0s autopkgtest [03:50:25]: starting date and time: 2026-02-05 03:50:25+0000 0s autopkgtest [03:50:25]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [03:50:25]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.5fig6ngm/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade fastqtl --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.42-2ubuntu5 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-ppc64el-29.secgroup --name adt-resolute-ppc64el-fastqtl-20260205-035024-juju-7f2275-prod-proposed-migration-environment-2-4826651b-7448-4e24-a20f-047964e2c3b8 --image adt/ubuntu-resolute-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-ppc64el -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-ppc64el-fastqtl-20260205-035024-juju-7f2275-prod-proposed-migration-environment-2-4826651b-7448-4e24-a20f-047964e2c3b8 from image adt/ubuntu-resolute-ppc64el-server-20260205.img (UUID f866c950-0b62-4023-bac6-0f13279e15ed)... 71s autopkgtest [03:51:36]: testbed dpkg architecture: ppc64el 71s autopkgtest [03:51:36]: testbed apt version: 3.1.14 72s autopkgtest [03:51:37]: @@@@@@@@@@@@@@@@@@@@ test bed setup 72s autopkgtest [03:51:37]: testbed release detected to be: None 73s autopkgtest [03:51:38]: updating testbed package index (apt update) 73s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 73s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 73s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 73s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 73s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [35.4 kB] 73s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5260 B] 73s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1719 kB] 74s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [227 kB] 74s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el Packages [257 kB] 74s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el Packages [1449 kB] 74s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse ppc64el Packages [21.6 kB] 75s Fetched 3839 kB in 1s (2744 kB/s) 75s Reading package lists... 76s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 76s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 76s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 76s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 77s Reading package lists... 77s Reading package lists... 77s Building dependency tree... 77s Reading state information... 78s Calculating upgrade... 78s The following packages will be upgraded: 78s libc-bin libc-gconv-modules-extra libc6 locales pollinate 78s python3-referencing sed 78s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 78s Need to get 8612 kB of archives. 78s After this operation, 0 B of additional disk space will be used. 78s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el sed ppc64el 4.9-2build3 [211 kB] 78s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el libc-gconv-modules-extra ppc64el 2.42-2ubuntu5 [1448 kB] 78s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el libc6 ppc64el 2.42-2ubuntu5 [1913 kB] 78s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el libc-bin ppc64el 2.42-2ubuntu5 [748 kB] 78s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el locales all 2.42-2ubuntu5 [4255 kB] 79s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el pollinate all 4.33-4ubuntu5 [14.0 kB] 79s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-referencing all 0.36.2-1ubuntu2 [22.2 kB] 79s dpkg-preconfigure: unable to re-open stdin: No such file or directory 79s Fetched 8612 kB in 1s (9602 kB/s) 79s (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 ... 82008 files and directories currently installed.) 79s Preparing to unpack .../sed_4.9-2build3_ppc64el.deb ... 79s Unpacking sed (4.9-2build3) over (4.9-2build2) ... 80s Setting up sed (4.9-2build3) ... 80s (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 ... 82008 files and directories currently installed.) 80s Preparing to unpack .../libc-gconv-modules-extra_2.42-2ubuntu5_ppc64el.deb ... 80s Unpacking libc-gconv-modules-extra:ppc64el (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 80s Setting up libc-gconv-modules-extra:ppc64el (2.42-2ubuntu5) ... 80s (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 ... 82008 files and directories currently installed.) 80s Preparing to unpack .../libc6_2.42-2ubuntu5_ppc64el.deb ... 81s Unpacking libc6:ppc64el (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 81s Setting up libc6:ppc64el (2.42-2ubuntu5) ... 82s (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 ... 82008 files and directories currently installed.) 82s Preparing to unpack .../libc-bin_2.42-2ubuntu5_ppc64el.deb ... 82s Unpacking libc-bin (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 82s Setting up libc-bin (2.42-2ubuntu5) ... 82s (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 ... 82008 files and directories currently installed.) 82s Preparing to unpack .../locales_2.42-2ubuntu5_all.deb ... 82s Unpacking locales (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 83s Preparing to unpack .../pollinate_4.33-4ubuntu5_all.deb ... 83s Unpacking pollinate (4.33-4ubuntu5) over (4.33-4ubuntu4) ... 83s Preparing to unpack .../python3-referencing_0.36.2-1ubuntu2_all.deb ... 83s Unpacking python3-referencing (0.36.2-1ubuntu2) over (0.36.2-1ubuntu1) ... 83s Setting up locales (2.42-2ubuntu5) ... 83s Generating locales (this might take a while)... 85s en_US.UTF-8... done 85s Generation complete. 85s Setting up pollinate (4.33-4ubuntu5) ... 95s Setting up python3-referencing (0.36.2-1ubuntu2) ... 95s Processing triggers for man-db (2.13.1-1) ... 97s Processing triggers for install-info (7.2-5) ... 98s Processing triggers for systemd (259-1ubuntu3) ... 99s autopkgtest [03:52:04]: upgrading testbed (apt dist-upgrade and autopurge) 99s Reading package lists... 99s Building dependency tree... 99s Reading state information... 99s Calculating upgrade... 99s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 99s Reading package lists... 100s Building dependency tree... 100s Reading state information... 100s Solving dependencies... 100s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 100s autopkgtest [03:52:05]: rebooting testbed after setup commands that affected boot 140s autopkgtest [03:52:45]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:45:54 UTC 2026 143s autopkgtest [03:52:48]: @@@@@@@@@@@@@@@@@@@@ apt-source fastqtl 147s Get:1 http://ftpmaster.internal/ubuntu resolute/universe fastqtl 2.184+v7+dfsg-5 (dsc) [2406 B] 147s Get:2 http://ftpmaster.internal/ubuntu resolute/universe fastqtl 2.184+v7+dfsg-5 (tar) [17.1 MB] 147s Get:3 http://ftpmaster.internal/ubuntu resolute/universe fastqtl 2.184+v7+dfsg-5 (diff) [21.0 kB] 147s gpgv: Signature made Mon Nov 17 21:53:57 2025 UTC 147s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 147s gpgv: issuer "emollier@debian.org" 147s gpgv: Can't check signature: No public key 147s dpkg-source: warning: cannot verify inline signature for ./fastqtl_2.184+v7+dfsg-5.dsc: no acceptable signature found 148s autopkgtest [03:52:53]: testing package fastqtl version 2.184+v7+dfsg-5 148s autopkgtest [03:52:53]: build not needed 151s autopkgtest [03:52:56]: test run-sample-analysis: preparing testbed 151s Reading package lists... 151s Building dependency tree... 151s Reading state information... 151s Solving dependencies... 151s The following NEW packages will be installed: 151s fastqtl fastqtl-doc libblas3 libboost-iostreams1.88.0 151s libboost-program-options1.88.0 libdeflate0 libgsl28 libgslcblas0 libhts3t64 151s libhtscodecs2 r-mathlib 151s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. 151s Need to get 23.3 MB of archives. 151s After this operation, 34.8 MB of additional disk space will be used. 151s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el libblas3 ppc64el 3.12.1-7ubuntu1 [291 kB] 151s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el libboost-iostreams1.88.0 ppc64el 1.88.0-1.4ubuntu3 [262 kB] 151s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el libboost-program-options1.88.0 ppc64el 1.88.0-1.4ubuntu3 [334 kB] 151s Get:4 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libgslcblas0 ppc64el 2.8+dfsg-6 [283 kB] 151s Get:5 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libgsl28 ppc64el 2.8+dfsg-6 [1411 kB] 151s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdeflate0 ppc64el 1.23-2 [63.3 kB] 151s Get:7 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhtscodecs2 ppc64el 1.6.1-2build1 [119 kB] 151s Get:8 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhts3t64 ppc64el 1.22.1+ds2-1 [617 kB] 151s Get:9 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-mathlib ppc64el 4.5.2-1ubuntu2 [2665 kB] 151s Get:10 http://ftpmaster.internal/ubuntu resolute/universe ppc64el fastqtl ppc64el 2.184+v7+dfsg-5 [250 kB] 152s Get:11 http://ftpmaster.internal/ubuntu resolute/universe ppc64el fastqtl-doc all 2.184+v7+dfsg-5 [17.1 MB] 152s Fetched 23.3 MB in 1s (31.4 MB/s) 152s Selecting previously unselected package libblas3:ppc64el. 152s (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 ... 82008 files and directories currently installed.) 152s Preparing to unpack .../00-libblas3_3.12.1-7ubuntu1_ppc64el.deb ... 152s Unpacking libblas3:ppc64el (3.12.1-7ubuntu1) ... 152s Selecting previously unselected package libboost-iostreams1.88.0:ppc64el. 152s Preparing to unpack .../01-libboost-iostreams1.88.0_1.88.0-1.4ubuntu3_ppc64el.deb ... 152s Unpacking libboost-iostreams1.88.0:ppc64el (1.88.0-1.4ubuntu3) ... 152s Selecting previously unselected package libboost-program-options1.88.0:ppc64el. 152s Preparing to unpack .../02-libboost-program-options1.88.0_1.88.0-1.4ubuntu3_ppc64el.deb ... 152s Unpacking libboost-program-options1.88.0:ppc64el (1.88.0-1.4ubuntu3) ... 152s Selecting previously unselected package libgslcblas0:ppc64el. 152s Preparing to unpack .../03-libgslcblas0_2.8+dfsg-6_ppc64el.deb ... 152s Unpacking libgslcblas0:ppc64el (2.8+dfsg-6) ... 152s Selecting previously unselected package libgsl28:ppc64el. 152s Preparing to unpack .../04-libgsl28_2.8+dfsg-6_ppc64el.deb ... 152s Unpacking libgsl28:ppc64el (2.8+dfsg-6) ... 152s Selecting previously unselected package libdeflate0:ppc64el. 152s Preparing to unpack .../05-libdeflate0_1.23-2_ppc64el.deb ... 152s Unpacking libdeflate0:ppc64el (1.23-2) ... 152s Selecting previously unselected package libhtscodecs2:ppc64el. 152s Preparing to unpack .../06-libhtscodecs2_1.6.1-2build1_ppc64el.deb ... 152s Unpacking libhtscodecs2:ppc64el (1.6.1-2build1) ... 152s Selecting previously unselected package libhts3t64:ppc64el. 152s Preparing to unpack .../07-libhts3t64_1.22.1+ds2-1_ppc64el.deb ... 152s Unpacking libhts3t64:ppc64el (1.22.1+ds2-1) ... 153s Selecting previously unselected package r-mathlib. 153s Preparing to unpack .../08-r-mathlib_4.5.2-1ubuntu2_ppc64el.deb ... 153s Unpacking r-mathlib (4.5.2-1ubuntu2) ... 153s Selecting previously unselected package fastqtl. 153s Preparing to unpack .../09-fastqtl_2.184+v7+dfsg-5_ppc64el.deb ... 153s Unpacking fastqtl (2.184+v7+dfsg-5) ... 153s Selecting previously unselected package fastqtl-doc. 153s Preparing to unpack .../10-fastqtl-doc_2.184+v7+dfsg-5_all.deb ... 153s Unpacking fastqtl-doc (2.184+v7+dfsg-5) ... 153s Setting up libhtscodecs2:ppc64el (1.6.1-2build1) ... 153s Setting up libboost-program-options1.88.0:ppc64el (1.88.0-1.4ubuntu3) ... 153s Setting up fastqtl-doc (2.184+v7+dfsg-5) ... 153s Setting up libgslcblas0:ppc64el (2.8+dfsg-6) ... 153s Setting up libdeflate0:ppc64el (1.23-2) ... 153s Setting up libboost-iostreams1.88.0:ppc64el (1.88.0-1.4ubuntu3) ... 153s Setting up libblas3:ppc64el (3.12.1-7ubuntu1) ... 153s 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 153s Setting up r-mathlib (4.5.2-1ubuntu2) ... 153s Setting up libhts3t64:ppc64el (1.22.1+ds2-1) ... 153s Setting up libgsl28:ppc64el (2.8+dfsg-6) ... 153s Setting up fastqtl (2.184+v7+dfsg-5) ... 153s Processing triggers for man-db (2.13.1-1) ... 154s Processing triggers for libc-bin (2.42-2ubuntu5) ... 155s autopkgtest [03:53:00]: test run-sample-analysis: [----------------------- 156s covariates.txt.gz 156s genotypes.vcf.gz 156s genotypes.vcf.gz.tbi 156s interaction.txt 156s phenotypes.bed.gz 156s phenotypes.bed.gz.tbi 156s 156s Fast QTL 156s * Authors : Olivier DELANEAU, Halit ONGEN, Alfonso BUIL & Manolis DERMITZAKIS 156s * Contact : olivier.delaneau@gmail.com 156s * Webpage : http://fastqtl.sourceforge.net/ 156s * Version : v2.184_gtex 156s 156s Perform permutation based interaction analysis (used to calculate corrected p-values for MPs) 156s * Perform 100 permutations 156s * Test interaction with term from [interaction.txt] 156s * Random number generator is seeded with 1 156s * Considering variants within 1e+06 bp of the MPs 156s * Using minor allele frequency threshold = 0.0000 156s * Using minor allele sample threshold = 0 156s * Using INFO field AF threshold = 0.0000 156s * Chunk processed 1 / 100 156s 156s Scanning phenotype data in [phenotypes.bed.gz] 156s * 364 phenotypes 156s 156s Reading phenotype data in [phenotypes.bed.gz] 156s * region = 22:17517460-17646177 156s * 373 samples included 156s * 4 phenotypes included 156s 156s Reading genotype data in [genotypes.vcf.gz] in VCF format 156s * region = 22:16517460-18646177 156s * 373 samples included 156s * 8580 sites included 156s 156s Reading covariates in [covariates.txt.gz] 156s * 373 samples included 156s * 4 covariate(s) included 156s 156s Reading interaction term in [interaction.txt] 156s * 373 samples included 156s 156s Imputing missing genotypes 156s 156s Imputing missing phenotypes 156s 156s Initialize covariate 156s 156s Processing gene [ENSG00000237438.1] 156s * Number of variants in cis = 7966 168s * Beta distribution parameters = 1.0382 2287.7101 168s * Progress = 25.0% 168s 168s Processing gene [ENSG00000177663.8] 168s * Number of variants in cis = 8165 180s * Beta distribution parameters = 0.7994 2826.0721 180s * Progress = 50.0% 180s 180s Processing gene [ENSG00000183307.3] 180s * Number of variants in cis = 8279 192s * Beta distribution parameters = 0.9595 9906.5566 192s * Progress = 75.0% 192s 192s Processing gene [ENSG00000069998.8] 192s * Number of variants in cis = 8466 204s * Beta distribution parameters = 0.9606 4564.2130 204s * Progress = 100.0% 204s 204s Running time: 49 seconds 205s autopkgtest [03:53:50]: test run-sample-analysis: -----------------------] 205s run-sample-analysis PASS 205s autopkgtest [03:53:50]: test run-sample-analysis: - - - - - - - - - - results - - - - - - - - - - 205s autopkgtest [03:53:50]: @@@@@@@@@@@@@@@@@@@@ summary 205s run-sample-analysis PASS