0s autopkgtest [11:08:03]: starting date and time: 2026-02-05 11:08:03+0000
  0s autopkgtest [11:08:03]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op
  0s autopkgtest [11:08:03]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.zdh8w1y5/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade shapeit4 --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.42-2ubuntu5 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-ppc64el-27.secgroup --name adt-resolute-ppc64el-shapeit4-20260205-110803-juju-7f2275-prod-proposed-migration-environment-2-17de414f-3d03-48fe-bbea-d58516135643 --image adt/ubuntu-resolute-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-ppc64el -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/
  4s Creating nova instance adt-resolute-ppc64el-shapeit4-20260205-110803-juju-7f2275-prod-proposed-migration-environment-2-17de414f-3d03-48fe-bbea-d58516135643 from image adt/ubuntu-resolute-ppc64el-server-20260205.img (UUID f866c950-0b62-4023-bac6-0f13279e15ed)...
 67s autopkgtest [11:09:10]: testbed dpkg architecture: ppc64el
 67s autopkgtest [11:09:10]: testbed apt version: 3.1.14
 67s autopkgtest [11:09:10]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 68s autopkgtest [11:09:11]: testbed release detected to be: None
 68s autopkgtest [11:09:11]: updating testbed package index (apt update)
 69s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB]
 69s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease
 69s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease
 69s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease
 69s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1696 kB]
 69s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [35.4 kB]
 69s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [227 kB]
 69s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5260 B]
 69s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el Packages [261 kB]
 69s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el Packages [1492 kB]
 69s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse ppc64el Packages [21.9 kB]
 70s Fetched 3863 kB in 1s (3594 kB/s)
 71s Reading package lists...
 71s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease
 71s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease
 71s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease
 71s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease
 72s Reading package lists...
 72s Reading package lists...
 73s Building dependency tree...
 73s Reading state information...
 73s Calculating upgrade...
 73s The following packages will be upgraded:
 73s   libc-bin libc-gconv-modules-extra libc6 locales pollinate
 73s   python3-referencing sed
 73s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 73s Need to get 8612 kB of archives.
 73s After this operation, 0 B of additional disk space will be used.
 73s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el sed ppc64el 4.9-2build3 [211 kB]
 73s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el libc-gconv-modules-extra ppc64el 2.42-2ubuntu5 [1448 kB]
 73s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el libc6 ppc64el 2.42-2ubuntu5 [1913 kB]
 73s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el libc-bin ppc64el 2.42-2ubuntu5 [748 kB]
 73s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el locales all 2.42-2ubuntu5 [4255 kB]
 73s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el pollinate all 4.33-4ubuntu5 [14.0 kB]
 73s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-referencing all 0.36.2-1ubuntu2 [22.2 kB]
 74s dpkg-preconfigure: unable to re-open stdin: No such file or directory
 74s Fetched 8612 kB in 1s (13.0 MB/s)
 76s (Reading database ... 
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(Reading database ... 82008 files and directories currently installed.)
 76s Preparing to unpack .../sed_4.9-2build3_ppc64el.deb ...
 76s Unpacking sed (4.9-2build3) over (4.9-2build2) ...
 76s Setting up sed (4.9-2build3) ...
 76s (Reading database ... 
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(Reading database ... 82008 files and directories currently installed.)
 76s Preparing to unpack .../libc-gconv-modules-extra_2.42-2ubuntu5_ppc64el.deb ...
 76s Unpacking libc-gconv-modules-extra:ppc64el (2.42-2ubuntu5) over (2.42-2ubuntu4) ...
 77s Setting up libc-gconv-modules-extra:ppc64el (2.42-2ubuntu5) ...
 77s (Reading database ... 
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 77s Preparing to unpack .../libc6_2.42-2ubuntu5_ppc64el.deb ...
 78s Unpacking libc6:ppc64el (2.42-2ubuntu5) over (2.42-2ubuntu4) ...
 78s Setting up libc6:ppc64el (2.42-2ubuntu5) ...
 79s (Reading database ... 
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 79s Preparing to unpack .../libc-bin_2.42-2ubuntu5_ppc64el.deb ...
 79s Unpacking libc-bin (2.42-2ubuntu5) over (2.42-2ubuntu4) ...
 80s Setting up libc-bin (2.42-2ubuntu5) ...
 81s (Reading database ... 
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(Reading database ... 82008 files and directories currently installed.)
 81s Preparing to unpack .../locales_2.42-2ubuntu5_all.deb ...
 81s Unpacking locales (2.42-2ubuntu5) over (2.42-2ubuntu4) ...
 81s Preparing to unpack .../pollinate_4.33-4ubuntu5_all.deb ...
 81s Unpacking pollinate (4.33-4ubuntu5) over (4.33-4ubuntu4) ...
 81s Preparing to unpack .../python3-referencing_0.36.2-1ubuntu2_all.deb ...
 81s Unpacking python3-referencing (0.36.2-1ubuntu2) over (0.36.2-1ubuntu1) ...
 82s Setting up locales (2.42-2ubuntu5) ...
 82s Generating locales (this might take a while)...
 84s   en_US.UTF-8... done
 84s Generation complete.
 84s Setting up pollinate (4.33-4ubuntu5) ...
 95s Setting up python3-referencing (0.36.2-1ubuntu2) ...
 95s Processing triggers for man-db (2.13.1-1) ...
 97s Processing triggers for install-info (7.2-5) ...
 97s Processing triggers for systemd (259-1ubuntu3) ...
 98s autopkgtest [11:09:41]: upgrading testbed (apt dist-upgrade and autopurge)
 99s Reading package lists...
 99s Building dependency tree...
 99s Reading state information...
 99s Calculating upgrade...
 99s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 99s Reading package lists...
 99s Building dependency tree...
 99s Reading state information...
 99s Solving dependencies...
100s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
100s autopkgtest [11:09:43]: rebooting testbed after setup commands that affected boot
142s autopkgtest [11:10:25]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:45:54 UTC 2026
144s autopkgtest [11:10:27]: @@@@@@@@@@@@@@@@@@@@ apt-source shapeit4
149s Get:1 http://ftpmaster.internal/ubuntu resolute/universe shapeit4 4.2.2+dfsg-1build5 (dsc) [2237 B]
149s Get:2 http://ftpmaster.internal/ubuntu resolute/universe shapeit4 4.2.2+dfsg-1build5 (tar) [59.0 MB]
149s Get:3 http://ftpmaster.internal/ubuntu resolute/universe shapeit4 4.2.2+dfsg-1build5 (diff) [5456 B]
149s gpgv: Signature made Wed Aug  6 15:09:14 2025 UTC
149s gpgv:                using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37
149s gpgv: Can't check signature: No public key
149s dpkg-source: warning: cannot verify inline signature for ./shapeit4_4.2.2+dfsg-1build5.dsc: no acceptable signature found
151s autopkgtest [11:10:34]: testing package shapeit4 version 4.2.2+dfsg-1build5
151s autopkgtest [11:10:34]: build not needed
154s autopkgtest [11:10:37]: test run-sample-analysis: preparing testbed
154s Reading package lists...
154s Building dependency tree...
154s Reading state information...
154s Solving dependencies...
155s The following NEW packages will be installed:
155s   libboost-iostreams1.88.0 libboost-program-options1.88.0 libdeflate0
155s   libhts3t64 libhtscodecs2 shapeit4 shapeit4-example
155s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded.
155s Need to get 53.8 MB of archives.
155s After this operation, 60.0 MB of additional disk space will be used.
155s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el libboost-iostreams1.88.0 ppc64el 1.88.0-1.4ubuntu3 [262 kB]
155s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el libboost-program-options1.88.0 ppc64el 1.88.0-1.4ubuntu3 [334 kB]
155s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdeflate0 ppc64el 1.23-2 [63.3 kB]
155s Get:4 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhtscodecs2 ppc64el 1.6.1-2build1 [119 kB]
155s Get:5 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhts3t64 ppc64el 1.22.1+ds2-1 [617 kB]
155s Get:6 http://ftpmaster.internal/ubuntu resolute/universe ppc64el shapeit4 ppc64el 4.2.2+dfsg-1build5 [191 kB]
155s Get:7 http://ftpmaster.internal/ubuntu resolute/universe ppc64el shapeit4-example all 4.2.2+dfsg-1build5 [52.3 MB]
158s Fetched 53.8 MB in 3s (18.8 MB/s)
158s Selecting previously unselected package libboost-iostreams1.88.0:ppc64el.
158s (Reading database ... 
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158s Preparing to unpack .../0-libboost-iostreams1.88.0_1.88.0-1.4ubuntu3_ppc64el.deb ...
158s Unpacking libboost-iostreams1.88.0:ppc64el (1.88.0-1.4ubuntu3) ...
158s Selecting previously unselected package libboost-program-options1.88.0:ppc64el.
158s Preparing to unpack .../1-libboost-program-options1.88.0_1.88.0-1.4ubuntu3_ppc64el.deb ...
158s Unpacking libboost-program-options1.88.0:ppc64el (1.88.0-1.4ubuntu3) ...
158s Selecting previously unselected package libdeflate0:ppc64el.
158s Preparing to unpack .../2-libdeflate0_1.23-2_ppc64el.deb ...
158s Unpacking libdeflate0:ppc64el (1.23-2) ...
158s Selecting previously unselected package libhtscodecs2:ppc64el.
158s Preparing to unpack .../3-libhtscodecs2_1.6.1-2build1_ppc64el.deb ...
158s Unpacking libhtscodecs2:ppc64el (1.6.1-2build1) ...
158s Selecting previously unselected package libhts3t64:ppc64el.
158s Preparing to unpack .../4-libhts3t64_1.22.1+ds2-1_ppc64el.deb ...
158s Unpacking libhts3t64:ppc64el (1.22.1+ds2-1) ...
158s Selecting previously unselected package shapeit4.
158s Preparing to unpack .../5-shapeit4_4.2.2+dfsg-1build5_ppc64el.deb ...
158s Unpacking shapeit4 (4.2.2+dfsg-1build5) ...
158s Selecting previously unselected package shapeit4-example.
158s Preparing to unpack .../6-shapeit4-example_4.2.2+dfsg-1build5_all.deb ...
158s Unpacking shapeit4-example (4.2.2+dfsg-1build5) ...
159s Setting up libhtscodecs2:ppc64el (1.6.1-2build1) ...
159s Setting up libboost-program-options1.88.0:ppc64el (1.88.0-1.4ubuntu3) ...
159s Setting up libdeflate0:ppc64el (1.23-2) ...
159s Setting up libboost-iostreams1.88.0:ppc64el (1.88.0-1.4ubuntu3) ...
159s Setting up shapeit4-example (4.2.2+dfsg-1build5) ...
159s Setting up libhts3t64:ppc64el (1.22.1+ds2-1) ...
159s Setting up shapeit4 (4.2.2+dfsg-1build5) ...
159s Processing triggers for man-db (2.13.1-1) ...
160s Processing triggers for libc-bin (2.42-2ubuntu5) ...
162s autopkgtest [11:10:45]: test run-sample-analysis: [-----------------------
162s + shapeit4 --input unphased.vcf.gz --map chr20.b37.gmap.gz --region 20:2000000-3000000 --thread 4 --output phased.vcf.gz
162s 
162s SHAPEIT
162s   * Author        : Olivier DELANEAU, University of Lausanne
162s   * Contact       : olivier.delaneau@gmail.com
162s   * Version       : 4.2.2
162s   * Run date      : 05/02/2026 - 11:10:45
162s 
162s Files:
162s   * Input VCF     : [unphased.vcf.gz]
162s   * Genetic Map   : [chr20.b37.gmap.gz]
162s   * Output VCF    : [phased.vcf.gz]
162s 
162s Parameters:
162s   * Seed    : 15052011
162s   * Threads : 4 threads
162s   * MCMC    : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m]
162s   * PBWT    : Depth of PBWT neighbours to condition on: 4
162s   * PBWT    : Store indexes at variants [MAC>=2 / MDR<=0.5 / Dist=0.02 cM]
162s   * HMM     : K is variable / min W is 2.50cM / Ne is 15000
162s   * HMM     : Recombination rates given by genetic map
162s   * HMM     : AVX2 optimization inactive / Activating AVX2 substantially improves performance
162s 
162s Initialization:
162s   * VCF/BCF scanning ...
[W::hts_idx_load3] The index file is older than the data file: unphased.vcf.gz.csi
162s   * VCF/BCF scanning [N=203 / L=8651 / Reg=20:2000000-3000000] (0.08s)
162s [W::hts_idx_load3] The index file is older than the data file: unphased.vcf.gz.csi
162s   * VCF/BCF parsing [0%]
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  * VCF/BCF parsing [100%]
  * VCF/BCF parsing [Hom=89.3% / Het=10.7% / Mis=0.0%] (0.10s)
162s   * GMAP parsing [n=82962] (0.06s)
162s   * cM interpolation [s=1236 / i=7415] (0.00s)
162s   * Region length [999850 bp / 2.5 cM]
162s   * HMM parameters [Ne=15000 / Error=0.0001 / #rare=2243]
162s   * PBWT indexing [l=120] (0.00s)
162s   * HAP update (0.01s)
162s   * H2V transpose (0.00s)
162s   * PBWT phase sweep [0%]
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162s   * Build genotype graphs [seg=62841] (0.01s)
162s 
162s Burn-in iteration [1/5]
162s   * V2H transpose (0.00s)
162s   * PBWT selection [0%]
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  * PBWT selection (0.01s)
162s   * C2H transpose (0.00s)
164s   * HMM computations [0%]
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  * HMM computations [K=291.522+/-9.938 / W=1.00Mb] (1.94s)
164s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
164s   * HAP update (0.01s)
164s   * H2V transpose (0.00s)
164s 
164s Burn-in iteration [2/5]
164s   * V2H transpose (0.00s)
164s   * PBWT selection [0%]
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164s   * C2H transpose (0.00s)
166s   * HMM computations [0%]
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  * HMM computations [K=250.581+/-11.160 / W=1.00Mb] (1.65s)
166s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
166s   * HAP update (0.01s)
166s   * H2V transpose (0.00s)
166s 
166s Burn-in iteration [3/5]
166s   * V2H transpose (0.00s)
166s   * PBWT selection [0%]
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  * PBWT selection (0.01s)
166s   * C2H transpose (0.00s)
168s   * HMM computations [0%]
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  * HMM computations [K=238.527+/-13.238 / W=1.00Mb] (1.54s)
168s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
168s   * HAP update (0.01s)
168s   * H2V transpose (0.00s)
168s 
168s Burn-in iteration [4/5]
168s   * V2H transpose (0.00s)
168s   * PBWT selection [0%]
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  * PBWT selection (0.01s)
168s   * C2H transpose (0.00s)
169s   * HMM computations [0%]
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  * HMM computations [K=231.020+/-13.413 / W=1.00Mb] (1.51s)
169s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
169s   * HAP update (0.01s)
169s   * H2V transpose (0.00s)
169s 
169s Burn-in iteration [5/5]
169s   * V2H transpose (0.00s)
169s   * PBWT selection [0%]
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169s   * C2H transpose (0.00s)
171s   * HMM computations [0%]
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  * HMM computations [K=226.039+/-13.430 / W=1.00Mb] (1.51s)
171s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
171s   * HAP update (0.01s)
171s   * H2V transpose (0.00s)
171s 
171s Pruning iteration [1/1]
171s   * V2H transpose (0.00s)
171s   * PBWT selection [0%]
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  * PBWT selection (0.01s)
171s   * C2H transpose (0.00s)
172s   * HMM computations [0%]
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  * HMM computations [K=222.094+/-13.589 / W=1.00Mb] (1.66s)
172s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
172s   * HAP update (0.01s)
172s   * H2V transpose (0.00s)
172s   * Trimming [pc=41.25%]
172s 
172s Burn-in iteration [1/1]
172s   * V2H transpose (0.00s)
172s   * PBWT selection [0%]
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  * PBWT selection (0.01s)
172s   * C2H transpose (0.00s)
174s   * HMM computations [0%]
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  * HMM computations [K=229.241+/-14.851 / W=1.00Mb] (1.41s)
174s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
174s   * HAP update (0.01s)
174s   * H2V transpose (0.00s)
174s 
174s Pruning iteration [1/1]
174s   * V2H transpose (0.00s)
174s   * PBWT selection [0%]
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  * PBWT selection (0.01s)
174s   * C2H transpose (0.00s)
175s   * HMM computations [0%]
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  * HMM computations [K=214.507+/-15.549 / W=1.00Mb] (1.41s)
175s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
175s   * HAP update (0.01s)
175s   * H2V transpose (0.00s)
175s   * Trimming [pc=65.05%]
175s 
175s Burn-in iteration [1/1]
175s   * V2H transpose (0.00s)
175s   * PBWT selection [0%]
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175s   * C2H transpose (0.00s)
176s   * HMM computations [0%]
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  * HMM computations [K=216.133+/-16.058 / W=1.00Mb] (1.12s)
176s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
176s   * HAP update (0.01s)
176s   * H2V transpose (0.00s)
176s 
176s Pruning iteration [1/1]
176s   * V2H transpose (0.00s)
176s   * PBWT selection [0%]
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  * PBWT selection (0.01s)
176s   * C2H transpose (0.00s)
177s   * HMM computations [0%]
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  * HMM computations [K=209.010+/-16.712 / W=1.00Mb] (1.19s)
177s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
177s   * HAP update (0.01s)
177s   * H2V transpose (0.00s)
177s   * Trimming [pc=77.76%]
177s 
177s Main iteration [1/5]
177s   * V2H transpose (0.00s)
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177s   * C2H transpose (0.00s)
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179s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
179s   * HAP update (0.01s)
179s   * H2V transpose (0.00s)
179s 
179s Main iteration [2/5]
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179s   * C2H transpose (0.00s)
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180s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
180s   * HAP update (0.01s)
180s   * H2V transpose (0.00s)
180s 
180s Main iteration [3/5]
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180s   * C2H transpose (0.00s)
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  * HMM computations [K=211.749+/-16.258 / W=1.00Mb] (1.06s)
181s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
181s   * HAP update (0.01s)
181s   * H2V transpose (0.00s)
181s 
181s Main iteration [4/5]
181s   * V2H transpose (0.00s)
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  * PBWT selection (0.01s)
181s   * C2H transpose (0.00s)
182s   * HMM computations [0%]
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  * HMM computations [K=209.443+/-16.662 / W=1.00Mb] (0.98s)
182s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
182s   * HAP update (0.01s)
182s   * H2V transpose (0.00s)
182s 
182s Main iteration [5/5]
182s   * V2H transpose (0.00s)
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  * PBWT selection (0.01s)
182s   * C2H transpose (0.00s)
183s   * HMM computations [0%]
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  * HMM computations [K=210.660+/-16.717 / W=1.00Mb] (0.99s)
183s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
183s   * HAP update (0.01s)
183s   * H2V transpose (0.00s)
183s 
183s Finalization:
183s   * HAP solving (0.02s)
183s   * HAP update (0.01s)
183s   * H2V transpose (0.00s)
183s   * VCF writing [0%]
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+ 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
183s   * VCF writing [Compressed / N=203 / L=8651] (0.12s)
183s   * Total running time = 20 seconds
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 - 11:11:06
183s 
183s Files:
183s   * Input VCF     : [unphased.bcf]
183s   * Reference VCF : [reference.bcf]
183s   * Scaffold VCF  : [scaffold.bcf]
183s   * Genetic Map   : [chr20.b37.gmap.gz]
183s   * Output VCF    : [phased.bcf]
183s   * Output LOG    : [phased.log]
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     : Inform phasing using VCF/PS field / Error rate of PS field is 0.0001
183s   * HMM     : AVX2 optimization inactive / Activating AVX2 substantially improves performance
183s 
183s Initialization:
183s   * VCF/BCF scanning ...
  * VCF/BCF scanning [Nm=203 / Nr=300 / L=24990 / Reg=20] (0.06s)
183s   * VCF/BCF parsing [0%]
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  * VCF/BCF parsing [Hom=90.0% / Het=10.0% / Pha=2.668% / Sca=0.778% / Mis=0.0%] (0.26s)
183s   * GMAP parsing [n=82962] (0.06s)
183s   * cM interpolation [s=3296 / i=21694] (0.00s)
183s   * Region length [2999624 bp / 6.6 cM]
183s   * HMM parameters [Ne=15000 / Error=0.0001 / #rare=9606]
183s   * PBWT indexing [l=328] (0.00s)
183s   * HAP update (0.04s)
183s   * H2V transpose (0.01s)
184s   * PBWT phase sweep [0%]
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  * PBWT phase sweep (0.26s)
184s   * Build genotype graphs [seg=164449] (0.04s)
184s 
184s Burn-in iteration [1/5]
184s   * V2H transpose (0.00s)
184s   * PBWT selection [0%]
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  * PBWT selection (0.04s)
184s   * C2H transpose (0.00s)
194s   * HMM computations [0%]
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  * HMM computations [K=572.985+/-107.628 / W=2.22Mb] (10.53s)
194s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
194s   * HAP update (0.01s)
194s   * H2V transpose (0.00s)
194s 
194s Burn-in iteration [2/5]
194s   * V2H transpose (0.00s)
194s   * PBWT selection [0%]
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  * PBWT selection (0.04s)
194s   * C2H transpose (0.00s)
203s   * HMM computations [0%]
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  * HMM computations [K=449.275+/-124.444 / W=2.26Mb] (8.49s)
203s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
203s   * HAP update (0.01s)
203s   * H2V transpose (0.00s)
203s 
203s Burn-in iteration [3/5]
203s   * V2H transpose (0.00s)
203s   * PBWT selection [0%]
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  * PBWT selection (0.04s)
203s   * C2H transpose (0.00s)
211s   * HMM computations [0%]
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  * HMM computations [K=430.838+/-116.372 / W=2.25Mb] (7.75s)
211s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
211s   * HAP update (0.01s)
211s   * H2V transpose (0.00s)
211s 
211s Burn-in iteration [4/5]
211s   * V2H transpose (0.00s)
211s   * PBWT selection [0%]
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  * PBWT selection (0.04s)
211s   * C2H transpose (0.00s)
219s   * HMM computations [0%]
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  * HMM computations [K=442.766+/-115.780 / W=2.33Mb] (7.98s)
219s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
219s   * HAP update (0.01s)
219s   * H2V transpose (0.00s)
219s 
219s Burn-in iteration [5/5]
219s   * V2H transpose (0.00s)
219s   * PBWT selection [0%]
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  * PBWT selection (0.04s)
219s   * C2H transpose (0.00s)
227s   * HMM computations [0%]
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  * HMM computations [K=423.109+/-117.840 / W=2.21Mb] (7.88s)
227s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
227s   * HAP update (0.01s)
227s   * H2V transpose (0.00s)
227s 
227s Pruning iteration [1/1]
227s   * V2H transpose (0.00s)
227s   * PBWT selection [0%]
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  * PBWT selection (0.04s)
227s   * C2H transpose (0.00s)
235s   * HMM computations [0%]
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  * HMM computations [K=435.045+/-117.465 / W=2.28Mb] (8.41s)
235s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
235s   * HAP update (0.01s)
235s   * H2V transpose (0.00s)
235s   * Trimming [pc=42.06%]
235s 
235s Burn-in iteration [1/1]
235s   * V2H transpose (0.00s)
235s   * PBWT selection [0%]
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  * PBWT selection (0.04s)
235s   * C2H transpose (0.00s)
242s   * HMM computations [0%]
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  * HMM computations [K=425.633+/-115.808 / W=2.22Mb] (6.63s)
242s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
242s   * HAP update (0.01s)
242s   * H2V transpose (0.00s)
242s 
242s Pruning iteration [1/1]
242s   * V2H transpose (0.00s)
242s   * PBWT selection [0%]
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  * PBWT selection (0.04s)
242s   * C2H transpose (0.00s)
248s   * HMM computations [0%]
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  * HMM computations [K=398.035+/-115.509 / W=2.12Mb] (6.42s)
248s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
248s   * HAP update (0.01s)
248s   * H2V transpose (0.00s)
248s   * Trimming [pc=66.14%]
248s 
248s Burn-in iteration [1/1]
248s   * V2H transpose (0.00s)
248s   * PBWT selection [0%]
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  * PBWT selection (0.04s)
248s   * C2H transpose (0.00s)
254s   * HMM computations [0%]
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  * HMM computations [K=406.586+/-114.863 / W=2.23Mb] (5.68s)
254s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
254s   * HAP update (0.01s)
254s   * H2V transpose (0.00s)
254s 
254s Pruning iteration [1/1]
254s   * V2H transpose (0.00s)
254s   * PBWT selection [0%]
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  * PBWT selection (0.04s)
254s   * C2H transpose (0.00s)
260s   * HMM computations [0%]
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  * HMM computations [K=396.123+/-115.290 / W=2.21Mb] (5.87s)
260s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
260s   * HAP update (0.01s)
260s   * H2V transpose (0.00s)
260s   * Trimming [pc=78.17%]
260s 
260s Main iteration [1/5]
260s   * V2H transpose (0.00s)
260s   * PBWT selection [0%]
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  * PBWT selection (0.04s)
260s   * C2H transpose (0.00s)
265s   * HMM computations [0%]
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  * HMM computations [K=387.637+/-113.994 / W=2.15Mb] (5.28s)
265s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
265s   * HAP update (0.01s)
265s   * H2V transpose (0.00s)
265s 
265s Main iteration [2/5]
265s   * V2H transpose (0.00s)
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265s   * C2H transpose (0.00s)
271s   * HMM computations [0%]
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  * HMM computations [K=398.802+/-109.985 / W=2.28Mb] (5.34s)
271s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
271s   * HAP update (0.01s)
271s   * H2V transpose (0.00s)
271s 
271s Main iteration [3/5]
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  * PBWT selection (0.04s)
271s   * C2H transpose (0.00s)
276s   * HMM computations [0%]
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  * HMM computations [K=385.606+/-111.399 / W=2.16Mb] (5.19s)
276s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
276s   * HAP update (0.01s)
276s   * H2V transpose (0.00s)
276s 
276s Main iteration [4/5]
276s   * V2H transpose (0.00s)
276s   * PBWT selection [0%]
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  * PBWT selection (0.04s)
276s   * C2H transpose (0.00s)
281s   * HMM computations [0%]
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  * HMM computations [K=391.710+/-110.573 / W=2.19Mb] (5.10s)
281s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
281s   * HAP update (0.01s)
281s   * H2V transpose (0.00s)
281s 
281s Main iteration [5/5]
281s   * V2H transpose (0.00s)
281s   * PBWT selection [0%]
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  * PBWT selection [100%]
  * PBWT selection (0.04s)
281s   * C2H transpose (0.00s)
286s   * HMM computations [0%]
  * HMM computations [1%]
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  * HMM computations [K=394.844+/-114.986 / W=2.22Mb] (5.05s)
286s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
286s   * HAP update (0.01s)
286s   * H2V transpose (0.00s)
286s 
286s Finalization:
286s   * HAP solving (0.03s)
286s   * HAP update (0.01s)
286s   * H2V transpose (0.00s)
286s   * VCF writing [0%]
  * VCF writing [1%]
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  * VCF writing [96%]
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  * VCF writing [98%]
  * VCF writing [99%]
  * VCF writing [100%]
  * BCF writing [Compressed / N=203 / L=24990] (0.21s)
286s   * Total running time = 103 seconds
287s autopkgtest [11:12:50]: test run-sample-analysis: -----------------------]
287s run-sample-analysis  PASS
287s autopkgtest [11:12:50]: test run-sample-analysis:  - - - - - - - - - - results - - - - - - - - - -
288s autopkgtest [11:12:51]: @@@@@@@@@@@@@@@@@@@@ summary
288s run-sample-analysis  PASS