0s autopkgtest [04:48:06]: starting date and time: 2024-04-12 04:48:06+0000 0s autopkgtest [04:48:06]: git checkout: 43bc6cdf gitlab-ci: do not include the salsa pipeline 0s autopkgtest [04:48:06]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.tg4hjclv/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:lapack --apt-upgrade qtltools --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=lapack/3.12.0-3build1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos02-ppc64el-18.secgroup --name adt-noble-ppc64el-qtltools-20240412-044806-juju-7f2275-prod-proposed-migration-environment-3-55db328d-b04f-4737-9f7b-d2168ae71c80 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,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 [04:49:59]: testbed dpkg architecture: ppc64el 114s autopkgtest [04:50:00]: testbed apt version: 2.7.14build2 114s autopkgtest [04:50:00]: @@@@@@@@@@@@@@@@@@@@ test bed setup 114s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 115s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [5776 B] 115s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [13.2 kB] 115s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [540 kB] 115s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [288 kB] 115s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [312 kB] 115s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 115s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1368 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 [624 kB] 115s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 115s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [2860 B] 115s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 117s Fetched 1915 kB in 1s (1666 kB/s) 118s Reading package lists... 120s Reading package lists... 120s Building dependency tree... 120s Reading state information... 121s Calculating upgrade... 121s The following packages will be upgraded: 121s bcache-tools bpftrace cloud-init eatmydata hostname htop iprutils libattr1 121s libeatmydata1 librtas2 librtasevent2 libservicelog-1.1-1 libvpd-2.2-3 lsvpd 121s nano pci.ids powerpc-ibm-utils powerpc-utils ppc64-diag servicelog tzdata 121s ufw usb.ids 121s 23 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 121s Need to get 4423 kB of archives. 121s After this operation, 11.3 kB of additional disk space will be used. 121s Get:1 http://ftpmaster.internal/ubuntu noble/main ppc64el hostname ppc64el 3.23+nmu2ubuntu2 [11.3 kB] 121s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el librtas2 ppc64el 2.0.4-1build1 [20.6 kB] 121s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el librtasevent2 ppc64el 2.0.4-1build1 [29.8 kB] 121s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el libservicelog-1.1-1 ppc64el 1.1.19-1build1 [59.0 kB] 121s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el libvpd-2.2-3 ppc64el 2.2.9-1build1 [64.4 kB] 121s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el iprutils ppc64el 2.4.19-2build1 [289 kB] 121s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el lsvpd ppc64el 1.7.14-1ubuntu2 [158 kB] 121s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el servicelog ppc64el 1.1.16-1build1 [33.3 kB] 121s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el powerpc-ibm-utils ppc64el 1.3.12-0ubuntu2 [261 kB] 121s Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el ppc64-diag ppc64el 2.7.9-1build1 [308 kB] 121s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el libattr1 ppc64el 1:2.5.2-1build1 [12.6 kB] 121s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el powerpc-utils ppc64el 1.3.12-0ubuntu2 [1644 B] 121s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el tzdata all 2024a-2ubuntu1 [273 kB] 121s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el nano ppc64el 7.2-2build1 [323 kB] 121s Get:15 http://ftpmaster.internal/ubuntu noble/main ppc64el pci.ids all 0.0~2024.03.31-1 [275 kB] 121s Get:16 http://ftpmaster.internal/ubuntu noble/main ppc64el ufw all 0.36.2-6 [169 kB] 121s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el usb.ids all 2024.03.18-1 [223 kB] 121s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el bcache-tools ppc64el 1.0.8-5build1 [20.3 kB] 121s Get:19 http://ftpmaster.internal/ubuntu noble/main ppc64el bpftrace ppc64el 0.20.2-1ubuntu4 [1058 kB] 121s Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el libeatmydata1 ppc64el 131-1ubuntu1 [7646 B] 121s Get:21 http://ftpmaster.internal/ubuntu noble/main ppc64el eatmydata all 131-1ubuntu1 [5584 B] 121s Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el htop ppc64el 3.3.0-4build1 [221 kB] 121s Get:23 http://ftpmaster.internal/ubuntu noble/main ppc64el cloud-init all 24.1.3-0ubuntu3 [598 kB] 122s Preconfiguring packages ... 122s Fetched 4423 kB in 1s (5895 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 ... 71991 files and directories currently installed.) 122s Preparing to unpack .../hostname_3.23+nmu2ubuntu2_ppc64el.deb ... 122s Unpacking hostname (3.23+nmu2ubuntu2) over (3.23+nmu2ubuntu1) ... 122s Setting up hostname (3.23+nmu2ubuntu2) ... 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 ... 71991 files and directories currently installed.) 122s Preparing to unpack .../0-librtas2_2.0.4-1build1_ppc64el.deb ... 122s Unpacking librtas2 (2.0.4-1build1) over (2.0.4-1) ... 122s Preparing to unpack .../1-librtasevent2_2.0.4-1build1_ppc64el.deb ... 122s Unpacking librtasevent2 (2.0.4-1build1) over (2.0.4-1) ... 122s Preparing to unpack .../2-libservicelog-1.1-1_1.1.19-1build1_ppc64el.deb ... 122s Unpacking libservicelog-1.1-1:ppc64el (1.1.19-1build1) over (1.1.19-1) ... 122s Preparing to unpack .../3-libvpd-2.2-3_2.2.9-1build1_ppc64el.deb ... 122s Unpacking libvpd-2.2-3 (2.2.9-1build1) over (2.2.9-1) ... 122s Preparing to unpack .../4-iprutils_2.4.19-2build1_ppc64el.deb ... 122s Unpacking iprutils (2.4.19-2build1) over (2.4.19-2) ... 122s Preparing to unpack .../5-lsvpd_1.7.14-1ubuntu2_ppc64el.deb ... 122s Unpacking lsvpd (1.7.14-1ubuntu2) over (1.7.14-1ubuntu1) ... 122s Preparing to unpack .../6-servicelog_1.1.16-1build1_ppc64el.deb ... 122s Unpacking servicelog (1.1.16-1build1) over (1.1.16-1) ... 122s Preparing to unpack .../7-powerpc-ibm-utils_1.3.12-0ubuntu2_ppc64el.deb ... 122s Unpacking powerpc-ibm-utils (1.3.12-0ubuntu2) over (1.3.12-0ubuntu1) ... 122s Preparing to unpack .../8-ppc64-diag_2.7.9-1build1_ppc64el.deb ... 122s Unpacking ppc64-diag (2.7.9-1build1) over (2.7.9-1) ... 122s Preparing to unpack .../9-libattr1_1%3a2.5.2-1build1_ppc64el.deb ... 122s Unpacking libattr1:ppc64el (1:2.5.2-1build1) over (1:2.5.2-1) ... 122s Setting up libattr1:ppc64el (1:2.5.2-1build1) ... 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 ... 71991 files and directories currently installed.) 122s Preparing to unpack .../00-powerpc-utils_1.3.12-0ubuntu2_ppc64el.deb ... 122s Unpacking powerpc-utils (1.3.12-0ubuntu2) over (1.3.12-0ubuntu1) ... 122s Preparing to unpack .../01-tzdata_2024a-2ubuntu1_all.deb ... 122s Unpacking tzdata (2024a-2ubuntu1) over (2024a-1ubuntu1) ... 123s Preparing to unpack .../02-nano_7.2-2build1_ppc64el.deb ... 123s Unpacking nano (7.2-2build1) over (7.2-2) ... 123s Preparing to unpack .../03-pci.ids_0.0~2024.03.31-1_all.deb ... 123s Unpacking pci.ids (0.0~2024.03.31-1) over (0.0~2024.02.02-1) ... 123s Preparing to unpack .../04-ufw_0.36.2-6_all.deb ... 123s Unpacking ufw (0.36.2-6) over (0.36.2-5) ... 123s Preparing to unpack .../05-usb.ids_2024.03.18-1_all.deb ... 123s Unpacking usb.ids (2024.03.18-1) over (2024.01.30-1) ... 123s Preparing to unpack .../06-bcache-tools_1.0.8-5build1_ppc64el.deb ... 123s Unpacking bcache-tools (1.0.8-5build1) over (1.0.8-5) ... 123s Preparing to unpack .../07-bpftrace_0.20.2-1ubuntu4_ppc64el.deb ... 123s Unpacking bpftrace (0.20.2-1ubuntu4) over (0.20.2-1ubuntu3) ... 123s Preparing to unpack .../08-libeatmydata1_131-1ubuntu1_ppc64el.deb ... 123s Unpacking libeatmydata1:ppc64el (131-1ubuntu1) over (131-1) ... 123s Preparing to unpack .../09-eatmydata_131-1ubuntu1_all.deb ... 123s Unpacking eatmydata (131-1ubuntu1) over (131-1) ... 123s Preparing to unpack .../10-htop_3.3.0-4build1_ppc64el.deb ... 123s Unpacking htop (3.3.0-4build1) over (3.3.0-4) ... 123s Preparing to unpack .../11-cloud-init_24.1.3-0ubuntu3_all.deb ... 123s Unpacking cloud-init (24.1.3-0ubuntu3) over (24.1.3-0ubuntu2) ... 123s Setting up bcache-tools (1.0.8-5build1) ... 123s Setting up pci.ids (0.0~2024.03.31-1) ... 123s Setting up cloud-init (24.1.3-0ubuntu3) ... 125s Setting up librtasevent2 (2.0.4-1build1) ... 125s Setting up iprutils (2.4.19-2build1) ... 127s Setting up bpftrace (0.20.2-1ubuntu4) ... 127s Setting up htop (3.3.0-4build1) ... 127s Setting up ufw (0.36.2-6) ... 129s Setting up libservicelog-1.1-1:ppc64el (1.1.19-1build1) ... 129s Setting up servicelog (1.1.16-1build1) ... 129s Setting up libvpd-2.2-3 (2.2.9-1build1) ... 129s Setting up tzdata (2024a-2ubuntu1) ... 129s 129s Current default time zone: 'Etc/UTC' 129s Local time is now: Fri Apr 12 04:50:15 UTC 2024. 129s Universal Time is now: Fri Apr 12 04:50:15 UTC 2024. 129s Run 'dpkg-reconfigure tzdata' if you wish to change it. 129s 129s Setting up usb.ids (2024.03.18-1) ... 129s Setting up nano (7.2-2build1) ... 129s Setting up librtas2 (2.0.4-1build1) ... 129s Setting up libeatmydata1:ppc64el (131-1ubuntu1) ... 129s Setting up eatmydata (131-1ubuntu1) ... 129s Setting up lsvpd (1.7.14-1ubuntu2) ... 129s Setting up powerpc-ibm-utils (1.3.12-0ubuntu2) ... 129s Setting up powerpc-utils (1.3.12-0ubuntu2) ... 129s Setting up ppc64-diag (2.7.9-1build1) ... 130s Processing triggers for initramfs-tools (0.142ubuntu24) ... 130s update-initramfs: Generating /boot/initrd.img-6.8.0-22-generic 130s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 137s Processing triggers for libc-bin (2.39-0ubuntu8) ... 137s Processing triggers for rsyslog (8.2312.0-3ubuntu8) ... 138s Processing triggers for man-db (2.12.0-4build1) ... 139s Processing triggers for install-info (7.1-3build2) ... 139s Reading package lists... 139s Building dependency tree... 139s Reading state information... 140s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 140s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 140s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 140s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 140s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 142s Reading package lists... 142s Reading package lists... 142s Building dependency tree... 142s Reading state information... 142s Calculating upgrade... 143s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 143s Reading package lists... 143s Building dependency tree... 143s Reading state information... 143s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 143s autopkgtest [04:50:29]: rebooting testbed after setup commands that affected boot 304s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 317s autopkgtest [04:53:23]: testbed running kernel: Linux 6.8.0-22-generic #22-Ubuntu SMP Thu Apr 4 22:47:57 UTC 2024 319s autopkgtest [04:53:25]: @@@@@@@@@@@@@@@@@@@@ apt-source qtltools 322s Get:1 http://ftpmaster.internal/ubuntu noble/universe qtltools 1.3.1+dfsg-4build3 (dsc) [2293 B] 322s Get:2 http://ftpmaster.internal/ubuntu noble/universe qtltools 1.3.1+dfsg-4build3 (tar) [141 kB] 322s Get:3 http://ftpmaster.internal/ubuntu noble/universe qtltools 1.3.1+dfsg-4build3 (diff) [13.6 MB] 323s gpgv: Signature made Mon Apr 1 07:33:53 2024 UTC 323s gpgv: using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984 323s gpgv: Can't check signature: No public key 323s dpkg-source: warning: cannot verify inline signature for ./qtltools_1.3.1+dfsg-4build3.dsc: no acceptable signature found 324s autopkgtest [04:53:30]: testing package qtltools version 1.3.1+dfsg-4build3 344s autopkgtest [04:53:50]: build not needed 359s autopkgtest [04:54:05]: test run-sample-analysis: preparing testbed 369s Reading package lists... 369s Building dependency tree... 369s Reading state information... 369s Starting pkgProblemResolver with broken count: 0 369s Starting 2 pkgProblemResolver with broken count: 0 369s Done 370s The following additional packages will be installed: 370s fontconfig libblas3 libboost-iostreams1.83.0 libboost-program-options1.83.0 370s libcairo2 libdatrie1 libgfortran5 libgomp1 libgraphite2-3 libgsl27 370s libgslcblas0 libharfbuzz0b libhts3t64 libhtscodecs2 libice6 liblapack3 370s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 370s libpaper1 libpixman-1-0 libsm6 libtcl8.6 libthai-data libthai0 libtk8.6 370s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 qtltools 370s qtltools-example r-base-core r-mathlib unzip x11-common xdg-utils zip 370s Suggested packages: 370s gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html tcl8.6 tk8.6 370s elpa-ess r-doc-info | r-doc-pdf r-base-html 370s Recommended packages: 370s r-bioc-qvalue r-recommended r-base-dev r-doc-html libfile-mimeinfo-perl 370s libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils 370s The following NEW packages will be installed: 370s autopkgtest-satdep fontconfig libblas3 libboost-iostreams1.83.0 370s libboost-program-options1.83.0 libcairo2 libdatrie1 libgfortran5 libgomp1 370s libgraphite2-3 libgsl27 libgslcblas0 libharfbuzz0b libhts3t64 libhtscodecs2 370s libice6 liblapack3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 370s libpaper-utils libpaper1 libpixman-1-0 libsm6 libtcl8.6 libthai-data 370s libthai0 libtk8.6 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 370s libxt6t64 qtltools qtltools-example r-base-core r-mathlib unzip x11-common 370s xdg-utils zip 370s 0 upgraded, 42 newly installed, 0 to remove and 0 not upgraded. 370s Need to get 56.0 MB/56.0 MB of archives. 370s After this operation, 108 MB of additional disk space will be used. 370s Get:1 /tmp/autopkgtest.MhXR9q/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [712 B] 370s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el fontconfig ppc64el 2.15.0-1.1ubuntu2 [192 kB] 370s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libblas3 ppc64el 3.12.0-3build1 [227 kB] 370s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el libboost-iostreams1.83.0 ppc64el 1.83.0-2.1ubuntu3 [260 kB] 370s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el libboost-program-options1.83.0 ppc64el 1.83.0-2.1ubuntu3 [329 kB] 370s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el libpixman-1-0 ppc64el 0.42.2-1 [300 kB] 370s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-render0 ppc64el 1.15-1 [17.2 kB] 370s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-shm0 ppc64el 1.15-1 [5896 B] 370s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1 [23.3 kB] 370s Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el libcairo2 ppc64el 1.18.0-3 [751 kB] 370s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el libdatrie1 ppc64el 0.2.13-3 [25.1 kB] 370s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240330-1ubuntu2 [575 kB] 370s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240330-1ubuntu2 [161 kB] 370s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el libgraphite2-3 ppc64el 1.3.14-2 [105 kB] 370s Get:15 http://ftpmaster.internal/ubuntu noble/universe ppc64el libgslcblas0 ppc64el 2.7.1+dfsg-6ubuntu1 [85.3 kB] 370s Get:16 http://ftpmaster.internal/ubuntu noble/universe ppc64el libgsl27 ppc64el 2.7.1+dfsg-6ubuntu1 [1064 kB] 370s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el libharfbuzz0b ppc64el 8.3.0-2build2 [580 kB] 370s Get:18 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 370s Get:19 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3t64 ppc64el 1.19+ds-1.1build3 [569 kB] 370s Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el x11-common all 1:7.7+23ubuntu2 [23.4 kB] 370s Get:21 http://ftpmaster.internal/ubuntu noble/main ppc64el libice6 ppc64el 2:1.0.10-1build2 [49.3 kB] 370s Get:22 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el liblapack3 ppc64el 3.12.0-3build1 [2804 kB] 371s Get:23 http://ftpmaster.internal/ubuntu noble/main ppc64el libthai-data all 0.1.29-2 [158 kB] 371s Get:24 http://ftpmaster.internal/ubuntu noble/main ppc64el libthai0 ppc64el 0.1.29-2 [21.4 kB] 371s Get:25 http://ftpmaster.internal/ubuntu noble/main ppc64el libpango-1.0-0 ppc64el 1.52.1+ds-1build1 [271 kB] 371s Get:26 http://ftpmaster.internal/ubuntu noble/main ppc64el libpangoft2-1.0-0 ppc64el 1.52.1+ds-1build1 [50.5 kB] 371s Get:27 http://ftpmaster.internal/ubuntu noble/main ppc64el libpangocairo-1.0-0 ppc64el 1.52.1+ds-1build1 [31.1 kB] 371s Get:28 http://ftpmaster.internal/ubuntu noble/main ppc64el libpaper1 ppc64el 1.1.29 [13.5 kB] 371s Get:29 http://ftpmaster.internal/ubuntu noble/main ppc64el libpaper-utils ppc64el 1.1.29 [8710 B] 371s Get:30 http://ftpmaster.internal/ubuntu noble/main ppc64el libsm6 ppc64el 2:1.2.3-1build2 [18.5 kB] 371s Get:31 http://ftpmaster.internal/ubuntu noble/main ppc64el libtcl8.6 ppc64el 8.6.14+dfsg-1build1 [1204 kB] 371s Get:32 http://ftpmaster.internal/ubuntu noble/main ppc64el libxft2 ppc64el 2.3.6-1 [59.8 kB] 371s Get:33 http://ftpmaster.internal/ubuntu noble/main ppc64el libxss1 ppc64el 1:1.2.3-1build2 [8982 B] 371s Get:34 http://ftpmaster.internal/ubuntu noble/main ppc64el libtk8.6 ppc64el 8.6.14-1build1 [944 kB] 371s Get:35 http://ftpmaster.internal/ubuntu noble/main ppc64el libxt6t64 ppc64el 1:1.2.1-1.2build1 [202 kB] 371s Get:36 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-mathlib ppc64el 4.3.3-2build2 [2440 kB] 371s Get:37 http://ftpmaster.internal/ubuntu noble/main ppc64el zip ppc64el 3.0-13 [192 kB] 371s Get:38 http://ftpmaster.internal/ubuntu noble/main ppc64el unzip ppc64el 6.0-28ubuntu3 [192 kB] 371s Get:39 http://ftpmaster.internal/ubuntu noble/main ppc64el xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 371s Get:40 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-base-core ppc64el 4.3.3-2build2 [27.4 MB] 371s Get:41 http://ftpmaster.internal/ubuntu noble/universe ppc64el qtltools ppc64el 1.3.1+dfsg-4build3 [828 kB] 372s Get:42 http://ftpmaster.internal/ubuntu noble/universe ppc64el qtltools-example all 1.3.1+dfsg-4build3 [13.6 MB] 372s Preconfiguring packages ... 372s Fetched 56.0 MB in 2s (25.6 MB/s) 372s Selecting previously unselected package fontconfig. 372s (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 ... 71990 files and directories currently installed.) 372s Preparing to unpack .../00-fontconfig_2.15.0-1.1ubuntu2_ppc64el.deb ... 372s Unpacking fontconfig (2.15.0-1.1ubuntu2) ... 372s Selecting previously unselected package libblas3:ppc64el. 372s Preparing to unpack .../01-libblas3_3.12.0-3build1_ppc64el.deb ... 372s Unpacking libblas3:ppc64el (3.12.0-3build1) ... 372s Selecting previously unselected package libboost-iostreams1.83.0:ppc64el. 372s Preparing 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libgraphite2-3:ppc64el. 373s Preparing to unpack .../12-libgraphite2-3_1.3.14-2_ppc64el.deb ... 373s Unpacking libgraphite2-3:ppc64el (1.3.14-2) ... 373s Selecting previously unselected package libgslcblas0:ppc64el. 373s Preparing to unpack .../13-libgslcblas0_2.7.1+dfsg-6ubuntu1_ppc64el.deb ... 373s Unpacking libgslcblas0:ppc64el (2.7.1+dfsg-6ubuntu1) ... 373s Selecting previously unselected package libgsl27:ppc64el. 373s Preparing to unpack .../14-libgsl27_2.7.1+dfsg-6ubuntu1_ppc64el.deb ... 373s Unpacking libgsl27:ppc64el (2.7.1+dfsg-6ubuntu1) ... 373s Selecting previously unselected package libharfbuzz0b:ppc64el. 373s Preparing to unpack .../15-libharfbuzz0b_8.3.0-2build2_ppc64el.deb ... 373s Unpacking libharfbuzz0b:ppc64el (8.3.0-2build2) ... 373s Selecting previously unselected package libhtscodecs2:ppc64el. 373s Preparing to unpack .../16-libhtscodecs2_1.6.0-1_ppc64el.deb ... 373s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 373s Selecting previously unselected package libhts3t64:ppc64el. 373s Preparing to unpack .../17-libhts3t64_1.19+ds-1.1build3_ppc64el.deb ... 373s Unpacking libhts3t64:ppc64el (1.19+ds-1.1build3) ... 373s Selecting previously unselected package x11-common. 373s Preparing to unpack .../18-x11-common_1%3a7.7+23ubuntu2_all.deb ... 373s Unpacking x11-common (1:7.7+23ubuntu2) ... 373s Selecting previously unselected package libice6:ppc64el. 373s Preparing to unpack .../19-libice6_2%3a1.0.10-1build2_ppc64el.deb ... 373s Unpacking libice6:ppc64el (2:1.0.10-1build2) ... 373s Selecting previously unselected package liblapack3:ppc64el. 373s Preparing to unpack .../20-liblapack3_3.12.0-3build1_ppc64el.deb ... 373s Unpacking liblapack3:ppc64el (3.12.0-3build1) ... 373s Selecting previously unselected package libthai-data. 373s Preparing to unpack .../21-libthai-data_0.1.29-2_all.deb ... 373s Unpacking libthai-data (0.1.29-2) ... 373s Selecting previously unselected package libthai0:ppc64el. 373s Preparing to unpack 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Creating config file /etc/papersize with new version 374s Setting up fontconfig (2.15.0-1.1ubuntu2) ... 376s Regenerating fonts cache... done. 376s Setting up libxrender1:ppc64el (1:0.9.10-1.1) ... 376s Setting up libdatrie1:ppc64el (0.2.13-3) ... 376s Setting up libgslcblas0:ppc64el (2.7.1+dfsg-6ubuntu1) ... 376s Setting up libxcb-render0:ppc64el (1.15-1) ... 376s Setting up unzip (6.0-28ubuntu3) ... 376s Setting up x11-common (1:7.7+23ubuntu2) ... 377s Setting up libgsl27:ppc64el (2.7.1+dfsg-6ubuntu1) ... 377s Setting up libxcb-shm0:ppc64el (1.15-1) ... 377s Setting up libpaper-utils (1.1.29) ... 377s Setting up libgomp1:ppc64el (14-20240330-1ubuntu2) ... 377s Setting up libcairo2:ppc64el (1.18.0-3) ... 377s Setting up zip (3.0-13) ... 377s Setting up libblas3:ppc64el (3.12.0-3build1) ... 377s 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 377s Setting up libboost-iostreams1.83.0:ppc64el (1.83.0-2.1ubuntu3) ... 377s Setting up libtcl8.6:ppc64el (8.6.14+dfsg-1build1) ... 377s Setting up libgfortran5:ppc64el (14-20240330-1ubuntu2) ... 377s Setting up r-mathlib (4.3.3-2build2) ... 377s Setting up libhts3t64:ppc64el (1.19+ds-1.1build3) ... 377s Setting up libharfbuzz0b:ppc64el (8.3.0-2build2) ... 377s Setting up libthai-data (0.1.29-2) ... 377s Setting up libxss1:ppc64el (1:1.2.3-1build2) ... 377s Setting up xdg-utils (1.1.3-4.1ubuntu3) ... 377s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 377s Setting up libice6:ppc64el (2:1.0.10-1build2) ... 377s Setting up liblapack3:ppc64el (3.12.0-3build1) ... 377s 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 377s Setting up libxft2:ppc64el (2.3.6-1) ... 377s Setting up libtk8.6:ppc64el (8.6.14-1build1) ... 377s Setting up libthai0:ppc64el (0.1.29-2) ... 377s Setting up libsm6:ppc64el (2:1.2.3-1build2) ... 377s Setting up libpango-1.0-0:ppc64el (1.52.1+ds-1build1) ... 377s Setting up libxt6t64:ppc64el (1:1.2.1-1.2build1) ... 377s Setting up libpangoft2-1.0-0:ppc64el (1.52.1+ds-1build1) ... 377s Setting up libpangocairo-1.0-0:ppc64el (1.52.1+ds-1build1) ... 377s Setting up r-base-core (4.3.3-2build2) ... 377s 377s Creating config file /etc/R/Renviron with new version 377s Setting up qtltools (1.3.1+dfsg-4build3) ... 377s Setting up autopkgtest-satdep (0) ... 377s Processing triggers for man-db (2.12.0-4build1) ... 378s Processing triggers for install-info (7.1-3build2) ... 379s Processing triggers for libc-bin (2.39-0ubuntu8) ... 382s (Reading database ... 73915 files and directories currently installed.) 382s Removing autopkgtest-satdep (0) ... 383s autopkgtest [04:54:29]: test run-sample-analysis: [----------------------- 383s ./genes.50percent.chr22.bed.gz 383s ./genes.50percent.chr22.bed.gz.tbi 383s ./genes.covariates.pc50.txt.gz 383s ./genes.simulated.chr22.bed.gz 383s ./genes.simulated.chr22.bed.gz.tbi 383s ./genotypes.chr22.vcf.gz 384s ./genotypes.chr22.vcf.gz.tbi 384s 384s QTLtools 384s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 384s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 384s * Webpage : https://qtltools.github.io/qtltools/ 384s * Version : 1.3.1 384s * Date : 12/04/2024 - 04:54:30 384s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 384s 384s CONDUCT PCA ON DATA 384s 384s Initialize random number generator 384s * Built-in seed is 15112011 384s * First Integer = 30553 384s * First Double = 0.0126695 384s 384s Reading sample list from [genes.50percent.chr22.bed.gz] 384s * #samples = 358 384s 384s Merging sample sets from all input files 384s * #files = 1 384s * #samples in all files = 358 384s 384s Reading phenotype data in [genes.50percent.chr22.bed.gz] 384s * 358 samples included 384s * 608 phenotypes included 384s 384s Calculating PCA with a matrix 358 x 608 384s * Calculated mean and sd 384s * 0 sd==0 columns removed 384s * Variables centered 384s * Variables scaled to unit variance 384s * Running SVD 385s * SVD complete 385s * Calculated sd and var for PCs 385s * Calculated cumulative var for PCs 385s * Done! 385s 385s Running time: 0 seconds 385s 385s QTLtools 385s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 385s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 385s * Webpage : https://qtltools.github.io/qtltools/ 385s * Version : 1.3.1 385s * Date : 12/04/2024 - 04:54:31 385s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 385s 385s MAPPING QTL IN CIS 385s * TASK: Report all nominal associations with p <= 0.01 385s * Linear model: Phe ~ Var + Cov 385s * Cis-window size is 1000000 bp 385s * Region = [chr22:17000000-18000000] 385s 385s Initialize random number generator 385s * Built-in seed is 15112011 385s * First Integer = 30553 385s * First Double = 0.0126695 385s 385s Reading sample list from [genes.50percent.chr22.bed.gz] 385s * #samples = 358 385s 385s Read sample list from [genotypes.chr22.vcf.gz] 385s * #samples = 358 385s 385s Reading sample list from [genes.covariates.pc50.txt.gz] 385s * #samples = 358 385s 385s Merging sample sets from all input files 385s * #files = 3 385s * #samples in all files = 358 385s 385s Reading phenotype data in [genes.50percent.chr22.bed.gz] 385s * target region [chr22:17000000-18000000] 385s * 8 phenotypes included 385s * 3 phenotypes are on the negative strand 385s 385s Reading genotype data in [genotypes.chr22.vcf.gz] 385s * File format detected: VCF 385s * target region [chr22:16000000-19000000] 385s * 6404 variants included 385s 385s Reading covariates in [genes.covariates.pc50.txt.gz] 385s * 53 covariates included 385s 385s Residualize phenotypes for covariates 385s * #covariates = 53 385s 385s Processing phenotype [ENSG00000237438.2] [1/8] 385s * #variants in cis = 5095 385s * Best hit: [id=22_17542810, d=25350, pv=1.1864e-25, s=-0.7518] 385s 385s Processing phenotype [ENSG00000273203.1] [2/8] 385s * #variants in cis = 5170 385s * Best hit: [id=22_17517388, d=-31323, pv=5.86611e-06, s=-0.1406] 385s 385s Processing phenotype [ENSG00000273442.1] [3/8] 385s * #variants in cis = 5188 385s * Best hit: [id=22_17553526, d=-8065, pv=0.000244522, s=0.1340] 385s 385s Processing phenotype [ENSG00000177663.9] [4/8] 385s * #variants in cis = 5193 385s * Best hit: [id=22_17513703, d=-52141, pv=8.03358e-14, s=-0.2096] 385s 385s Processing phenotype [ENSG00000183307.3] [5/8] 385s * #variants in cis = 5230 385s * Best hit: [id=22_17587975, d=14282, pv=1.56789e-07, s=-0.0078] 385s 385s Processing phenotype [ENSG00000069998.8] [6/8] 385s * #variants in cis = 5291 385s * Best hit: [id=22_17620429, d=25748, pv=1.37287e-14, s=-1.5147] 385s 385s Processing phenotype [ENSG00000093072.11] [7/8] 385s * #variants in cis = 5293 385s * Best hit: [id=22_17699630, d=3249, pv=0.000578649, s=0.6404] 385s 385s Processing phenotype [ENSG00000099954.14] [8/8] 385s * #variants in cis = 5435 385s * Best hit: [id=22_17175937, d=-664900, pv=0.000866455, s=0.0067] 385s 385s Running time: 0 seconds 385s 385s QTLtools 385s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 385s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 385s * Webpage : https://qtltools.github.io/qtltools/ 385s * Version : 1.3.1 385s * Date : 12/04/2024 - 04:54:31 385s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 385s 385s MAPPING QTL IN CIS 385s * TASK: Perform 1000 permutations 385s * Linear model: Phe ~ Var + Cov 385s * Cis-window size is 1000000 bp 385s * Region = [chr22:17000000-18000000] 385s 385s Initialize random number generator 385s * Built-in seed is 15112011 385s * First Integer = 30553 385s * First Double = 0.0126695 385s 385s Reading sample list from [genes.50percent.chr22.bed.gz] 385s * #samples = 358 385s 385s Read sample list from [genotypes.chr22.vcf.gz] 385s * #samples = 358 385s 385s Reading sample list from [genes.covariates.pc50.txt.gz] 385s * #samples = 358 385s 385s Merging sample sets from all input files 385s * #files = 3 385s * #samples in all files = 358 385s 385s Reading phenotype data in [genes.50percent.chr22.bed.gz] 385s * target region [chr22:17000000-18000000] 385s * 8 phenotypes included 385s * 3 phenotypes are on the negative strand 385s 385s Reading genotype data in [genotypes.chr22.vcf.gz] 385s * File format detected: VCF 385s * target region [chr22:16000000-19000000] 385s * 6404 variants included 385s 385s Reading covariates in [genes.covariates.pc50.txt.gz] 385s * 53 covariates included 385s 385s Residualize phenotypes for covariates 385s * #covariates = 53 385s 385s Processing phenotype [ENSG00000237438.2] [1/8] 385s * #variants in cis = 5095 386s * Best hit: [id=22_17542810, d=25350, pv=1.1864e-25, s=-0.7518] 386s * Beta parameters: [s1=1.00995, s2=621.053] 386s * Adjusted p-values: [emp=0.000999001, beta=1.28062e-20] 386s 386s Processing phenotype [ENSG00000273203.1] [2/8] 386s * #variants in cis = 5170 388s * Best hit: [id=22_17517388, d=-31323, pv=5.86611e-06, s=-0.1406] 388s * Beta parameters: [s1=1.11817, s2=641.379] 388s * Adjusted p-values: [emp=0.00799201, beta=0.00751892] 388s 388s Processing phenotype [ENSG00000273442.1] [3/8] 388s * #variants in cis = 5188 389s * Best hit: [id=22_17553526, d=-8065, pv=0.000244522, s=0.1340] 389s * Beta parameters: [s1=1.08364, s2=467.63] 389s * Adjusted p-values: [emp=0.297702, beta=0.293948] 389s 389s Processing phenotype [ENSG00000177663.9] [4/8] 389s * #variants in cis = 5193 390s * Best hit: [id=22_17513703, d=-52141, pv=8.03358e-14, s=-0.2096] 390s * Beta parameters: [s1=0.989061, s2=704.553] 390s * Adjusted p-values: [emp=0.000999001, beta=7.91291e-10] 390s 390s Processing phenotype [ENSG00000183307.3] [5/8] 390s * #variants in cis = 5230 392s * Best hit: [id=22_17587975, d=14282, pv=1.56789e-07, s=-0.0078] 392s * Beta parameters: [s1=1.01322, s2=559.49] 392s * Adjusted p-values: [emp=0.000999001, beta=0.00050707] 392s 392s Processing phenotype [ENSG00000069998.8] [6/8] 392s * #variants in cis = 5291 393s * Best hit: [id=22_17620429, d=25748, pv=1.37287e-14, s=-1.5147] 393s * Beta parameters: [s1=1.02312, s2=563.339] 393s * Adjusted p-values: [emp=0.000999001, beta=2.56935e-10] 393s 393s Processing phenotype [ENSG00000093072.11] [7/8] 393s * #variants in cis = 5293 394s * Best hit: [id=22_17699630, d=3249, pv=0.000578649, s=0.6404] 395s * Beta parameters: [s1=0.957514, s2=559.397] 395s * Adjusted p-values: [emp=0.574426, beta=0.562826] 395s 395s Processing phenotype [ENSG00000099954.14] [8/8] 395s * #variants in cis = 5435 396s * Best hit: [id=22_17175937, d=-664900, pv=0.000866455, s=0.0067] 396s * Beta parameters: [s1=0.938041, s2=226.852] 396s * Adjusted p-values: [emp=0.842158, beta=0.84836] 396s 396s Running time: 10 seconds 396s 396s QTLtools 396s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 396s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 396s * Webpage : https://qtltools.github.io/qtltools/ 396s * Version : 1.3.1 396s * Date : 12/04/2024 - 04:54:42 396s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 396s 396s MAPPING QTL IN TRANS 396s * TASK: Perform a full nominal pass, do not adjust p-values 396s * Cis-window size is 5000000 bp 396s * #bins = 1000 396s * threshold = 1e-05 396s 396s Initialize random number generator 396s * Built-in seed is 15112011 396s * First Integer = 30553 396s * First Double = 0.0126695 396s 396s Read sample list from [genotypes.chr22.vcf.gz] 396s * #samples = 358 396s 396s Checking sample list in [genes.simulated.chr22.bed.gz] 396s * #samples = 358 396s 396s Reading phenotype data in [genes.simulated.chr22.bed.gz] from line 0 to 0 396s * 358 samples included 396s * 608 phenotypes included 396s * 275 phenotypes is on the negative strand 396s 396s Calculate correlation threshold 396s * thres = 1e-05 396s * corr = 0.2311 396s 396s Sweep through genotype data in [genotypes.chr22.vcf.gz] 396s * #variants=1950 #multi_allelic=0 #not_processed=0 #hits=101/1000000 speed=3.47MT/s 396s * #variants=4001 #multi_allelic=0 #not_processed=0 #hits=153/2000000 speed=3.39MT/s 397s * #variants=6187 #multi_allelic=0 #not_processed=0 #hits=244/3000000 speed=3.36MT/s 397s * #variants=8537 #multi_allelic=0 #not_processed=0 #hits=285/4000000 speed=3.37MT/s 397s * #variants=11025 #multi_allelic=0 #not_processed=0 #hits=312/5000000 speed=3.34MT/s 398s * #variants=13621 #multi_allelic=0 #not_processed=0 #hits=320/6000000 speed=3.33MT/s 398s * #variants=16217 #multi_allelic=0 #not_processed=0 #hits=342/7000000 speed=3.29MT/s 398s * #variants=18755 #multi_allelic=0 #not_processed=0 #hits=401/8000000 speed=3.29MT/s 399s * #variants=21237 #multi_allelic=0 #not_processed=0 #hits=402/9000000 speed=3.31MT/s 399s * #variants=23680 #multi_allelic=0 #not_processed=0 #hits=455/10000000 speed=3.31MT/s 399s * #variants=26171 #multi_allelic=0 #not_processed=0 #hits=463/11000000 speed=3.31MT/s 399s * #variants=28609 #multi_allelic=0 #not_processed=0 #hits=469/12000000 speed=3.32MT/s 400s * #variants=30861 #multi_allelic=0 #not_processed=0 #hits=973/13000000 speed=3.23MT/s 400s * #variants=32932 #multi_allelic=0 #not_processed=0 #hits=979/14000000 speed=3.34MT/s 400s * #variants=34974 #multi_allelic=0 #not_processed=0 #hits=1085/15000000 speed=3.41MT/s 401s * #variants=37021 #multi_allelic=0 #not_processed=0 #hits=1086/16000000 speed=3.44MT/s 401s * #variants=39122 #multi_allelic=0 #not_processed=0 #hits=1089/17000000 speed=3.34MT/s 401s * #variants=41334 #multi_allelic=0 #not_processed=0 #hits=1089/18000000 speed=3.33MT/s 402s * #variants=43627 #multi_allelic=0 #not_processed=0 #hits=1096/19000000 speed=3.32MT/s 402s * #variants=45897 #multi_allelic=0 #not_processed=0 #hits=1153/20000000 speed=3.28MT/s 402s * #variants=48114 #multi_allelic=0 #not_processed=0 #hits=1243/21000000 speed=3.31MT/s 402s * #variants=50410 #multi_allelic=0 #not_processed=0 #hits=1249/22000000 speed=3.28MT/s 403s * #variants=52820 #multi_allelic=0 #not_processed=0 #hits=1259/23000000 speed=3.31MT/s 403s * #variants=55279 #multi_allelic=0 #not_processed=0 #hits=1498/24000000 speed=3.31MT/s 403s * #variants=57789 #multi_allelic=0 #not_processed=0 #hits=1724/25000000 speed=3.27MT/s 404s * #variants=60201 #multi_allelic=0 #not_processed=0 #hits=2168/26000000 speed=3.28MT/s 404s * #variants=62476 #multi_allelic=0 #not_processed=0 #hits=2452/27000000 speed=3.36MT/s 404s * #variants=64608 #multi_allelic=0 #not_processed=0 #hits=2544/28000000 speed=3.41MT/s 405s * #variants=66709 #multi_allelic=0 #not_processed=0 #hits=2684/29000000 speed=3.41MT/s 405s * #variants=68871 #multi_allelic=0 #not_processed=0 #hits=2688/30000000 speed=3.36MT/s 405s * #variants=71070 #multi_allelic=0 #not_processed=0 #hits=2720/31000000 speed=3.40MT/s 405s * #variants=73151 #multi_allelic=0 #not_processed=0 #hits=2891/32000000 speed=3.40MT/s 406s * #variants=75122 #multi_allelic=0 #not_processed=0 #hits=3110/33000000 speed=3.42MT/s 406s * #variants=77058 #multi_allelic=0 #not_processed=0 #hits=3209/34000000 speed=3.45MT/s 406s * #variants=78989 #multi_allelic=0 #not_processed=0 #hits=3218/35000000 speed=3.44MT/s 407s * #variants=80903 #multi_allelic=0 #not_processed=0 #hits=3250/36000000 speed=3.46MT/s 407s * #variants=82811 #multi_allelic=0 #not_processed=0 #hits=3463/37000000 speed=3.45MT/s 407s * #variants=84694 #multi_allelic=0 #not_processed=0 #hits=4035/38000000 speed=3.34MT/s 407s * #variants=85485 #multi_allelic=0 #not_processed=0 #hits=4036/38425275 speed=3.49MT/s 407s 407s Running time: 11 seconds 407s 407s QTLtools 407s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 407s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 407s * Webpage : https://qtltools.github.io/qtltools/ 407s * Version : 1.3.1 407s * Date : 12/04/2024 - 04:54:53 407s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 407s 407s MAPPING QTL IN TRANS 407s * TASK: Permute randomly chosen phenotypes 1000 times and test 407s * Cis-window size is 5000000 bp 407s * #bins = 1000 407s * threshold = 1e-05 407s 407s Initialize random number generator 407s * Built-in seed is 15112011 407s * First Integer = 30553 407s * First Double = 0.0126695 407s 407s Read sample list from [genotypes.chr22.vcf.gz] 407s * #samples = 358 407s 407s Checking sample list in [genes.simulated.chr22.bed.gz] 407s * #samples = 358 407s 407s Reading phenotype data in [genes.simulated.chr22.bed.gz] from line 0 to 0 407s * 358 samples included 407s * 608 phenotypes included 407s * 275 phenotypes is on the negative strand 407s 407s Normal transform phenotypes 407s 407s Calculate correlation threshold 407s * thres = 1e-05 407s * corr = 0.2311 407s 407s Sweep through genotype data in [genotypes.chr22.vcf.gz] 408s * #variants=1177 #multi_allelic=0 #not_processed=0 #hits=28/1000000 speed=3.57MT/s 408s * #variants=2383 #multi_allelic=0 #not_processed=0 #hits=38/2000000 speed=3.57MT/s 408s * #variants=3633 #multi_allelic=0 #not_processed=0 #hits=53/3000000 speed=3.52MT/s 409s * #variants=4928 #multi_allelic=0 #not_processed=0 #hits=53/4000000 speed=3.51MT/s 409s * #variants=6269 #multi_allelic=0 #not_processed=0 #hits=71/5000000 speed=3.47MT/s 409s * #variants=7675 #multi_allelic=0 #not_processed=0 #hits=72/6000000 speed=3.42MT/s 410s * #variants=9151 #multi_allelic=0 #not_processed=0 #hits=88/7000000 speed=3.38MT/s 410s * #variants=10663 #multi_allelic=0 #not_processed=0 #hits=96/8000000 speed=3.33MT/s 410s * #variants=12202 #multi_allelic=0 #not_processed=0 #hits=96/9000000 speed=3.32MT/s 410s * #variants=13804 #multi_allelic=0 #not_processed=0 #hits=96/10000000 speed=3.27MT/s 411s * #variants=15381 #multi_allelic=0 #not_processed=0 #hits=120/11000000 speed=3.29MT/s 411s * #variants=16946 #multi_allelic=0 #not_processed=0 #hits=123/12000000 speed=3.29MT/s 411s * #variants=18483 #multi_allelic=0 #not_processed=0 #hits=129/13000000 speed=3.32MT/s 412s * #variants=19995 #multi_allelic=0 #not_processed=0 #hits=131/14000000 speed=3.34MT/s 412s * #variants=21489 #multi_allelic=0 #not_processed=0 #hits=132/15000000 speed=3.32MT/s 412s * #variants=22947 #multi_allelic=0 #not_processed=0 #hits=151/16000000 speed=3.36MT/s 413s * #variants=24445 #multi_allelic=0 #not_processed=0 #hits=168/17000000 speed=3.33MT/s 413s * #variants=25965 #multi_allelic=0 #not_processed=0 #hits=175/18000000 speed=3.32MT/s 413s * #variants=27472 #multi_allelic=0 #not_processed=0 #hits=179/19000000 speed=3.33MT/s 413s * #variants=28933 #multi_allelic=0 #not_processed=0 #hits=181/20000000 speed=3.37MT/s 414s * #variants=30325 #multi_allelic=0 #not_processed=0 #hits=181/21000000 speed=3.42MT/s 414s * #variants=31617 #multi_allelic=0 #not_processed=0 #hits=182/22000000 speed=3.50MT/s 414s * #variants=32875 #multi_allelic=0 #not_processed=0 #hits=190/23000000 speed=3.52MT/s 415s * #variants=34127 #multi_allelic=0 #not_processed=0 #hits=192/24000000 speed=3.52MT/s 415s * #variants=35392 #multi_allelic=0 #not_processed=0 #hits=206/25000000 speed=3.53MT/s 415s * #variants=36652 #multi_allelic=0 #not_processed=0 #hits=206/26000000 speed=3.52MT/s 415s * #variants=37940 #multi_allelic=0 #not_processed=0 #hits=213/27000000 speed=3.50MT/s 416s * #variants=39255 #multi_allelic=0 #not_processed=0 #hits=238/28000000 speed=3.39MT/s 416s * #variants=40602 #multi_allelic=0 #not_processed=0 #hits=239/29000000 speed=3.46MT/s 416s * #variants=41998 #multi_allelic=0 #not_processed=0 #hits=245/30000000 speed=3.41MT/s 417s * #variants=43398 #multi_allelic=0 #not_processed=0 #hits=245/31000000 speed=3.41MT/s 417s * #variants=44803 #multi_allelic=0 #not_processed=0 #hits=260/32000000 speed=3.40MT/s 417s * #variants=46187 #multi_allelic=0 #not_processed=0 #hits=261/33000000 speed=3.42MT/s 417s * #variants=47545 #multi_allelic=0 #not_processed=0 #hits=268/34000000 speed=3.44MT/s 418s * #variants=48904 #multi_allelic=0 #not_processed=0 #hits=280/35000000 speed=3.45MT/s 418s * #variants=50309 #multi_allelic=0 #not_processed=0 #hits=306/36000000 speed=3.41MT/s 418s * #variants=51731 #multi_allelic=0 #not_processed=0 #hits=314/37000000 speed=3.40MT/s 419s * #variants=53171 #multi_allelic=0 #not_processed=0 #hits=320/38000000 speed=3.39MT/s 419s * #variants=54621 #multi_allelic=0 #not_processed=0 #hits=323/39000000 speed=3.39MT/s 419s * #variants=56099 #multi_allelic=0 #not_processed=0 #hits=323/40000000 speed=3.38MT/s 420s * #variants=57584 #multi_allelic=0 #not_processed=0 #hits=340/41000000 speed=3.36MT/s 420s * #variants=59032 #multi_allelic=0 #not_processed=0 #hits=344/42000000 speed=3.39MT/s 420s * #variants=60437 #multi_allelic=0 #not_processed=0 #hits=345/43000000 speed=3.40MT/s 420s * #variants=61810 #multi_allelic=0 #not_processed=0 #hits=357/44000000 speed=3.44MT/s 421s * #variants=63129 #multi_allelic=0 #not_processed=0 #hits=384/45000000 speed=3.47MT/s 421s * #variants=64409 #multi_allelic=0 #not_processed=0 #hits=391/46000000 speed=3.51MT/s 421s * #variants=65679 #multi_allelic=0 #not_processed=0 #hits=430/47000000 speed=3.51MT/s 422s * #variants=66953 #multi_allelic=0 #not_processed=0 #hits=436/48000000 speed=3.47MT/s 422s * #variants=68247 #multi_allelic=0 #not_processed=0 #hits=446/49000000 speed=3.50MT/s 422s * #variants=69595 #multi_allelic=0 #not_processed=0 #hits=460/50000000 speed=3.45MT/s 422s * #variants=70918 #multi_allelic=0 #not_processed=0 #hits=481/51000000 speed=3.46MT/s 423s * #variants=72211 #multi_allelic=0 #not_processed=0 #hits=492/52000000 speed=3.48MT/s 423s * #variants=73449 #multi_allelic=0 #not_processed=0 #hits=492/53000000 speed=3.53MT/s 423s * #variants=74662 #multi_allelic=0 #not_processed=0 #hits=500/54000000 speed=3.55MT/s 424s * #variants=75863 #multi_allelic=0 #not_processed=0 #hits=506/55000000 speed=3.56MT/s 424s * #variants=77058 #multi_allelic=0 #not_processed=0 #hits=513/56000000 speed=3.56MT/s 424s * #variants=78253 #multi_allelic=0 #not_processed=0 #hits=515/57000000 speed=3.56MT/s 424s * #variants=79446 #multi_allelic=0 #not_processed=0 #hits=530/58000000 speed=3.48MT/s 425s * #variants=80634 #multi_allelic=0 #not_processed=0 #hits=581/59000000 speed=3.56MT/s 425s * #variants=81817 #multi_allelic=0 #not_processed=0 #hits=594/60000000 speed=3.56MT/s 425s * #variants=82993 #multi_allelic=0 #not_processed=0 #hits=598/61000000 speed=3.56MT/s 426s * #variants=84160 #multi_allelic=0 #not_processed=0 #hits=599/62000000 speed=3.58MT/s 426s * #variants=85304 #multi_allelic=0 #not_processed=0 #hits=609/63000000 speed=3.60MT/s 426s * #variants=85485 #multi_allelic=0 #not_processed=0 #hits=609/63157827 speed=3.67MT/s 426s 426s Running time: 18 seconds 426s autopkgtest [04:55:12]: test run-sample-analysis: -----------------------] 427s run-sample-analysis PASS 427s autopkgtest [04:55:13]: test run-sample-analysis: - - - - - - - - - - results - - - - - - - - - - 427s autopkgtest [04:55:13]: @@@@@@@@@@@@@@@@@@@@ summary 427s run-sample-analysis PASS 439s Creating nova instance adt-noble-ppc64el-qtltools-20240412-044806-juju-7f2275-prod-proposed-migration-environment-3-55db328d-b04f-4737-9f7b-d2168ae71c80 from image adt/ubuntu-noble-ppc64el-server-20240411.img (UUID 011dc926-2757-46f5-8272-d10ae3620829)...