0s autopkgtest [07:49:06]: starting date and time: 2026-02-05 07:49:06+0000 0s autopkgtest [07:49:06]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [07:49:06]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.i3f6wp6d/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 shapeit4 --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-20@sto01-arm64-15.secgroup --name adt-resolute-arm64-shapeit4-20260205-074906-juju-7f2275-prod-proposed-migration-environment-20-beebb1ff-a384-490b-af58-104a70ae2511 --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-autopkgtest-workers-arm64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-arm64-shapeit4-20260205-074906-juju-7f2275-prod-proposed-migration-environment-20-beebb1ff-a384-490b-af58-104a70ae2511 from image adt/ubuntu-resolute-arm64-server-20260204.img (UUID f58d981d-b271-4157-b9b1-fd704695563c)... 80s autopkgtest [07:50:26]: testbed dpkg architecture: arm64 80s autopkgtest [07:50:26]: testbed apt version: 3.1.14 81s autopkgtest [07:50:27]: @@@@@@@@@@@@@@@@@@@@ test bed setup 81s autopkgtest [07:50:27]: testbed release detected to be: None 82s autopkgtest [07:50:28]: updating testbed package index (apt update) 82s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 82s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 82s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 82s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 82s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5260 B] 82s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [228 kB] 82s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1719 kB] 83s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [35.4 kB] 84s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [269 kB] 85s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [7264 B] 85s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [52.9 kB] 85s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [328 B] 85s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [1556 kB] 85s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [41.9 kB] 85s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [26.0 kB] 85s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [792 B] 87s Fetched 4067 kB in 2s (2523 kB/s) 88s Reading package lists... 88s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 88s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 88s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 88s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 89s Reading package lists... 89s Reading package lists... 90s Building dependency tree... 90s Reading state information... 90s Calculating upgrade... 90s The following packages will be upgraded: 90s libc-bin libc-gconv-modules-extra libc6 locales pollinate python3-linkify-it 90s python3-referencing sed 90s 8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 90s Need to get 8110 kB of archives. 90s After this operation, 0 B of additional disk space will be used. 90s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 sed arm64 4.9-2build3 [193 kB] 90s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libc-gconv-modules-extra arm64 2.42-2ubuntu5 [1413 kB] 90s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libc6 arm64 2.42-2ubuntu5 [1594 kB] 91s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libc-bin arm64 2.42-2ubuntu5 [599 kB] 91s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 locales all 2.42-2ubuntu5 [4255 kB] 91s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-linkify-it all 2.0.3-1ubuntu3 [19.4 kB] 91s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 pollinate all 4.33-4ubuntu5 [14.0 kB] 91s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-referencing all 0.36.2-1ubuntu2 [22.2 kB] 91s dpkg-preconfigure: unable to re-open stdin: No such file or directory 91s Fetched 8110 kB in 0s (17.3 MB/s) 91s (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.) 91s Preparing to unpack .../sed_4.9-2build3_arm64.deb ... 91s Unpacking sed (4.9-2build3) over (4.9-2build2) ... 92s Setting up sed (4.9-2build3) ... 92s (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.) 92s Preparing to unpack .../libc-gconv-modules-extra_2.42-2ubuntu5_arm64.deb ... 92s Unpacking libc-gconv-modules-extra:arm64 (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 92s Setting up libc-gconv-modules-extra:arm64 (2.42-2ubuntu5) ... 92s (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.) 92s Preparing to unpack .../libc6_2.42-2ubuntu5_arm64.deb ... 92s Unpacking libc6:arm64 (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 92s Setting up libc6:arm64 (2.42-2ubuntu5) ... 93s (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.) 93s Preparing to unpack .../libc-bin_2.42-2ubuntu5_arm64.deb ... 93s Unpacking libc-bin (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 93s Setting up libc-bin (2.42-2ubuntu5) ... 93s (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.) 93s Preparing to unpack .../locales_2.42-2ubuntu5_all.deb ... 93s Unpacking locales (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 93s Preparing to unpack .../python3-linkify-it_2.0.3-1ubuntu3_all.deb ... 93s Unpacking python3-linkify-it (2.0.3-1ubuntu3) over (2.0.3-1ubuntu2) ... 93s Preparing to unpack .../pollinate_4.33-4ubuntu5_all.deb ... 93s Unpacking pollinate (4.33-4ubuntu5) over (4.33-4ubuntu4) ... 93s Preparing to unpack .../python3-referencing_0.36.2-1ubuntu2_all.deb ... 93s Unpacking python3-referencing (0.36.2-1ubuntu2) over (0.36.2-1ubuntu1) ... 93s Setting up locales (2.42-2ubuntu5) ... 94s Generating locales (this might take a while)... 96s en_US.UTF-8... done 96s Generation complete. 96s Setting up pollinate (4.33-4ubuntu5) ... 106s Setting up python3-linkify-it (2.0.3-1ubuntu3) ... 106s Setting up python3-referencing (0.36.2-1ubuntu2) ... 107s Processing triggers for man-db (2.13.1-1) ... 108s Processing triggers for install-info (7.2-5) ... 108s Processing triggers for systemd (259-1ubuntu3) ... 109s autopkgtest [07:50:55]: upgrading testbed (apt dist-upgrade and autopurge) 109s Reading package lists... 109s Building dependency tree... 109s Reading state information... 110s Calculating upgrade... 110s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 111s Solving dependencies... 111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 111s autopkgtest [07:50:57]: rebooting testbed after setup commands that affected boot 155s autopkgtest [07:51:41]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:41:39 UTC 2026 158s autopkgtest [07:51:44]: @@@@@@@@@@@@@@@@@@@@ apt-source shapeit4 165s Get:1 http://ftpmaster.internal/ubuntu resolute/universe shapeit4 4.2.2+dfsg-1build5 (dsc) [2237 B] 165s Get:2 http://ftpmaster.internal/ubuntu resolute/universe shapeit4 4.2.2+dfsg-1build5 (tar) [59.0 MB] 165s Get:3 http://ftpmaster.internal/ubuntu resolute/universe shapeit4 4.2.2+dfsg-1build5 (diff) [5456 B] 165s gpgv: Signature made Wed Aug 6 15:09:14 2025 UTC 165s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 165s gpgv: Can't check signature: No public key 165s dpkg-source: warning: cannot verify inline signature for ./shapeit4_4.2.2+dfsg-1build5.dsc: no acceptable signature found 166s autopkgtest [07:51:52]: testing package shapeit4 version 4.2.2+dfsg-1build5 167s autopkgtest [07:51:53]: build not needed 172s autopkgtest [07:51:58]: test run-sample-analysis: preparing testbed 176s Reading package lists... 176s Building dependency tree... 176s Reading state information... 176s Solving dependencies... 176s The following NEW packages will be installed: 176s libboost-iostreams1.88.0 libboost-program-options1.88.0 libdeflate0 176s libhts3t64 libhtscodecs2 shapeit4 shapeit4-example 176s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 176s Need to get 53.6 MB of archives. 176s After this operation, 59.3 MB of additional disk space will be used. 176s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 libboost-iostreams1.88.0 arm64 1.88.0-1.4ubuntu3 [261 kB] 176s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libboost-program-options1.88.0 arm64 1.88.0-1.4ubuntu3 [326 kB] 176s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB] 176s Get:4 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhtscodecs2 arm64 1.6.1-2build1 [83.8 kB] 176s Get:5 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhts3t64 arm64 1.22.1+ds2-1 [442 kB] 176s Get:6 http://ftpmaster.internal/ubuntu resolute/universe arm64 shapeit4 arm64 4.2.2+dfsg-1build5 [172 kB] 176s Get:7 http://ftpmaster.internal/ubuntu resolute/universe arm64 shapeit4-example all 4.2.2+dfsg-1build5 [52.3 MB] 180s Fetched 53.6 MB in 6s (8341 kB/s) 180s Selecting previously unselected package libboost-iostreams1.88.0:arm64. 180s (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.) 180s Preparing to unpack .../0-libboost-iostreams1.88.0_1.88.0-1.4ubuntu3_arm64.deb ... 180s Unpacking libboost-iostreams1.88.0:arm64 (1.88.0-1.4ubuntu3) ... 180s Selecting previously unselected package libboost-program-options1.88.0:arm64. 180s Preparing to unpack .../1-libboost-program-options1.88.0_1.88.0-1.4ubuntu3_arm64.deb ... 180s Unpacking libboost-program-options1.88.0:arm64 (1.88.0-1.4ubuntu3) ... 180s Selecting previously unselected package libdeflate0:arm64. 180s Preparing to unpack .../2-libdeflate0_1.23-2_arm64.deb ... 180s Unpacking libdeflate0:arm64 (1.23-2) ... 180s Selecting previously unselected package libhtscodecs2:arm64. 180s Preparing to unpack .../3-libhtscodecs2_1.6.1-2build1_arm64.deb ... 180s Unpacking libhtscodecs2:arm64 (1.6.1-2build1) ... 180s Selecting previously unselected package libhts3t64:arm64. 180s Preparing to unpack .../4-libhts3t64_1.22.1+ds2-1_arm64.deb ... 180s Unpacking libhts3t64:arm64 (1.22.1+ds2-1) ... 180s Selecting previously unselected package shapeit4. 180s Preparing to unpack .../5-shapeit4_4.2.2+dfsg-1build5_arm64.deb ... 180s Unpacking shapeit4 (4.2.2+dfsg-1build5) ... 180s Selecting previously unselected package shapeit4-example. 180s Preparing to unpack .../6-shapeit4-example_4.2.2+dfsg-1build5_all.deb ... 180s Unpacking shapeit4-example (4.2.2+dfsg-1build5) ... 180s Setting up libhtscodecs2:arm64 (1.6.1-2build1) ... 180s Setting up libboost-program-options1.88.0:arm64 (1.88.0-1.4ubuntu3) ... 180s Setting up libdeflate0:arm64 (1.23-2) ... 180s Setting up libboost-iostreams1.88.0:arm64 (1.88.0-1.4ubuntu3) ... 180s Setting up shapeit4-example (4.2.2+dfsg-1build5) ... 180s Setting up libhts3t64:arm64 (1.22.1+ds2-1) ... 180s Setting up shapeit4 (4.2.2+dfsg-1build5) ... 180s Processing triggers for man-db (2.13.1-1) ... 181s Processing triggers for libc-bin (2.42-2ubuntu5) ... 182s autopkgtest [07:52:08]: test run-sample-analysis: [----------------------- 183s + shapeit4 --input unphased.vcf.gz --map chr20.b37.gmap.gz --region 20:2000000-3000000 --thread 4 --output phased.vcf.gz 183s 183s SHAPEIT 183s * Author : Olivier DELANEAU, University of Lausanne 183s * Contact : olivier.delaneau@gmail.com 183s * Version : 4.2.2 183s * Run date : 05/02/2026 - 07:52:09 183s 183s Files: 183s * Input VCF : [unphased.vcf.gz] 183s * Genetic Map : [chr20.b37.gmap.gz] 183s * Output VCF : [phased.vcf.gz] 183s 183s Parameters: 183s * Seed : 15052011 183s * Threads : 4 threads 183s * MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m] 183s * PBWT : Depth of PBWT neighbours to condition on: 4 183s * PBWT : Store indexes at variants [MAC>=2 / MDR<=0.5 / Dist=0.02 cM] 183s * HMM : K is variable / min W is 2.50cM / Ne is 15000 183s * HMM : Recombination rates given by genetic map 183s * HMM : AVX2 optimization inactive / Activating AVX2 substantially improves performance 183s 183s Initialization: 183s * VCF/BCF scanning ... [W::hts_idx_load3] The index file is older than the data file: unphased.vcf.gz.csi 183s * VCF/BCF scanning [N=203 / L=8651 / Reg=20:2000000-3000000] (0.07s) 183s [W::hts_idx_load3] The index file is older than the data file: unphased.vcf.gz.csi 183s * 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 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transpose (0.00s) 183s * 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 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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 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[100%] * VCF writing [Compressed / N=203 / L=8651] (0.10s) 197s * Total running time = 14 seconds 197s + 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 198s 198s SHAPEIT 198s * Author : Olivier DELANEAU, University of Lausanne 198s * Contact : olivier.delaneau@gmail.com 198s * Version : 4.2.2 198s * Run date : 05/02/2026 - 07:52:24 198s 198s Files: 198s * Input VCF : [unphased.bcf] 198s * Reference VCF : [reference.bcf] 198s * Scaffold VCF : [scaffold.bcf] 198s * Genetic Map : [chr20.b37.gmap.gz] 198s * Output VCF : [phased.bcf] 198s * Output LOG : [phased.log] 198s 198s Parameters: 198s * Seed : 15052011 198s * Threads : 4 threads 198s * MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m] 198s * PBWT : Depth of PBWT neighbours to condition on: 4 198s * PBWT : Store indexes at variants [MAC>=2 / MDR<=0.5 / Dist=0.02 cM] 198s * HMM : K is variable / min W is 2.50cM / Ne is 15000 198s * HMM : Recombination rates given by genetic map 198s * HMM : Inform phasing using VCF/PS field / Error rate of PS field is 0.0001 198s * HMM : AVX2 optimization inactive / Activating AVX2 substantially improves performance 198s 198s Initialization: 198s * VCF/BCF scanning ... * VCF/BCF scanning [Nm=203 / Nr=300 / L=24990 / Reg=20] (0.03s) 198s * 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 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[2999624 bp / 6.6 cM] 198s * HMM parameters [Ne=15000 / Error=0.0001 / #rare=9606] 198s * PBWT indexing [l=328] (0.00s) 198s * HAP update (0.02s) 198s * H2V transpose (0.01s) 198s * 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%] * 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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) 198s * C2H transpose (0.00s) 207s * 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 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#contraints=0 / #merged = 0] 213s * HAP update (0.01s) 213s * H2V transpose (0.01s) 213s 213s Burn-in iteration [3/5] 213s * V2H transpose (0.01s) 214s * 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 [99%] * HMM computations [100%] * HMM computations [K=433.739+/-118.320 / W=2.27Mb] (6.27s) 220s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 220s * HAP update (0.01s) 220s * H2V transpose (0.01s) 220s 220s Burn-in iteration [4/5] 220s * V2H transpose (0.01s) 220s * 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%] * 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PBWT selection [97%] * PBWT selection [98%] * PBWT selection [99%] * PBWT selection [100%] * PBWT selection (0.04s) 239s * C2H transpose (0.00s) 244s * 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%] * HMM computations [33%] * HMM 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249s * Trimming [pc=66.15%] 249s 249s Burn-in iteration [1/1] 249s * V2H transpose (0.01s) 249s * 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 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273s * 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 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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 (0.04s) 273s * C2H transpose (0.00s) 277s * 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 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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=407.582+/-115.110 / W=2.28Mb] (3.85s) 277s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 277s * HAP update (0.01s) 277s * H2V transpose (0.01s) 277s 277s Finalization: 277s * HAP solving (0.03s) 277s * HAP update (0.01s) 277s * H2V transpose (0.01s) 277s * 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] (0.13s) 277s * Total running time = 79 seconds 277s autopkgtest [07:53:43]: test run-sample-analysis: -----------------------] 278s run-sample-analysis PASS 278s autopkgtest [07:53:44]: test run-sample-analysis: - - - - - - - - - - results - - - - - - - - - - 278s autopkgtest [07:53:44]: @@@@@@@@@@@@@@@@@@@@ summary 278s run-sample-analysis PASS