0s autopkgtest [23:42:22]: starting date and time: 2024-03-24 23:42:22+0000 0s autopkgtest [23:42:22]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [23:42:22]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.b5brkwfc/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-3@bos02-ppc64el-10.secgroup --name adt-noble-ppc64el-qtltools-20240324-234219-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 270s autopkgtest [23:46:52]: testbed dpkg architecture: ppc64el 270s autopkgtest [23:46:52]: testbed apt version: 2.7.12 270s autopkgtest [23:46:52]: @@@@@@@@@@@@@@@@@@@@ test bed setup 271s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 272s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 272s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 272s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3986 kB] 272s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.5 kB] 272s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [701 kB] 272s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 272s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 272s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 272s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4271 kB] 273s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 273s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [62.6 kB] 273s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 276s Fetched 9710 kB in 3s (3784 kB/s) 276s Reading package lists... 279s Reading package lists... 279s Building dependency tree... 279s Reading state information... 279s Calculating upgrade... 280s The following packages will be REMOVED: 280s libssl3 280s The following NEW packages will be installed: 280s libssl3t64 280s The following packages have been kept back: 280s curl 280s The following packages will be upgraded: 280s openssl 280s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 280s Need to get 3151 kB of archives. 280s After this operation, 73.7 kB of additional disk space will be used. 280s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu2 [1026 kB] 280s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu2 [2125 kB] 281s Fetched 3151 kB in 1s (4197 kB/s) 281s (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.) 281s Preparing to unpack .../openssl_3.0.13-0ubuntu2_ppc64el.deb ... 281s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 281s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested: 281s wget depends on libssl3 (>= 3.0.0). 281s tnftp depends on libssl3 (>= 3.0.0). 281s tcpdump depends on libssl3 (>= 3.0.0). 281s systemd-resolved depends on libssl3 (>= 3.0.0). 281s systemd depends on libssl3 (>= 3.0.0). 281s sudo depends on libssl3 (>= 3.0.0). 281s rsync depends on libssl3 (>= 3.0.0). 281s python3-cryptography depends on libssl3 (>= 3.0.0). 281s openssh-server depends on libssl3 (>= 3.0.10). 281s openssh-client depends on libssl3 (>= 3.0.10). 281s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 281s libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0). 281s libssh-4:ppc64el depends on libssl3 (>= 3.0.0). 281s libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0). 281s libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0). 281s libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0). 281s libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0). 281s libnvme1 depends on libssl3 (>= 3.0.0). 281s libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0). 281s libkmod2:ppc64el depends on libssl3 (>= 3.0.0). 281s libfido2-1:ppc64el depends on libssl3 (>= 3.0.0). 281s libcurl4:ppc64el depends on libssl3 (>= 3.0.0). 281s libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0). 281s kmod depends on libssl3 (>= 3.0.0). 281s dhcpcd-base depends on libssl3 (>= 3.0.0). 281s bind9-libs:ppc64el depends on libssl3 (>= 3.0.0). 281s 281s (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.) 281s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ... 281s Selecting previously unselected package libssl3t64:ppc64el. 281s (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.) 281s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_ppc64el.deb ... 281s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 281s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 281s Setting up openssl (3.0.13-0ubuntu2) ... 281s Processing triggers for man-db (2.12.0-3) ... 282s Processing triggers for libc-bin (2.39-0ubuntu6) ... 282s Reading package lists... 282s Building dependency tree... 282s Reading state information... 282s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 283s sh: Attempting to set up Debian/Ubuntu apt sources automatically 283s sh: Distribution appears to be Ubuntu 284s Reading package lists... 284s Building dependency tree... 284s Reading state information... 284s eatmydata is already the newest version (131-1). 284s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 284s Reading package lists... 284s Building dependency tree... 284s Reading state information... 285s dbus is already the newest version (1.14.10-4ubuntu1). 285s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 285s Reading package lists... 285s Building dependency tree... 285s Reading state information... 285s rng-tools-debian is already the newest version (2.4). 285s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 285s Reading package lists... 285s Building dependency tree... 285s Reading state information... 285s The following packages will be REMOVED: 285s cloud-init* python3-configobj* python3-debconf* 286s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 286s After this operation, 3256 kB disk space will be freed. 286s (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.) 286s Removing cloud-init (24.1.2-0ubuntu1) ... 286s Removing python3-configobj (5.0.8-3) ... 286s Removing python3-debconf (1.5.86) ... 286s Processing triggers for man-db (2.12.0-3) ... 287s (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.) 287s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 287s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 287s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 287s invoke-rc.d: policy-rc.d denied execution of try-restart. 288s Reading package lists... 288s Building dependency tree... 288s Reading state information... 288s linux-generic is already the newest version (6.8.0-11.11+1). 288s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 288s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 288s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 288s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 291s Reading package lists... 291s Reading package lists... 291s Building dependency tree... 291s Reading state information... 292s Calculating upgrade... 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 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 293s autopkgtest [23:47:15]: rebooting testbed after setup commands that affected boot 334s autopkgtest [23:47:56]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 337s autopkgtest [23:47:59]: @@@@@@@@@@@@@@@@@@@@ apt-source qtltools 340s Get:1 http://ftpmaster.internal/ubuntu noble/universe qtltools 1.3.1+dfsg-4build1 (dsc) [2214 B] 340s Get:2 http://ftpmaster.internal/ubuntu noble/universe qtltools 1.3.1+dfsg-4build1 (tar) [141 kB] 340s Get:3 http://ftpmaster.internal/ubuntu noble/universe qtltools 1.3.1+dfsg-4build1 (diff) [13.6 MB] 340s gpgv: Signature made Tue Dec 19 15:02:56 2023 UTC 340s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 340s gpgv: Can't check signature: No public key 340s dpkg-source: warning: cannot verify inline signature for ./qtltools_1.3.1+dfsg-4build1.dsc: no acceptable signature found 341s autopkgtest [23:48:03]: testing package qtltools version 1.3.1+dfsg-4build1 342s autopkgtest [23:48:04]: build not needed 343s autopkgtest [23:48:05]: test run-sample-analysis: preparing testbed 344s Reading package lists... 344s Building dependency tree... 344s Reading state information... 345s Starting pkgProblemResolver with broken count: 0 345s Starting 2 pkgProblemResolver with broken count: 0 345s Done 345s The following additional packages will be installed: 345s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 345s libboost-iostreams1.83.0 libboost-program-options1.83.0 libcairo2 libdatrie1 345s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 libgsl27 345s libgslcblas0 libharfbuzz0b libhts3 libhtscodecs2 libice6 libjbig0 345s libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0 345s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 345s libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 345s libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6 345s qtltools qtltools-example r-base-core r-mathlib unzip x11-common xdg-utils 345s zip 345s Suggested packages: 345s gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html tcl8.6 tk8.6 345s elpa-ess r-doc-info | r-doc-pdf r-base-html 345s Recommended packages: 345s r-bioc-qvalue r-recommended r-base-dev r-doc-html libfile-mimeinfo-perl 345s libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils 345s The following NEW packages will be installed: 345s autopkgtest-satdep fontconfig fontconfig-config fonts-dejavu-core 345s fonts-dejavu-mono libblas3 libboost-iostreams1.83.0 345s libboost-program-options1.83.0 libcairo2 libdatrie1 libdeflate0 345s libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 libgsl27 libgslcblas0 345s libharfbuzz0b libhts3 libhtscodecs2 libice6 libjbig0 libjpeg-turbo8 libjpeg8 345s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 345s libpaper-utils libpaper1 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 345s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 345s libxft2 libxrender1 libxss1 libxt6 qtltools qtltools-example r-base-core 345s r-mathlib unzip x11-common xdg-utils zip 345s 0 upgraded, 54 newly installed, 0 to remove and 0 not upgraded. 345s Need to get 58.8 MB/58.8 MB of archives. 345s After this operation, 115 MB of additional disk space will be used. 345s Get:1 /tmp/autopkgtest.1zpbUa/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [716 B] 345s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB] 345s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB] 345s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el fontconfig-config ppc64el 2.15.0-1ubuntu1 [37.0 kB] 345s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el libfontconfig1 ppc64el 2.15.0-1ubuntu1 [190 kB] 345s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el fontconfig ppc64el 2.15.0-1ubuntu1 [192 kB] 345s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3 [227 kB] 345s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el libboost-iostreams1.83.0 ppc64el 1.83.0-2ubuntu1 [340 kB] 345s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el libboost-program-options1.83.0 ppc64el 1.83.0-2ubuntu1 [421 kB] 346s Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el libpixman-1-0 ppc64el 0.42.2-1 [300 kB] 346s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-render0 ppc64el 1.15-1 [17.2 kB] 346s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-shm0 ppc64el 1.15-1 [5896 B] 346s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1 [23.3 kB] 346s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el libcairo2 ppc64el 1.18.0-1 [735 kB] 346s Get:15 http://ftpmaster.internal/ubuntu noble/main ppc64el libdatrie1 ppc64el 0.2.13-3 [25.1 kB] 346s Get:16 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 346s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240303-1ubuntu1 [574 kB] 346s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240303-1ubuntu1 [161 kB] 346s Get:19 http://ftpmaster.internal/ubuntu noble/main ppc64el libgraphite2-3 ppc64el 1.3.14-2 [105 kB] 346s Get:20 http://ftpmaster.internal/ubuntu noble/universe ppc64el libgslcblas0 ppc64el 2.7.1+dfsg-6ubuntu1 [85.3 kB] 346s Get:21 http://ftpmaster.internal/ubuntu noble/universe ppc64el libgsl27 ppc64el 2.7.1+dfsg-6ubuntu1 [1064 kB] 346s Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el libharfbuzz0b ppc64el 8.3.0-2 [576 kB] 346s Get:23 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 346s Get:24 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB] 346s Get:25 http://ftpmaster.internal/ubuntu noble/main ppc64el x11-common all 1:7.7+23ubuntu2 [23.4 kB] 346s Get:26 http://ftpmaster.internal/ubuntu noble/main ppc64el libice6 ppc64el 2:1.0.10-1build2 [49.3 kB] 346s Get:27 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu1 [212 kB] 346s Get:28 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 346s Get:29 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3 [2804 kB] 346s Get:30 http://ftpmaster.internal/ubuntu noble/main ppc64el liblerc4 ppc64el 4.0.0+ds-4ubuntu1 [266 kB] 346s Get:31 http://ftpmaster.internal/ubuntu noble/main ppc64el libthai-data all 0.1.29-2 [158 kB] 346s Get:32 http://ftpmaster.internal/ubuntu noble/main ppc64el libthai0 ppc64el 0.1.29-2 [21.4 kB] 346s Get:33 http://ftpmaster.internal/ubuntu noble/main ppc64el libpango-1.0-0 ppc64el 1.51.0+ds-4 [266 kB] 346s Get:34 http://ftpmaster.internal/ubuntu noble/main ppc64el libpangoft2-1.0-0 ppc64el 1.51.0+ds-4 [49.5 kB] 346s Get:35 http://ftpmaster.internal/ubuntu noble/main ppc64el libpangocairo-1.0-0 ppc64el 1.51.0+ds-4 [31.2 kB] 346s Get:36 http://ftpmaster.internal/ubuntu noble/main ppc64el libpaper1 ppc64el 1.1.29 [13.5 kB] 346s Get:37 http://ftpmaster.internal/ubuntu noble/main ppc64el libpaper-utils ppc64el 1.1.29 [8710 B] 346s Get:38 http://ftpmaster.internal/ubuntu noble/main ppc64el libsharpyuv0 ppc64el 1.3.2-0.4 [28.7 kB] 346s Get:39 http://ftpmaster.internal/ubuntu noble/main ppc64el libsm6 ppc64el 2:1.2.3-1build2 [18.5 kB] 346s Get:40 http://ftpmaster.internal/ubuntu noble/main ppc64el libtcl8.6 ppc64el 8.6.13+dfsg-2 [1179 kB] 346s Get:41 http://ftpmaster.internal/ubuntu noble/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu1 [34.7 kB] 346s Get:42 http://ftpmaster.internal/ubuntu noble/main ppc64el libwebp7 ppc64el 1.3.2-0.4 [312 kB] 346s Get:43 http://ftpmaster.internal/ubuntu noble/main ppc64el libtiff6 ppc64el 4.5.1+git230720-3ubuntu1 [323 kB] 346s Get:44 http://ftpmaster.internal/ubuntu noble/main ppc64el libxft2 ppc64el 2.3.6-1 [59.8 kB] 346s Get:45 http://ftpmaster.internal/ubuntu noble/main ppc64el libxss1 ppc64el 1:1.2.3-1build2 [8982 B] 346s Get:46 http://ftpmaster.internal/ubuntu noble/main ppc64el libtk8.6 ppc64el 8.6.14-1 [944 kB] 346s Get:47 http://ftpmaster.internal/ubuntu noble/main ppc64el libxt6 ppc64el 1:1.2.1-1.1 [198 kB] 346s Get:48 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-mathlib ppc64el 4.3.2-1build1 [2425 kB] 346s Get:49 http://ftpmaster.internal/ubuntu noble/main ppc64el zip ppc64el 3.0-13 [192 kB] 346s Get:50 http://ftpmaster.internal/ubuntu noble/main ppc64el unzip ppc64el 6.0-28ubuntu3 [192 kB] 346s Get:51 http://ftpmaster.internal/ubuntu noble/main ppc64el xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 346s Get:52 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-base-core ppc64el 4.3.2-1build1 [27.4 MB] 347s Get:53 http://ftpmaster.internal/ubuntu noble/universe ppc64el qtltools ppc64el 1.3.1+dfsg-4build1 [823 kB] 347s Get:54 http://ftpmaster.internal/ubuntu noble/universe ppc64el qtltools-example all 1.3.1+dfsg-4build1 [13.6 MB] 348s Preconfiguring packages ... 348s Fetched 58.8 MB in 3s (22.7 MB/s) 348s Selecting previously unselected package fonts-dejavu-mono. 348s (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.) 348s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 348s Unpacking fonts-dejavu-mono (2.37-8) ... 348s Selecting previously unselected package fonts-dejavu-core. 348s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 348s Unpacking fonts-dejavu-core (2.37-8) ... 348s Selecting previously unselected package fontconfig-config. 348s Preparing to unpack .../02-fontconfig-config_2.15.0-1ubuntu1_ppc64el.deb ... 348s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 348s Selecting previously unselected package libfontconfig1:ppc64el. 348s Preparing to unpack .../03-libfontconfig1_2.15.0-1ubuntu1_ppc64el.deb ... 348s Unpacking libfontconfig1:ppc64el (2.15.0-1ubuntu1) ... 348s Selecting previously unselected package fontconfig. 348s Preparing to unpack .../04-fontconfig_2.15.0-1ubuntu1_ppc64el.deb ... 348s Unpacking fontconfig (2.15.0-1ubuntu1) ... 348s Selecting previously unselected package libblas3:ppc64el. 348s Preparing to unpack .../05-libblas3_3.12.0-3_ppc64el.deb ... 348s Unpacking libblas3:ppc64el (3.12.0-3) ... 348s Selecting previously unselected package libboost-iostreams1.83.0:ppc64el. 348s Preparing to unpack .../06-libboost-iostreams1.83.0_1.83.0-2ubuntu1_ppc64el.deb ... 348s Unpacking libboost-iostreams1.83.0:ppc64el (1.83.0-2ubuntu1) ... 348s Selecting previously unselected package libboost-program-options1.83.0:ppc64el. 348s Preparing to unpack .../07-libboost-program-options1.83.0_1.83.0-2ubuntu1_ppc64el.deb ... 348s Unpacking libboost-program-options1.83.0:ppc64el (1.83.0-2ubuntu1) ... 348s Selecting previously unselected package libpixman-1-0:ppc64el. 348s Preparing to unpack .../08-libpixman-1-0_0.42.2-1_ppc64el.deb ... 348s Unpacking libpixman-1-0:ppc64el (0.42.2-1) ... 348s Selecting previously unselected package libxcb-render0:ppc64el. 348s Preparing to unpack .../09-libxcb-render0_1.15-1_ppc64el.deb ... 348s Unpacking libxcb-render0:ppc64el (1.15-1) ... 348s Selecting previously unselected package libxcb-shm0:ppc64el. 348s Preparing to unpack .../10-libxcb-shm0_1.15-1_ppc64el.deb ... 348s Unpacking libxcb-shm0:ppc64el (1.15-1) ... 348s Selecting previously unselected package libxrender1:ppc64el. 348s Preparing to unpack .../11-libxrender1_1%3a0.9.10-1.1_ppc64el.deb ... 348s Unpacking libxrender1:ppc64el (1:0.9.10-1.1) ... 348s Selecting previously unselected package libcairo2:ppc64el. 348s Preparing to unpack .../12-libcairo2_1.18.0-1_ppc64el.deb ... 348s Unpacking libcairo2:ppc64el (1.18.0-1) ... 348s Selecting previously unselected package libdatrie1:ppc64el. 348s Preparing to unpack .../13-libdatrie1_0.2.13-3_ppc64el.deb ... 348s Unpacking libdatrie1:ppc64el (0.2.13-3) ... 348s Selecting previously unselected package libdeflate0:ppc64el. 348s Preparing to unpack .../14-libdeflate0_1.19-1_ppc64el.deb ... 348s Unpacking libdeflate0:ppc64el (1.19-1) ... 348s Selecting previously unselected package libgfortran5:ppc64el. 348s Preparing to unpack .../15-libgfortran5_14-20240303-1ubuntu1_ppc64el.deb ... 348s Unpacking libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 348s Selecting previously unselected package libgomp1:ppc64el. 348s Preparing to unpack .../16-libgomp1_14-20240303-1ubuntu1_ppc64el.deb ... 348s Unpacking libgomp1:ppc64el (14-20240303-1ubuntu1) ... 348s Selecting previously unselected package libgraphite2-3:ppc64el. 348s Preparing to unpack .../17-libgraphite2-3_1.3.14-2_ppc64el.deb ... 348s Unpacking libgraphite2-3:ppc64el (1.3.14-2) ... 348s Selecting previously unselected package libgslcblas0:ppc64el. 348s Preparing to unpack .../18-libgslcblas0_2.7.1+dfsg-6ubuntu1_ppc64el.deb ... 348s Unpacking libgslcblas0:ppc64el (2.7.1+dfsg-6ubuntu1) ... 348s Selecting previously unselected package libgsl27:ppc64el. 348s Preparing to unpack .../19-libgsl27_2.7.1+dfsg-6ubuntu1_ppc64el.deb ... 348s Unpacking libgsl27:ppc64el (2.7.1+dfsg-6ubuntu1) ... 348s Selecting previously unselected package libharfbuzz0b:ppc64el. 348s Preparing to unpack .../20-libharfbuzz0b_8.3.0-2_ppc64el.deb ... 348s Unpacking libharfbuzz0b:ppc64el (8.3.0-2) ... 349s Selecting previously unselected package libhtscodecs2:ppc64el. 349s Preparing to unpack .../21-libhtscodecs2_1.6.0-1_ppc64el.deb ... 349s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 349s Selecting previously unselected package libhts3:ppc64el. 349s Preparing to unpack .../22-libhts3_1.18+ds-1_ppc64el.deb ... 349s Unpacking libhts3:ppc64el (1.18+ds-1) ... 349s Selecting previously unselected package x11-common. 349s Preparing to unpack .../23-x11-common_1%3a7.7+23ubuntu2_all.deb ... 349s Unpacking x11-common (1:7.7+23ubuntu2) ... 349s Selecting previously unselected package libice6:ppc64el. 349s Preparing to unpack .../24-libice6_2%3a1.0.10-1build2_ppc64el.deb ... 349s Unpacking libice6:ppc64el (2:1.0.10-1build2) ... 349s Selecting previously unselected package libjpeg-turbo8:ppc64el. 349s Preparing to unpack .../25-libjpeg-turbo8_2.1.5-2ubuntu1_ppc64el.deb ... 349s Unpacking libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 349s Selecting previously unselected package libjpeg8:ppc64el. 349s Preparing to unpack .../26-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 349s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 349s Selecting previously unselected package liblapack3:ppc64el. 349s Preparing to unpack .../27-liblapack3_3.12.0-3_ppc64el.deb ... 349s Unpacking liblapack3:ppc64el (3.12.0-3) ... 349s Selecting previously unselected package liblerc4:ppc64el. 349s Preparing to unpack .../28-liblerc4_4.0.0+ds-4ubuntu1_ppc64el.deb ... 349s Unpacking liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ... 349s Selecting previously unselected package libthai-data. 349s Preparing to unpack .../29-libthai-data_0.1.29-2_all.deb ... 349s Unpacking libthai-data (0.1.29-2) ... 349s Selecting previously unselected package libthai0:ppc64el. 349s Preparing to unpack .../30-libthai0_0.1.29-2_ppc64el.deb ... 349s Unpacking libthai0:ppc64el (0.1.29-2) ... 349s Selecting previously unselected package libpango-1.0-0:ppc64el. 349s Preparing to unpack .../31-libpango-1.0-0_1.51.0+ds-4_ppc64el.deb ... 349s Unpacking libpango-1.0-0:ppc64el (1.51.0+ds-4) ... 349s Selecting previously unselected package libpangoft2-1.0-0:ppc64el. 349s Preparing to unpack .../32-libpangoft2-1.0-0_1.51.0+ds-4_ppc64el.deb ... 349s Unpacking libpangoft2-1.0-0:ppc64el (1.51.0+ds-4) ... 349s Selecting previously unselected package libpangocairo-1.0-0:ppc64el. 349s Preparing to unpack .../33-libpangocairo-1.0-0_1.51.0+ds-4_ppc64el.deb ... 349s Unpacking libpangocairo-1.0-0:ppc64el (1.51.0+ds-4) ... 349s Selecting previously unselected package libpaper1:ppc64el. 349s Preparing to unpack .../34-libpaper1_1.1.29_ppc64el.deb ... 349s Unpacking libpaper1:ppc64el (1.1.29) ... 349s Selecting previously unselected package libpaper-utils. 349s Preparing to unpack .../35-libpaper-utils_1.1.29_ppc64el.deb ... 349s Unpacking libpaper-utils (1.1.29) ... 349s Selecting previously unselected package libsharpyuv0:ppc64el. 349s Preparing to unpack .../36-libsharpyuv0_1.3.2-0.4_ppc64el.deb ... 349s Unpacking libsharpyuv0:ppc64el (1.3.2-0.4) ... 349s Selecting previously unselected package libsm6:ppc64el. 349s Preparing to unpack .../37-libsm6_2%3a1.2.3-1build2_ppc64el.deb ... 349s Unpacking libsm6:ppc64el (2:1.2.3-1build2) ... 349s Selecting previously unselected package libtcl8.6:ppc64el. 349s Preparing to unpack .../38-libtcl8.6_8.6.13+dfsg-2_ppc64el.deb ... 349s Unpacking libtcl8.6:ppc64el (8.6.13+dfsg-2) ... 349s Selecting previously unselected package libjbig0:ppc64el. 349s Preparing to unpack .../39-libjbig0_2.1-6.1ubuntu1_ppc64el.deb ... 349s Unpacking libjbig0:ppc64el (2.1-6.1ubuntu1) ... 349s Selecting previously unselected package libwebp7:ppc64el. 349s Preparing to unpack .../40-libwebp7_1.3.2-0.4_ppc64el.deb ... 349s Unpacking libwebp7:ppc64el (1.3.2-0.4) ... 349s Selecting previously unselected package libtiff6:ppc64el. 349s Preparing to unpack .../41-libtiff6_4.5.1+git230720-3ubuntu1_ppc64el.deb ... 349s Unpacking libtiff6:ppc64el (4.5.1+git230720-3ubuntu1) ... 349s Selecting previously unselected package libxft2:ppc64el. 349s Preparing to unpack .../42-libxft2_2.3.6-1_ppc64el.deb ... 349s Unpacking libxft2:ppc64el (2.3.6-1) ... 349s Selecting previously unselected package libxss1:ppc64el. 349s Preparing to unpack .../43-libxss1_1%3a1.2.3-1build2_ppc64el.deb ... 349s Unpacking libxss1:ppc64el (1:1.2.3-1build2) ... 349s Selecting previously unselected package libtk8.6:ppc64el. 349s Preparing to unpack .../44-libtk8.6_8.6.14-1_ppc64el.deb ... 349s Unpacking libtk8.6:ppc64el (8.6.14-1) ... 349s Selecting previously unselected package libxt6:ppc64el. 349s Preparing to unpack .../45-libxt6_1%3a1.2.1-1.1_ppc64el.deb ... 349s Unpacking libxt6:ppc64el (1:1.2.1-1.1) ... 349s Selecting previously unselected package r-mathlib. 349s Preparing to unpack .../46-r-mathlib_4.3.2-1build1_ppc64el.deb ... 349s Unpacking r-mathlib (4.3.2-1build1) ... 349s Selecting previously unselected package zip. 349s Preparing to unpack .../47-zip_3.0-13_ppc64el.deb ... 349s Unpacking zip (3.0-13) ... 349s Selecting previously unselected package unzip. 349s Preparing to unpack .../48-unzip_6.0-28ubuntu3_ppc64el.deb ... 349s Unpacking unzip (6.0-28ubuntu3) ... 349s Selecting previously unselected package xdg-utils. 349s Preparing to unpack .../49-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 349s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 349s Selecting previously unselected package r-base-core. 349s Preparing to unpack .../50-r-base-core_4.3.2-1build1_ppc64el.deb ... 349s Unpacking r-base-core (4.3.2-1build1) ... 350s Selecting previously unselected package qtltools. 350s Preparing to unpack .../51-qtltools_1.3.1+dfsg-4build1_ppc64el.deb ... 350s Unpacking qtltools (1.3.1+dfsg-4build1) ... 350s Selecting previously unselected package qtltools-example. 350s Preparing to unpack .../52-qtltools-example_1.3.1+dfsg-4build1_all.deb ... 350s Unpacking qtltools-example (1.3.1+dfsg-4build1) ... 350s Selecting previously unselected package autopkgtest-satdep. 350s Preparing to unpack .../53-1-autopkgtest-satdep.deb ... 350s Unpacking autopkgtest-satdep (0) ... 350s Setting up libhtscodecs2:ppc64el (1.6.0-1) ... 350s Setting up libgraphite2-3:ppc64el (1.3.14-2) ... 350s Setting up qtltools-example (1.3.1+dfsg-4build1) ... 350s Setting up libboost-program-options1.83.0:ppc64el (1.83.0-2ubuntu1) ... 350s Setting up libpixman-1-0:ppc64el (0.42.2-1) ... 350s Setting up libsharpyuv0:ppc64el (1.3.2-0.4) ... 350s Setting up libpaper1:ppc64el (1.1.29) ... 350s 350s Creating config file /etc/papersize with new version 350s Setting up liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ... 350s Setting up libxrender1:ppc64el (1:0.9.10-1.1) ... 350s Setting up libdatrie1:ppc64el (0.2.13-3) ... 350s Setting up libgslcblas0:ppc64el (2.7.1+dfsg-6ubuntu1) ... 350s Setting up libxcb-render0:ppc64el (1.15-1) ... 350s Setting up unzip (6.0-28ubuntu3) ... 350s Setting up x11-common (1:7.7+23ubuntu2) ... 351s Setting up libdeflate0:ppc64el (1.19-1) ... 351s Setting up libgsl27:ppc64el (2.7.1+dfsg-6ubuntu1) ... 351s Setting up libxcb-shm0:ppc64el (1.15-1) ... 351s Setting up libpaper-utils (1.1.29) ... 351s Setting up libgomp1:ppc64el (14-20240303-1ubuntu1) ... 351s Setting up libjbig0:ppc64el (2.1-6.1ubuntu1) ... 351s Setting up zip (3.0-13) ... 351s Setting up libblas3:ppc64el (3.12.0-3) ... 351s 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 351s Setting up libboost-iostreams1.83.0:ppc64el (1.83.0-2ubuntu1) ... 351s Setting up fonts-dejavu-mono (2.37-8) ... 351s Setting up libtcl8.6:ppc64el (8.6.13+dfsg-2) ... 351s Setting up fonts-dejavu-core (2.37-8) ... 351s Setting up libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 351s Setting up libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 351s Setting up libwebp7:ppc64el (1.3.2-0.4) ... 351s Setting up r-mathlib (4.3.2-1build1) ... 351s Setting up libharfbuzz0b:ppc64el (8.3.0-2) ... 351s Setting up libthai-data (0.1.29-2) ... 351s Setting up libxss1:ppc64el (1:1.2.3-1build2) ... 351s Setting up xdg-utils (1.1.3-4.1ubuntu3) ... 351s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 351s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 351s Setting up libice6:ppc64el (2:1.0.10-1build2) ... 351s Setting up liblapack3:ppc64el (3.12.0-3) ... 351s 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 351s Setting up libhts3:ppc64el (1.18+ds-1) ... 351s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 351s Setting up libthai0:ppc64el (0.1.29-2) ... 351s Setting up libtiff6:ppc64el (4.5.1+git230720-3ubuntu1) ... 351s Setting up libfontconfig1:ppc64el (2.15.0-1ubuntu1) ... 351s Setting up libsm6:ppc64el (2:1.2.3-1build2) ... 351s Setting up fontconfig (2.15.0-1ubuntu1) ... 353s Regenerating fonts cache... done. 353s Setting up libxft2:ppc64el (2.3.6-1) ... 353s Setting up libtk8.6:ppc64el (8.6.14-1) ... 353s Setting up libpango-1.0-0:ppc64el (1.51.0+ds-4) ... 353s Setting up libcairo2:ppc64el (1.18.0-1) ... 353s Setting up libxt6:ppc64el (1:1.2.1-1.1) ... 353s Setting up libpangoft2-1.0-0:ppc64el (1.51.0+ds-4) ... 353s Setting up libpangocairo-1.0-0:ppc64el (1.51.0+ds-4) ... 353s Setting up r-base-core (4.3.2-1build1) ... 353s 353s Creating config file /etc/R/Renviron with new version 353s Setting up qtltools (1.3.1+dfsg-4build1) ... 353s Setting up autopkgtest-satdep (0) ... 353s Processing triggers for man-db (2.12.0-3) ... 354s Processing triggers for install-info (7.1-3) ... 354s Processing triggers for libc-bin (2.39-0ubuntu6) ... 357s (Reading database ... 71810 files and directories currently installed.) 357s Removing autopkgtest-satdep (0) ... 358s autopkgtest [23:48:20]: test run-sample-analysis: [----------------------- 358s ./genes.50percent.chr22.bed.gz 358s ./genes.50percent.chr22.bed.gz.tbi 358s ./genes.covariates.pc50.txt.gz 358s ./genes.simulated.chr22.bed.gz 358s ./genes.simulated.chr22.bed.gz.tbi 358s ./genotypes.chr22.vcf.gz 359s ./genotypes.chr22.vcf.gz.tbi 359s 359s QTLtools 359s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 359s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 359s * Webpage : https://qtltools.github.io/qtltools/ 359s * Version : 1.3.1 359s * Date : 24/03/2024 - 23:48:22 359s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 359s 359s CONDUCT PCA ON DATA 359s 359s Initialize random number generator 359s * Built-in seed is 15112011 359s * First Integer = 30553 359s * First Double = 0.0126695 359s 359s Reading sample list from [genes.50percent.chr22.bed.gz] 359s * #samples = 358 359s 359s Merging sample sets from all input files 359s * #files = 1 359s * #samples in all files = 358 359s 359s Reading phenotype data in [genes.50percent.chr22.bed.gz] 359s * 358 samples included 359s * 608 phenotypes included 359s 359s Calculating PCA with a matrix 358 x 608 359s * Calculated mean and sd 359s * 0 sd==0 columns removed 359s * Variables centered 359s * Variables scaled to unit variance 359s * Running SVD 359s * SVD complete 359s * Calculated sd and var for PCs 359s * Calculated cumulative var for PCs 359s * Done! 359s 359s Running time: 0 seconds 359s 359s QTLtools 359s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 359s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 359s * Webpage : https://qtltools.github.io/qtltools/ 359s * Version : 1.3.1 359s * Date : 24/03/2024 - 23:48:23 359s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 359s 359s MAPPING QTL IN CIS 359s * TASK: Report all nominal associations with p <= 0.01 359s * Linear model: Phe ~ Var + Cov 359s * Cis-window size is 1000000 bp 359s * Region = [chr22:17000000-18000000] 359s 359s Initialize random number generator 359s * Built-in seed is 15112011 359s * First Integer = 30553 359s * First Double = 0.0126695 359s 359s Reading sample list from [genes.50percent.chr22.bed.gz] 359s * #samples = 358 359s 359s Read sample list from [genotypes.chr22.vcf.gz] 359s * #samples = 358 359s 359s Reading sample list from [genes.covariates.pc50.txt.gz] 359s * #samples = 358 359s 359s Merging sample sets from all input files 359s * #files = 3 359s * #samples in all files = 358 359s 359s Reading phenotype data in [genes.50percent.chr22.bed.gz] 359s * target region [chr22:17000000-18000000] 359s * 8 phenotypes included 359s * 3 phenotypes are on the negative strand 359s 359s Reading genotype data in [genotypes.chr22.vcf.gz] 359s * File format detected: VCF 359s * target region [chr22:16000000-19000000] 360s * 6404 variants included 360s 360s Reading covariates in [genes.covariates.pc50.txt.gz] 360s * 53 covariates included 360s 360s Residualize phenotypes for covariates 360s * #covariates = 53 360s 360s Processing phenotype [ENSG00000237438.2] [1/8] 360s * #variants in cis = 5095 360s * Best hit: [id=22_17542810, d=25350, pv=1.1864e-25, s=-0.7518] 360s 360s Processing phenotype [ENSG00000273203.1] [2/8] 360s * #variants in cis = 5170 360s * Best hit: [id=22_17517388, d=-31323, pv=5.86611e-06, s=-0.1406] 360s 360s Processing phenotype [ENSG00000273442.1] [3/8] 360s * #variants in cis = 5188 360s * Best hit: [id=22_17553526, d=-8065, pv=0.000244522, s=0.1340] 360s 360s Processing phenotype [ENSG00000177663.9] [4/8] 360s * #variants in cis = 5193 360s * Best hit: [id=22_17513703, d=-52141, pv=8.03358e-14, s=-0.2096] 360s 360s Processing phenotype [ENSG00000183307.3] [5/8] 360s * #variants in cis = 5230 360s * Best hit: [id=22_17587975, d=14282, pv=1.56789e-07, s=-0.0078] 360s 360s Processing phenotype [ENSG00000069998.8] [6/8] 360s * #variants in cis = 5291 360s * Best hit: [id=22_17620429, d=25748, pv=1.37287e-14, s=-1.5147] 360s 360s Processing phenotype [ENSG00000093072.11] [7/8] 360s * #variants in cis = 5293 360s * Best hit: [id=22_17699630, d=3249, pv=0.000578649, s=0.6404] 360s 360s Processing phenotype [ENSG00000099954.14] [8/8] 360s * #variants in cis = 5435 360s * Best hit: [id=22_17175937, d=-664900, pv=0.000866455, s=0.0067] 360s 360s Running time: 4294967295 seconds 360s 360s QTLtools 360s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 360s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 360s * Webpage : https://qtltools.github.io/qtltools/ 360s * Version : 1.3.1 360s * Date : 24/03/2024 - 23:48:22 360s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 360s 360s MAPPING QTL IN CIS 360s * TASK: Perform 1000 permutations 360s * Linear model: Phe ~ Var + Cov 360s * Cis-window size is 1000000 bp 360s * Region = [chr22:17000000-18000000] 360s 360s Initialize random number generator 360s * Built-in seed is 15112011 360s * First Integer = 30553 360s * First Double = 0.0126695 360s 360s Reading sample list from [genes.50percent.chr22.bed.gz] 360s * #samples = 358 360s 360s Read sample list from [genotypes.chr22.vcf.gz] 360s * #samples = 358 360s 360s Reading sample list from [genes.covariates.pc50.txt.gz] 360s * #samples = 358 360s 360s Merging sample sets from all input files 360s * #files = 3 360s * #samples in all files = 358 360s 360s Reading phenotype data in [genes.50percent.chr22.bed.gz] 360s * target region [chr22:17000000-18000000] 360s * 8 phenotypes included 360s * 3 phenotypes are on the negative strand 360s 360s Reading genotype data in [genotypes.chr22.vcf.gz] 360s * File format detected: VCF 360s * target region [chr22:16000000-19000000] 360s * 6404 variants included 360s 360s Reading covariates in [genes.covariates.pc50.txt.gz] 360s * 53 covariates included 360s 360s Residualize phenotypes for covariates 360s * #covariates = 53 360s 360s Processing phenotype [ENSG00000237438.2] [1/8] 360s * #variants in cis = 5095 361s * Best hit: [id=22_17542810, d=25350, pv=1.1864e-25, s=-0.7518] 361s * Beta parameters: [s1=1.00995, s2=621.053] 361s * Adjusted p-values: [emp=0.000999001, beta=1.28062e-20] 361s 361s Processing phenotype [ENSG00000273203.1] [2/8] 361s * #variants in cis = 5170 363s * Best hit: [id=22_17517388, d=-31323, pv=5.86611e-06, s=-0.1406] 363s * Beta parameters: [s1=1.11817, s2=641.379] 363s * Adjusted p-values: [emp=0.00799201, beta=0.00751892] 363s 363s Processing phenotype [ENSG00000273442.1] [3/8] 363s * #variants in cis = 5188 364s * Best hit: [id=22_17553526, d=-8065, pv=0.000244522, s=0.1340] 364s * Beta parameters: [s1=1.08364, s2=467.63] 364s * Adjusted p-values: [emp=0.297702, beta=0.293948] 364s 364s Processing phenotype [ENSG00000177663.9] [4/8] 364s * #variants in cis = 5193 365s * Best hit: [id=22_17513703, d=-52141, pv=8.03358e-14, s=-0.2096] 365s * Beta parameters: [s1=0.989061, s2=704.553] 365s * Adjusted p-values: [emp=0.000999001, beta=7.91291e-10] 365s 365s Processing phenotype [ENSG00000183307.3] [5/8] 365s * #variants in cis = 5230 366s * Best hit: [id=22_17587975, d=14282, pv=1.56789e-07, s=-0.0078] 366s * Beta parameters: [s1=1.01322, s2=559.49] 366s * Adjusted p-values: [emp=0.000999001, beta=0.00050707] 366s 366s Processing phenotype [ENSG00000069998.8] [6/8] 366s * #variants in cis = 5291 368s * Best hit: [id=22_17620429, d=25748, pv=1.37287e-14, s=-1.5147] 368s * Beta parameters: [s1=1.02312, s2=563.339] 368s * Adjusted p-values: [emp=0.000999001, beta=2.56935e-10] 368s 368s Processing phenotype [ENSG00000093072.11] [7/8] 368s * #variants in cis = 5293 369s * Best hit: [id=22_17699630, d=3249, pv=0.000578649, s=0.6404] 369s * Beta parameters: [s1=0.957514, s2=559.397] 369s * Adjusted p-values: [emp=0.574426, beta=0.562826] 369s 369s Processing phenotype [ENSG00000099954.14] [8/8] 369s * #variants in cis = 5435 370s * Best hit: [id=22_17175937, d=-664900, pv=0.000866455, s=0.0067] 370s * Beta parameters: [s1=0.938041, s2=226.852] 370s * Adjusted p-values: [emp=0.842158, beta=0.84836] 370s 370s Running time: 10 seconds 370s 370s QTLtools 370s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 370s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 370s * Webpage : https://qtltools.github.io/qtltools/ 370s * Version : 1.3.1 370s * Date : 24/03/2024 - 23:48:32 370s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 370s 370s MAPPING QTL IN TRANS 370s * TASK: Perform a full nominal pass, do not adjust p-values 370s * Cis-window size is 5000000 bp 370s * #bins = 1000 370s * threshold = 1e-05 370s 370s Initialize random number generator 370s * Built-in seed is 15112011 370s * First Integer = 30553 370s * First Double = 0.0126695 370s 370s Read sample list from [genotypes.chr22.vcf.gz] 370s * #samples = 358 370s 370s Checking sample list in [genes.simulated.chr22.bed.gz] 370s * #samples = 358 370s 370s Reading phenotype data in [genes.simulated.chr22.bed.gz] from line 0 to 0 370s * 358 samples included 370s * 608 phenotypes included 370s * 275 phenotypes is on the negative strand 370s 370s Calculate correlation threshold 370s * thres = 1e-05 370s * corr = 0.2311 370s 370s Sweep through genotype data in [genotypes.chr22.vcf.gz] 371s * #variants=1950 #multi_allelic=0 #not_processed=0 #hits=101/1000000 speed=3.29MT/s 371s * #variants=4001 #multi_allelic=0 #not_processed=0 #hits=153/2000000 speed=3.26MT/s 371s * #variants=6187 #multi_allelic=0 #not_processed=0 #hits=244/3000000 speed=3.21MT/s 372s * #variants=8537 #multi_allelic=0 #not_processed=0 #hits=285/4000000 speed=3.16MT/s 372s * #variants=11025 #multi_allelic=0 #not_processed=0 #hits=312/5000000 speed=3.12MT/s 372s * #variants=13621 #multi_allelic=0 #not_processed=0 #hits=320/6000000 speed=3.10MT/s 373s * #variants=16217 #multi_allelic=0 #not_processed=0 #hits=342/7000000 speed=3.09MT/s 373s * #variants=18755 #multi_allelic=0 #not_processed=0 #hits=401/8000000 speed=3.11MT/s 373s * #variants=21237 #multi_allelic=0 #not_processed=0 #hits=402/9000000 speed=3.12MT/s 373s * #variants=23680 #multi_allelic=0 #not_processed=0 #hits=455/10000000 speed=3.12MT/s 374s * #variants=26171 #multi_allelic=0 #not_processed=0 #hits=463/11000000 speed=2.96MT/s 374s * #variants=28609 #multi_allelic=0 #not_processed=0 #hits=469/12000000 speed=3.13MT/s 374s * #variants=30861 #multi_allelic=0 #not_processed=0 #hits=973/13000000 speed=3.15MT/s 375s * #variants=32932 #multi_allelic=0 #not_processed=0 #hits=979/14000000 speed=3.25MT/s 375s * #variants=34974 #multi_allelic=0 #not_processed=0 #hits=1085/15000000 speed=3.23MT/s 375s * #variants=37021 #multi_allelic=0 #not_processed=0 #hits=1086/16000000 speed=3.25MT/s 376s * #variants=39122 #multi_allelic=0 #not_processed=0 #hits=1089/17000000 speed=3.24MT/s 376s * #variants=41334 #multi_allelic=0 #not_processed=0 #hits=1089/18000000 speed=3.19MT/s 376s * #variants=43627 #multi_allelic=0 #not_processed=0 #hits=1096/19000000 speed=3.16MT/s 377s * #variants=45897 #multi_allelic=0 #not_processed=0 #hits=1153/20000000 speed=3.16MT/s 377s * #variants=48114 #multi_allelic=0 #not_processed=0 #hits=1243/21000000 speed=2.92MT/s 378s * #variants=50410 #multi_allelic=0 #not_processed=0 #hits=1249/22000000 speed=3.16MT/s 378s * #variants=52820 #multi_allelic=0 #not_processed=0 #hits=1259/23000000 speed=3.13MT/s 378s * #variants=55279 #multi_allelic=0 #not_processed=0 #hits=1498/24000000 speed=3.10MT/s 378s * #variants=57789 #multi_allelic=0 #not_processed=0 #hits=1724/25000000 speed=3.09MT/s 379s * #variants=60201 #multi_allelic=0 #not_processed=0 #hits=2168/26000000 speed=3.09MT/s 379s * #variants=62476 #multi_allelic=0 #not_processed=0 #hits=2452/27000000 speed=3.15MT/s 379s * #variants=64608 #multi_allelic=0 #not_processed=0 #hits=2544/28000000 speed=3.22MT/s 380s * #variants=66709 #multi_allelic=0 #not_processed=0 #hits=2684/29000000 speed=3.23MT/s 380s * #variants=68871 #multi_allelic=0 #not_processed=0 #hits=2688/30000000 speed=3.23MT/s 380s * #variants=71070 #multi_allelic=0 #not_processed=0 #hits=2720/31000000 speed=3.19MT/s 380s * #variants=73151 #multi_allelic=0 #not_processed=0 #hits=2891/32000000 speed=3.24MT/s 381s * #variants=75122 #multi_allelic=0 #not_processed=0 #hits=3110/33000000 speed=3.07MT/s 381s * #variants=77058 #multi_allelic=0 #not_processed=0 #hits=3209/34000000 speed=3.29MT/s 382s * #variants=78989 #multi_allelic=0 #not_processed=0 #hits=3218/35000000 speed=3.30MT/s 382s * #variants=80903 #multi_allelic=0 #not_processed=0 #hits=3250/36000000 speed=3.30MT/s 382s * #variants=82811 #multi_allelic=0 #not_processed=0 #hits=3463/37000000 speed=3.29MT/s 382s * #variants=84694 #multi_allelic=0 #not_processed=0 #hits=4035/38000000 speed=3.27MT/s 382s * #variants=85485 #multi_allelic=0 #not_processed=0 #hits=4036/38425275 speed=3.32MT/s 382s 382s Running time: 12 seconds 382s 382s QTLtools 382s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 382s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 382s * Webpage : https://qtltools.github.io/qtltools/ 382s * Version : 1.3.1 382s * Date : 24/03/2024 - 23:48:44 382s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 382s 382s MAPPING QTL IN TRANS 382s * TASK: Permute randomly chosen phenotypes 1000 times and test 382s * Cis-window size is 5000000 bp 382s * #bins = 1000 382s * threshold = 1e-05 382s 382s Initialize random number generator 382s * Built-in seed is 15112011 382s * First Integer = 30553 382s * First Double = 0.0126695 382s 382s Read sample list from [genotypes.chr22.vcf.gz] 382s * #samples = 358 382s 382s Checking sample list in [genes.simulated.chr22.bed.gz] 382s * #samples = 358 382s 382s Reading phenotype data in [genes.simulated.chr22.bed.gz] from line 0 to 0 382s * 358 samples included 383s * 608 phenotypes included 383s * 275 phenotypes is on the negative strand 383s 383s Normal transform phenotypes 383s 383s Calculate correlation threshold 383s * thres = 1e-05 383s * corr = 0.2311 383s 383s Sweep through genotype data in [genotypes.chr22.vcf.gz] 383s * #variants=1177 #multi_allelic=0 #not_processed=0 #hits=28/1000000 speed=3.46MT/s 383s * #variants=2383 #multi_allelic=0 #not_processed=0 #hits=38/2000000 speed=3.42MT/s 383s * #variants=3633 #multi_allelic=0 #not_processed=0 #hits=53/3000000 speed=3.40MT/s 384s * #variants=4928 #multi_allelic=0 #not_processed=0 #hits=53/4000000 speed=3.37MT/s 384s * #variants=6269 #multi_allelic=0 #not_processed=0 #hits=71/5000000 speed=3.25MT/s 384s * #variants=7675 #multi_allelic=0 #not_processed=0 #hits=72/6000000 speed=3.28MT/s 385s * #variants=9151 #multi_allelic=0 #not_processed=0 #hits=88/7000000 speed=3.24MT/s 385s * #variants=10663 #multi_allelic=0 #not_processed=0 #hits=96/8000000 speed=3.21MT/s 385s * #variants=12202 #multi_allelic=0 #not_processed=0 #hits=96/9000000 speed=3.14MT/s 386s * #variants=13804 #multi_allelic=0 #not_processed=0 #hits=96/10000000 speed=3.15MT/s 386s * #variants=15381 #multi_allelic=0 #not_processed=0 #hits=120/11000000 speed=3.16MT/s 386s * #variants=16946 #multi_allelic=0 #not_processed=0 #hits=123/12000000 speed=3.17MT/s 387s * #variants=18483 #multi_allelic=0 #not_processed=0 #hits=129/13000000 speed=3.18MT/s 387s * #variants=19995 #multi_allelic=0 #not_processed=0 #hits=131/14000000 speed=2.94MT/s 387s * #variants=21489 #multi_allelic=0 #not_processed=0 #hits=132/15000000 speed=3.22MT/s 388s * #variants=22947 #multi_allelic=0 #not_processed=0 #hits=151/16000000 speed=3.24MT/s 388s * #variants=24445 #multi_allelic=0 #not_processed=0 #hits=168/17000000 speed=3.18MT/s 388s * #variants=25965 #multi_allelic=0 #not_processed=0 #hits=175/18000000 speed=3.21MT/s 389s * #variants=27472 #multi_allelic=0 #not_processed=0 #hits=179/19000000 speed=3.21MT/s 389s * #variants=28933 #multi_allelic=0 #not_processed=0 #hits=181/20000000 speed=3.25MT/s 389s * #variants=30325 #multi_allelic=0 #not_processed=0 #hits=181/21000000 speed=3.28MT/s 390s * #variants=31617 #multi_allelic=0 #not_processed=0 #hits=182/22000000 speed=3.36MT/s 390s * #variants=32875 #multi_allelic=0 #not_processed=0 #hits=190/23000000 speed=3.39MT/s 390s * #variants=34127 #multi_allelic=0 #not_processed=0 #hits=192/24000000 speed=3.39MT/s 390s * #variants=35392 #multi_allelic=0 #not_processed=0 #hits=206/25000000 speed=3.39MT/s 391s * #variants=36652 #multi_allelic=0 #not_processed=0 #hits=206/26000000 speed=3.24MT/s 391s * #variants=37940 #multi_allelic=0 #not_processed=0 #hits=213/27000000 speed=3.37MT/s 391s * #variants=39255 #multi_allelic=0 #not_processed=0 #hits=238/28000000 speed=3.34MT/s 392s * #variants=40602 #multi_allelic=0 #not_processed=0 #hits=239/29000000 speed=3.32MT/s 392s * #variants=41998 #multi_allelic=0 #not_processed=0 #hits=245/30000000 speed=3.29MT/s 392s * #variants=43398 #multi_allelic=0 #not_processed=0 #hits=245/31000000 speed=3.29MT/s 392s * #variants=44803 #multi_allelic=0 #not_processed=0 #hits=260/32000000 speed=3.28MT/s 393s * #variants=46187 #multi_allelic=0 #not_processed=0 #hits=261/33000000 speed=3.30MT/s 393s * #variants=47545 #multi_allelic=0 #not_processed=0 #hits=268/34000000 speed=3.31MT/s 393s * #variants=48904 #multi_allelic=0 #not_processed=0 #hits=280/35000000 speed=3.33MT/s 394s * #variants=50309 #multi_allelic=0 #not_processed=0 #hits=306/36000000 speed=3.29MT/s 394s * #variants=51731 #multi_allelic=0 #not_processed=0 #hits=314/37000000 speed=3.15MT/s 394s * #variants=53171 #multi_allelic=0 #not_processed=0 #hits=320/38000000 speed=3.26MT/s 395s * #variants=54621 #multi_allelic=0 #not_processed=0 #hits=323/39000000 speed=3.26MT/s 395s * #variants=56099 #multi_allelic=0 #not_processed=0 #hits=323/40000000 speed=3.23MT/s 395s * #variants=57584 #multi_allelic=0 #not_processed=0 #hits=340/41000000 speed=3.23MT/s 396s * #variants=59032 #multi_allelic=0 #not_processed=0 #hits=344/42000000 speed=3.27MT/s 396s * #variants=60437 #multi_allelic=0 #not_processed=0 #hits=345/43000000 speed=3.29MT/s 396s * #variants=61810 #multi_allelic=0 #not_processed=0 #hits=357/44000000 speed=3.31MT/s 396s * #variants=63129 #multi_allelic=0 #not_processed=0 #hits=384/45000000 speed=3.36MT/s 397s * #variants=64409 #multi_allelic=0 #not_processed=0 #hits=391/46000000 speed=3.39MT/s 397s * #variants=65679 #multi_allelic=0 #not_processed=0 #hits=430/47000000 speed=3.39MT/s 397s * #variants=66953 #multi_allelic=0 #not_processed=0 #hits=436/48000000 speed=3.39MT/s 398s * #variants=68247 #multi_allelic=0 #not_processed=0 #hits=446/49000000 speed=3.38MT/s 398s * #variants=69595 #multi_allelic=0 #not_processed=0 #hits=460/50000000 speed=3.34MT/s 398s * #variants=70918 #multi_allelic=0 #not_processed=0 #hits=481/51000000 speed=3.36MT/s 399s * #variants=72211 #multi_allelic=0 #not_processed=0 #hits=492/52000000 speed=3.38MT/s 399s * #variants=73449 #multi_allelic=0 #not_processed=0 #hits=492/53000000 speed=3.42MT/s 399s * #variants=74662 #multi_allelic=0 #not_processed=0 #hits=500/54000000 speed=3.44MT/s 399s * #variants=75863 #multi_allelic=0 #not_processed=0 #hits=506/55000000 speed=3.45MT/s 400s * #variants=77058 #multi_allelic=0 #not_processed=0 #hits=513/56000000 speed=3.46MT/s 400s * #variants=78253 #multi_allelic=0 #not_processed=0 #hits=515/57000000 speed=3.46MT/s 400s * #variants=79446 #multi_allelic=0 #not_processed=0 #hits=530/58000000 speed=3.22MT/s 401s * #variants=80634 #multi_allelic=0 #not_processed=0 #hits=581/59000000 speed=3.46MT/s 402s * #variants=81817 #multi_allelic=0 #not_processed=0 #hits=594/60000000 speed=3.46MT/s 402s * #variants=82993 #multi_allelic=0 #not_processed=0 #hits=598/61000000 speed=3.47MT/s 402s * #variants=84160 #multi_allelic=0 #not_processed=0 #hits=599/62000000 speed=3.48MT/s 402s * #variants=85304 #multi_allelic=0 #not_processed=0 #hits=609/63000000 speed=3.50MT/s 402s * #variants=85485 #multi_allelic=0 #not_processed=0 #hits=609/63157827 speed=3.51MT/s 402s 402s Running time: 19 seconds 402s autopkgtest [23:49:04]: test run-sample-analysis: -----------------------] 403s run-sample-analysis PASS 403s autopkgtest [23:49:05]: test run-sample-analysis: - - - - - - - - - - results - - - - - - - - - - 403s autopkgtest [23:49:05]: @@@@@@@@@@@@@@@@@@@@ summary 403s run-sample-analysis PASS 434s Creating nova instance adt-noble-ppc64el-qtltools-20240324-234219-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-ppc64el-server-20240324.img (UUID 456c38b1-f024-4aa9-9fc9-7cea731b220e)...