1s autopkgtest [17:35:44]: starting date and time: 2025-03-15 17:35:44+0000
  1s autopkgtest [17:35:44]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production'
  1s autopkgtest [17:35:44]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.rol39b5i/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,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\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/2.41-1ubuntu2 -- lxd -r lxd-armhf-10.145.243.210 lxd-armhf-10.145.243.210:autopkgtest/ubuntu/plucky/armhf
 21s autopkgtest [17:36:04]: testbed dpkg architecture: armhf
 23s autopkgtest [17:36:06]: testbed apt version: 2.9.33
 27s autopkgtest [17:36:10]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 28s autopkgtest [17:36:11]: testbed release detected to be: None
 36s autopkgtest [17:36:19]: updating testbed package index (apt update)
 38s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB]
 38s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB]
 39s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB]
 39s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB]
 39s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB]
 39s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB]
 40s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB]
 40s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [114 kB]
 40s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1832 B]
 40s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B]
 40s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [312 kB]
 40s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [11.1 kB]
 40s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B]
 40s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [240 B]
 40s Get:15 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB]
 40s Get:16 http://ftpmaster.internal/ubuntu plucky/main Sources [1394 kB]
 42s Get:17 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB]
 62s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB]
 63s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB]
 63s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B]
 63s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB]
 77s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB]
 79s Fetched 41.0 MB in 41s (996 kB/s)
 80s Reading package lists...
 86s autopkgtest [17:37:09]: upgrading testbed (apt dist-upgrade and autopurge)
 87s Reading package lists...
 88s Building dependency tree...
 88s Reading state information...
 88s Calculating upgrade...Starting pkgProblemResolver with broken count: 0
 88s Starting 2 pkgProblemResolver with broken count: 0
 88s Done
 89s Entering ResolveByKeep
 89s 
 89s Calculating upgrade...
 90s The following packages will be upgraded:
 90s   libc-bin libc6 locales pinentry-curses python3-jinja2 sos strace
 90s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 90s Need to get 8683 kB of archives.
 90s After this operation, 23.6 kB of additional disk space will be used.
 90s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB]
 94s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB]
 94s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB]
 99s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB]
 99s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf pinentry-curses armhf 1.3.1-2ubuntu3 [40.6 kB]
 99s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB]
 99s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB]
100s Preconfiguring packages ...
100s Fetched 8683 kB in 10s (888 kB/s)
101s (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 ... 64655 files and directories currently installed.)
101s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ...
101s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
101s Setting up libc6:armhf (2.41-1ubuntu2) ...
101s (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 ... 64655 files and directories currently installed.)
101s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ...
101s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
101s Setting up libc-bin (2.41-1ubuntu2) ...
102s (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 ... 64655 files and directories currently installed.)
102s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ...
102s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
102s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ...
102s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ...
102s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_armhf.deb ...
102s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ...
102s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ...
102s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ...
102s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ...
103s Unpacking sos (4.9.0-5) over (4.9.0-4) ...
103s Setting up sos (4.9.0-5) ...
104s Setting up pinentry-curses (1.3.1-2ubuntu3) ...
104s Setting up locales (2.41-1ubuntu2) ...
105s Generating locales (this might take a while)...
107s   en_US.UTF-8... done
107s Generation complete.
107s Setting up python3-jinja2 (3.1.5-2ubuntu1) ...
107s Setting up strace (6.13+ds-1ubuntu1) ...
107s Processing triggers for man-db (2.13.0-1) ...
108s Processing triggers for systemd (257.3-1ubuntu3) ...
111s Reading package lists...
112s Building dependency tree...
112s Reading state information...
112s Starting pkgProblemResolver with broken count: 0
112s Starting 2 pkgProblemResolver with broken count: 0
112s Done
113s Solving dependencies...
113s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
115s autopkgtest [17:37:38]: rebooting testbed after setup commands that affected boot
155s autopkgtest [17:38:18]: testbed running kernel: Linux 6.8.0-52-generic #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 18:10:51 UTC 2
179s autopkgtest [17:38:42]: @@@@@@@@@@@@@@@@@@@@ apt-source shapeit4
242s Get:1 http://ftpmaster.internal/ubuntu plucky/universe shapeit4 4.2.2+dfsg-1build3 (dsc) [2237 B]
242s Get:2 http://ftpmaster.internal/ubuntu plucky/universe shapeit4 4.2.2+dfsg-1build3 (tar) [59.0 MB]
242s Get:3 http://ftpmaster.internal/ubuntu plucky/universe shapeit4 4.2.2+dfsg-1build3 (diff) [5424 B]
242s gpgv: Signature made Mon Apr  1 08:00:11 2024 UTC
242s gpgv:                using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984
242s gpgv: Can't check signature: No public key
242s dpkg-source: warning: cannot verify inline signature for ./shapeit4_4.2.2+dfsg-1build3.dsc: no acceptable signature found
243s autopkgtest [17:39:46]: testing package shapeit4 version 4.2.2+dfsg-1build3
245s autopkgtest [17:39:48]: build not needed
249s autopkgtest [17:39:52]: test run-sample-analysis: preparing testbed
251s Reading package lists...
251s Building dependency tree...
251s Reading state information...
252s Starting pkgProblemResolver with broken count: 0
252s Starting 2 pkgProblemResolver with broken count: 0
252s Done
253s The following NEW packages will be installed:
253s   libboost-iostreams1.83.0 libboost-program-options1.83.0 libdeflate0
253s   libhts3t64 libhtscodecs2 shapeit4 shapeit4-example
253s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded.
253s Need to get 53.6 MB of archives.
253s After this operation, 58.7 MB of additional disk space will be used.
253s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf libboost-iostreams1.83.0 armhf 1.83.0-4.1ubuntu2 [258 kB]
253s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libboost-program-options1.83.0 armhf 1.83.0-4.1ubuntu2 [345 kB]
253s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.23-1 [38.5 kB]
253s Get:4 http://ftpmaster.internal/ubuntu plucky/universe armhf libhtscodecs2 armhf 1.6.1-2 [67.5 kB]
253s Get:5 http://ftpmaster.internal/ubuntu plucky/universe armhf libhts3t64 armhf 1.21+ds-1 [399 kB]
254s Get:6 http://ftpmaster.internal/ubuntu plucky/universe armhf shapeit4 armhf 4.2.2+dfsg-1build3 [200 kB]
254s Get:7 http://ftpmaster.internal/ubuntu plucky/universe armhf shapeit4-example all 4.2.2+dfsg-1build3 [52.3 MB]
293s Fetched 53.6 MB in 40s (1332 kB/s)
293s Selecting previously unselected package libboost-iostreams1.83.0:armhf.
293s (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 ... 64655 files and directories currently installed.)
293s Preparing to unpack .../0-libboost-iostreams1.83.0_1.83.0-4.1ubuntu2_armhf.deb ...
293s Unpacking libboost-iostreams1.83.0:armhf (1.83.0-4.1ubuntu2) ...
293s Selecting previously unselected package libboost-program-options1.83.0:armhf.
293s Preparing to unpack .../1-libboost-program-options1.83.0_1.83.0-4.1ubuntu2_armhf.deb ...
293s Unpacking libboost-program-options1.83.0:armhf (1.83.0-4.1ubuntu2) ...
293s Selecting previously unselected package libdeflate0:armhf.
293s Preparing to unpack .../2-libdeflate0_1.23-1_armhf.deb ...
293s Unpacking libdeflate0:armhf (1.23-1) ...
293s Selecting previously unselected package libhtscodecs2:armhf.
294s Preparing to unpack .../3-libhtscodecs2_1.6.1-2_armhf.deb ...
294s Unpacking libhtscodecs2:armhf (1.6.1-2) ...
294s Selecting previously unselected package libhts3t64:armhf.
294s Preparing to unpack .../4-libhts3t64_1.21+ds-1_armhf.deb ...
294s Unpacking libhts3t64:armhf (1.21+ds-1) ...
294s Selecting previously unselected package shapeit4.
294s Preparing to unpack .../5-shapeit4_4.2.2+dfsg-1build3_armhf.deb ...
294s Unpacking shapeit4 (4.2.2+dfsg-1build3) ...
294s Selecting previously unselected package shapeit4-example.
294s Preparing to unpack .../6-shapeit4-example_4.2.2+dfsg-1build3_all.deb ...
294s Unpacking shapeit4-example (4.2.2+dfsg-1build3) ...
294s Setting up libhtscodecs2:armhf (1.6.1-2) ...
294s Setting up libboost-program-options1.83.0:armhf (1.83.0-4.1ubuntu2) ...
294s Setting up libdeflate0:armhf (1.23-1) ...
294s Setting up shapeit4-example (4.2.2+dfsg-1build3) ...
294s Setting up libboost-iostreams1.83.0:armhf (1.83.0-4.1ubuntu2) ...
294s Setting up libhts3t64:armhf (1.21+ds-1) ...
294s Setting up shapeit4 (4.2.2+dfsg-1build3) ...
294s Processing triggers for man-db (2.13.0-1) ...
295s Processing triggers for libc-bin (2.41-1ubuntu2) ...
304s autopkgtest [17:40:47]: test run-sample-analysis: [-----------------------
306s + shapeit4 --input unphased.vcf.gz --map chr20.b37.gmap.gz --region 20:2000000-3000000 --thread 4 --output phased.vcf.gz
306s 
306s SHAPEIT
306s   * Author        : Olivier DELANEAU, University of Lausanne
306s   * Contact       : olivier.delaneau@gmail.com
306s   * Version       : 4.2.2
306s   * Run date      : 15/03/2025 - 17:40:49
306s 
306s Files:
306s   * Input VCF     : [unphased.vcf.gz]
306s   * Genetic Map   : [chr20.b37.gmap.gz]
306s   * Output VCF    : [phased.vcf.gz]
306s 
306s Parameters:
306s   * Seed    : 15052011
306s   * Threads : 4 threads
306s   * MCMC    : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m]
306s   * PBWT    : Depth of PBWT neighbours to condition on: 4
306s   * PBWT    : Store indexes at variants [MAC>=2 / MDR<=0.5 / Dist=0.02 cM]
306s   * HMM     : K is variable / min W is 2.50cM / Ne is 15000
306s   * HMM     : Recombination rates given by genetic map
306s   * HMM     : AVX2 optimization inactive / Activating AVX2 substantially improves performance
306s 
306s Initialization:
306s   * VCF/BCF scanning ...
  * VCF/BCF scanning [N=203 / L=8651 / Reg=20:2000000-3000000] (0.08s)
307s   * VCF/BCF parsing [0%]
  * VCF/BCF parsing [1%]
  * VCF/BCF parsing [2%]
  * VCF/BCF parsing [3%]
  * VCF/BCF parsing [4%]
  * VCF/BCF parsing [5%]
  * VCF/BCF parsing [6%]
  * VCF/BCF parsing [7%]
  * VCF/BCF parsing [8%]
  * VCF/BCF parsing [9%]
  * VCF/BCF parsing [10%]
  * VCF/BCF parsing [11%]
  * VCF/BCF parsing [12%]
  * VCF/BCF parsing [13%]
  * VCF/BCF parsing [14%]
  * VCF/BCF parsing [15%]
  * VCF/BCF parsing [16%]
  * VCF/BCF parsing [17%]
  * VCF/BCF parsing [18%]
  * VCF/BCF parsing [19%]
  * VCF/BCF parsing [20%]
  * VCF/BCF parsing [21%]
  * VCF/BCF parsing [22%]
  * VCF/BCF parsing [23%]
  * VCF/BCF parsing [24%]
  * VCF/BCF parsing [25%]
  * VCF/BCF parsing [26%]
  * VCF/BCF parsing [27%]
  * VCF/BCF parsing [28%]
  * VCF/BCF parsing [29%]
  * VCF/BCF parsing [30%]
  * VCF/BCF parsing [31%]
  * VCF/BCF parsing [32%]
  * VCF/BCF parsing [33%]
  * VCF/BCF parsing [34%]
  * VCF/BCF parsing [35%]
  * VCF/BCF parsing [36%]
  * VCF/BCF parsing [37%]
  * VCF/BCF parsing [38%]
  * VCF/BCF parsing [39%]
  * VCF/BCF parsing [40%]
  * VCF/BCF parsing [41%]
  * VCF/BCF parsing [42%]
  * VCF/BCF parsing [43%]
  * VCF/BCF parsing [44%]
  * VCF/BCF parsing [45%]
  * VCF/BCF parsing [46%]
  * VCF/BCF parsing [47%]
  * VCF/BCF parsing [48%]
  * VCF/BCF parsing [49%]
  * VCF/BCF parsing [50%]
  * VCF/BCF parsing [51%]
  * VCF/BCF parsing [52%]
  * VCF/BCF parsing [53%]
  * VCF/BCF parsing [54%]
  * VCF/BCF parsing [55%]
  * VCF/BCF parsing [56%]
  * VCF/BCF parsing [57%]
  * VCF/BCF parsing [58%]
  * VCF/BCF parsing [59%]
  * VCF/BCF parsing [60%]
  * VCF/BCF parsing [61%]
  * VCF/BCF parsing [62%]
  * VCF/BCF parsing [63%]
  * VCF/BCF parsing [64%]
  * VCF/BCF parsing [65%]
  * VCF/BCF parsing [66%]
  * VCF/BCF parsing [67%]
  * VCF/BCF parsing [68%]
  * VCF/BCF parsing [69%]
  * VCF/BCF parsing [70%]
  * VCF/BCF parsing [71%]
  * VCF/BCF parsing [72%]
  * VCF/BCF parsing [73%]
  * VCF/BCF parsing [74%]
  * VCF/BCF parsing [75%]
  * VCF/BCF parsing [76%]
  * VCF/BCF parsing [77%]
  * VCF/BCF parsing [78%]
  * VCF/BCF parsing [79%]
  * VCF/BCF parsing [80%]
  * VCF/BCF parsing [81%]
  * VCF/BCF parsing [82%]
  * VCF/BCF parsing [83%]
  * VCF/BCF parsing [84%]
  * VCF/BCF parsing [85%]
  * VCF/BCF parsing [86%]
  * VCF/BCF parsing [87%]
  * VCF/BCF parsing [88%]
  * VCF/BCF parsing [89%]
  * VCF/BCF parsing [90%]
  * VCF/BCF parsing [91%]
  * VCF/BCF parsing [92%]
  * VCF/BCF parsing [93%]
  * VCF/BCF parsing [94%]
  * VCF/BCF parsing [95%]
  * VCF/BCF parsing [96%]
  * VCF/BCF parsing [97%]
  * VCF/BCF parsing [98%]
  * VCF/BCF parsing [99%]
  * VCF/BCF parsing [100%]
  * VCF/BCF parsing [Hom=89.3% / Het=10.7% / Mis=0.0%] (0.11s)
307s   * GMAP parsing [n=82962] (0.06s)
307s   * cM interpolation [s=1236 / i=7415] (0.01s)
307s   * Region length [999850 bp / 2.5 cM]
307s   * HMM parameters [Ne=15000 / Error=0.0001 / #rare=2243]
307s   * PBWT indexing [l=120] (0.00s)
307s   * HAP update (0.01s)
307s   * H2V transpose (0.00s)
307s   * PBWT phase sweep [0%]
  * PBWT phase sweep [1%]
  * PBWT phase sweep [2%]
  * PBWT phase sweep [3%]
  * PBWT phase sweep [4%]
  * PBWT phase sweep [5%]
  * PBWT phase sweep [6%]
  * PBWT phase sweep [7%]
  * PBWT phase sweep [8%]
  * PBWT phase sweep [9%]
  * PBWT phase sweep [10%]
  * PBWT phase sweep [11%]
  * PBWT phase sweep [12%]
  * PBWT phase sweep [13%]
  * PBWT phase sweep [14%]
  * PBWT phase sweep [15%]
  * PBWT phase sweep [16%]
  * PBWT phase sweep [17%]
  * PBWT phase sweep [18%]
  * PBWT phase sweep [19%]
  * PBWT phase sweep [20%]
  * PBWT phase sweep [21%]
  * PBWT phase sweep [22%]
  * PBWT phase sweep [23%]
  * PBWT phase sweep [24%]
  * PBWT phase sweep [25%]
  * PBWT phase sweep [26%]
  * PBWT phase sweep [27%]
  * PBWT phase sweep [28%]
  * PBWT phase sweep [29%]
  * PBWT phase sweep [30%]
  * PBWT phase sweep [31%]
  * PBWT phase sweep [32%]
  * PBWT phase sweep [33%]
  * PBWT phase sweep [34%]
  * PBWT phase sweep [35%]
  * PBWT phase sweep [36%]
  * PBWT phase sweep [37%]
  * PBWT phase sweep [38%]
  * PBWT phase sweep [39%]
  * PBWT phase sweep [40%]
  * PBWT phase sweep [41%]
  * PBWT phase sweep [42%]
  * PBWT phase sweep [43%]
  * PBWT phase sweep [44%]
  * PBWT phase sweep [45%]
  * PBWT phase sweep [46%]
  * PBWT phase sweep [47%]
  * PBWT phase sweep [48%]
  * PBWT phase sweep [49%]
  * PBWT phase sweep [50%]
  * PBWT phase sweep [51%]
  * PBWT phase sweep [52%]
  * PBWT phase sweep [53%]
  * PBWT phase sweep [54%]
  * PBWT phase sweep [55%]
  * PBWT phase sweep [56%]
  * PBWT phase sweep [57%]
  * PBWT phase sweep [58%]
  * PBWT phase sweep [59%]
  * PBWT phase sweep [60%]
  * PBWT phase sweep [61%]
  * PBWT phase sweep [62%]
  * PBWT phase sweep [63%]
  * PBWT phase sweep [64%]
  * PBWT phase sweep [65%]
  * PBWT phase sweep [66%]
  * PBWT phase sweep [67%]
  * PBWT phase sweep [68%]
  * PBWT phase sweep [69%]
  * PBWT phase sweep [70%]
  * PBWT phase sweep [71%]
  * PBWT phase sweep [72%]
  * PBWT phase sweep [73%]
  * PBWT phase sweep [74%]
  * PBWT phase sweep [75%]
  * PBWT phase sweep [76%]
  * PBWT phase sweep [77%]
  * PBWT phase sweep [78%]
  * PBWT phase sweep [79%]
  * PBWT phase sweep [80%]
  * PBWT phase sweep [81%]
  * PBWT phase sweep [82%]
  * PBWT phase sweep [83%]
  * PBWT phase sweep [84%]
  * PBWT phase sweep [85%]
  * PBWT phase sweep [86%]
  * PBWT phase sweep [87%]
  * PBWT phase sweep [88%]
  * PBWT phase sweep [89%]
  * PBWT phase sweep [90%]
  * PBWT phase sweep [91%]
  * PBWT phase sweep [92%]
  * PBWT phase sweep [93%]
  * PBWT phase sweep [94%]
  * PBWT phase sweep [95%]
  * PBWT phase sweep [96%]
  * PBWT phase sweep [97%]
  * PBWT phase sweep [98%]
  * PBWT phase sweep [99%]
  * PBWT phase sweep [100%]
  * PBWT phase sweep (0.07s)
307s   * Build genotype graphs [seg=62841] (0.01s)
307s 
307s Burn-in iteration [1/5]
307s   * V2H transpose (0.00s)
307s   * PBWT selection [0%]
  * PBWT selection [1%]
  * PBWT selection [2%]
  * PBWT selection [3%]
  * PBWT selection [4%]
  * PBWT selection [5%]
  * PBWT selection [6%]
  * PBWT selection [7%]
  * PBWT selection [8%]
  * PBWT selection [9%]
  * PBWT selection [10%]
  * PBWT selection [11%]
  * PBWT selection [12%]
  * PBWT selection [13%]
  * PBWT selection [14%]
  * PBWT selection [15%]
  * PBWT selection [16%]
  * PBWT selection [17%]
  * PBWT selection [18%]
  * PBWT selection [19%]
  * PBWT selection [20%]
  * PBWT selection [21%]
  * PBWT selection [22%]
  * PBWT selection [23%]
  * PBWT selection [24%]
  * PBWT selection [25%]
  * PBWT selection [26%]
  * PBWT selection [27%]
  * PBWT selection [28%]
  * PBWT selection [29%]
  * PBWT selection [30%]
  * PBWT selection [31%]
  * PBWT selection [32%]
  * PBWT selection [33%]
  * PBWT selection [34%]
  * PBWT selection [35%]
  * PBWT selection [36%]
  * PBWT selection [37%]
  * PBWT selection [38%]
  * PBWT selection [39%]
  * PBWT selection [40%]
  * PBWT selection [41%]
  * PBWT selection [42%]
  * PBWT selection [43%]
  * PBWT selection [44%]
  * PBWT selection [45%]
  * PBWT selection [46%]
  * PBWT selection [47%]
  * PBWT selection [48%]
  * PBWT selection [49%]
  * PBWT selection [50%]
  * PBWT selection [51%]
  * PBWT selection [52%]
  * PBWT selection [53%]
  * PBWT selection [54%]
  * PBWT selection [55%]
  * PBWT selection [56%]
  * PBWT selection [57%]
  * PBWT selection [58%]
  * PBWT selection [59%]
  * PBWT selection [60%]
  * PBWT selection [61%]
  * PBWT selection [62%]
  * PBWT selection [63%]
  * PBWT selection [64%]
  * PBWT selection [65%]
  * PBWT selection [66%]
  * PBWT selection [67%]
  * PBWT selection [68%]
  * PBWT selection [69%]
  * PBWT selection [70%]
  * PBWT selection [71%]
  * PBWT selection [72%]
  * PBWT selection [73%]
  * PBWT selection [74%]
  * PBWT selection [75%]
  * PBWT selection [76%]
  * PBWT selection [77%]
  * PBWT selection [78%]
  * PBWT selection [79%]
  * PBWT selection [80%]
  * PBWT selection [81%]
  * PBWT selection [82%]
  * PBWT selection [83%]
  * PBWT selection [84%]
  * PBWT selection [85%]
  * PBWT selection [86%]
  * PBWT selection [87%]
  * PBWT selection [88%]
  * PBWT selection [89%]
  * PBWT selection [90%]
  * PBWT selection [91%]
  * PBWT selection [92%]
  * PBWT selection [93%]
  * PBWT selection [94%]
  * PBWT selection [95%]
  * PBWT selection [96%]
  * PBWT selection [97%]
  * PBWT selection [98%]
  * PBWT selection [99%]
  * PBWT selection [100%]
  * PBWT selection (0.01s)
307s   * C2H transpose (0.00s)
308s   * 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=302.315+/-10.774 / W=1.00Mb] (0.92s)
308s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
308s   * HAP update (0.01s)
308s   * H2V transpose (0.00s)
308s 
308s Burn-in iteration [2/5]
308s   * V2H transpose (0.00s)
308s   * PBWT selection [0%]
  * PBWT selection [1%]
  * PBWT selection [2%]
  * PBWT selection [3%]
  * PBWT selection [4%]
  * PBWT selection [5%]
  * PBWT selection [6%]
  * PBWT selection [7%]
  * PBWT selection [8%]
  * PBWT selection [9%]
  * PBWT selection [10%]
  * PBWT selection [11%]
  * PBWT selection [12%]
  * PBWT selection [13%]
  * PBWT selection [14%]
  * PBWT selection [15%]
  * PBWT selection [16%]
  * PBWT selection [17%]
  * PBWT selection [18%]
  * PBWT selection [19%]
  * PBWT selection [20%]
  * PBWT selection [21%]
  * PBWT selection [22%]
  * PBWT selection [23%]
  * PBWT selection [24%]
  * PBWT selection [25%]
  * PBWT selection [26%]
  * PBWT selection [27%]
  * PBWT selection [28%]
  * PBWT selection [29%]
  * PBWT selection [30%]
  * PBWT selection [31%]
  * PBWT selection [32%]
  * PBWT selection [33%]
  * PBWT selection [34%]
  * PBWT selection [35%]
  * PBWT selection [36%]
  * PBWT selection [37%]
  * PBWT selection [38%]
  * PBWT selection [39%]
  * PBWT selection [40%]
  * PBWT selection [41%]
  * PBWT selection [42%]
  * PBWT selection [43%]
  * PBWT selection [44%]
  * PBWT selection [45%]
  * PBWT selection [46%]
  * PBWT selection [47%]
  * PBWT selection [48%]
  * PBWT selection [49%]
  * PBWT selection [50%]
  * PBWT selection [51%]
  * PBWT selection [52%]
  * PBWT selection [53%]
  * PBWT selection [54%]
  * PBWT selection [55%]
  * PBWT selection [56%]
  * PBWT selection [57%]
  * PBWT selection [58%]
  * PBWT selection [59%]
  * PBWT selection [60%]
  * PBWT selection [61%]
  * PBWT selection [62%]
  * PBWT selection [63%]
  * PBWT selection [64%]
  * PBWT selection [65%]
  * PBWT selection [66%]
  * PBWT selection [67%]
  * PBWT selection [68%]
  * PBWT selection [69%]
  * PBWT selection [70%]
  * PBWT selection [71%]
  * PBWT selection [72%]
  * PBWT selection [73%]
  * PBWT selection [74%]
  * PBWT selection [75%]
  * PBWT selection [76%]
  * PBWT selection [77%]
  * PBWT selection [78%]
  * PBWT selection [79%]
  * PBWT selection [80%]
  * PBWT selection [81%]
  * PBWT selection [82%]
  * PBWT selection [83%]
  * PBWT selection [84%]
  * PBWT selection [85%]
  * PBWT selection [86%]
  * PBWT selection [87%]
  * PBWT selection [88%]
  * PBWT selection [89%]
  * PBWT selection [90%]
  * PBWT selection [91%]
  * PBWT selection [92%]
  * PBWT selection [93%]
  * PBWT selection [94%]
  * PBWT selection [95%]
  * PBWT selection [96%]
  * PBWT selection [97%]
  * PBWT selection [98%]
  * PBWT selection [99%]
  * PBWT selection [100%]
  * PBWT selection (0.01s)
308s   * C2H transpose (0.00s)
308s   * 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=7.941+/-0.441 / W=1.00Mb] (0.08s)
308s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
308s   * HAP update (0.01s)
308s   * H2V transpose (0.00s)
308s 
308s Burn-in iteration [3/5]
308s   * V2H transpose (0.00s)
308s   * PBWT selection [0%]
  * PBWT selection [1%]
  * PBWT selection [2%]
  * PBWT selection [3%]
  * PBWT selection [4%]
  * PBWT selection [5%]
  * PBWT selection [6%]
  * PBWT selection [7%]
  * PBWT selection [8%]
  * PBWT selection [9%]
  * PBWT selection [10%]
  * PBWT selection [11%]
  * PBWT selection [12%]
  * PBWT selection [13%]
  * PBWT selection [14%]
  * PBWT selection [15%]
  * PBWT selection [16%]
  * PBWT selection [17%]
  * PBWT selection [18%]
  * PBWT selection [19%]
  * PBWT selection [20%]
  * PBWT selection [21%]
  * PBWT selection [22%]
  * PBWT selection [23%]
  * PBWT selection [24%]
  * PBWT selection [25%]
  * PBWT selection [26%]
  * PBWT selection [27%]
  * PBWT selection [28%]
  * PBWT selection [29%]
  * PBWT selection [30%]
  * PBWT selection [31%]
  * PBWT selection [32%]
  * PBWT selection [33%]
  * PBWT selection [34%]
  * PBWT selection [35%]
  * PBWT selection [36%]
  * PBWT selection [37%]
  * PBWT selection [38%]
  * PBWT selection [39%]
  * PBWT selection [40%]
  * PBWT selection [41%]
  * PBWT selection [42%]
  * PBWT selection [43%]
  * PBWT selection [44%]
  * PBWT selection [45%]
  * PBWT selection [46%]
  * PBWT selection [47%]
  * PBWT selection [48%]
  * PBWT selection [49%]
  * PBWT selection [50%]
  * PBWT selection [51%]
  * PBWT selection [52%]
  * PBWT selection [53%]
  * PBWT selection [54%]
  * PBWT selection [55%]
  * PBWT selection [56%]
  * PBWT selection [57%]
  * PBWT selection [58%]
  * PBWT selection [59%]
  * PBWT selection [60%]
  * PBWT selection [61%]
  * PBWT selection [62%]
  * PBWT selection [63%]
  * PBWT selection [64%]
  * PBWT selection [65%]
  * PBWT selection [66%]
  * PBWT selection [67%]
  * PBWT selection [68%]
  * PBWT selection [69%]
  * PBWT selection [70%]
  * PBWT selection [71%]
  * PBWT selection [72%]
  * PBWT selection [73%]
  * PBWT selection [74%]
  * PBWT selection [75%]
  * PBWT selection [76%]
  * PBWT selection [77%]
  * PBWT selection [78%]
  * PBWT selection [79%]
  * PBWT selection [80%]
  * PBWT selection [81%]
  * PBWT selection [82%]
  * PBWT selection [83%]
  * PBWT selection [84%]
  * PBWT selection [85%]
  * PBWT selection [86%]
  * PBWT selection [87%]
  * PBWT selection [88%]
  * PBWT selection [89%]
  * PBWT selection [90%]
  * PBWT selection [91%]
  * PBWT selection [92%]
  * PBWT selection [93%]
  * PBWT selection [94%]
  * PBWT selection [95%]
  * PBWT selection [96%]
  * PBWT selection [97%]
  * PBWT selection [98%]
  * PBWT selection [99%]
  * PBWT selection [100%]
  * PBWT selection (0.01s)
308s   * C2H transpose (0.00s)
308s   * 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=7.941+/-0.441 / W=1.00Mb] (0.07s)
308s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
308s   * HAP update (0.01s)
308s   * H2V transpose (0.00s)
308s 
308s Burn-in iteration [4/5]
308s   * V2H transpose (0.00s)
308s   * PBWT selection [0%]
  * PBWT selection [1%]
  * PBWT selection [2%]
  * PBWT selection [3%]
  * PBWT selection [4%]
  * PBWT selection [5%]
  * PBWT selection [6%]
  * PBWT selection [7%]
  * PBWT selection [8%]
  * PBWT selection [9%]
  * PBWT selection [10%]
  * PBWT selection [11%]
  * PBWT selection [12%]
  * PBWT selection [13%]
  * PBWT selection [14%]
  * PBWT selection [15%]
  * PBWT selection [16%]
  * PBWT selection [17%]
  * PBWT selection [18%]
  * PBWT selection [19%]
  * PBWT selection [20%]
  * PBWT selection [21%]
  * PBWT selection [22%]
  * PBWT selection [23%]
  * PBWT selection [24%]
  * PBWT selection [25%]
  * PBWT selection [26%]
  * PBWT selection [27%]
  * PBWT selection [28%]
  * PBWT selection [29%]
  * PBWT selection [30%]
  * PBWT selection [31%]
  * PBWT selection [32%]
  * PBWT selection [33%]
  * PBWT selection [34%]
  * PBWT selection [35%]
  * PBWT selection [36%]
  * PBWT selection [37%]
  * PBWT selection [38%]
  * PBWT selection [39%]
  * PBWT selection [40%]
  * PBWT selection [41%]
  * PBWT selection [42%]
  * PBWT selection [43%]
  * PBWT selection [44%]
  * PBWT selection [45%]
  * PBWT selection [46%]
  * PBWT selection [47%]
  * PBWT selection [48%]
  * PBWT selection [49%]
  * PBWT selection [50%]
  * PBWT selection [51%]
  * PBWT selection [52%]
  * PBWT selection [53%]
  * PBWT selection [54%]
  * PBWT selection [55%]
  * PBWT selection [56%]
  * PBWT selection [57%]
  * PBWT selection [58%]
  * PBWT selection [59%]
  * PBWT selection [60%]
  * PBWT selection [61%]
  * PBWT selection [62%]
  * PBWT selection [63%]
  * PBWT selection [64%]
  * PBWT selection [65%]
  * PBWT selection [66%]
  * PBWT selection [67%]
  * PBWT selection [68%]
  * PBWT selection [69%]
  * PBWT selection [70%]
  * PBWT selection [71%]
  * PBWT selection [72%]
  * PBWT selection [73%]
  * PBWT selection [74%]
  * PBWT selection [75%]
  * PBWT selection [76%]
  * PBWT selection [77%]
  * PBWT selection [78%]
  * PBWT selection [79%]
  * PBWT selection [80%]
  * PBWT selection [81%]
  * PBWT selection [82%]
  * PBWT selection [83%]
  * PBWT selection [84%]
  * PBWT selection [85%]
  * PBWT selection [86%]
  * PBWT selection [87%]
  * PBWT selection [88%]
  * PBWT selection [89%]
  * PBWT selection [90%]
  * PBWT selection [91%]
  * PBWT selection [92%]
  * PBWT selection [93%]
  * PBWT selection [94%]
  * PBWT selection [95%]
  * PBWT selection [96%]
  * PBWT selection [97%]
  * PBWT selection [98%]
  * PBWT selection [99%]
  * PBWT selection [100%]
  * PBWT selection (0.01s)
308s   * C2H transpose (0.00s)
308s   * 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=7.941+/-0.441 / W=1.00Mb] (0.08s)
308s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
308s   * HAP update (0.01s)
308s   * H2V transpose (0.00s)
308s 
308s Burn-in iteration [5/5]
308s   * V2H transpose (0.00s)
308s   * PBWT selection [0%]
  * PBWT selection [1%]
  * PBWT selection [2%]
  * PBWT selection [3%]
  * PBWT selection [4%]
  * PBWT selection [5%]
  * PBWT selection [6%]
  * PBWT selection [7%]
  * PBWT selection [8%]
  * PBWT selection [9%]
  * PBWT selection [10%]
  * PBWT selection [11%]
  * PBWT selection [12%]
  * PBWT selection [13%]
  * PBWT selection [14%]
  * PBWT selection [15%]
  * PBWT selection [16%]
  * PBWT selection [17%]
  * PBWT selection [18%]
  * PBWT selection [19%]
  * PBWT selection [20%]
  * PBWT selection [21%]
  * PBWT selection [22%]
  * PBWT selection [23%]
  * PBWT selection [24%]
  * PBWT selection [25%]
  * PBWT selection [26%]
  * PBWT selection [27%]
  * PBWT selection [28%]
  * PBWT selection [29%]
  * PBWT selection [30%]
  * PBWT selection [31%]
  * PBWT selection [32%]
  * PBWT selection [33%]
  * PBWT selection [34%]
  * PBWT selection [35%]
  * PBWT selection [36%]
  * PBWT selection [37%]
  * PBWT selection [38%]
  * PBWT selection [39%]
  * PBWT selection [40%]
  * PBWT selection [41%]
  * PBWT selection [42%]
  * PBWT selection [43%]
  * PBWT selection [44%]
  * PBWT selection [45%]
  * PBWT selection [46%]
  * PBWT selection [47%]
  * PBWT selection [48%]
  * PBWT selection [49%]
  * PBWT selection [50%]
  * PBWT selection [51%]
  * PBWT selection [52%]
  * PBWT selection [53%]
  * PBWT selection [54%]
  * PBWT selection [55%]
  * PBWT selection [56%]
  * PBWT selection [57%]
  * PBWT selection [58%]
  * PBWT selection [59%]
  * PBWT selection [60%]
  * PBWT selection [61%]
  * PBWT selection [62%]
  * PBWT selection [63%]
  * PBWT selection [64%]
  * PBWT selection [65%]
  * PBWT selection [66%]
  * PBWT selection [67%]
  * PBWT selection [68%]
  * PBWT selection [69%]
  * PBWT selection [70%]
  * PBWT selection [71%]
  * PBWT selection [72%]
  * PBWT selection [73%]
  * PBWT selection [74%]
  * PBWT selection [75%]
  * PBWT selection [76%]
  * PBWT selection [77%]
  * PBWT selection [78%]
  * PBWT selection [79%]
  * PBWT selection [80%]
  * PBWT selection [81%]
  * PBWT selection [82%]
  * PBWT selection [83%]
  * PBWT selection [84%]
  * PBWT selection [85%]
  * PBWT selection [86%]
  * PBWT selection [87%]
  * PBWT selection [88%]
  * PBWT selection [89%]
  * PBWT selection [90%]
  * PBWT selection [91%]
  * PBWT selection [92%]
  * PBWT selection [93%]
  * PBWT selection [94%]
  * PBWT selection [95%]
  * PBWT selection [96%]
  * PBWT selection [97%]
  * PBWT selection [98%]
  * PBWT selection [99%]
  * PBWT selection [100%]
  * PBWT selection (0.01s)
308s   * C2H transpose (0.00s)
308s   * 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=7.941+/-0.441 / W=1.00Mb] (0.11s)
308s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
308s   * HAP update (0.01s)
308s   * H2V transpose (0.00s)
308s 
308s Pruning iteration [1/1]
308s   * V2H transpose (0.00s)
308s   * PBWT selection [0%]
  * PBWT selection [1%]
  * PBWT selection [2%]
  * PBWT selection [3%]
  * PBWT selection [4%]
  * PBWT selection [5%]
  * PBWT selection [6%]
  * PBWT selection [7%]
  * PBWT selection [8%]
  * PBWT selection [9%]
  * PBWT selection [10%]
  * PBWT selection [11%]
  * PBWT selection [12%]
  * PBWT selection [13%]
  * PBWT selection [14%]
  * PBWT selection [15%]
  * PBWT selection [16%]
  * PBWT selection [17%]
  * PBWT selection [18%]
  * PBWT selection [19%]
  * PBWT selection [20%]
  * PBWT selection [21%]
  * PBWT selection [22%]
  * PBWT selection [23%]
  * PBWT selection [24%]
  * PBWT selection [25%]
  * PBWT selection [26%]
  * PBWT selection [27%]
  * PBWT selection [28%]
  * PBWT selection [29%]
  * PBWT selection [30%]
  * PBWT selection [31%]
  * PBWT selection [32%]
  * PBWT selection [33%]
  * PBWT selection [34%]
  * PBWT selection [35%]
  * PBWT selection [36%]
  * PBWT selection [37%]
  * PBWT selection [38%]
  * PBWT selection [39%]
  * PBWT selection [40%]
  * PBWT selection [41%]
  * PBWT selection [42%]
  * PBWT selection [43%]
  * PBWT selection [44%]
  * PBWT selection [45%]
  * PBWT selection [46%]
  * PBWT selection [47%]
  * PBWT selection [48%]
  * PBWT selection [49%]
  * PBWT selection [50%]
  * PBWT selection [51%]
  * PBWT selection [52%]
  * PBWT selection [53%]
  * PBWT selection [54%]
  * PBWT selection [55%]
  * PBWT selection [56%]
  * PBWT selection [57%]
  * PBWT selection [58%]
  * PBWT selection [59%]
  * PBWT selection [60%]
  * PBWT selection [61%]
  * PBWT selection [62%]
  * PBWT selection [63%]
  * PBWT selection [64%]
  * PBWT selection [65%]
  * PBWT selection [66%]
  * PBWT selection [67%]
  * PBWT selection [68%]
  * PBWT selection [69%]
  * PBWT selection [70%]
  * PBWT selection [71%]
  * PBWT selection [72%]
  * PBWT selection [73%]
  * PBWT selection [74%]
  * PBWT selection [75%]
  * PBWT selection [76%]
  * PBWT selection [77%]
  * PBWT selection [78%]
  * PBWT selection [79%]
  * PBWT selection [80%]
  * PBWT selection [81%]
  * PBWT selection [82%]
  * PBWT selection [83%]
  * PBWT selection [84%]
  * PBWT selection [85%]
  * PBWT selection [86%]
  * PBWT selection [87%]
  * PBWT selection [88%]
  * PBWT selection [89%]
  * PBWT selection [90%]
  * PBWT selection [91%]
  * PBWT selection [92%]
  * PBWT selection [93%]
  * PBWT selection [94%]
  * PBWT selection [95%]
  * PBWT selection [96%]
  * PBWT selection [97%]
  * PBWT selection [98%]
  * PBWT selection [99%]
  * PBWT selection [100%]
  * PBWT selection (0.01s)
308s   * C2H transpose (0.00s)
308s   * 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=7.941+/-0.441 / W=1.00Mb] (0.14s)
308s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
308s   * HAP update (0.01s)
308s   * H2V transpose (0.00s)
308s   * Trimming [pc=0.00%]
308s 
308s Burn-in iteration [1/1]
308s   * V2H transpose (0.00s)
308s   * PBWT selection [0%]
  * PBWT selection [1%]
  * PBWT selection [2%]
  * PBWT selection [3%]
  * PBWT selection [4%]
  * PBWT selection [5%]
  * PBWT selection [6%]
  * PBWT selection [7%]
  * PBWT selection [8%]
  * PBWT selection [9%]
  * PBWT selection [10%]
  * PBWT selection [11%]
  * PBWT selection [12%]
  * PBWT selection [13%]
  * PBWT selection [14%]
  * PBWT selection [15%]
  * PBWT selection [16%]
  * PBWT selection [17%]
  * PBWT selection [18%]
  * PBWT selection [19%]
  * PBWT selection [20%]
  * PBWT selection [21%]
  * PBWT selection [22%]
  * PBWT selection [23%]
  * PBWT selection [24%]
  * PBWT selection [25%]
  * PBWT selection [26%]
  * PBWT selection [27%]
  * PBWT selection [28%]
  * PBWT selection [29%]
  * PBWT selection [30%]
  * PBWT selection [31%]
  * PBWT selection [32%]
  * PBWT selection [33%]
  * PBWT selection [34%]
  * PBWT selection [35%]
  * PBWT selection [36%]
  * PBWT selection [37%]
  * PBWT selection [38%]
  * PBWT selection [39%]
  * PBWT selection [40%]
  * PBWT selection [41%]
  * PBWT selection [42%]
  * PBWT selection [43%]
  * PBWT selection [44%]
  * PBWT selection [45%]
  * PBWT selection [46%]
  * PBWT selection [47%]
  * PBWT selection [48%]
  * PBWT selection [49%]
  * PBWT selection [50%]
  * PBWT selection [51%]
  * PBWT selection [52%]
  * PBWT selection [53%]
  * PBWT selection [54%]
  * PBWT selection [55%]
  * PBWT selection [56%]
  * PBWT selection [57%]
  * PBWT selection [58%]
  * PBWT selection [59%]
  * PBWT selection [60%]
  * PBWT selection [61%]
  * PBWT selection [62%]
  * PBWT selection [63%]
  * PBWT selection [64%]
  * PBWT selection [65%]
  * PBWT selection [66%]
  * PBWT selection [67%]
  * PBWT selection [68%]
  * PBWT selection [69%]
  * PBWT selection [70%]
  * PBWT selection [71%]
  * PBWT selection [72%]
  * PBWT selection [73%]
  * PBWT selection [74%]
  * PBWT selection [75%]
  * PBWT selection [76%]
  * PBWT selection [77%]
  * PBWT selection [78%]
  * PBWT selection [79%]
  * PBWT selection [80%]
  * PBWT selection [81%]
  * PBWT selection [82%]
  * PBWT selection [83%]
  * PBWT selection [84%]
  * PBWT selection [85%]
  * PBWT selection [86%]
  * PBWT selection [87%]
  * PBWT selection [88%]
  * PBWT selection [89%]
  * PBWT selection [90%]
  * PBWT selection [91%]
  * PBWT selection [92%]
  * PBWT selection [93%]
  * PBWT selection [94%]
  * PBWT selection [95%]
  * PBWT selection [96%]
  * PBWT selection [97%]
  * PBWT selection [98%]
  * PBWT selection [99%]
  * PBWT selection [100%]
  * PBWT selection (0.01s)
308s   * C2H transpose (0.00s)
308s   * 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=7.941+/-0.441 / W=1.00Mb] (0.12s)
308s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
308s   * HAP update (0.01s)
308s   * H2V transpose (0.00s)
308s 
308s Pruning iteration [1/1]
308s   * V2H transpose (0.00s)
308s   * PBWT selection [0%]
  * PBWT selection [1%]
  * PBWT selection [2%]
  * PBWT selection [3%]
  * PBWT selection [4%]
  * PBWT selection [5%]
  * PBWT selection [6%]
  * PBWT selection [7%]
  * PBWT selection [8%]
  * PBWT selection [9%]
  * PBWT selection [10%]
  * PBWT selection [11%]
  * PBWT selection [12%]
  * PBWT selection [13%]
  * PBWT selection [14%]
  * PBWT selection [15%]
  * PBWT selection [16%]
  * PBWT selection [17%]
  * PBWT selection [18%]
  * PBWT selection [19%]
  * PBWT selection [20%]
  * PBWT selection [21%]
  * PBWT selection [22%]
  * PBWT selection [23%]
  * PBWT selection [24%]
  * PBWT selection [25%]
  * PBWT selection [26%]
  * PBWT selection [27%]
  * PBWT selection [28%]
  * PBWT selection [29%]
  * PBWT selection [30%]
  * PBWT selection [31%]
  * PBWT selection [32%]
  * PBWT selection [33%]
  * PBWT selection [34%]
  * PBWT selection [35%]
  * PBWT selection [36%]
  * PBWT selection [37%]
  * PBWT selection [38%]
  * PBWT selection [39%]
  * PBWT selection [40%]
  * PBWT selection [41%]
  * PBWT selection [42%]
  * PBWT selection [43%]
  * PBWT selection [44%]
  * PBWT selection [45%]
  * PBWT selection [46%]
  * PBWT selection [47%]
  * PBWT selection [48%]
  * PBWT selection [49%]
  * PBWT selection [50%]
  * PBWT selection [51%]
  * PBWT selection [52%]
  * PBWT selection [53%]
  * PBWT selection [54%]
  * PBWT selection [55%]
  * PBWT selection [56%]
  * PBWT selection [57%]
  * PBWT selection [58%]
  * PBWT selection [59%]
  * PBWT selection [60%]
  * PBWT selection [61%]
  * PBWT selection [62%]
  * PBWT selection [63%]
  * PBWT selection [64%]
  * PBWT selection [65%]
  * PBWT selection [66%]
  * PBWT selection [67%]
  * PBWT selection [68%]
  * PBWT selection [69%]
  * PBWT selection [70%]
  * PBWT selection [71%]
  * PBWT selection [72%]
  * PBWT selection [73%]
  * PBWT selection [74%]
  * PBWT selection [75%]
  * PBWT selection [76%]
  * PBWT selection [77%]
  * PBWT selection [78%]
  * PBWT selection [79%]
  * PBWT selection [80%]
  * PBWT selection [81%]
  * PBWT selection [82%]
  * PBWT selection [83%]
  * PBWT selection [84%]
  * PBWT selection [85%]
  * PBWT selection [86%]
  * PBWT selection [87%]
  * PBWT selection [88%]
  * PBWT selection [89%]
  * PBWT selection [90%]
  * PBWT selection [91%]
  * PBWT selection [92%]
  * PBWT selection [93%]
  * PBWT selection [94%]
  * PBWT selection [95%]
  * PBWT selection [96%]
  * PBWT selection [97%]
  * PBWT selection [98%]
  * PBWT selection [99%]
  * PBWT selection [100%]
  * PBWT selection (0.01s)
308s   * C2H transpose (0.00s)
309s   * 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=7.941+/-0.441 / W=1.00Mb] (0.18s)
309s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
309s   * HAP update (0.01s)
309s   * H2V transpose (0.00s)
309s   * Trimming [pc=0.00%]
309s 
309s Burn-in iteration [1/1]
309s   * V2H transpose (0.00s)
309s   * PBWT selection [0%]
  * PBWT selection [1%]
  * PBWT selection [2%]
  * PBWT selection [3%]
  * PBWT selection [4%]
  * PBWT selection [5%]
  * PBWT selection [6%]
  * PBWT selection [7%]
  * PBWT selection [8%]
  * PBWT selection [9%]
  * PBWT selection [10%]
  * PBWT selection [11%]
  * PBWT selection [12%]
  * PBWT selection [13%]
  * PBWT selection [14%]
  * PBWT selection [15%]
  * PBWT selection [16%]
  * PBWT selection [17%]
  * PBWT selection [18%]
  * PBWT selection [19%]
  * PBWT selection [20%]
  * PBWT selection [21%]
  * PBWT selection [22%]
  * PBWT selection [23%]
  * PBWT selection [24%]
  * PBWT selection [25%]
  * PBWT selection [26%]
  * PBWT selection [27%]
  * PBWT selection [28%]
  * PBWT selection [29%]
  * PBWT selection [30%]
  * PBWT selection [31%]
  * PBWT selection [32%]
  * PBWT selection [33%]
  * PBWT selection [34%]
  * PBWT selection [35%]
  * PBWT selection [36%]
  * PBWT selection [37%]
  * PBWT selection [38%]
  * PBWT selection [39%]
  * PBWT selection [40%]
  * PBWT selection [41%]
  * PBWT selection [42%]
  * PBWT selection [43%]
  * PBWT selection [44%]
  * PBWT selection [45%]
  * PBWT selection [46%]
  * PBWT selection [47%]
  * PBWT selection [48%]
  * PBWT selection [49%]
  * PBWT selection [50%]
  * PBWT selection [51%]
  * PBWT selection [52%]
  * PBWT selection [53%]
  * PBWT selection [54%]
  * PBWT selection [55%]
  * PBWT selection [56%]
  * PBWT selection [57%]
  * PBWT selection [58%]
  * PBWT selection [59%]
  * PBWT selection [60%]
  * PBWT selection [61%]
  * PBWT selection [62%]
  * PBWT selection [63%]
  * PBWT selection [64%]
  * PBWT selection [65%]
  * PBWT selection [66%]
  * PBWT selection [67%]
  * PBWT selection [68%]
  * PBWT selection [69%]
  * PBWT selection [70%]
  * PBWT selection [71%]
  * PBWT selection [72%]
  * PBWT selection [73%]
  * PBWT selection [74%]
  * PBWT selection [75%]
  * PBWT selection [76%]
  * PBWT selection [77%]
  * PBWT selection [78%]
  * PBWT selection [79%]
  * PBWT selection [80%]
  * PBWT selection [81%]
  * PBWT selection [82%]
  * PBWT selection [83%]
  * PBWT selection [84%]
  * PBWT selection [85%]
  * PBWT selection [86%]
  * PBWT selection [87%]
  * PBWT selection [88%]
  * PBWT selection [89%]
  * PBWT selection [90%]
  * PBWT selection [91%]
  * PBWT selection [92%]
  * PBWT selection [93%]
  * PBWT selection [94%]
  * PBWT selection [95%]
  * PBWT selection [96%]
  * PBWT selection [97%]
  * PBWT selection [98%]
  * PBWT selection [99%]
  * PBWT selection [100%]
  * PBWT selection (0.01s)
309s   * C2H transpose (0.00s)
309s   * 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=7.941+/-0.441 / W=1.00Mb] (0.10s)
309s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
309s   * HAP update (0.01s)
309s   * H2V transpose (0.00s)
309s 
309s Pruning iteration [1/1]
309s   * V2H transpose (0.00s)
309s   * PBWT selection [0%]
  * PBWT selection [1%]
  * PBWT selection [2%]
  * PBWT selection [3%]
  * PBWT selection [4%]
  * PBWT selection [5%]
  * PBWT selection [6%]
  * PBWT selection [7%]
  * PBWT selection [8%]
  * PBWT selection [9%]
  * PBWT selection [10%]
  * PBWT selection [11%]
  * PBWT selection [12%]
  * PBWT selection [13%]
  * PBWT selection [14%]
  * PBWT selection [15%]
  * PBWT selection [16%]
  * PBWT selection [17%]
  * PBWT selection [18%]
  * PBWT selection [19%]
  * PBWT selection [20%]
  * PBWT selection [21%]
  * PBWT selection [22%]
  * PBWT selection [23%]
  * PBWT selection [24%]
  * PBWT selection [25%]
  * PBWT selection [26%]
  * PBWT selection [27%]
  * PBWT selection [28%]
  * PBWT selection [29%]
  * PBWT selection [30%]
  * PBWT selection [31%]
  * PBWT selection [32%]
  * PBWT selection [33%]
  * PBWT selection [34%]
  * PBWT selection [35%]
  * PBWT selection [36%]
  * PBWT selection [37%]
  * PBWT selection [38%]
  * PBWT selection [39%]
  * PBWT selection [40%]
  * PBWT selection [41%]
  * PBWT selection [42%]
  * PBWT selection [43%]
  * PBWT selection [44%]
  * PBWT selection [45%]
  * PBWT selection [46%]
  * PBWT selection [47%]
  * PBWT selection [48%]
  * PBWT selection [49%]
  * PBWT selection [50%]
  * PBWT selection [51%]
  * PBWT selection [52%]
  * PBWT selection [53%]
  * PBWT selection [54%]
  * PBWT selection [55%]
  * PBWT selection [56%]
  * PBWT selection [57%]
  * PBWT selection [58%]
  * PBWT selection [59%]
  * PBWT selection [60%]
  * PBWT selection [61%]
  * PBWT selection [62%]
  * PBWT selection [63%]
  * PBWT selection [64%]
  * PBWT selection [65%]
  * PBWT selection [66%]
  * PBWT selection [67%]
  * PBWT selection [68%]
  * PBWT selection [69%]
  * PBWT selection [70%]
  * PBWT selection [71%]
  * PBWT selection [72%]
  * PBWT selection [73%]
  * PBWT selection [74%]
  * PBWT selection [75%]
  * PBWT selection [76%]
  * PBWT selection [77%]
  * PBWT selection [78%]
  * PBWT selection [79%]
  * PBWT selection [80%]
  * PBWT selection [81%]
  * PBWT selection [82%]
  * PBWT selection [83%]
  * PBWT selection [84%]
  * PBWT selection [85%]
  * PBWT selection [86%]
  * PBWT selection [87%]
  * PBWT selection [88%]
  * PBWT selection [89%]
  * PBWT selection [90%]
  * PBWT selection [91%]
  * PBWT selection [92%]
  * PBWT selection [93%]
  * PBWT selection [94%]
  * PBWT selection [95%]
  * PBWT selection [96%]
  * PBWT selection [97%]
  * PBWT selection [98%]
  * PBWT selection [99%]
  * PBWT selection [100%]
  * PBWT selection (0.01s)
309s   * C2H transpose (0.00s)
309s   * 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=7.941+/-0.441 / W=1.00Mb] (0.12s)
309s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
309s   * HAP update (0.01s)
309s   * H2V transpose (0.00s)
309s   * Trimming [pc=0.00%]
309s 
309s Main iteration [1/5]
309s   * V2H transpose (0.00s)
309s   * PBWT selection [0%]
  * PBWT selection [1%]
  * PBWT selection [2%]
  * PBWT selection [3%]
  * PBWT selection [4%]
  * PBWT selection [5%]
  * PBWT selection [6%]
  * PBWT selection [7%]
  * PBWT selection [8%]
  * PBWT selection [9%]
  * PBWT selection [10%]
  * PBWT selection [11%]
  * PBWT selection [12%]
  * PBWT selection [13%]
  * PBWT selection [14%]
  * PBWT selection [15%]
  * PBWT selection [16%]
  * PBWT selection [17%]
  * PBWT selection [18%]
  * PBWT selection [19%]
  * PBWT selection [20%]
  * PBWT selection [21%]
  * PBWT selection [22%]
  * PBWT selection [23%]
  * PBWT selection [24%]
  * PBWT selection [25%]
  * PBWT selection [26%]
  * PBWT selection [27%]
  * PBWT selection [28%]
  * PBWT selection [29%]
  * PBWT selection [30%]
  * PBWT selection [31%]
  * PBWT selection [32%]
  * PBWT selection [33%]
  * PBWT selection [34%]
  * PBWT selection [35%]
  * PBWT selection [36%]
  * PBWT selection [37%]
  * PBWT selection [38%]
  * PBWT selection [39%]
  * PBWT selection [40%]
  * PBWT selection [41%]
  * PBWT selection [42%]
  * PBWT selection [43%]
  * PBWT selection [44%]
  * PBWT selection [45%]
  * PBWT selection [46%]
  * PBWT selection [47%]
  * PBWT selection [48%]
  * PBWT selection [49%]
  * PBWT selection [50%]
  * PBWT selection [51%]
  * PBWT selection [52%]
  * PBWT selection [53%]
  * PBWT selection [54%]
  * PBWT selection [55%]
  * PBWT selection [56%]
  * PBWT selection [57%]
  * PBWT selection [58%]
  * PBWT selection [59%]
  * PBWT selection [60%]
  * PBWT selection [61%]
  * PBWT selection [62%]
  * PBWT selection [63%]
  * PBWT selection [64%]
  * PBWT selection [65%]
  * PBWT selection [66%]
  * PBWT selection [67%]
  * PBWT selection [68%]
  * PBWT selection [69%]
  * PBWT selection [70%]
  * PBWT selection [71%]
  * PBWT selection [72%]
  * PBWT selection [73%]
  * PBWT selection [74%]
  * PBWT selection [75%]
  * PBWT selection [76%]
  * PBWT selection [77%]
  * PBWT selection [78%]
  * PBWT selection [79%]
  * PBWT selection [80%]
  * PBWT selection [81%]
  * PBWT selection [82%]
  * PBWT selection [83%]
  * PBWT selection [84%]
  * PBWT selection [85%]
  * PBWT selection [86%]
  * PBWT selection [87%]
  * PBWT selection [88%]
  * PBWT selection [89%]
  * PBWT selection [90%]
  * PBWT selection [91%]
  * PBWT selection [92%]
  * PBWT selection [93%]
  * PBWT selection [94%]
  * PBWT selection [95%]
  * PBWT selection [96%]
  * PBWT selection [97%]
  * PBWT selection [98%]
  * PBWT selection [99%]
  * PBWT selection [100%]
  * PBWT selection (0.01s)
309s   * C2H transpose (0.00s)
309s   * 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=7.941+/-0.441 / W=1.00Mb] (0.11s)
309s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
309s   * HAP update (0.01s)
309s   * H2V transpose (0.00s)
309s 
309s Main iteration [2/5]
309s   * V2H transpose (0.00s)
309s   * PBWT selection [0%]
  * PBWT selection [1%]
  * PBWT selection [2%]
  * PBWT selection [3%]
  * PBWT selection [4%]
  * PBWT selection [5%]
  * PBWT selection [6%]
  * PBWT selection [7%]
  * PBWT selection [8%]
  * PBWT selection [9%]
  * PBWT selection [10%]
  * PBWT selection [11%]
  * PBWT selection [12%]
  * PBWT selection [13%]
  * PBWT selection [14%]
  * PBWT selection [15%]
  * PBWT selection [16%]
  * PBWT selection [17%]
  * PBWT selection [18%]
  * PBWT selection [19%]
  * PBWT selection [20%]
  * PBWT selection [21%]
  * PBWT selection [22%]
  * PBWT selection [23%]
  * PBWT selection [24%]
  * PBWT selection [25%]
  * PBWT selection [26%]
  * PBWT selection [27%]
  * PBWT selection [28%]
  * PBWT selection [29%]
  * PBWT selection [30%]
  * PBWT selection [31%]
  * PBWT selection [32%]
  * PBWT selection [33%]
  * PBWT selection [34%]
  * PBWT selection [35%]
  * PBWT selection [36%]
  * PBWT selection [37%]
  * PBWT selection [38%]
  * PBWT selection [39%]
  * PBWT selection [40%]
  * PBWT selection [41%]
  * PBWT selection [42%]
  * PBWT selection [43%]
  * PBWT selection [44%]
  * PBWT selection [45%]
  * PBWT selection [46%]
  * PBWT selection [47%]
  * PBWT selection [48%]
  * PBWT selection [49%]
  * PBWT selection [50%]
  * PBWT selection [51%]
  * PBWT selection [52%]
  * PBWT selection [53%]
  * PBWT selection [54%]
  * PBWT selection [55%]
  * PBWT selection [56%]
  * PBWT selection [57%]
  * PBWT selection [58%]
  * PBWT selection [59%]
  * PBWT selection [60%]
  * PBWT selection [61%]
  * PBWT selection [62%]
  * PBWT selection [63%]
  * PBWT selection [64%]
  * PBWT selection [65%]
  * PBWT selection [66%]
  * PBWT selection [67%]
  * PBWT selection [68%]
  * PBWT selection [69%]
  * PBWT selection [70%]
  * PBWT selection [71%]
  * PBWT selection [72%]
  * PBWT selection [73%]
  * PBWT selection [74%]
  * PBWT selection [75%]
  * PBWT selection [76%]
  * PBWT selection [77%]
  * PBWT selection [78%]
  * PBWT selection [79%]
  * PBWT selection [80%]
  * PBWT selection [81%]
  * PBWT selection [82%]
  * PBWT selection [83%]
  * PBWT selection [84%]
  * PBWT selection [85%]
  * PBWT selection [86%]
  * PBWT selection [87%]
  * PBWT selection [88%]
  * PBWT selection [89%]
  * PBWT selection [90%]
  * PBWT selection [91%]
  * PBWT selection [92%]
  * PBWT selection [93%]
  * PBWT selection [94%]
  * PBWT selection [95%]
  * PBWT selection [96%]
  * PBWT selection [97%]
  * PBWT selection [98%]
  * PBWT selection [99%]
  * PBWT selection [100%]
  * PBWT selection (0.01s)
309s   * C2H transpose (0.00s)
309s   * 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=7.941+/-0.441 / W=1.00Mb] (0.11s)
309s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
309s   * HAP update (0.01s)
309s   * H2V transpose (0.00s)
309s 
309s Main iteration [3/5]
309s   * V2H transpose (0.00s)
309s   * PBWT selection [0%]
  * PBWT selection [1%]
  * PBWT selection [2%]
  * PBWT selection [3%]
  * PBWT selection [4%]
  * PBWT selection [5%]
  * PBWT selection [6%]
  * PBWT selection [7%]
  * PBWT selection [8%]
  * PBWT selection [9%]
  * PBWT selection [10%]
  * PBWT selection [11%]
  * PBWT selection [12%]
  * PBWT selection [13%]
  * PBWT selection [14%]
  * PBWT selection [15%]
  * PBWT selection [16%]
  * PBWT selection [17%]
  * PBWT selection [18%]
  * PBWT selection [19%]
  * PBWT selection [20%]
  * PBWT selection [21%]
  * PBWT selection [22%]
  * PBWT selection [23%]
  * PBWT selection [24%]
  * PBWT selection [25%]
  * PBWT selection [26%]
  * PBWT selection [27%]
  * PBWT selection [28%]
  * PBWT selection [29%]
  * PBWT selection [30%]
  * PBWT selection [31%]
  * PBWT selection [32%]
  * PBWT selection [33%]
  * PBWT selection [34%]
  * PBWT selection [35%]
  * PBWT selection [36%]
  * PBWT selection [37%]
  * PBWT selection [38%]
  * PBWT selection [39%]
  * PBWT selection [40%]
  * PBWT selection [41%]
  * PBWT selection [42%]
  * PBWT selection [43%]
  * PBWT selection [44%]
  * PBWT selection [45%]
  * PBWT selection [46%]
  * PBWT selection [47%]
  * PBWT selection [48%]
  * PBWT selection [49%]
  * PBWT selection [50%]
  * PBWT selection [51%]
  * PBWT selection [52%]
  * PBWT selection [53%]
  * PBWT selection [54%]
  * PBWT selection [55%]
  * PBWT selection [56%]
  * PBWT selection [57%]
  * PBWT selection [58%]
  * PBWT selection [59%]
  * PBWT selection [60%]
  * PBWT selection [61%]
  * PBWT selection [62%]
  * PBWT selection [63%]
  * PBWT selection [64%]
  * PBWT selection [65%]
  * PBWT selection [66%]
  * PBWT selection [67%]
  * PBWT selection [68%]
  * PBWT selection [69%]
  * PBWT selection [70%]
  * PBWT selection [71%]
  * PBWT selection [72%]
  * PBWT selection [73%]
  * PBWT selection [74%]
  * PBWT selection [75%]
  * PBWT selection [76%]
  * PBWT selection [77%]
  * PBWT selection [78%]
  * PBWT selection [79%]
  * PBWT selection [80%]
  * PBWT selection [81%]
  * PBWT selection [82%]
  * PBWT selection [83%]
  * PBWT selection [84%]
  * PBWT selection [85%]
  * PBWT selection [86%]
  * PBWT selection [87%]
  * PBWT selection [88%]
  * PBWT selection [89%]
  * PBWT selection [90%]
  * PBWT selection [91%]
  * PBWT selection [92%]
  * PBWT selection [93%]
  * PBWT selection [94%]
  * PBWT selection [95%]
  * PBWT selection [96%]
  * PBWT selection [97%]
  * PBWT selection [98%]
  * PBWT selection [99%]
  * PBWT selection [100%]
  * PBWT selection (0.01s)
309s   * C2H transpose (0.00s)
309s   * 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=7.941+/-0.441 / W=1.00Mb] (0.13s)
309s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
309s   * HAP update (0.01s)
309s   * H2V transpose (0.00s)
309s 
309s Main iteration [4/5]
309s   * V2H transpose (0.00s)
309s   * PBWT selection [0%]
  * PBWT selection [1%]
  * PBWT selection [2%]
  * PBWT selection [3%]
  * PBWT selection [4%]
  * PBWT selection [5%]
  * PBWT selection [6%]
  * PBWT selection [7%]
  * PBWT selection [8%]
  * PBWT selection [9%]
  * PBWT selection [10%]
  * PBWT selection [11%]
  * PBWT selection [12%]
  * PBWT selection [13%]
  * PBWT selection [14%]
  * PBWT selection [15%]
  * PBWT selection [16%]
  * PBWT selection [17%]
  * PBWT selection [18%]
  * PBWT selection [19%]
  * PBWT selection [20%]
  * PBWT selection [21%]
  * PBWT selection [22%]
  * PBWT selection [23%]
  * PBWT selection [24%]
  * PBWT selection [25%]
  * PBWT selection [26%]
  * PBWT selection [27%]
  * PBWT selection [28%]
  * PBWT selection [29%]
  * PBWT selection [30%]
  * PBWT selection [31%]
  * PBWT selection [32%]
  * PBWT selection [33%]
  * PBWT selection [34%]
  * PBWT selection [35%]
  * PBWT selection [36%]
  * PBWT selection [37%]
  * PBWT selection [38%]
  * PBWT selection [39%]
  * PBWT selection [40%]
  * PBWT selection [41%]
  * PBWT selection [42%]
  * PBWT selection [43%]
  * PBWT selection [44%]
  * PBWT selection [45%]
  * PBWT selection [46%]
  * PBWT selection [47%]
  * PBWT selection [48%]
  * PBWT selection [49%]
  * PBWT selection [50%]
  * PBWT selection [51%]
  * PBWT selection [52%]
  * PBWT selection [53%]
  * PBWT selection [54%]
  * PBWT selection [55%]
  * PBWT selection [56%]
  * PBWT selection [57%]
  * PBWT selection [58%]
  * PBWT selection [59%]
  * PBWT selection [60%]
  * PBWT selection [61%]
  * PBWT selection [62%]
  * PBWT selection [63%]
  * PBWT selection [64%]
  * PBWT selection [65%]
  * PBWT selection [66%]
  * PBWT selection [67%]
  * PBWT selection [68%]
  * PBWT selection [69%]
  * PBWT selection [70%]
  * PBWT selection [71%]
  * PBWT selection [72%]
  * PBWT selection [73%]
  * PBWT selection [74%]
  * PBWT selection [75%]
  * PBWT selection [76%]
  * PBWT selection [77%]
  * PBWT selection [78%]
  * PBWT selection [79%]
  * PBWT selection [80%]
  * PBWT selection [81%]
  * PBWT selection [82%]
  * PBWT selection [83%]
  * PBWT selection [84%]
  * PBWT selection [85%]
  * PBWT selection [86%]
  * PBWT selection [87%]
  * PBWT selection [88%]
  * PBWT selection [89%]
  * PBWT selection [90%]
  * PBWT selection [91%]
  * PBWT selection [92%]
  * PBWT selection [93%]
  * PBWT selection [94%]
  * PBWT selection [95%]
  * PBWT selection [96%]
  * PBWT selection [97%]
  * PBWT selection [98%]
  * PBWT selection [99%]
  * PBWT selection [100%]
  * PBWT selection (0.01s)
309s   * C2H transpose (0.00s)
309s   * 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=7.941+/-0.441 / W=1.00Mb] (0.10s)
309s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
309s   * HAP update (0.01s)
309s   * H2V transpose (0.00s)
309s 
309s Main iteration [5/5]
309s   * V2H transpose (0.00s)
309s   * PBWT selection [0%]
  * PBWT selection [1%]
  * PBWT selection [2%]
  * PBWT selection [3%]
  * PBWT selection [4%]
  * PBWT selection [5%]
  * PBWT selection [6%]
  * PBWT selection [7%]
  * PBWT selection [8%]
  * PBWT selection [9%]
  * PBWT selection [10%]
  * PBWT selection [11%]
  * PBWT selection [12%]
  * PBWT selection [13%]
  * PBWT selection [14%]
  * PBWT selection [15%]
  * PBWT selection [16%]
  * PBWT selection [17%]
  * PBWT selection [18%]
  * PBWT selection [19%]
  * PBWT selection [20%]
  * PBWT selection [21%]
  * PBWT selection [22%]
  * PBWT selection [23%]
  * PBWT selection [24%]
  * PBWT selection [25%]
  * PBWT selection [26%]
  * PBWT selection [27%]
  * PBWT selection [28%]
  * PBWT selection [29%]
  * PBWT selection [30%]
  * PBWT selection [31%]
  * PBWT selection [32%]
  * PBWT selection [33%]
  * PBWT selection [34%]
  * PBWT selection [35%]
  * PBWT selection [36%]
  * PBWT selection [37%]
  * PBWT selection [38%]
  * PBWT selection [39%]
  * PBWT selection [40%]
  * PBWT selection [41%]
  * PBWT selection [42%]
  * PBWT selection [43%]
  * PBWT selection [44%]
  * PBWT selection [45%]
  * PBWT selection [46%]
  * PBWT selection [47%]
  * PBWT selection [48%]
  * PBWT selection [49%]
  * PBWT selection [50%]
  * PBWT selection [51%]
  * PBWT selection [52%]
  * PBWT selection [53%]
  * PBWT selection [54%]
  * PBWT selection [55%]
  * PBWT selection [56%]
  * PBWT selection [57%]
  * PBWT selection [58%]
  * PBWT selection [59%]
  * PBWT selection [60%]
  * PBWT selection [61%]
  * PBWT selection [62%]
  * PBWT selection [63%]
  * PBWT selection [64%]
  * PBWT selection [65%]
  * PBWT selection [66%]
  * PBWT selection [67%]
  * PBWT selection [68%]
  * PBWT selection [69%]
  * PBWT selection [70%]
  * PBWT selection [71%]
  * PBWT selection [72%]
  * PBWT selection [73%]
  * PBWT selection [74%]
  * PBWT selection [75%]
  * PBWT selection [76%]
  * PBWT selection [77%]
  * PBWT selection [78%]
  * PBWT selection [79%]
  * PBWT selection [80%]
  * PBWT selection [81%]
  * PBWT selection [82%]
  * PBWT selection [83%]
  * PBWT selection [84%]
  * PBWT selection [85%]
  * PBWT selection [86%]
  * PBWT selection [87%]
  * PBWT selection [88%]
  * PBWT selection [89%]
  * PBWT selection [90%]
  * PBWT selection [91%]
  * PBWT selection [92%]
  * PBWT selection [93%]
  * PBWT selection [94%]
  * PBWT selection [95%]
  * PBWT selection [96%]
  * PBWT selection [97%]
  * PBWT selection [98%]
  * PBWT selection [99%]
  * PBWT selection [100%]
  * PBWT selection (0.01s)
309s   * C2H transpose (0.00s)
309s   * 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=7.941+/-0.441 / W=1.00Mb] (0.11s)
309s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
309s   * HAP update (0.01s)
309s   * H2V transpose (0.00s)
309s 
309s Finalization:
309s   * HAP solving (0.04s)
309s   * HAP update (0.01s)
309s   * H2V transpose (0.00s)
310s   * 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] (0.14s)
310s   * Total running time = 3 seconds
310s + 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
310s 
310s SHAPEIT
310s   * Author        : Olivier DELANEAU, University of Lausanne
310s   * Contact       : olivier.delaneau@gmail.com
310s   * Version       : 4.2.2
310s   * Run date      : 15/03/2025 - 17:40:53
310s 
310s Files:
310s   * Input VCF     : [unphased.bcf]
310s   * Reference VCF : [reference.bcf]
310s   * Scaffold VCF  : [scaffold.bcf]
310s   * Genetic Map   : [chr20.b37.gmap.gz]
310s   * Output VCF    : [phased.bcf]
310s   * Output LOG    : [phased.log]
310s 
310s Parameters:
310s   * Seed    : 15052011
310s   * Threads : 4 threads
310s   * MCMC    : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m]
310s   * PBWT    : Depth of PBWT neighbours to condition on: 4
310s   * PBWT    : Store indexes at variants [MAC>=2 / MDR<=0.5 / Dist=0.02 cM]
310s   * HMM     : K is variable / min W is 2.50cM / Ne is 15000
310s   * HMM     : Recombination rates given by genetic map
310s   * HMM     : Inform phasing using VCF/PS field / Error rate of PS field is 0.0001
310s   * HMM     : AVX2 optimization inactive / Activating AVX2 substantially improves performance
310s 
310s Initialization:
310s   * VCF/BCF scanning ...
  * VCF/BCF scanning [Nm=203 / Nr=300 / L=24990 / Reg=20] (0.06s)
310s   * 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%] (0.36s)
310s   * GMAP parsing [n=82962] (0.06s)
310s   * cM interpolation [s=3296 / i=21694] (0.01s)
310s   * Region length [2999624 bp / 6.6 cM]
310s   * HMM parameters [Ne=15000 / Error=0.0001 / #rare=9606]
310s   * PBWT indexing [l=328] (0.00s)
310s   * HAP update (0.03s)
310s   * H2V transpose (0.01s)
310s   * PBWT phase sweep [0%]
  * PBWT phase sweep [1%]
  * PBWT phase sweep [2%]
  * PBWT phase sweep [3%]
  * PBWT phase sweep [4%]
  * PBWT phase sweep [5%]
  * PBWT phase sweep [6%]
  * PBWT phase sweep [7%]
  * PBWT phase sweep [8%]
  * PBWT phase sweep [9%]
  * PBWT phase sweep [10%]
  * PBWT phase sweep [11%]
  * PBWT phase sweep [12%]
  * PBWT phase sweep [13%]
  * PBWT phase sweep [14%]
  * PBWT phase sweep [15%]
  * PBWT phase sweep [16%]
  * PBWT phase sweep [17%]
  * PBWT phase sweep [18%]
  * PBWT phase sweep [19%]
  * PBWT phase sweep [20%]
  * PBWT phase sweep [21%]
  * PBWT phase sweep [22%]
  * PBWT phase sweep [23%]
  * PBWT phase sweep [24%]
  * PBWT phase sweep [25%]
  * PBWT phase sweep [26%]
  * PBWT phase sweep [27%]
  * PBWT phase sweep [28%]
  * PBWT phase sweep [29%]
  * PBWT phase sweep [30%]
  * PBWT phase sweep [31%]
  * PBWT phase sweep [32%]
  * PBWT phase sweep [33%]
  * PBWT phase sweep [34%]
  * PBWT phase sweep [35%]
  * PBWT phase sweep [36%]
  * PBWT phase sweep [37%]
  * PBWT phase sweep [38%]
  * PBWT phase sweep [39%]
  * PBWT phase sweep [40%]
  * PBWT phase sweep [41%]
  * PBWT phase sweep [42%]
  * PBWT phase sweep [43%]
  * PBWT phase sweep [44%]
  * PBWT phase sweep [45%]
  * PBWT phase sweep [46%]
  * PBWT phase sweep [47%]
  * PBWT phase sweep [48%]
  * PBWT phase sweep [49%]
  * PBWT phase sweep [50%]
  * PBWT phase sweep [51%]
  * PBWT phase sweep [52%]
  * PBWT phase sweep [53%]
  * PBWT phase sweep [54%]
  * PBWT phase sweep [55%]
  * PBWT phase sweep [56%]
  * PBWT phase sweep [57%]
  * PBWT phase sweep [58%]
  * PBWT phase sweep [59%]
  * PBWT phase sweep [60%]
  * PBWT phase sweep [61%]
  * PBWT phase sweep [62%]
  * PBWT phase sweep [63%]
  * PBWT phase sweep [64%]
  * PBWT phase sweep [65%]
  * PBWT phase sweep [66%]
  * PBWT phase sweep [67%]
  * PBWT phase sweep [68%]
  * PBWT phase sweep [69%]
  * PBWT phase sweep [70%]
  * PBWT phase sweep [71%]
  * PBWT phase sweep [72%]
  * PBWT phase sweep [73%]
  * PBWT phase sweep [74%]
  * PBWT phase sweep [75%]
  * PBWT phase sweep [76%]
  * PBWT phase sweep [77%]
  * PBWT phase sweep [78%]
  * PBWT phase sweep [79%]
  * PBWT phase sweep [80%]
  * PBWT phase sweep [81%]
  * PBWT phase sweep [82%]
  * PBWT phase sweep [83%]
  * PBWT phase sweep [84%]
  * PBWT phase sweep [85%]
  * PBWT phase sweep [86%]
  * PBWT phase sweep [87%]
  * PBWT phase sweep [88%]
  * PBWT phase sweep [89%]
  * PBWT phase sweep [90%]
  * PBWT phase sweep [91%]
  * PBWT phase sweep [92%]
  * PBWT phase sweep [93%]
  * PBWT phase sweep [94%]
  * PBWT phase sweep [95%]
  * PBWT phase sweep [96%]
  * PBWT phase sweep [97%]
  * PBWT phase sweep [98%]
  * PBWT phase sweep [99%]
  * PBWT phase sweep [100%]
  * PBWT phase sweep (0.28s)
311s   * Build genotype graphs [seg=164449] (0.05s)
311s 
311s Burn-in iteration [1/5]
311s   * V2H transpose (0.00s)
311s   * PBWT selection [0%]
  * PBWT selection [1%]
  * PBWT selection [2%]
  * PBWT selection [3%]
  * PBWT selection [4%]
  * PBWT selection [5%]
  * PBWT selection [6%]
  * PBWT selection [7%]
  * PBWT selection [8%]
  * PBWT selection [9%]
  * PBWT selection [10%]
  * PBWT selection [11%]
  * PBWT selection [12%]
  * PBWT selection [13%]
  * PBWT selection [14%]
  * PBWT selection [15%]
  * PBWT selection [16%]
  * PBWT selection [17%]
  * PBWT selection [18%]
  * PBWT selection [19%]
  * PBWT selection [20%]
  * PBWT selection [21%]
  * PBWT selection [22%]
  * PBWT selection [23%]
  * PBWT selection [24%]
  * PBWT selection [25%]
  * PBWT selection [26%]
  * PBWT selection [27%]
  * PBWT selection [28%]
  * PBWT selection [29%]
  * PBWT selection [30%]
  * PBWT selection [31%]
  * PBWT selection [32%]
  * PBWT selection [33%]
  * PBWT selection [34%]
  * PBWT selection [35%]
  * PBWT selection [36%]
  * PBWT selection [37%]
  * PBWT selection [38%]
  * PBWT selection [39%]
  * PBWT selection [40%]
  * PBWT selection [41%]
  * PBWT selection [42%]
  * PBWT selection [43%]
  * PBWT selection [44%]
  * PBWT selection [45%]
  * PBWT selection [46%]
  * PBWT selection [47%]
  * PBWT selection [48%]
  * PBWT selection [49%]
  * PBWT selection [50%]
  * PBWT selection [51%]
  * PBWT selection [52%]
  * PBWT selection [53%]
  * PBWT selection [54%]
  * PBWT selection [55%]
  * PBWT selection [56%]
  * PBWT selection [57%]
  * PBWT selection [58%]
  * PBWT selection [59%]
  * PBWT selection [60%]
  * PBWT selection [61%]
  * PBWT selection [62%]
  * PBWT selection [63%]
  * PBWT selection [64%]
  * PBWT selection [65%]
  * PBWT selection [66%]
  * PBWT selection [67%]
  * PBWT selection [68%]
  * PBWT selection [69%]
  * PBWT selection [70%]
  * PBWT selection [71%]
  * PBWT selection [72%]
  * PBWT selection [73%]
  * PBWT selection [74%]
  * PBWT selection [75%]
  * PBWT selection [76%]
  * PBWT selection [77%]
  * PBWT selection [78%]
  * PBWT selection [79%]
  * PBWT selection [80%]
  * PBWT selection [81%]
  * PBWT selection [82%]
  * PBWT selection [83%]
  * PBWT selection [84%]
  * PBWT selection [85%]
  * PBWT selection [86%]
  * PBWT selection [87%]
  * PBWT selection [88%]
  * PBWT selection [89%]
  * PBWT selection [90%]
  * PBWT selection [91%]
  * PBWT selection [92%]
  * PBWT selection [93%]
  * PBWT selection [94%]
  * PBWT selection [95%]
  * PBWT selection [96%]
  * PBWT selection [97%]
  * PBWT selection [98%]
  * PBWT selection [99%]
  * PBWT selection [100%]
  * PBWT selection (0.05s)
311s   * C2H transpose (0.00s)
314s   * 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=368.515+/-30.516 / W=2.27Mb] (3.52s)
314s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
314s   * HAP update (0.01s)
314s   * H2V transpose (0.00s)
314s 
314s Burn-in iteration [2/5]
314s   * V2H transpose (0.00s)
314s   * PBWT selection [0%]
  * PBWT selection [1%]
  * PBWT selection [2%]
  * PBWT selection [3%]
  * PBWT selection [4%]
  * PBWT selection [5%]
  * PBWT selection [6%]
  * PBWT selection [7%]
  * PBWT selection [8%]
  * PBWT selection [9%]
  * PBWT selection [10%]
  * PBWT selection [11%]
  * PBWT selection [12%]
  * PBWT selection [13%]
  * PBWT selection [14%]
  * PBWT selection [15%]
  * PBWT selection [16%]
  * PBWT selection [17%]
  * PBWT selection [18%]
  * PBWT selection [19%]
  * PBWT selection [20%]
  * PBWT selection [21%]
  * PBWT selection [22%]
  * PBWT selection [23%]
  * PBWT selection [24%]
  * PBWT selection [25%]
  * PBWT selection [26%]
  * PBWT selection [27%]
  * PBWT selection [28%]
  * PBWT selection [29%]
  * PBWT selection [30%]
  * PBWT selection [31%]
  * PBWT selection [32%]
  * PBWT selection [33%]
  * PBWT selection [34%]
  * PBWT selection [35%]
  * PBWT selection [36%]
  * PBWT selection [37%]
  * PBWT selection [38%]
  * PBWT selection [39%]
  * PBWT selection [40%]
  * PBWT selection [41%]
  * PBWT selection [42%]
  * PBWT selection [43%]
  * PBWT selection [44%]
  * PBWT selection [45%]
  * PBWT selection [46%]
  * PBWT selection [47%]
  * PBWT selection [48%]
  * PBWT selection [49%]
  * PBWT selection [50%]
  * PBWT selection [51%]
  * PBWT selection [52%]
  * PBWT selection [53%]
  * PBWT selection [54%]
  * PBWT selection [55%]
  * PBWT selection [56%]
  * PBWT selection [57%]
  * PBWT selection [58%]
  * PBWT selection [59%]
  * PBWT selection [60%]
  * PBWT selection [61%]
  * PBWT selection [62%]
  * PBWT selection [63%]
  * PBWT selection [64%]
  * PBWT selection [65%]
  * PBWT selection [66%]
  * PBWT selection [67%]
  * PBWT selection [68%]
  * PBWT selection [69%]
  * PBWT selection [70%]
  * PBWT selection [71%]
  * PBWT selection [72%]
  * PBWT selection [73%]
  * PBWT selection [74%]
  * PBWT selection [75%]
  * PBWT selection [76%]
  * PBWT selection [77%]
  * PBWT selection [78%]
  * PBWT selection [79%]
  * PBWT selection [80%]
  * PBWT selection [81%]
  * PBWT selection [82%]
  * PBWT selection [83%]
  * PBWT selection [84%]
  * PBWT selection [85%]
  * PBWT selection [86%]
  * PBWT selection [87%]
  * PBWT selection [88%]
  * PBWT selection [89%]
  * PBWT selection [90%]
  * PBWT selection [91%]
  * PBWT selection [92%]
  * PBWT selection [93%]
  * PBWT selection [94%]
  * PBWT selection [95%]
  * PBWT selection [96%]
  * PBWT selection [97%]
  * PBWT selection [98%]
  * PBWT selection [99%]
  * PBWT selection [100%]
  * PBWT selection (0.04s)
314s   * C2H transpose (0.00s)
314s   * 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=7.970+/-0.298 / W=2.26Mb] (0.21s)
314s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
314s   * HAP update (0.02s)
314s   * H2V transpose (0.02s)
314s 
314s Burn-in iteration [3/5]
314s   * V2H transpose (0.00s)
314s   * PBWT selection [0%]
  * PBWT selection [1%]
  * PBWT selection [2%]
  * PBWT selection [3%]
  * PBWT selection [4%]
  * PBWT selection [5%]
  * PBWT selection [6%]
  * PBWT selection [7%]
  * PBWT selection [8%]
  * PBWT selection [9%]
  * PBWT selection [10%]
  * PBWT selection [11%]
  * PBWT selection [12%]
  * PBWT selection [13%]
  * PBWT selection [14%]
  * PBWT selection [15%]
  * PBWT selection [16%]
  * PBWT selection [17%]
  * PBWT selection [18%]
  * PBWT selection [19%]
  * PBWT selection [20%]
  * PBWT selection [21%]
  * PBWT selection [22%]
  * PBWT selection [23%]
  * PBWT selection [24%]
  * PBWT selection [25%]
  * PBWT selection [26%]
  * PBWT selection [27%]
  * PBWT selection [28%]
  * PBWT selection [29%]
  * PBWT selection [30%]
  * PBWT selection [31%]
  * PBWT selection [32%]
  * PBWT selection [33%]
  * PBWT selection [34%]
  * PBWT selection [35%]
  * PBWT selection [36%]
  * PBWT selection [37%]
  * PBWT selection [38%]
  * PBWT selection [39%]
  * PBWT selection [40%]
  * PBWT selection [41%]
  * PBWT selection [42%]
  * PBWT selection [43%]
  * PBWT selection [44%]
  * PBWT selection [45%]
  * PBWT selection [46%]
  * PBWT selection [47%]
  * PBWT selection [48%]
  * PBWT selection [49%]
  * PBWT selection [50%]
  * PBWT selection [51%]
  * PBWT selection [52%]
  * PBWT selection [53%]
  * PBWT selection [54%]
  * PBWT selection [55%]
  * PBWT selection [56%]
  * PBWT selection [57%]
  * PBWT selection [58%]
  * PBWT selection [59%]
  * PBWT selection [60%]
  * PBWT selection [61%]
  * PBWT selection [62%]
  * PBWT selection [63%]
  * PBWT selection [64%]
  * PBWT selection [65%]
  * PBWT selection [66%]
  * PBWT selection [67%]
  * PBWT selection [68%]
  * PBWT selection [69%]
  * PBWT selection [70%]
  * PBWT selection [71%]
  * PBWT selection [72%]
  * PBWT selection [73%]
  * PBWT selection [74%]
  * PBWT selection [75%]
  * PBWT selection [76%]
  * PBWT selection [77%]
  * PBWT selection [78%]
  * PBWT selection [79%]
  * PBWT selection [80%]
  * PBWT selection [81%]
  * PBWT selection [82%]
  * PBWT selection [83%]
  * PBWT selection [84%]
  * PBWT selection [85%]
  * PBWT selection [86%]
  * PBWT selection [87%]
  * PBWT selection [88%]
  * PBWT selection [89%]
  * PBWT selection [90%]
  * PBWT selection [91%]
  * PBWT selection [92%]
  * PBWT selection [93%]
  * PBWT selection [94%]
  * PBWT selection [95%]
  * PBWT selection [96%]
  * PBWT selection [97%]
  * PBWT selection [98%]
  * PBWT selection [99%]
  * PBWT selection [100%]
  * PBWT selection (0.05s)
314s   * C2H transpose (0.01s)
315s   * 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=7.965+/-0.356 / W=2.15Mb] (0.20s)
315s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
315s   * HAP update (0.02s)
315s   * H2V transpose (0.01s)
315s 
315s Burn-in iteration [4/5]
315s   * V2H transpose (0.00s)
315s   * PBWT selection [0%]
  * PBWT selection [1%]
  * PBWT selection [2%]
  * PBWT selection [3%]
  * PBWT selection [4%]
  * PBWT selection [5%]
  * PBWT selection [6%]
  * PBWT selection [7%]
  * PBWT selection [8%]
  * PBWT selection [9%]
  * PBWT selection [10%]
  * PBWT selection [11%]
  * PBWT selection [12%]
  * PBWT selection [13%]
  * PBWT selection [14%]
  * PBWT selection [15%]
  * PBWT selection [16%]
  * PBWT selection [17%]
  * PBWT selection [18%]
  * PBWT selection [19%]
  * PBWT selection [20%]
  * PBWT selection [21%]
  * PBWT selection [22%]
  * PBWT selection [23%]
  * PBWT selection [24%]
  * PBWT selection [25%]
  * PBWT selection [26%]
  * PBWT selection [27%]
  * PBWT selection [28%]
  * PBWT selection [29%]
  * PBWT selection [30%]
  * PBWT selection [31%]
  * PBWT selection [32%]
  * PBWT selection [33%]
  * PBWT selection [34%]
  * PBWT selection [35%]
  * PBWT selection [36%]
  * PBWT selection [37%]
  * PBWT selection [38%]
  * PBWT selection [39%]
  * PBWT selection [40%]
  * PBWT selection [41%]
  * PBWT selection [42%]
  * PBWT selection [43%]
  * PBWT selection [44%]
  * PBWT selection [45%]
  * PBWT selection [46%]
  * PBWT selection [47%]
  * PBWT selection [48%]
  * PBWT selection [49%]
  * PBWT selection [50%]
  * PBWT selection [51%]
  * PBWT selection [52%]
  * PBWT selection [53%]
  * PBWT selection [54%]
  * PBWT selection [55%]
  * PBWT selection [56%]
  * PBWT selection [57%]
  * PBWT selection [58%]
  * PBWT selection [59%]
  * PBWT selection [60%]
  * PBWT selection [61%]
  * PBWT selection [62%]
  * PBWT selection [63%]
  * PBWT selection [64%]
  * PBWT selection [65%]
  * PBWT selection [66%]
  * PBWT selection [67%]
  * PBWT selection [68%]
  * PBWT selection [69%]
  * PBWT selection [70%]
  * PBWT selection [71%]
  * PBWT selection [72%]
  * PBWT selection [73%]
  * PBWT selection [74%]
  * PBWT selection [75%]
  * PBWT selection [76%]
  * PBWT selection [77%]
  * PBWT selection [78%]
  * PBWT selection [79%]
  * PBWT selection [80%]
  * PBWT selection [81%]
  * PBWT selection [82%]
  * PBWT selection [83%]
  * PBWT selection [84%]
  * PBWT selection [85%]
  * PBWT selection [86%]
  * PBWT selection [87%]
  * PBWT selection [88%]
  * PBWT selection [89%]
  * PBWT selection [90%]
  * PBWT selection [91%]
  * PBWT selection [92%]
  * PBWT selection [93%]
  * PBWT selection [94%]
  * PBWT selection [95%]
  * PBWT selection [96%]
  * PBWT selection [97%]
  * PBWT selection [98%]
  * PBWT selection [99%]
  * PBWT selection [100%]
  * PBWT selection (0.04s)
315s   * C2H transpose (0.00s)
315s   * 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=7.978+/-0.272 / W=2.26Mb] (0.19s)
315s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
315s   * HAP update (0.01s)
315s   * H2V transpose (0.00s)
315s 
315s Burn-in iteration [5/5]
315s   * V2H transpose (0.00s)
315s   * PBWT selection [0%]
  * PBWT selection [1%]
  * PBWT selection [2%]
  * PBWT selection [3%]
  * PBWT selection [4%]
  * PBWT selection [5%]
  * PBWT selection [6%]
  * PBWT selection [7%]
  * PBWT selection [8%]
  * PBWT selection [9%]
  * PBWT selection [10%]
  * PBWT selection [11%]
  * PBWT selection [12%]
  * PBWT selection [13%]
  * PBWT selection [14%]
  * PBWT selection [15%]
  * PBWT selection [16%]
  * PBWT selection [17%]
  * PBWT selection [18%]
  * PBWT selection [19%]
  * PBWT selection [20%]
  * PBWT selection [21%]
  * PBWT selection [22%]
  * PBWT selection [23%]
  * PBWT selection [24%]
  * PBWT selection [25%]
  * PBWT selection [26%]
  * PBWT selection [27%]
  * PBWT selection [28%]
  * PBWT selection [29%]
  * PBWT selection [30%]
  * PBWT selection [31%]
  * PBWT selection [32%]
  * PBWT selection [33%]
  * PBWT selection [34%]
  * PBWT selection [35%]
  * PBWT selection [36%]
  * PBWT selection [37%]
  * PBWT selection [38%]
  * PBWT selection [39%]
  * PBWT selection [40%]
  * PBWT selection [41%]
  * PBWT selection [42%]
  * PBWT selection [43%]
  * PBWT selection [44%]
  * PBWT selection [45%]
  * PBWT selection [46%]
  * PBWT selection [47%]
  * PBWT selection [48%]
  * PBWT selection [49%]
  * PBWT selection [50%]
  * PBWT selection [51%]
  * PBWT selection [52%]
  * PBWT selection [53%]
  * PBWT selection [54%]
  * PBWT selection [55%]
  * PBWT selection [56%]
  * PBWT selection [57%]
  * PBWT selection [58%]
  * PBWT selection [59%]
  * PBWT selection [60%]
  * PBWT selection [61%]
  * PBWT selection [62%]
  * PBWT selection [63%]
  * PBWT selection [64%]
  * PBWT selection [65%]
  * PBWT selection [66%]
  * PBWT selection [67%]
  * PBWT selection [68%]
  * PBWT selection [69%]
  * PBWT selection [70%]
  * PBWT selection [71%]
  * PBWT selection [72%]
  * PBWT selection [73%]
  * PBWT selection [74%]
  * PBWT selection [75%]
  * PBWT selection [76%]
  * PBWT selection [77%]
  * PBWT selection [78%]
  * PBWT selection [79%]
  * PBWT selection [80%]
  * PBWT selection [81%]
  * PBWT selection [82%]
  * PBWT selection [83%]
  * PBWT selection [84%]
  * PBWT selection [85%]
  * PBWT selection [86%]
  * PBWT selection [87%]
  * PBWT selection [88%]
  * PBWT selection [89%]
  * PBWT selection [90%]
  * PBWT selection [91%]
  * PBWT selection [92%]
  * PBWT selection [93%]
  * PBWT selection [94%]
  * PBWT selection [95%]
  * PBWT selection [96%]
  * PBWT selection [97%]
  * PBWT selection [98%]
  * PBWT selection [99%]
  * PBWT selection [100%]
  * PBWT selection (0.04s)
315s   * C2H transpose (0.00s)
315s   * 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=7.957+/-0.376 / W=2.17Mb] (0.19s)
315s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
315s   * HAP update (0.02s)
315s   * H2V transpose (0.00s)
315s 
315s Pruning iteration [1/1]
315s   * V2H transpose (0.00s)
315s   * PBWT selection [0%]
  * PBWT selection [1%]
  * PBWT selection [2%]
  * PBWT selection [3%]
  * PBWT selection [4%]
  * PBWT selection [5%]
  * PBWT selection [6%]
  * PBWT selection [7%]
  * PBWT selection [8%]
  * PBWT selection [9%]
  * PBWT selection [10%]
  * PBWT selection [11%]
  * PBWT selection [12%]
  * PBWT selection [13%]
  * PBWT selection [14%]
  * PBWT selection [15%]
  * PBWT selection [16%]
  * PBWT selection [17%]
  * PBWT selection [18%]
  * PBWT selection [19%]
  * PBWT selection [20%]
  * PBWT selection [21%]
  * PBWT selection [22%]
  * PBWT selection [23%]
  * PBWT selection [24%]
  * PBWT selection [25%]
  * PBWT selection [26%]
  * PBWT selection [27%]
  * PBWT selection [28%]
  * PBWT selection [29%]
  * PBWT selection [30%]
  * PBWT selection [31%]
  * PBWT selection [32%]
  * PBWT selection [33%]
  * PBWT selection [34%]
  * PBWT selection [35%]
  * PBWT selection [36%]
  * PBWT selection [37%]
  * PBWT selection [38%]
  * PBWT selection [39%]
  * PBWT selection [40%]
  * PBWT selection [41%]
  * PBWT selection [42%]
  * PBWT selection [43%]
  * PBWT selection [44%]
  * PBWT selection [45%]
  * PBWT selection [46%]
  * PBWT selection [47%]
  * PBWT selection [48%]
  * PBWT selection [49%]
  * PBWT selection [50%]
  * PBWT selection [51%]
  * PBWT selection [52%]
  * PBWT selection [53%]
  * PBWT selection [54%]
  * PBWT selection [55%]
  * PBWT selection [56%]
  * PBWT selection [57%]
  * PBWT selection [58%]
  * PBWT selection [59%]
  * PBWT selection [60%]
  * PBWT selection [61%]
  * PBWT selection [62%]
  * PBWT selection [63%]
  * PBWT selection [64%]
  * PBWT selection [65%]
  * PBWT selection [66%]
  * PBWT selection [67%]
  * PBWT selection [68%]
  * PBWT selection [69%]
  * PBWT selection [70%]
  * PBWT selection [71%]
  * PBWT selection [72%]
  * PBWT selection [73%]
  * PBWT selection [74%]
  * PBWT selection [75%]
  * PBWT selection [76%]
  * PBWT selection [77%]
  * PBWT selection [78%]
  * PBWT selection [79%]
  * PBWT selection [80%]
  * PBWT selection [81%]
  * PBWT selection [82%]
  * PBWT selection [83%]
  * PBWT selection [84%]
  * PBWT selection [85%]
  * PBWT selection [86%]
  * PBWT selection [87%]
  * PBWT selection [88%]
  * PBWT selection [89%]
  * PBWT selection [90%]
  * PBWT selection [91%]
  * PBWT selection [92%]
  * PBWT selection [93%]
  * PBWT selection [94%]
  * PBWT selection [95%]
  * PBWT selection [96%]
  * PBWT selection [97%]
  * PBWT selection [98%]
  * PBWT selection [99%]
  * PBWT selection [100%]
  * PBWT selection (0.04s)
315s   * C2H transpose (0.00s)
315s   * 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=7.978+/-0.272 / W=2.26Mb] (0.23s)
315s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
316s   * HAP update (0.01s)
316s   * H2V transpose (0.00s)
316s   * Trimming [pc=3.72%]
316s 
316s Burn-in iteration [1/1]
316s   * V2H transpose (0.00s)
316s   * PBWT selection [0%]
  * PBWT selection [1%]
  * PBWT selection [2%]
  * PBWT selection [3%]
  * PBWT selection [4%]
  * PBWT selection [5%]
  * PBWT selection [6%]
  * PBWT selection [7%]
  * PBWT selection [8%]
  * PBWT selection [9%]
  * PBWT selection [10%]
  * PBWT selection [11%]
  * PBWT selection [12%]
  * PBWT selection [13%]
  * PBWT selection [14%]
  * PBWT selection [15%]
  * PBWT selection [16%]
  * PBWT selection [17%]
  * PBWT selection [18%]
  * PBWT selection [19%]
  * PBWT selection [20%]
  * PBWT selection [21%]
  * PBWT selection [22%]
  * PBWT selection [23%]
  * PBWT selection [24%]
  * PBWT selection [25%]
  * PBWT selection [26%]
  * PBWT selection [27%]
  * PBWT selection [28%]
  * PBWT selection [29%]
  * PBWT selection [30%]
  * PBWT selection [31%]
  * PBWT selection [32%]
  * PBWT selection [33%]
  * PBWT selection [34%]
  * PBWT selection [35%]
  * PBWT selection [36%]
  * PBWT selection [37%]
  * PBWT selection [38%]
  * PBWT selection [39%]
  * PBWT selection [40%]
  * PBWT selection [41%]
  * PBWT selection [42%]
  * PBWT selection [43%]
  * PBWT selection [44%]
  * PBWT selection [45%]
  * PBWT selection [46%]
  * PBWT selection [47%]
  * PBWT selection [48%]
  * PBWT selection [49%]
  * PBWT selection [50%]
  * PBWT selection [51%]
  * PBWT selection [52%]
  * PBWT selection [53%]
  * PBWT selection [54%]
  * PBWT selection [55%]
  * PBWT selection [56%]
  * PBWT selection [57%]
  * PBWT selection [58%]
  * PBWT selection [59%]
  * PBWT selection [60%]
  * PBWT selection [61%]
  * PBWT selection [62%]
  * PBWT selection [63%]
  * PBWT selection [64%]
  * PBWT selection [65%]
  * PBWT selection [66%]
  * PBWT selection [67%]
  * PBWT selection [68%]
  * PBWT selection [69%]
  * PBWT selection [70%]
  * PBWT selection [71%]
  * PBWT selection [72%]
  * PBWT selection [73%]
  * PBWT selection [74%]
  * PBWT selection [75%]
  * PBWT selection [76%]
  * PBWT selection [77%]
  * PBWT selection [78%]
  * PBWT selection [79%]
  * PBWT selection [80%]
  * PBWT selection [81%]
  * PBWT selection [82%]
  * PBWT selection [83%]
  * PBWT selection [84%]
  * PBWT selection [85%]
  * PBWT selection [86%]
  * PBWT selection [87%]
  * PBWT selection [88%]
  * PBWT selection [89%]
  * PBWT selection [90%]
  * PBWT selection [91%]
  * PBWT selection [92%]
  * PBWT selection [93%]
  * PBWT selection [94%]
  * PBWT selection [95%]
  * PBWT selection [96%]
  * PBWT selection [97%]
  * PBWT selection [98%]
  * PBWT selection [99%]
  * PBWT selection [100%]
  * PBWT selection (0.04s)
316s   * C2H transpose (0.00s)
316s   * 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=7.971+/-0.295 / W=2.21Mb] (0.18s)
316s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
316s   * HAP update (0.02s)
316s   * H2V transpose (0.01s)
316s 
316s Pruning iteration [1/1]
316s   * V2H transpose (0.00s)
316s   * PBWT selection [0%]
  * PBWT selection [1%]
  * PBWT selection [2%]
  * PBWT selection [3%]
  * PBWT selection [4%]
  * PBWT selection [5%]
  * PBWT selection [6%]
  * PBWT selection [7%]
  * PBWT selection [8%]
  * PBWT selection [9%]
  * PBWT selection [10%]
  * PBWT selection [11%]
  * PBWT selection [12%]
  * PBWT selection [13%]
  * PBWT selection [14%]
  * PBWT selection [15%]
  * PBWT selection [16%]
  * PBWT selection [17%]
  * PBWT selection [18%]
  * PBWT selection [19%]
  * PBWT selection [20%]
  * PBWT selection [21%]
  * PBWT selection [22%]
  * PBWT selection [23%]
  * PBWT selection [24%]
  * PBWT selection [25%]
  * PBWT selection [26%]
  * PBWT selection [27%]
  * PBWT selection [28%]
  * PBWT selection [29%]
  * PBWT selection [30%]
  * PBWT selection [31%]
  * PBWT selection [32%]
  * PBWT selection [33%]
  * PBWT selection [34%]
  * PBWT selection [35%]
  * PBWT selection [36%]
  * PBWT selection [37%]
  * PBWT selection [38%]
  * PBWT selection [39%]
  * PBWT selection [40%]
  * PBWT selection [41%]
  * PBWT selection [42%]
  * PBWT selection [43%]
  * PBWT selection [44%]
  * PBWT selection [45%]
  * PBWT selection [46%]
  * PBWT selection [47%]
  * PBWT selection [48%]
  * PBWT selection [49%]
  * PBWT selection [50%]
  * PBWT selection [51%]
  * PBWT selection [52%]
  * PBWT selection [53%]
  * PBWT selection [54%]
  * PBWT selection [55%]
  * PBWT selection [56%]
  * PBWT selection [57%]
  * PBWT selection [58%]
  * PBWT selection [59%]
  * PBWT selection [60%]
  * PBWT selection [61%]
  * PBWT selection [62%]
  * PBWT selection [63%]
  * PBWT selection [64%]
  * PBWT selection [65%]
  * PBWT selection [66%]
  * PBWT selection [67%]
  * PBWT selection [68%]
  * PBWT selection [69%]
  * PBWT selection [70%]
  * PBWT selection [71%]
  * PBWT selection [72%]
  * PBWT selection [73%]
  * PBWT selection [74%]
  * PBWT selection [75%]
  * PBWT selection [76%]
  * PBWT selection [77%]
  * PBWT selection [78%]
  * PBWT selection [79%]
  * PBWT selection [80%]
  * PBWT selection [81%]
  * PBWT selection [82%]
  * PBWT selection [83%]
  * PBWT selection [84%]
  * PBWT selection [85%]
  * PBWT selection [86%]
  * PBWT selection [87%]
  * PBWT selection [88%]
  * PBWT selection [89%]
  * PBWT selection [90%]
  * PBWT selection [91%]
  * PBWT selection [92%]
  * PBWT selection [93%]
  * PBWT selection [94%]
  * PBWT selection [95%]
  * PBWT selection [96%]
  * PBWT selection [97%]
  * PBWT selection [98%]
  * PBWT selection [99%]
  * PBWT selection [100%]
  * PBWT selection (0.05s)
316s   * C2H transpose (0.00s)
316s   * 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=7.970+/-0.298 / W=2.26Mb] (0.23s)
316s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
316s   * HAP update (0.02s)
316s   * H2V transpose (0.00s)
316s   * Trimming [pc=4.94%]
316s 
316s Burn-in iteration [1/1]
316s   * V2H transpose (0.00s)
316s   * PBWT selection [0%]
  * PBWT selection [1%]
  * PBWT selection [2%]
  * PBWT selection [3%]
  * PBWT selection [4%]
  * PBWT selection [5%]
  * PBWT selection [6%]
  * PBWT selection [7%]
  * PBWT selection [8%]
  * PBWT selection [9%]
  * PBWT selection [10%]
  * PBWT selection [11%]
  * PBWT selection [12%]
  * PBWT selection [13%]
  * PBWT selection [14%]
  * PBWT selection [15%]
  * PBWT selection [16%]
  * PBWT selection [17%]
  * PBWT selection [18%]
  * PBWT selection [19%]
  * PBWT selection [20%]
  * PBWT selection [21%]
  * PBWT selection [22%]
  * PBWT selection [23%]
  * PBWT selection [24%]
  * PBWT selection [25%]
  * PBWT selection [26%]
  * PBWT selection [27%]
  * PBWT selection [28%]
  * PBWT selection [29%]
  * PBWT selection [30%]
  * PBWT selection [31%]
  * PBWT selection [32%]
  * PBWT selection [33%]
  * PBWT selection [34%]
  * PBWT selection [35%]
  * PBWT selection [36%]
  * PBWT selection [37%]
  * PBWT selection [38%]
  * PBWT selection [39%]
  * PBWT selection [40%]
  * PBWT selection [41%]
  * PBWT selection [42%]
  * PBWT selection [43%]
  * PBWT selection [44%]
  * PBWT selection [45%]
  * PBWT selection [46%]
  * PBWT selection [47%]
  * PBWT selection [48%]
  * PBWT selection [49%]
  * PBWT selection [50%]
  * PBWT selection [51%]
  * PBWT selection [52%]
  * PBWT selection [53%]
  * PBWT selection [54%]
  * PBWT selection [55%]
  * PBWT selection [56%]
  * PBWT selection [57%]
  * PBWT selection [58%]
  * PBWT selection [59%]
  * PBWT selection [60%]
  * PBWT selection [61%]
  * PBWT selection [62%]
  * PBWT selection [63%]
  * PBWT selection [64%]
  * PBWT selection [65%]
  * PBWT selection [66%]
  * PBWT selection [67%]
  * PBWT selection [68%]
  * PBWT selection [69%]
  * PBWT selection [70%]
  * PBWT selection [71%]
  * PBWT selection [72%]
  * PBWT selection [73%]
  * PBWT selection [74%]
  * PBWT selection [75%]
  * PBWT selection [76%]
  * PBWT selection [77%]
  * PBWT selection [78%]
  * PBWT selection [79%]
  * PBWT selection [80%]
  * PBWT selection [81%]
  * PBWT selection [82%]
  * PBWT selection [83%]
  * PBWT selection [84%]
  * PBWT selection [85%]
  * PBWT selection [86%]
  * PBWT selection [87%]
  * PBWT selection [88%]
  * PBWT selection [89%]
  * PBWT selection [90%]
  * PBWT selection [91%]
  * PBWT selection [92%]
  * PBWT selection [93%]
  * PBWT selection [94%]
  * PBWT selection [95%]
  * PBWT selection [96%]
  * PBWT selection [97%]
  * PBWT selection [98%]
  * PBWT selection [99%]
  * PBWT selection [100%]
  * PBWT selection (0.06s)
316s   * C2H transpose (0.00s)
316s   * 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=7.971+/-0.295 / W=2.22Mb] (0.18s)
316s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
316s   * HAP update (0.02s)
316s   * H2V transpose (0.00s)
316s 
316s Pruning iteration [1/1]
316s   * V2H transpose (0.00s)
316s   * PBWT selection [0%]
  * PBWT selection [1%]
  * PBWT selection [2%]
  * PBWT selection [3%]
  * PBWT selection [4%]
  * PBWT selection [5%]
  * PBWT selection [6%]
  * PBWT selection [7%]
  * PBWT selection [8%]
  * PBWT selection [9%]
  * PBWT selection [10%]
  * PBWT selection [11%]
  * PBWT selection [12%]
  * PBWT selection [13%]
  * PBWT selection [14%]
  * PBWT selection [15%]
  * PBWT selection [16%]
  * PBWT selection [17%]
  * PBWT selection [18%]
  * PBWT selection [19%]
  * PBWT selection [20%]
  * PBWT selection [21%]
  * PBWT selection [22%]
  * PBWT selection [23%]
  * PBWT selection [24%]
  * PBWT selection [25%]
  * PBWT selection [26%]
  * PBWT selection [27%]
  * PBWT selection [28%]
  * PBWT selection [29%]
  * PBWT selection [30%]
  * PBWT selection [31%]
  * PBWT selection [32%]
  * PBWT selection [33%]
  * PBWT selection [34%]
  * PBWT selection [35%]
  * PBWT selection [36%]
  * PBWT selection [37%]
  * PBWT selection [38%]
  * PBWT selection [39%]
  * PBWT selection [40%]
  * PBWT selection [41%]
  * PBWT selection [42%]
  * PBWT selection [43%]
  * PBWT selection [44%]
  * PBWT selection [45%]
  * PBWT selection [46%]
  * PBWT selection [47%]
  * PBWT selection [48%]
  * PBWT selection [49%]
  * PBWT selection [50%]
  * PBWT selection [51%]
  * PBWT selection [52%]
  * PBWT selection [53%]
  * PBWT selection [54%]
  * PBWT selection [55%]
  * PBWT selection [56%]
  * PBWT selection [57%]
  * PBWT selection [58%]
  * PBWT selection [59%]
  * PBWT selection [60%]
  * PBWT selection [61%]
  * PBWT selection [62%]
  * PBWT selection [63%]
  * PBWT selection [64%]
  * PBWT selection [65%]
  * PBWT selection [66%]
  * PBWT selection [67%]
  * PBWT selection [68%]
  * PBWT selection [69%]
  * PBWT selection [70%]
  * PBWT selection [71%]
  * PBWT selection [72%]
  * PBWT selection [73%]
  * PBWT selection [74%]
  * PBWT selection [75%]
  * PBWT selection [76%]
  * PBWT selection [77%]
  * PBWT selection [78%]
  * PBWT selection [79%]
  * PBWT selection [80%]
  * PBWT selection [81%]
  * PBWT selection [82%]
  * PBWT selection [83%]
  * PBWT selection [84%]
  * PBWT selection [85%]
  * PBWT selection [86%]
  * PBWT selection [87%]
  * PBWT selection [88%]
  * PBWT selection [89%]
  * PBWT selection [90%]
  * PBWT selection [91%]
  * PBWT selection [92%]
  * PBWT selection [93%]
  * PBWT selection [94%]
  * PBWT selection [95%]
  * PBWT selection [96%]
  * PBWT selection [97%]
  * PBWT selection [98%]
  * PBWT selection [99%]
  * PBWT selection [100%]
  * PBWT selection (0.05s)
316s   * C2H transpose (0.00s)
317s   * 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+/-0.290 / W=2.15Mb] (0.22s)
317s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
317s   * HAP update (0.01s)
317s   * H2V transpose (0.00s)
317s   * Trimming [pc=5.17%]
317s 
317s Main iteration [1/5]
317s   * V2H transpose (0.00s)
317s   * PBWT selection [0%]
  * PBWT selection [1%]
  * PBWT selection [2%]
  * PBWT selection [3%]
  * PBWT selection [4%]
  * PBWT selection [5%]
  * PBWT selection [6%]
  * PBWT selection [7%]
  * PBWT selection [8%]
  * PBWT selection [9%]
  * PBWT selection [10%]
  * PBWT selection [11%]
  * PBWT selection [12%]
  * PBWT selection [13%]
  * PBWT selection [14%]
  * PBWT selection [15%]
  * PBWT selection [16%]
  * PBWT selection [17%]
  * PBWT selection [18%]
  * PBWT selection [19%]
  * PBWT selection [20%]
  * PBWT selection [21%]
  * PBWT selection [22%]
  * PBWT selection [23%]
  * PBWT selection [24%]
  * PBWT selection [25%]
  * PBWT selection [26%]
  * PBWT selection [27%]
  * PBWT selection [28%]
  * PBWT selection [29%]
  * PBWT selection [30%]
  * PBWT selection [31%]
  * PBWT selection [32%]
  * PBWT selection [33%]
  * PBWT selection [34%]
  * PBWT selection [35%]
  * PBWT selection [36%]
  * PBWT selection [37%]
  * PBWT selection [38%]
  * PBWT selection [39%]
  * PBWT selection [40%]
  * PBWT selection [41%]
  * PBWT selection [42%]
  * PBWT selection [43%]
  * PBWT selection [44%]
  * PBWT selection [45%]
  * PBWT selection [46%]
  * PBWT selection [47%]
  * PBWT selection [48%]
  * PBWT selection [49%]
  * PBWT selection [50%]
  * PBWT selection [51%]
  * PBWT selection [52%]
  * PBWT selection [53%]
  * PBWT selection [54%]
  * PBWT selection [55%]
  * PBWT selection [56%]
  * PBWT selection [57%]
  * PBWT selection [58%]
  * PBWT selection [59%]
  * PBWT selection [60%]
  * PBWT selection [61%]
  * PBWT selection [62%]
  * PBWT selection [63%]
  * PBWT selection [64%]
  * PBWT selection [65%]
  * PBWT selection [66%]
  * PBWT selection [67%]
  * PBWT selection [68%]
  * PBWT selection [69%]
  * PBWT selection [70%]
  * PBWT selection [71%]
  * PBWT selection [72%]
  * PBWT selection [73%]
  * PBWT selection [74%]
  * PBWT selection [75%]
  * PBWT selection [76%]
  * PBWT selection [77%]
  * PBWT selection [78%]
  * PBWT selection [79%]
  * PBWT selection [80%]
  * PBWT selection [81%]
  * PBWT selection [82%]
  * PBWT selection [83%]
  * PBWT selection [84%]
  * PBWT selection [85%]
  * PBWT selection [86%]
  * PBWT selection [87%]
  * PBWT selection [88%]
  * PBWT selection [89%]
  * PBWT selection [90%]
  * PBWT selection [91%]
  * PBWT selection [92%]
  * PBWT selection [93%]
  * PBWT selection [94%]
  * PBWT selection [95%]
  * PBWT selection [96%]
  * PBWT selection [97%]
  * PBWT selection [98%]
  * PBWT selection [99%]
  * PBWT selection [100%]
  * PBWT selection (0.04s)
317s   * C2H transpose (0.00s)
317s   * 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=7.971+/-0.294 / W=2.21Mb] (0.18s)
317s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
317s   * HAP update (0.02s)
317s   * H2V transpose (0.00s)
317s 
317s Main iteration [2/5]
317s   * V2H transpose (0.00s)
317s   * PBWT selection [0%]
  * PBWT selection [1%]
  * PBWT selection [2%]
  * PBWT selection [3%]
  * PBWT selection [4%]
  * PBWT selection [5%]
  * PBWT selection [6%]
  * PBWT selection [7%]
  * PBWT selection [8%]
  * PBWT selection [9%]
  * PBWT selection [10%]
  * PBWT selection [11%]
  * PBWT selection [12%]
  * PBWT selection [13%]
  * PBWT selection [14%]
  * PBWT selection [15%]
  * PBWT selection [16%]
  * PBWT selection [17%]
  * PBWT selection [18%]
  * PBWT selection [19%]
  * PBWT selection [20%]
  * PBWT selection [21%]
  * PBWT selection [22%]
  * PBWT selection [23%]
  * PBWT selection [24%]
  * PBWT selection [25%]
  * PBWT selection [26%]
  * PBWT selection [27%]
  * PBWT selection [28%]
  * PBWT selection [29%]
  * PBWT selection [30%]
  * PBWT selection [31%]
  * PBWT selection [32%]
  * PBWT selection [33%]
  * PBWT selection [34%]
  * PBWT selection [35%]
  * PBWT selection [36%]
  * PBWT selection [37%]
  * PBWT selection [38%]
  * PBWT selection [39%]
  * PBWT selection [40%]
  * PBWT selection [41%]
  * PBWT selection [42%]
  * PBWT selection [43%]
  * PBWT selection [44%]
  * PBWT selection [45%]
  * PBWT selection [46%]
  * PBWT selection [47%]
  * PBWT selection [48%]
  * PBWT selection [49%]
  * PBWT selection [50%]
  * PBWT selection [51%]
  * PBWT selection [52%]
  * PBWT selection [53%]
  * PBWT selection [54%]
  * PBWT selection [55%]
  * PBWT selection [56%]
  * PBWT selection [57%]
  * PBWT selection [58%]
  * PBWT selection [59%]
  * PBWT selection [60%]
  * PBWT selection [61%]
  * PBWT selection [62%]
  * PBWT selection [63%]
  * PBWT selection [64%]
  * PBWT selection [65%]
  * PBWT selection [66%]
  * PBWT selection [67%]
  * PBWT selection [68%]
  * PBWT selection [69%]
  * PBWT selection [70%]
  * PBWT selection [71%]
  * PBWT selection [72%]
  * PBWT selection [73%]
  * PBWT selection [74%]
  * PBWT selection [75%]
  * PBWT selection [76%]
  * PBWT selection [77%]
  * PBWT selection [78%]
  * PBWT selection [79%]
  * PBWT selection [80%]
  * PBWT selection [81%]
  * PBWT selection [82%]
  * PBWT selection [83%]
  * PBWT selection [84%]
  * PBWT selection [85%]
  * PBWT selection [86%]
  * PBWT selection [87%]
  * PBWT selection [88%]
  * PBWT selection [89%]
  * PBWT selection [90%]
  * PBWT selection [91%]
  * PBWT selection [92%]
  * PBWT selection [93%]
  * PBWT selection [94%]
  * PBWT selection [95%]
  * PBWT selection [96%]
  * PBWT selection [97%]
  * PBWT selection [98%]
  * PBWT selection [99%]
  * PBWT selection [100%]
  * PBWT selection (0.05s)
317s   * C2H transpose (0.00s)
317s   * 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=7.969+/-0.304 / W=2.36Mb] (0.19s)
317s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
317s   * HAP update (0.02s)
317s   * H2V transpose (0.01s)
317s 
317s Main iteration [3/5]
317s   * V2H transpose (0.00s)
317s   * PBWT selection [0%]
  * PBWT selection [1%]
  * PBWT selection [2%]
  * PBWT selection [3%]
  * PBWT selection [4%]
  * PBWT selection [5%]
  * PBWT selection [6%]
  * PBWT selection [7%]
  * PBWT selection [8%]
  * PBWT selection [9%]
  * PBWT selection [10%]
  * PBWT selection [11%]
  * PBWT selection [12%]
  * PBWT selection [13%]
  * PBWT selection [14%]
  * PBWT selection [15%]
  * PBWT selection [16%]
  * PBWT selection [17%]
  * PBWT selection [18%]
  * PBWT selection [19%]
  * PBWT selection [20%]
  * PBWT selection [21%]
  * PBWT selection [22%]
  * PBWT selection [23%]
  * PBWT selection [24%]
  * PBWT selection [25%]
  * PBWT selection [26%]
  * PBWT selection [27%]
  * PBWT selection [28%]
  * PBWT selection [29%]
  * PBWT selection [30%]
  * PBWT selection [31%]
  * PBWT selection [32%]
  * PBWT selection [33%]
  * PBWT selection [34%]
  * PBWT selection [35%]
  * PBWT selection [36%]
  * PBWT selection [37%]
  * PBWT selection [38%]
  * PBWT selection [39%]
  * PBWT selection [40%]
  * PBWT selection [41%]
  * PBWT selection [42%]
  * PBWT selection [43%]
  * PBWT selection [44%]
  * PBWT selection [45%]
  * PBWT selection [46%]
  * PBWT selection [47%]
  * PBWT selection [48%]
  * PBWT selection [49%]
  * PBWT selection [50%]
  * PBWT selection [51%]
  * PBWT selection [52%]
  * PBWT selection [53%]
  * PBWT selection [54%]
  * PBWT selection [55%]
  * PBWT selection [56%]
  * PBWT selection [57%]
  * PBWT selection [58%]
  * PBWT selection [59%]
  * PBWT selection [60%]
  * PBWT selection [61%]
  * PBWT selection [62%]
  * PBWT selection [63%]
  * PBWT selection [64%]
  * PBWT selection [65%]
  * PBWT selection [66%]
  * PBWT selection [67%]
  * PBWT selection [68%]
  * PBWT selection [69%]
  * PBWT selection [70%]
  * PBWT selection [71%]
  * PBWT selection [72%]
  * PBWT selection [73%]
  * PBWT selection [74%]
  * PBWT selection [75%]
  * PBWT selection [76%]
  * PBWT selection [77%]
  * PBWT selection [78%]
  * PBWT selection [79%]
  * PBWT selection [80%]
  * PBWT selection [81%]
  * PBWT selection [82%]
  * PBWT selection [83%]
  * PBWT selection [84%]
  * PBWT selection [85%]
  * PBWT selection [86%]
  * PBWT selection [87%]
  * PBWT selection [88%]
  * PBWT selection [89%]
  * PBWT selection [90%]
  * PBWT selection [91%]
  * PBWT selection [92%]
  * PBWT selection [93%]
  * PBWT selection [94%]
  * PBWT selection [95%]
  * PBWT selection [96%]
  * PBWT selection [97%]
  * PBWT selection [98%]
  * PBWT selection [99%]
  * PBWT selection [100%]
  * PBWT selection (0.05s)
317s   * C2H transpose (0.00s)
317s   * 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=7.970+/-0.300 / W=2.30Mb] (0.20s)
317s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
317s   * HAP update (0.02s)
317s   * H2V transpose (0.01s)
317s 
317s Main iteration [4/5]
317s   * V2H transpose (0.00s)
317s   * PBWT selection [0%]
  * PBWT selection [1%]
  * PBWT selection [2%]
  * PBWT selection [3%]
  * PBWT selection [4%]
  * PBWT selection [5%]
  * PBWT selection [6%]
  * PBWT selection [7%]
  * PBWT selection [8%]
  * PBWT selection [9%]
  * PBWT selection [10%]
  * PBWT selection [11%]
  * PBWT selection [12%]
  * PBWT selection [13%]
  * PBWT selection [14%]
  * PBWT selection [15%]
  * PBWT selection [16%]
  * PBWT selection [17%]
  * PBWT selection [18%]
  * PBWT selection [19%]
  * PBWT selection [20%]
  * PBWT selection [21%]
  * PBWT selection [22%]
  * PBWT selection [23%]
  * PBWT selection [24%]
  * PBWT selection [25%]
  * PBWT selection [26%]
  * PBWT selection [27%]
  * PBWT selection [28%]
  * PBWT selection [29%]
  * PBWT selection [30%]
  * PBWT selection [31%]
  * PBWT selection [32%]
  * PBWT selection [33%]
  * PBWT selection [34%]
  * PBWT selection [35%]
  * PBWT selection [36%]
  * PBWT selection [37%]
  * PBWT selection [38%]
  * PBWT selection [39%]
  * PBWT selection [40%]
  * PBWT selection [41%]
  * PBWT selection [42%]
  * PBWT selection [43%]
  * PBWT selection [44%]
  * PBWT selection [45%]
  * PBWT selection [46%]
  * PBWT selection [47%]
  * PBWT selection [48%]
  * PBWT selection [49%]
  * PBWT selection [50%]
  * PBWT selection [51%]
  * PBWT selection [52%]
  * PBWT selection [53%]
  * PBWT selection [54%]
  * PBWT selection [55%]
  * PBWT selection [56%]
  * PBWT selection [57%]
  * PBWT selection [58%]
  * PBWT selection [59%]
  * PBWT selection [60%]
  * PBWT selection [61%]
  * PBWT selection [62%]
  * PBWT selection [63%]
  * PBWT selection [64%]
  * PBWT selection [65%]
  * PBWT selection [66%]
  * PBWT selection [67%]
  * PBWT selection [68%]
  * PBWT selection [69%]
  * PBWT selection [70%]
  * PBWT selection [71%]
  * PBWT selection [72%]
  * PBWT selection [73%]
  * PBWT selection [74%]
  * PBWT selection [75%]
  * PBWT selection [76%]
  * PBWT selection [77%]
  * PBWT selection [78%]
  * PBWT selection [79%]
  * PBWT selection [80%]
  * PBWT selection [81%]
  * PBWT selection [82%]
  * PBWT selection [83%]
  * PBWT selection [84%]
  * PBWT selection [85%]
  * PBWT selection [86%]
  * PBWT selection [87%]
  * PBWT selection [88%]
  * PBWT selection [89%]
  * PBWT selection [90%]
  * PBWT selection [91%]
  * PBWT selection [92%]
  * PBWT selection [93%]
  * PBWT selection [94%]
  * PBWT selection [95%]
  * PBWT selection [96%]
  * PBWT selection [97%]
  * PBWT selection [98%]
  * PBWT selection [99%]
  * PBWT selection [100%]
  * PBWT selection (0.04s)
317s   * C2H transpose (0.00s)
318s   * 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=7.963+/-0.362 / W=2.23Mb] (0.18s)
318s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
318s   * HAP update (0.01s)
318s   * H2V transpose (0.00s)
318s 
318s Main iteration [5/5]
318s   * V2H transpose (0.00s)
318s   * PBWT selection [0%]
  * PBWT selection [1%]
  * PBWT selection [2%]
  * PBWT selection [3%]
  * PBWT selection [4%]
  * PBWT selection [5%]
  * PBWT selection [6%]
  * PBWT selection [7%]
  * PBWT selection [8%]
  * PBWT selection [9%]
  * PBWT selection [10%]
  * PBWT selection [11%]
  * PBWT selection [12%]
  * PBWT selection [13%]
  * PBWT selection [14%]
  * PBWT selection [15%]
  * PBWT selection [16%]
  * PBWT selection [17%]
  * PBWT selection [18%]
  * PBWT selection [19%]
  * PBWT selection [20%]
  * PBWT selection [21%]
  * PBWT selection [22%]
  * PBWT selection [23%]
  * PBWT selection [24%]
  * PBWT selection [25%]
  * PBWT selection [26%]
  * PBWT selection [27%]
  * PBWT selection [28%]
  * PBWT selection [29%]
  * PBWT selection [30%]
  * PBWT selection [31%]
  * PBWT selection [32%]
  * PBWT selection [33%]
  * PBWT selection [34%]
  * PBWT selection [35%]
  * PBWT selection [36%]
  * PBWT selection [37%]
  * PBWT selection [38%]
  * PBWT selection [39%]
  * PBWT selection [40%]
  * PBWT selection [41%]
  * PBWT selection [42%]
  * PBWT selection [43%]
  * PBWT selection [44%]
  * PBWT selection [45%]
  * PBWT selection [46%]
  * PBWT selection [47%]
  * PBWT selection [48%]
  * PBWT selection [49%]
  * PBWT selection [50%]
  * PBWT selection [51%]
  * PBWT selection [52%]
  * PBWT selection [53%]
  * PBWT selection [54%]
  * PBWT selection [55%]
  * PBWT selection [56%]
  * PBWT selection [57%]
  * PBWT selection [58%]
  * PBWT selection [59%]
  * PBWT selection [60%]
  * PBWT selection [61%]
  * PBWT selection [62%]
  * PBWT selection [63%]
  * PBWT selection [64%]
  * PBWT selection [65%]
  * PBWT selection [66%]
  * PBWT selection [67%]
  * PBWT selection [68%]
  * PBWT selection [69%]
  * PBWT selection [70%]
  * PBWT selection [71%]
  * PBWT selection [72%]
  * PBWT selection [73%]
  * PBWT selection [74%]
  * PBWT selection [75%]
  * PBWT selection [76%]
  * PBWT selection [77%]
  * PBWT selection [78%]
  * PBWT selection [79%]
  * PBWT selection [80%]
  * PBWT selection [81%]
  * PBWT selection [82%]
  * PBWT selection [83%]
  * PBWT selection [84%]
  * PBWT selection [85%]
  * PBWT selection [86%]
  * PBWT selection [87%]
  * PBWT selection [88%]
  * PBWT selection [89%]
  * PBWT selection [90%]
  * PBWT selection [91%]
  * PBWT selection [92%]
  * PBWT selection [93%]
  * PBWT selection [94%]
  * PBWT selection [95%]
  * PBWT selection [96%]
  * PBWT selection [97%]
  * PBWT selection [98%]
  * PBWT selection [99%]
  * PBWT selection [100%]
  * PBWT selection (0.04s)
318s   * C2H transpose (0.00s)
318s   * 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=7.971+/-0.293 / W=2.20Mb] (0.18s)
318s   * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0]
318s   * HAP update (0.01s)
318s   * H2V transpose (0.01s)
318s 
318s Finalization:
318s   * HAP solving (0.10s)
318s   * HAP update (0.01s)
318s   * H2V transpose (0.00s)
318s   * 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)
318s   * Total running time = 8 seconds
319s autopkgtest [17:41:02]: test run-sample-analysis: -----------------------]
323s run-sample-analysis  PASS
323s autopkgtest [17:41:06]: test run-sample-analysis:  - - - - - - - - - - results - - - - - - - - - -
326s autopkgtest [17:41:09]: @@@@@@@@@@@@@@@@@@@@ summary
326s run-sample-analysis  PASS