0s autopkgtest [13:01:22]: starting date and time: 2024-03-24 13:01:22+0000 0s autopkgtest [13:01:22]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [13:01:22]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.lfj6lysv/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-ppc64el-10.secgroup --name adt-noble-ppc64el-qtltools-20240324-130122-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-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/ 277s autopkgtest [13:05:59]: testbed dpkg architecture: ppc64el 277s autopkgtest [13:05:59]: testbed apt version: 2.7.12 277s autopkgtest [13:05:59]: @@@@@@@@@@@@@@@@@@@@ test bed setup 278s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 279s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4044 kB] 279s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 279s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 279s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [539 kB] 279s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [726 kB] 279s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 279s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 279s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 279s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4274 kB] 280s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 280s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [61.1 kB] 280s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 283s Fetched 9838 kB in 3s (3679 kB/s) 283s Reading package lists... 286s Reading package lists... 287s Building dependency tree... 287s Reading state information... 287s Calculating upgrade... 287s The following packages will be REMOVED: 287s libssl3 287s The following NEW packages will be installed: 287s libssl3t64 287s The following packages have been kept back: 287s curl 287s The following packages will be upgraded: 287s openssl 287s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 287s Need to get 3151 kB of archives. 287s After this operation, 73.7 kB of additional disk space will be used. 287s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu2 [1026 kB] 288s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu2 [2125 kB] 288s Fetched 3151 kB in 1s (3975 kB/s) 288s (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 ... 70156 files and directories currently installed.) 288s Preparing to unpack .../openssl_3.0.13-0ubuntu2_ppc64el.deb ... 288s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 288s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested: 288s wget depends on libssl3 (>= 3.0.0). 288s tnftp depends on libssl3 (>= 3.0.0). 288s tcpdump depends on libssl3 (>= 3.0.0). 288s systemd-resolved depends on libssl3 (>= 3.0.0). 288s systemd depends on libssl3 (>= 3.0.0). 288s sudo depends on libssl3 (>= 3.0.0). 288s rsync depends on libssl3 (>= 3.0.0). 288s python3-cryptography depends on libssl3 (>= 3.0.0). 288s openssh-server depends on libssl3 (>= 3.0.10). 288s openssh-client depends on libssl3 (>= 3.0.10). 288s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 288s libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0). 288s libssh-4:ppc64el depends on libssl3 (>= 3.0.0). 288s libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0). 288s libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0). 288s libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0). 288s libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0). 288s libnvme1 depends on libssl3 (>= 3.0.0). 288s libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0). 288s libkmod2:ppc64el depends on libssl3 (>= 3.0.0). 288s libfido2-1:ppc64el depends on libssl3 (>= 3.0.0). 288s libcurl4:ppc64el depends on libssl3 (>= 3.0.0). 288s libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0). 288s kmod depends on libssl3 (>= 3.0.0). 288s dhcpcd-base depends on libssl3 (>= 3.0.0). 288s bind9-libs:ppc64el depends on libssl3 (>= 3.0.0). 288s 288s (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 ... 70156 files and directories currently installed.) 288s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ... 288s Selecting previously unselected package libssl3t64:ppc64el. 288s (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 ... 70145 files and directories currently installed.) 288s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_ppc64el.deb ... 288s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 288s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 288s Setting up openssl (3.0.13-0ubuntu2) ... 288s Processing triggers for man-db (2.12.0-3) ... 289s Processing triggers for libc-bin (2.39-0ubuntu6) ... 289s Reading package lists... 289s Building dependency tree... 289s Reading state information... 290s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 290s sh: Attempting to set up Debian/Ubuntu apt sources automatically 290s sh: Distribution appears to be Ubuntu 291s Reading package lists... 291s Building dependency tree... 291s Reading state information... 292s eatmydata is already the newest version (131-1). 292s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 292s Reading package lists... 292s Building dependency tree... 292s Reading state information... 292s dbus is already the newest version (1.14.10-4ubuntu1). 292s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 292s Reading package lists... 292s Building dependency tree... 292s Reading state information... 292s rng-tools-debian is already the newest version (2.4). 292s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 292s Reading package lists... 293s Building dependency tree... 293s Reading state information... 293s The following packages will be REMOVED: 293s cloud-init* python3-configobj* python3-debconf* 293s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 293s After this operation, 3256 kB disk space will be freed. 293s (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 ... 70158 files and directories currently installed.) 293s Removing cloud-init (24.1.2-0ubuntu1) ... 294s Removing python3-configobj (5.0.8-3) ... 294s Removing python3-debconf (1.5.86) ... 294s Processing triggers for man-db (2.12.0-3) ... 294s (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 ... 69769 files and directories currently installed.) 294s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 295s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 295s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 295s invoke-rc.d: policy-rc.d denied execution of try-restart. 295s Reading package lists... 296s Building dependency tree... 296s Reading state information... 296s linux-generic is already the newest version (6.8.0-11.11+1). 296s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 296s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 296s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 296s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 299s Reading package lists... 299s Reading package lists... 299s Building dependency tree... 299s Reading state information... 299s Calculating upgrade... 299s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 300s Reading package lists... 300s Building dependency tree... 300s Reading state information... 300s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 300s autopkgtest [13:06:22]: rebooting testbed after setup commands that affected boot 466s autopkgtest [13:09:08]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 469s autopkgtest [13:09:11]: @@@@@@@@@@@@@@@@@@@@ apt-source qtltools 474s Get:1 http://ftpmaster.internal/ubuntu noble/universe qtltools 1.3.1+dfsg-4build1 (dsc) [2214 B] 474s Get:2 http://ftpmaster.internal/ubuntu noble/universe qtltools 1.3.1+dfsg-4build1 (tar) [141 kB] 474s Get:3 http://ftpmaster.internal/ubuntu noble/universe qtltools 1.3.1+dfsg-4build1 (diff) [13.6 MB] 474s gpgv: Signature made Tue Dec 19 15:02:56 2023 UTC 474s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 474s gpgv: Can't check signature: No public key 474s dpkg-source: warning: cannot verify inline signature for ./qtltools_1.3.1+dfsg-4build1.dsc: no acceptable signature found 475s autopkgtest [13:09:17]: testing package qtltools version 1.3.1+dfsg-4build1 478s autopkgtest [13:09:20]: build not needed 479s autopkgtest [13:09:21]: test run-sample-analysis: preparing testbed 485s Reading package lists... 486s Building dependency tree... 486s Reading state information... 486s Starting pkgProblemResolver with broken count: 0 486s Starting 2 pkgProblemResolver with broken count: 0 486s Done 486s The following additional packages will be installed: 486s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 486s libboost-iostreams1.83.0 libboost-program-options1.83.0 libcairo2 libdatrie1 486s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 libgsl27 486s libgslcblas0 libharfbuzz0b libhts3 libhtscodecs2 libice6 libjbig0 486s libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0 486s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 486s libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 486s libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6 486s qtltools qtltools-example r-base-core r-mathlib unzip x11-common xdg-utils 486s zip 486s Suggested packages: 486s gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html tcl8.6 tk8.6 486s elpa-ess r-doc-info | r-doc-pdf r-base-html 486s Recommended packages: 486s r-bioc-qvalue r-recommended r-base-dev r-doc-html libfile-mimeinfo-perl 486s libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils 486s The following NEW packages will be installed: 486s autopkgtest-satdep fontconfig fontconfig-config fonts-dejavu-core 486s fonts-dejavu-mono libblas3 libboost-iostreams1.83.0 486s libboost-program-options1.83.0 libcairo2 libdatrie1 libdeflate0 486s libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 libgsl27 libgslcblas0 486s libharfbuzz0b libhts3 libhtscodecs2 libice6 libjbig0 libjpeg-turbo8 libjpeg8 486s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 486s libpaper-utils libpaper1 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 486s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 486s libxft2 libxrender1 libxss1 libxt6 qtltools qtltools-example r-base-core 486s r-mathlib unzip x11-common xdg-utils zip 486s 0 upgraded, 54 newly installed, 0 to remove and 0 not upgraded. 486s Need to get 58.8 MB/58.8 MB of archives. 486s After this operation, 115 MB of additional disk space will be used. 486s Get:1 /tmp/autopkgtest.tCFqvK/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [712 B] 486s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB] 487s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB] 487s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el fontconfig-config ppc64el 2.15.0-1ubuntu1 [37.0 kB] 487s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el libfontconfig1 ppc64el 2.15.0-1ubuntu1 [190 kB] 487s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el fontconfig ppc64el 2.15.0-1ubuntu1 [192 kB] 488s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3 [227 kB] 488s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el libboost-iostreams1.83.0 ppc64el 1.83.0-2ubuntu1 [340 kB] 488s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el libboost-program-options1.83.0 ppc64el 1.83.0-2ubuntu1 [421 kB] 488s Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el libpixman-1-0 ppc64el 0.42.2-1 [300 kB] 488s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-render0 ppc64el 1.15-1 [17.2 kB] 488s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-shm0 ppc64el 1.15-1 [5896 B] 488s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1 [23.3 kB] 488s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el libcairo2 ppc64el 1.18.0-1 [735 kB] 489s Get:15 http://ftpmaster.internal/ubuntu noble/main ppc64el libdatrie1 ppc64el 0.2.13-3 [25.1 kB] 489s Get:16 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 489s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240303-1ubuntu1 [574 kB] 489s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240303-1ubuntu1 [161 kB] 489s Get:19 http://ftpmaster.internal/ubuntu noble/main ppc64el libgraphite2-3 ppc64el 1.3.14-2 [105 kB] 489s Get:20 http://ftpmaster.internal/ubuntu noble/universe ppc64el libgslcblas0 ppc64el 2.7.1+dfsg-6ubuntu1 [85.3 kB] 489s Get:21 http://ftpmaster.internal/ubuntu noble/universe ppc64el libgsl27 ppc64el 2.7.1+dfsg-6ubuntu1 [1064 kB] 489s Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el libharfbuzz0b ppc64el 8.3.0-2 [576 kB] 489s Get:23 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 489s Get:24 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB] 489s Get:25 http://ftpmaster.internal/ubuntu noble/main ppc64el x11-common all 1:7.7+23ubuntu2 [23.4 kB] 489s Get:26 http://ftpmaster.internal/ubuntu noble/main ppc64el libice6 ppc64el 2:1.0.10-1build2 [49.3 kB] 490s Get:27 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu1 [212 kB] 490s Get:28 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 490s Get:29 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3 [2804 kB] 490s Get:30 http://ftpmaster.internal/ubuntu noble/main ppc64el liblerc4 ppc64el 4.0.0+ds-4ubuntu1 [266 kB] 491s Get:31 http://ftpmaster.internal/ubuntu noble/main ppc64el libthai-data all 0.1.29-2 [158 kB] 491s Get:32 http://ftpmaster.internal/ubuntu noble/main ppc64el libthai0 ppc64el 0.1.29-2 [21.4 kB] 491s Get:33 http://ftpmaster.internal/ubuntu noble/main ppc64el libpango-1.0-0 ppc64el 1.51.0+ds-4 [266 kB] 491s Get:34 http://ftpmaster.internal/ubuntu noble/main ppc64el libpangoft2-1.0-0 ppc64el 1.51.0+ds-4 [49.5 kB] 491s Get:35 http://ftpmaster.internal/ubuntu noble/main ppc64el libpangocairo-1.0-0 ppc64el 1.51.0+ds-4 [31.2 kB] 491s Get:36 http://ftpmaster.internal/ubuntu noble/main ppc64el libpaper1 ppc64el 1.1.29 [13.5 kB] 491s Get:37 http://ftpmaster.internal/ubuntu noble/main ppc64el libpaper-utils ppc64el 1.1.29 [8710 B] 491s Get:38 http://ftpmaster.internal/ubuntu noble/main ppc64el libsharpyuv0 ppc64el 1.3.2-0.4 [28.7 kB] 491s Get:39 http://ftpmaster.internal/ubuntu noble/main ppc64el libsm6 ppc64el 2:1.2.3-1build2 [18.5 kB] 491s Get:40 http://ftpmaster.internal/ubuntu noble/main ppc64el libtcl8.6 ppc64el 8.6.13+dfsg-2 [1179 kB] 491s Get:41 http://ftpmaster.internal/ubuntu noble/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu1 [34.7 kB] 491s Get:42 http://ftpmaster.internal/ubuntu noble/main ppc64el libwebp7 ppc64el 1.3.2-0.4 [312 kB] 491s Get:43 http://ftpmaster.internal/ubuntu noble/main ppc64el libtiff6 ppc64el 4.5.1+git230720-3ubuntu1 [323 kB] 491s Get:44 http://ftpmaster.internal/ubuntu noble/main ppc64el libxft2 ppc64el 2.3.6-1 [59.8 kB] 491s Get:45 http://ftpmaster.internal/ubuntu noble/main ppc64el libxss1 ppc64el 1:1.2.3-1build2 [8982 B] 491s Get:46 http://ftpmaster.internal/ubuntu noble/main ppc64el libtk8.6 ppc64el 8.6.14-1 [944 kB] 492s Get:47 http://ftpmaster.internal/ubuntu noble/main ppc64el libxt6 ppc64el 1:1.2.1-1.1 [198 kB] 492s Get:48 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-mathlib ppc64el 4.3.2-1build1 [2425 kB] 492s Get:49 http://ftpmaster.internal/ubuntu noble/main ppc64el zip ppc64el 3.0-13 [192 kB] 492s Get:50 http://ftpmaster.internal/ubuntu noble/main ppc64el unzip ppc64el 6.0-28ubuntu3 [192 kB] 492s Get:51 http://ftpmaster.internal/ubuntu noble/main ppc64el xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 492s Get:52 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-base-core ppc64el 4.3.2-1build1 [27.4 MB] 500s Get:53 http://ftpmaster.internal/ubuntu noble/universe ppc64el qtltools ppc64el 1.3.1+dfsg-4build1 [823 kB] 501s Get:54 http://ftpmaster.internal/ubuntu noble/universe ppc64el qtltools-example all 1.3.1+dfsg-4build1 [13.6 MB] 505s Preconfiguring packages ... 505s Fetched 58.8 MB in 19s (3097 kB/s) 505s Selecting previously unselected package fonts-dejavu-mono. 505s (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 ... 69714 files and directories currently installed.) 505s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 505s Unpacking fonts-dejavu-mono (2.37-8) ... 506s Selecting previously unselected package fonts-dejavu-core. 506s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 506s Unpacking fonts-dejavu-core (2.37-8) ... 506s Selecting previously unselected package fontconfig-config. 506s Preparing to unpack .../02-fontconfig-config_2.15.0-1ubuntu1_ppc64el.deb ... 506s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 506s Selecting previously unselected package libfontconfig1:ppc64el. 506s Preparing to unpack .../03-libfontconfig1_2.15.0-1ubuntu1_ppc64el.deb ... 506s Unpacking libfontconfig1:ppc64el (2.15.0-1ubuntu1) ... 506s Selecting previously unselected package fontconfig. 506s Preparing to unpack .../04-fontconfig_2.15.0-1ubuntu1_ppc64el.deb ... 506s Unpacking fontconfig (2.15.0-1ubuntu1) ... 506s Selecting previously unselected package libblas3:ppc64el. 506s Preparing to unpack .../05-libblas3_3.12.0-3_ppc64el.deb ... 506s Unpacking libblas3:ppc64el (3.12.0-3) ... 506s Selecting previously unselected package libboost-iostreams1.83.0:ppc64el. 506s Preparing to unpack .../06-libboost-iostreams1.83.0_1.83.0-2ubuntu1_ppc64el.deb ... 506s Unpacking libboost-iostreams1.83.0:ppc64el (1.83.0-2ubuntu1) ... 506s Selecting previously unselected package libboost-program-options1.83.0:ppc64el. 506s Preparing to unpack .../07-libboost-program-options1.83.0_1.83.0-2ubuntu1_ppc64el.deb ... 506s Unpacking libboost-program-options1.83.0:ppc64el (1.83.0-2ubuntu1) ... 506s Selecting previously unselected package libpixman-1-0:ppc64el. 506s Preparing to unpack .../08-libpixman-1-0_0.42.2-1_ppc64el.deb ... 506s Unpacking libpixman-1-0:ppc64el (0.42.2-1) ... 506s Selecting previously unselected package libxcb-render0:ppc64el. 506s Preparing to unpack .../09-libxcb-render0_1.15-1_ppc64el.deb ... 506s Unpacking libxcb-render0:ppc64el (1.15-1) ... 506s Selecting previously unselected package libxcb-shm0:ppc64el. 506s Preparing to unpack .../10-libxcb-shm0_1.15-1_ppc64el.deb ... 506s Unpacking libxcb-shm0:ppc64el (1.15-1) ... 506s Selecting previously unselected package libxrender1:ppc64el. 506s Preparing to unpack .../11-libxrender1_1%3a0.9.10-1.1_ppc64el.deb ... 506s Unpacking libxrender1:ppc64el (1:0.9.10-1.1) ... 506s Selecting previously unselected package libcairo2:ppc64el. 506s 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.../22-libhts3_1.18+ds-1_ppc64el.deb ... 506s Unpacking libhts3:ppc64el (1.18+ds-1) ... 506s Selecting previously unselected package x11-common. 506s Preparing to unpack .../23-x11-common_1%3a7.7+23ubuntu2_all.deb ... 506s Unpacking x11-common (1:7.7+23ubuntu2) ... 506s Selecting previously unselected package libice6:ppc64el. 506s Preparing to unpack .../24-libice6_2%3a1.0.10-1build2_ppc64el.deb ... 506s Unpacking libice6:ppc64el (2:1.0.10-1build2) ... 506s Selecting previously unselected package libjpeg-turbo8:ppc64el. 506s Preparing to unpack .../25-libjpeg-turbo8_2.1.5-2ubuntu1_ppc64el.deb ... 506s Unpacking libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 506s Selecting previously unselected package libjpeg8:ppc64el. 506s Preparing to unpack .../26-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 506s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 506s Selecting previously unselected package liblapack3:ppc64el. 506s Preparing to unpack .../27-liblapack3_3.12.0-3_ppc64el.deb ... 506s Unpacking liblapack3:ppc64el (3.12.0-3) ... 506s Selecting previously unselected package liblerc4:ppc64el. 506s Preparing to unpack .../28-liblerc4_4.0.0+ds-4ubuntu1_ppc64el.deb ... 506s Unpacking liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ... 506s Selecting previously unselected package libthai-data. 506s Preparing to unpack .../29-libthai-data_0.1.29-2_all.deb ... 506s Unpacking libthai-data (0.1.29-2) ... 506s Selecting previously unselected package libthai0:ppc64el. 506s Preparing to unpack .../30-libthai0_0.1.29-2_ppc64el.deb ... 506s Unpacking libthai0:ppc64el (0.1.29-2) ... 506s Selecting previously unselected package libpango-1.0-0:ppc64el. 506s Preparing to unpack .../31-libpango-1.0-0_1.51.0+ds-4_ppc64el.deb ... 506s Unpacking libpango-1.0-0:ppc64el (1.51.0+ds-4) ... 506s Selecting previously unselected package libpangoft2-1.0-0:ppc64el. 506s Preparing to unpack .../32-libpangoft2-1.0-0_1.51.0+ds-4_ppc64el.deb ... 506s Unpacking libpangoft2-1.0-0:ppc64el (1.51.0+ds-4) ... 506s Selecting previously unselected package libpangocairo-1.0-0:ppc64el. 506s Preparing to unpack .../33-libpangocairo-1.0-0_1.51.0+ds-4_ppc64el.deb ... 506s Unpacking libpangocairo-1.0-0:ppc64el (1.51.0+ds-4) ... 506s Selecting previously unselected package libpaper1:ppc64el. 506s Preparing to unpack .../34-libpaper1_1.1.29_ppc64el.deb ... 506s Unpacking libpaper1:ppc64el (1.1.29) ... 506s Selecting previously unselected package libpaper-utils. 506s Preparing to unpack .../35-libpaper-utils_1.1.29_ppc64el.deb ... 506s Unpacking libpaper-utils (1.1.29) ... 506s Selecting previously unselected package libsharpyuv0:ppc64el. 506s Preparing to unpack .../36-libsharpyuv0_1.3.2-0.4_ppc64el.deb ... 506s Unpacking libsharpyuv0:ppc64el (1.3.2-0.4) ... 506s Selecting previously unselected package libsm6:ppc64el. 506s Preparing to unpack .../37-libsm6_2%3a1.2.3-1build2_ppc64el.deb ... 506s Unpacking libsm6:ppc64el (2:1.2.3-1build2) ... 507s Selecting previously unselected package libtcl8.6:ppc64el. 507s 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libboost-program-options1.83.0:ppc64el (1.83.0-2ubuntu1) ... 507s Setting up libpixman-1-0:ppc64el (0.42.2-1) ... 507s Setting up libsharpyuv0:ppc64el (1.3.2-0.4) ... 507s Setting up libpaper1:ppc64el (1.1.29) ... 508s 508s Creating config file /etc/papersize with new version 508s Setting up liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ... 508s Setting up libxrender1:ppc64el (1:0.9.10-1.1) ... 508s Setting up libdatrie1:ppc64el (0.2.13-3) ... 508s Setting up libgslcblas0:ppc64el (2.7.1+dfsg-6ubuntu1) ... 508s Setting up libxcb-render0:ppc64el (1.15-1) ... 508s Setting up unzip (6.0-28ubuntu3) ... 508s Setting up x11-common (1:7.7+23ubuntu2) ... 508s Setting up libdeflate0:ppc64el (1.19-1) ... 508s Setting up libgsl27:ppc64el (2.7.1+dfsg-6ubuntu1) ... 508s Setting up libxcb-shm0:ppc64el (1.15-1) ... 508s Setting up libpaper-utils (1.1.29) ... 508s Setting up libgomp1:ppc64el (14-20240303-1ubuntu1) ... 508s Setting up libjbig0:ppc64el (2.1-6.1ubuntu1) ... 508s Setting up zip (3.0-13) ... 508s Setting up libblas3:ppc64el (3.12.0-3) ... 508s 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 508s Setting up libboost-iostreams1.83.0:ppc64el (1.83.0-2ubuntu1) ... 508s Setting up fonts-dejavu-mono (2.37-8) ... 508s Setting up libtcl8.6:ppc64el (8.6.13+dfsg-2) ... 508s Setting up fonts-dejavu-core (2.37-8) ... 508s Setting up libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 508s Setting up libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 508s Setting up libwebp7:ppc64el (1.3.2-0.4) ... 508s Setting up r-mathlib (4.3.2-1build1) ... 508s Setting up libharfbuzz0b:ppc64el (8.3.0-2) ... 508s Setting up libthai-data (0.1.29-2) ... 508s Setting up libxss1:ppc64el (1:1.2.3-1build2) ... 508s Setting up xdg-utils (1.1.3-4.1ubuntu3) ... 508s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 508s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 508s Setting up libice6:ppc64el (2:1.0.10-1build2) ... 508s Setting up liblapack3:ppc64el (3.12.0-3) ... 508s 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 508s Setting up libhts3:ppc64el (1.18+ds-1) ... 508s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 508s Setting up libthai0:ppc64el (0.1.29-2) ... 508s Setting up libtiff6:ppc64el (4.5.1+git230720-3ubuntu1) ... 508s Setting up libfontconfig1:ppc64el (2.15.0-1ubuntu1) ... 508s Setting up libsm6:ppc64el (2:1.2.3-1build2) ... 508s Setting up fontconfig (2.15.0-1ubuntu1) ... 510s Regenerating fonts cache... done. 510s Setting up libxft2:ppc64el (2.3.6-1) ... 510s Setting up libtk8.6:ppc64el (8.6.14-1) ... 510s Setting up libpango-1.0-0:ppc64el (1.51.0+ds-4) ... 510s Setting up libcairo2:ppc64el (1.18.0-1) ... 510s Setting up libxt6:ppc64el (1:1.2.1-1.1) ... 510s Setting up libpangoft2-1.0-0:ppc64el (1.51.0+ds-4) ... 510s Setting up libpangocairo-1.0-0:ppc64el (1.51.0+ds-4) ... 510s Setting up r-base-core (4.3.2-1build1) ... 511s 511s Creating config file /etc/R/Renviron with new version 511s Setting up qtltools (1.3.1+dfsg-4build1) ... 511s Setting up autopkgtest-satdep (0) ... 511s Processing triggers for man-db (2.12.0-3) ... 512s Processing triggers for install-info (7.1-3) ... 512s Processing triggers for libc-bin (2.39-0ubuntu6) ... 515s (Reading database ... 71810 files and directories currently installed.) 515s Removing autopkgtest-satdep (0) ... 516s autopkgtest [13:09:58]: test run-sample-analysis: [----------------------- 516s ./genes.50percent.chr22.bed.gz 516s ./genes.50percent.chr22.bed.gz.tbi 516s ./genes.covariates.pc50.txt.gz 516s ./genes.simulated.chr22.bed.gz 516s ./genes.simulated.chr22.bed.gz.tbi 516s ./genotypes.chr22.vcf.gz 517s ./genotypes.chr22.vcf.gz.tbi 517s 517s QTLtools 517s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 517s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 517s * Webpage : https://qtltools.github.io/qtltools/ 517s * Version : 1.3.1 517s * Date : 24/03/2024 - 13:09:59 517s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 517s 517s CONDUCT PCA ON DATA 517s 517s Initialize random number generator 517s * Built-in seed is 15112011 517s * First Integer = 30553 517s * First Double = 0.0126695 517s 517s Reading sample list from [genes.50percent.chr22.bed.gz] 517s * #samples = 358 517s 517s Merging sample sets from all input files 517s * #files = 1 517s * #samples in all files = 358 517s 517s Reading phenotype data in [genes.50percent.chr22.bed.gz] 517s * 358 samples included 517s * 608 phenotypes included 517s 517s Calculating PCA with a matrix 358 x 608 517s * Calculated mean and sd 517s * 0 sd==0 columns removed 517s * Variables centered 517s * Variables scaled to unit variance 517s * Running SVD 518s * SVD complete 518s * Calculated sd and var for PCs 518s * Calculated cumulative var for PCs 518s * Done! 518s 518s Running time: 0 seconds 518s 518s QTLtools 518s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 518s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 518s * Webpage : https://qtltools.github.io/qtltools/ 518s * Version : 1.3.1 518s * Date : 24/03/2024 - 13:09:59 518s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 518s 518s MAPPING QTL IN CIS 518s * TASK: Report all nominal associations with p <= 0.01 518s * Linear model: Phe ~ Var + Cov 518s * Cis-window size is 1000000 bp 518s * Region = [chr22:17000000-18000000] 518s 518s Initialize random number generator 518s * Built-in seed is 15112011 518s * First Integer = 30553 518s * First Double = 0.0126695 518s 518s Reading sample list from [genes.50percent.chr22.bed.gz] 518s * #samples = 358 518s 518s Read sample list from [genotypes.chr22.vcf.gz] 518s * #samples = 358 518s 518s Reading sample list from [genes.covariates.pc50.txt.gz] 518s * #samples = 358 518s 518s Merging sample sets from all input files 518s * #files = 3 518s * #samples in all files = 358 518s 518s Reading phenotype data in [genes.50percent.chr22.bed.gz] 518s * target region [chr22:17000000-18000000] 518s * 8 phenotypes included 518s * 3 phenotypes are on the negative strand 518s 518s Reading genotype data in [genotypes.chr22.vcf.gz] 518s * File format detected: VCF 518s * target region [chr22:16000000-19000000] 518s * 6404 variants included 518s 518s Reading covariates in [genes.covariates.pc50.txt.gz] 518s * 53 covariates included 518s 518s Residualize phenotypes for covariates 518s * #covariates = 53 518s 518s Processing phenotype [ENSG00000237438.2] [1/8] 518s * #variants in cis = 5095 518s * Best hit: [id=22_17542810, d=25350, pv=1.1864e-25, s=-0.7518] 518s 518s Processing phenotype [ENSG00000273203.1] [2/8] 518s * #variants in cis = 5170 518s * Best hit: [id=22_17517388, d=-31323, pv=5.86611e-06, s=-0.1406] 518s 518s Processing phenotype [ENSG00000273442.1] [3/8] 518s * #variants in cis = 5188 518s * Best hit: [id=22_17553526, d=-8065, pv=0.000244522, s=0.1340] 518s 518s Processing phenotype [ENSG00000177663.9] [4/8] 518s * #variants in cis = 5193 518s * Best hit: [id=22_17513703, d=-52141, pv=8.03358e-14, s=-0.2096] 518s 518s Processing phenotype [ENSG00000183307.3] [5/8] 518s * #variants in cis = 5230 518s * Best hit: [id=22_17587975, d=14282, pv=1.56789e-07, s=-0.0078] 518s 518s Processing phenotype [ENSG00000069998.8] [6/8] 518s * #variants in cis = 5291 518s * Best hit: [id=22_17620429, d=25748, pv=1.37287e-14, s=-1.5147] 518s 518s Processing phenotype [ENSG00000093072.11] [7/8] 518s * #variants in cis = 5293 518s * Best hit: [id=22_17699630, d=3249, pv=0.000578649, s=0.6404] 518s 518s Processing phenotype [ENSG00000099954.14] [8/8] 518s * #variants in cis = 5435 518s * Best hit: [id=22_17175937, d=-664900, pv=0.000866455, s=0.0067] 518s 518s Running time: 0 seconds 518s 518s QTLtools 518s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 518s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 518s * Webpage : https://qtltools.github.io/qtltools/ 518s * Version : 1.3.1 518s * Date : 24/03/2024 - 13:10:00 518s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 518s 518s MAPPING QTL IN CIS 518s * TASK: Perform 1000 permutations 518s * Linear model: Phe ~ Var + Cov 518s * Cis-window size is 1000000 bp 518s * Region = [chr22:17000000-18000000] 518s 518s Initialize random number generator 518s * Built-in seed is 15112011 518s * First Integer = 30553 518s * First Double = 0.0126695 518s 518s Reading sample list from [genes.50percent.chr22.bed.gz] 518s * #samples = 358 518s 518s Read sample list from [genotypes.chr22.vcf.gz] 518s * #samples = 358 518s 518s Reading sample list from [genes.covariates.pc50.txt.gz] 518s * #samples = 358 518s 518s Merging sample sets from all input files 518s * #files = 3 518s * #samples in all files = 358 518s 518s Reading phenotype data in [genes.50percent.chr22.bed.gz] 518s * target region [chr22:17000000-18000000] 518s * 8 phenotypes included 518s * 3 phenotypes are on the negative strand 518s 518s Reading genotype data in [genotypes.chr22.vcf.gz] 518s * File format detected: VCF 518s * target region [chr22:16000000-19000000] 518s * 6404 variants included 518s 518s Reading covariates in [genes.covariates.pc50.txt.gz] 518s * 53 covariates included 518s 518s Residualize phenotypes for covariates 518s * #covariates = 53 518s 518s Processing phenotype [ENSG00000237438.2] [1/8] 518s * #variants in cis = 5095 519s * Best hit: [id=22_17542810, d=25350, pv=1.1864e-25, s=-0.7518] 519s * Beta parameters: [s1=1.00995, s2=621.053] 519s * Adjusted p-values: [emp=0.000999001, beta=1.28062e-20] 519s 519s Processing phenotype [ENSG00000273203.1] [2/8] 519s * #variants in cis = 5170 520s * Best hit: [id=22_17517388, d=-31323, pv=5.86611e-06, s=-0.1406] 520s * Beta parameters: [s1=1.11817, s2=641.379] 520s * Adjusted p-values: [emp=0.00799201, beta=0.00751892] 520s 520s Processing phenotype [ENSG00000273442.1] [3/8] 520s * #variants in cis = 5188 522s * Best hit: [id=22_17553526, d=-8065, pv=0.000244522, s=0.1340] 522s * Beta parameters: [s1=1.08364, s2=467.63] 522s * Adjusted p-values: [emp=0.297702, beta=0.293948] 522s 522s Processing phenotype [ENSG00000177663.9] [4/8] 522s * #variants in cis = 5193 523s * Best hit: [id=22_17513703, d=-52141, pv=8.03358e-14, s=-0.2096] 523s * Beta parameters: [s1=0.989061, s2=704.553] 523s * Adjusted p-values: [emp=0.000999001, beta=7.91291e-10] 523s 523s Processing phenotype [ENSG00000183307.3] [5/8] 523s * #variants in cis = 5230 524s * Best hit: [id=22_17587975, d=14282, pv=1.56789e-07, s=-0.0078] 524s * Beta parameters: [s1=1.01322, s2=559.49] 524s * Adjusted p-values: [emp=0.000999001, beta=0.00050707] 524s 524s Processing phenotype [ENSG00000069998.8] [6/8] 524s * #variants in cis = 5291 526s * Best hit: [id=22_17620429, d=25748, pv=1.37287e-14, s=-1.5147] 526s * Beta parameters: [s1=1.02312, s2=563.339] 526s * Adjusted p-values: [emp=0.000999001, beta=2.56935e-10] 526s 526s Processing phenotype [ENSG00000093072.11] [7/8] 526s * #variants in cis = 5293 527s * Best hit: [id=22_17699630, d=3249, pv=0.000578649, s=0.6404] 527s * Beta parameters: [s1=0.957514, s2=559.397] 527s * Adjusted p-values: [emp=0.574426, beta=0.562826] 527s 527s Processing phenotype [ENSG00000099954.14] [8/8] 527s * #variants in cis = 5435 528s * Best hit: [id=22_17175937, d=-664900, pv=0.000866455, s=0.0067] 528s * Beta parameters: [s1=0.938041, s2=226.852] 528s * Adjusted p-values: [emp=0.842158, beta=0.84836] 528s 528s Running time: 10 seconds 528s 528s QTLtools 528s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 528s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 528s * Webpage : https://qtltools.github.io/qtltools/ 528s * Version : 1.3.1 528s * Date : 24/03/2024 - 13:10:10 528s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 528s 528s MAPPING QTL IN TRANS 528s * TASK: Perform a full nominal pass, do not adjust p-values 528s * Cis-window size is 5000000 bp 528s * #bins = 1000 528s * threshold = 1e-05 528s 528s Initialize random number generator 528s * Built-in seed is 15112011 528s * First Integer = 30553 528s * First Double = 0.0126695 528s 528s Read sample list from [genotypes.chr22.vcf.gz] 528s * #samples = 358 528s 528s Checking sample list in [genes.simulated.chr22.bed.gz] 528s * #samples = 358 528s 528s Reading phenotype data in [genes.simulated.chr22.bed.gz] from line 0 to 0 528s * 358 samples included 528s * 608 phenotypes included 528s * 275 phenotypes is on the negative strand 528s 528s Calculate correlation threshold 528s * thres = 1e-05 528s * corr = 0.2311 528s 528s Sweep through genotype data in [genotypes.chr22.vcf.gz] 529s * #variants=1950 #multi_allelic=0 #not_processed=0 #hits=101/1000000 speed=3.28MT/s 529s * #variants=4001 #multi_allelic=0 #not_processed=0 #hits=153/2000000 speed=3.25MT/s 529s * #variants=6187 #multi_allelic=0 #not_processed=0 #hits=244/3000000 speed=3.21MT/s 530s * #variants=8537 #multi_allelic=0 #not_processed=0 #hits=285/4000000 speed=3.16MT/s 530s * #variants=11025 #multi_allelic=0 #not_processed=0 #hits=312/5000000 speed=3.12MT/s 530s * #variants=13621 #multi_allelic=0 #not_processed=0 #hits=320/6000000 speed=3.09MT/s 531s * #variants=16217 #multi_allelic=0 #not_processed=0 #hits=342/7000000 speed=3.02MT/s 531s * #variants=18755 #multi_allelic=0 #not_processed=0 #hits=401/8000000 speed=3.10MT/s 531s * #variants=21237 #multi_allelic=0 #not_processed=0 #hits=402/9000000 speed=3.12MT/s 531s * #variants=23680 #multi_allelic=0 #not_processed=0 #hits=455/10000000 speed=3.12MT/s 532s * #variants=26171 #multi_allelic=0 #not_processed=0 #hits=463/11000000 speed=3.11MT/s 532s * #variants=28609 #multi_allelic=0 #not_processed=0 #hits=469/12000000 speed=3.12MT/s 532s * #variants=30861 #multi_allelic=0 #not_processed=0 #hits=973/13000000 speed=3.15MT/s 533s * #variants=32932 #multi_allelic=0 #not_processed=0 #hits=979/14000000 speed=2.94MT/s 533s * #variants=34974 #multi_allelic=0 #not_processed=0 #hits=1085/15000000 speed=3.26MT/s 533s * #variants=37021 #multi_allelic=0 #not_processed=0 #hits=1086/16000000 speed=3.27MT/s 534s * #variants=39122 #multi_allelic=0 #not_processed=0 #hits=1089/17000000 speed=3.25MT/s 534s * #variants=41334 #multi_allelic=0 #not_processed=0 #hits=1089/18000000 speed=3.21MT/s 534s * #variants=43627 #multi_allelic=0 #not_processed=0 #hits=1096/19000000 speed=3.17MT/s 535s * #variants=45897 #multi_allelic=0 #not_processed=0 #hits=1153/20000000 speed=3.17MT/s 535s * #variants=48114 #multi_allelic=0 #not_processed=0 #hits=1243/21000000 speed=3.19MT/s 535s * #variants=50410 #multi_allelic=0 #not_processed=0 #hits=1249/22000000 speed=3.17MT/s 536s * #variants=52820 #multi_allelic=0 #not_processed=0 #hits=1259/23000000 speed=3.14MT/s 536s * #variants=55279 #multi_allelic=0 #not_processed=0 #hits=1498/24000000 speed=3.10MT/s 536s * #variants=57789 #multi_allelic=0 #not_processed=0 #hits=1724/25000000 speed=3.09MT/s 537s * #variants=60201 #multi_allelic=0 #not_processed=0 #hits=2168/26000000 speed=3.11MT/s 537s * #variants=62476 #multi_allelic=0 #not_processed=0 #hits=2452/27000000 speed=3.16MT/s 537s * #variants=64608 #multi_allelic=0 #not_processed=0 #hits=2544/28000000 speed=3.23MT/s 537s * #variants=66709 #multi_allelic=0 #not_processed=0 #hits=2684/29000000 speed=3.24MT/s 538s * #variants=68871 #multi_allelic=0 #not_processed=0 #hits=2688/30000000 speed=3.23MT/s 538s * #variants=71070 #multi_allelic=0 #not_processed=0 #hits=2720/31000000 speed=3.19MT/s 538s * #variants=73151 #multi_allelic=0 #not_processed=0 #hits=2891/32000000 speed=3.24MT/s 539s * #variants=75122 #multi_allelic=0 #not_processed=0 #hits=3110/33000000 speed=3.27MT/s 539s * #variants=77058 #multi_allelic=0 #not_processed=0 #hits=3209/34000000 speed=3.28MT/s 539s * #variants=78989 #multi_allelic=0 #not_processed=0 #hits=3218/35000000 speed=3.29MT/s 540s * #variants=80903 #multi_allelic=0 #not_processed=0 #hits=3250/36000000 speed=3.30MT/s 540s * #variants=82811 #multi_allelic=0 #not_processed=0 #hits=3463/37000000 speed=3.25MT/s 540s * #variants=84694 #multi_allelic=0 #not_processed=0 #hits=4035/38000000 speed=3.26MT/s 540s * #variants=85485 #multi_allelic=0 #not_processed=0 #hits=4036/38425275 speed=3.32MT/s 540s 540s Running time: 12 seconds 540s 540s QTLtools 540s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 540s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 540s * Webpage : https://qtltools.github.io/qtltools/ 540s * Version : 1.3.1 540s * Date : 24/03/2024 - 13:10:22 540s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 540s 540s MAPPING QTL IN TRANS 540s * TASK: Permute randomly chosen phenotypes 1000 times and test 540s * Cis-window size is 5000000 bp 540s * #bins = 1000 540s * threshold = 1e-05 540s 540s Initialize random number generator 540s * Built-in seed is 15112011 540s * First Integer = 30553 540s * First Double = 0.0126695 540s 540s Read sample list from [genotypes.chr22.vcf.gz] 540s * #samples = 358 540s 540s Checking sample list in [genes.simulated.chr22.bed.gz] 540s * #samples = 358 540s 540s Reading phenotype data in [genes.simulated.chr22.bed.gz] from line 0 to 0 540s * 358 samples included 541s * 608 phenotypes included 541s * 275 phenotypes is on the negative strand 541s 541s Normal transform phenotypes 541s 541s Calculate correlation threshold 541s * thres = 1e-05 541s * corr = 0.2311 541s 541s Sweep through genotype data in [genotypes.chr22.vcf.gz] 541s * #variants=1177 #multi_allelic=0 #not_processed=0 #hits=28/1000000 speed=3.45MT/s 541s * #variants=2383 #multi_allelic=0 #not_processed=0 #hits=38/2000000 speed=3.42MT/s 541s * #variants=3633 #multi_allelic=0 #not_processed=0 #hits=53/3000000 speed=3.39MT/s 542s * #variants=4928 #multi_allelic=0 #not_processed=0 #hits=53/4000000 speed=3.36MT/s 542s * #variants=6269 #multi_allelic=0 #not_processed=0 #hits=71/5000000 speed=3.31MT/s 542s * #variants=7675 #multi_allelic=0 #not_processed=0 #hits=72/6000000 speed=3.27MT/s 543s * #variants=9151 #multi_allelic=0 #not_processed=0 #hits=88/7000000 speed=3.23MT/s 543s * #variants=10663 #multi_allelic=0 #not_processed=0 #hits=96/8000000 speed=3.19MT/s 543s * #variants=12202 #multi_allelic=0 #not_processed=0 #hits=96/9000000 speed=3.17MT/s 544s * #variants=13804 #multi_allelic=0 #not_processed=0 #hits=96/10000000 speed=3.13MT/s 544s * #variants=15381 #multi_allelic=0 #not_processed=0 #hits=120/11000000 speed=3.14MT/s 544s * #variants=16946 #multi_allelic=0 #not_processed=0 #hits=123/12000000 speed=3.15MT/s 545s * #variants=18483 #multi_allelic=0 #not_processed=0 #hits=129/13000000 speed=3.17MT/s 545s * #variants=19995 #multi_allelic=0 #not_processed=0 #hits=131/14000000 speed=3.19MT/s 545s * #variants=21489 #multi_allelic=0 #not_processed=0 #hits=132/15000000 speed=3.22MT/s 545s * #variants=22947 #multi_allelic=0 #not_processed=0 #hits=151/16000000 speed=3.22MT/s 546s * #variants=24445 #multi_allelic=0 #not_processed=0 #hits=168/17000000 speed=3.19MT/s 546s * #variants=25965 #multi_allelic=0 #not_processed=0 #hits=175/18000000 speed=3.18MT/s 546s * #variants=27472 #multi_allelic=0 #not_processed=0 #hits=179/19000000 speed=3.18MT/s 547s * #variants=28933 #multi_allelic=0 #not_processed=0 #hits=181/20000000 speed=3.24MT/s 547s * #variants=30325 #multi_allelic=0 #not_processed=0 #hits=181/21000000 speed=3.28MT/s 547s * #variants=31617 #multi_allelic=0 #not_processed=0 #hits=182/22000000 speed=3.36MT/s 548s * #variants=32875 #multi_allelic=0 #not_processed=0 #hits=190/23000000 speed=3.39MT/s 548s * #variants=34127 #multi_allelic=0 #not_processed=0 #hits=192/24000000 speed=3.39MT/s 548s * #variants=35392 #multi_allelic=0 #not_processed=0 #hits=206/25000000 speed=3.36MT/s 549s * #variants=36652 #multi_allelic=0 #not_processed=0 #hits=206/26000000 speed=3.37MT/s 549s * #variants=37940 #multi_allelic=0 #not_processed=0 #hits=213/27000000 speed=3.36MT/s 549s * #variants=39255 #multi_allelic=0 #not_processed=0 #hits=238/28000000 speed=3.33MT/s 549s * #variants=40602 #multi_allelic=0 #not_processed=0 #hits=239/29000000 speed=3.32MT/s 550s * #variants=41998 #multi_allelic=0 #not_processed=0 #hits=245/30000000 speed=3.28MT/s 550s * #variants=43398 #multi_allelic=0 #not_processed=0 #hits=245/31000000 speed=3.28MT/s 550s * #variants=44803 #multi_allelic=0 #not_processed=0 #hits=260/32000000 speed=3.28MT/s 551s * #variants=46187 #multi_allelic=0 #not_processed=0 #hits=261/33000000 speed=3.29MT/s 551s * #variants=47545 #multi_allelic=0 #not_processed=0 #hits=268/34000000 speed=3.29MT/s 551s * #variants=48904 #multi_allelic=0 #not_processed=0 #hits=280/35000000 speed=3.29MT/s 552s * #variants=50309 #multi_allelic=0 #not_processed=0 #hits=306/36000000 speed=3.27MT/s 552s * #variants=51731 #multi_allelic=0 #not_processed=0 #hits=314/37000000 speed=3.26MT/s 552s * #variants=53171 #multi_allelic=0 #not_processed=0 #hits=320/38000000 speed=3.25MT/s 553s * #variants=54621 #multi_allelic=0 #not_processed=0 #hits=323/39000000 speed=3.23MT/s 553s * #variants=56099 #multi_allelic=0 #not_processed=0 #hits=323/40000000 speed=3.22MT/s 553s * #variants=57584 #multi_allelic=0 #not_processed=0 #hits=340/41000000 speed=3.22MT/s 553s * #variants=59032 #multi_allelic=0 #not_processed=0 #hits=344/42000000 speed=3.18MT/s 554s * #variants=60437 #multi_allelic=0 #not_processed=0 #hits=345/43000000 speed=3.28MT/s 554s * #variants=61810 #multi_allelic=0 #not_processed=0 #hits=357/44000000 speed=3.29MT/s 554s * #variants=63129 #multi_allelic=0 #not_processed=0 #hits=384/45000000 speed=3.34MT/s 555s * #variants=64409 #multi_allelic=0 #not_processed=0 #hits=391/46000000 speed=3.38MT/s 555s * #variants=65679 #multi_allelic=0 #not_processed=0 #hits=430/47000000 speed=3.38MT/s 555s * #variants=66953 #multi_allelic=0 #not_processed=0 #hits=436/48000000 speed=3.37MT/s 556s * #variants=68247 #multi_allelic=0 #not_processed=0 #hits=446/49000000 speed=3.34MT/s 556s * #variants=69595 #multi_allelic=0 #not_processed=0 #hits=460/50000000 speed=3.31MT/s 556s * #variants=70918 #multi_allelic=0 #not_processed=0 #hits=481/51000000 speed=3.29MT/s 556s * #variants=72211 #multi_allelic=0 #not_processed=0 #hits=492/52000000 speed=3.33MT/s 557s * #variants=73449 #multi_allelic=0 #not_processed=0 #hits=492/53000000 speed=3.40MT/s 557s * #variants=74662 #multi_allelic=0 #not_processed=0 #hits=500/54000000 speed=3.42MT/s 558s * #variants=75863 #multi_allelic=0 #not_processed=0 #hits=506/55000000 speed=3.44MT/s 558s * #variants=77058 #multi_allelic=0 #not_processed=0 #hits=513/56000000 speed=3.44MT/s 558s * #variants=78253 #multi_allelic=0 #not_processed=0 #hits=515/57000000 speed=3.44MT/s 558s * #variants=79446 #multi_allelic=0 #not_processed=0 #hits=530/58000000 speed=3.44MT/s 558s * #variants=80634 #multi_allelic=0 #not_processed=0 #hits=581/59000000 speed=3.44MT/s 559s * #variants=81817 #multi_allelic=0 #not_processed=0 #hits=594/60000000 speed=3.46MT/s 559s * #variants=82993 #multi_allelic=0 #not_processed=0 #hits=598/61000000 speed=3.47MT/s 559s * #variants=84160 #multi_allelic=0 #not_processed=0 #hits=599/62000000 speed=3.47MT/s 560s * #variants=85304 #multi_allelic=0 #not_processed=0 #hits=609/63000000 speed=3.47MT/s 560s * #variants=85485 #multi_allelic=0 #not_processed=0 #hits=609/63157827 speed=3.51MT/s 560s 560s Running time: 19 seconds 560s autopkgtest [13:10:42]: test run-sample-analysis: -----------------------] 561s run-sample-analysis PASS 561s autopkgtest [13:10:43]: test run-sample-analysis: - - - - - - - - - - results - - - - - - - - - - 561s autopkgtest [13:10:43]: @@@@@@@@@@@@@@@@@@@@ summary 561s run-sample-analysis PASS 609s Creating nova instance adt-noble-ppc64el-qtltools-20240324-130122-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240323.img (UUID ff8abf95-5243-4ea5-b7f5-3bf690534a1d)...