0s autopkgtest [01:45:58]: starting date and time: 2026-02-05 01:45:58+0000 0s autopkgtest [01:45:58]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [01:45:58]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.u6hurlzo/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc,src:chiark-tcl --apt-upgrade fastqtl --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=glibc/2.42-2ubuntu5 chiark-tcl/1.3.7build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-arm64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@sto01-arm64-5.secgroup --name adt-resolute-arm64-fastqtl-20260205-014558-juju-7f2275-prod-proposed-migration-environment-15-6fe59253-8b18-418b-a261-ea20cbddbb8e --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-autopkgtest-workers-arm64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 5s Creating nova instance adt-resolute-arm64-fastqtl-20260205-014558-juju-7f2275-prod-proposed-migration-environment-15-6fe59253-8b18-418b-a261-ea20cbddbb8e from image adt/ubuntu-resolute-arm64-server-20260204.img (UUID f58d981d-b271-4157-b9b1-fd704695563c)... 60s autopkgtest [01:46:58]: testbed dpkg architecture: arm64 60s autopkgtest [01:46:58]: testbed apt version: 3.1.14 61s autopkgtest [01:46:59]: @@@@@@@@@@@@@@@@@@@@ test bed setup 61s autopkgtest [01:46:59]: testbed release detected to be: None 63s autopkgtest [01:47:01]: updating testbed package index (apt update) 63s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 63s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 63s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 63s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 63s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [35.4 kB] 63s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5260 B] 63s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [228 kB] 63s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1768 kB] 64s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [262 kB] 64s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [7248 B] 64s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [52.9 kB] 64s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [328 B] 64s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [1540 kB] 64s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [40.2 kB] 64s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [26.0 kB] 64s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [776 B] 68s Fetched 4091 kB in 1s (4346 kB/s) 69s Reading package lists... 70s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 70s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 70s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 70s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 71s Reading package lists... 71s Reading package lists... 71s Building dependency tree... 71s Reading state information... 71s Calculating upgrade... 72s The following packages will be upgraded: 72s libc-bin libc-gconv-modules-extra libc6 locales python3-linkify-it 72s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 72s Need to get 7881 kB of archives. 72s After this operation, 0 B of additional disk space will be used. 72s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libc-gconv-modules-extra arm64 2.42-2ubuntu5 [1413 kB] 72s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libc6 arm64 2.42-2ubuntu5 [1594 kB] 72s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libc-bin arm64 2.42-2ubuntu5 [599 kB] 72s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 locales all 2.42-2ubuntu5 [4255 kB] 72s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-linkify-it all 2.0.3-1ubuntu3 [19.4 kB] 73s dpkg-preconfigure: unable to re-open stdin: No such file or directory 73s Fetched 7881 kB in 1s (12.2 MB/s) 73s (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 ... 89360 files and directories currently installed.) 73s Preparing to unpack .../libc-gconv-modules-extra_2.42-2ubuntu5_arm64.deb ... 73s Unpacking libc-gconv-modules-extra:arm64 (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 73s Setting up libc-gconv-modules-extra:arm64 (2.42-2ubuntu5) ... 74s (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 ... 89360 files and directories currently installed.) 74s Preparing to unpack .../libc6_2.42-2ubuntu5_arm64.deb ... 74s Unpacking libc6:arm64 (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 74s Setting up libc6:arm64 (2.42-2ubuntu5) ... 74s (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 ... 89360 files and directories currently installed.) 74s Preparing to unpack .../libc-bin_2.42-2ubuntu5_arm64.deb ... 74s Unpacking libc-bin (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 74s Setting up libc-bin (2.42-2ubuntu5) ... 74s (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 ... 89360 files and directories currently installed.) 74s Preparing to unpack .../locales_2.42-2ubuntu5_all.deb ... 75s Unpacking locales (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 75s Preparing to unpack .../python3-linkify-it_2.0.3-1ubuntu3_all.deb ... 75s Unpacking python3-linkify-it (2.0.3-1ubuntu3) over (2.0.3-1ubuntu2) ... 75s Setting up locales (2.42-2ubuntu5) ... 76s Generating locales (this might take a while)... 78s en_US.UTF-8... done 78s Generation complete. 78s Setting up python3-linkify-it (2.0.3-1ubuntu3) ... 78s Processing triggers for man-db (2.13.1-1) ... 80s Processing triggers for systemd (259-1ubuntu3) ... 81s autopkgtest [01:47:19]: upgrading testbed (apt dist-upgrade and autopurge) 81s Reading package lists... 81s Building dependency tree... 81s Reading state information... 81s Calculating upgrade... 82s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 82s Reading package lists... 83s Building dependency tree... 83s Reading state information... 83s Solving dependencies... 83s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 87s autopkgtest [01:47:25]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:41:39 UTC 2026 88s autopkgtest [01:47:26]: @@@@@@@@@@@@@@@@@@@@ apt-source fastqtl 93s Get:1 http://ftpmaster.internal/ubuntu resolute/universe fastqtl 2.184+v7+dfsg-5 (dsc) [2406 B] 93s Get:2 http://ftpmaster.internal/ubuntu resolute/universe fastqtl 2.184+v7+dfsg-5 (tar) [17.1 MB] 93s Get:3 http://ftpmaster.internal/ubuntu resolute/universe fastqtl 2.184+v7+dfsg-5 (diff) [21.0 kB] 93s gpgv: Signature made Mon Nov 17 21:53:57 2025 UTC 93s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 93s gpgv: issuer "emollier@debian.org" 93s gpgv: Can't check signature: No public key 93s dpkg-source: warning: cannot verify inline signature for ./fastqtl_2.184+v7+dfsg-5.dsc: no acceptable signature found 94s autopkgtest [01:47:32]: testing package fastqtl version 2.184+v7+dfsg-5 94s autopkgtest [01:47:32]: build not needed 96s autopkgtest [01:47:34]: test run-sample-analysis: preparing testbed 97s Reading package lists... 97s Building dependency tree... 97s Reading state information... 97s Solving dependencies... 98s The following NEW packages will be installed: 98s fastqtl fastqtl-doc libblas3 libboost-iostreams1.88.0 98s libboost-program-options1.88.0 libdeflate0 libgsl28 libgslcblas0 libhts3t64 98s libhtscodecs2 r-mathlib 98s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. 98s Need to get 22.3 MB of archives. 98s After this operation, 31.7 MB of additional disk space will be used. 98s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-7ubuntu1 [181 kB] 98s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libboost-iostreams1.88.0 arm64 1.88.0-1.4ubuntu3 [261 kB] 98s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libboost-program-options1.88.0 arm64 1.88.0-1.4ubuntu3 [326 kB] 98s Get:4 http://ftpmaster.internal/ubuntu resolute/universe arm64 libgslcblas0 arm64 2.8+dfsg-6 [93.1 kB] 98s Get:5 http://ftpmaster.internal/ubuntu resolute/universe arm64 libgsl28 arm64 2.8+dfsg-6 [966 kB] 98s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB] 98s Get:7 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhtscodecs2 arm64 1.6.1-2build1 [83.8 kB] 98s Get:8 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhts3t64 arm64 1.22.1+ds2-1 [442 kB] 98s Get:9 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-mathlib arm64 4.5.2-1ubuntu2 [2621 kB] 98s Get:10 http://ftpmaster.internal/ubuntu resolute/universe arm64 fastqtl arm64 2.184+v7+dfsg-5 [212 kB] 98s Get:11 http://ftpmaster.internal/ubuntu resolute/universe arm64 fastqtl-doc all 2.184+v7+dfsg-5 [17.1 MB] 99s Fetched 22.3 MB in 1s (30.5 MB/s) 99s Selecting previously unselected package libblas3:arm64. 99s (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 ... 89360 files and directories currently installed.) 99s Preparing to unpack .../00-libblas3_3.12.1-7ubuntu1_arm64.deb ... 99s Unpacking libblas3:arm64 (3.12.1-7ubuntu1) ... 99s Selecting previously unselected package libboost-iostreams1.88.0:arm64. 99s Preparing to unpack .../01-libboost-iostreams1.88.0_1.88.0-1.4ubuntu3_arm64.deb ... 99s Unpacking libboost-iostreams1.88.0:arm64 (1.88.0-1.4ubuntu3) ... 99s Selecting previously unselected package libboost-program-options1.88.0:arm64. 99s Preparing to unpack .../02-libboost-program-options1.88.0_1.88.0-1.4ubuntu3_arm64.deb ... 99s Unpacking libboost-program-options1.88.0:arm64 (1.88.0-1.4ubuntu3) ... 99s Selecting previously unselected package libgslcblas0:arm64. 99s Preparing to unpack .../03-libgslcblas0_2.8+dfsg-6_arm64.deb ... 99s Unpacking libgslcblas0:arm64 (2.8+dfsg-6) ... 99s Selecting previously unselected package libgsl28:arm64. 99s Preparing to unpack .../04-libgsl28_2.8+dfsg-6_arm64.deb ... 99s Unpacking libgsl28:arm64 (2.8+dfsg-6) ... 99s Selecting previously unselected package libdeflate0:arm64. 99s Preparing to unpack .../05-libdeflate0_1.23-2_arm64.deb ... 99s Unpacking libdeflate0:arm64 (1.23-2) ... 99s Selecting previously unselected package libhtscodecs2:arm64. 99s Preparing to unpack .../06-libhtscodecs2_1.6.1-2build1_arm64.deb ... 99s Unpacking libhtscodecs2:arm64 (1.6.1-2build1) ... 99s Selecting previously unselected package libhts3t64:arm64. 99s Preparing to unpack .../07-libhts3t64_1.22.1+ds2-1_arm64.deb ... 99s Unpacking libhts3t64:arm64 (1.22.1+ds2-1) ... 99s Selecting previously unselected package r-mathlib. 99s Preparing to unpack .../08-r-mathlib_4.5.2-1ubuntu2_arm64.deb ... 99s Unpacking r-mathlib (4.5.2-1ubuntu2) ... 99s Selecting previously unselected package fastqtl. 99s Preparing to unpack .../09-fastqtl_2.184+v7+dfsg-5_arm64.deb ... 99s Unpacking fastqtl (2.184+v7+dfsg-5) ... 99s Selecting previously unselected package fastqtl-doc. 99s Preparing to unpack .../10-fastqtl-doc_2.184+v7+dfsg-5_all.deb ... 99s Unpacking fastqtl-doc (2.184+v7+dfsg-5) ... 100s Setting up libhtscodecs2:arm64 (1.6.1-2build1) ... 100s Setting up libboost-program-options1.88.0:arm64 (1.88.0-1.4ubuntu3) ... 100s Setting up fastqtl-doc (2.184+v7+dfsg-5) ... 100s Setting up libgslcblas0:arm64 (2.8+dfsg-6) ... 100s Setting up libdeflate0:arm64 (1.23-2) ... 100s Setting up libboost-iostreams1.88.0:arm64 (1.88.0-1.4ubuntu3) ... 100s Setting up libblas3:arm64 (3.12.1-7ubuntu1) ... 100s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 100s Setting up r-mathlib (4.5.2-1ubuntu2) ... 100s Setting up libhts3t64:arm64 (1.22.1+ds2-1) ... 100s Setting up libgsl28:arm64 (2.8+dfsg-6) ... 100s Setting up fastqtl (2.184+v7+dfsg-5) ... 100s Processing triggers for man-db (2.13.1-1) ... 100s Processing triggers for libc-bin (2.42-2ubuntu5) ... 102s autopkgtest [01:47:40]: test run-sample-analysis: [----------------------- 102s covariates.txt.gz 102s genotypes.vcf.gz 102s genotypes.vcf.gz.tbi 102s interaction.txt 102s phenotypes.bed.gz 102s phenotypes.bed.gz.tbi 102s 102s Fast QTL 102s * Authors : Olivier DELANEAU, Halit ONGEN, Alfonso BUIL & Manolis DERMITZAKIS 102s * Contact : olivier.delaneau@gmail.com 102s * Webpage : http://fastqtl.sourceforge.net/ 102s * Version : v2.184_gtex 102s 102s Perform permutation based interaction analysis (used to calculate corrected p-values for MPs) 102s * Perform 100 permutations 102s * Test interaction with term from [interaction.txt] 102s * Random number generator is seeded with 1 102s * Considering variants within 1e+06 bp of the MPs 102s * Using minor allele frequency threshold = 0.0000 102s * Using minor allele sample threshold = 0 102s * Using INFO field AF threshold = 0.0000 102s * Chunk processed 1 / 100 102s 102s Scanning phenotype data in [phenotypes.bed.gz] 102s * 364 phenotypes 102s 102s Reading phenotype data in [phenotypes.bed.gz] 102s * region = 22:17517460-17646177 102s * 373 samples included 102s * 4 phenotypes included 102s 102s Reading genotype data in [genotypes.vcf.gz] in VCF format 102s * region = 22:16517460-18646177 103s * 373 samples included 103s * 8580 sites included 103s 103s Reading covariates in [covariates.txt.gz] 103s * 373 samples included 103s * 4 covariate(s) included 103s 103s Reading interaction term in [interaction.txt] 103s * 373 samples included 103s 103s Imputing missing genotypes 103s 103s Imputing missing phenotypes 103s 103s Initialize covariate 103s 103s Processing gene [ENSG00000237438.1] 103s * Number of variants in cis = 7966 111s * Beta distribution parameters = 1.0382 2287.7101 111s * Progress = 25.0% 111s 111s Processing gene [ENSG00000177663.8] 111s * Number of variants in cis = 8165 119s * Beta distribution parameters = 0.7994 2826.0721 119s * Progress = 50.0% 119s 119s Processing gene [ENSG00000183307.3] 119s * Number of variants in cis = 8279 128s * Beta distribution parameters = 0.9595 9906.5566 128s * Progress = 75.0% 128s 128s Processing gene [ENSG00000069998.8] 128s * Number of variants in cis = 8466 136s * Beta distribution parameters = 0.9606 4564.2130 136s * Progress = 100.0% 136s 136s Running time: 33 seconds 136s autopkgtest [01:48:14]: test run-sample-analysis: -----------------------] 137s run-sample-analysis PASS 137s autopkgtest [01:48:15]: test run-sample-analysis: - - - - - - - - - - results - - - - - - - - - - 137s autopkgtest [01:48:15]: @@@@@@@@@@@@@@@@@@@@ summary 137s run-sample-analysis PASS