0s autopkgtest [21:15:56]: starting date and time: 2024-03-25 21:15:56+0000 0s autopkgtest [21:15:56]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [21:15:56]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.nfmddw39/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:qtltools,src:curl,src:gnutls28,src:htslib,src:libpsl,src:nettle,src:openssl,src:r-base --apt-upgrade qtltools --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=qtltools/1.3.1+dfsg-4build2 curl/8.5.0-2ubuntu8 gnutls28/3.8.3-1.1ubuntu2 htslib/1.19+ds-1.1build2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu2 r-base/4.3.3-2build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-s390x-7.secgroup --name adt-noble-s390x-qtltools-20240325-211556-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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/ 137s autopkgtest [21:18:13]: testbed dpkg architecture: s390x 137s autopkgtest [21:18:13]: testbed apt version: 2.7.12 137s autopkgtest [21:18:13]: @@@@@@@@@@@@@@@@@@@@ test bed setup 138s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 139s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [7608 B] 139s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.0 kB] 139s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [497 kB] 139s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4038 kB] 141s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [692 kB] 142s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 142s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 142s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 142s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4136 kB] 144s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 144s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [47.8 kB] 144s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 146s Fetched 9603 kB in 6s (1482 kB/s) 147s Reading package lists... 151s Reading package lists... 151s Building dependency tree... 151s Reading state information... 152s Calculating upgrade... 152s The following packages will be REMOVED: 152s libssl3 152s The following NEW packages will be installed: 152s libssl3t64 152s The following packages have been kept back: 152s curl 152s The following packages will be upgraded: 152s openssl 152s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 152s Need to get 2685 kB of archives. 152s After this operation, 239 kB of additional disk space will be used. 152s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main s390x openssl s390x 3.0.13-0ubuntu2 [1010 kB] 153s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libssl3t64 s390x 3.0.13-0ubuntu2 [1675 kB] 154s Fetched 2685 kB in 1s (2255 kB/s) 154s (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 ... 52170 files and directories currently installed.) 154s Preparing to unpack .../openssl_3.0.13-0ubuntu2_s390x.deb ... 154s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 158s dpkg: libssl3:s390x: dependency problems, but removing anyway as you requested: 158s wget depends on libssl3 (>= 3.0.0). 158s tnftp depends on libssl3 (>= 3.0.0). 158s tcpdump depends on libssl3 (>= 3.0.0). 158s systemd-resolved depends on libssl3 (>= 3.0.0). 158s systemd depends on libssl3 (>= 3.0.0). 158s sudo depends on libssl3 (>= 3.0.0). 158s s390-tools depends on libssl3 (>= 3.0.0). 158s rsync depends on libssl3 (>= 3.0.0). 158s python3-cryptography depends on libssl3 (>= 3.0.0). 158s openssh-server depends on libssl3 (>= 3.0.10). 158s openssh-client depends on libssl3 (>= 3.0.10). 158s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 158s libsystemd-shared:s390x depends on libssl3 (>= 3.0.0). 158s libssh-4:s390x depends on libssl3 (>= 3.0.0). 158s libsasl2-modules:s390x depends on libssl3 (>= 3.0.0). 158s libsasl2-2:s390x depends on libssl3 (>= 3.0.0). 158s libpython3.12-minimal:s390x depends on libssl3 (>= 3.0.0). 158s libpython3.11-minimal:s390x depends on libssl3 (>= 3.0.0). 158s libnvme1 depends on libssl3 (>= 3.0.0). 158s libkrb5-3:s390x depends on libssl3 (>= 3.0.0). 158s libkmod2:s390x depends on libssl3 (>= 3.0.0). 158s libfido2-1:s390x depends on libssl3 (>= 3.0.0). 158s libcurl4:s390x depends on libssl3 (>= 3.0.0). 158s libcryptsetup12:s390x depends on libssl3 (>= 3.0.0). 158s kmod depends on libssl3 (>= 3.0.0). 158s dhcpcd-base depends on libssl3 (>= 3.0.0). 158s bind9-libs:s390x depends on libssl3 (>= 3.0.0). 158s 158s (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 ... 52170 files and directories currently installed.) 158s Removing libssl3:s390x (3.0.10-1ubuntu4) ... 158s Selecting previously unselected package libssl3t64:s390x. 158s (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 ... 52159 files and directories currently installed.) 158s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_s390x.deb ... 158s Unpacking libssl3t64:s390x (3.0.13-0ubuntu2) ... 158s Setting up libssl3t64:s390x (3.0.13-0ubuntu2) ... 158s Setting up openssl (3.0.13-0ubuntu2) ... 158s Processing triggers for man-db (2.12.0-3) ... 159s Processing triggers for libc-bin (2.39-0ubuntu6) ... 159s Reading package lists... 160s Building dependency tree... 160s Reading state information... 160s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 160s Unknown architecture, assuming PC-style ttyS0 160s sh: Attempting to set up Debian/Ubuntu apt sources automatically 160s sh: Distribution appears to be Ubuntu 162s Reading package lists... 162s Building dependency tree... 162s Reading state information... 162s eatmydata is already the newest version (131-1). 162s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 163s Reading package lists... 163s Building dependency tree... 163s Reading state information... 163s dbus is already the newest version (1.14.10-4ubuntu1). 163s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 163s Reading package lists... 164s Building dependency tree... 164s Reading state information... 164s rng-tools-debian is already the newest version (2.4). 164s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 164s Reading package lists... 165s Building dependency tree... 165s Reading state information... 165s The following packages will be REMOVED: 165s cloud-init* python3-configobj* python3-debconf* 165s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 165s After this operation, 3256 kB disk space will be freed. 166s (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 ... 52172 files and directories currently installed.) 166s Removing cloud-init (24.1.2-0ubuntu1) ... 166s Removing python3-configobj (5.0.8-3) ... 166s Removing python3-debconf (1.5.86) ... 167s Processing triggers for man-db (2.12.0-3) ... 167s (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 ... 51783 files and directories currently installed.) 167s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 168s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 168s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 168s invoke-rc.d: policy-rc.d denied execution of try-restart. 169s Reading package lists... 169s Building dependency tree... 169s Reading state information... 170s linux-generic is already the newest version (6.8.0-11.11+1). 170s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 170s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 170s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 170s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 175s Reading package lists... 175s Reading package lists... 175s Building dependency tree... 175s Reading state information... 175s Calculating upgrade... 175s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 175s Reading package lists... 175s Building dependency tree... 175s Reading state information... 175s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 176s autopkgtest [21:18:52]: rebooting testbed after setup commands that affected boot 210s autopkgtest [21:19:26]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 214s autopkgtest [21:19:30]: @@@@@@@@@@@@@@@@@@@@ apt-source qtltools 219s Get:1 http://ftpmaster.internal/ubuntu noble/universe qtltools 1.3.1+dfsg-4build1 (dsc) [2214 B] 219s Get:2 http://ftpmaster.internal/ubuntu noble/universe qtltools 1.3.1+dfsg-4build1 (tar) [141 kB] 219s Get:3 http://ftpmaster.internal/ubuntu noble/universe qtltools 1.3.1+dfsg-4build1 (diff) [13.6 MB] 219s gpgv: Signature made Tue Dec 19 15:02:56 2023 UTC 219s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 219s gpgv: Can't check signature: No public key 219s dpkg-source: warning: cannot verify inline signature for ./qtltools_1.3.1+dfsg-4build1.dsc: no acceptable signature found 221s autopkgtest [21:19:37]: testing package qtltools version 1.3.1+dfsg-4build1 235s autopkgtest [21:19:51]: build not needed 242s autopkgtest [21:19:58]: test run-sample-analysis: preparing testbed 243s Reading package lists... 244s Building dependency tree... 244s Reading state information... 244s Starting pkgProblemResolver with broken count: 0 244s Starting 2 pkgProblemResolver with broken count: 0 244s Done 245s The following additional packages will be installed: 245s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 245s libboost-iostreams1.83.0 libboost-program-options1.83.0 libcairo2 libdatrie1 245s libdeflate0 libfontconfig1 libfreetype6 libgfortran5 libgomp1 libgraphite2-3 245s libgsl27 libgslcblas0 libharfbuzz0b libhts3 libhtscodecs2 libice6 libjbig0 245s libjpeg-turbo8 libjpeg8 liblapack3 libpango-1.0-0 libpangocairo-1.0-0 245s libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libsharpyuv0 libsm6 245s libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 245s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6 qtltools qtltools-example 245s r-base-core r-mathlib unzip x11-common xdg-utils zip 245s Suggested packages: 245s gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html tcl8.6 tk8.6 245s elpa-ess r-doc-info | r-doc-pdf r-base-html 245s Recommended packages: 245s r-bioc-qvalue r-recommended r-base-dev r-doc-html libfile-mimeinfo-perl 245s libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils 245s The following NEW packages will be installed: 245s autopkgtest-satdep fontconfig fontconfig-config fonts-dejavu-core 245s fonts-dejavu-mono libblas3 libboost-iostreams1.83.0 245s libboost-program-options1.83.0 libcairo2 libdatrie1 libdeflate0 245s libfontconfig1 libfreetype6 libgfortran5 libgomp1 libgraphite2-3 libgsl27 245s libgslcblas0 libharfbuzz0b libhts3 libhtscodecs2 libice6 libjbig0 245s libjpeg-turbo8 libjpeg8 liblapack3 libpango-1.0-0 libpangocairo-1.0-0 245s libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libsharpyuv0 libsm6 245s libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 245s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6 qtltools qtltools-example 245s r-base-core r-mathlib unzip x11-common xdg-utils zip 245s 0 upgraded, 54 newly installed, 0 to remove and 0 not upgraded. 245s Need to get 57.6 MB/57.6 MB of archives. 245s After this operation, 105 MB of additional disk space will be used. 245s Get:1 /tmp/autopkgtest.Ml0JfY/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [712 B] 245s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libfreetype6 s390x 2.13.2+dfsg-1 [431 kB] 246s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 246s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 246s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x fontconfig-config s390x 2.15.0-1ubuntu1 [37.0 kB] 246s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x libfontconfig1 s390x 2.15.0-1ubuntu1 [150 kB] 246s Get:7 http://ftpmaster.internal/ubuntu noble/main s390x fontconfig s390x 2.15.0-1ubuntu1 [191 kB] 246s Get:8 http://ftpmaster.internal/ubuntu noble/main s390x libblas3 s390x 3.12.0-3 [245 kB] 247s Get:9 http://ftpmaster.internal/ubuntu noble/main s390x libboost-iostreams1.83.0 s390x 1.83.0-2ubuntu1 [340 kB] 247s Get:10 http://ftpmaster.internal/ubuntu noble/main s390x libboost-program-options1.83.0 s390x 1.83.0-2ubuntu1 [418 kB] 247s Get:11 http://ftpmaster.internal/ubuntu noble/main s390x libpixman-1-0 s390x 0.42.2-1 [173 kB] 247s Get:12 http://ftpmaster.internal/ubuntu noble/main s390x libxcb-render0 s390x 1.15-1 [17.0 kB] 247s Get:13 http://ftpmaster.internal/ubuntu noble/main s390x libxcb-shm0 s390x 1.15-1 [5782 B] 247s Get:14 http://ftpmaster.internal/ubuntu noble/main s390x libxrender1 s390x 1:0.9.10-1.1 [19.4 kB] 247s Get:15 http://ftpmaster.internal/ubuntu noble/main s390x libcairo2 s390x 1.18.0-1 [578 kB] 247s Get:16 http://ftpmaster.internal/ubuntu noble/main s390x libdatrie1 s390x 0.2.13-3 [22.6 kB] 247s Get:17 http://ftpmaster.internal/ubuntu noble/main s390x libdeflate0 s390x 1.19-1 [46.0 kB] 247s Get:18 http://ftpmaster.internal/ubuntu noble/main s390x libgfortran5 s390x 14-20240303-1ubuntu1 [598 kB] 247s Get:19 http://ftpmaster.internal/ubuntu noble/main s390x libgomp1 s390x 14-20240303-1ubuntu1 [151 kB] 247s Get:20 http://ftpmaster.internal/ubuntu noble/main s390x libgraphite2-3 s390x 1.3.14-2 [90.4 kB] 247s Get:21 http://ftpmaster.internal/ubuntu noble/universe s390x libgslcblas0 s390x 2.7.1+dfsg-6ubuntu1 [147 kB] 247s Get:22 http://ftpmaster.internal/ubuntu noble/universe s390x libgsl27 s390x 2.7.1+dfsg-6ubuntu1 [1069 kB] 247s Get:23 http://ftpmaster.internal/ubuntu noble/main s390x libharfbuzz0b s390x 8.3.0-2 [515 kB] 247s Get:24 http://ftpmaster.internal/ubuntu noble/universe s390x libhtscodecs2 s390x 1.6.0-1 [87.2 kB] 247s Get:25 http://ftpmaster.internal/ubuntu noble/universe s390x libhts3 s390x 1.18+ds-1 [463 kB] 247s Get:26 http://ftpmaster.internal/ubuntu noble/main s390x x11-common all 1:7.7+23ubuntu2 [23.4 kB] 247s Get:27 http://ftpmaster.internal/ubuntu noble/main s390x libice6 s390x 2:1.0.10-1build2 [40.8 kB] 247s Get:28 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg-turbo8 s390x 2.1.5-2ubuntu1 [128 kB] 247s Get:29 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 247s Get:30 http://ftpmaster.internal/ubuntu noble/main s390x liblapack3 s390x 3.12.0-3 [2979 kB] 247s Get:31 http://ftpmaster.internal/ubuntu noble/main s390x libthai-data all 0.1.29-2 [158 kB] 247s Get:32 http://ftpmaster.internal/ubuntu noble/main s390x libthai0 s390x 0.1.29-2 [20.6 kB] 247s Get:33 http://ftpmaster.internal/ubuntu noble/main s390x libpango-1.0-0 s390x 1.51.0+ds-4 [240 kB] 247s Get:34 http://ftpmaster.internal/ubuntu noble/main s390x libpangoft2-1.0-0 s390x 1.51.0+ds-4 [43.6 kB] 247s Get:35 http://ftpmaster.internal/ubuntu noble/main s390x libpangocairo-1.0-0 s390x 1.51.0+ds-4 [28.9 kB] 247s Get:36 http://ftpmaster.internal/ubuntu noble/main s390x libpaper1 s390x 1.1.29 [13.3 kB] 247s Get:37 http://ftpmaster.internal/ubuntu noble/main s390x libpaper-utils s390x 1.1.29 [8452 B] 247s Get:38 http://ftpmaster.internal/ubuntu noble/main s390x libsharpyuv0 s390x 1.3.2-0.4 [14.8 kB] 247s Get:39 http://ftpmaster.internal/ubuntu noble/main s390x libsm6 s390x 2:1.2.3-1build2 [16.9 kB] 247s Get:40 http://ftpmaster.internal/ubuntu noble/main s390x libtcl8.6 s390x 8.6.13+dfsg-2 [948 kB] 248s Get:41 http://ftpmaster.internal/ubuntu noble/main s390x libjbig0 s390x 2.1-6.1ubuntu1 [29.8 kB] 248s Get:42 http://ftpmaster.internal/ubuntu noble/main s390x libwebp7 s390x 1.3.2-0.4 [207 kB] 248s Get:43 http://ftpmaster.internal/ubuntu noble/main s390x libtiff6 s390x 4.5.1+git230720-3ubuntu1 [253 kB] 248s Get:44 http://ftpmaster.internal/ubuntu noble/main s390x libxft2 s390x 2.3.6-1 [44.3 kB] 248s Get:45 http://ftpmaster.internal/ubuntu noble/main s390x libxss1 s390x 1:1.2.3-1build2 [8192 B] 248s Get:46 http://ftpmaster.internal/ubuntu noble/main s390x libtk8.6 s390x 8.6.14-1 [833 kB] 248s Get:47 http://ftpmaster.internal/ubuntu noble/main s390x libxt6 s390x 1:1.2.1-1.1 [166 kB] 248s Get:48 http://ftpmaster.internal/ubuntu noble/universe s390x r-mathlib s390x 4.3.2-1build1 [2370 kB] 248s Get:49 http://ftpmaster.internal/ubuntu noble/main s390x zip s390x 3.0-13 [175 kB] 248s Get:50 http://ftpmaster.internal/ubuntu noble/main s390x unzip s390x 6.0-28ubuntu3 [180 kB] 248s Get:51 http://ftpmaster.internal/ubuntu noble/main s390x xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 248s Get:52 http://ftpmaster.internal/ubuntu noble/universe s390x r-base-core s390x 4.3.2-1build1 [27.1 MB] 250s Get:53 http://ftpmaster.internal/ubuntu noble/universe s390x qtltools s390x 1.3.1+dfsg-4build1 [831 kB] 250s Get:54 http://ftpmaster.internal/ubuntu noble/universe s390x qtltools-example all 1.3.1+dfsg-4build1 [13.6 MB] 252s Preconfiguring packages ... 252s Fetched 57.6 MB in 6s (9487 kB/s) 252s Selecting previously unselected package libfreetype6:s390x. 252s (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 ... 51728 files and directories currently installed.) 252s Preparing to unpack .../00-libfreetype6_2.13.2+dfsg-1_s390x.deb ... 252s Unpacking libfreetype6:s390x (2.13.2+dfsg-1) ... 252s Selecting previously unselected package fonts-dejavu-mono. 252s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 252s Unpacking fonts-dejavu-mono (2.37-8) ... 252s Selecting previously unselected package fonts-dejavu-core. 252s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 252s Unpacking fonts-dejavu-core (2.37-8) ... 252s Selecting previously unselected package fontconfig-config. 252s Preparing to unpack .../03-fontconfig-config_2.15.0-1ubuntu1_s390x.deb ... 252s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 252s Selecting previously unselected package libfontconfig1:s390x. 252s Preparing to unpack .../04-libfontconfig1_2.15.0-1ubuntu1_s390x.deb ... 252s Unpacking libfontconfig1:s390x (2.15.0-1ubuntu1) ... 252s Selecting previously unselected package fontconfig. 252s Preparing to unpack .../05-fontconfig_2.15.0-1ubuntu1_s390x.deb ... 252s Unpacking fontconfig (2.15.0-1ubuntu1) ... 252s Selecting previously unselected package libblas3:s390x. 252s Preparing to unpack .../06-libblas3_3.12.0-3_s390x.deb ... 252s Unpacking libblas3:s390x (3.12.0-3) ... 252s Selecting previously unselected package libboost-iostreams1.83.0:s390x. 252s Preparing to unpack .../07-libboost-iostreams1.83.0_1.83.0-2ubuntu1_s390x.deb ... 252s Unpacking libboost-iostreams1.83.0:s390x (1.83.0-2ubuntu1) ... 252s Selecting previously unselected package libboost-program-options1.83.0:s390x. 252s Preparing to unpack .../08-libboost-program-options1.83.0_1.83.0-2ubuntu1_s390x.deb ... 252s Unpacking libboost-program-options1.83.0:s390x (1.83.0-2ubuntu1) ... 252s Selecting previously unselected package libpixman-1-0:s390x. 252s Preparing to unpack .../09-libpixman-1-0_0.42.2-1_s390x.deb ... 252s Unpacking libpixman-1-0:s390x (0.42.2-1) ... 252s Selecting previously unselected package libxcb-render0:s390x. 252s Preparing to unpack .../10-libxcb-render0_1.15-1_s390x.deb ... 252s Unpacking libxcb-render0:s390x (1.15-1) ... 252s Selecting previously unselected package libxcb-shm0:s390x. 252s Preparing to unpack .../11-libxcb-shm0_1.15-1_s390x.deb ... 252s Unpacking libxcb-shm0:s390x (1.15-1) ... 252s Selecting previously unselected package libxrender1:s390x. 252s Preparing to unpack .../12-libxrender1_1%3a0.9.10-1.1_s390x.deb ... 252s Unpacking libxrender1:s390x (1:0.9.10-1.1) ... 252s Selecting previously unselected package libcairo2:s390x. 252s Preparing to unpack .../13-libcairo2_1.18.0-1_s390x.deb ... 252s Unpacking libcairo2:s390x (1.18.0-1) ... 252s Selecting previously unselected package libdatrie1:s390x. 252s Preparing to unpack .../14-libdatrie1_0.2.13-3_s390x.deb ... 252s Unpacking libdatrie1:s390x (0.2.13-3) ... 252s Selecting previously unselected package libdeflate0:s390x. 252s Preparing to unpack .../15-libdeflate0_1.19-1_s390x.deb ... 252s Unpacking libdeflate0:s390x (1.19-1) ... 252s Selecting previously unselected package libgfortran5:s390x. 252s Preparing to unpack .../16-libgfortran5_14-20240303-1ubuntu1_s390x.deb ... 252s Unpacking libgfortran5:s390x (14-20240303-1ubuntu1) ... 252s Selecting previously unselected package libgomp1:s390x. 252s Preparing to unpack .../17-libgomp1_14-20240303-1ubuntu1_s390x.deb ... 252s Unpacking libgomp1:s390x (14-20240303-1ubuntu1) ... 253s Selecting previously unselected package libgraphite2-3:s390x. 253s Preparing to unpack .../18-libgraphite2-3_1.3.14-2_s390x.deb ... 253s Unpacking libgraphite2-3:s390x (1.3.14-2) ... 253s Selecting previously unselected package libgslcblas0:s390x. 253s Preparing to unpack .../19-libgslcblas0_2.7.1+dfsg-6ubuntu1_s390x.deb ... 253s Unpacking libgslcblas0:s390x (2.7.1+dfsg-6ubuntu1) ... 253s Selecting previously unselected package libgsl27:s390x. 253s Preparing to unpack .../20-libgsl27_2.7.1+dfsg-6ubuntu1_s390x.deb ... 253s Unpacking libgsl27:s390x (2.7.1+dfsg-6ubuntu1) ... 253s Selecting previously unselected package libharfbuzz0b:s390x. 253s Preparing to unpack .../21-libharfbuzz0b_8.3.0-2_s390x.deb ... 253s Unpacking libharfbuzz0b:s390x (8.3.0-2) ... 253s Selecting previously unselected package libhtscodecs2:s390x. 253s Preparing to unpack .../22-libhtscodecs2_1.6.0-1_s390x.deb ... 253s Unpacking libhtscodecs2:s390x (1.6.0-1) ... 253s Selecting previously unselected package libhts3:s390x. 253s Preparing to unpack .../23-libhts3_1.18+ds-1_s390x.deb ... 253s Unpacking libhts3:s390x (1.18+ds-1) ... 253s Selecting previously unselected package x11-common. 253s Preparing to unpack .../24-x11-common_1%3a7.7+23ubuntu2_all.deb ... 253s Unpacking x11-common (1:7.7+23ubuntu2) ... 253s Selecting previously unselected package libice6:s390x. 253s Preparing to unpack .../25-libice6_2%3a1.0.10-1build2_s390x.deb ... 253s Unpacking libice6:s390x (2:1.0.10-1build2) ... 253s Selecting previously unselected package libjpeg-turbo8:s390x. 253s Preparing to unpack .../26-libjpeg-turbo8_2.1.5-2ubuntu1_s390x.deb ... 253s Unpacking libjpeg-turbo8:s390x (2.1.5-2ubuntu1) ... 253s Selecting previously unselected package libjpeg8:s390x. 253s Preparing to unpack .../27-libjpeg8_8c-2ubuntu11_s390x.deb ... 253s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 253s Selecting previously unselected package liblapack3:s390x. 253s Preparing to unpack .../28-liblapack3_3.12.0-3_s390x.deb ... 253s Unpacking liblapack3:s390x (3.12.0-3) ... 253s Selecting previously unselected package libthai-data. 253s Preparing to unpack .../29-libthai-data_0.1.29-2_all.deb ... 253s Unpacking libthai-data (0.1.29-2) ... 253s Selecting previously unselected package libthai0:s390x. 253s Preparing to unpack .../30-libthai0_0.1.29-2_s390x.deb ... 253s Unpacking libthai0:s390x (0.1.29-2) ... 253s Selecting previously unselected package libpango-1.0-0:s390x. 253s Preparing to unpack .../31-libpango-1.0-0_1.51.0+ds-4_s390x.deb ... 253s Unpacking libpango-1.0-0:s390x (1.51.0+ds-4) ... 253s Selecting previously unselected package libpangoft2-1.0-0:s390x. 253s Preparing to unpack .../32-libpangoft2-1.0-0_1.51.0+ds-4_s390x.deb ... 253s Unpacking libpangoft2-1.0-0:s390x (1.51.0+ds-4) ... 253s Selecting previously unselected package libpangocairo-1.0-0:s390x. 253s Preparing to unpack .../33-libpangocairo-1.0-0_1.51.0+ds-4_s390x.deb ... 253s Unpacking libpangocairo-1.0-0:s390x (1.51.0+ds-4) ... 253s Selecting previously unselected package libpaper1:s390x. 253s Preparing to unpack .../34-libpaper1_1.1.29_s390x.deb ... 253s Unpacking libpaper1:s390x (1.1.29) ... 253s Selecting previously unselected package libpaper-utils. 253s Preparing to unpack .../35-libpaper-utils_1.1.29_s390x.deb ... 253s Unpacking libpaper-utils (1.1.29) ... 253s Selecting previously unselected package libsharpyuv0:s390x. 253s Preparing to unpack .../36-libsharpyuv0_1.3.2-0.4_s390x.deb ... 253s Unpacking libsharpyuv0:s390x (1.3.2-0.4) ... 253s Selecting previously unselected package libsm6:s390x. 253s Preparing to unpack .../37-libsm6_2%3a1.2.3-1build2_s390x.deb ... 253s Unpacking libsm6:s390x (2:1.2.3-1build2) ... 253s Selecting previously unselected package libtcl8.6:s390x. 253s Preparing to unpack .../38-libtcl8.6_8.6.13+dfsg-2_s390x.deb ... 253s Unpacking libtcl8.6:s390x (8.6.13+dfsg-2) ... 253s Selecting previously unselected package libjbig0:s390x. 253s Preparing to unpack .../39-libjbig0_2.1-6.1ubuntu1_s390x.deb ... 253s Unpacking libjbig0:s390x (2.1-6.1ubuntu1) ... 253s Selecting previously unselected package libwebp7:s390x. 253s Preparing to unpack .../40-libwebp7_1.3.2-0.4_s390x.deb ... 253s Unpacking libwebp7:s390x (1.3.2-0.4) ... 253s Selecting previously unselected package libtiff6:s390x. 253s Preparing to unpack .../41-libtiff6_4.5.1+git230720-3ubuntu1_s390x.deb ... 253s Unpacking libtiff6:s390x (4.5.1+git230720-3ubuntu1) ... 253s Selecting previously unselected package libxft2:s390x. 253s Preparing to unpack .../42-libxft2_2.3.6-1_s390x.deb ... 253s Unpacking libxft2:s390x (2.3.6-1) ... 253s Selecting previously unselected package libxss1:s390x. 253s Preparing to unpack .../43-libxss1_1%3a1.2.3-1build2_s390x.deb ... 253s Unpacking libxss1:s390x (1:1.2.3-1build2) ... 253s Selecting previously unselected package libtk8.6:s390x. 253s Preparing to unpack .../44-libtk8.6_8.6.14-1_s390x.deb ... 253s Unpacking libtk8.6:s390x (8.6.14-1) ... 253s Selecting previously unselected package libxt6:s390x. 253s Preparing to unpack .../45-libxt6_1%3a1.2.1-1.1_s390x.deb ... 253s Unpacking libxt6:s390x (1:1.2.1-1.1) ... 253s Selecting previously unselected package r-mathlib. 253s Preparing to unpack .../46-r-mathlib_4.3.2-1build1_s390x.deb ... 253s Unpacking r-mathlib (4.3.2-1build1) ... 254s Selecting previously unselected package zip. 254s Preparing to unpack .../47-zip_3.0-13_s390x.deb ... 254s Unpacking zip (3.0-13) ... 254s Selecting previously unselected package unzip. 254s Preparing to unpack .../48-unzip_6.0-28ubuntu3_s390x.deb ... 254s Unpacking unzip (6.0-28ubuntu3) ... 254s Selecting previously unselected package xdg-utils. 254s Preparing to unpack .../49-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 254s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 254s Selecting previously unselected package r-base-core. 254s Preparing to unpack .../50-r-base-core_4.3.2-1build1_s390x.deb ... 254s Unpacking r-base-core (4.3.2-1build1) ... 254s Selecting previously unselected package qtltools. 254s Preparing to unpack .../51-qtltools_1.3.1+dfsg-4build1_s390x.deb ... 254s Unpacking qtltools (1.3.1+dfsg-4build1) ... 254s Selecting previously unselected package qtltools-example. 254s Preparing to unpack .../52-qtltools-example_1.3.1+dfsg-4build1_all.deb ... 254s Unpacking qtltools-example (1.3.1+dfsg-4build1) ... 254s Selecting previously unselected package autopkgtest-satdep. 254s Preparing to unpack .../53-1-autopkgtest-satdep.deb ... 254s Unpacking autopkgtest-satdep (0) ... 254s Setting up libhtscodecs2:s390x (1.6.0-1) ... 254s Setting up libgraphite2-3:s390x (1.3.14-2) ... 254s Setting up qtltools-example (1.3.1+dfsg-4build1) ... 254s Setting up libboost-program-options1.83.0:s390x (1.83.0-2ubuntu1) ... 254s Setting up libpixman-1-0:s390x (0.42.2-1) ... 254s Setting up libsharpyuv0:s390x (1.3.2-0.4) ... 254s Setting up libpaper1:s390x (1.1.29) ... 254s 254s Creating config file /etc/papersize with new version 255s Setting up libxrender1:s390x (1:0.9.10-1.1) ... 255s Setting up libdatrie1:s390x (0.2.13-3) ... 255s Setting up libgslcblas0:s390x (2.7.1+dfsg-6ubuntu1) ... 256s Setting up libxcb-render0:s390x (1.15-1) ... 256s Setting up unzip (6.0-28ubuntu3) ... 256s Setting up x11-common (1:7.7+23ubuntu2) ... 256s Setting up libdeflate0:s390x (1.19-1) ... 256s Setting up libgsl27:s390x (2.7.1+dfsg-6ubuntu1) ... 256s Setting up libxcb-shm0:s390x (1.15-1) ... 256s Setting up libpaper-utils (1.1.29) ... 256s Setting up libgomp1:s390x (14-20240303-1ubuntu1) ... 256s Setting up libjbig0:s390x (2.1-6.1ubuntu1) ... 256s Setting up zip (3.0-13) ... 256s Setting up libblas3:s390x (3.12.0-3) ... 256s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 256s Setting up libfreetype6:s390x (2.13.2+dfsg-1) ... 256s Setting up libboost-iostreams1.83.0:s390x (1.83.0-2ubuntu1) ... 256s Setting up fonts-dejavu-mono (2.37-8) ... 256s Setting up libtcl8.6:s390x (8.6.13+dfsg-2) ... 256s Setting up fonts-dejavu-core (2.37-8) ... 256s Setting up libjpeg-turbo8:s390x (2.1.5-2ubuntu1) ... 256s Setting up libgfortran5:s390x (14-20240303-1ubuntu1) ... 256s Setting up libwebp7:s390x (1.3.2-0.4) ... 256s Setting up r-mathlib (4.3.2-1build1) ... 256s Setting up libharfbuzz0b:s390x (8.3.0-2) ... 256s Setting up libthai-data (0.1.29-2) ... 256s Setting up libxss1:s390x (1:1.2.3-1build2) ... 256s Setting up xdg-utils (1.1.3-4.1ubuntu3) ... 256s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 256s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 256s Setting up libice6:s390x (2:1.0.10-1build2) ... 256s Setting up liblapack3:s390x (3.12.0-3) ... 256s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 256s Setting up libhts3:s390x (1.18+ds-1) ... 256s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 256s Setting up libthai0:s390x (0.1.29-2) ... 256s Setting up libtiff6:s390x (4.5.1+git230720-3ubuntu1) ... 256s Setting up libfontconfig1:s390x (2.15.0-1ubuntu1) ... 256s Setting up libsm6:s390x (2:1.2.3-1build2) ... 256s Setting up fontconfig (2.15.0-1ubuntu1) ... 258s Regenerating fonts cache... done. 258s Setting up libxft2:s390x (2.3.6-1) ... 258s Setting up libtk8.6:s390x (8.6.14-1) ... 258s Setting up libpango-1.0-0:s390x (1.51.0+ds-4) ... 258s Setting up libcairo2:s390x (1.18.0-1) ... 259s Setting up libxt6:s390x (1:1.2.1-1.1) ... 259s Setting up libpangoft2-1.0-0:s390x (1.51.0+ds-4) ... 259s Setting up libpangocairo-1.0-0:s390x (1.51.0+ds-4) ... 259s Setting up r-base-core (4.3.2-1build1) ... 259s 259s Creating config file /etc/R/Renviron with new version 260s Setting up qtltools (1.3.1+dfsg-4build1) ... 260s Setting up autopkgtest-satdep (0) ... 260s Processing triggers for man-db (2.12.0-3) ... 262s Processing triggers for install-info (7.1-3) ... 262s Processing triggers for libc-bin (2.39-0ubuntu6) ... 276s (Reading database ... 53825 files and directories currently installed.) 276s Removing autopkgtest-satdep (0) ... 277s autopkgtest [21:20:33]: test run-sample-analysis: [----------------------- 279s ./genes.50percent.chr22.bed.gz 279s ./genes.50percent.chr22.bed.gz.tbi 279s ./genes.covariates.pc50.txt.gz 279s ./genes.simulated.chr22.bed.gz 279s ./genes.simulated.chr22.bed.gz.tbi 279s ./genotypes.chr22.vcf.gz 280s ./genotypes.chr22.vcf.gz.tbi 280s 280s QTLtools 280s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 280s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 280s * Webpage : https://qtltools.github.io/qtltools/ 280s * Version : 1.3.1 280s * Date : 25/03/2024 - 21:20:36 280s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 280s 280s CONDUCT PCA ON DATA 280s 280s Initialize random number generator 280s * Built-in seed is 15112011 280s * First Integer = 30553 280s * First Double = 0.0126695 280s 280s Reading sample list from [genes.50percent.chr22.bed.gz] 280s * #samples = 358 280s 280s Merging sample sets from all input files 280s * #files = 1 280s * #samples in all files = 358 280s 280s Reading phenotype data in [genes.50percent.chr22.bed.gz] 280s * 358 samples included 280s * 608 phenotypes included 280s 280s Calculating PCA with a matrix 358 x 608 280s * Calculated mean and sd 280s * 0 sd==0 columns removed 280s * Variables centered 280s * Variables scaled to unit variance 280s * Running SVD 282s * SVD complete 282s * Calculated sd and var for PCs 282s * Calculated cumulative var for PCs 282s * Done! 282s 282s Running time: 2 seconds 282s 282s QTLtools 282s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 282s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 282s * Webpage : https://qtltools.github.io/qtltools/ 282s * Version : 1.3.1 282s * Date : 25/03/2024 - 21:20:38 282s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 282s 282s MAPPING QTL IN CIS 282s * TASK: Report all nominal associations with p <= 0.01 282s * Linear model: Phe ~ Var + Cov 282s * Cis-window size is 1000000 bp 282s * Region = [chr22:17000000-18000000] 282s 282s Initialize random number generator 282s * Built-in seed is 15112011 282s * First Integer = 30553 282s * First Double = 0.0126695 282s 282s Reading sample list from [genes.50percent.chr22.bed.gz] 282s * #samples = 358 282s 282s Read sample list from [genotypes.chr22.vcf.gz] 282s * #samples = 358 282s 282s Reading sample list from [genes.covariates.pc50.txt.gz] 282s * #samples = 358 282s 282s Merging sample sets from all input files 282s * #files = 3 282s * #samples in all files = 358 282s 282s Reading phenotype data in [genes.50percent.chr22.bed.gz] 282s * target region [chr22:17000000-18000000] 282s * 8 phenotypes included 282s * 3 phenotypes are on the negative strand 282s 282s Reading genotype data in [genotypes.chr22.vcf.gz] 282s * File format detected: VCF 282s * target region [chr22:16000000-19000000] 283s * 6404 variants included 283s 283s Reading covariates in [genes.covariates.pc50.txt.gz] 283s * 53 covariates included 283s 283s Residualize phenotypes for covariates 283s * #covariates = 53 283s 283s Processing phenotype [ENSG00000237438.2] [1/8] 283s * #variants in cis = 5095 283s * Best hit: [id=22_17542810, d=25350, pv=1.1864e-25, s=-0.7518] 283s 283s Processing phenotype [ENSG00000273203.1] [2/8] 283s * #variants in cis = 5170 283s * Best hit: [id=22_17517388, d=-31323, pv=5.86611e-06, s=-0.1406] 283s 283s Processing phenotype [ENSG00000273442.1] [3/8] 283s * #variants in cis = 5188 283s * Best hit: [id=22_17553526, d=-8065, pv=0.000244522, s=0.1340] 283s 283s Processing phenotype [ENSG00000177663.9] [4/8] 283s * #variants in cis = 5193 283s * Best hit: [id=22_17513703, d=-52141, pv=8.03358e-14, s=-0.2096] 283s 283s Processing phenotype [ENSG00000183307.3] [5/8] 283s * #variants in cis = 5230 283s * Best hit: [id=22_17587975, d=14282, pv=1.56789e-07, s=-0.0078] 283s 283s Processing phenotype [ENSG00000069998.8] [6/8] 283s * #variants in cis = 5291 283s * Best hit: [id=22_17620429, d=25748, pv=1.37287e-14, s=-1.5147] 283s 283s Processing phenotype [ENSG00000093072.11] [7/8] 283s * #variants in cis = 5293 283s * Best hit: [id=22_17699630, d=3249, pv=0.000578649, s=0.6404] 283s 283s Processing phenotype [ENSG00000099954.14] [8/8] 283s * #variants in cis = 5435 283s * Best hit: [id=22_17175937, d=-664900, pv=0.000866455, s=0.0067] 283s 283s Running time: 0 seconds 283s 283s QTLtools 283s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 283s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 283s * Webpage : https://qtltools.github.io/qtltools/ 283s * Version : 1.3.1 283s * Date : 25/03/2024 - 21:20:39 283s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 283s 283s MAPPING QTL IN CIS 283s * TASK: Perform 1000 permutations 283s * Linear model: Phe ~ Var + Cov 283s * Cis-window size is 1000000 bp 283s * Region = [chr22:17000000-18000000] 283s 283s Initialize random number generator 283s * Built-in seed is 15112011 283s * First Integer = 30553 283s * First Double = 0.0126695 283s 283s Reading sample list from [genes.50percent.chr22.bed.gz] 283s * #samples = 358 283s 283s Read sample list from [genotypes.chr22.vcf.gz] 283s * #samples = 358 283s 283s Reading sample list from [genes.covariates.pc50.txt.gz] 283s * #samples = 358 283s 283s Merging sample sets from all input files 283s * #files = 3 283s * #samples in all files = 358 283s 283s Reading phenotype data in [genes.50percent.chr22.bed.gz] 283s * target region [chr22:17000000-18000000] 283s * 8 phenotypes included 283s * 3 phenotypes are on the negative strand 283s 283s Reading genotype data in [genotypes.chr22.vcf.gz] 283s * File format detected: VCF 283s * target region [chr22:16000000-19000000] 283s * 6404 variants included 283s 283s Reading covariates in [genes.covariates.pc50.txt.gz] 283s * 53 covariates included 283s 283s Residualize phenotypes for covariates 283s * #covariates = 53 283s 283s Processing phenotype [ENSG00000237438.2] [1/8] 283s * #variants in cis = 5095 286s * Best hit: [id=22_17542810, d=25350, pv=1.1864e-25, s=-0.7518] 286s * Beta parameters: [s1=1.00995, s2=621.053] 286s * Adjusted p-values: [emp=0.000999001, beta=1.28062e-20] 286s 286s Processing phenotype [ENSG00000273203.1] [2/8] 286s * #variants in cis = 5170 288s * Best hit: [id=22_17517388, d=-31323, pv=5.86611e-06, s=-0.1406] 288s * Beta parameters: [s1=1.11817, s2=641.379] 288s * Adjusted p-values: [emp=0.00799201, beta=0.00751892] 288s 288s Processing phenotype [ENSG00000273442.1] [3/8] 288s * #variants in cis = 5188 290s * Best hit: [id=22_17553526, d=-8065, pv=0.000244522, s=0.1340] 290s * Beta parameters: [s1=1.08364, s2=467.63] 290s * Adjusted p-values: [emp=0.297702, beta=0.293948] 290s 290s Processing phenotype [ENSG00000177663.9] [4/8] 290s * #variants in cis = 5193 292s * Best hit: [id=22_17513703, d=-52141, pv=8.03358e-14, s=-0.2096] 292s * Beta parameters: [s1=0.989061, s2=704.553] 292s * Adjusted p-values: [emp=0.000999001, beta=7.91291e-10] 292s 292s Processing phenotype [ENSG00000183307.3] [5/8] 292s * #variants in cis = 5230 294s * Best hit: [id=22_17587975, d=14282, pv=1.56789e-07, s=-0.0078] 294s * Beta parameters: [s1=1.01322, s2=559.49] 294s * Adjusted p-values: [emp=0.000999001, beta=0.00050707] 294s 294s Processing phenotype [ENSG00000069998.8] [6/8] 294s * #variants in cis = 5291 296s * Best hit: [id=22_17620429, d=25748, pv=1.37287e-14, s=-1.5147] 296s * Beta parameters: [s1=1.02312, s2=563.339] 296s * Adjusted p-values: [emp=0.000999001, beta=2.56935e-10] 296s 296s Processing phenotype [ENSG00000093072.11] [7/8] 296s * #variants in cis = 5293 299s * Best hit: [id=22_17699630, d=3249, pv=0.000578649, s=0.6404] 299s * Beta parameters: [s1=0.957514, s2=559.397] 299s * Adjusted p-values: [emp=0.574426, beta=0.562826] 299s 299s Processing phenotype [ENSG00000099954.14] [8/8] 299s * #variants in cis = 5435 301s * Best hit: [id=22_17175937, d=-664900, pv=0.000866455, s=0.0067] 301s * Beta parameters: [s1=0.938041, s2=226.852] 301s * Adjusted p-values: [emp=0.842158, beta=0.84836] 301s 301s Running time: 17 seconds 301s 301s QTLtools 301s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 301s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 301s * Webpage : https://qtltools.github.io/qtltools/ 301s * Version : 1.3.1 301s * Date : 25/03/2024 - 21:20:57 301s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 301s 301s MAPPING QTL IN TRANS 301s * TASK: Perform a full nominal pass, do not adjust p-values 301s * Cis-window size is 5000000 bp 301s * #bins = 1000 301s * threshold = 1e-05 301s 301s Initialize random number generator 301s * Built-in seed is 15112011 301s * First Integer = 30553 301s * First Double = 0.0126695 301s 301s Read sample list from [genotypes.chr22.vcf.gz] 301s * #samples = 358 301s 301s Checking sample list in [genes.simulated.chr22.bed.gz] 301s * #samples = 358 301s 301s Reading phenotype data in [genes.simulated.chr22.bed.gz] from line 0 to 0 301s * 358 samples included 301s * 608 phenotypes included 301s * 275 phenotypes is on the negative strand 301s 301s Calculate correlation threshold 301s * thres = 1e-05 301s * corr = 0.2311 301s 301s Sweep through genotype data in [genotypes.chr22.vcf.gz] 301s * #variants=1950 #multi_allelic=0 #not_processed=0 #hits=101/1000000 speed=2.56MT/s 302s * #variants=4001 #multi_allelic=0 #not_processed=0 #hits=153/2000000 speed=2.35MT/s 302s * #variants=6187 #multi_allelic=0 #not_processed=0 #hits=244/3000000 speed=2.00MT/s 303s * #variants=8537 #multi_allelic=0 #not_processed=0 #hits=285/4000000 speed=2.53MT/s 303s * #variants=11025 #multi_allelic=0 #not_processed=0 #hits=312/5000000 speed=2.17MT/s 303s * #variants=13621 #multi_allelic=0 #not_processed=0 #hits=320/6000000 speed=2.11MT/s 304s * #variants=16217 #multi_allelic=0 #not_processed=0 #hits=342/7000000 speed=1.94MT/s 304s * #variants=18755 #multi_allelic=0 #not_processed=0 #hits=401/8000000 speed=2.51MT/s 305s * #variants=21237 #multi_allelic=0 #not_processed=0 #hits=402/9000000 speed=1.74MT/s 305s * #variants=23680 #multi_allelic=0 #not_processed=0 #hits=455/10000000 speed=2.06MT/s 306s * #variants=26171 #multi_allelic=0 #not_processed=0 #hits=463/11000000 speed=2.13MT/s 306s * #variants=28609 #multi_allelic=0 #not_processed=0 #hits=469/12000000 speed=2.07MT/s 307s * #variants=30861 #multi_allelic=0 #not_processed=0 #hits=973/13000000 speed=1.96MT/s 308s * #variants=32932 #multi_allelic=0 #not_processed=0 #hits=979/14000000 speed=1.76MT/s 308s * #variants=34974 #multi_allelic=0 #not_processed=0 #hits=1085/15000000 speed=1.82MT/s 308s * #variants=37021 #multi_allelic=0 #not_processed=0 #hits=1086/16000000 speed=2.40MT/s 309s * #variants=39122 #multi_allelic=0 #not_processed=0 #hits=1089/17000000 speed=2.13MT/s 310s * #variants=41334 #multi_allelic=0 #not_processed=0 #hits=1089/18000000 speed=1.49MT/s 310s * #variants=43627 #multi_allelic=0 #not_processed=0 #hits=1096/19000000 speed=1.93MT/s 311s * #variants=45897 #multi_allelic=0 #not_processed=0 #hits=1153/20000000 speed=2.06MT/s 311s * #variants=48114 #multi_allelic=0 #not_processed=0 #hits=1243/21000000 speed=2.04MT/s 312s * #variants=50410 #multi_allelic=0 #not_processed=0 #hits=1249/22000000 speed=2.33MT/s 312s * #variants=52820 #multi_allelic=0 #not_processed=0 #hits=1259/23000000 speed=2.35MT/s 313s * #variants=55279 #multi_allelic=0 #not_processed=0 #hits=1498/24000000 speed=1.83MT/s 313s * #variants=57789 #multi_allelic=0 #not_processed=0 #hits=1724/25000000 speed=2.26MT/s 313s * #variants=60201 #multi_allelic=0 #not_processed=0 #hits=2168/26000000 speed=2.20MT/s 314s * #variants=62476 #multi_allelic=0 #not_processed=0 #hits=2452/27000000 speed=2.14MT/s 314s * #variants=64608 #multi_allelic=0 #not_processed=0 #hits=2544/28000000 speed=2.26MT/s 315s * #variants=66709 #multi_allelic=0 #not_processed=0 #hits=2684/29000000 speed=2.19MT/s 315s * #variants=68871 #multi_allelic=0 #not_processed=0 #hits=2688/30000000 speed=2.10MT/s 316s * #variants=71070 #multi_allelic=0 #not_processed=0 #hits=2720/31000000 speed=1.72MT/s 316s * #variants=73151 #multi_allelic=0 #not_processed=0 #hits=2891/32000000 speed=1.90MT/s 317s * #variants=75122 #multi_allelic=0 #not_processed=0 #hits=3110/33000000 speed=1.72MT/s 317s * #variants=77058 #multi_allelic=0 #not_processed=0 #hits=3209/34000000 speed=2.21MT/s 318s * #variants=78989 #multi_allelic=0 #not_processed=0 #hits=3218/35000000 speed=2.15MT/s 318s * #variants=80903 #multi_allelic=0 #not_processed=0 #hits=3250/36000000 speed=1.74MT/s 319s * #variants=82811 #multi_allelic=0 #not_processed=0 #hits=3463/37000000 speed=2.02MT/s 319s * #variants=84694 #multi_allelic=0 #not_processed=0 #hits=4035/38000000 speed=1.83MT/s 320s * #variants=85485 #multi_allelic=0 #not_processed=0 #hits=4036/38425275 speed=2.23MT/s 320s 320s Running time: 18 seconds 320s 320s QTLtools 320s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 320s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 320s * Webpage : https://qtltools.github.io/qtltools/ 320s * Version : 1.3.1 320s * Date : 25/03/2024 - 21:21:16 320s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 320s 320s MAPPING QTL IN TRANS 320s * TASK: Permute randomly chosen phenotypes 1000 times and test 320s * Cis-window size is 5000000 bp 320s * #bins = 1000 320s * threshold = 1e-05 320s 320s Initialize random number generator 320s * Built-in seed is 15112011 320s * First Integer = 30553 320s * First Double = 0.0126695 320s 320s Read sample list from [genotypes.chr22.vcf.gz] 320s * #samples = 358 320s 320s Checking sample list in [genes.simulated.chr22.bed.gz] 320s * #samples = 358 320s 320s Reading phenotype data in [genes.simulated.chr22.bed.gz] from line 0 to 0 320s * 358 samples included 320s * 608 phenotypes included 320s * 275 phenotypes is on the negative strand 320s 320s Normal transform phenotypes 320s 320s Calculate correlation threshold 320s * thres = 1e-05 320s * corr = 0.2311 320s 320s Sweep through genotype data in [genotypes.chr22.vcf.gz] 320s * #variants=1177 #multi_allelic=0 #not_processed=0 #hits=28/1000000 speed=2.96MT/s 321s * #variants=2383 #multi_allelic=0 #not_processed=0 #hits=38/2000000 speed=2.25MT/s 321s * #variants=3633 #multi_allelic=0 #not_processed=0 #hits=53/3000000 speed=2.38MT/s 322s * #variants=4928 #multi_allelic=0 #not_processed=0 #hits=53/4000000 speed=2.25MT/s 322s * #variants=6269 #multi_allelic=0 #not_processed=0 #hits=71/5000000 speed=2.18MT/s 322s * #variants=7675 #multi_allelic=0 #not_processed=0 #hits=72/6000000 speed=2.10MT/s 323s * #variants=9151 #multi_allelic=0 #not_processed=0 #hits=88/7000000 speed=2.22MT/s 323s * #variants=10663 #multi_allelic=0 #not_processed=0 #hits=96/8000000 speed=1.97MT/s 324s * #variants=12202 #multi_allelic=0 #not_processed=0 #hits=96/9000000 speed=2.33MT/s 324s * #variants=13804 #multi_allelic=0 #not_processed=0 #hits=96/10000000 speed=2.70MT/s 325s * #variants=15381 #multi_allelic=0 #not_processed=0 #hits=120/11000000 speed=2.42MT/s 325s * #variants=16946 #multi_allelic=0 #not_processed=0 #hits=123/12000000 speed=2.87MT/s 325s * #variants=18483 #multi_allelic=0 #not_processed=0 #hits=129/13000000 speed=2.67MT/s 326s * #variants=19995 #multi_allelic=0 #not_processed=0 #hits=131/14000000 speed=2.53MT/s 326s * #variants=21489 #multi_allelic=0 #not_processed=0 #hits=132/15000000 speed=2.95MT/s 327s * #variants=22947 #multi_allelic=0 #not_processed=0 #hits=151/16000000 speed=2.49MT/s 327s * #variants=24445 #multi_allelic=0 #not_processed=0 #hits=168/17000000 speed=2.75MT/s 327s * #variants=25965 #multi_allelic=0 #not_processed=0 #hits=175/18000000 speed=2.96MT/s 328s * #variants=27472 #multi_allelic=0 #not_processed=0 #hits=179/19000000 speed=2.95MT/s 328s * #variants=28933 #multi_allelic=0 #not_processed=0 #hits=181/20000000 speed=3.23MT/s 328s * #variants=30325 #multi_allelic=0 #not_processed=0 #hits=181/21000000 speed=2.87MT/s 329s * #variants=31617 #multi_allelic=0 #not_processed=0 #hits=182/22000000 speed=2.32MT/s 329s * #variants=32875 #multi_allelic=0 #not_processed=0 #hits=190/23000000 speed=2.56MT/s 330s * #variants=34127 #multi_allelic=0 #not_processed=0 #hits=192/24000000 speed=1.50MT/s 330s * #variants=35392 #multi_allelic=0 #not_processed=0 #hits=206/25000000 speed=1.91MT/s 331s * #variants=36652 #multi_allelic=0 #not_processed=0 #hits=206/26000000 speed=3.24MT/s 331s * #variants=37940 #multi_allelic=0 #not_processed=0 #hits=213/27000000 speed=3.36MT/s 331s * #variants=39255 #multi_allelic=0 #not_processed=0 #hits=238/28000000 speed=2.85MT/s 332s * #variants=40602 #multi_allelic=0 #not_processed=0 #hits=239/29000000 speed=2.70MT/s 332s * #variants=41998 #multi_allelic=0 #not_processed=0 #hits=245/30000000 speed=3.07MT/s 332s * #variants=43398 #multi_allelic=0 #not_processed=0 #hits=245/31000000 speed=3.22MT/s 333s * #variants=44803 #multi_allelic=0 #not_processed=0 #hits=260/32000000 speed=2.77MT/s 333s * #variants=46187 #multi_allelic=0 #not_processed=0 #hits=261/33000000 speed=3.04MT/s 333s * #variants=47545 #multi_allelic=0 #not_processed=0 #hits=268/34000000 speed=3.14MT/s 334s * #variants=48904 #multi_allelic=0 #not_processed=0 #hits=280/35000000 speed=2.71MT/s 334s * #variants=50309 #multi_allelic=0 #not_processed=0 #hits=306/36000000 speed=2.86MT/s 334s * #variants=51731 #multi_allelic=0 #not_processed=0 #hits=314/37000000 speed=2.93MT/s 335s * #variants=53171 #multi_allelic=0 #not_processed=0 #hits=320/38000000 speed=2.82MT/s 335s * #variants=54621 #multi_allelic=0 #not_processed=0 #hits=323/39000000 speed=2.72MT/s 335s * #variants=56099 #multi_allelic=0 #not_processed=0 #hits=323/40000000 speed=2.95MT/s 336s * #variants=57584 #multi_allelic=0 #not_processed=0 #hits=340/41000000 speed=2.92MT/s 336s * #variants=59032 #multi_allelic=0 #not_processed=0 #hits=344/42000000 speed=3.01MT/s 336s * #variants=60437 #multi_allelic=0 #not_processed=0 #hits=345/43000000 speed=2.88MT/s 337s * #variants=61810 #multi_allelic=0 #not_processed=0 #hits=357/44000000 speed=3.40MT/s 337s * #variants=63129 #multi_allelic=0 #not_processed=0 #hits=384/45000000 speed=3.15MT/s 337s * #variants=64409 #multi_allelic=0 #not_processed=0 #hits=391/46000000 speed=2.90MT/s 338s * #variants=65679 #multi_allelic=0 #not_processed=0 #hits=430/47000000 speed=2.79MT/s 338s * #variants=66953 #multi_allelic=0 #not_processed=0 #hits=436/48000000 speed=2.19MT/s 339s * #variants=68247 #multi_allelic=0 #not_processed=0 #hits=446/49000000 speed=2.18MT/s 339s * #variants=69595 #multi_allelic=0 #not_processed=0 #hits=460/50000000 speed=2.57MT/s 339s * #variants=70918 #multi_allelic=0 #not_processed=0 #hits=481/51000000 speed=2.85MT/s 340s * #variants=72211 #multi_allelic=0 #not_processed=0 #hits=492/52000000 speed=3.08MT/s 340s * #variants=73449 #multi_allelic=0 #not_processed=0 #hits=492/53000000 speed=2.51MT/s 340s * #variants=74662 #multi_allelic=0 #not_processed=0 #hits=500/54000000 speed=2.97MT/s 341s * #variants=75863 #multi_allelic=0 #not_processed=0 #hits=506/55000000 speed=2.07MT/s 341s * #variants=77058 #multi_allelic=0 #not_processed=0 #hits=513/56000000 speed=3.00MT/s 342s * #variants=78253 #multi_allelic=0 #not_processed=0 #hits=515/57000000 speed=2.99MT/s 342s * #variants=79446 #multi_allelic=0 #not_processed=0 #hits=530/58000000 speed=2.45MT/s 342s * #variants=80634 #multi_allelic=0 #not_processed=0 #hits=581/59000000 speed=3.50MT/s 343s * #variants=81817 #multi_allelic=0 #not_processed=0 #hits=594/60000000 speed=3.23MT/s 343s * #variants=82993 #multi_allelic=0 #not_processed=0 #hits=598/61000000 speed=3.51MT/s 343s * #variants=84160 #multi_allelic=0 #not_processed=0 #hits=599/62000000 speed=3.61MT/s 343s * #variants=85304 #multi_allelic=0 #not_processed=0 #hits=609/63000000 speed=3.79MT/s 343s * #variants=85485 #multi_allelic=0 #not_processed=0 #hits=609/63157827 speed=3.95MT/s 343s 343s Running time: 23 seconds 344s autopkgtest [21:21:40]: test run-sample-analysis: -----------------------] 344s autopkgtest [21:21:40]: test run-sample-analysis: - - - - - - - - - - results - - - - - - - - - - 344s run-sample-analysis PASS 345s autopkgtest [21:21:41]: @@@@@@@@@@@@@@@@@@@@ summary 345s run-sample-analysis PASS 375s Creating nova instance adt-noble-s390x-qtltools-20240325-211556-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-s390x-server-20240325.img (UUID 9f25d9bc-613c-4979-9452-2ea8e4d84cd0)...