams1.83.0 141s libboost-program-options1.83.0 libcairo2 libdatrie1 libgfortran5 libgomp1 141s libgraphite2-3 libgsl27 libgslcblas0 libharfbuzz0b libhts3t64 libhtscodecs2 141s libice6 liblapack3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 141s libpaper-utils libpaper1 libpixman-1-0 libsm6 libtcl8.6 libthai-data 141s libthai0 libtk8.6 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 141s libxt6t64 qtltools qtltools-example r-base-core r-mathlib unzip x11-common 141s xdg-utils zip 141s 0 upgraded, 42 newly installed, 0 to remove and 0 not upgraded. 141s Need to get 56.0 MB/56.0 MB of archives. 141s After this operation, 108 MB of additional disk space will be used. 141s Get:1 /tmp/autopkgtest.ognG95/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [716 B] 142s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el fontconfig ppc64el 2.15.0-1.1ubuntu2 [192 kB] 142s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3build1 [227 kB] 142s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el libboost-iostreams1.83.0 ppc64el 1.83.0-2.1ubuntu3 [260 kB] 142s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el libboost-program-options1.83.0 ppc64el 1.83.0-2.1ubuntu3 [329 kB] 142s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el libpixman-1-0 ppc64el 0.42.2-1build1 [336 kB] 142s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-render0 ppc64el 1.15-1ubuntu2 [17.7 kB] 142s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-shm0 ppc64el 1.15-1ubuntu2 [6184 B] 142s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1build1 [23.1 kB] 142s Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el libcairo2 ppc64el 1.18.0-3build1 [751 kB] 142s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el libdatrie1 ppc64el 0.2.13-3build1 [22.7 kB] 142s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240412-0ubuntu1 [574 kB] 142s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240412-0ubuntu1 [161 kB] 142s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el libgraphite2-3 ppc64el 1.3.14-2build1 [84.6 kB] 142s Get:15 http://ftpmaster.internal/ubuntu noble/universe ppc64el libgslcblas0 ppc64el 2.7.1+dfsg-6ubuntu2 [86.6 kB] 142s Get:16 http://ftpmaster.internal/ubuntu noble/universe ppc64el libgsl27 ppc64el 2.7.1+dfsg-6ubuntu2 [1090 kB] 142s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el libharfbuzz0b ppc64el 8.3.0-2build2 [580 kB] 142s Get:18 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1build1 [110 kB] 142s Get:19 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3t64 ppc64el 1.19+ds-1.1build3 [569 kB] 142s Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el x11-common all 1:7.7+23ubuntu3 [21.7 kB] 142s Get:21 http://ftpmaster.internal/ubuntu noble/main ppc64el libice6 ppc64el 2:1.0.10-1build3 [49.1 kB] 142s Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3build1 [2804 kB] 143s Get:23 http://ftpmaster.internal/ubuntu noble/main ppc64el libthai-data all 0.1.29-2build1 [158 kB] 143s Get:24 http://ftpmaster.internal/ubuntu noble/main ppc64el libthai0 ppc64el 0.1.29-2build1 [21.8 kB] 143s Get:25 http://ftpmaster.internal/ubuntu noble/main ppc64el libpango-1.0-0 ppc64el 1.52.1+ds-1build1 [271 kB] 143s Get:26 http://ftpmaster.internal/ubuntu noble/main ppc64el libpangoft2-1.0-0 ppc64el 1.52.1+ds-1build1 [50.5 kB] 143s Get:27 http://ftpmaster.internal/ubuntu noble/main ppc64el libpangocairo-1.0-0 ppc64el 1.52.1+ds-1build1 [31.1 kB] 143s Get:28 http://ftpmaster.internal/ubuntu noble/main ppc64el libpaper1 ppc64el 1.1.29build1 [13.7 kB] 143s Get:29 http://ftpmaster.internal/ubuntu noble/main ppc64el libpaper-utils ppc64el 1.1.29build1 [8742 B] 143s Get:30 http://ftpmaster.internal/ubuntu noble/main ppc64el libsm6 ppc64el 2:1.2.3-1build3 [17.6 kB] 143s Get:31 http://ftpmaster.internal/ubuntu noble/main ppc64el libtcl8.6 ppc64el 8.6.14+dfsg-1build1 [1204 kB] 143s Get:32 http://ftpmaster.internal/ubuntu noble/main ppc64el libxft2 ppc64el 2.3.6-1build1 [61.5 kB] 143s Get:33 http://ftpmaster.internal/ubuntu noble/main ppc64el libxss1 ppc64el 1:1.2.3-1build3 [7980 B] 143s Get:34 http://ftpmaster.internal/ubuntu noble/main ppc64el libtk8.6 ppc64el 8.6.14-1build1 [944 kB] 143s Get:35 http://ftpmaster.internal/ubuntu noble/main ppc64el libxt6t64 ppc64el 1:1.2.1-1.2build1 [202 kB] 143s Get:36 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-mathlib ppc64el 4.3.3-2build2 [2440 kB] 143s Get:37 http://ftpmaster.internal/ubuntu noble/main ppc64el zip ppc64el 3.0-13build1 [198 kB] 143s Get:38 http://ftpmaster.internal/ubuntu noble/main ppc64el unzip ppc64el 6.0-28ubuntu4 [192 kB] 143s Get:39 http://ftpmaster.internal/ubuntu noble/main ppc64el xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 143s Get:40 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-base-core ppc64el 4.3.3-2build2 [27.4 MB] 144s Get:41 http://ftpmaster.internal/ubuntu noble/universe ppc64el qtltools ppc64el 1.3.1+dfsg-4build3 [828 kB] 144s Get:42 http://ftpmaster.internal/ubuntu noble/universe ppc64el qtltools-example all 1.3.1+dfsg-4build3 [13.6 MB] 145s Preconfiguring packages ... 145s Fetched 56.0 MB in 3s (17.5 MB/s) 145s Selecting previously unselected package fontconfig. 145s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 72217 files and directories currently installed.) 145s Preparing to unpack .../00-fontconfig_2.15.0-1.1ubuntu2_ppc64el.deb ... 145s Unpacking fontconfig (2.15.0-1.1ubuntu2) ... 145s Selecting previously unselected package libblas3:ppc64el. 145s Preparing to unpack .../01-libblas3_3.12.0-3build1_ppc64el.deb ... 145s Unpacking libblas3:ppc64el (3.12.0-3build1) ... 145s Selecting previously unselected package libboost-iostreams1.83.0:ppc64el. 145s Preparing to unpack .../02-libboost-iostreams1.83.0_1.83.0-2.1ubuntu3_ppc64el.deb ... 145s Unpacking libboost-iostreams1.83.0:ppc64el (1.83.0-2.1ubuntu3) ... 145s Selecting previously unselected package libboost-program-options1.83.0:ppc64el. 145s Preparing to unpack .../03-libboost-program-options1.83.0_1.83.0-2.1ubuntu3_ppc64el.deb ... 145s Unpacking libboost-program-options1.83.0:ppc64el (1.83.0-2.1ubuntu3) ... 145s Selecting previously unselected package libpixman-1-0:ppc64el. 145s Preparing to unpack .../04-libpixman-1-0_0.42.2-1build1_ppc64el.deb ... 145s Unpacking libpixman-1-0:ppc64el (0.42.2-1build1) ... 145s Selecting previously unselected package libxcb-render0:ppc64el. 145s Preparing to unpack .../05-libxcb-render0_1.15-1ubuntu2_ppc64el.deb ... 145s Unpacking libxcb-render0:ppc64el (1.15-1ubuntu2) ... 145s Selecting previously unselected package libxcb-shm0:ppc64el. 145s Preparing to unpack .../06-libxcb-shm0_1.15-1ubuntu2_ppc64el.deb ... 145s Unpacking libxcb-shm0:ppc64el (1.15-1ubuntu2) ... 145s Selecting previously unselected package libxrender1:ppc64el. 145s Preparing to unpack .../07-libxrender1_1%3a0.9.10-1.1build1_ppc64el.deb ... 145s Unpacking libxrender1:ppc64el (1:0.9.10-1.1build1) ... 145s Selecting previously unselected package libcairo2:ppc64el. 145s Preparing to unpack .../08-libcairo2_1.18.0-3build1_ppc64el.deb ... 145s Unpacking libcairo2:ppc64el (1.18.0-3build1) ... 145s Selecting previously unselected package libdatrie1:ppc64el. 145s Preparing to unpack .../09-libdatrie1_0.2.13-3build1_ppc64el.deb ... 145s Unpacking libdatrie1:ppc64el (0.2.13-3build1) ... 145s Selecting previously unselected package libgfortran5:ppc64el. 145s Preparing to unpack .../10-libgfortran5_14-20240412-0ubuntu1_ppc64el.deb ... 145s Unpacking libgfortran5:ppc64el (14-20240412-0ubuntu1) ... 145s Selecting previously unselected package libgomp1:ppc64el. 145s Preparing to unpack .../11-libgomp1_14-20240412-0ubuntu1_ppc64el.deb ... 145s Unpacking libgomp1:ppc64el (14-20240412-0ubuntu1) ... 145s Selecting previously unselected package libgraphite2-3:ppc64el. 145s Preparing to unpack .../12-libgraphite2-3_1.3.14-2build1_ppc64el.deb ... 145s Unpacking libgraphite2-3:ppc64el (1.3.14-2build1) ... 145s Selecting previously unselected package libgslcblas0:ppc64el. 145s Preparing to unpack .../13-libgslcblas0_2.7.1+dfsg-6ubuntu2_ppc64el.deb ... 145s Unpacking libgslcblas0:ppc64el (2.7.1+dfsg-6ubuntu2) ... 145s Selecting previously unselected package libgsl27:ppc64el. 145s Preparing to unpack .../14-libgsl27_2.7.1+dfsg-6ubuntu2_ppc64el.deb ... 145s Unpacking libgsl27:ppc64el (2.7.1+dfsg-6ubuntu2) ... 145s Selecting previously unselected package libharfbuzz0b:ppc64el. 145s Preparing to unpack .../15-libharfbuzz0b_8.3.0-2build2_ppc64el.deb ... 145s Unpacking libharfbuzz0b:ppc64el (8.3.0-2build2) ... 145s Selecting previously unselected package libhtscodecs2:ppc64el. 145s Preparing to unpack .../16-libhtscodecs2_1.6.0-1build1_ppc64el.deb ... 145s Unpacking libhtscodecs2:ppc64el (1.6.0-1build1) ... 145s Selecting previously unselected package libhts3t64:ppc64el. 145s Preparing to unpack .../17-libhts3t64_1.19+ds-1.1build3_ppc64el.deb ... 145s Unpacking libhts3t64:ppc64el (1.19+ds-1.1build3) ... 145s Selecting previously unselected package x11-common. 145s Preparing to unpack .../18-x11-common_1%3a7.7+23ubuntu3_all.deb ... 145s Unpacking x11-common (1:7.7+23ubuntu3) ... 145s Selecting previously unselected package libice6:ppc64el. 145s Preparing to unpack .../19-libice6_2%3a1.0.10-1build3_ppc64el.deb ... 145s Unpacking libice6:ppc64el (2:1.0.10-1build3) ... 145s Selecting previously unselected package liblapack3:ppc64el. 145s Preparing to unpack .../20-liblapack3_3.12.0-3build1_ppc64el.deb ... 145s Unpacking liblapack3:ppc64el (3.12.0-3build1) ... 146s Selecting previously unselected package libthai-data. 146s Preparing to unpack .../21-libthai-data_0.1.29-2build1_all.deb ... 146s Unpacking libthai-data (0.1.29-2build1) ... 146s Selecting previously unselected package libthai0:ppc64el. 146s Preparing to unpack .../22-libthai0_0.1.29-2build1_ppc64el.deb ... 146s Unpacking libthai0:ppc64el (0.1.29-2build1) ... 146s Selecting previously unselected package libpango-1.0-0:ppc64el. 146s Preparing to unpack .../23-libpango-1.0-0_1.52.1+ds-1build1_ppc64el.deb ... 146s Unpacking libpango-1.0-0:ppc64el (1.52.1+ds-1build1) ... 146s Selecting previously unselected package libpangoft2-1.0-0:ppc64el. 146s Preparing to unpack .../24-libpangoft2-1.0-0_1.52.1+ds-1build1_ppc64el.deb ... 146s Unpacking libpangoft2-1.0-0:ppc64el (1.52.1+ds-1build1) ... 146s Selecting previously unselected package libpangocairo-1.0-0:ppc64el. 146s Preparing to unpack .../25-libpangocairo-1.0-0_1.52.1+ds-1build1_ppc64el.deb ... 146s Unpacking libpangocairo-1.0-0:ppc64el (1.52.1+ds-1build1) ... 146s Selecting previously unselected package libpaper1:ppc64el. 146s Preparing to unpack .../26-libpaper1_1.1.29build1_ppc64el.deb ... 146s Unpacking libpaper1:ppc64el (1.1.29build1) ... 146s Selecting previously unselected package libpaper-utils. 146s Preparing to unpack .../27-libpaper-utils_1.1.29build1_ppc64el.deb ... 146s Unpacking libpaper-utils (1.1.29build1) ... 146s Selecting previously unselected package libsm6:ppc64el. 146s Preparing to unpack .../28-libsm6_2%3a1.2.3-1build3_ppc64el.deb ... 146s Unpacking libsm6:ppc64el (2:1.2.3-1build3) ... 146s Selecting previously unselected package libtcl8.6:ppc64el. 146s Preparing to unpack .../29-libtcl8.6_8.6.14+dfsg-1build1_ppc64el.deb ... 146s Unpacking libtcl8.6:ppc64el (8.6.14+dfsg-1build1) ... 146s Selecting previously unselected package libxft2:ppc64el. 146s Preparing to unpack .../30-libxft2_2.3.6-1build1_ppc64el.deb ... 146s Unpacking libxft2:ppc64el (2.3.6-1build1) ... 146s Selecting previously unselected package libxss1:ppc64el. 146s Preparing to unpack .../31-libxss1_1%3a1.2.3-1build3_ppc64el.deb ... 146s Unpacking libxss1:ppc64el (1:1.2.3-1build3) ... 146s Selecting previously unselected package libtk8.6:ppc64el. 146s Preparing to unpack .../32-libtk8.6_8.6.14-1build1_ppc64el.deb ... 146s Unpacking libtk8.6:ppc64el (8.6.14-1build1) ... 146s Selecting previously unselected package libxt6t64:ppc64el. 146s Preparing to unpack .../33-libxt6t64_1%3a1.2.1-1.2build1_ppc64el.deb ... 146s Unpacking libxt6t64:ppc64el (1:1.2.1-1.2build1) ... 146s Selecting previously unselected package r-mathlib. 146s Preparing to unpack .../34-r-mathlib_4.3.3-2build2_ppc64el.deb ... 146s Unpacking r-mathlib (4.3.3-2build2) ... 146s Selecting previously unselected package zip. 146s Preparing to unpack .../35-zip_3.0-13build1_ppc64el.deb ... 146s Unpacking zip (3.0-13build1) ... 146s Selecting previously unselected package unzip. 146s Preparing to unpack .../36-unzip_6.0-28ubuntu4_ppc64el.deb ... 146s Unpacking unzip (6.0-28ubuntu4) ... 146s Selecting previously unselected package xdg-utils. 146s Preparing to unpack .../37-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 146s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 146s Selecting previously unselected package r-base-core. 146s Preparing to unpack .../38-r-base-core_4.3.3-2build2_ppc64el.deb ... 146s Unpacking r-base-core (4.3.3-2build2) ... 146s Selecting previously unselected package qtltools. 146s Preparing to unpack .../39-qtltools_1.3.1+dfsg-4build3_ppc64el.deb ... 146s Unpacking qtltools (1.3.1+dfsg-4build3) ... 146s Selecting previously unselected package qtltools-example. 146s Preparing to unpack .../40-qtltools-example_1.3.1+dfsg-4build3_all.deb ... 146s Unpacking qtltools-example (1.3.1+dfsg-4build3) ... 146s Selecting previously unselected package autopkgtest-satdep. 146s Preparing to unpack .../41-1-autopkgtest-satdep.deb ... 146s Unpacking autopkgtest-satdep (0) ... 146s Setting up libhtscodecs2:ppc64el (1.6.0-1build1) ... 146s Setting up libgraphite2-3:ppc64el (1.3.14-2build1) ... 146s Setting up qtltools-example (1.3.1+dfsg-4build3) ... 146s Setting up libboost-program-options1.83.0:ppc64el (1.83.0-2.1ubuntu3) ... 146s Setting up libpixman-1-0:ppc64el (0.42.2-1build1) ... 146s Setting up libpaper1:ppc64el (1.1.29build1) ... 147s 147s Creating config file /etc/papersize with new version 147s Setting up fontconfig (2.15.0-1.1ubuntu2) ... 149s Regenerating fonts cache... done. 149s Setting up libxrender1:ppc64el (1:0.9.10-1.1build1) ... 149s Setting up libdatrie1:ppc64el (0.2.13-3build1) ... 149s Setting up libgslcblas0:ppc64el (2.7.1+dfsg-6ubuntu2) ... 149s Setting up libxcb-render0:ppc64el (1.15-1ubuntu2) ... 149s Setting up unzip (6.0-28ubuntu4) ... 149s Setting up x11-common (1:7.7+23ubuntu3) ... 149s Setting up libgsl27:ppc64el (2.7.1+dfsg-6ubuntu2) ... 149s Setting up libxcb-shm0:ppc64el (1.15-1ubuntu2) ... 149s Setting up libpaper-utils (1.1.29build1) ... 149s Setting up libgomp1:ppc64el (14-20240412-0ubuntu1) ... 149s Setting up libcairo2:ppc64el (1.18.0-3build1) ... 149s Setting up zip (3.0-13build1) ... 149s Setting up libblas3:ppc64el (3.12.0-3build1) ... 149s 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 149s Setting up libboost-iostreams1.83.0:ppc64el (1.83.0-2.1ubuntu3) ... 149s Setting up libtcl8.6:ppc64el (8.6.14+dfsg-1build1) ... 149s Setting up libgfortran5:ppc64el (14-20240412-0ubuntu1) ... 149s Setting up r-mathlib (4.3.3-2build2) ... 149s Setting up libhts3t64:ppc64el (1.19+ds-1.1build3) ... 149s Setting up libharfbuzz0b:ppc64el (8.3.0-2build2) ... 149s Setting up libthai-data (0.1.29-2build1) ... 149s Setting up libxss1:ppc64el (1:1.2.3-1build3) ... 149s Setting up xdg-utils (1.1.3-4.1ubuntu3) ... 149s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 149s Setting up libice6:ppc64el (2:1.0.10-1build3) ... 149s Setting up liblapack3:ppc64el (3.12.0-3build1) ... 149s 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 149s Setting up libxft2:ppc64el (2.3.6-1build1) ... 149s Setting up libtk8.6:ppc64el (8.6.14-1build1) ... 149s Setting up libthai0:ppc64el (0.1.29-2build1) ... 149s Setting up libsm6:ppc64el (2:1.2.3-1build3) ... 149s Setting up libpango-1.0-0:ppc64el (1.52.1+ds-1build1) ... 149s Setting up libxt6t64:ppc64el (1:1.2.1-1.2build1) ... 149s Setting up libpangoft2-1.0-0:ppc64el (1.52.1+ds-1build1) ... 149s Setting up libpangocairo-1.0-0:ppc64el (1.52.1+ds-1build1) ... 149s Setting up r-base-core (4.3.3-2build2) ... 149s 149s Creating config file /etc/R/Renviron with new version 149s Setting up qtltools (1.3.1+dfsg-4build3) ... 149s Setting up autopkgtest-satdep (0) ... 149s Processing triggers for man-db (2.12.0-4build2) ... 150s Processing triggers for install-info (7.1-3build2) ... 150s Processing triggers for libc-bin (2.39-0ubuntu8.3) ... 154s (Reading database ... 74141 files and directories currently installed.) 154s Removing autopkgtest-satdep (0) ... 154s autopkgtest [00:16:56]: test run-sample-analysis: [----------------------- 155s ./genes.50percent.chr22.bed.gz 155s ./genes.50percent.chr22.bed.gz.tbi 155s ./genes.covariates.pc50.txt.gz 155s ./genes.simulated.chr22.bed.gz 155s ./genes.simulated.chr22.bed.gz.tbi 155s ./genotypes.chr22.vcf.gz 155s ./genotypes.chr22.vcf.gz.tbi 155s 155s QTLtools 155s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 155s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 155s * Webpage : https://qtltools.github.io/qtltools/ 155s * Version : 1.3.1 155s * Date : 13/08/2024 - 00:16:57 155s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 155s 155s CONDUCT PCA ON DATA 155s 155s Initialize random number generator 155s * Built-in seed is 15112011 155s * First Integer = 30553 155s * First Double = 0.0126695 155s 155s Reading sample list from [genes.50percent.chr22.bed.gz] 155s * #samples = 358 155s 155s Merging sample sets from all input files 155s * #files = 1 155s * #samples in all files = 358 155s 155s Reading phenotype data in [genes.50percent.chr22.bed.gz] 155s * 358 samples included 155s * 608 phenotypes included 155s 155s Calculating PCA with a matrix 358 x 608 155s * Calculated mean and sd 155s * 0 sd==0 columns removed 155s * Variables centered 155s * Variables scaled to unit variance 155s * Running SVD 156s * SVD complete 156s * Calculated sd and var for PCs 156s * Calculated cumulative var for PCs 156s * Done! 156s 156s Running time: 0 seconds 156s 156s QTLtools 156s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 156s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 156s * Webpage : https://qtltools.github.io/qtltools/ 156s * Version : 1.3.1 156s * Date : 13/08/2024 - 00:16:58 156s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 156s 156s MAPPING QTL IN CIS 156s * TASK: Report all nominal associations with p <= 0.01 156s * Linear model: Phe ~ Var + Cov 156s * Cis-window size is 1000000 bp 156s * Region = [chr22:17000000-18000000] 156s 156s Initialize random number generator 156s * Built-in seed is 15112011 156s * First Integer = 30553 156s * First Double = 0.0126695 156s 156s Reading sample list from [genes.50percent.chr22.bed.gz] 156s * #samples = 358 156s 156s Read sample list from [genotypes.chr22.vcf.gz] 156s * #samples = 358 156s 156s Reading sample list from [genes.covariates.pc50.txt.gz] 156s * #samples = 358 156s 156s Merging sample sets from all input files 156s * #files = 3 156s * #samples in all files = 358 156s 156s Reading phenotype data in [genes.50percent.chr22.bed.gz] 156s * target region [chr22:17000000-18000000] 156s * 8 phenotypes included 156s * 3 phenotypes are on the negative strand 156s 156s Reading genotype data in [genotypes.chr22.vcf.gz] 156s * File format detected: VCF 156s * target region [chr22:16000000-19000000] 156s * 6404 variants included 156s 156s Reading covariates in [genes.covariates.pc50.txt.gz] 156s * 53 covariates included 156s 156s Residualize phenotypes for covariates 156s * #covariates = 53 156s 156s Processing phenotype [ENSG00000237438.2] [1/8] 156s * #variants in cis = 5095 156s * Best hit: [id=22_17542810, d=25350, pv=1.1864e-25, s=-0.7518] 156s 156s Processing phenotype [ENSG00000273203.1] [2/8] 156s * #variants in cis = 5170 156s * Best hit: [id=22_17517388, d=-31323, pv=5.86611e-06, s=-0.1406] 156s 156s Processing phenotype [ENSG00000273442.1] [3/8] 156s * #variants in cis = 5188 156s * Best hit: [id=22_17553526, d=-8065, pv=0.000244522, s=0.1340] 156s 156s Processing phenotype [ENSG00000177663.9] [4/8] 156s * #variants in cis = 5193 156s * Best hit: [id=22_17513703, d=-52141, pv=8.03358e-14, s=-0.2096] 156s 156s Processing phenotype [ENSG00000183307.3] [5/8] 156s * #variants in cis = 5230 156s * Best hit: [id=22_17587975, d=14282, pv=1.56789e-07, s=-0.0078] 156s 156s Processing phenotype [ENSG00000069998.8] [6/8] 156s * #variants in cis = 5291 156s * Best hit: [id=22_17620429, d=25748, pv=1.37287e-14, s=-1.5147] 156s 156s Processing phenotype [ENSG00000093072.11] [7/8] 156s * #variants in cis = 5293 156s * Best hit: [id=22_17699630, d=3249, pv=0.000578649, s=0.6404] 156s 156s Processing phenotype [ENSG00000099954.14] [8/8] 156s * #variants in cis = 5435 156s * Best hit: [id=22_17175937, d=-664900, pv=0.000866455, s=0.0067] 156s 156s Running time: 0 seconds 156s 156s QTLtools 156s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 156s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 156s * Webpage : https://qtltools.github.io/qtltools/ 156s * Version : 1.3.1 156s * Date : 13/08/2024 - 00:16:58 156s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 156s 156s MAPPING QTL IN CIS 156s * TASK: Perform 1000 permutations 156s * Linear model: Phe ~ Var + Cov 156s * Cis-window size is 1000000 bp 156s * Region = [chr22:17000000-18000000] 156s 156s Initialize random number generator 156s * Built-in seed is 15112011 156s * First Integer = 30553 156s * First Double = 0.0126695 156s 156s Reading sample list from [genes.50percent.chr22.bed.gz] 156s * #samples = 358 156s 156s Read sample list from [genotypes.chr22.vcf.gz] 156s * #samples = 358 156s 156s Reading sample list from [genes.covariates.pc50.txt.gz] 156s * #samples = 358 156s 156s Merging sample sets from all input files 156s * #files = 3 156s * #samples in all files = 358 156s 156s Reading phenotype data in [genes.50percent.chr22.bed.gz] 156s * target region [chr22:17000000-18000000] 156s * 8 phenotypes included 156s * 3 phenotypes are on the negative strand 156s 156s Reading genotype data in [genotypes.chr22.vcf.gz] 156s * File format detected: VCF 156s * target region [chr22:16000000-19000000] 156s * 6404 variants included 156s 156s Reading covariates in [genes.covariates.pc50.txt.gz] 156s * 53 covariates included 156s 156s Residualize phenotypes for covariates 156s * #covariates = 53 156s 156s Processing phenotype [ENSG00000237438.2] [1/8] 156s * #variants in cis = 5095 158s * Best hit: [id=22_17542810, d=25350, pv=1.1864e-25, s=-0.7518] 158s * Beta parameters: [s1=1.00995, s2=621.053] 158s * Adjusted p-values: [emp=0.000999001, beta=1.28062e-20] 158s 158s Processing phenotype [ENSG00000273203.1] [2/8] 158s * #variants in cis = 5170 159s * Best hit: [id=22_17517388, d=-31323, pv=5.86611e-06, s=-0.1406] 159s * Beta parameters: [s1=1.11817, s2=641.379] 159s * Adjusted p-values: [emp=0.00799201, beta=0.00751892] 159s 159s Processing phenotype [ENSG00000273442.1] [3/8] 159s * #variants in cis = 5188 160s * Best hit: [id=22_17553526, d=-8065, pv=0.000244522, s=0.1340] 160s * Beta parameters: [s1=1.08364, s2=467.63] 160s * Adjusted p-values: [emp=0.297702, beta=0.293948] 160s 160s Processing phenotype [ENSG00000177663.9] [4/8] 160s * #variants in cis = 5193 161s * Best hit: [id=22_17513703, d=-52141, pv=8.03358e-14, s=-0.2096] 161s * Beta parameters: [s1=0.989061, s2=704.553] 161s * Adjusted p-values: [emp=0.000999001, beta=7.91291e-10] 161s 161s Processing phenotype [ENSG00000183307.3] [5/8] 161s * #variants in cis = 5230 162s * Best hit: [id=22_17587975, d=14282, pv=1.56789e-07, s=-0.0078] 162s * Beta parameters: [s1=1.01322, s2=559.49] 162s * Adjusted p-values: [emp=0.000999001, beta=0.00050707] 162s 162s Processing phenotype [ENSG00000069998.8] [6/8] 162s * #variants in cis = 5291 164s * Best hit: [id=22_17620429, d=25748, pv=1.37287e-14, s=-1.5147] 164s * Beta parameters: [s1=1.02312, s2=563.339] 164s * Adjusted p-values: [emp=0.000999001, beta=2.56935e-10] 164s 164s Processing phenotype [ENSG00000093072.11] [7/8] 164s * #variants in cis = 5293 165s * Best hit: [id=22_17699630, d=3249, pv=0.000578649, s=0.6404] 165s * Beta parameters: [s1=0.957514, s2=559.397] 165s * Adjusted p-values: [emp=0.574426, beta=0.562826] 165s 165s Processing phenotype [ENSG00000099954.14] [8/8] 165s * #variants in cis = 5435 166s * Best hit: [id=22_17175937, d=-664900, pv=0.000866455, s=0.0067] 166s * Beta parameters: [s1=0.938041, s2=226.852] 166s * Adjusted p-values: [emp=0.842158, beta=0.84836] 166s 166s Running time: 9 seconds 166s 166s QTLtools 166s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 166s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 166s * Webpage : https://qtltools.github.io/qtltools/ 166s * Version : 1.3.1 166s * Date : 13/08/2024 - 00:17:08 166s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 166s 166s MAPPING QTL IN TRANS 166s * TASK: Perform a full nominal pass, do not adjust p-values 166s * Cis-window size is 5000000 bp 166s * #bins = 1000 166s * threshold = 1e-05 166s 166s Initialize random number generator 166s * Built-in seed is 15112011 166s * First Integer = 30553 166s * First Double = 0.0126695 166s 166s Read sample list from [genotypes.chr22.vcf.gz] 166s * #samples = 358 166s 166s Checking sample list in [genes.simulated.chr22.bed.gz] 166s * #samples = 358 166s 166s Reading phenotype data in [genes.simulated.chr22.bed.gz] from line 0 to 0 166s * 358 samples included 166s * 608 phenotypes included 166s * 275 phenotypes is on the negative strand 166s 166s Calculate correlation threshold 166s * thres = 1e-05 166s * corr = 0.2311 166s 166s Sweep through genotype data in [genotypes.chr22.vcf.gz] 166s * #variants=1950 #multi_allelic=0 #not_processed=0 #hits=101/1000000 speed=3.70MT/s 167s * #variants=4001 #multi_allelic=0 #not_processed=0 #hits=153/2000000 speed=3.58MT/s 167s * #variants=6187 #multi_allelic=0 #not_processed=0 #hits=244/3000000 speed=3.64MT/s 167s * #variants=8537 #multi_allelic=0 #not_processed=0 #hits=285/4000000 speed=3.37MT/s 168s * #variants=11025 #multi_allelic=0 #not_processed=0 #hits=312/5000000 speed=3.24MT/s 168s * #variants=13621 #multi_allelic=0 #not_processed=0 #hits=320/6000000 speed=3.33MT/s 168s * #variants=16217 #multi_allelic=0 #not_processed=0 #hits=342/7000000 speed=3.64MT/s 168s * #variants=18755 #multi_allelic=0 #not_processed=0 #hits=401/8000000 speed=3.53MT/s 169s * #variants=21237 #multi_allelic=0 #not_processed=0 #hits=402/9000000 speed=3.05MT/s 169s * #variants=23680 #multi_allelic=0 #not_processed=0 #hits=455/10000000 speed=3.42MT/s 169s * #variants=26171 #multi_allelic=0 #not_processed=0 #hits=463/11000000 speed=3.69MT/s 170s * #variants=28609 #multi_allelic=0 #not_processed=0 #hits=469/12000000 speed=3.72MT/s 170s * #variants=30861 #multi_allelic=0 #not_processed=0 #hits=973/13000000 speed=3.70MT/s 170s * #variants=32932 #multi_allelic=0 #not_processed=0 #hits=979/14000000 speed=3.82MT/s 170s * #variants=34974 #multi_allelic=0 #not_processed=0 #hits=1085/15000000 speed=3.79MT/s 171s * #variants=37021 #multi_allelic=0 #not_processed=0 #hits=1086/16000000 speed=3.83MT/s 171s * #variants=39122 #multi_allelic=0 #not_processed=0 #hits=1089/17000000 speed=3.70MT/s 171s * #variants=41334 #multi_allelic=0 #not_processed=0 #hits=1089/18000000 speed=3.79MT/s 171s * #variants=43627 #multi_allelic=0 #not_processed=0 #hits=1096/19000000 speed=3.76MT/s 172s * #variants=45897 #multi_allelic=0 #not_processed=0 #hits=1153/20000000 speed=3.80MT/s 172s * #variants=48114 #multi_allelic=0 #not_processed=0 #hits=1243/21000000 speed=3.66MT/s 172s * #variants=50410 #multi_allelic=0 #not_processed=0 #hits=1249/22000000 speed=3.82MT/s 172s * #variants=52820 #multi_allelic=0 #not_processed=0 #hits=1259/23000000 speed=3.75MT/s 173s * #variants=55279 #multi_allelic=0 #not_processed=0 #hits=1498/24000000 speed=3.72MT/s 173s * #variants=57789 #multi_allelic=0 #not_processed=0 #hits=1724/25000000 speed=2.99MT/s 173s * #variants=60201 #multi_allelic=0 #not_processed=0 #hits=2168/26000000 speed=3.34MT/s 174s * #variants=62476 #multi_allelic=0 #not_processed=0 #hits=2452/27000000 speed=3.37MT/s 174s * #variants=64608 #multi_allelic=0 #not_processed=0 #hits=2544/28000000 speed=3.80MT/s 174s * #variants=66709 #multi_allelic=0 #not_processed=0 #hits=2684/29000000 speed=3.80MT/s 174s * #variants=68871 #multi_allelic=0 #not_processed=0 #hits=2688/30000000 speed=3.77MT/s 175s * #variants=71070 #multi_allelic=0 #not_processed=0 #hits=2720/31000000 speed=3.83MT/s 175s * #variants=73151 #multi_allelic=0 #not_processed=0 #hits=2891/32000000 speed=3.80MT/s 175s * #variants=75122 #multi_allelic=0 #not_processed=0 #hits=3110/33000000 speed=3.70MT/s 176s * #variants=77058 #multi_allelic=0 #not_processed=0 #hits=3209/34000000 speed=3.89MT/s 176s * #variants=78989 #multi_allelic=0 #not_processed=0 #hits=3218/35000000 speed=3.91MT/s 176s * #variants=80903 #multi_allelic=0 #not_processed=0 #hits=3250/36000000 speed=3.92MT/s 176s * #variants=82811 #multi_allelic=0 #not_processed=0 #hits=3463/37000000 speed=3.94MT/s 177s * #variants=84694 #multi_allelic=0 #not_processed=0 #hits=4035/38000000 speed=3.88MT/s 177s * #variants=85485 #multi_allelic=0 #not_processed=0 #hits=4036/38425275 speed=3.97MT/s 177s 177s Running time: 10 seconds 177s 177s QTLtools 177s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 177s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 177s * Webpage : https://qtltools.github.io/qtltools/ 177s * Version : 1.3.1 177s * Date : 13/08/2024 - 00:17:19 177s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 177s 177s MAPPING QTL IN TRANS 177s * TASK: Permute randomly chosen phenotypes 1000 times and test 177s * Cis-window size is 5000000 bp 177s * #bins = 1000 177s * threshold = 1e-05 177s 177s Initialize random number generator 177s * Built-in seed is 15112011 177s * First Integer = 30553 177s * First Double = 0.0126695 177s 177s Read sample list from [genotypes.chr22.vcf.gz] 177s * #samples = 358 177s 177s Checking sample list in [genes.simulated.chr22.bed.gz] 177s * #samples = 358 177s 177s Reading phenotype data in [genes.simulated.chr22.bed.gz] from line 0 to 0 177s * 358 samples included 177s * 608 phenotypes included 177s * 275 phenotypes is on the negative strand 177s 177s Normal transform phenotypes 177s 177s Calculate correlation threshold 177s * thres = 1e-05 177s * corr = 0.2311 177s 177s Sweep through genotype data in [genotypes.chr22.vcf.gz] 177s * #variants=1177 #multi_allelic=0 #not_processed=0 #hits=28/1000000 speed=4.05MT/s 177s * #variants=2383 #multi_allelic=0 #not_processed=0 #hits=38/2000000 speed=4.05MT/s 178s * #variants=3633 #multi_allelic=0 #not_processed=0 #hits=53/3000000 speed=4.03MT/s 178s * #variants=4928 #multi_allelic=0 #not_processed=0 #hits=53/4000000 speed=3.97MT/s 178s * #variants=6269 #multi_allelic=0 #not_processed=0 #hits=71/5000000 speed=3.91MT/s 178s * #variants=7675 #multi_allelic=0 #not_processed=0 #hits=72/6000000 speed=3.85MT/s 179s * #variants=9151 #multi_allelic=0 #not_processed=0 #hits=88/7000000 speed=3.76MT/s 179s * #variants=10663 #multi_allelic=0 #not_processed=0 #hits=96/8000000 speed=3.76MT/s 179s * #variants=12202 #multi_allelic=0 #not_processed=0 #hits=96/9000000 speed=3.73MT/s 179s * #variants=13804 #multi_allelic=0 #not_processed=0 #hits=96/10000000 speed=3.68MT/s 180s * #variants=15381 #multi_allelic=0 #not_processed=0 #hits=120/11000000 speed=3.68MT/s 180s * #variants=16946 #multi_allelic=0 #not_processed=0 #hits=123/12000000 speed=3.83MT/s 180s * #variants=18483 #multi_allelic=0 #not_processed=0 #hits=129/13000000 speed=3.85MT/s 180s * #variants=19995 #multi_allelic=0 #not_processed=0 #hits=131/14000000 speed=3.79MT/s 181s * #variants=21489 #multi_allelic=0 #not_processed=0 #hits=132/15000000 speed=3.75MT/s 181s * #variants=22947 #multi_allelic=0 #not_processed=0 #hits=151/16000000 speed=3.82MT/s 181s * #variants=24445 #multi_allelic=0 #not_processed=0 #hits=168/17000000 speed=3.79MT/s 182s * #variants=25965 #multi_allelic=0 #not_processed=0 #hits=175/18000000 speed=3.75MT/s 182s * #variants=27472 #multi_allelic=0 #not_processed=0 #hits=179/19000000 speed=3.76MT/s 182s * #variants=28933 #multi_allelic=0 #not_processed=0 #hits=181/20000000 speed=3.80MT/s 182s * #variants=30325 #multi_allelic=0 #not_processed=0 #hits=181/21000000 speed=3.86MT/s 183s * #variants=31617 #multi_allelic=0 #not_processed=0 #hits=182/22000000 speed=3.92MT/s 183s * #variants=32875 #multi_allelic=0 #not_processed=0 #hits=190/23000000 speed=3.98MT/s 183s * #variants=34127 #multi_allelic=0 #not_processed=0 #hits=192/24000000 speed=3.62MT/s 183s * #variants=35392 #multi_allelic=0 #not_processed=0 #hits=206/25000000 speed=3.70MT/s 184s * #variants=36652 #multi_allelic=0 #not_processed=0 #hits=206/26000000 speed=3.76MT/s 184s * #variants=37940 #multi_allelic=0 #not_processed=0 #hits=213/27000000 speed=3.83MT/s 184s * #variants=39255 #multi_allelic=0 #not_processed=0 #hits=238/28000000 speed=3.82MT/s 184s * #variants=40602 #multi_allelic=0 #not_processed=0 #hits=239/29000000 speed=3.79MT/s 185s * #variants=41998 #multi_allelic=0 #not_processed=0 #hits=245/30000000 speed=3.73MT/s 185s * #variants=43398 #multi_allelic=0 #not_processed=0 #hits=245/31000000 speed=3.77MT/s 185s * #variants=44803 #multi_allelic=0 #not_processed=0 #hits=260/32000000 speed=3.72MT/s 185s * #variants=46187 #multi_allelic=0 #not_processed=0 #hits=261/33000000 speed=3.72MT/s 186s * #variants=47545 #multi_allelic=0 #not_processed=0 #hits=268/34000000 speed=3.62MT/s 186s * #variants=48904 #multi_allelic=0 #not_processed=0 #hits=280/35000000 speed=3.68MT/s 186s * #variants=50309 #multi_allelic=0 #not_processed=0 #hits=306/36000000 speed=3.75MT/s 187s * #variants=51731 #multi_allelic=0 #not_processed=0 #hits=314/37000000 speed=3.75MT/s 187s * #variants=53171 #multi_allelic=0 #not_processed=0 #hits=320/38000000 speed=3.53MT/s 187s * #variants=54621 #multi_allelic=0 #not_processed=0 #hits=323/39000000 speed=3.61MT/s 187s * #variants=56099 #multi_allelic=0 #not_processed=0 #hits=323/40000000 speed=3.51MT/s 188s * #variants=57584 #multi_allelic=0 #not_processed=0 #hits=340/41000000 speed=3.60MT/s 188s * #variants=59032 #multi_allelic=0 #not_processed=0 #hits=344/42000000 speed=3.65MT/s 188s * #variants=60437 #multi_allelic=0 #not_processed=0 #hits=345/43000000 speed=3.61MT/s 189s * #variants=61810 #multi_allelic=0 #not_processed=0 #hits=357/44000000 speed=3.77MT/s 189s * #variants=63129 #multi_allelic=0 #not_processed=0 #hits=384/45000000 speed=3.79MT/s 189s * #variants=64409 #multi_allelic=0 #not_processed=0 #hits=391/46000000 speed=3.77MT/s 189s * #variants=65679 #multi_allelic=0 #not_processed=0 #hits=430/47000000 speed=3.79MT/s 190s * #variants=66953 #multi_allelic=0 #not_processed=0 #hits=436/48000000 speed=3.82MT/s 190s * #variants=68247 #multi_allelic=0 #not_processed=0 #hits=446/49000000 speed=3.79MT/s 190s * #variants=69595 #multi_allelic=0 #not_processed=0 #hits=460/50000000 speed=3.76MT/s 190s * #variants=70918 #multi_allelic=0 #not_processed=0 #hits=481/51000000 speed=3.75MT/s 191s * #variants=72211 #multi_allelic=0 #not_processed=0 #hits=492/52000000 speed=3.72MT/s 191s * #variants=73449 #multi_allelic=0 #not_processed=0 #hits=492/53000000 speed=3.75MT/s 191s * #variants=74662 #multi_allelic=0 #not_processed=0 #hits=500/54000000 speed=3.80MT/s 191s * #variants=75863 #multi_allelic=0 #not_processed=0 #hits=506/55000000 speed=3.94MT/s 192s * #variants=77058 #multi_allelic=0 #not_processed=0 #hits=513/56000000 speed=4.02MT/s 192s * #variants=78253 #multi_allelic=0 #not_processed=0 #hits=515/57000000 speed=3.98MT/s 192s * #variants=79446 #multi_allelic=0 #not_processed=0 #hits=530/58000000 speed=4.00MT/s 192s * #variants=80634 #multi_allelic=0 #not_processed=0 #hits=581/59000000 speed=4.02MT/s 193s * #variants=81817 #multi_allelic=0 #not_processed=0 #hits=594/60000000 speed=4.02MT/s 193s * #variants=82993 #multi_allelic=0 #not_processed=0 #hits=598/61000000 speed=4.03MT/s 193s * #variants=84160 #multi_allelic=0 #not_processed=0 #hits=599/62000000 speed=4.03MT/s 193s * #variants=85304 #multi_allelic=0 #not_processed=0 #hits=609/63000000 speed=4.05MT/s 193s * #variants=85485 #multi_allelic=0 #not_processed=0 #hits=609/63157827 speed=4.15MT/s 193s 193s Running time: 16 seconds 194s autopkgtest [00:17:36]: test run-sample-analysis: -----------------------] 194s autopkgtest [00:17:36]: test run-sample-analysis: - - - - - - - - - - results - - - - - - - - - - 194s run-sample-analysis PASS 195s autopkgtest [00:17:37]: @@@@@@@@@@@@@@@@@@@@ summary 195s run-sample-analysis PASS 200s nova [W] Using flock in prodstack6-ppc64el 200s Creating nova instance adt-noble-ppc64el-qtltools-20240813-001421-juju-7f2275-prod-proposed-migration-environment-2-39bbe0a2-a0e1-4d9e-9f42-e11a29e740cc from image adt/ubuntu-noble-ppc64el-server-20240812.img (UUID 897171f4-60c5-48b4-94c3-092604e7e237)...