0s autopkgtest [09:56:12]: starting date and time: 2024-03-25 09:56:12+0000 0s autopkgtest [09:56:12]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [09:56:12]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.n6i743xn/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@bos01-ppc64el-6.secgroup --name adt-noble-ppc64el-qtltools-20240325-095612-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://us.ports.ubuntu.com/ubuntu-ports/ 145s autopkgtest [09:58:37]: testbed dpkg architecture: ppc64el 145s autopkgtest [09:58:37]: testbed apt version: 2.7.12 145s autopkgtest [09:58:37]: @@@@@@@@@@@@@@@@@@@@ test bed setup 146s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 147s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 147s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3987 kB] 147s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.8 kB] 147s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 147s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [700 kB] 147s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 147s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 147s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 147s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4271 kB] 147s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 147s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [62.3 kB] 147s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 151s Fetched 9710 kB in 2s (4180 kB/s) 151s Reading package lists... 154s Reading package lists... 154s Building dependency tree... 154s Reading state information... 154s Calculating upgrade... 154s The following packages will be REMOVED: 154s libssl3 154s The following NEW packages will be installed: 154s libssl3t64 154s The following packages have been kept back: 154s curl 154s The following packages will be upgraded: 154s openssl 154s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 154s Need to get 3151 kB of archives. 154s After this operation, 73.7 kB of additional disk space will be used. 154s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu2 [1026 kB] 155s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu2 [2125 kB] 155s Fetched 3151 kB in 1s (4443 kB/s) 155s (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.) 155s Preparing to unpack .../openssl_3.0.13-0ubuntu2_ppc64el.deb ... 155s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 155s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested: 155s wget depends on libssl3 (>= 3.0.0). 155s tnftp depends on libssl3 (>= 3.0.0). 155s tcpdump depends on libssl3 (>= 3.0.0). 155s systemd-resolved depends on libssl3 (>= 3.0.0). 155s systemd depends on libssl3 (>= 3.0.0). 155s sudo depends on libssl3 (>= 3.0.0). 155s rsync depends on libssl3 (>= 3.0.0). 155s python3-cryptography depends on libssl3 (>= 3.0.0). 155s openssh-server depends on libssl3 (>= 3.0.10). 155s openssh-client depends on libssl3 (>= 3.0.10). 155s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 155s libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0). 155s libssh-4:ppc64el depends on libssl3 (>= 3.0.0). 155s libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0). 155s libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0). 155s libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0). 155s libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0). 155s libnvme1 depends on libssl3 (>= 3.0.0). 155s libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0). 155s libkmod2:ppc64el depends on libssl3 (>= 3.0.0). 155s libfido2-1:ppc64el depends on libssl3 (>= 3.0.0). 155s libcurl4:ppc64el depends on libssl3 (>= 3.0.0). 155s libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0). 155s kmod depends on libssl3 (>= 3.0.0). 155s dhcpcd-base depends on libssl3 (>= 3.0.0). 155s bind9-libs:ppc64el depends on libssl3 (>= 3.0.0). 155s 155s (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.) 155s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ... 155s Selecting previously unselected package libssl3t64:ppc64el. 155s (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.) 155s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_ppc64el.deb ... 155s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 155s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 155s Setting up openssl (3.0.13-0ubuntu2) ... 155s Processing triggers for man-db (2.12.0-3) ... 156s Processing triggers for libc-bin (2.39-0ubuntu6) ... 156s Reading package lists... 156s Building dependency tree... 156s Reading state information... 156s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 159s sh: Attempting to set up Debian/Ubuntu apt sources automatically 159s Reading package lists...sh: Distribution appears to be Ubuntu 159s 159s Building dependency tree... 159s Reading state information... 159s eatmydata is already the newest version (131-1). 159s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 159s Reading package lists... 159s Building dependency tree... 159s Reading state information... 159s dbus is already the newest version (1.14.10-4ubuntu1). 159s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 159s Reading package lists... 159s Building dependency tree... 159s Reading state information... 159s rng-tools-debian is already the newest version (2.4). 159s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 159s Reading package lists... 159s Building dependency tree... 159s Reading state information... 159s The following packages will be REMOVED: 159s cloud-init* python3-configobj* python3-debconf* 159s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 159s After this operation, 3256 kB disk space will be freed. 159s (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.) 159s Removing cloud-init (24.1.2-0ubuntu1) ... 160s Removing python3-configobj (5.0.8-3) ... 160s Removing python3-debconf (1.5.86) ... 160s Processing triggers for man-db (2.12.0-3) ... 160s (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.) 160s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 161s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 161s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 161s invoke-rc.d: policy-rc.d denied execution of try-restart. 161s Reading package lists... 161s Building dependency tree... 161s Reading state information... 161s linux-generic is already the newest version (6.8.0-11.11+1). 161s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 162s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 162s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 162s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 164s Reading package lists... 164s Reading package lists... 164s Building dependency tree... 164s Reading state information... 164s Calculating upgrade... 164s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 165s Reading package lists... 165s Building dependency tree... 165s Reading state information... 165s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 165s autopkgtest [09:58:57]: rebooting testbed after setup commands that affected boot 331s autopkgtest [10:01:42]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 334s autopkgtest [10:01:46]: @@@@@@@@@@@@@@@@@@@@ apt-source qtltools 337s Get:1 http://ftpmaster.internal/ubuntu noble/universe qtltools 1.3.1+dfsg-4build1 (dsc) [2214 B] 337s Get:2 http://ftpmaster.internal/ubuntu noble/universe qtltools 1.3.1+dfsg-4build1 (tar) [141 kB] 337s Get:3 http://ftpmaster.internal/ubuntu noble/universe qtltools 1.3.1+dfsg-4build1 (diff) [13.6 MB] 337s gpgv: Signature made Tue Dec 19 15:02:56 2023 UTC 337s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 337s gpgv: Can't check signature: No public key 337s dpkg-source: warning: cannot verify inline signature for ./qtltools_1.3.1+dfsg-4build1.dsc: no acceptable signature found 338s autopkgtest [10:01:50]: testing package qtltools version 1.3.1+dfsg-4build1 346s autopkgtest [10:01:58]: build not needed 346s autopkgtest [10:01:58]: test run-sample-analysis: preparing testbed 353s Reading package lists... 353s Building dependency tree... 353s Reading state information... 353s Starting pkgProblemResolver with broken count: 0 353s Starting 2 pkgProblemResolver with broken count: 0 353s Done 353s The following additional packages will be installed: 353s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 353s libboost-iostreams1.83.0 libboost-program-options1.83.0 libcairo2 libdatrie1 353s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 libgsl27 353s libgslcblas0 libharfbuzz0b libhts3 libhtscodecs2 libice6 libjbig0 353s libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0 353s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 353s libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 353s libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6 353s qtltools qtltools-example r-base-core r-mathlib unzip x11-common xdg-utils 353s zip 353s Suggested packages: 353s gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html tcl8.6 tk8.6 353s elpa-ess r-doc-info | r-doc-pdf r-base-html 353s Recommended packages: 353s r-bioc-qvalue r-recommended r-base-dev r-doc-html libfile-mimeinfo-perl 353s libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils 353s The following NEW packages will be installed: 353s autopkgtest-satdep fontconfig fontconfig-config fonts-dejavu-core 353s fonts-dejavu-mono libblas3 libboost-iostreams1.83.0 353s libboost-program-options1.83.0 libcairo2 libdatrie1 libdeflate0 353s libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 libgsl27 libgslcblas0 353s libharfbuzz0b libhts3 libhtscodecs2 libice6 libjbig0 libjpeg-turbo8 libjpeg8 353s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 353s libpaper-utils libpaper1 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 353s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 353s libxft2 libxrender1 libxss1 libxt6 qtltools qtltools-example r-base-core 353s r-mathlib unzip x11-common xdg-utils zip 353s 0 upgraded, 54 newly installed, 0 to remove and 0 not upgraded. 353s Need to get 58.8 MB/58.8 MB of archives. 353s After this operation, 115 MB of additional disk space will be used. 353s Get:1 /tmp/autopkgtest.Z3CTMp/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [720 B] 353s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB] 354s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB] 354s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el fontconfig-config ppc64el 2.15.0-1ubuntu1 [37.0 kB] 354s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el libfontconfig1 ppc64el 2.15.0-1ubuntu1 [190 kB] 354s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el fontconfig ppc64el 2.15.0-1ubuntu1 [192 kB] 354s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3 [227 kB] 354s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el libboost-iostreams1.83.0 ppc64el 1.83.0-2ubuntu1 [340 kB] 354s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el libboost-program-options1.83.0 ppc64el 1.83.0-2ubuntu1 [421 kB] 354s Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el libpixman-1-0 ppc64el 0.42.2-1 [300 kB] 354s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-render0 ppc64el 1.15-1 [17.2 kB] 354s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-shm0 ppc64el 1.15-1 [5896 B] 354s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1 [23.3 kB] 354s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el libcairo2 ppc64el 1.18.0-1 [735 kB] 354s Get:15 http://ftpmaster.internal/ubuntu noble/main ppc64el libdatrie1 ppc64el 0.2.13-3 [25.1 kB] 354s Get:16 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 354s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240303-1ubuntu1 [574 kB] 354s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240303-1ubuntu1 [161 kB] 354s Get:19 http://ftpmaster.internal/ubuntu noble/main ppc64el libgraphite2-3 ppc64el 1.3.14-2 [105 kB] 354s Get:20 http://ftpmaster.internal/ubuntu noble/universe ppc64el libgslcblas0 ppc64el 2.7.1+dfsg-6ubuntu1 [85.3 kB] 354s Get:21 http://ftpmaster.internal/ubuntu noble/universe ppc64el libgsl27 ppc64el 2.7.1+dfsg-6ubuntu1 [1064 kB] 354s Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el libharfbuzz0b ppc64el 8.3.0-2 [576 kB] 354s Get:23 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 354s Get:24 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB] 354s Get:25 http://ftpmaster.internal/ubuntu noble/main ppc64el x11-common all 1:7.7+23ubuntu2 [23.4 kB] 354s Get:26 http://ftpmaster.internal/ubuntu noble/main ppc64el libice6 ppc64el 2:1.0.10-1build2 [49.3 kB] 354s Get:27 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu1 [212 kB] 354s Get:28 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 354s Get:29 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3 [2804 kB] 354s Get:30 http://ftpmaster.internal/ubuntu noble/main ppc64el liblerc4 ppc64el 4.0.0+ds-4ubuntu1 [266 kB] 354s Get:31 http://ftpmaster.internal/ubuntu noble/main ppc64el libthai-data all 0.1.29-2 [158 kB] 354s Get:32 http://ftpmaster.internal/ubuntu noble/main ppc64el libthai0 ppc64el 0.1.29-2 [21.4 kB] 354s Get:33 http://ftpmaster.internal/ubuntu noble/main ppc64el libpango-1.0-0 ppc64el 1.51.0+ds-4 [266 kB] 354s Get:34 http://ftpmaster.internal/ubuntu noble/main ppc64el libpangoft2-1.0-0 ppc64el 1.51.0+ds-4 [49.5 kB] 354s Get:35 http://ftpmaster.internal/ubuntu noble/main ppc64el libpangocairo-1.0-0 ppc64el 1.51.0+ds-4 [31.2 kB] 354s Get:36 http://ftpmaster.internal/ubuntu noble/main ppc64el libpaper1 ppc64el 1.1.29 [13.5 kB] 354s Get:37 http://ftpmaster.internal/ubuntu noble/main ppc64el libpaper-utils ppc64el 1.1.29 [8710 B] 354s Get:38 http://ftpmaster.internal/ubuntu noble/main ppc64el libsharpyuv0 ppc64el 1.3.2-0.4 [28.7 kB] 354s Get:39 http://ftpmaster.internal/ubuntu noble/main ppc64el libsm6 ppc64el 2:1.2.3-1build2 [18.5 kB] 354s Get:40 http://ftpmaster.internal/ubuntu noble/main ppc64el libtcl8.6 ppc64el 8.6.13+dfsg-2 [1179 kB] 354s Get:41 http://ftpmaster.internal/ubuntu noble/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu1 [34.7 kB] 354s Get:42 http://ftpmaster.internal/ubuntu noble/main ppc64el libwebp7 ppc64el 1.3.2-0.4 [312 kB] 354s Get:43 http://ftpmaster.internal/ubuntu noble/main ppc64el libtiff6 ppc64el 4.5.1+git230720-3ubuntu1 [323 kB] 354s Get:44 http://ftpmaster.internal/ubuntu noble/main ppc64el libxft2 ppc64el 2.3.6-1 [59.8 kB] 354s Get:45 http://ftpmaster.internal/ubuntu noble/main ppc64el libxss1 ppc64el 1:1.2.3-1build2 [8982 B] 354s Get:46 http://ftpmaster.internal/ubuntu noble/main ppc64el libtk8.6 ppc64el 8.6.14-1 [944 kB] 354s Get:47 http://ftpmaster.internal/ubuntu noble/main ppc64el libxt6 ppc64el 1:1.2.1-1.1 [198 kB] 354s Get:48 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-mathlib ppc64el 4.3.2-1build1 [2425 kB] 354s Get:49 http://ftpmaster.internal/ubuntu noble/main ppc64el zip ppc64el 3.0-13 [192 kB] 354s Get:50 http://ftpmaster.internal/ubuntu noble/main ppc64el unzip ppc64el 6.0-28ubuntu3 [192 kB] 354s Get:51 http://ftpmaster.internal/ubuntu noble/main ppc64el xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 355s Get:52 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-base-core ppc64el 4.3.2-1build1 [27.4 MB] 355s Get:53 http://ftpmaster.internal/ubuntu noble/universe ppc64el qtltools ppc64el 1.3.1+dfsg-4build1 [823 kB] 355s Get:54 http://ftpmaster.internal/ubuntu noble/universe ppc64el qtltools-example all 1.3.1+dfsg-4build1 [13.6 MB] 356s Preconfiguring packages ... 356s Fetched 58.8 MB in 2s (24.5 MB/s) 356s Selecting previously unselected package fonts-dejavu-mono. 356s (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.) 356s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 356s Unpacking fonts-dejavu-mono (2.37-8) ... 356s Selecting previously unselected package fonts-dejavu-core. 356s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 356s Unpacking fonts-dejavu-core (2.37-8) ... 356s Selecting previously unselected package fontconfig-config. 356s Preparing to unpack .../02-fontconfig-config_2.15.0-1ubuntu1_ppc64el.deb ... 356s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 356s Selecting previously unselected package libfontconfig1:ppc64el. 356s Preparing to unpack .../03-libfontconfig1_2.15.0-1ubuntu1_ppc64el.deb ... 356s Unpacking libfontconfig1:ppc64el (2.15.0-1ubuntu1) ... 356s Selecting previously unselected package fontconfig. 356s Preparing to unpack .../04-fontconfig_2.15.0-1ubuntu1_ppc64el.deb ... 356s Unpacking fontconfig (2.15.0-1ubuntu1) ... 356s Selecting previously unselected package libblas3:ppc64el. 356s Preparing to unpack .../05-libblas3_3.12.0-3_ppc64el.deb ... 356s Unpacking libblas3:ppc64el (3.12.0-3) ... 356s Selecting previously unselected package libboost-iostreams1.83.0:ppc64el. 356s Preparing to unpack .../06-libboost-iostreams1.83.0_1.83.0-2ubuntu1_ppc64el.deb ... 356s Unpacking libboost-iostreams1.83.0:ppc64el (1.83.0-2ubuntu1) ... 356s Selecting previously unselected package libboost-program-options1.83.0:ppc64el. 356s Preparing to unpack .../07-libboost-program-options1.83.0_1.83.0-2ubuntu1_ppc64el.deb ... 356s Unpacking libboost-program-options1.83.0:ppc64el (1.83.0-2ubuntu1) ... 356s Selecting previously unselected package libpixman-1-0:ppc64el. 356s Preparing to unpack .../08-libpixman-1-0_0.42.2-1_ppc64el.deb ... 356s Unpacking libpixman-1-0:ppc64el (0.42.2-1) ... 356s Selecting previously unselected package libxcb-render0:ppc64el. 356s Preparing to unpack .../09-libxcb-render0_1.15-1_ppc64el.deb ... 356s Unpacking libxcb-render0:ppc64el (1.15-1) ... 356s Selecting previously unselected package libxcb-shm0:ppc64el. 356s Preparing to unpack .../10-libxcb-shm0_1.15-1_ppc64el.deb ... 356s Unpacking libxcb-shm0:ppc64el (1.15-1) ... 356s Selecting previously unselected package libxrender1:ppc64el. 356s Preparing to unpack .../11-libxrender1_1%3a0.9.10-1.1_ppc64el.deb ... 356s Unpacking libxrender1:ppc64el (1:0.9.10-1.1) ... 356s Selecting previously unselected package libcairo2:ppc64el. 356s Preparing to unpack .../12-libcairo2_1.18.0-1_ppc64el.deb ... 356s Unpacking libcairo2:ppc64el (1.18.0-1) ... 356s Selecting previously unselected package libdatrie1:ppc64el. 356s Preparing to unpack .../13-libdatrie1_0.2.13-3_ppc64el.deb ... 356s Unpacking libdatrie1:ppc64el (0.2.13-3) ... 356s Selecting previously unselected package libdeflate0:ppc64el. 356s Preparing to unpack .../14-libdeflate0_1.19-1_ppc64el.deb ... 356s Unpacking libdeflate0:ppc64el (1.19-1) ... 356s Selecting previously unselected package libgfortran5:ppc64el. 356s Preparing to unpack .../15-libgfortran5_14-20240303-1ubuntu1_ppc64el.deb ... 356s Unpacking libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 356s Selecting previously unselected package libgomp1:ppc64el. 356s Preparing to unpack .../16-libgomp1_14-20240303-1ubuntu1_ppc64el.deb ... 356s Unpacking libgomp1:ppc64el (14-20240303-1ubuntu1) ... 356s Selecting previously unselected package libgraphite2-3:ppc64el. 356s Preparing to unpack .../17-libgraphite2-3_1.3.14-2_ppc64el.deb ... 356s Unpacking libgraphite2-3:ppc64el (1.3.14-2) ... 356s Selecting previously unselected package libgslcblas0:ppc64el. 356s Preparing to unpack .../18-libgslcblas0_2.7.1+dfsg-6ubuntu1_ppc64el.deb ... 356s Unpacking libgslcblas0:ppc64el (2.7.1+dfsg-6ubuntu1) ... 356s Selecting previously unselected package libgsl27:ppc64el. 356s Preparing to unpack .../19-libgsl27_2.7.1+dfsg-6ubuntu1_ppc64el.deb ... 356s Unpacking libgsl27:ppc64el (2.7.1+dfsg-6ubuntu1) ... 356s Selecting previously unselected package libharfbuzz0b:ppc64el. 356s Preparing to unpack .../20-libharfbuzz0b_8.3.0-2_ppc64el.deb ... 357s Unpacking libharfbuzz0b:ppc64el (8.3.0-2) ... 357s Selecting previously unselected package libhtscodecs2:ppc64el. 357s Preparing to unpack .../21-libhtscodecs2_1.6.0-1_ppc64el.deb ... 357s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 357s Selecting previously unselected package libhts3:ppc64el. 357s Preparing to unpack .../22-libhts3_1.18+ds-1_ppc64el.deb ... 357s Unpacking libhts3:ppc64el (1.18+ds-1) ... 357s Selecting previously unselected package x11-common. 357s Preparing to unpack .../23-x11-common_1%3a7.7+23ubuntu2_all.deb ... 357s Unpacking x11-common (1:7.7+23ubuntu2) ... 357s Selecting previously unselected package libice6:ppc64el. 357s Preparing to unpack .../24-libice6_2%3a1.0.10-1build2_ppc64el.deb ... 357s Unpacking libice6:ppc64el (2:1.0.10-1build2) ... 357s Selecting previously unselected package libjpeg-turbo8:ppc64el. 357s Preparing to unpack .../25-libjpeg-turbo8_2.1.5-2ubuntu1_ppc64el.deb ... 357s Unpacking libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 357s Selecting previously unselected package libjpeg8:ppc64el. 357s Preparing to unpack .../26-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 357s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 357s Selecting previously unselected package liblapack3:ppc64el. 357s Preparing to unpack .../27-liblapack3_3.12.0-3_ppc64el.deb ... 357s Unpacking liblapack3:ppc64el (3.12.0-3) ... 357s Selecting previously unselected package liblerc4:ppc64el. 357s Preparing to unpack .../28-liblerc4_4.0.0+ds-4ubuntu1_ppc64el.deb ... 357s Unpacking liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ... 357s Selecting previously unselected package libthai-data. 357s Preparing to unpack .../29-libthai-data_0.1.29-2_all.deb ... 357s Unpacking libthai-data (0.1.29-2) ... 357s Selecting previously unselected package libthai0:ppc64el. 357s Preparing to unpack .../30-libthai0_0.1.29-2_ppc64el.deb ... 357s Unpacking libthai0:ppc64el (0.1.29-2) ... 357s Selecting previously unselected package libpango-1.0-0:ppc64el. 357s Preparing to unpack .../31-libpango-1.0-0_1.51.0+ds-4_ppc64el.deb ... 357s Unpacking libpango-1.0-0:ppc64el (1.51.0+ds-4) ... 357s Selecting previously unselected package libpangoft2-1.0-0:ppc64el. 357s Preparing to unpack .../32-libpangoft2-1.0-0_1.51.0+ds-4_ppc64el.deb ... 357s Unpacking libpangoft2-1.0-0:ppc64el (1.51.0+ds-4) ... 357s Selecting previously unselected package libpangocairo-1.0-0:ppc64el. 357s Preparing to unpack .../33-libpangocairo-1.0-0_1.51.0+ds-4_ppc64el.deb ... 357s Unpacking libpangocairo-1.0-0:ppc64el (1.51.0+ds-4) ... 357s Selecting previously unselected package libpaper1:ppc64el. 357s Preparing to unpack .../34-libpaper1_1.1.29_ppc64el.deb ... 357s Unpacking libpaper1:ppc64el (1.1.29) ... 357s Selecting previously unselected package libpaper-utils. 357s Preparing to unpack .../35-libpaper-utils_1.1.29_ppc64el.deb ... 357s Unpacking libpaper-utils (1.1.29) ... 357s Selecting previously unselected package libsharpyuv0:ppc64el. 357s Preparing to unpack .../36-libsharpyuv0_1.3.2-0.4_ppc64el.deb ... 357s Unpacking libsharpyuv0:ppc64el (1.3.2-0.4) ... 357s Selecting previously unselected package libsm6:ppc64el. 357s Preparing to unpack .../37-libsm6_2%3a1.2.3-1build2_ppc64el.deb ... 357s Unpacking libsm6:ppc64el (2:1.2.3-1build2) ... 357s Selecting previously unselected package libtcl8.6:ppc64el. 357s Preparing to unpack .../38-libtcl8.6_8.6.13+dfsg-2_ppc64el.deb ... 357s Unpacking libtcl8.6:ppc64el (8.6.13+dfsg-2) ... 357s Selecting previously unselected package libjbig0:ppc64el. 357s Preparing to unpack .../39-libjbig0_2.1-6.1ubuntu1_ppc64el.deb ... 357s Unpacking libjbig0:ppc64el (2.1-6.1ubuntu1) ... 357s Selecting previously unselected package libwebp7:ppc64el. 357s Preparing to unpack .../40-libwebp7_1.3.2-0.4_ppc64el.deb ... 357s Unpacking libwebp7:ppc64el (1.3.2-0.4) ... 357s Selecting previously unselected package libtiff6:ppc64el. 357s Preparing to unpack .../41-libtiff6_4.5.1+git230720-3ubuntu1_ppc64el.deb ... 357s Unpacking libtiff6:ppc64el (4.5.1+git230720-3ubuntu1) ... 357s Selecting previously unselected package libxft2:ppc64el. 357s Preparing to unpack .../42-libxft2_2.3.6-1_ppc64el.deb ... 357s Unpacking libxft2:ppc64el (2.3.6-1) ... 357s Selecting previously unselected package libxss1:ppc64el. 357s Preparing to unpack .../43-libxss1_1%3a1.2.3-1build2_ppc64el.deb ... 357s Unpacking libxss1:ppc64el (1:1.2.3-1build2) ... 357s Selecting previously unselected package libtk8.6:ppc64el. 357s Preparing to unpack .../44-libtk8.6_8.6.14-1_ppc64el.deb ... 357s Unpacking libtk8.6:ppc64el (8.6.14-1) ... 357s Selecting previously unselected package libxt6:ppc64el. 357s Preparing to unpack .../45-libxt6_1%3a1.2.1-1.1_ppc64el.deb ... 357s Unpacking libxt6:ppc64el (1:1.2.1-1.1) ... 357s Selecting previously unselected package r-mathlib. 357s Preparing to unpack .../46-r-mathlib_4.3.2-1build1_ppc64el.deb ... 357s Unpacking r-mathlib (4.3.2-1build1) ... 357s Selecting previously unselected package zip. 357s Preparing to unpack .../47-zip_3.0-13_ppc64el.deb ... 357s Unpacking zip (3.0-13) ... 357s Selecting previously unselected package unzip. 357s Preparing to unpack .../48-unzip_6.0-28ubuntu3_ppc64el.deb ... 357s Unpacking unzip (6.0-28ubuntu3) ... 357s Selecting previously unselected package xdg-utils. 357s Preparing to unpack .../49-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 357s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 357s Selecting previously unselected package r-base-core. 357s Preparing to unpack .../50-r-base-core_4.3.2-1build1_ppc64el.deb ... 357s Unpacking r-base-core (4.3.2-1build1) ... 358s Selecting previously unselected package qtltools. 358s Preparing to unpack .../51-qtltools_1.3.1+dfsg-4build1_ppc64el.deb ... 358s Unpacking qtltools (1.3.1+dfsg-4build1) ... 358s Selecting previously unselected package qtltools-example. 358s Preparing to unpack .../52-qtltools-example_1.3.1+dfsg-4build1_all.deb ... 358s Unpacking qtltools-example (1.3.1+dfsg-4build1) ... 358s Selecting previously unselected package autopkgtest-satdep. 358s Preparing to unpack .../53-1-autopkgtest-satdep.deb ... 358s Unpacking autopkgtest-satdep (0) ... 358s Setting up libhtscodecs2:ppc64el (1.6.0-1) ... 358s Setting up libgraphite2-3:ppc64el (1.3.14-2) ... 358s Setting up qtltools-example (1.3.1+dfsg-4build1) ... 358s Setting up libboost-program-options1.83.0:ppc64el (1.83.0-2ubuntu1) ... 358s Setting up libpixman-1-0:ppc64el (0.42.2-1) ... 358s Setting up libsharpyuv0:ppc64el (1.3.2-0.4) ... 358s Setting up libpaper1:ppc64el (1.1.29) ... 358s 358s Creating config file /etc/papersize with new version 358s Setting up liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ... 358s Setting up libxrender1:ppc64el (1:0.9.10-1.1) ... 358s Setting up libdatrie1:ppc64el (0.2.13-3) ... 358s Setting up libgslcblas0:ppc64el (2.7.1+dfsg-6ubuntu1) ... 358s Setting up libxcb-render0:ppc64el (1.15-1) ... 358s Setting up unzip (6.0-28ubuntu3) ... 358s Setting up x11-common (1:7.7+23ubuntu2) ... 358s Setting up libdeflate0:ppc64el (1.19-1) ... 358s Setting up libgsl27:ppc64el (2.7.1+dfsg-6ubuntu1) ... 358s Setting up libxcb-shm0:ppc64el (1.15-1) ... 358s Setting up libpaper-utils (1.1.29) ... 358s Setting up libgomp1:ppc64el (14-20240303-1ubuntu1) ... 358s Setting up libjbig0:ppc64el (2.1-6.1ubuntu1) ... 358s Setting up zip (3.0-13) ... 358s Setting up libblas3:ppc64el (3.12.0-3) ... 358s 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 358s Setting up libboost-iostreams1.83.0:ppc64el (1.83.0-2ubuntu1) ... 358s Setting up fonts-dejavu-mono (2.37-8) ... 358s Setting up libtcl8.6:ppc64el (8.6.13+dfsg-2) ... 358s Setting up fonts-dejavu-core (2.37-8) ... 358s Setting up libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 358s Setting up libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 358s Setting up libwebp7:ppc64el (1.3.2-0.4) ... 358s Setting up r-mathlib (4.3.2-1build1) ... 358s Setting up libharfbuzz0b:ppc64el (8.3.0-2) ... 358s Setting up libthai-data (0.1.29-2) ... 358s Setting up libxss1:ppc64el (1:1.2.3-1build2) ... 358s Setting up xdg-utils (1.1.3-4.1ubuntu3) ... 358s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 358s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 358s Setting up libice6:ppc64el (2:1.0.10-1build2) ... 358s Setting up liblapack3:ppc64el (3.12.0-3) ... 358s 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 358s Setting up libhts3:ppc64el (1.18+ds-1) ... 358s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 359s Setting up libthai0:ppc64el (0.1.29-2) ... 359s Setting up libtiff6:ppc64el (4.5.1+git230720-3ubuntu1) ... 359s Setting up libfontconfig1:ppc64el (2.15.0-1ubuntu1) ... 359s Setting up libsm6:ppc64el (2:1.2.3-1build2) ... 359s Setting up fontconfig (2.15.0-1ubuntu1) ... 361s Regenerating fonts cache... done. 361s Setting up libxft2:ppc64el (2.3.6-1) ... 361s Setting up libtk8.6:ppc64el (8.6.14-1) ... 361s Setting up libpango-1.0-0:ppc64el (1.51.0+ds-4) ... 361s Setting up libcairo2:ppc64el (1.18.0-1) ... 361s Setting up libxt6:ppc64el (1:1.2.1-1.1) ... 361s Setting up libpangoft2-1.0-0:ppc64el (1.51.0+ds-4) ... 361s Setting up libpangocairo-1.0-0:ppc64el (1.51.0+ds-4) ... 361s Setting up r-base-core (4.3.2-1build1) ... 361s 361s Creating config file /etc/R/Renviron with new version 361s Setting up qtltools (1.3.1+dfsg-4build1) ... 361s Setting up autopkgtest-satdep (0) ... 361s Processing triggers for man-db (2.12.0-3) ... 362s Processing triggers for install-info (7.1-3) ... 362s Processing triggers for libc-bin (2.39-0ubuntu6) ... 365s (Reading database ... 71810 files and directories currently installed.) 365s Removing autopkgtest-satdep (0) ... 365s autopkgtest [10:02:17]: test run-sample-analysis: [----------------------- 366s ./genes.50percent.chr22.bed.gz 366s ./genes.50percent.chr22.bed.gz.tbi 366s ./genes.covariates.pc50.txt.gz 366s ./genes.simulated.chr22.bed.gz 366s ./genes.simulated.chr22.bed.gz.tbi 366s ./genotypes.chr22.vcf.gz 366s ./genotypes.chr22.vcf.gz.tbi 366s 366s QTLtools 366s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 366s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 366s * Webpage : https://qtltools.github.io/qtltools/ 366s * Version : 1.3.1 366s * Date : 25/03/2024 - 10:02:18 366s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 366s 366s CONDUCT PCA ON DATA 366s 366s Initialize random number generator 366s * Built-in seed is 15112011 366s * First Integer = 30553 366s * First Double = 0.0126695 366s 366s Reading sample list from [genes.50percent.chr22.bed.gz] 366s * #samples = 358 366s 366s Merging sample sets from all input files 366s * #files = 1 366s * #samples in all files = 358 366s 366s Reading phenotype data in [genes.50percent.chr22.bed.gz] 366s * 358 samples included 366s * 608 phenotypes included 366s 366s Calculating PCA with a matrix 358 x 608 366s * Calculated mean and sd 366s * 0 sd==0 columns removed 366s * Variables centered 366s * Variables scaled to unit variance 366s * Running SVD 367s * SVD complete 367s * Calculated sd and var for PCs 367s * Calculated cumulative var for PCs 367s * Done! 367s 367s Running time: 0 seconds 367s 367s QTLtools 367s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 367s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 367s * Webpage : https://qtltools.github.io/qtltools/ 367s * Version : 1.3.1 367s * Date : 25/03/2024 - 10:02:19 367s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 367s 367s MAPPING QTL IN CIS 367s * TASK: Report all nominal associations with p <= 0.01 367s * Linear model: Phe ~ Var + Cov 367s * Cis-window size is 1000000 bp 367s * Region = [chr22:17000000-18000000] 367s 367s Initialize random number generator 367s * Built-in seed is 15112011 367s * First Integer = 30553 367s * First Double = 0.0126695 367s 367s Reading sample list from [genes.50percent.chr22.bed.gz] 367s * #samples = 358 367s 367s Read sample list from [genotypes.chr22.vcf.gz] 367s * #samples = 358 367s 367s Reading sample list from [genes.covariates.pc50.txt.gz] 367s * #samples = 358 367s 367s Merging sample sets from all input files 367s * #files = 3 367s * #samples in all files = 358 367s 367s Reading phenotype data in [genes.50percent.chr22.bed.gz] 367s * target region [chr22:17000000-18000000] 367s * 8 phenotypes included 367s * 3 phenotypes are on the negative strand 367s 367s Reading genotype data in [genotypes.chr22.vcf.gz] 367s * File format detected: VCF 367s * target region [chr22:16000000-19000000] 367s * 6404 variants included 367s 367s Reading covariates in [genes.covariates.pc50.txt.gz] 367s * 53 covariates included 367s 367s Residualize phenotypes for covariates 367s * #covariates = 53 367s 367s Processing phenotype [ENSG00000237438.2] [1/8] 367s * #variants in cis = 5095 367s * Best hit: [id=22_17542810, d=25350, pv=1.1864e-25, s=-0.7518] 367s 367s Processing phenotype [ENSG00000273203.1] [2/8] 367s * #variants in cis = 5170 367s * Best hit: [id=22_17517388, d=-31323, pv=5.86611e-06, s=-0.1406] 367s 367s Processing phenotype [ENSG00000273442.1] [3/8] 367s * #variants in cis = 5188 367s * Best hit: [id=22_17553526, d=-8065, pv=0.000244522, s=0.1340] 367s 367s Processing phenotype [ENSG00000177663.9] [4/8] 367s * #variants in cis = 5193 367s * Best hit: [id=22_17513703, d=-52141, pv=8.03358e-14, s=-0.2096] 367s 367s Processing phenotype [ENSG00000183307.3] [5/8] 367s * #variants in cis = 5230 367s * Best hit: [id=22_17587975, d=14282, pv=1.56789e-07, s=-0.0078] 367s 367s Processing phenotype [ENSG00000069998.8] [6/8] 367s * #variants in cis = 5291 367s * Best hit: [id=22_17620429, d=25748, pv=1.37287e-14, s=-1.5147] 367s 367s Processing phenotype [ENSG00000093072.11] [7/8] 367s * #variants in cis = 5293 367s * Best hit: [id=22_17699630, d=3249, pv=0.000578649, s=0.6404] 367s 367s Processing phenotype [ENSG00000099954.14] [8/8] 367s * #variants in cis = 5435 367s * Best hit: [id=22_17175937, d=-664900, pv=0.000866455, s=0.0067] 367s 367s Running time: 0 seconds 367s 367s QTLtools 367s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 367s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 367s * Webpage : https://qtltools.github.io/qtltools/ 367s * Version : 1.3.1 367s * Date : 25/03/2024 - 10:02:19 367s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 367s 367s MAPPING QTL IN CIS 367s * TASK: Perform 1000 permutations 367s * Linear model: Phe ~ Var + Cov 367s * Cis-window size is 1000000 bp 367s * Region = [chr22:17000000-18000000] 367s 367s Initialize random number generator 367s * Built-in seed is 15112011 367s * First Integer = 30553 367s * First Double = 0.0126695 367s 367s Reading sample list from [genes.50percent.chr22.bed.gz] 367s * #samples = 358 367s 367s Read sample list from [genotypes.chr22.vcf.gz] 367s * #samples = 358 367s 367s Reading sample list from [genes.covariates.pc50.txt.gz] 367s * #samples = 358 367s 367s Merging sample sets from all input files 367s * #files = 3 367s * #samples in all files = 358 367s 367s Reading phenotype data in [genes.50percent.chr22.bed.gz] 367s * target region [chr22:17000000-18000000] 367s * 8 phenotypes included 367s * 3 phenotypes are on the negative strand 367s 367s Reading genotype data in [genotypes.chr22.vcf.gz] 367s * File format detected: VCF 367s * target region [chr22:16000000-19000000] 367s * 6404 variants included 367s 367s Reading covariates in [genes.covariates.pc50.txt.gz] 367s * 53 covariates included 367s 367s Residualize phenotypes for covariates 367s * #covariates = 53 367s 367s Processing phenotype [ENSG00000237438.2] [1/8] 367s * #variants in cis = 5095 369s * Best hit: [id=22_17542810, d=25350, pv=1.1864e-25, s=-0.7518] 369s * Beta parameters: [s1=1.00995, s2=621.053] 369s * Adjusted p-values: [emp=0.000999001, beta=1.28062e-20] 369s 369s Processing phenotype [ENSG00000273203.1] [2/8] 369s * #variants in cis = 5170 370s * Best hit: [id=22_17517388, d=-31323, pv=5.86611e-06, s=-0.1406] 370s * Beta parameters: [s1=1.11817, s2=641.379] 370s * Adjusted p-values: [emp=0.00799201, beta=0.00751892] 370s 370s Processing phenotype [ENSG00000273442.1] [3/8] 370s * #variants in cis = 5188 374s * Best hit: [id=22_17553526, d=-8065, pv=0.000244522, s=0.1340] 374s * Beta parameters: [s1=1.08364, s2=467.63] 374s * Adjusted p-values: [emp=0.297702, beta=0.293948] 374s 374s Processing phenotype [ENSG00000177663.9] [4/8] 374s * #variants in cis = 5193 374s * Best hit: [id=22_17513703, d=-52141, pv=8.03358e-14, s=-0.2096] 374s * Beta parameters: [s1=0.989061, s2=704.553] 374s * Adjusted p-values: [emp=0.000999001, beta=7.91291e-10] 374s 374s Processing phenotype [ENSG00000183307.3] [5/8] 374s * #variants in cis = 5230 374s * Best hit: [id=22_17587975, d=14282, pv=1.56789e-07, s=-0.0078] 374s * Beta parameters: [s1=1.01322, s2=559.49] 374s * Adjusted p-values: [emp=0.000999001, beta=0.00050707] 374s 374s Processing phenotype [ENSG00000069998.8] [6/8] 374s * #variants in cis = 5291 374s * Best hit: [id=22_17620429, d=25748, pv=1.37287e-14, s=-1.5147] 374s * Beta parameters: [s1=1.02312, s2=563.339] 374s * Adjusted p-values: [emp=0.000999001, beta=2.56935e-10] 374s 374s Processing phenotype [ENSG00000093072.11] [7/8] 374s * #variants in cis = 5293 375s * Best hit: [id=22_17699630, d=3249, pv=0.000578649, s=0.6404] 375s * Beta parameters: [s1=0.957514, s2=559.397] 375s * Adjusted p-values: [emp=0.574426, beta=0.562826] 375s 375s Processing phenotype [ENSG00000099954.14] [8/8] 375s * #variants in cis = 5435 377s * Best hit: [id=22_17175937, d=-664900, pv=0.000866455, s=0.0067] 377s * Beta parameters: [s1=0.938041, s2=226.852] 377s * Adjusted p-values: [emp=0.842158, beta=0.84836] 377s 377s Running time: 9 seconds 377s 377s QTLtools 377s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 377s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 377s * Webpage : https://qtltools.github.io/qtltools/ 377s * Version : 1.3.1 377s * Date : 25/03/2024 - 10:02:29 377s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 377s 377s MAPPING QTL IN TRANS 377s * TASK: Perform a full nominal pass, do not adjust p-values 377s * Cis-window size is 5000000 bp 377s * #bins = 1000 377s * threshold = 1e-05 377s 377s Initialize random number generator 377s * Built-in seed is 15112011 377s * First Integer = 30553 377s * First Double = 0.0126695 377s 377s Read sample list from [genotypes.chr22.vcf.gz] 377s * #samples = 358 377s 377s Checking sample list in [genes.simulated.chr22.bed.gz] 377s * #samples = 358 377s 377s Reading phenotype data in [genes.simulated.chr22.bed.gz] from line 0 to 0 377s * 358 samples included 377s * 608 phenotypes included 377s * 275 phenotypes is on the negative strand 377s 377s Calculate correlation threshold 377s * thres = 1e-05 377s * corr = 0.2311 377s 377s Sweep through genotype data in [genotypes.chr22.vcf.gz] 377s * #variants=1950 #multi_allelic=0 #not_processed=0 #hits=101/1000000 speed=3.66MT/s 377s * #variants=4001 #multi_allelic=0 #not_processed=0 #hits=153/2000000 speed=3.64MT/s 378s * #variants=6187 #multi_allelic=0 #not_processed=0 #hits=244/3000000 speed=3.58MT/s 378s * #variants=8537 #multi_allelic=0 #not_processed=0 #hits=285/4000000 speed=3.53MT/s 378s * #variants=11025 #multi_allelic=0 #not_processed=0 #hits=312/5000000 speed=3.47MT/s 378s * #variants=13621 #multi_allelic=0 #not_processed=0 #hits=320/6000000 speed=3.45MT/s 379s * #variants=16217 #multi_allelic=0 #not_processed=0 #hits=342/7000000 speed=3.45MT/s 379s * #variants=18755 #multi_allelic=0 #not_processed=0 #hits=401/8000000 speed=3.46MT/s 379s * #variants=21237 #multi_allelic=0 #not_processed=0 #hits=402/9000000 speed=3.47MT/s 380s * #variants=23680 #multi_allelic=0 #not_processed=0 #hits=455/10000000 speed=3.46MT/s 380s * #variants=26171 #multi_allelic=0 #not_processed=0 #hits=463/11000000 speed=3.48MT/s 380s * #variants=28609 #multi_allelic=0 #not_processed=0 #hits=469/12000000 speed=3.46MT/s 380s * #variants=30861 #multi_allelic=0 #not_processed=0 #hits=973/13000000 speed=3.52MT/s 381s * #variants=32932 #multi_allelic=0 #not_processed=0 #hits=979/14000000 speed=3.64MT/s 381s * #variants=34974 #multi_allelic=0 #not_processed=0 #hits=1085/15000000 speed=3.62MT/s 381s * #variants=37021 #multi_allelic=0 #not_processed=0 #hits=1086/16000000 speed=3.64MT/s 382s * #variants=39122 #multi_allelic=0 #not_processed=0 #hits=1089/17000000 speed=3.61MT/s 382s * #variants=41334 #multi_allelic=0 #not_processed=0 #hits=1089/18000000 speed=3.57MT/s 382s * #variants=43627 #multi_allelic=0 #not_processed=0 #hits=1096/19000000 speed=3.53MT/s 382s * #variants=45897 #multi_allelic=0 #not_processed=0 #hits=1153/20000000 speed=3.55MT/s 383s * #variants=48114 #multi_allelic=0 #not_processed=0 #hits=1243/21000000 speed=3.56MT/s 383s * #variants=50410 #multi_allelic=0 #not_processed=0 #hits=1249/22000000 speed=3.53MT/s 383s * #variants=52820 #multi_allelic=0 #not_processed=0 #hits=1259/23000000 speed=3.50MT/s 383s * #variants=55279 #multi_allelic=0 #not_processed=0 #hits=1498/24000000 speed=3.46MT/s 384s * #variants=57789 #multi_allelic=0 #not_processed=0 #hits=1724/25000000 speed=3.45MT/s 384s * #variants=60201 #multi_allelic=0 #not_processed=0 #hits=2168/26000000 speed=3.46MT/s 384s * #variants=62476 #multi_allelic=0 #not_processed=0 #hits=2452/27000000 speed=3.52MT/s 385s * #variants=64608 #multi_allelic=0 #not_processed=0 #hits=2544/28000000 speed=3.58MT/s 385s * #variants=66709 #multi_allelic=0 #not_processed=0 #hits=2684/29000000 speed=3.61MT/s 385s * #variants=68871 #multi_allelic=0 #not_processed=0 #hits=2688/30000000 speed=3.58MT/s 385s * #variants=71070 #multi_allelic=0 #not_processed=0 #hits=2720/31000000 speed=3.57MT/s 387s * #variants=73151 #multi_allelic=0 #not_processed=0 #hits=2891/32000000 speed=3.61MT/s 387s * #variants=75122 #multi_allelic=0 #not_processed=0 #hits=3110/33000000 speed=3.65MT/s 387s * #variants=77058 #multi_allelic=0 #not_processed=0 #hits=3209/34000000 speed=3.66MT/s 387s * #variants=78989 #multi_allelic=0 #not_processed=0 #hits=3218/35000000 speed=3.68MT/s 387s * #variants=80903 #multi_allelic=0 #not_processed=0 #hits=3250/36000000 speed=3.68MT/s 387s * #variants=82811 #multi_allelic=0 #not_processed=0 #hits=3463/37000000 speed=3.68MT/s 387s * #variants=84694 #multi_allelic=0 #not_processed=0 #hits=4035/38000000 speed=3.65MT/s 388s * #variants=85485 #multi_allelic=0 #not_processed=0 #hits=4036/38425275 speed=3.73MT/s 388s 388s Running time: 10 seconds 388s 388s QTLtools 388s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 388s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 388s * Webpage : https://qtltools.github.io/qtltools/ 388s * Version : 1.3.1 388s * Date : 25/03/2024 - 10:02:39 388s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 388s 388s MAPPING QTL IN TRANS 388s * TASK: Permute randomly chosen phenotypes 1000 times and test 388s * Cis-window size is 5000000 bp 388s * #bins = 1000 388s * threshold = 1e-05 388s 388s Initialize random number generator 388s * Built-in seed is 15112011 388s * First Integer = 30553 388s * First Double = 0.0126695 388s 388s Read sample list from [genotypes.chr22.vcf.gz] 388s * #samples = 358 388s 388s Checking sample list in [genes.simulated.chr22.bed.gz] 388s * #samples = 358 388s 388s Reading phenotype data in [genes.simulated.chr22.bed.gz] from line 0 to 0 388s * 358 samples included 388s * 608 phenotypes included 388s * 275 phenotypes is on the negative strand 388s 388s Normal transform phenotypes 388s 388s Calculate correlation threshold 388s * thres = 1e-05 388s * corr = 0.2311 388s 388s Sweep through genotype data in [genotypes.chr22.vcf.gz] 388s * #variants=1177 #multi_allelic=0 #not_processed=0 #hits=28/1000000 speed=3.86MT/s 388s * #variants=2383 #multi_allelic=0 #not_processed=0 #hits=38/2000000 speed=3.83MT/s 388s * #variants=3633 #multi_allelic=0 #not_processed=0 #hits=53/3000000 speed=3.80MT/s 389s * #variants=4928 #multi_allelic=0 #not_processed=0 #hits=53/4000000 speed=3.75MT/s 389s * #variants=6269 #multi_allelic=0 #not_processed=0 #hits=71/5000000 speed=3.70MT/s 389s * #variants=7675 #multi_allelic=0 #not_processed=0 #hits=72/6000000 speed=3.65MT/s 390s * #variants=9151 #multi_allelic=0 #not_processed=0 #hits=88/7000000 speed=3.58MT/s 390s * #variants=10663 #multi_allelic=0 #not_processed=0 #hits=96/8000000 speed=3.57MT/s 390s * #variants=12202 #multi_allelic=0 #not_processed=0 #hits=96/9000000 speed=3.50MT/s 390s * #variants=13804 #multi_allelic=0 #not_processed=0 #hits=96/10000000 speed=3.51MT/s 391s * #variants=15381 #multi_allelic=0 #not_processed=0 #hits=120/11000000 speed=3.52MT/s 391s * #variants=16946 #multi_allelic=0 #not_processed=0 #hits=123/12000000 speed=3.53MT/s 391s * #variants=18483 #multi_allelic=0 #not_processed=0 #hits=129/13000000 speed=3.55MT/s 392s * #variants=19995 #multi_allelic=0 #not_processed=0 #hits=131/14000000 speed=3.57MT/s 392s * #variants=21489 #multi_allelic=0 #not_processed=0 #hits=132/15000000 speed=3.62MT/s 392s * #variants=22947 #multi_allelic=0 #not_processed=0 #hits=151/16000000 speed=3.60MT/s 392s * #variants=24445 #multi_allelic=0 #not_processed=0 #hits=168/17000000 speed=3.58MT/s 393s * #variants=25965 #multi_allelic=0 #not_processed=0 #hits=175/18000000 speed=3.52MT/s 393s * #variants=27472 #multi_allelic=0 #not_processed=0 #hits=179/19000000 speed=3.57MT/s 393s * #variants=28933 #multi_allelic=0 #not_processed=0 #hits=181/20000000 speed=3.61MT/s 393s * #variants=30325 #multi_allelic=0 #not_processed=0 #hits=181/21000000 speed=3.68MT/s 394s * #variants=31617 #multi_allelic=0 #not_processed=0 #hits=182/22000000 speed=3.76MT/s 394s * #variants=32875 #multi_allelic=0 #not_processed=0 #hits=190/23000000 speed=3.80MT/s 394s * #variants=34127 #multi_allelic=0 #not_processed=0 #hits=192/24000000 speed=3.80MT/s 395s * #variants=35392 #multi_allelic=0 #not_processed=0 #hits=206/25000000 speed=3.79MT/s 395s * #variants=36652 #multi_allelic=0 #not_processed=0 #hits=206/26000000 speed=3.77MT/s 395s * #variants=37940 #multi_allelic=0 #not_processed=0 #hits=213/27000000 speed=3.73MT/s 395s * #variants=39255 #multi_allelic=0 #not_processed=0 #hits=238/28000000 speed=3.72MT/s 396s * #variants=40602 #multi_allelic=0 #not_processed=0 #hits=239/29000000 speed=3.64MT/s 396s * #variants=41998 #multi_allelic=0 #not_processed=0 #hits=245/30000000 speed=3.66MT/s 396s * #variants=43398 #multi_allelic=0 #not_processed=0 #hits=245/31000000 speed=3.60MT/s 396s * #variants=44803 #multi_allelic=0 #not_processed=0 #hits=260/32000000 speed=3.65MT/s 397s * #variants=46187 #multi_allelic=0 #not_processed=0 #hits=261/33000000 speed=3.68MT/s 397s * #variants=47545 #multi_allelic=0 #not_processed=0 #hits=268/34000000 speed=3.70MT/s 397s * #variants=48904 #multi_allelic=0 #not_processed=0 #hits=280/35000000 speed=3.69MT/s 398s * #variants=50309 #multi_allelic=0 #not_processed=0 #hits=306/36000000 speed=3.66MT/s 398s * #variants=51731 #multi_allelic=0 #not_processed=0 #hits=314/37000000 speed=3.64MT/s 398s * #variants=53171 #multi_allelic=0 #not_processed=0 #hits=320/38000000 speed=3.57MT/s 398s * #variants=54621 #multi_allelic=0 #not_processed=0 #hits=323/39000000 speed=3.61MT/s 399s * #variants=56099 #multi_allelic=0 #not_processed=0 #hits=323/40000000 speed=3.60MT/s 399s * #variants=57584 #multi_allelic=0 #not_processed=0 #hits=340/41000000 speed=3.58MT/s 399s * #variants=59032 #multi_allelic=0 #not_processed=0 #hits=344/42000000 speed=3.61MT/s 399s * #variants=60437 #multi_allelic=0 #not_processed=0 #hits=345/43000000 speed=3.65MT/s 400s * #variants=61810 #multi_allelic=0 #not_processed=0 #hits=357/44000000 speed=3.66MT/s 400s * #variants=63129 #multi_allelic=0 #not_processed=0 #hits=384/45000000 speed=3.73MT/s 400s * #variants=64409 #multi_allelic=0 #not_processed=0 #hits=391/46000000 speed=3.76MT/s 401s * #variants=65679 #multi_allelic=0 #not_processed=0 #hits=430/47000000 speed=3.77MT/s 401s * #variants=66953 #multi_allelic=0 #not_processed=0 #hits=436/48000000 speed=3.77MT/s 401s * #variants=68247 #multi_allelic=0 #not_processed=0 #hits=446/49000000 speed=3.76MT/s 401s * #variants=69595 #multi_allelic=0 #not_processed=0 #hits=460/50000000 speed=3.72MT/s 402s * #variants=70918 #multi_allelic=0 #not_processed=0 #hits=481/51000000 speed=3.73MT/s 402s * #variants=72211 #multi_allelic=0 #not_processed=0 #hits=492/52000000 speed=3.76MT/s 402s * #variants=73449 #multi_allelic=0 #not_processed=0 #hits=492/53000000 speed=3.82MT/s 402s * #variants=74662 #multi_allelic=0 #not_processed=0 #hits=500/54000000 speed=3.83MT/s 403s * #variants=75863 #multi_allelic=0 #not_processed=0 #hits=506/55000000 speed=3.83MT/s 403s * #variants=77058 #multi_allelic=0 #not_processed=0 #hits=513/56000000 speed=3.85MT/s 403s * #variants=78253 #multi_allelic=0 #not_processed=0 #hits=515/57000000 speed=3.85MT/s 403s * #variants=79446 #multi_allelic=0 #not_processed=0 #hits=530/58000000 speed=3.83MT/s 404s * #variants=80634 #multi_allelic=0 #not_processed=0 #hits=581/59000000 speed=3.86MT/s 404s * #variants=81817 #multi_allelic=0 #not_processed=0 #hits=594/60000000 speed=3.86MT/s 404s * #variants=82993 #multi_allelic=0 #not_processed=0 #hits=598/61000000 speed=3.86MT/s 404s * #variants=84160 #multi_allelic=0 #not_processed=0 #hits=599/62000000 speed=3.86MT/s 405s * #variants=85304 #multi_allelic=0 #not_processed=0 #hits=609/63000000 speed=3.83MT/s 405s * #variants=85485 #multi_allelic=0 #not_processed=0 #hits=609/63157827 speed=3.76MT/s 405s 405s Running time: 17 seconds 405s autopkgtest [10:02:57]: test run-sample-analysis: -----------------------] 406s run-sample-analysis PASS 406s autopkgtest [10:02:58]: test run-sample-analysis: - - - - - - - - - - results - - - - - - - - - - 406s autopkgtest [10:02:58]: @@@@@@@@@@@@@@@@@@@@ summary 406s run-sample-analysis PASS 425s Creating nova instance adt-noble-ppc64el-qtltools-20240325-095612-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240325.img (UUID 2c4a456c-136a-4a3a-993e-7f82eda3b6c0)...