0s autopkgtest [23:43:06]: starting date and time: 2025-03-15 23:43:06+0000 0s autopkgtest [23:43:06]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [23:43:06]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.73kr943p/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade shapeit4 --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-s390x-11.secgroup --name adt-plucky-s390x-shapeit4-20250315-234306-juju-7f2275-prod-proposed-migration-environment-2-0b09e17a-234f-4353-bc0b-8685ff0df875 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-s390x -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,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 120s autopkgtest [23:45:06]: testbed dpkg architecture: s390x 120s autopkgtest [23:45:06]: testbed apt version: 2.9.33 121s autopkgtest [23:45:07]: @@@@@@@@@@@@@@@@@@@@ test bed setup 121s autopkgtest [23:45:07]: testbed release detected to be: None 121s autopkgtest [23:45:07]: updating testbed package index (apt update) 122s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 122s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 122s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 122s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 122s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [369 kB] 123s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.5 kB] 123s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [44.1 kB] 123s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [76.2 kB] 123s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1788 B] 123s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 123s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [321 kB] 123s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [13.0 kB] 123s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3532 B] 123s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [240 B] 123s Fetched 970 kB in 1s (698 kB/s) 124s Reading package lists... 124s Reading package lists... 124s Building dependency tree... 124s Reading state information... 125s Calculating upgrade... 125s Calculating upgrade... 125s The following packages were automatically installed and are no longer required: 125s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 125s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 125s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 125s linux-tools-6.11.0-8-generic 125s Use 'sudo apt autoremove' to remove them. 125s The following packages will be upgraded: 125s pinentry-curses python3-jinja2 strace 125s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 125s Need to get 652 kB of archives. 125s After this operation, 27.6 kB of additional disk space will be used. 125s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB] 125s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pinentry-curses s390x 1.3.1-2ubuntu3 [42.9 kB] 125s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 126s Fetched 652 kB in 1s (886 kB/s) 126s (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 ... 81428 files and directories currently installed.) 126s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ... 126s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 126s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_s390x.deb ... 126s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 126s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 126s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 126s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 126s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 126s Setting up strace (6.13+ds-1ubuntu1) ... 126s Processing triggers for man-db (2.13.0-1) ... 127s Reading package lists... 127s Building dependency tree... 127s Reading state information... 127s Solving dependencies... 127s The following packages will be REMOVED: 127s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 127s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 127s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 127s linux-tools-6.11.0-8-generic* 127s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded. 127s After this operation, 167 MB disk space will be freed. 127s (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 ... 81428 files and directories currently installed.) 127s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 127s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 127s Removing libpython3.12t64:s390x (3.12.9-1) ... 127s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 127s Removing libnsl2:s390x (1.3.0-3build3) ... 127s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 127s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 127s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 128s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 128s Processing triggers for libc-bin (2.41-1ubuntu1) ... 128s (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 ... 56328 files and directories currently installed.) 128s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 128s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 128s autopkgtest [23:45:14]: upgrading testbed (apt dist-upgrade and autopurge) 128s Reading package lists... 128s Building dependency tree... 128s Reading state information... 129s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 129s Starting 2 pkgProblemResolver with broken count: 0 129s Done 129s Entering ResolveByKeep 129s 129s Calculating upgrade... 129s The following packages will be upgraded: 129s libc-bin libc-dev-bin libc6 libc6-dev locales 129s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 129s Need to get 9512 kB of archives. 129s After this operation, 8192 B of additional disk space will be used. 129s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB] 130s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB] 130s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB] 130s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB] 130s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB] 130s Preconfiguring packages ... 131s Fetched 9512 kB in 1s (8092 kB/s) 131s (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 ... 56326 files and directories currently installed.) 131s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ... 131s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 131s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ... 131s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 131s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ... 131s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 131s Setting up libc6:s390x (2.41-1ubuntu2) ... 131s (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 ... 56326 files and directories currently installed.) 131s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ... 131s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 131s Setting up libc-bin (2.41-1ubuntu2) ... 131s (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 ... 56326 files and directories currently installed.) 131s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 131s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 131s Setting up locales (2.41-1ubuntu2) ... 131s Generating locales (this might take a while)... 132s en_US.UTF-8... done 132s Generation complete. 132s Setting up libc-dev-bin (2.41-1ubuntu2) ... 132s Setting up libc6-dev:s390x (2.41-1ubuntu2) ... 132s Processing triggers for man-db (2.13.0-1) ... 133s Processing triggers for systemd (257.3-1ubuntu3) ... 134s Reading package lists... 134s Building dependency tree... 134s Reading state information... 134s Starting pkgProblemResolver with broken count: 0 134s Starting 2 pkgProblemResolver with broken count: 0 134s Done 134s Solving dependencies... 134s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 135s autopkgtest [23:45:21]: rebooting testbed after setup commands that affected boot 152s autopkgtest [23:45:38]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025 155s autopkgtest [23:45:41]: @@@@@@@@@@@@@@@@@@@@ apt-source shapeit4 160s Get:1 http://ftpmaster.internal/ubuntu plucky/universe shapeit4 4.2.2+dfsg-1build3 (dsc) [2237 B] 160s Get:2 http://ftpmaster.internal/ubuntu plucky/universe shapeit4 4.2.2+dfsg-1build3 (tar) [59.0 MB] 160s Get:3 http://ftpmaster.internal/ubuntu plucky/universe shapeit4 4.2.2+dfsg-1build3 (diff) [5424 B] 160s gpgv: Signature made Mon Apr 1 08:00:11 2024 UTC 160s gpgv: using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984 160s gpgv: Can't check signature: No public key 160s dpkg-source: warning: cannot verify inline signature for ./shapeit4_4.2.2+dfsg-1build3.dsc: no acceptable signature found 161s autopkgtest [23:45:47]: testing package shapeit4 version 4.2.2+dfsg-1build3 161s autopkgtest [23:45:47]: build not needed 164s autopkgtest [23:45:50]: test run-sample-analysis: preparing testbed 165s Reading package lists... 165s Building dependency tree... 165s Reading state information... 165s Starting pkgProblemResolver with broken count: 0 165s Starting 2 pkgProblemResolver with broken count: 0 165s Done 165s The following NEW packages will be installed: 165s libboost-iostreams1.83.0 libboost-program-options1.83.0 libdeflate0 165s libhts3t64 libhtscodecs2 shapeit4 shapeit4-example 165s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 165s Need to get 53.7 MB of archives. 165s After this operation, 59.1 MB of additional disk space will be used. 165s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libboost-iostreams1.83.0 s390x 1.83.0-4.1ubuntu2 [259 kB] 165s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libboost-program-options1.83.0 s390x 1.83.0-4.1ubuntu2 [326 kB] 166s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate0 s390x 1.23-1 [46.1 kB] 166s Get:4 http://ftpmaster.internal/ubuntu plucky/universe s390x libhtscodecs2 s390x 1.6.1-2 [91.0 kB] 166s Get:5 http://ftpmaster.internal/ubuntu plucky/universe s390x libhts3t64 s390x 1.21+ds-1 [479 kB] 166s Get:6 http://ftpmaster.internal/ubuntu plucky/universe s390x shapeit4 s390x 4.2.2+dfsg-1build3 [198 kB] 166s Get:7 http://ftpmaster.internal/ubuntu plucky/universe s390x shapeit4-example all 4.2.2+dfsg-1build3 [52.3 MB] 170s Fetched 53.7 MB in 5s (11.2 MB/s) 170s Selecting previously unselected package libboost-iostreams1.83.0:s390x. 170s (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 ... 56326 files and directories currently installed.) 170s Preparing to unpack .../0-libboost-iostreams1.83.0_1.83.0-4.1ubuntu2_s390x.deb ... 170s Unpacking libboost-iostreams1.83.0:s390x (1.83.0-4.1ubuntu2) ... 170s Selecting previously unselected package libboost-program-options1.83.0:s390x. 170s Preparing to unpack .../1-libboost-program-options1.83.0_1.83.0-4.1ubuntu2_s390x.deb ... 170s Unpacking libboost-program-options1.83.0:s390x (1.83.0-4.1ubuntu2) ... 170s Selecting previously unselected package libdeflate0:s390x. 170s Preparing to unpack .../2-libdeflate0_1.23-1_s390x.deb ... 170s Unpacking libdeflate0:s390x (1.23-1) ... 170s Selecting previously unselected package libhtscodecs2:s390x. 170s Preparing to unpack .../3-libhtscodecs2_1.6.1-2_s390x.deb ... 170s Unpacking libhtscodecs2:s390x (1.6.1-2) ... 170s Selecting previously unselected package libhts3t64:s390x. 170s Preparing to unpack .../4-libhts3t64_1.21+ds-1_s390x.deb ... 170s Unpacking libhts3t64:s390x (1.21+ds-1) ... 170s Selecting previously unselected package shapeit4. 170s Preparing to unpack .../5-shapeit4_4.2.2+dfsg-1build3_s390x.deb ... 170s Unpacking shapeit4 (4.2.2+dfsg-1build3) ... 170s Selecting previously unselected package shapeit4-example. 170s Preparing to unpack .../6-shapeit4-example_4.2.2+dfsg-1build3_all.deb ... 170s Unpacking shapeit4-example (4.2.2+dfsg-1build3) ... 170s Setting up libhtscodecs2:s390x (1.6.1-2) ... 170s Setting up libboost-program-options1.83.0:s390x (1.83.0-4.1ubuntu2) ... 170s Setting up libdeflate0:s390x (1.23-1) ... 170s Setting up shapeit4-example (4.2.2+dfsg-1build3) ... 170s Setting up libboost-iostreams1.83.0:s390x (1.83.0-4.1ubuntu2) ... 170s Setting up libhts3t64:s390x (1.21+ds-1) ... 170s Setting up shapeit4 (4.2.2+dfsg-1build3) ... 170s Processing triggers for man-db (2.13.0-1) ... 171s Processing triggers for libc-bin (2.41-1ubuntu2) ... 172s autopkgtest [23:45:58]: test run-sample-analysis: [----------------------- 172s + shapeit4 --input unphased.vcf.gz --map chr20.b37.gmap.gz --region 20:2000000-3000000 --thread 4 --output phased.vcf.gz 172s 172s SHAPEIT 172s * Author : Olivier DELANEAU, University of Lausanne 172s * Contact : olivier.delaneau@gmail.com 172s * Version : 4.2.2 172s * Run date : 15/03/2025 - 23:47:24 172s 172s Files: 172s * Input VCF : [unphased.vcf.gz] 172s * Genetic Map : [chr20.b37.gmap.gz] 172s * Output VCF : [phased.vcf.gz] 172s 172s Parameters: 172s * Seed : 15052011 172s * Threads : 4 threads 172s * MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m] 172s * PBWT : Depth of PBWT neighbours to condition on: 4 172s * PBWT : Store indexes at variants [MAC>=2 / MDR<=0.5 / Dist=0.02 cM] 172s * HMM : K is variable / min W is 2.50cM / Ne is 15000 172s * HMM : Recombination rates given by genetic map 172s * HMM : AVX2 optimization inactive / Activating AVX2 substantially improves performance 172s 172s Initialization: 172s * VCF/BCF scanning ... * VCF/BCF scanning [N=203 / L=8651 / Reg=20:2000000-3000000] (0.06s) 172s * VCF/BCF parsing [0%] * VCF/BCF parsing [1%] * VCF/BCF parsing [2%] * VCF/BCF parsing [3%] * VCF/BCF parsing [4%] * VCF/BCF parsing [5%] * VCF/BCF parsing [6%] * VCF/BCF parsing [7%] * VCF/BCF parsing [8%] * VCF/BCF parsing [9%] * VCF/BCF parsing [10%] * VCF/BCF parsing [11%] * VCF/BCF parsing [12%] * VCF/BCF parsing [13%] * VCF/BCF parsing [14%] * VCF/BCF parsing [15%] * VCF/BCF parsing [16%] * VCF/BCF parsing [17%] * VCF/BCF parsing [18%] * VCF/BCF parsing [19%] * VCF/BCF parsing [20%] * VCF/BCF parsing [21%] * VCF/BCF parsing [22%] * VCF/BCF parsing [23%] * VCF/BCF parsing [24%] * VCF/BCF parsing [25%] * VCF/BCF parsing [26%] * VCF/BCF parsing [27%] * VCF/BCF parsing [28%] * VCF/BCF parsing [29%] * VCF/BCF parsing [30%] * VCF/BCF parsing [31%] * VCF/BCF parsing [32%] * VCF/BCF parsing [33%] * VCF/BCF parsing [34%] * VCF/BCF parsing [35%] * VCF/BCF parsing [36%] * VCF/BCF parsing [37%] * VCF/BCF parsing [38%] * VCF/BCF parsing [39%] * VCF/BCF parsing [40%] * VCF/BCF parsing [41%] * VCF/BCF parsing [42%] * VCF/BCF parsing [43%] * VCF/BCF parsing [44%] * VCF/BCF parsing [45%] * VCF/BCF parsing [46%] * VCF/BCF parsing [47%] * VCF/BCF parsing [48%] * VCF/BCF parsing [49%] * VCF/BCF parsing [50%] * VCF/BCF parsing [51%] * VCF/BCF parsing [52%] * VCF/BCF parsing [53%] * VCF/BCF parsing [54%] * VCF/BCF parsing [55%] * VCF/BCF parsing [56%] * VCF/BCF parsing [57%] * VCF/BCF parsing [58%] * VCF/BCF parsing [59%] * VCF/BCF parsing [60%] * VCF/BCF parsing [61%] * VCF/BCF parsing [62%] * VCF/BCF parsing [63%] * VCF/BCF parsing [64%] * VCF/BCF parsing [65%] * VCF/BCF parsing [66%] * VCF/BCF parsing [67%] * VCF/BCF parsing [68%] * VCF/BCF parsing [69%] * VCF/BCF parsing [70%] * VCF/BCF parsing [71%] * VCF/BCF parsing [72%] * VCF/BCF parsing [73%] * VCF/BCF parsing [74%] * VCF/BCF parsing [75%] * VCF/BCF parsing [76%] * VCF/BCF parsing [77%] * VCF/BCF parsing [78%] * VCF/BCF parsing [79%] * VCF/BCF parsing [80%] * VCF/BCF parsing [81%] * VCF/BCF parsing [82%] * VCF/BCF parsing [83%] * VCF/BCF parsing [84%] * VCF/BCF parsing [85%] * VCF/BCF parsing [86%] * VCF/BCF parsing [87%] * VCF/BCF parsing [88%] * VCF/BCF parsing [89%] * VCF/BCF parsing [90%] * VCF/BCF parsing [91%] * VCF/BCF parsing [92%] * VCF/BCF parsing [93%] * VCF/BCF parsing [94%] * VCF/BCF parsing [95%] * VCF/BCF parsing [96%] * VCF/BCF parsing [97%] * VCF/BCF parsing [98%] * VCF/BCF parsing [99%] * VCF/BCF parsing [100%] * VCF/BCF parsing [Hom=89.3% / Het=10.7% / Mis=0.0%] (0.08s) 172s * GMAP parsing [n=82962] (0.05s) 172s * cM interpolation [s=1236 / i=7415] (0.00s) 172s * Region length [999850 bp / 2.5 cM] 172s * HMM parameters [Ne=15000 / Error=0.0001 / #rare=2243] 172s * PBWT indexing [l=120] (0.00s) 172s * HAP update (0.03s) 172s * H2V transpose (0.00s) 173s * PBWT phase sweep [0%] * PBWT phase sweep [1%] * PBWT phase sweep [2%] * PBWT phase sweep [3%] * PBWT phase sweep [4%] * PBWT phase sweep [5%] * PBWT phase sweep [6%] * PBWT phase sweep [7%] * PBWT phase sweep [8%] * PBWT phase sweep [9%] * PBWT phase sweep [10%] * PBWT phase sweep [11%] * PBWT phase sweep [12%] * PBWT phase sweep [13%] * PBWT phase sweep [14%] * PBWT phase sweep [15%] * PBWT phase sweep [16%] * PBWT phase sweep [17%] * PBWT phase sweep [18%] * PBWT phase sweep [19%] * PBWT phase sweep [20%] * PBWT phase sweep [21%] * PBWT phase sweep [22%] * PBWT phase sweep [23%] * PBWT phase sweep [24%] * PBWT phase sweep [25%] * PBWT phase sweep [26%] * 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#contraints=0 / #merged = 0] 174s * HAP update (0.00s) 174s * H2V transpose (0.00s) 174s 174s Burn-in iteration [2/5] 174s * V2H transpose (0.00s) 174s * PBWT selection [0%] * PBWT selection [1%] * PBWT selection [2%] * PBWT selection [3%] * PBWT selection [4%] * PBWT selection [5%] * PBWT selection [6%] * PBWT selection [7%] * PBWT selection [8%] * PBWT selection [9%] * PBWT selection [10%] * PBWT selection [11%] * PBWT selection [12%] * PBWT selection [13%] * PBWT selection [14%] * PBWT selection [15%] * PBWT selection [16%] * PBWT selection [17%] * PBWT selection [18%] * PBWT selection [19%] * PBWT selection [20%] * PBWT selection [21%] * PBWT selection [22%] * PBWT selection [23%] * PBWT selection [24%] * PBWT selection [25%] * PBWT selection [26%] * PBWT selection [27%] * PBWT selection [28%] * PBWT selection [29%] * PBWT selection [30%] * PBWT selection [31%] * PBWT selection [32%] * PBWT selection [33%] * PBWT selection [34%] * PBWT selection [35%] * PBWT selection [36%] * PBWT 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computations [K=327.187+/-8.138 / W=1.00Mb] (1.24s) 195s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 195s * HAP update (0.00s) 195s * H2V transpose (0.00s) 195s 195s Finalization: 195s * HAP solving (0.02s) 195s * HAP update (0.00s) 195s * H2V transpose (0.00s) 195s * VCF writing [0%] * VCF writing [1%] * VCF writing [2%] * VCF writing [3%] * VCF writing [4%] * VCF writing [5%] * VCF writing [6%] * VCF writing [7%] * VCF writing [8%] * VCF writing [9%] * VCF writing [10%] * VCF writing [11%] * VCF writing [12%] * VCF writing [13%] * VCF writing [14%] * VCF writing [15%] * VCF writing [16%] * VCF writing [17%] * VCF writing [18%] * VCF writing [19%] * VCF writing [20%] * VCF writing [21%] * VCF writing [22%] * VCF writing [23%] * VCF writing [24%] * VCF writing [25%] * VCF writing [26%] * VCF writing [27%] * VCF writing [28%] * VCF writing [29%] * VCF writing [30%] * VCF writing [31%] * VCF writing [32%] * VCF writing [33%] * VCF writing [34%] * VCF writing [35%] * VCF writing [36%] * VCF writing [37%] * VCF writing [38%] * VCF writing [39%] * VCF writing [40%] * VCF writing [41%] * VCF writing [42%] * VCF writing [43%] * VCF writing [44%] * VCF writing [45%] * VCF writing [46%] * VCF writing [47%] * VCF writing [48%] * VCF writing [49%] * VCF writing [50%] * VCF writing [51%] * VCF writing [52%] * VCF writing [53%] * VCF writing [54%] * VCF writing [55%] * VCF writing [56%] * VCF writing [57%] * VCF writing [58%] * VCF writing [59%] * VCF writing [60%] * VCF writing [61%] * VCF writing [62%] * VCF writing [63%] * VCF writing [64%] * VCF writing [65%] * VCF writing [66%] * VCF writing [67%] * VCF writing [68%] * VCF writing [69%] * VCF writing [70%] * VCF writing [71%] * VCF writing [72%] * VCF writing [73%] * VCF writing [74%] * VCF writing [75%] * VCF writing [76%] * VCF writing [77%] * VCF writing [78%] * VCF writing [79%] * VCF writing [80%] * VCF writing [81%] * VCF writing [82%] * VCF writing [83%] * VCF writing [84%] * VCF writing [85%] * VCF writing [86%] * VCF writing [87%] * VCF writing [88%] * VCF writing [89%] * VCF writing [90%] * VCF writing [91%] * VCF writing [92%] * VCF writing [93%] * VCF writing [94%] * VCF writing [95%] * VCF writing [96%] * VCF writing [97%] * VCF writing [98%] * VCF writing [99%] * VCF writing [100%] * VCF writing [Compressed / N=203 / L=8651] (0.18s) 195s * Total running time = 4294967234 seconds 195s + shapeit4 --input unphased.bcf --map chr20.b37.gmap.gz --region 20 --reference reference.bcf --scaffold scaffold.bcf --use-PS 0.0001 --thread 4 --log phased.log --output phased.bcf 195s 195s SHAPEIT 195s * Author : Olivier DELANEAU, University of Lausanne 195s * Contact : olivier.delaneau@gmail.com 195s * Version : 4.2.2 195s * Run date : 15/03/2025 - 23:46:21 195s 195s Files: 195s * Input VCF : [unphased.bcf] 195s * Reference VCF : [reference.bcf] 195s * Scaffold VCF : [scaffold.bcf] 195s * Genetic Map : [chr20.b37.gmap.gz] 195s * Output VCF : [phased.bcf] 195s * Output LOG : [phased.log] 195s 195s Parameters: 195s * Seed : 15052011 195s * Threads : 4 threads 195s * MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m] 195s * PBWT : Depth of PBWT neighbours to condition on: 4 195s * PBWT : Store indexes at variants [MAC>=2 / MDR<=0.5 / Dist=0.02 cM] 195s * HMM : K is variable / min W is 2.50cM / Ne is 15000 195s * HMM : Recombination rates given by genetic map 195s * HMM : Inform phasing using VCF/PS field / Error rate of PS field is 0.0001 195s * HMM : AVX2 optimization inactive / Activating AVX2 substantially improves performance 195s 195s Initialization: 196s * VCF/BCF scanning ... * VCF/BCF scanning [Nm=203 / Nr=300 / L=24990 / Reg=20] (0.07s) 196s * VCF/BCF parsing [0%] * VCF/BCF parsing [1%] * VCF/BCF parsing [2%] * VCF/BCF parsing [3%] * VCF/BCF parsing [4%] * VCF/BCF parsing [5%] * VCF/BCF parsing [6%] * VCF/BCF parsing [7%] * VCF/BCF parsing [8%] * VCF/BCF parsing [9%] * VCF/BCF parsing [10%] * VCF/BCF parsing [11%] * VCF/BCF parsing [12%] * VCF/BCF parsing 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parsing [55%] * VCF/BCF parsing [56%] * VCF/BCF parsing [57%] * VCF/BCF parsing [58%] * VCF/BCF parsing [59%] * VCF/BCF parsing [60%] * VCF/BCF parsing [61%] * VCF/BCF parsing [62%] * VCF/BCF parsing [63%] * VCF/BCF parsing [64%] * VCF/BCF parsing [65%] * VCF/BCF parsing [66%] * VCF/BCF parsing [67%] * VCF/BCF parsing [68%] * VCF/BCF parsing [69%] * VCF/BCF parsing [70%] * VCF/BCF parsing [71%] * VCF/BCF parsing [72%] * VCF/BCF parsing [73%] * VCF/BCF parsing [74%] * VCF/BCF parsing [75%] * VCF/BCF parsing [76%] * VCF/BCF parsing [77%] * VCF/BCF parsing [78%] * VCF/BCF parsing [79%] * VCF/BCF parsing [80%] * VCF/BCF parsing [81%] * VCF/BCF parsing [82%] * VCF/BCF parsing [83%] * VCF/BCF parsing [84%] * VCF/BCF parsing [85%] * VCF/BCF parsing [86%] * VCF/BCF parsing [87%] * VCF/BCF parsing [88%] * VCF/BCF parsing [89%] * VCF/BCF parsing [90%] * VCF/BCF parsing [91%] * VCF/BCF parsing [92%] * VCF/BCF parsing [93%] * VCF/BCF parsing [94%] * VCF/BCF parsing [95%] * VCF/BCF parsing [96%] * VCF/BCF parsing [97%] * VCF/BCF parsing [98%] * VCF/BCF parsing [99%] * VCF/BCF parsing [100%] * VCF/BCF parsing [Hom=90.0% / Het=10.0% / Pha=2.668% / Sca=0.778% / Mis=0.0%] (0.21s) 196s * GMAP parsing [n=82962] (0.05s) 196s * cM interpolation [s=3296 / i=21694] (0.00s) 196s * Region length [2999624 bp / 6.6 cM] 196s * HMM parameters [Ne=15000 / Error=0.0001 / #rare=9606] 196s * PBWT indexing [l=328] (0.00s) 196s * HAP update (0.10s) 196s * H2V transpose (0.01s) 196s * PBWT phase sweep [0%] * PBWT phase sweep [1%] * PBWT phase sweep [2%] * PBWT phase sweep [3%] * PBWT phase sweep [4%] * PBWT phase sweep [5%] * PBWT phase sweep [6%] * PBWT phase sweep [7%] * PBWT phase sweep [8%] * PBWT phase sweep [9%] * PBWT phase sweep [10%] * PBWT phase sweep [11%] * PBWT phase sweep [12%] * PBWT phase sweep [13%] * PBWT phase sweep [14%] * PBWT phase sweep [15%] * PBWT phase sweep [16%] * PBWT phase sweep [17%] * PBWT phase sweep [18%] * PBWT phase sweep [19%] * PBWT phase sweep [20%] * PBWT phase sweep [21%] * PBWT phase sweep [22%] * PBWT phase sweep [23%] * PBWT phase sweep [24%] * PBWT phase sweep [25%] * PBWT phase sweep [26%] * PBWT phase sweep [27%] * PBWT phase sweep [28%] * PBWT phase sweep [29%] * PBWT phase sweep [30%] * PBWT phase sweep [31%] * PBWT phase sweep [32%] * PBWT phase sweep [33%] * PBWT phase sweep [34%] * PBWT phase sweep [35%] * PBWT phase sweep [36%] * PBWT phase sweep [37%] * PBWT phase sweep [38%] * PBWT phase sweep [39%] * PBWT phase sweep [40%] * PBWT phase sweep [41%] * PBWT phase sweep [42%] * PBWT phase sweep [43%] * PBWT phase sweep [44%] * PBWT phase sweep [45%] * PBWT phase sweep [46%] * PBWT phase sweep [47%] * PBWT phase sweep [48%] * PBWT phase sweep [49%] * PBWT phase sweep [50%] * PBWT phase sweep [51%] * PBWT phase sweep [52%] * PBWT phase sweep [53%] * PBWT phase sweep [54%] * PBWT phase sweep [55%] * PBWT phase sweep [56%] * PBWT phase sweep [57%] * PBWT phase sweep [58%] * PBWT phase sweep [59%] * PBWT phase sweep [60%] * PBWT phase sweep [61%] * PBWT phase sweep [62%] * PBWT phase sweep [63%] * PBWT phase sweep [64%] * PBWT phase sweep [65%] * PBWT phase sweep [66%] * PBWT phase sweep [67%] * PBWT phase sweep [68%] * PBWT phase sweep [69%] * PBWT phase sweep [70%] * PBWT phase sweep [71%] * PBWT phase sweep [72%] * PBWT phase sweep [73%] * PBWT phase sweep [74%] * PBWT phase sweep [75%] * PBWT phase sweep [76%] * PBWT phase sweep [77%] * PBWT phase sweep [78%] * PBWT phase sweep [79%] * PBWT phase sweep [80%] * PBWT phase sweep [81%] * PBWT phase sweep [82%] * PBWT phase sweep [83%] * PBWT phase sweep [84%] * PBWT phase sweep [85%] * PBWT phase sweep [86%] * PBWT phase sweep [87%] * PBWT phase sweep [88%] * PBWT phase sweep [89%] * PBWT phase sweep [90%] * PBWT phase sweep [91%] * PBWT phase sweep [92%] * PBWT phase sweep [93%] * PBWT phase sweep [94%] * PBWT phase sweep [95%] * PBWT phase sweep [96%] * PBWT phase sweep [97%] * PBWT phase sweep [98%] * PBWT phase sweep [99%] * PBWT phase sweep [100%] * PBWT phase sweep (0.25s) 196s * Build genotype graphs [seg=164449] (0.04s) 196s 196s Burn-in iteration [1/5] 196s * V2H transpose (0.01s) 196s * PBWT selection [0%] * PBWT selection [1%] * PBWT selection [2%] * PBWT selection [3%] * PBWT selection [4%] * PBWT selection [5%] * PBWT selection [6%] * PBWT selection [7%] * PBWT selection [8%] * PBWT selection [9%] * PBWT selection [10%] * PBWT selection [11%] * PBWT selection [12%] * PBWT selection [13%] * PBWT selection [14%] * PBWT selection [15%] * PBWT selection [16%] * PBWT selection [17%] * PBWT selection [18%] * PBWT selection [19%] * PBWT selection [20%] * PBWT selection [21%] * PBWT selection [22%] * PBWT selection [23%] * PBWT selection [24%] * PBWT selection [25%] * PBWT selection [26%] * PBWT selection [27%] * PBWT selection [28%] * PBWT selection [29%] * PBWT selection [30%] * PBWT selection [31%] * PBWT selection [32%] * PBWT selection [33%] * PBWT selection [34%] * PBWT selection [35%] * PBWT selection [36%] * PBWT selection [37%] * PBWT selection [38%] * PBWT selection [39%] * PBWT selection [40%] * PBWT selection [41%] * PBWT selection [42%] * PBWT selection [43%] * PBWT selection [44%] * PBWT selection [45%] * PBWT selection [46%] * PBWT selection [47%] * PBWT selection [48%] * PBWT selection [49%] * PBWT selection [50%] * PBWT selection [51%] * PBWT selection [52%] * PBWT selection [53%] * PBWT selection [54%] * PBWT selection [55%] * PBWT selection [56%] * PBWT selection [57%] * PBWT selection [58%] * PBWT selection [59%] * PBWT selection [60%] * PBWT selection [61%] * PBWT selection [62%] * PBWT selection [63%] * PBWT selection [64%] * PBWT selection [65%] * PBWT selection [66%] * PBWT selection [67%] * PBWT selection [68%] * PBWT selection [69%] * PBWT selection [70%] * PBWT selection [71%] * PBWT selection [72%] * PBWT selection [73%] * PBWT selection [74%] * PBWT selection [75%] * PBWT selection [76%] * PBWT selection [77%] * PBWT selection [78%] * PBWT selection [79%] * PBWT selection [80%] * PBWT selection [81%] * PBWT selection [82%] * PBWT selection [83%] * PBWT selection [84%] * PBWT selection [85%] * PBWT selection [86%] * PBWT selection [87%] * PBWT selection [88%] * PBWT selection [89%] * PBWT selection [90%] * PBWT selection [91%] * PBWT selection [92%] * PBWT selection [93%] * PBWT selection [94%] * PBWT selection [95%] * PBWT selection [96%] * PBWT selection [97%] * PBWT selection [98%] * PBWT selection [99%] * PBWT selection [100%] * PBWT selection (0.05s) 196s * C2H transpose (0.00s) 205s * HMM computations [0%] * HMM computations [1%] * HMM computations [2%] * HMM computations [3%] * HMM computations [4%] * HMM computations [5%] * HMM computations [6%] * HMM computations [7%] * HMM computations [8%] * HMM computations [9%] * HMM computations [10%] * HMM computations [11%] * HMM computations [12%] * HMM computations [13%] * HMM computations [14%] * HMM computations [15%] * HMM computations [16%] * HMM computations [17%] * HMM computations [18%] * HMM computations 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[99%] * HMM computations [100%] * HMM computations [K=589.089+/-99.944 / W=2.25Mb] (8.40s) 205s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 205s * HAP update (0.01s) 205s * H2V transpose (0.01s) 205s 205s Burn-in iteration [2/5] 205s * V2H transpose (0.00s) 205s * PBWT selection [0%] * PBWT selection [1%] * PBWT selection [2%] * PBWT selection [3%] * PBWT selection [4%] * PBWT selection [5%] * PBWT selection [6%] * PBWT selection [7%] * PBWT selection [8%] * PBWT selection [9%] * PBWT selection [10%] * PBWT selection [11%] * PBWT selection [12%] * PBWT selection [13%] * PBWT selection [14%] * PBWT selection [15%] * PBWT selection [16%] * PBWT selection [17%] * PBWT selection [18%] * PBWT selection [19%] * PBWT selection [20%] * PBWT selection [21%] * PBWT selection [22%] * PBWT selection [23%] * PBWT selection [24%] * PBWT selection [25%] * PBWT selection [26%] * PBWT selection [27%] * PBWT selection [28%] * PBWT selection [29%] * PBWT selection [30%] * PBWT selection 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HMM computations [94%] * HMM computations [95%] * HMM computations [96%] * HMM computations [97%] * HMM computations [98%] * HMM computations [99%] * HMM computations [100%] * HMM computations [K=473.839+/-63.355 / W=2.23Mb] (6.36s) 211s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 211s * HAP update (0.01s) 211s * H2V transpose (0.01s) 211s 211s Burn-in iteration [3/5] 211s * V2H transpose (0.00s) 211s * PBWT selection [0%] * PBWT selection [1%] * PBWT selection [2%] * PBWT selection [3%] * PBWT selection [4%] * PBWT selection [5%] * PBWT selection [6%] * PBWT selection [7%] * PBWT selection [8%] * PBWT selection [9%] * PBWT selection [10%] * PBWT selection [11%] * PBWT selection [12%] * PBWT selection [13%] * PBWT selection [14%] * PBWT selection [15%] * PBWT selection [16%] * PBWT selection [17%] * PBWT selection [18%] * PBWT selection [19%] * PBWT selection [20%] * PBWT selection [21%] * PBWT selection [22%] * PBWT selection [23%] * PBWT selection [24%] * PBWT 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constraints [#inds=0 / #contraints=0 / #merged = 0] 250s * HAP update (0.01s) 250s * H2V transpose (0.01s) 250s 250s Pruning iteration [1/1] 250s * V2H transpose (0.00s) 250s * PBWT selection [0%] * PBWT selection [1%] * PBWT selection [2%] * PBWT selection [3%] * PBWT selection [4%] * PBWT selection [5%] * PBWT selection [6%] * PBWT selection [7%] * PBWT selection [8%] * PBWT selection [9%] * PBWT selection [10%] * PBWT selection [11%] * PBWT selection [12%] * PBWT selection [13%] * PBWT selection [14%] * PBWT selection [15%] * PBWT selection [16%] * PBWT selection [17%] * PBWT selection [18%] * PBWT selection [19%] * PBWT selection [20%] * PBWT selection [21%] * PBWT selection [22%] * PBWT selection [23%] * PBWT selection [24%] * PBWT selection [25%] * PBWT selection [26%] * PBWT selection [27%] * PBWT selection [28%] * PBWT selection [29%] * PBWT selection [30%] * PBWT selection [31%] * PBWT selection [32%] * PBWT selection [33%] * PBWT selection [34%] * PBWT selection [35%] * PBWT 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computations [58%] * HMM computations [59%] * HMM computations [60%] * HMM computations [61%] * HMM computations [62%] * HMM computations [63%] * HMM computations [64%] * HMM computations [65%] * HMM computations [66%] * HMM computations [67%] * HMM computations [68%] * HMM computations [69%] * HMM computations [70%] * HMM computations [71%] * HMM computations [72%] * HMM computations [73%] * HMM computations [74%] * HMM computations [75%] * HMM computations [76%] * HMM computations [77%] * HMM computations [78%] * HMM computations [79%] * HMM computations [80%] * HMM computations [81%] * HMM computations [82%] * HMM computations [83%] * HMM computations [84%] * HMM computations [85%] * HMM computations [86%] * HMM computations [87%] * HMM computations [88%] * HMM computations [89%] * HMM computations [90%] * HMM computations [91%] * HMM computations [92%] * HMM computations [93%] * HMM computations [94%] * HMM computations [95%] * HMM computations [96%] * HMM computations [97%] * HMM computations [98%] * HMM computations [99%] * HMM computations [100%] * HMM computations [K=486.119+/-67.527 / W=2.27Mb] (6.22s) 256s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 256s * HAP update (0.01s) 256s * H2V transpose (0.01s) 256s * Trimming [pc=62.39%] 256s 256s Burn-in iteration [1/1] 256s * V2H transpose (0.00s) 256s * PBWT selection [0%] * PBWT selection [1%] * PBWT selection [2%] * PBWT selection [3%] * PBWT selection [4%] * PBWT selection [5%] * PBWT selection [6%] * PBWT selection [7%] * PBWT selection [8%] * PBWT selection [9%] * PBWT selection [10%] * PBWT selection [11%] * PBWT selection [12%] * PBWT selection [13%] * PBWT selection [14%] * PBWT selection [15%] * PBWT selection [16%] * PBWT selection [17%] * PBWT selection [18%] * PBWT selection [19%] * PBWT selection [20%] * PBWT selection [21%] * PBWT selection [22%] * PBWT selection [23%] * PBWT selection [24%] * PBWT selection [25%] * PBWT selection [26%] * PBWT selection [27%] * PBWT selection [28%] 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[95%] * PBWT selection [96%] * PBWT selection [97%] * PBWT selection [98%] * PBWT selection [99%] * PBWT selection [100%] * PBWT selection (0.05s) 274s * C2H transpose (0.00s) 279s * HMM computations [0%] * HMM computations [1%] * HMM computations [2%] * HMM computations [3%] * HMM computations [4%] * HMM computations [5%] * HMM computations [6%] * HMM computations [7%] * HMM computations [8%] * HMM computations [9%] * HMM computations [10%] * HMM computations [11%] * HMM computations [12%] * HMM computations [13%] * HMM computations [14%] * HMM computations [15%] * HMM computations [16%] * HMM computations [17%] * HMM computations [18%] * HMM computations [19%] * HMM computations [20%] * HMM computations [21%] * HMM computations [22%] * HMM computations [23%] * HMM computations [24%] * HMM computations [25%] * HMM computations [26%] * HMM computations [27%] * HMM computations [28%] * HMM computations [29%] * HMM computations [30%] * HMM computations [31%] * HMM computations [32%] * 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HMM computations [73%] * HMM computations [74%] * HMM computations [75%] * HMM computations [76%] * HMM computations [77%] * HMM computations [78%] * HMM computations [79%] * HMM computations [80%] * HMM computations [81%] * HMM computations [82%] * HMM computations [83%] * HMM computations [84%] * HMM computations [85%] * HMM computations [86%] * HMM computations [87%] * HMM computations [88%] * HMM computations [89%] * HMM computations [90%] * HMM computations [91%] * HMM computations [92%] * HMM computations [93%] * HMM computations [94%] * HMM computations [95%] * HMM computations [96%] * HMM computations [97%] * HMM computations [98%] * HMM computations [99%] * HMM computations [100%] * HMM computations [K=480.695+/-69.896 / W=2.24Mb] (4.80s) 279s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 279s * HAP update (0.01s) 279s * H2V transpose (0.01s) 279s 279s Main iteration [3/5] 279s * V2H transpose (0.00s) 279s * PBWT selection [0%] * PBWT selection [1%] * PBWT 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[K=482.369+/-66.830 / W=2.25Mb] (4.77s) 290s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 290s * HAP update (0.01s) 290s * H2V transpose (0.01s) 290s 290s Main iteration [5/5] 290s * V2H transpose (0.00s) 290s * PBWT selection [0%] * PBWT selection [1%] * PBWT selection [2%] * PBWT selection [3%] * PBWT selection [4%] * PBWT selection [5%] * PBWT selection [6%] * PBWT selection [7%] * PBWT selection [8%] * PBWT selection [9%] * PBWT selection [10%] * PBWT selection [11%] * PBWT selection [12%] * PBWT selection [13%] * PBWT selection [14%] * PBWT selection [15%] * PBWT selection [16%] * PBWT selection [17%] * PBWT selection [18%] * PBWT selection [19%] * PBWT selection [20%] * PBWT selection [21%] * PBWT selection [22%] * PBWT selection [23%] * PBWT selection [24%] * PBWT selection [25%] * PBWT selection [26%] * PBWT selection [27%] * PBWT selection [28%] * PBWT selection [29%] * PBWT selection [30%] * PBWT selection [31%] * PBWT selection [32%] * PBWT selection [33%] * 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computations [96%] * HMM computations [97%] * HMM computations [98%] * HMM computations [99%] * HMM computations [100%] * HMM computations [K=578.785+/-98.263 / W=2.22Mb] (5.78s) 296s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 296s * HAP update (0.01s) 296s * H2V transpose (0.01s) 296s 296s Finalization: 296s * HAP solving (0.04s) 296s * HAP update (0.01s) 296s * H2V transpose (0.00s) 296s * VCF writing [0%] * VCF writing [1%] * VCF writing [2%] * VCF writing [3%] * VCF writing [4%] * VCF writing [5%] * VCF writing [6%] * VCF writing [7%] * VCF writing [8%] * VCF writing [9%] * VCF writing [10%] * VCF writing [11%] * VCF writing [12%] * VCF writing [13%] * VCF writing [14%] * VCF writing [15%] * VCF writing [16%] * VCF writing [17%] * VCF writing [18%] * VCF writing [19%] * VCF writing [20%] * VCF writing [21%] * VCF writing [22%] * VCF writing [23%] * VCF writing [24%] * VCF writing [25%] * VCF writing [26%] * VCF writing [27%] * VCF writing [28%] * VCF writing [29%] * VCF writing [30%] * VCF writing [31%] * VCF writing [32%] * VCF writing [33%] * VCF writing [34%] * VCF writing [35%] * VCF writing [36%] * VCF writing [37%] * VCF writing [38%] * VCF writing [39%] * VCF writing [40%] * VCF writing [41%] * VCF writing [42%] * VCF writing [43%] * VCF writing [44%] * VCF writing [45%] * VCF writing [46%] * VCF writing [47%] * VCF writing [48%] * VCF writing [49%] * VCF writing [50%] * VCF writing [51%] * VCF writing [52%] * VCF writing [53%] * VCF writing [54%] * VCF writing [55%] * VCF writing [56%] * VCF writing [57%] * VCF writing [58%] * VCF writing [59%] * VCF writing [60%] * VCF writing [61%] * VCF writing [62%] * VCF writing [63%] * VCF writing [64%] * VCF writing [65%] * VCF writing [66%] * VCF writing [67%] * VCF writing [68%] * VCF writing [69%] * VCF writing [70%] * VCF writing [71%] * VCF writing [72%] * VCF writing [73%] * VCF writing [74%] * VCF writing [75%] * VCF writing [76%] * VCF writing [77%] * VCF writing [78%] * VCF writing [79%] * VCF writing [80%] * VCF writing [81%] * VCF writing [82%] * VCF writing [83%] * VCF writing [84%] * VCF writing [85%] * VCF writing [86%] * VCF writing [87%] * VCF writing [88%] * VCF writing [89%] * VCF writing [90%] * VCF writing [91%] * VCF writing [92%] * VCF writing [93%] * VCF writing [94%] * VCF writing [95%] * VCF writing [96%] * VCF writing [97%] * VCF writing [98%] * VCF writing [99%] * VCF writing [100%] * BCF writing [Compressed / N=203 / L=24990] (0.33s) 296s * Total running time = 100 seconds 296s autopkgtest [23:48:02]: test run-sample-analysis: -----------------------] 297s autopkgtest [23:48:03]: test run-sample-analysis: - - - - - - - - - - results - - - - - - - - - - 297s run-sample-analysis PASS 297s autopkgtest [23:48:03]: @@@@@@@@@@@@@@@@@@@@ summary 297s run-sample-analysis PASS 302s nova [W] Using flock in prodstack6-s390x 302s Creating nova instance adt-plucky-s390x-shapeit4-20250315-234306-juju-7f2275-prod-proposed-migration-environment-2-0b09e17a-234f-4353-bc0b-8685ff0df875 from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 302s nova [W] Timed out waiting for 42ca334d-c552-4d9f-96d1-bd77666b8916 to get deleted.