0s autopkgtest [01:28:51]: starting date and time: 2024-04-19 01:28:51+0000 0s autopkgtest [01:28:51]: git checkout: 43bc6cdf gitlab-ci: do not include the salsa pipeline 0s autopkgtest [01:28:51]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.mjket0jc/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:gsl --apt-upgrade gemma --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=gsl/2.7.1+dfsg-6ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos01-s390x-6.secgroup --name adt-noble-s390x-gemma-20240419-012851-juju-7f2275-prod-proposed-migration-environment-3-7ccc2a65-38f3-4f95-a342-c7d11caf536e --image adt/ubuntu-noble-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://us.ports.ubuntu.com/ubuntu-ports/ 202s autopkgtest [01:32:13]: testbed dpkg architecture: s390x 202s autopkgtest [01:32:13]: testbed apt version: 2.7.14build2 202s autopkgtest [01:32:13]: @@@@@@@@@@@@@@@@@@@@ test bed setup 203s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 203s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [2340 B] 203s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [338 kB] 203s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [53.4 kB] 203s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [12.2 kB] 203s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [93.9 kB] 203s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 203s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [976 B] 203s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 203s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [427 kB] 203s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 203s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 204s Fetched 1055 kB in 1s (1146 kB/s) 204s Reading package lists... 209s sh: 4: dhclient: not found 210s Reading package lists... 210s Building dependency tree... 210s Reading state information... 210s Calculating upgrade... 210s The following packages will be upgraded: 210s apport apport-core-dump-handler libkeyutils1 libnetplan1 libnuma1 make 210s man-db netcat-openbsd netplan-generator netplan.io numactl python3-apport 210s python3-netplan python3-problem-report 210s 14 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 210s Need to get 2057 kB of archives. 210s After this operation, 1024 B of additional disk space will be used. 210s Get:1 http://ftpmaster.internal/ubuntu noble/main s390x python3-problem-report all 2.28.1-0ubuntu1 [23.8 kB] 211s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x python3-apport all 2.28.1-0ubuntu1 [92.1 kB] 211s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x apport-core-dump-handler all 2.28.1-0ubuntu1 [16.8 kB] 211s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x apport all 2.28.1-0ubuntu1 [83.5 kB] 211s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x libkeyutils1 s390x 1.6.3-3build1 [9556 B] 211s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x netplan-generator s390x 1.0-2ubuntu1 [59.2 kB] 211s Get:7 http://ftpmaster.internal/ubuntu noble/main s390x python3-netplan s390x 1.0-2ubuntu1 [23.0 kB] 211s Get:8 http://ftpmaster.internal/ubuntu noble/main s390x netplan.io s390x 1.0-2ubuntu1 [65.8 kB] 211s Get:9 http://ftpmaster.internal/ubuntu noble/main s390x libnetplan1 s390x 1.0-2ubuntu1 [126 kB] 211s Get:10 http://ftpmaster.internal/ubuntu noble/main s390x netcat-openbsd s390x 1.226-1ubuntu2 [44.0 kB] 211s Get:11 http://ftpmaster.internal/ubuntu noble/main s390x libnuma1 s390x 2.0.18-1build1 [25.1 kB] 211s Get:12 http://ftpmaster.internal/ubuntu noble/main s390x man-db s390x 2.12.0-4build2 [1253 kB] 211s Get:13 http://ftpmaster.internal/ubuntu noble/main s390x make s390x 4.3-4.1build2 [196 kB] 211s Get:14 http://ftpmaster.internal/ubuntu noble/main s390x numactl s390x 2.0.18-1build1 [40.0 kB] 211s Preconfiguring packages ... 211s Fetched 2057 kB in 1s (2904 kB/s) 212s (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 ... 78323 files and directories currently installed.) 212s Preparing to unpack .../00-python3-problem-report_2.28.1-0ubuntu1_all.deb ... 212s Unpacking python3-problem-report (2.28.1-0ubuntu1) over (2.28.0-0ubuntu1) ... 212s Preparing to unpack .../01-python3-apport_2.28.1-0ubuntu1_all.deb ... 212s Unpacking python3-apport (2.28.1-0ubuntu1) over (2.28.0-0ubuntu1) ... 212s Preparing to unpack .../02-apport-core-dump-handler_2.28.1-0ubuntu1_all.deb ... 212s Unpacking apport-core-dump-handler (2.28.1-0ubuntu1) over (2.28.0-0ubuntu1) ... 212s Preparing to unpack .../03-apport_2.28.1-0ubuntu1_all.deb ... 212s Unpacking apport (2.28.1-0ubuntu1) over (2.28.0-0ubuntu1) ... 212s Preparing to unpack .../04-libkeyutils1_1.6.3-3build1_s390x.deb ... 212s Unpacking libkeyutils1:s390x (1.6.3-3build1) over (1.6.3-3) ... 212s Preparing to unpack .../05-netplan-generator_1.0-2ubuntu1_s390x.deb ... 212s Adding 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 212s Unpacking netplan-generator (1.0-2ubuntu1) over (1.0-2build1) ... 212s Preparing to unpack .../06-python3-netplan_1.0-2ubuntu1_s390x.deb ... 212s Unpacking python3-netplan (1.0-2ubuntu1) over (1.0-2build1) ... 212s Preparing to unpack .../07-netplan.io_1.0-2ubuntu1_s390x.deb ... 212s Unpacking netplan.io (1.0-2ubuntu1) over (1.0-2build1) ... 212s Preparing to unpack .../08-libnetplan1_1.0-2ubuntu1_s390x.deb ... 212s Unpacking libnetplan1:s390x (1.0-2ubuntu1) over (1.0-2build1) ... 212s Preparing to unpack .../09-netcat-openbsd_1.226-1ubuntu2_s390x.deb ... 212s Unpacking netcat-openbsd (1.226-1ubuntu2) over (1.226-1ubuntu1) ... 212s Preparing to unpack .../10-libnuma1_2.0.18-1build1_s390x.deb ... 212s Unpacking libnuma1:s390x (2.0.18-1build1) over (2.0.18-1) ... 212s Preparing to unpack .../11-man-db_2.12.0-4build2_s390x.deb ... 212s Unpacking man-db (2.12.0-4build2) over (2.12.0-4build1) ... 212s Preparing to unpack .../12-make_4.3-4.1build2_s390x.deb ... 212s Unpacking make (4.3-4.1build2) over (4.3-4.1build1) ... 212s Preparing to unpack .../13-numactl_2.0.18-1build1_s390x.deb ... 212s Unpacking numactl (2.0.18-1build1) over (2.0.18-1) ... 212s Setting up libkeyutils1:s390x (1.6.3-3build1) ... 212s Setting up python3-problem-report (2.28.1-0ubuntu1) ... 212s Setting up netcat-openbsd (1.226-1ubuntu2) ... 212s Setting up libnetplan1:s390x (1.0-2ubuntu1) ... 212s Setting up man-db (2.12.0-4build2) ... 212s Updating database of manual pages ... 214s man-db.service is a disabled or a static unit not running, not starting it. 214s Setting up python3-apport (2.28.1-0ubuntu1) ... 214s Setting up make (4.3-4.1build2) ... 214s Setting up libnuma1:s390x (2.0.18-1build1) ... 214s Setting up python3-netplan (1.0-2ubuntu1) ... 214s Setting up netplan-generator (1.0-2ubuntu1) ... 214s Removing 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 214s Setting up numactl (2.0.18-1build1) ... 214s Setting up netplan.io (1.0-2ubuntu1) ... 214s Setting up apport-core-dump-handler (2.28.1-0ubuntu1) ... 215s Setting up apport (2.28.1-0ubuntu1) ... 215s Installing new version of config file /etc/apport/crashdb.conf ... 216s apport-autoreport.service is a disabled or a static unit not running, not starting it. 216s Processing triggers for dbus (1.14.10-4ubuntu4) ... 216s Processing triggers for libc-bin (2.39-0ubuntu8) ... 216s Reading package lists... 217s Building dependency tree... 217s Reading state information... 217s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 217s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 217s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 217s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 217s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 218s Reading package lists... 219s Reading package lists... 219s Building dependency tree... 219s Reading state information... 219s Calculating upgrade... 219s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 219s Reading package lists... 219s Building dependency tree... 219s Reading state information... 219s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 220s autopkgtest [01:32:31]: rebooting testbed after setup commands that affected boot 272s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 293s autopkgtest [01:33:44]: testbed running kernel: Linux 6.8.0-22-generic #22-Ubuntu SMP Thu Apr 4 21:54:17 UTC 2024 296s autopkgtest [01:33:47]: @@@@@@@@@@@@@@@@@@@@ apt-source gemma 358s Get:1 http://ftpmaster.internal/ubuntu noble/universe gemma 0.98.5+dfsg-2 (dsc) [2130 B] 358s Get:2 http://ftpmaster.internal/ubuntu noble/universe gemma 0.98.5+dfsg-2 (tar) [44.2 MB] 358s Get:3 http://ftpmaster.internal/ubuntu noble/universe gemma 0.98.5+dfsg-2 (diff) [6636 B] 358s gpgv: Signature made Fri Nov 18 11:18:27 2022 UTC 358s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 358s gpgv: issuer "tille@debian.org" 358s gpgv: Can't check signature: No public key 358s dpkg-source: warning: cannot verify inline signature for ./gemma_0.98.5+dfsg-2.dsc: no acceptable signature found 364s autopkgtest [01:34:55]: testing package gemma version 0.98.5+dfsg-2 364s autopkgtest [01:34:55]: build not needed 370s autopkgtest [01:35:01]: test run-unit-test: preparing testbed 371s Reading package lists... 372s Building dependency tree... 372s Reading state information... 372s Starting pkgProblemResolver with broken count: 0 372s Starting 2 pkgProblemResolver with broken count: 0 372s Done 372s The following additional packages will be installed: 372s gemma gemma-doc libgfortran5 libgsl27 libgslcblas0 libopenblas0 372s libopenblas0-pthread 372s Suggested packages: 372s gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html 372s The following NEW packages will be installed: 372s autopkgtest-satdep gemma gemma-doc libgfortran5 libgsl27 libgslcblas0 372s libopenblas0 libopenblas0-pthread 372s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. 372s Need to get 42.5 MB/42.5 MB of archives. 372s After this operation, 62.4 MB of additional disk space will be used. 372s Get:1 /tmp/autopkgtest.tDKaIY/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [708 B] 372s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libgslcblas0 s390x 2.7.1+dfsg-6ubuntu2 [150 kB] 373s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libgsl27 s390x 2.7.1+dfsg-6ubuntu2 [1084 kB] 374s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x libgfortran5 s390x 14-20240412-0ubuntu1 [600 kB] 375s Get:5 http://ftpmaster.internal/ubuntu noble/universe s390x libopenblas0-pthread s390x 0.3.26+ds-1 [6974 kB] 377s Get:6 http://ftpmaster.internal/ubuntu noble/universe s390x libopenblas0 s390x 0.3.26+ds-1 [6170 B] 377s Get:7 http://ftpmaster.internal/ubuntu noble/universe s390x gemma s390x 0.98.5+dfsg-2 [336 kB] 377s Get:8 http://ftpmaster.internal/ubuntu noble/universe s390x gemma-doc all 0.98.5+dfsg-2 [33.4 MB] 379s Fetched 42.5 MB in 7s (6189 kB/s) 379s Selecting previously unselected package libgslcblas0:s390x. 380s (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 ... 78322 files and directories currently installed.) 380s Preparing to unpack .../0-libgslcblas0_2.7.1+dfsg-6ubuntu2_s390x.deb ... 380s Unpacking libgslcblas0:s390x (2.7.1+dfsg-6ubuntu2) ... 380s Selecting previously unselected package libgsl27:s390x. 380s Preparing to unpack .../1-libgsl27_2.7.1+dfsg-6ubuntu2_s390x.deb ... 380s Unpacking libgsl27:s390x (2.7.1+dfsg-6ubuntu2) ... 380s Selecting previously unselected package libgfortran5:s390x. 380s Preparing to unpack .../2-libgfortran5_14-20240412-0ubuntu1_s390x.deb ... 380s Unpacking libgfortran5:s390x (14-20240412-0ubuntu1) ... 380s Selecting previously unselected package libopenblas0-pthread:s390x. 380s Preparing to unpack .../3-libopenblas0-pthread_0.3.26+ds-1_s390x.deb ... 380s Unpacking libopenblas0-pthread:s390x (0.3.26+ds-1) ... 380s Selecting previously unselected package libopenblas0:s390x. 380s Preparing to unpack .../4-libopenblas0_0.3.26+ds-1_s390x.deb ... 380s Unpacking libopenblas0:s390x (0.3.26+ds-1) ... 380s Selecting previously unselected package gemma. 380s Preparing to unpack .../5-gemma_0.98.5+dfsg-2_s390x.deb ... 380s Unpacking gemma (0.98.5+dfsg-2) ... 380s Selecting previously unselected package gemma-doc. 380s Preparing to unpack .../6-gemma-doc_0.98.5+dfsg-2_all.deb ... 380s Unpacking gemma-doc (0.98.5+dfsg-2) ... 380s Selecting previously unselected package autopkgtest-satdep. 380s Preparing to unpack .../7-1-autopkgtest-satdep.deb ... 380s Unpacking autopkgtest-satdep (0) ... 380s Setting up libgslcblas0:s390x (2.7.1+dfsg-6ubuntu2) ... 380s Setting up libgsl27:s390x (2.7.1+dfsg-6ubuntu2) ... 380s Setting up libgfortran5:s390x (14-20240412-0ubuntu1) ... 380s Setting up gemma-doc (0.98.5+dfsg-2) ... 380s Setting up libopenblas0-pthread:s390x (0.3.26+ds-1) ... 380s update-alternatives: using /usr/lib/s390x-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 380s update-alternatives: using /usr/lib/s390x-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 380s update-alternatives: using /usr/lib/s390x-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/s390x-linux-gnu/libopenblas.so.0 (libopenblas.so.0-s390x-linux-gnu) in auto mode 380s Setting up libopenblas0:s390x (0.3.26+ds-1) ... 380s Setting up gemma (0.98.5+dfsg-2) ... 380s Setting up autopkgtest-satdep (0) ... 380s Processing triggers for libc-bin (2.39-0ubuntu8) ... 383s (Reading database ... 78384 files and directories currently installed.) 383s Removing autopkgtest-satdep (0) ... 383s autopkgtest [01:35:14]: test run-unit-test: [----------------------- 384s GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 384s Reading Files ... 386s ## number of total individuals = 1940 386s ## number of analyzed individuals = 1410 386s ## number of covariates = 1 386s ## number of phenotypes = 1 386s ## number of total SNPs/var = 12226 386s ## number of analyzed SNPs = 10768 386s Calculating Relatedness Matrix ... 398s 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% 399s **** INFO: Done. 400s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 400s GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 400s Reading Files ... 401s ## number of total individuals = 1940 401s ## number of analyzed individuals = 1410 401s ## number of covariates = 1 401s ## number of phenotypes = 1 401s ## number of total SNPs/var = 12226 401s ## number of analyzed SNPs = 10768 402s Start Eigen-Decomposition... 403s pve estimate =0.608801 403s se(pve) =0.032774 417s 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% ================================================== 100% 418s **** INFO: Done. 418s GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 418s Reading Files ... 419s ## number of total individuals = 1940 419s ## number of analyzed individuals = 1197 419s ## number of covariates = 1 419s ## number of phenotypes = 2 419s ## number of total SNPs/var = 12226 419s ## number of analyzed SNPs = 10758 419s Start Eigen-Decomposition... 420s REMLE estimate for Vg in the null model: 420s 1.3940 420s -0.2267 2.0817 420s se(Vg): 420s 0.1567 420s 0.1363 0.2359 420s REMLE estimate for Ve in the null model: 420s 0.3489 420s 0.0491 0.4144 420s se(Ve): 420s 0.0206 420s 0.0166 0.0267 420s REMLE likelihood = -2855.1664 420s MLE estimate for Vg in the null model: 420s 1.3959 420s -0.2267 2.0854 420s se(Vg): 420s 0.1568 420s 0.1365 0.2361 420s MLE estimate for Ve in the null model: 420s 0.3483 420s 0.0490 0.4136 420s se(Ve): 420s 0.0206 420s 0.0166 0.0266 420s MLE likelihood = -2856.0280 462s 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% 462s **** INFO: Done. 462s GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 462s Reading Files ... 463s ## number of total individuals = 1940 463s ## number of analyzed individuals = 1940 463s ## number of individuals with full phenotypes = 1197 463s ## number of covariates = 1 463s ## number of phenotypes = 2 463s ## number of observed data = 2990 463s ## number of missing data = 890 465s Start Eigen-Decomposition... 465s REMLE estimate for Vg in the null model: 465s 1.39398 465s -0.226714 2.08168 465s REMLE estimate for Ve in the null model: 465s 0.348882 465s 0.0490525 0.414433 466s Predicting Missing Phentypes ... 467s **** INFO: Done. 467s GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 467s Reading Files ... 469s ## number of total individuals = 1940 469s ## number of analyzed individuals = 1940 469s ## number of covariates = 1 469s ## number of phenotypes = 2 469s ## number of total SNPs/var = 12226 469s ## number of analyzed SNPs = 10783 470s Start Eigen-Decomposition... 473s REMLE estimate for Vg in the null model: 473s 1.3918 473s -0.1223 2.0525 473s se(Vg): 473s 0.1163 473s 0.1015 0.1769 473s REMLE estimate for Ve in the null model: 473s 0.2245 473s 0.0365 0.3270 473s se(Ve): 473s 0.0101 473s 0.0088 0.0150 473s REMLE likelihood = -4007.1527 473s MLE estimate for Vg in the null model: 473s 1.3928 473s -0.1222 2.0542 473s se(Vg): 473s 0.1163 473s 0.1015 0.1768 473s MLE estimate for Ve in the null model: 473s 0.2243 473s 0.0365 0.3266 473s se(Ve): 473s 0.0101 473s 0.0088 0.0150 473s MLE likelihood = -4007.6750 522s 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% 522s **** INFO: Done. 522s GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 522s Reading Files ... 523s ## number of total individuals = 1940 523s ## number of analyzed individuals = 757 523s ## number of covariates = 1 523s ## number of phenotypes = 1 523s ## number of total SNPs/var = 12226 523s ## number of analyzed SNPs = 10775 526s Start Eigen-Decomposition... 526s pve estimate =0.372151 526s se(pve) =0.0522377 526s Calculating UtX... 530s initial value of h = 0.372151 530s initial value of rho = 0.393216 530s initial value of pi = 0.00194896 530s initial value of |gamma| = 21 534s 0% 0.00 ==== 9% 0.26 ========= 18% 0.25 ============= 27% 0.24 ================== 36% 0.23 ====================== 45% 0.23 =========================== 55% 0.23 =============================== 64% 0.23 ==================================== 73% 0.23 ======================================== 82% 0.22 ============================================= 91% 0.22 ================================================== 100% 0.22 534s **** INFO: Done. 534s GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 534s Reading Files ... 535s ## number of total individuals = 1940 535s ## number of analyzed individuals = 757 535s ## number of covariates = 1 535s ## number of phenotypes = 1 535s ## number of total SNPs/var = 12226 535s ## number of analyzed SNPs = 10775 535s ## number of cases = 409 535s ## number of controls = 348 538s Start Eigen-Decomposition... 538s pve estimate =0.372151 538s se(pve) =0.0522377 538s Calculating UtX... 543s initial value of h = 0.372151 543s initial value of rho = 0.393216 543s initial value of pi = 0.00194896 543s initial value of |gamma| = 21 610s 0% 0.00 ==== 9% 0.11 ========= 18% 0.11 ============= 27% 0.10 ================== 36% 0.10 ====================== 45% 0.10 =========================== 55% 0.10 =============================== 64% 0.10 ==================================== 73% 0.11 ======================================== 82% 0.10 ============================================= 91% 0.10 ================================================== 100% 0.10 610s **** INFO: Done. 610s GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 610s Reading Files ... 611s ## number of total individuals = 1940 611s ## number of analyzed individuals = 757 611s ## number of covariates = 1 611s ## number of phenotypes = 1 611s ## number of total SNPs/var = 12226 611s ## number of analyzed SNPs = 10775 611s Calculating Relatedness Matrix ... 622s 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% 624s **** INFO: Done. 624s GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 624s Reading Files ... 624s ## number of total individuals = 1940 624s ## number of analyzed individuals = 757 624s ## number of covariates = 1 624s ## number of phenotypes = 1 624s Adding Breeding Values ... 625s Start Eigen-Decomposition... 627s 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% 627s **** INFO: Done. 627s GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 627s Reading Files ... 627s ## number of total individuals = 1940 627s ## number of analyzed individuals = 757 627s ## number of covariates = 1 627s ## number of phenotypes = 1 629s 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% 629s **** INFO: Done. 629s GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 629s Reading Files ... 629s ## number of total individuals = 1940 629s ## number of analyzed individuals = 757 629s ## number of covariates = 1 629s ## number of phenotypes = 1 631s 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% 631s **** INFO: Done. 631s GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 631s Reading Files ... 631s ## number of total individuals = 1940 631s ## number of analyzed individuals = 757 631s ## number of covariates = 1 631s ## number of phenotypes = 1 633s 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% **** INFO: Done. 633s ================================================== 100% 633s autopkgtest [01:39:24]: test run-unit-test: -----------------------] 634s run-unit-test PASS 634s autopkgtest [01:39:25]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 634s autopkgtest [01:39:25]: @@@@@@@@@@@@@@@@@@@@ summary 634s run-unit-test PASS 649s Creating nova instance adt-noble-s390x-gemma-20240419-012851-juju-7f2275-prod-proposed-migration-environment-3-7ccc2a65-38f3-4f95-a342-c7d11caf536e from image adt/ubuntu-noble-s390x-server-20240418.img (UUID 85e53509-ea4e-4742-afdb-a30c7e328507)...