0s autopkgtest [10:37:08]: starting date and time: 2026-02-05 10:37:08+0000 0s autopkgtest [10:37:08]: git checkout: 508d4a25 a-v-ssh wait_for_ssh: demote "ssh connection failed" to a debug message 0s autopkgtest [10:37:08]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.8i7sz79a/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,localhost,localdomain,internal,login.ubuntu.com,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:glibc --apt-upgrade shapeit4 --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.42-2ubuntu5 -- lxd -r lxd-armhf-10.145.243.85 lxd-armhf-10.145.243.85:autopkgtest/ubuntu/resolute/armhf 28s autopkgtest [10:37:36]: testbed dpkg architecture: armhf 29s autopkgtest [10:37:37]: testbed apt version: 3.1.14 34s autopkgtest [10:37:42]: @@@@@@@@@@@@@@@@@@@@ test bed setup 36s autopkgtest [10:37:44]: testbed release detected to be: None 45s autopkgtest [10:37:53]: updating testbed package index (apt update) 47s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 48s Get:2 http://ftpmaster.internal/ubuntu resolute InRelease [124 kB] 48s Get:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease [124 kB] 48s Get:4 http://ftpmaster.internal/ubuntu resolute-security InRelease [124 kB] 48s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [227 kB] 48s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1696 kB] 48s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [35.4 kB] 48s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5260 B] 48s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf Packages [253 kB] 48s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf Packages [1396 kB] 48s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse armhf Packages [9664 B] 48s Get:12 http://ftpmaster.internal/ubuntu resolute/main Sources [1402 kB] 48s Get:13 http://ftpmaster.internal/ubuntu resolute/universe Sources [21.3 MB] 49s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf Packages [1374 kB] 49s Get:15 http://ftpmaster.internal/ubuntu resolute/universe armhf Packages [14.9 MB] 52s Fetched 43.1 MB in 5s (8164 kB/s) 54s Reading package lists... 60s autopkgtest [10:38:08]: upgrading testbed (apt dist-upgrade and autopurge) 62s Reading package lists... 62s Building dependency tree... 62s Reading state information... 63s Calculating upgrade... 63s The following packages will be upgraded: 63s libc-bin libc-gconv-modules-extra libc6 locales 63s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 63s Need to get 7850 kB of archives. 63s After this operation, 0 B of additional disk space will be used. 63s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libc-gconv-modules-extra armhf 2.42-2ubuntu5 [1417 kB] 64s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libc6 armhf 2.42-2ubuntu5 [1632 kB] 64s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libc-bin armhf 2.42-2ubuntu5 [545 kB] 64s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf locales all 2.42-2ubuntu5 [4255 kB] 65s Preconfiguring packages ... 65s Fetched 7850 kB in 1s (8626 kB/s) 65s (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 ... 68395 files and directories currently installed.) 65s Preparing to unpack .../libc-gconv-modules-extra_2.42-2ubuntu5_armhf.deb ... 65s Unpacking libc-gconv-modules-extra:armhf (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 65s Setting up libc-gconv-modules-extra:armhf (2.42-2ubuntu5) ... 66s (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 ... 68395 files and directories currently installed.) 66s Preparing to unpack .../libc6_2.42-2ubuntu5_armhf.deb ... 66s readlink: /usr/lib/libeatmydata: No such file or directory 66s Unpacking libc6:armhf (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 66s Setting up libc6:armhf (2.42-2ubuntu5) ... 66s (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 ... 68395 files and directories currently installed.) 66s Preparing to unpack .../libc-bin_2.42-2ubuntu5_armhf.deb ... 66s Unpacking libc-bin (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 66s Setting up libc-bin (2.42-2ubuntu5) ... 67s (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 ... 68395 files and directories currently installed.) 67s Preparing to unpack .../locales_2.42-2ubuntu5_all.deb ... 67s Unpacking locales (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 67s Setting up locales (2.42-2ubuntu5) ... 69s Generating locales (this might take a while)... 71s en_US.UTF-8... done 71s Generation complete. 71s Processing triggers for systemd (259-1ubuntu3) ... 72s Processing triggers for man-db (2.13.1-1) ... 76s Reading package lists... 76s Building dependency tree... 76s Reading state information... 76s Solving dependencies... 77s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 79s autopkgtest [10:38:27]: rebooting testbed after setup commands that affected boot 121s autopkgtest [10:39:09]: testbed running kernel: Linux 6.8.0-87-generic #88~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 14 14:00:09 UTC 2 147s autopkgtest [10:39:35]: @@@@@@@@@@@@@@@@@@@@ apt-source shapeit4 164s Get:1 http://ftpmaster.internal/ubuntu resolute/universe shapeit4 4.2.2+dfsg-1build5 (dsc) [2237 B] 164s Get:2 http://ftpmaster.internal/ubuntu resolute/universe shapeit4 4.2.2+dfsg-1build5 (tar) [59.0 MB] 164s Get:3 http://ftpmaster.internal/ubuntu resolute/universe shapeit4 4.2.2+dfsg-1build5 (diff) [5456 B] 164s gpgv: Signature made Wed Aug 6 15:09:14 2025 UTC 164s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 164s gpgv: Can't check signature: No public key 164s dpkg-source: warning: cannot verify inline signature for ./shapeit4_4.2.2+dfsg-1build5.dsc: no acceptable signature found 166s autopkgtest [10:39:54]: testing package shapeit4 version 4.2.2+dfsg-1build5 168s autopkgtest [10:39:56]: build not needed 321s autopkgtest [10:42:29]: test run-sample-analysis: preparing testbed 323s Reading package lists... 323s Building dependency tree... 323s Reading state information... 323s Solving dependencies... 324s The following NEW packages will be installed: 324s libboost-iostreams1.88.0 libboost-program-options1.88.0 libdeflate0 324s libhts3t64 libhtscodecs2 shapeit4 shapeit4-example 324s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 324s Need to get 53.6 MB of archives. 324s After this operation, 58.7 MB of additional disk space will be used. 324s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf libboost-iostreams1.88.0 armhf 1.88.0-1.4ubuntu3 [260 kB] 324s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf libboost-program-options1.88.0 armhf 1.88.0-1.4ubuntu3 [345 kB] 325s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libdeflate0 armhf 1.23-2 [38.7 kB] 325s Get:4 http://ftpmaster.internal/ubuntu resolute/universe armhf libhtscodecs2 armhf 1.6.1-2build1 [67.0 kB] 325s Get:5 http://ftpmaster.internal/ubuntu resolute/universe armhf libhts3t64 armhf 1.22.1+ds2-1 [408 kB] 325s Get:6 http://ftpmaster.internal/ubuntu resolute/universe armhf shapeit4 armhf 4.2.2+dfsg-1build5 [201 kB] 325s Get:7 http://ftpmaster.internal/ubuntu resolute/universe armhf shapeit4-example all 4.2.2+dfsg-1build5 [52.3 MB] 330s Fetched 53.6 MB in 6s (9577 kB/s) 330s Selecting previously unselected package libboost-iostreams1.88.0:armhf. 330s (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 ... 68395 files and directories currently installed.) 330s Preparing to unpack .../0-libboost-iostreams1.88.0_1.88.0-1.4ubuntu3_armhf.deb ... 330s Unpacking libboost-iostreams1.88.0:armhf (1.88.0-1.4ubuntu3) ... 330s Selecting previously unselected package libboost-program-options1.88.0:armhf. 330s Preparing to unpack .../1-libboost-program-options1.88.0_1.88.0-1.4ubuntu3_armhf.deb ... 330s Unpacking libboost-program-options1.88.0:armhf (1.88.0-1.4ubuntu3) ... 330s Selecting previously unselected package libdeflate0:armhf. 330s Preparing to unpack .../2-libdeflate0_1.23-2_armhf.deb ... 330s Unpacking libdeflate0:armhf (1.23-2) ... 330s Selecting previously unselected package libhtscodecs2:armhf. 330s Preparing to unpack .../3-libhtscodecs2_1.6.1-2build1_armhf.deb ... 330s Unpacking libhtscodecs2:armhf (1.6.1-2build1) ... 330s Selecting previously unselected package libhts3t64:armhf. 330s Preparing to unpack .../4-libhts3t64_1.22.1+ds2-1_armhf.deb ... 330s Unpacking libhts3t64:armhf (1.22.1+ds2-1) ... 330s Selecting previously unselected package shapeit4. 330s Preparing to unpack .../5-shapeit4_4.2.2+dfsg-1build5_armhf.deb ... 330s Unpacking shapeit4 (4.2.2+dfsg-1build5) ... 330s Selecting previously unselected package shapeit4-example. 330s Preparing to unpack .../6-shapeit4-example_4.2.2+dfsg-1build5_all.deb ... 330s Unpacking shapeit4-example (4.2.2+dfsg-1build5) ... 331s Setting up libhtscodecs2:armhf (1.6.1-2build1) ... 331s Setting up libboost-program-options1.88.0:armhf (1.88.0-1.4ubuntu3) ... 331s Setting up libdeflate0:armhf (1.23-2) ... 331s Setting up libboost-iostreams1.88.0:armhf (1.88.0-1.4ubuntu3) ... 331s Setting up shapeit4-example (4.2.2+dfsg-1build5) ... 331s Setting up libhts3t64:armhf (1.22.1+ds2-1) ... 331s Setting up shapeit4 (4.2.2+dfsg-1build5) ... 331s Processing triggers for man-db (2.13.1-1) ... 332s Processing triggers for libc-bin (2.42-2ubuntu5) ... 342s autopkgtest [10:42:50]: test run-sample-analysis: [----------------------- 344s + shapeit4 --input unphased.vcf.gz --map chr20.b37.gmap.gz --region 20:2000000-3000000 --thread 4 --output phased.vcf.gz 344s 344s SHAPEIT 344s * Author : Olivier DELANEAU, University of Lausanne 344s * Contact : olivier.delaneau@gmail.com 344s * Version : 4.2.2 344s * Run date : 05/02/2026 - 10:42:52 344s 344s Files: 344s * Input VCF : [unphased.vcf.gz] 344s * Genetic Map : [chr20.b37.gmap.gz] 344s * Output VCF : [phased.vcf.gz] 344s 344s Parameters: 344s * Seed : 15052011 344s * Threads : 4 threads 344s * MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m] 344s * PBWT : Depth of PBWT neighbours to condition on: 4 344s * PBWT : Store indexes at variants [MAC>=2 / MDR<=0.5 / Dist=0.02 cM] 344s * HMM : K is variable / min W is 2.50cM / Ne is 15000 344s * HMM : Recombination rates given by genetic map 344s * HMM : AVX2 optimization inactive / Activating AVX2 substantially improves performance 344s 344s Initialization: 344s * VCF/BCF scanning ... [W::hts_idx_load3] The index file is older than the data file: unphased.vcf.gz.csi 344s * VCF/BCF scanning [N=203 / L=8651 / Reg=20:2000000-3000000] (0.08s) 344s [W::hts_idx_load3] The index file is older than the data file: unphased.vcf.gz.csi 344s * 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) 344s * 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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/ #merged = 0] 346s * HAP update (0.01s) 346s * H2V transpose (0.00s) 346s * Trimming [pc=0.00%] 346s 346s Main iteration [1/5] 346s * V2H transpose (0.00s) 346s * 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 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[99%] * PBWT selection [100%] * PBWT selection (0.01s) 346s * C2H transpose (0.00s) 346s * 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 computations [34%] * HMM computations [35%] * HMM computations 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[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=7.941+/-0.441 / W=1.00Mb] (0.06s) 346s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 346s * HAP update (0.01s) 346s * H2V transpose (0.00s) 346s 346s Finalization: 346s * HAP solving (0.04s) 346s * HAP update (0.01s) 346s * H2V transpose (0.00s) 346s * 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] (0.11s) 346s * Total running time = 2 seconds 346s + 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 346s 346s SHAPEIT 346s * Author : Olivier DELANEAU, University of Lausanne 346s * Contact : olivier.delaneau@gmail.com 346s * Version : 4.2.2 346s * Run date : 05/02/2026 - 10:42:54 346s 346s Files: 346s * Input VCF : [unphased.bcf] 346s * Reference VCF : [reference.bcf] 346s * Scaffold VCF : [scaffold.bcf] 346s * Genetic Map : [chr20.b37.gmap.gz] 346s * Output VCF : [phased.bcf] 346s * Output LOG : [phased.log] 346s 346s Parameters: 346s * Seed : 15052011 346s * Threads : 4 threads 346s * MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m] 346s * PBWT : Depth of PBWT neighbours to condition on: 4 346s * PBWT : Store indexes at variants [MAC>=2 / MDR<=0.5 / Dist=0.02 cM] 346s * HMM : K is variable / min W is 2.50cM / Ne is 15000 346s * HMM : Recombination rates given by genetic map 346s * HMM : Inform phasing using VCF/PS field / Error rate of PS field is 0.0001 346s * HMM : AVX2 optimization inactive / Activating AVX2 substantially improves performance 346s 346s Initialization: 346s * VCF/BCF scanning ... * VCF/BCF scanning [Nm=203 / Nr=300 / L=24990 / Reg=20] (0.03s) 346s * 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=90.0% / Het=10.0% / Pha=2.668% / Sca=0.778% / Mis=0.0%] (0.30s) 347s * GMAP parsing [n=82962] (0.06s) 347s * cM interpolation [s=3296 / i=21694] (0.01s) 347s * Region length [2999624 bp / 6.6 cM] 347s * HMM parameters [Ne=15000 / Error=0.0001 / #rare=9606] 347s * PBWT indexing [l=328] (0.00s) 347s * HAP update (0.03s) 347s * H2V transpose (0.01s) 347s * 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 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[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 (0.27s) 347s * Build genotype graphs [seg=164449] (0.02s) 347s 347s Burn-in iteration [1/5] 347s * V2H transpose (0.00s) 347s * 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%] * 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350s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 350s * HAP update (0.01s) 350s * H2V transpose (0.01s) 350s 350s Burn-in iteration [4/5] 350s * V2H transpose (0.00s) 350s * 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 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PBWT selection [96%] * PBWT selection [97%] * PBWT selection [98%] * PBWT selection [99%] * PBWT selection [100%] * PBWT selection (0.04s) 351s * C2H transpose (0.00s) 352s * 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 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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) 352s * C2H transpose (0.00s) 352s * 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 computations [34%] * HMM computations [35%] * HMM computations [36%] * HMM computations [37%] * HMM computations [38%] * HMM computations [39%] * HMM computations [40%] * HMM computations [41%] * HMM computations [42%] * HMM computations [43%] * HMM computations [44%] * HMM computations [45%] * HMM computations [46%] * HMM computations [47%] * HMM computations [48%] * HMM computations [49%] * HMM computations [50%] * HMM computations [51%] * HMM computations [52%] * HMM computations [53%] * HMM computations [54%] * HMM computations [55%] * HMM computations [56%] * HMM computations [57%] * HMM 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=7.972+/-0.291 / W=2.17Mb] (0.17s) 352s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 352s * HAP update (0.01s) 352s * H2V transpose (0.00s) 352s 352s Pruning iteration [1/1] 352s * V2H transpose (0.00s) 352s * 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%] * 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[100%] * HMM computations [K=7.970+/-0.299 / W=2.29Mb] (0.22s) 352s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 352s * HAP update (0.01s) 352s * H2V transpose (0.00s) 352s * Trimming [pc=5.17%] 352s 352s Main iteration [1/5] 352s * V2H transpose (0.00s) 352s * 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%] 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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 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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 computations [34%] * HMM computations [35%] * HMM computations [36%] * HMM computations [37%] * HMM computations [38%] * HMM computations [39%] * HMM computations [40%] * HMM computations [41%] * HMM computations [42%] * HMM 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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=7.978+/-0.273 / W=2.27Mb] (0.18s) 353s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 353s * HAP update (0.01s) 353s * H2V transpose (0.00s) 353s 353s Main iteration [4/5] 353s * V2H transpose (0.00s) 353s * 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%] * 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[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=7.971+/-0.292 / W=2.18Mb] (0.20s) 353s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 353s * HAP update (0.01s) 353s * H2V transpose (0.00s) 353s 353s Main iteration [5/5] 353s * V2H transpose (0.00s) 353s * PBWT selection [0%] * PBWT selection [1%] * PBWT selection [2%] * PBWT selection [3%] * PBWT selection [4%] * PBWT selection [5%] * PBWT selection [6%] * PBWT selection [7%] * 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[94%] * PBWT selection [95%] * PBWT selection [96%] * PBWT selection [97%] * PBWT selection [98%] * PBWT selection [99%] * PBWT selection [100%] * PBWT selection (0.04s) 353s * C2H transpose (0.00s) 353s * 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 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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=7.971+/-0.295 / W=2.22Mb] (0.19s) 353s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 353s * HAP update (0.01s) 353s * H2V transpose (0.00s) 353s 353s Finalization: 353s * HAP solving (0.09s) 353s * HAP update (0.01s) 353s * H2V transpose (0.00s) 354s * 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] (0.10s) 354s * Total running time = 7 seconds 354s autopkgtest [10:43:02]: test run-sample-analysis: -----------------------] 358s autopkgtest [10:43:06]: test run-sample-analysis: - - - - - - - - - - results - - - - - - - - - - 358s run-sample-analysis PASS 362s autopkgtest [10:43:10]: @@@@@@@@@@@@@@@@@@@@ summary 362s run-sample-analysis PASS