0s autopkgtest [22:08:07]: starting date and time: 2024-04-02 22:08:07+0000 0s autopkgtest [22:08:07]: git checkout: 31124158 autopkgtest: take Paride's WIP change regarding wrong src pkg selection 0s autopkgtest [22:08:07]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.72ficpod/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:htslib,src:boost1.83 --apt-upgrade qtltools --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=htslib/1.19+ds-1.1build3 boost1.83/1.83.0-2.1ubuntu3' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos01-ppc64el-20.secgroup --name adt-noble-ppc64el-qtltools-20240402-220807-juju-7f2275-prod-proposed-migration-environment-3-6942a73a-50d7-4ac4-b0da-bebf53075ab6 --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://us.ports.ubuntu.com/ubuntu-ports/ 195s autopkgtest [22:11:22]: testbed dpkg architecture: ppc64el 196s autopkgtest [22:11:23]: testbed apt version: 2.7.14 196s autopkgtest [22:11:23]: @@@@@@@@@@@@@@@@@@@@ test bed setup 197s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 198s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [61.8 kB] 198s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [469 kB] 198s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3879 kB] 202s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [7348 B] 202s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [655 kB] 203s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 203s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1192 B] 203s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 203s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4028 kB] 207s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 207s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [30.7 kB] 207s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 210s Fetched 9260 kB in 10s (933 kB/s) 210s Reading package lists... 213s Reading package lists... 213s Building dependency tree... 213s Reading state information... 213s Calculating upgrade... 214s The following packages will be upgraded: 214s dash ftp kbd libcbor0.10 libmbim-glib4 libmbim-proxy libnewt0.52 214s libpipeline1 libprotobuf-c1 libreiserfscore0t64 librtmp1 libsensors-config 214s libsensors5 libtext-charwidth-perl libvolume-key1 python3-newt 214s python3-pyrsistent tnftp ubuntu-kernel-accessories ubuntu-minimal 214s ubuntu-standard whiptail 214s 22 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 214s Need to get 1264 kB of archives. 214s After this operation, 70.7 kB disk space will be freed. 214s Get:1 http://ftpmaster.internal/ubuntu noble/main ppc64el dash ppc64el 0.5.12-6ubuntu5 [108 kB] 214s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el kbd ppc64el 2.6.4-2ubuntu2 [245 kB] 214s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-newt ppc64el 0.52.24-2ubuntu2 [21.9 kB] 214s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el libnewt0.52 ppc64el 0.52.24-2ubuntu2 [61.9 kB] 214s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el libtext-charwidth-perl ppc64el 0.04-11build3 [9536 B] 214s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el whiptail ppc64el 0.52.24-2ubuntu2 [19.7 kB] 214s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el ubuntu-minimal ppc64el 1.538build1 [10.9 kB] 214s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el tnftp ppc64el 20230507-2build2 [116 kB] 215s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el ftp all 20230507-2build2 [4724 B] 215s Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el libcbor0.10 ppc64el 0.10.2-1.2ubuntu2 [28.5 kB] 215s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el libpipeline1 ppc64el 1.5.7-2 [26.9 kB] 215s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el ubuntu-standard ppc64el 1.538build1 [10.9 kB] 215s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el libmbim-proxy ppc64el 1.31.2-0ubuntu3 [6290 B] 215s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el libmbim-glib4 ppc64el 1.31.2-0ubuntu3 [254 kB] 215s Get:15 http://ftpmaster.internal/ubuntu noble/main ppc64el libprotobuf-c1 ppc64el 1.4.1-1ubuntu4 [26.0 kB] 215s Get:16 http://ftpmaster.internal/ubuntu noble/main ppc64el libreiserfscore0t64 ppc64el 1:3.6.27-7.1build1 [92.8 kB] 215s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el librtmp1 ppc64el 2.4+20151223.gitfa8646d.1-2build7 [64.4 kB] 215s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el libsensors-config all 1:3.6.0-9build1 [5546 B] 215s Get:19 http://ftpmaster.internal/ubuntu noble/main ppc64el libsensors5 ppc64el 1:3.6.0-9build1 [32.4 kB] 215s Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el libvolume-key1 ppc64el 0.3.12-7build2 [47.9 kB] 215s Get:21 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-pyrsistent ppc64el 0.20.0-1build2 [60.4 kB] 215s Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el ubuntu-kernel-accessories ppc64el 1.538build1 [10.7 kB] 215s Fetched 1264 kB in 1s (1084 kB/s) 215s (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 ... 103426 files and directories currently installed.) 215s Preparing to unpack .../dash_0.5.12-6ubuntu5_ppc64el.deb ... 215s Unpacking dash (0.5.12-6ubuntu5) over (0.5.12-6ubuntu4) ... 215s Setting up dash (0.5.12-6ubuntu5) ... 215s (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 ... 103426 files and directories currently installed.) 215s Preparing to unpack .../00-kbd_2.6.4-2ubuntu2_ppc64el.deb ... 215s Unpacking kbd (2.6.4-2ubuntu2) over (2.6.4-2ubuntu1) ... 215s Preparing to unpack .../01-python3-newt_0.52.24-2ubuntu2_ppc64el.deb ... 215s Unpacking python3-newt:ppc64el (0.52.24-2ubuntu2) over (0.52.24-2ubuntu1) ... 216s Preparing to unpack .../02-libnewt0.52_0.52.24-2ubuntu2_ppc64el.deb ... 216s Unpacking libnewt0.52:ppc64el (0.52.24-2ubuntu2) over (0.52.24-2ubuntu1) ... 216s Preparing to unpack .../03-libtext-charwidth-perl_0.04-11build3_ppc64el.deb ... 216s Unpacking libtext-charwidth-perl:ppc64el (0.04-11build3) over (0.04-11build2) ... 216s Preparing to unpack .../04-whiptail_0.52.24-2ubuntu2_ppc64el.deb ... 216s Unpacking whiptail (0.52.24-2ubuntu2) over (0.52.24-2ubuntu1) ... 216s Preparing to unpack .../05-ubuntu-minimal_1.538build1_ppc64el.deb ... 216s Unpacking ubuntu-minimal (1.538build1) over (1.538) ... 216s Preparing to unpack .../06-tnftp_20230507-2build2_ppc64el.deb ... 216s Unpacking tnftp (20230507-2build2) over (20230507-2build1) ... 216s Preparing to unpack .../07-ftp_20230507-2build2_all.deb ... 216s Unpacking ftp (20230507-2build2) over (20230507-2build1) ... 216s Preparing to unpack .../08-libcbor0.10_0.10.2-1.2ubuntu2_ppc64el.deb ... 216s Unpacking libcbor0.10:ppc64el (0.10.2-1.2ubuntu2) over (0.10.2-1.2ubuntu1) ... 216s Preparing to unpack .../09-libpipeline1_1.5.7-2_ppc64el.deb ... 216s Unpacking libpipeline1:ppc64el (1.5.7-2) over (1.5.7-1) ... 216s Preparing to unpack .../10-ubuntu-standard_1.538build1_ppc64el.deb ... 216s Unpacking ubuntu-standard (1.538build1) over (1.538) ... 216s Preparing to unpack .../11-libmbim-proxy_1.31.2-0ubuntu3_ppc64el.deb ... 216s Unpacking libmbim-proxy (1.31.2-0ubuntu3) over (1.31.2-0ubuntu2) ... 216s Preparing to unpack .../12-libmbim-glib4_1.31.2-0ubuntu3_ppc64el.deb ... 216s Unpacking libmbim-glib4:ppc64el (1.31.2-0ubuntu3) over (1.31.2-0ubuntu2) ... 216s Preparing to unpack .../13-libprotobuf-c1_1.4.1-1ubuntu4_ppc64el.deb ... 216s Unpacking libprotobuf-c1:ppc64el (1.4.1-1ubuntu4) over (1.4.1-1ubuntu3) ... 216s Preparing to unpack .../14-libreiserfscore0t64_1%3a3.6.27-7.1build1_ppc64el.deb ... 216s Unpacking libreiserfscore0t64 (1:3.6.27-7.1build1) over (1:3.6.27-7.1) ... 216s Preparing to unpack .../15-librtmp1_2.4+20151223.gitfa8646d.1-2build7_ppc64el.deb ... 216s Unpacking librtmp1:ppc64el (2.4+20151223.gitfa8646d.1-2build7) over (2.4+20151223.gitfa8646d.1-2build6) ... 216s Preparing to unpack .../16-libsensors-config_1%3a3.6.0-9build1_all.deb ... 216s Unpacking libsensors-config (1:3.6.0-9build1) over (1:3.6.0-9) ... 216s Preparing to unpack .../17-libsensors5_1%3a3.6.0-9build1_ppc64el.deb ... 216s Unpacking libsensors5:ppc64el (1:3.6.0-9build1) over (1:3.6.0-9) ... 216s Preparing to unpack .../18-libvolume-key1_0.3.12-7build2_ppc64el.deb ... 216s Unpacking libvolume-key1:ppc64el (0.3.12-7build2) over (0.3.12-7build1) ... 216s Preparing to unpack .../19-python3-pyrsistent_0.20.0-1build2_ppc64el.deb ... 216s Unpacking python3-pyrsistent:ppc64el (0.20.0-1build2) over (0.20.0-1) ... 216s Preparing to unpack .../20-ubuntu-kernel-accessories_1.538build1_ppc64el.deb ... 216s Unpacking ubuntu-kernel-accessories (1.538build1) over (1.538) ... 216s Setting up libpipeline1:ppc64el (1.5.7-2) ... 216s Setting up libtext-charwidth-perl:ppc64el (0.04-11build3) ... 216s Setting up ubuntu-kernel-accessories (1.538build1) ... 216s Setting up libnewt0.52:ppc64el (0.52.24-2ubuntu2) ... 216s Setting up libcbor0.10:ppc64el (0.10.2-1.2ubuntu2) ... 216s Setting up libsensors-config (1:3.6.0-9build1) ... 216s Setting up libreiserfscore0t64 (1:3.6.27-7.1build1) ... 216s Setting up python3-newt:ppc64el (0.52.24-2ubuntu2) ... 216s Setting up libprotobuf-c1:ppc64el (1.4.1-1ubuntu4) ... 216s Setting up librtmp1:ppc64el (2.4+20151223.gitfa8646d.1-2build7) ... 216s Setting up libsensors5:ppc64el (1:3.6.0-9build1) ... 216s Setting up python3-pyrsistent:ppc64el (0.20.0-1build2) ... 216s Setting up whiptail (0.52.24-2ubuntu2) ... 216s Setting up kbd (2.6.4-2ubuntu2) ... 216s Setting up libvolume-key1:ppc64el (0.3.12-7build2) ... 216s Setting up tnftp (20230507-2build2) ... 216s Setting up libmbim-glib4:ppc64el (1.31.2-0ubuntu3) ... 216s Setting up ubuntu-minimal (1.538build1) ... 216s Setting up libmbim-proxy (1.31.2-0ubuntu3) ... 216s Setting up ubuntu-standard (1.538build1) ... 216s Setting up ftp (20230507-2build2) ... 216s Processing triggers for initramfs-tools (0.142ubuntu23) ... 217s update-initramfs: Generating /boot/initrd.img-6.8.0-20-generic 217s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 223s Processing triggers for libc-bin (2.39-0ubuntu6) ... 223s Processing triggers for man-db (2.12.0-3build4) ... 224s Processing triggers for debianutils (5.17) ... 225s Reading package lists... 225s Building dependency tree... 225s Reading state information... 225s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 225s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 226s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 226s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 226s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 227s Reading package lists... 227s Reading package lists... 228s Building dependency tree... 228s Reading state information... 228s Calculating upgrade... 228s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 228s Reading package lists... 228s Building dependency tree... 228s Reading state information... 228s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 229s autopkgtest [22:11:56]: rebooting testbed after setup commands that affected boot 407s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 426s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 433s autopkgtest [22:15:20]: testbed running kernel: Linux 6.8.0-20-generic #20-Ubuntu SMP Mon Mar 18 11:46:05 UTC 2024 436s autopkgtest [22:15:23]: @@@@@@@@@@@@@@@@@@@@ apt-source qtltools 442s Get:1 http://ftpmaster.internal/ubuntu noble/universe qtltools 1.3.1+dfsg-4build2 (dsc) [2322 B] 442s Get:2 http://ftpmaster.internal/ubuntu noble/universe qtltools 1.3.1+dfsg-4build2 (tar) [141 kB] 442s Get:3 http://ftpmaster.internal/ubuntu noble/universe qtltools 1.3.1+dfsg-4build2 (diff) [13.6 MB] 443s gpgv: Signature made Fri Mar 22 16:52:46 2024 UTC 443s gpgv: using RSA key 4FB588A84C2DDE79A74C77876FA458DD1DB03F71 443s gpgv: issuer "juliank@ubuntu.com" 443s gpgv: Can't check signature: No public key 443s dpkg-source: warning: cannot verify inline signature for ./qtltools_1.3.1+dfsg-4build2.dsc: no acceptable signature found 444s autopkgtest [22:15:31]: testing package qtltools version 1.3.1+dfsg-4build2 445s autopkgtest [22:15:32]: build not needed 447s autopkgtest [22:15:34]: test run-sample-analysis: preparing testbed 450s Reading package lists... 450s Building dependency tree... 450s Reading state information... 451s Starting pkgProblemResolver with broken count: 0 451s Starting 2 pkgProblemResolver with broken count: 0 451s Done 452s The following additional packages will be installed: 452s fontconfig libblas3 libboost-iostreams1.83.0 libboost-program-options1.83.0 452s libcairo2 libdatrie1 libgfortran5 libgomp1 libgraphite2-3 libgsl27 452s libgslcblas0 libharfbuzz0b libhts3t64 libhtscodecs2 libice6 liblapack3 452s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 452s libpaper1 libpixman-1-0 libsm6 libtcl8.6 libthai-data libthai0 libtk8.6 452s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 qtltools 452s qtltools-example r-base-core r-mathlib unzip x11-common xdg-utils zip 452s Suggested packages: 452s gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html tcl8.6 tk8.6 452s elpa-ess r-doc-info | r-doc-pdf r-base-html 452s Recommended packages: 452s r-bioc-qvalue r-recommended r-base-dev r-doc-html libfile-mimeinfo-perl 452s libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils 452s The following NEW packages will be installed: 452s autopkgtest-satdep fontconfig libblas3 libboost-iostreams1.83.0 452s libboost-program-options1.83.0 libcairo2 libdatrie1 libgfortran5 libgomp1 452s libgraphite2-3 libgsl27 libgslcblas0 libharfbuzz0b libhts3t64 libhtscodecs2 452s libice6 liblapack3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 452s libpaper-utils libpaper1 libpixman-1-0 libsm6 libtcl8.6 libthai-data 452s libthai0 libtk8.6 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 452s libxt6t64 qtltools qtltools-example r-base-core r-mathlib unzip x11-common 452s xdg-utils zip 452s 0 upgraded, 42 newly installed, 0 to remove and 0 not upgraded. 452s Need to get 56.0 MB/56.0 MB of archives. 452s After this operation, 108 MB of additional disk space will be used. 452s Get:1 /tmp/autopkgtest.RCzPJr/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [712 B] 452s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el fontconfig ppc64el 2.15.0-1.1ubuntu1 [192 kB] 452s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3 [227 kB] 452s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libboost-iostreams1.83.0 ppc64el 1.83.0-2.1ubuntu3 [260 kB] 452s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libboost-program-options1.83.0 ppc64el 1.83.0-2.1ubuntu3 [329 kB] 452s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el libpixman-1-0 ppc64el 0.42.2-1 [300 kB] 453s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-render0 ppc64el 1.15-1 [17.2 kB] 453s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-shm0 ppc64el 1.15-1 [5896 B] 453s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1 [23.3 kB] 453s Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el libcairo2 ppc64el 1.18.0-1ubuntu1 [751 kB] 453s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el libdatrie1 ppc64el 0.2.13-3 [25.1 kB] 453s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240315-1ubuntu1 [574 kB] 453s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240315-1ubuntu1 [161 kB] 453s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el libgraphite2-3 ppc64el 1.3.14-2 [105 kB] 453s Get:15 http://ftpmaster.internal/ubuntu noble/universe ppc64el libgslcblas0 ppc64el 2.7.1+dfsg-6ubuntu1 [85.3 kB] 453s Get:16 http://ftpmaster.internal/ubuntu noble/universe ppc64el libgsl27 ppc64el 2.7.1+dfsg-6ubuntu1 [1064 kB] 453s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el libharfbuzz0b ppc64el 8.3.0-2build1 [580 kB] 453s Get:18 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 453s Get:19 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libhts3t64 ppc64el 1.19+ds-1.1build3 [569 kB] 453s Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el x11-common all 1:7.7+23ubuntu2 [23.4 kB] 453s Get:21 http://ftpmaster.internal/ubuntu noble/main ppc64el libice6 ppc64el 2:1.0.10-1build2 [49.3 kB] 453s Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3 [2804 kB] 453s Get:23 http://ftpmaster.internal/ubuntu noble/main ppc64el libthai-data all 0.1.29-2 [158 kB] 453s Get:24 http://ftpmaster.internal/ubuntu noble/main ppc64el libthai0 ppc64el 0.1.29-2 [21.4 kB] 453s Get:25 http://ftpmaster.internal/ubuntu noble/main ppc64el libpango-1.0-0 ppc64el 1.52.1+ds-1 [271 kB] 453s Get:26 http://ftpmaster.internal/ubuntu noble/main ppc64el libpangoft2-1.0-0 ppc64el 1.52.1+ds-1 [50.5 kB] 453s Get:27 http://ftpmaster.internal/ubuntu noble/main ppc64el libpangocairo-1.0-0 ppc64el 1.52.1+ds-1 [31.1 kB] 453s Get:28 http://ftpmaster.internal/ubuntu noble/main ppc64el libpaper1 ppc64el 1.1.29 [13.5 kB] 453s Get:29 http://ftpmaster.internal/ubuntu noble/main ppc64el libpaper-utils ppc64el 1.1.29 [8710 B] 453s Get:30 http://ftpmaster.internal/ubuntu noble/main ppc64el libsm6 ppc64el 2:1.2.3-1build2 [18.5 kB] 453s Get:31 http://ftpmaster.internal/ubuntu noble/main ppc64el libtcl8.6 ppc64el 8.6.14+dfsg-1 [1204 kB] 454s Get:32 http://ftpmaster.internal/ubuntu noble/main ppc64el libxft2 ppc64el 2.3.6-1 [59.8 kB] 454s Get:33 http://ftpmaster.internal/ubuntu noble/main ppc64el libxss1 ppc64el 1:1.2.3-1build2 [8982 B] 454s Get:34 http://ftpmaster.internal/ubuntu noble/main ppc64el libtk8.6 ppc64el 8.6.14-1 [944 kB] 454s Get:35 http://ftpmaster.internal/ubuntu noble/main ppc64el libxt6t64 ppc64el 1:1.2.1-1.2 [204 kB] 454s Get:36 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-mathlib ppc64el 4.3.3-2build1 [2439 kB] 454s Get:37 http://ftpmaster.internal/ubuntu noble/main ppc64el zip ppc64el 3.0-13 [192 kB] 454s Get:38 http://ftpmaster.internal/ubuntu noble/main ppc64el unzip ppc64el 6.0-28ubuntu3 [192 kB] 454s Get:39 http://ftpmaster.internal/ubuntu noble/main ppc64el xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 454s Get:40 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-base-core ppc64el 4.3.3-2build1 [27.4 MB] 455s Get:41 http://ftpmaster.internal/ubuntu noble/universe ppc64el qtltools ppc64el 1.3.1+dfsg-4build2 [828 kB] 455s Get:42 http://ftpmaster.internal/ubuntu noble/universe ppc64el qtltools-example all 1.3.1+dfsg-4build2 [13.6 MB] 456s Preconfiguring packages ... 456s Fetched 56.0 MB in 4s (13.7 MB/s) 456s Selecting previously unselected package fontconfig. 457s (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 ... 103425 files and directories currently installed.) 457s Preparing to unpack .../00-fontconfig_2.15.0-1.1ubuntu1_ppc64el.deb ... 457s Unpacking fontconfig (2.15.0-1.1ubuntu1) ... 457s Selecting previously unselected package libblas3:ppc64el. 457s Preparing to unpack .../01-libblas3_3.12.0-3_ppc64el.deb ... 457s Unpacking libblas3:ppc64el (3.12.0-3) ... 457s Selecting previously unselected package libboost-iostreams1.83.0:ppc64el. 457s Preparing to unpack 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package libxrender1:ppc64el. 457s Preparing to unpack .../07-libxrender1_1%3a0.9.10-1.1_ppc64el.deb ... 457s Unpacking libxrender1:ppc64el (1:0.9.10-1.1) ... 457s Selecting previously unselected package libcairo2:ppc64el. 457s Preparing to unpack .../08-libcairo2_1.18.0-1ubuntu1_ppc64el.deb ... 457s Unpacking libcairo2:ppc64el (1.18.0-1ubuntu1) ... 457s Selecting previously unselected package libdatrie1:ppc64el. 457s Preparing to unpack .../09-libdatrie1_0.2.13-3_ppc64el.deb ... 457s Unpacking libdatrie1:ppc64el (0.2.13-3) ... 457s Selecting previously unselected package libgfortran5:ppc64el. 457s Preparing to unpack .../10-libgfortran5_14-20240315-1ubuntu1_ppc64el.deb ... 457s Unpacking libgfortran5:ppc64el (14-20240315-1ubuntu1) ... 457s Selecting previously unselected package libgomp1:ppc64el. 457s Preparing to unpack .../11-libgomp1_14-20240315-1ubuntu1_ppc64el.deb ... 457s Unpacking libgomp1:ppc64el (14-20240315-1ubuntu1) ... 457s Selecting previously unselected package libgraphite2-3:ppc64el. 457s Preparing to unpack .../12-libgraphite2-3_1.3.14-2_ppc64el.deb ... 457s Unpacking libgraphite2-3:ppc64el (1.3.14-2) ... 457s Selecting previously unselected package libgslcblas0:ppc64el. 457s Preparing to unpack .../13-libgslcblas0_2.7.1+dfsg-6ubuntu1_ppc64el.deb ... 457s Unpacking libgslcblas0:ppc64el (2.7.1+dfsg-6ubuntu1) ... 457s Selecting previously unselected package libgsl27:ppc64el. 457s Preparing to unpack .../14-libgsl27_2.7.1+dfsg-6ubuntu1_ppc64el.deb ... 457s Unpacking libgsl27:ppc64el (2.7.1+dfsg-6ubuntu1) ... 457s Selecting previously unselected package libharfbuzz0b:ppc64el. 457s Preparing to unpack .../15-libharfbuzz0b_8.3.0-2build1_ppc64el.deb ... 457s Unpacking libharfbuzz0b:ppc64el (8.3.0-2build1) ... 457s Selecting previously unselected package libhtscodecs2:ppc64el. 457s Preparing to unpack .../16-libhtscodecs2_1.6.0-1_ppc64el.deb ... 457s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 457s Selecting previously unselected package 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... 457s Unpacking libthai0:ppc64el (0.1.29-2) ... 457s Selecting previously unselected package libpango-1.0-0:ppc64el. 457s Preparing to unpack .../23-libpango-1.0-0_1.52.1+ds-1_ppc64el.deb ... 457s Unpacking libpango-1.0-0:ppc64el (1.52.1+ds-1) ... 457s Selecting previously unselected package libpangoft2-1.0-0:ppc64el. 457s Preparing to unpack .../24-libpangoft2-1.0-0_1.52.1+ds-1_ppc64el.deb ... 457s Unpacking libpangoft2-1.0-0:ppc64el (1.52.1+ds-1) ... 457s Selecting previously unselected package libpangocairo-1.0-0:ppc64el. 457s Preparing to unpack .../25-libpangocairo-1.0-0_1.52.1+ds-1_ppc64el.deb ... 457s Unpacking libpangocairo-1.0-0:ppc64el (1.52.1+ds-1) ... 457s Selecting previously unselected package libpaper1:ppc64el. 457s Preparing to unpack .../26-libpaper1_1.1.29_ppc64el.deb ... 457s Unpacking libpaper1:ppc64el (1.1.29) ... 457s Selecting previously unselected package libpaper-utils. 457s Preparing to unpack .../27-libpaper-utils_1.1.29_ppc64el.deb ... 457s Unpacking 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libxt6t64:ppc64el. 458s Preparing to unpack .../33-libxt6t64_1%3a1.2.1-1.2_ppc64el.deb ... 458s Unpacking libxt6t64:ppc64el (1:1.2.1-1.2) ... 458s Selecting previously unselected package r-mathlib. 458s Preparing to unpack .../34-r-mathlib_4.3.3-2build1_ppc64el.deb ... 458s Unpacking r-mathlib (4.3.3-2build1) ... 458s Selecting previously unselected package zip. 458s Preparing to unpack .../35-zip_3.0-13_ppc64el.deb ... 458s Unpacking zip (3.0-13) ... 458s Selecting previously unselected package unzip. 458s Preparing to unpack .../36-unzip_6.0-28ubuntu3_ppc64el.deb ... 458s Unpacking unzip (6.0-28ubuntu3) ... 458s Selecting previously unselected package xdg-utils. 458s Preparing to unpack .../37-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 458s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 458s Selecting previously unselected package r-base-core. 458s Preparing to unpack .../38-r-base-core_4.3.3-2build1_ppc64el.deb ... 458s Unpacking r-base-core (4.3.3-2build1) ... 458s Selecting previously unselected package qtltools. 458s Preparing to unpack .../39-qtltools_1.3.1+dfsg-4build2_ppc64el.deb ... 458s Unpacking qtltools (1.3.1+dfsg-4build2) ... 458s Selecting previously unselected package qtltools-example. 458s Preparing to unpack .../40-qtltools-example_1.3.1+dfsg-4build2_all.deb ... 458s Unpacking qtltools-example (1.3.1+dfsg-4build2) ... 459s Selecting previously unselected package autopkgtest-satdep. 459s Preparing to unpack .../41-1-autopkgtest-satdep.deb ... 459s Unpacking autopkgtest-satdep (0) ... 459s Setting up libhtscodecs2:ppc64el (1.6.0-1) ... 459s Setting up libgraphite2-3:ppc64el (1.3.14-2) ... 459s Setting up qtltools-example (1.3.1+dfsg-4build2) ... 459s Setting up libboost-program-options1.83.0:ppc64el (1.83.0-2.1ubuntu3) ... 459s Setting up libpixman-1-0:ppc64el (0.42.2-1) ... 459s Setting up libpaper1:ppc64el (1.1.29) ... 459s 459s Creating config file /etc/papersize with new version 459s Setting up fontconfig (2.15.0-1.1ubuntu1) ... 461s Regenerating fonts cache... done. 461s Setting up libxrender1:ppc64el (1:0.9.10-1.1) ... 461s Setting up libdatrie1:ppc64el (0.2.13-3) ... 461s Setting up libgslcblas0:ppc64el (2.7.1+dfsg-6ubuntu1) ... 461s Setting up libxcb-render0:ppc64el (1.15-1) ... 461s Setting up unzip (6.0-28ubuntu3) ... 461s Setting up x11-common (1:7.7+23ubuntu2) ... 461s Setting up libgsl27:ppc64el (2.7.1+dfsg-6ubuntu1) ... 461s Setting up libxcb-shm0:ppc64el (1.15-1) ... 461s Setting up libpaper-utils (1.1.29) ... 461s Setting up libgomp1:ppc64el (14-20240315-1ubuntu1) ... 461s Setting up libcairo2:ppc64el (1.18.0-1ubuntu1) ... 461s Setting up zip (3.0-13) ... 461s Setting up libblas3:ppc64el (3.12.0-3) ... 461s 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 461s Setting up libboost-iostreams1.83.0:ppc64el (1.83.0-2.1ubuntu3) ... 461s Setting up libtcl8.6:ppc64el (8.6.14+dfsg-1) ... 461s Setting up libgfortran5:ppc64el (14-20240315-1ubuntu1) ... 461s Setting up r-mathlib (4.3.3-2build1) ... 461s Setting up libhts3t64:ppc64el (1.19+ds-1.1build3) ... 461s Setting up libharfbuzz0b:ppc64el (8.3.0-2build1) ... 461s Setting up libthai-data (0.1.29-2) ... 461s Setting up libxss1:ppc64el (1:1.2.3-1build2) ... 461s Setting up xdg-utils (1.1.3-4.1ubuntu3) ... 461s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 461s Setting up libice6:ppc64el (2:1.0.10-1build2) ... 461s Setting up liblapack3:ppc64el (3.12.0-3) ... 461s 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 461s Setting up libxft2:ppc64el (2.3.6-1) ... 461s Setting up libtk8.6:ppc64el (8.6.14-1) ... 461s Setting up libthai0:ppc64el (0.1.29-2) ... 461s Setting up libsm6:ppc64el (2:1.2.3-1build2) ... 461s Setting up libpango-1.0-0:ppc64el (1.52.1+ds-1) ... 461s Setting up libxt6t64:ppc64el (1:1.2.1-1.2) ... 461s Setting up libpangoft2-1.0-0:ppc64el (1.52.1+ds-1) ... 461s Setting up libpangocairo-1.0-0:ppc64el (1.52.1+ds-1) ... 461s Setting up r-base-core (4.3.3-2build1) ... 462s 462s Creating config file /etc/R/Renviron with new version 462s Setting up qtltools (1.3.1+dfsg-4build2) ... 462s Setting up autopkgtest-satdep (0) ... 462s Processing triggers for man-db (2.12.0-3build4) ... 464s Processing triggers for install-info (7.1-3build1) ... 464s Processing triggers for libc-bin (2.39-0ubuntu6) ... 469s (Reading database ... 105350 files and directories currently installed.) 469s Removing autopkgtest-satdep (0) ... 470s autopkgtest [22:15:57]: test run-sample-analysis: [----------------------- 470s ./genes.50percent.chr22.bed.gz 470s ./genes.50percent.chr22.bed.gz.tbi 470s ./genes.covariates.pc50.txt.gz 470s ./genes.simulated.chr22.bed.gz 470s ./genes.simulated.chr22.bed.gz.tbi 470s ./genotypes.chr22.vcf.gz 471s ./genotypes.chr22.vcf.gz.tbi 471s 471s QTLtools 471s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 471s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 471s * Webpage : https://qtltools.github.io/qtltools/ 471s * Version : 1.3.1 471s * Date : 02/04/2024 - 22:15:58 471s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 471s 471s CONDUCT PCA ON DATA 471s 471s Initialize random number generator 471s * Built-in seed is 15112011 471s * First Integer = 30553 471s * First Double = 0.0126695 471s 471s Reading sample list from [genes.50percent.chr22.bed.gz] 471s * #samples = 358 471s 471s Merging sample sets from all input files 471s * #files = 1 471s * #samples in all files = 358 471s 471s Reading phenotype data in [genes.50percent.chr22.bed.gz] 471s * 358 samples included 471s * 608 phenotypes included 471s 471s Calculating PCA with a matrix 358 x 608 471s * Calculated mean and sd 471s * 0 sd==0 columns removed 471s * Variables centered 471s * Variables scaled to unit variance 471s * Running SVD 472s * SVD complete 472s * Calculated sd and var for PCs 472s * Calculated cumulative var for PCs 472s * Done! 472s 472s Running time: 0 seconds 472s 472s QTLtools 472s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 472s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 472s * Webpage : https://qtltools.github.io/qtltools/ 472s * Version : 1.3.1 472s * Date : 02/04/2024 - 22:15:59 472s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 472s 472s MAPPING QTL IN CIS 472s * TASK: Report all nominal associations with p <= 0.01 472s * Linear model: Phe ~ Var + Cov 472s * Cis-window size is 1000000 bp 472s * Region = [chr22:17000000-18000000] 472s 472s Initialize random number generator 472s * Built-in seed is 15112011 472s * First Integer = 30553 472s * First Double = 0.0126695 472s 472s Reading sample list from [genes.50percent.chr22.bed.gz] 472s * #samples = 358 472s 472s Read sample list from [genotypes.chr22.vcf.gz] 472s * #samples = 358 472s 472s Reading sample list from [genes.covariates.pc50.txt.gz] 472s * #samples = 358 472s 472s Merging sample sets from all input files 472s * #files = 3 472s * #samples in all files = 358 472s 472s Reading phenotype data in [genes.50percent.chr22.bed.gz] 472s * target region [chr22:17000000-18000000] 472s * 8 phenotypes included 472s * 3 phenotypes are on the negative strand 472s 472s Reading genotype data in [genotypes.chr22.vcf.gz] 472s * File format detected: VCF 472s * target region [chr22:16000000-19000000] 472s * 6404 variants included 472s 472s Reading covariates in [genes.covariates.pc50.txt.gz] 472s * 53 covariates included 472s 472s Residualize phenotypes for covariates 472s * #covariates = 53 472s 472s Processing phenotype [ENSG00000237438.2] [1/8] 472s * #variants in cis = 5095 472s * Best hit: [id=22_17542810, d=25350, pv=1.1864e-25, s=-0.7518] 472s 472s Processing phenotype [ENSG00000273203.1] [2/8] 472s * #variants in cis = 5170 472s * Best hit: [id=22_17517388, d=-31323, pv=5.86611e-06, s=-0.1406] 472s 472s Processing phenotype [ENSG00000273442.1] [3/8] 472s * #variants in cis = 5188 472s * Best hit: [id=22_17553526, d=-8065, pv=0.000244522, s=0.1340] 472s 472s Processing phenotype [ENSG00000177663.9] [4/8] 472s * #variants in cis = 5193 472s * Best hit: [id=22_17513703, d=-52141, pv=8.03358e-14, s=-0.2096] 472s 472s Processing phenotype [ENSG00000183307.3] [5/8] 472s * #variants in cis = 5230 472s * Best hit: [id=22_17587975, d=14282, pv=1.56789e-07, s=-0.0078] 472s 472s Processing phenotype [ENSG00000069998.8] [6/8] 472s * #variants in cis = 5291 472s * Best hit: [id=22_17620429, d=25748, pv=1.37287e-14, s=-1.5147] 472s 472s Processing phenotype [ENSG00000093072.11] [7/8] 472s * #variants in cis = 5293 472s * Best hit: [id=22_17699630, d=3249, pv=0.000578649, s=0.6404] 472s 472s Processing phenotype [ENSG00000099954.14] [8/8] 472s * #variants in cis = 5435 472s * Best hit: [id=22_17175937, d=-664900, pv=0.000866455, s=0.0067] 472s 472s Running time: 0 seconds 472s 472s QTLtools 472s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 472s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 472s * Webpage : https://qtltools.github.io/qtltools/ 472s * Version : 1.3.1 472s * Date : 02/04/2024 - 22:15:59 472s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 472s 472s MAPPING QTL IN CIS 472s * TASK: Perform 1000 permutations 472s * Linear model: Phe ~ Var + Cov 472s * Cis-window size is 1000000 bp 472s * Region = [chr22:17000000-18000000] 472s 472s Initialize random number generator 472s * Built-in seed is 15112011 472s * First Integer = 30553 472s * First Double = 0.0126695 472s 472s Reading sample list from [genes.50percent.chr22.bed.gz] 472s * #samples = 358 472s 472s Read sample list from [genotypes.chr22.vcf.gz] 472s * #samples = 358 472s 472s Reading sample list from [genes.covariates.pc50.txt.gz] 472s * #samples = 358 472s 472s Merging sample sets from all input files 472s * #files = 3 472s * #samples in all files = 358 472s 472s Reading phenotype data in [genes.50percent.chr22.bed.gz] 472s * target region [chr22:17000000-18000000] 472s * 8 phenotypes included 472s * 3 phenotypes are on the negative strand 472s 472s Reading genotype data in [genotypes.chr22.vcf.gz] 472s * File format detected: VCF 472s * target region [chr22:16000000-19000000] 472s * 6404 variants included 472s 472s Reading covariates in [genes.covariates.pc50.txt.gz] 472s * 53 covariates included 472s 472s Residualize phenotypes for covariates 472s * #covariates = 53 472s 472s Processing phenotype [ENSG00000237438.2] [1/8] 472s * #variants in cis = 5095 473s * Best hit: [id=22_17542810, d=25350, pv=1.1864e-25, s=-0.7518] 473s * Beta parameters: [s1=1.00995, s2=621.053] 473s * Adjusted p-values: [emp=0.000999001, beta=1.28062e-20] 473s 473s Processing phenotype [ENSG00000273203.1] [2/8] 473s * #variants in cis = 5170 475s * Best hit: [id=22_17517388, d=-31323, pv=5.86611e-06, s=-0.1406] 475s * Beta parameters: [s1=1.11817, s2=641.379] 475s * Adjusted p-values: [emp=0.00799201, beta=0.00751892] 475s 475s Processing phenotype [ENSG00000273442.1] [3/8] 475s * #variants in cis = 5188 476s * Best hit: [id=22_17553526, d=-8065, pv=0.000244522, s=0.1340] 476s * Beta parameters: [s1=1.08364, s2=467.63] 476s * Adjusted p-values: [emp=0.297702, beta=0.293948] 476s 476s Processing phenotype [ENSG00000177663.9] [4/8] 476s * #variants in cis = 5193 477s * Best hit: [id=22_17513703, d=-52141, pv=8.03358e-14, s=-0.2096] 477s * Beta parameters: [s1=0.989061, s2=704.553] 477s * Adjusted p-values: [emp=0.000999001, beta=7.91291e-10] 477s 477s Processing phenotype [ENSG00000183307.3] [5/8] 477s * #variants in cis = 5230 479s * Best hit: [id=22_17587975, d=14282, pv=1.56789e-07, s=-0.0078] 479s * Beta parameters: [s1=1.01322, s2=559.49] 479s * Adjusted p-values: [emp=0.000999001, beta=0.00050707] 479s 479s Processing phenotype [ENSG00000069998.8] [6/8] 479s * #variants in cis = 5291 480s * Best hit: [id=22_17620429, d=25748, pv=1.37287e-14, s=-1.5147] 480s * Beta parameters: [s1=1.02312, s2=563.339] 480s * Adjusted p-values: [emp=0.000999001, beta=2.56935e-10] 480s 480s Processing phenotype [ENSG00000093072.11] [7/8] 480s * #variants in cis = 5293 481s * Best hit: [id=22_17699630, d=3249, pv=0.000578649, s=0.6404] 481s * Beta parameters: [s1=0.957514, s2=559.397] 481s * Adjusted p-values: [emp=0.574426, beta=0.562826] 481s 481s Processing phenotype [ENSG00000099954.14] [8/8] 481s * #variants in cis = 5435 482s * Best hit: [id=22_17175937, d=-664900, pv=0.000866455, s=0.0067] 482s * Beta parameters: [s1=0.938041, s2=226.852] 482s * Adjusted p-values: [emp=0.842158, beta=0.84836] 482s 482s Running time: 10 seconds 482s 482s QTLtools 482s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 482s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 482s * Webpage : https://qtltools.github.io/qtltools/ 482s * Version : 1.3.1 482s * Date : 02/04/2024 - 22:16:09 482s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 482s 482s MAPPING QTL IN TRANS 482s * TASK: Perform a full nominal pass, do not adjust p-values 482s * Cis-window size is 5000000 bp 482s * #bins = 1000 482s * threshold = 1e-05 482s 482s Initialize random number generator 482s * Built-in seed is 15112011 482s * First Integer = 30553 482s * First Double = 0.0126695 482s 482s Read sample list from [genotypes.chr22.vcf.gz] 482s * #samples = 358 482s 482s Checking sample list in [genes.simulated.chr22.bed.gz] 482s * #samples = 358 482s 482s Reading phenotype data in [genes.simulated.chr22.bed.gz] from line 0 to 0 482s * 358 samples included 482s * 608 phenotypes included 482s * 275 phenotypes is on the negative strand 482s 482s Calculate correlation threshold 482s * thres = 1e-05 482s * corr = 0.2311 482s 482s Sweep through genotype data in [genotypes.chr22.vcf.gz] 483s * #variants=1950 #multi_allelic=0 #not_processed=0 #hits=101/1000000 speed=3.83MT/s 483s * #variants=4001 #multi_allelic=0 #not_processed=0 #hits=153/2000000 speed=3.82MT/s 483s * #variants=6187 #multi_allelic=0 #not_processed=0 #hits=244/3000000 speed=3.79MT/s 483s * #variants=8537 #multi_allelic=0 #not_processed=0 #hits=285/4000000 speed=3.70MT/s 484s * #variants=11025 #multi_allelic=0 #not_processed=0 #hits=312/5000000 speed=3.69MT/s 484s * #variants=13621 #multi_allelic=0 #not_processed=0 #hits=320/6000000 speed=3.66MT/s 484s * #variants=16217 #multi_allelic=0 #not_processed=0 #hits=342/7000000 speed=3.65MT/s 485s * #variants=18755 #multi_allelic=0 #not_processed=0 #hits=401/8000000 speed=3.64MT/s 485s * #variants=21237 #multi_allelic=0 #not_processed=0 #hits=402/9000000 speed=3.69MT/s 485s * #variants=23680 #multi_allelic=0 #not_processed=0 #hits=455/10000000 speed=3.70MT/s 485s * #variants=26171 #multi_allelic=0 #not_processed=0 #hits=463/11000000 speed=3.68MT/s 486s * #variants=28609 #multi_allelic=0 #not_processed=0 #hits=469/12000000 speed=3.60MT/s 486s * #variants=30861 #multi_allelic=0 #not_processed=0 #hits=973/13000000 speed=3.70MT/s 486s * #variants=32932 #multi_allelic=0 #not_processed=0 #hits=979/14000000 speed=3.77MT/s 486s * #variants=34974 #multi_allelic=0 #not_processed=0 #hits=1085/15000000 speed=3.77MT/s 487s * #variants=37021 #multi_allelic=0 #not_processed=0 #hits=1086/16000000 speed=3.79MT/s 487s * #variants=39122 #multi_allelic=0 #not_processed=0 #hits=1089/17000000 speed=3.77MT/s 487s * #variants=41334 #multi_allelic=0 #not_processed=0 #hits=1089/18000000 speed=3.72MT/s 487s * #variants=43627 #multi_allelic=0 #not_processed=0 #hits=1096/19000000 speed=3.75MT/s 488s * #variants=45897 #multi_allelic=0 #not_processed=0 #hits=1153/20000000 speed=3.79MT/s 488s * #variants=48114 #multi_allelic=0 #not_processed=0 #hits=1243/21000000 speed=3.80MT/s 488s * #variants=50410 #multi_allelic=0 #not_processed=0 #hits=1249/22000000 speed=3.77MT/s 489s * #variants=52820 #multi_allelic=0 #not_processed=0 #hits=1259/23000000 speed=3.73MT/s 489s * #variants=55279 #multi_allelic=0 #not_processed=0 #hits=1498/24000000 speed=3.68MT/s 489s * #variants=57789 #multi_allelic=0 #not_processed=0 #hits=1724/25000000 speed=3.66MT/s 489s * #variants=60201 #multi_allelic=0 #not_processed=0 #hits=2168/26000000 speed=3.65MT/s 490s * #variants=62476 #multi_allelic=0 #not_processed=0 #hits=2452/27000000 speed=3.72MT/s 490s * #variants=64608 #multi_allelic=0 #not_processed=0 #hits=2544/28000000 speed=3.77MT/s 490s * #variants=66709 #multi_allelic=0 #not_processed=0 #hits=2684/29000000 speed=3.66MT/s 490s * #variants=68871 #multi_allelic=0 #not_processed=0 #hits=2688/30000000 speed=3.77MT/s 491s * #variants=71070 #multi_allelic=0 #not_processed=0 #hits=2720/31000000 speed=3.77MT/s 491s * #variants=73151 #multi_allelic=0 #not_processed=0 #hits=2891/32000000 speed=3.80MT/s 491s * #variants=75122 #multi_allelic=0 #not_processed=0 #hits=3110/33000000 speed=3.82MT/s 492s * #variants=77058 #multi_allelic=0 #not_processed=0 #hits=3209/34000000 speed=3.85MT/s 492s * #variants=78989 #multi_allelic=0 #not_processed=0 #hits=3218/35000000 speed=3.83MT/s 492s * #variants=80903 #multi_allelic=0 #not_processed=0 #hits=3250/36000000 speed=3.86MT/s 492s * #variants=82811 #multi_allelic=0 #not_processed=0 #hits=3463/37000000 speed=3.86MT/s 493s * #variants=84694 #multi_allelic=0 #not_processed=0 #hits=4035/38000000 speed=3.83MT/s 493s * #variants=85485 #multi_allelic=0 #not_processed=0 #hits=4036/38425275 speed=3.90MT/s 493s 493s Running time: 10 seconds 493s 493s QTLtools 493s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 493s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 493s * Webpage : https://qtltools.github.io/qtltools/ 493s * Version : 1.3.1 493s * Date : 02/04/2024 - 22:16:20 493s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 493s 493s MAPPING QTL IN TRANS 493s * TASK: Permute randomly chosen phenotypes 1000 times and test 493s * Cis-window size is 5000000 bp 493s * #bins = 1000 493s * threshold = 1e-05 493s 493s Initialize random number generator 493s * Built-in seed is 15112011 493s * First Integer = 30553 493s * First Double = 0.0126695 493s 493s Read sample list from [genotypes.chr22.vcf.gz] 493s * #samples = 358 493s 493s Checking sample list in [genes.simulated.chr22.bed.gz] 493s * #samples = 358 493s 493s Reading phenotype data in [genes.simulated.chr22.bed.gz] from line 0 to 0 493s * 358 samples included 493s * 608 phenotypes included 493s * 275 phenotypes is on the negative strand 493s 493s Normal transform phenotypes 493s 493s Calculate correlation threshold 493s * thres = 1e-05 493s * corr = 0.2311 493s 493s Sweep through genotype data in [genotypes.chr22.vcf.gz] 493s * #variants=1177 #multi_allelic=0 #not_processed=0 #hits=28/1000000 speed=3.94MT/s 493s * #variants=2383 #multi_allelic=0 #not_processed=0 #hits=38/2000000 speed=3.91MT/s 494s * #variants=3633 #multi_allelic=0 #not_processed=0 #hits=53/3000000 speed=3.85MT/s 494s * #variants=4928 #multi_allelic=0 #not_processed=0 #hits=53/4000000 speed=3.83MT/s 494s * #variants=6269 #multi_allelic=0 #not_processed=0 #hits=71/5000000 speed=3.77MT/s 494s * #variants=7675 #multi_allelic=0 #not_processed=0 #hits=72/6000000 speed=3.72MT/s 495s * #variants=9151 #multi_allelic=0 #not_processed=0 #hits=88/7000000 speed=3.66MT/s 495s * #variants=10663 #multi_allelic=0 #not_processed=0 #hits=96/8000000 speed=3.66MT/s 495s * #variants=12202 #multi_allelic=0 #not_processed=0 #hits=96/9000000 speed=3.66MT/s 495s * #variants=13804 #multi_allelic=0 #not_processed=0 #hits=96/10000000 speed=3.61MT/s 496s * #variants=15381 #multi_allelic=0 #not_processed=0 #hits=120/11000000 speed=3.61MT/s 496s * #variants=16946 #multi_allelic=0 #not_processed=0 #hits=123/12000000 speed=3.65MT/s 496s * #variants=18483 #multi_allelic=0 #not_processed=0 #hits=129/13000000 speed=3.65MT/s 497s * #variants=19995 #multi_allelic=0 #not_processed=0 #hits=131/14000000 speed=3.68MT/s 497s * #variants=21489 #multi_allelic=0 #not_processed=0 #hits=132/15000000 speed=3.69MT/s 497s * #variants=22947 #multi_allelic=0 #not_processed=0 #hits=151/16000000 speed=3.75MT/s 497s * #variants=24445 #multi_allelic=0 #not_processed=0 #hits=168/17000000 speed=3.69MT/s 498s * #variants=25965 #multi_allelic=0 #not_processed=0 #hits=175/18000000 speed=3.62MT/s 498s * #variants=27472 #multi_allelic=0 #not_processed=0 #hits=179/19000000 speed=3.69MT/s 498s * #variants=28933 #multi_allelic=0 #not_processed=0 #hits=181/20000000 speed=3.75MT/s 498s * #variants=30325 #multi_allelic=0 #not_processed=0 #hits=181/21000000 speed=3.80MT/s 499s * #variants=31617 #multi_allelic=0 #not_processed=0 #hits=182/22000000 speed=3.88MT/s 499s * #variants=32875 #multi_allelic=0 #not_processed=0 #hits=190/23000000 speed=3.88MT/s 499s * #variants=34127 #multi_allelic=0 #not_processed=0 #hits=192/24000000 speed=3.91MT/s 499s * #variants=35392 #multi_allelic=0 #not_processed=0 #hits=206/25000000 speed=3.82MT/s 500s * #variants=36652 #multi_allelic=0 #not_processed=0 #hits=206/26000000 speed=3.89MT/s 500s * #variants=37940 #multi_allelic=0 #not_processed=0 #hits=213/27000000 speed=3.85MT/s 500s * #variants=39255 #multi_allelic=0 #not_processed=0 #hits=238/28000000 speed=3.85MT/s 501s * #variants=40602 #multi_allelic=0 #not_processed=0 #hits=239/29000000 speed=3.83MT/s 501s * #variants=41998 #multi_allelic=0 #not_processed=0 #hits=245/30000000 speed=3.77MT/s 501s * #variants=43398 #multi_allelic=0 #not_processed=0 #hits=245/31000000 speed=3.66MT/s 501s * #variants=44803 #multi_allelic=0 #not_processed=0 #hits=260/32000000 speed=3.73MT/s 502s * #variants=46187 #multi_allelic=0 #not_processed=0 #hits=261/33000000 speed=3.83MT/s 502s * #variants=47545 #multi_allelic=0 #not_processed=0 #hits=268/34000000 speed=3.79MT/s 502s * #variants=48904 #multi_allelic=0 #not_processed=0 #hits=280/35000000 speed=3.80MT/s 502s * #variants=50309 #multi_allelic=0 #not_processed=0 #hits=306/36000000 speed=3.77MT/s 503s * #variants=51731 #multi_allelic=0 #not_processed=0 #hits=314/37000000 speed=3.70MT/s 503s * #variants=53171 #multi_allelic=0 #not_processed=0 #hits=320/38000000 speed=3.72MT/s 503s * #variants=54621 #multi_allelic=0 #not_processed=0 #hits=323/39000000 speed=3.79MT/s 503s * #variants=56099 #multi_allelic=0 #not_processed=0 #hits=323/40000000 speed=3.76MT/s 504s * #variants=57584 #multi_allelic=0 #not_processed=0 #hits=340/41000000 speed=3.75MT/s 504s * #variants=59032 #multi_allelic=0 #not_processed=0 #hits=344/42000000 speed=3.77MT/s 504s * #variants=60437 #multi_allelic=0 #not_processed=0 #hits=345/43000000 speed=3.77MT/s 505s * #variants=61810 #multi_allelic=0 #not_processed=0 #hits=357/44000000 speed=3.82MT/s 505s * #variants=63129 #multi_allelic=0 #not_processed=0 #hits=384/45000000 speed=3.85MT/s 505s * #variants=64409 #multi_allelic=0 #not_processed=0 #hits=391/46000000 speed=3.89MT/s 505s * #variants=65679 #multi_allelic=0 #not_processed=0 #hits=430/47000000 speed=3.91MT/s 506s * #variants=66953 #multi_allelic=0 #not_processed=0 #hits=436/48000000 speed=3.89MT/s 506s * #variants=68247 #multi_allelic=0 #not_processed=0 #hits=446/49000000 speed=3.85MT/s 506s * #variants=69595 #multi_allelic=0 #not_processed=0 #hits=460/50000000 speed=3.76MT/s 506s * #variants=70918 #multi_allelic=0 #not_processed=0 #hits=481/51000000 speed=3.86MT/s 507s * #variants=72211 #multi_allelic=0 #not_processed=0 #hits=492/52000000 speed=3.89MT/s 507s * #variants=73449 #multi_allelic=0 #not_processed=0 #hits=492/53000000 speed=3.89MT/s 507s * #variants=74662 #multi_allelic=0 #not_processed=0 #hits=500/54000000 speed=3.91MT/s 507s * #variants=75863 #multi_allelic=0 #not_processed=0 #hits=506/55000000 speed=3.92MT/s 508s * #variants=77058 #multi_allelic=0 #not_processed=0 #hits=513/56000000 speed=3.92MT/s 508s * #variants=78253 #multi_allelic=0 #not_processed=0 #hits=515/57000000 speed=3.95MT/s 508s * #variants=79446 #multi_allelic=0 #not_processed=0 #hits=530/58000000 speed=3.89MT/s 508s * #variants=80634 #multi_allelic=0 #not_processed=0 #hits=581/59000000 speed=3.91MT/s 509s * #variants=81817 #multi_allelic=0 #not_processed=0 #hits=594/60000000 speed=3.94MT/s 509s * #variants=82993 #multi_allelic=0 #not_processed=0 #hits=598/61000000 speed=3.92MT/s 509s * #variants=84160 #multi_allelic=0 #not_processed=0 #hits=599/62000000 speed=3.97MT/s 509s * #variants=85304 #multi_allelic=0 #not_processed=0 #hits=609/63000000 speed=3.86MT/s 509s * #variants=85485 #multi_allelic=0 #not_processed=0 #hits=609/63157827 speed=4.05MT/s 509s 509s Running time: 16 seconds 510s autopkgtest [22:16:37]: test run-sample-analysis: -----------------------] 510s run-sample-analysis PASS 510s autopkgtest [22:16:37]: test run-sample-analysis: - - - - - - - - - - results - - - - - - - - - - 511s autopkgtest [22:16:38]: @@@@@@@@@@@@@@@@@@@@ summary 511s run-sample-analysis PASS 538s Creating nova instance adt-noble-ppc64el-qtltools-20240402-220807-juju-7f2275-prod-proposed-migration-environment-3-6942a73a-50d7-4ac4-b0da-bebf53075ab6 from image adt/ubuntu-noble-ppc64el-server-20240401.img (UUID 40bf39fa-e644-4434-8f27-6e8b4e3ba74a)...