0s autopkgtest [13:05:38]: starting date and time: 2024-03-24 13:05:38+0000 0s autopkgtest [13:05:38]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [13:05:38]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.f9u_gvag/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:shapeit4,src:curl,src:gnutls28,src:htslib,src:libpsl,src:nettle,src:openssl --apt-upgrade shapeit4 --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=shapeit4/4.2.2+dfsg-1build2 curl/8.5.0-2ubuntu8 gnutls28/3.8.3-1.1ubuntu2 htslib/1.19+ds-1.1build2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos01-ppc64el-12.secgroup --name adt-noble-ppc64el-shapeit4-20240324-130538-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://us.ports.ubuntu.com/ubuntu-ports/ 120s autopkgtest [13:07:38]: testbed dpkg architecture: ppc64el 120s autopkgtest [13:07:38]: testbed apt version: 2.7.12 120s autopkgtest [13:07:38]: @@@@@@@@@@@@@@@@@@@@ test bed setup 121s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 121s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 121s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 121s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [539 kB] 121s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4044 kB] 121s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [726 kB] 121s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 121s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 121s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 121s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4274 kB] 122s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 122s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [61.1 kB] 122s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 125s Fetched 9838 kB in 2s (4261 kB/s) 125s Reading package lists... 128s Reading package lists... 128s Building dependency tree... 128s Reading state information... 128s Calculating upgrade... 128s The following packages will be REMOVED: 128s libssl3 128s The following NEW packages will be installed: 128s libssl3t64 128s The following packages have been kept back: 128s curl 128s The following packages will be upgraded: 128s cloud-init fonts-ubuntu-console libbsd0 libc-bin libc6 locales openssl 128s python3-markupsafe 128s 8 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 128s Need to get 12.1 MB of archives. 128s After this operation, 10.2 kB of additional disk space will be used. 128s Get:1 http://ftpmaster.internal/ubuntu noble/main ppc64el libc6 ppc64el 2.39-0ubuntu6 [3274 kB] 129s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libc-bin ppc64el 2.39-0ubuntu6 [751 kB] 129s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu2 [1026 kB] 129s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu2 [2125 kB] 129s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el libbsd0 ppc64el 0.12.1-1 [56.9 kB] 129s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el locales all 2.39-0ubuntu6 [4232 kB] 129s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-ubuntu-console all 0.869+git20240321-0ubuntu1 [18.7 kB] 129s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-markupsafe ppc64el 2.1.5-1build1 [13.2 kB] 129s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el cloud-init all 24.1.2-0ubuntu1 [597 kB] 130s Preconfiguring packages ... 130s Fetched 12.1 MB in 1s (11.3 MB/s) 130s (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 ... 70157 files and directories currently installed.) 130s Preparing to unpack .../libc6_2.39-0ubuntu6_ppc64el.deb ... 130s Unpacking libc6:ppc64el (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 130s Setting up libc6:ppc64el (2.39-0ubuntu6) ... 131s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70157 files and directories currently installed.) 131s Preparing to unpack .../libc-bin_2.39-0ubuntu6_ppc64el.deb ... 131s Unpacking libc-bin (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 131s Setting up libc-bin (2.39-0ubuntu6) ... 131s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70157 files and directories currently installed.) 131s Preparing to unpack .../openssl_3.0.13-0ubuntu2_ppc64el.deb ... 131s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 131s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested: 131s wget depends on libssl3 (>= 3.0.0). 131s tnftp depends on libssl3 (>= 3.0.0). 131s tcpdump depends on libssl3 (>= 3.0.0). 131s systemd-resolved depends on libssl3 (>= 3.0.0). 131s systemd depends on libssl3 (>= 3.0.0). 131s sudo depends on libssl3 (>= 3.0.0). 131s rsync depends on libssl3 (>= 3.0.0). 131s python3-cryptography depends on libssl3 (>= 3.0.0). 131s openssh-server depends on libssl3 (>= 3.0.10). 131s openssh-client depends on libssl3 (>= 3.0.10). 131s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 131s libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0). 131s libssh-4:ppc64el depends on libssl3 (>= 3.0.0). 131s libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0). 131s libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0). 131s libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0). 131s libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0). 131s libnvme1 depends on libssl3 (>= 3.0.0). 131s libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0). 131s libkmod2:ppc64el depends on libssl3 (>= 3.0.0). 131s libfido2-1:ppc64el depends on libssl3 (>= 3.0.0). 131s libcurl4:ppc64el depends on libssl3 (>= 3.0.0). 131s libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0). 131s kmod depends on libssl3 (>= 3.0.0). 131s dhcpcd-base depends on libssl3 (>= 3.0.0). 131s bind9-libs:ppc64el depends on libssl3 (>= 3.0.0). 131s 131s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70157 files and directories currently installed.) 131s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ... 131s Selecting previously unselected package libssl3t64:ppc64el. 131s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70146 files and directories currently installed.) 131s Preparing to unpack .../0-libssl3t64_3.0.13-0ubuntu2_ppc64el.deb ... 131s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 131s Preparing to unpack .../1-libbsd0_0.12.1-1_ppc64el.deb ... 131s Unpacking libbsd0:ppc64el (0.12.1-1) over (0.11.8-1) ... 131s Preparing to unpack .../2-locales_2.39-0ubuntu6_all.deb ... 131s Unpacking locales (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 131s Preparing to unpack .../3-fonts-ubuntu-console_0.869+git20240321-0ubuntu1_all.deb ... 131s Unpacking fonts-ubuntu-console (0.869+git20240321-0ubuntu1) over (0.869-0ubuntu1) ... 131s Preparing to unpack .../4-python3-markupsafe_2.1.5-1build1_ppc64el.deb ... 131s Unpacking python3-markupsafe (2.1.5-1build1) over (2.1.5-1) ... 131s Preparing to unpack .../5-cloud-init_24.1.2-0ubuntu1_all.deb ... 131s Unpacking cloud-init (24.1.2-0ubuntu1) over (24.1.1-0ubuntu1) ... 132s Setting up fonts-ubuntu-console (0.869+git20240321-0ubuntu1) ... 132s Setting up cloud-init (24.1.2-0ubuntu1) ... 133s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 133s Setting up locales (2.39-0ubuntu6) ... 133s Generating locales (this might take a while)... 135s en_US.UTF-8... done 135s Generation complete. 135s Setting up python3-markupsafe (2.1.5-1build1) ... 135s Setting up openssl (3.0.13-0ubuntu2) ... 135s Setting up libbsd0:ppc64el (0.12.1-1) ... 135s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 135s Processing triggers for man-db (2.12.0-3) ... 136s Processing triggers for libc-bin (2.39-0ubuntu6) ... 136s Reading package lists... 136s Building dependency tree... 136s Reading state information... 136s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 137s sh: Attempting to set up Debian/Ubuntu apt sources automatically 137s sh: Distribution appears to be Ubuntu 138s Reading package lists... 138s Building dependency tree... 138s Reading state information... 138s eatmydata is already the newest version (131-1). 138s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 138s Reading package lists... 138s Building dependency tree... 138s Reading state information... 138s dbus is already the newest version (1.14.10-4ubuntu1). 138s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 138s Reading package lists... 139s Building dependency tree... 139s Reading state information... 139s rng-tools-debian is already the newest version (2.4). 139s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 139s Reading package lists... 139s Building dependency tree... 139s Reading state information... 139s The following packages will be REMOVED: 139s cloud-init* python3-configobj* python3-debconf* 139s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 139s After this operation, 3256 kB disk space will be freed. 139s (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 ... 70158 files and directories currently installed.) 139s Removing cloud-init (24.1.2-0ubuntu1) ... 140s Removing python3-configobj (5.0.8-3) ... 140s Removing python3-debconf (1.5.86) ... 140s Processing triggers for man-db (2.12.0-3) ... 141s (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 ... 69769 files and directories currently installed.) 141s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 142s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 142s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 142s invoke-rc.d: policy-rc.d denied execution of try-restart. 142s Reading package lists... 142s Building dependency tree... 142s Reading state information... 142s linux-generic is already the newest version (6.8.0-11.11+1). 142s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 142s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 143s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 143s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 145s Reading package lists... 145s Reading package lists... 145s Building dependency tree... 145s Reading state information... 145s Calculating upgrade... 145s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 145s Reading package lists... 145s Building dependency tree... 145s Reading state information... 146s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 146s autopkgtest [13:08:04]: rebooting testbed after setup commands that affected boot 312s autopkgtest [13:10:50]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 315s autopkgtest [13:10:53]: @@@@@@@@@@@@@@@@@@@@ apt-source shapeit4 322s Get:1 http://ftpmaster.internal/ubuntu noble/universe shapeit4 4.2.2+dfsg-1build1 (dsc) [2158 B] 322s Get:2 http://ftpmaster.internal/ubuntu noble/universe shapeit4 4.2.2+dfsg-1build1 (tar) [59.0 MB] 322s Get:3 http://ftpmaster.internal/ubuntu noble/universe shapeit4 4.2.2+dfsg-1build1 (diff) [5280 B] 323s gpgv: Signature made Tue Dec 19 15:03:10 2023 UTC 323s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 323s gpgv: Can't check signature: No public key 323s dpkg-source: warning: cannot verify inline signature for ./shapeit4_4.2.2+dfsg-1build1.dsc: no acceptable signature found 324s autopkgtest [13:11:02]: testing package shapeit4 version 4.2.2+dfsg-1build1 324s autopkgtest [13:11:02]: build not needed 329s autopkgtest [13:11:07]: test run-sample-analysis: preparing testbed 332s Reading package lists... 332s Building dependency tree... 332s Reading state information... 332s Starting pkgProblemResolver with broken count: 0 332s Starting 2 pkgProblemResolver with broken count: 0 332s Done 332s The following additional packages will be installed: 332s libboost-iostreams1.83.0 libboost-program-options1.83.0 libdeflate0 libhts3 332s libhtscodecs2 shapeit4 shapeit4-example 332s The following NEW packages will be installed: 332s autopkgtest-satdep libboost-iostreams1.83.0 libboost-program-options1.83.0 332s libdeflate0 libhts3 libhtscodecs2 shapeit4 shapeit4-example 332s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. 332s Need to get 53.9 MB/53.9 MB of archives. 332s After this operation, 59.8 MB of additional disk space will be used. 332s Get:1 /tmp/autopkgtest.nVwGG6/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [712 B] 333s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libboost-iostreams1.83.0 ppc64el 1.83.0-2ubuntu1 [340 kB] 333s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libboost-program-options1.83.0 ppc64el 1.83.0-2ubuntu1 [421 kB] 333s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 333s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 333s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB] 333s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el shapeit4 ppc64el 4.2.2+dfsg-1build1 [186 kB] 333s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el shapeit4-example all 4.2.2+dfsg-1build1 [52.3 MB] 335s Fetched 53.9 MB in 2s (24.7 MB/s) 335s Selecting previously unselected package libboost-iostreams1.83.0:ppc64el. 335s (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 ... 69714 files and directories currently installed.) 335s Preparing to unpack .../0-libboost-iostreams1.83.0_1.83.0-2ubuntu1_ppc64el.deb ... 335s Unpacking libboost-iostreams1.83.0:ppc64el (1.83.0-2ubuntu1) ... 335s Selecting previously unselected package libboost-program-options1.83.0:ppc64el. 335s Preparing to unpack .../1-libboost-program-options1.83.0_1.83.0-2ubuntu1_ppc64el.deb ... 335s Unpacking libboost-program-options1.83.0:ppc64el (1.83.0-2ubuntu1) ... 335s Selecting previously unselected package libdeflate0:ppc64el. 335s Preparing to unpack .../2-libdeflate0_1.19-1_ppc64el.deb ... 335s Unpacking libdeflate0:ppc64el (1.19-1) ... 335s Selecting previously unselected package libhtscodecs2:ppc64el. 335s Preparing to unpack .../3-libhtscodecs2_1.6.0-1_ppc64el.deb ... 335s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 335s Selecting previously unselected package libhts3:ppc64el. 335s Preparing to unpack .../4-libhts3_1.18+ds-1_ppc64el.deb ... 335s Unpacking libhts3:ppc64el (1.18+ds-1) ... 335s Selecting previously unselected package shapeit4. 335s Preparing to unpack .../5-shapeit4_4.2.2+dfsg-1build1_ppc64el.deb ... 335s Unpacking shapeit4 (4.2.2+dfsg-1build1) ... 335s Selecting previously unselected package shapeit4-example. 335s Preparing to unpack .../6-shapeit4-example_4.2.2+dfsg-1build1_all.deb ... 335s Unpacking shapeit4-example (4.2.2+dfsg-1build1) ... 335s Selecting previously unselected package autopkgtest-satdep. 335s Preparing to unpack .../7-1-autopkgtest-satdep.deb ... 335s Unpacking autopkgtest-satdep (0) ... 335s Setting up libhtscodecs2:ppc64el (1.6.0-1) ... 335s Setting up libboost-program-options1.83.0:ppc64el (1.83.0-2ubuntu1) ... 335s Setting up libdeflate0:ppc64el (1.19-1) ... 335s Setting up shapeit4-example (4.2.2+dfsg-1build1) ... 335s Setting up libboost-iostreams1.83.0:ppc64el (1.83.0-2ubuntu1) ... 335s Setting up libhts3:ppc64el (1.18+ds-1) ... 335s Setting up shapeit4 (4.2.2+dfsg-1build1) ... 335s Setting up autopkgtest-satdep (0) ... 335s Processing triggers for man-db (2.12.0-3) ... 336s Processing triggers for libc-bin (2.39-0ubuntu6) ... 338s (Reading database ... 69776 files and directories currently installed.) 338s Removing autopkgtest-satdep (0) ... 339s autopkgtest [13:11:17]: test run-sample-analysis: [----------------------- 339s 339s SHAPEIT 339s * Author : Olivier DELANEAU, University of Lausanne 339s * Contact : olivier.delaneau@gmail.com 339s + shapeit4 --input unphased.vcf.gz --map chr20.b37.gmap.gz --region 20:2000000-3000000 --thread 4 --output phased.vcf.gz 339s * Version : 4.2.2 339s * Run date : 24/03/2024 - 13:11:17 339s 339s Files: 339s * Input VCF : [unphased.vcf.gz] 339s * Genetic Map : [chr20.b37.gmap.gz] 339s * Output VCF : [phased.vcf.gz] 339s 339s Parameters: 339s * Seed : 15052011 339s * Threads : 4 threads 339s * MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m] 339s * PBWT : Depth of PBWT neighbours to condition on: 4 339s * PBWT : Store indexes at variants [MAC>=2 / MDR<=0.5 / Dist=0.02 cM] 339s * HMM : K is variable / min W is 2.50cM / Ne is 15000 339s * HMM : Recombination rates given by genetic map 339s * HMM : AVX2 optimization inactive / Activating AVX2 substantially improves performance 339s 339s Initialization: 339s * VCF/BCF scanning ... * VCF/BCF scanning [N=203 / L=8651 / Reg=20:2000000-3000000] (0.12s) 339s * 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%] (0.15s) 339s * GMAP parsing [n=82962] (0.06s) 339s * cM interpolation [s=1236 / i=7415] (0.00s) 339s * Region length [999850 bp / 2.5 cM] 339s * HMM parameters [Ne=15000 / Error=0.0001 / #rare=2243] 339s * PBWT indexing [l=120] (0.00s) 339s * HAP update (0.01s) 339s * H2V transpose (0.00s) 339s * 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) 339s * Build genotype graphs [seg=62841] (0.03s) 339s 339s Burn-in iteration [1/5] 339s * V2H transpose (0.00s) 339s * 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) 339s * C2H transpose (0.00s) 343s * 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=291.522+/-9.938 / W=1.00Mb] (3.56s) 343s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 343s * HAP update (0.01s) 343s * H2V transpose (0.00s) 343s 343s Burn-in iteration [2/5] 343s * V2H transpose (0.00s) 343s * 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) 343s * C2H transpose (0.00s) 346s * HMM computations [0%] * HMM computations [1%] * HMM computations [2%] * HMM computations [3%] * HMM computations [4%] * HMM computations [5%] * HMM computations [6%] * HMM computations [7%] * HMM computations [8%] * HMM computations [9%] * HMM computations [10%] * HMM computations [11%] * HMM computations [12%] * HMM computations [13%] * HMM computations [14%] * HMM computations [15%] * HMM computations [16%] * HMM computations [17%] * HMM computations [18%] * HMM computations [19%] * HMM computations [20%] * HMM computations [21%] * HMM computations [22%] * HMM computations [23%] * HMM computations [24%] * HMM computations [25%] * HMM computations [26%] * HMM computations [27%] * HMM computations [28%] * HMM computations [29%] * HMM computations [30%] * HMM computations [31%] * HMM computations [32%] * HMM computations [33%] * HMM computations [34%] * HMM computations [35%] * HMM computations [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=254.576+/-12.725 / W=1.00Mb] (3.13s) 346s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 346s * HAP update (0.01s) 346s * H2V transpose (0.00s) 346s 346s Burn-in iteration [3/5] 346s * V2H transpose (0.00s) 346s * PBWT selection [0%] * PBWT selection [1%] * PBWT selection [2%] * PBWT selection [3%] * PBWT selection [4%] * PBWT selection [5%] * PBWT selection [6%] * PBWT selection [7%] * PBWT selection [8%] * PBWT selection [9%] * PBWT selection [10%] * PBWT selection [11%] * PBWT selection [12%] * PBWT selection [13%] * PBWT selection [14%] * PBWT selection [15%] * PBWT selection [16%] * PBWT selection [17%] * PBWT selection [18%] * PBWT selection [19%] * PBWT selection [20%] * PBWT selection [21%] * PBWT selection [22%] * PBWT selection [23%] * PBWT selection [24%] * PBWT selection [25%] * PBWT selection [26%] * PBWT selection [27%] * PBWT selection [28%] * PBWT selection [29%] * PBWT selection [30%] * PBWT selection [31%] * PBWT selection [32%] * PBWT selection [33%] * PBWT selection [34%] * PBWT selection [35%] * PBWT selection [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) 346s * C2H transpose (0.00s) 349s * 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=239.975+/-13.811 / W=1.00Mb] (2.93s) 349s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 349s * HAP update (0.01s) 349s * H2V transpose (0.00s) 349s 349s Burn-in iteration [4/5] 349s * V2H transpose (0.00s) 349s * 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) 349s * C2H transpose (0.00s) 352s * HMM computations [0%] * HMM computations [1%] * HMM computations [2%] * HMM computations [3%] * HMM computations [4%] * HMM computations [5%] * HMM computations [6%] * HMM computations [7%] * HMM computations [8%] * HMM computations [9%] * HMM computations [10%] * HMM computations [11%] * HMM computations [12%] * HMM computations [13%] * HMM computations [14%] * HMM computations [15%] * HMM computations [16%] * HMM computations [17%] * HMM computations [18%] * HMM computations [19%] * HMM computations [20%] * HMM computations [21%] * HMM computations [22%] * HMM computations [23%] * HMM computations [24%] * HMM computations [25%] * HMM computations [26%] * HMM computations [27%] * HMM computations [28%] * HMM computations [29%] * HMM computations [30%] * HMM computations [31%] * HMM computations [32%] * HMM computations [33%] * HMM computations [34%] * HMM computations [35%] * HMM computations [36%] * HMM computations [37%] * HMM computations [38%] * HMM computations [39%] * HMM computations [40%] * HMM computations [41%] * HMM computations [42%] * HMM computations [43%] * HMM computations [44%] * HMM computations [45%] * HMM computations [46%] * HMM computations [47%] * HMM computations [48%] * HMM computations [49%] * HMM computations [50%] * HMM computations [51%] * HMM computations [52%] * HMM computations [53%] * HMM computations [54%] * HMM computations [55%] * HMM computations [56%] * HMM computations [57%] * HMM computations [58%] * HMM computations [59%] * HMM computations [60%] * HMM computations [61%] * HMM computations [62%] * HMM computations [63%] * HMM computations [64%] * HMM computations [65%] * HMM computations [66%] * HMM computations [67%] * HMM computations [68%] * HMM computations [69%] * HMM computations [70%] * HMM computations [71%] * HMM computations [72%] * HMM computations [73%] * HMM computations [74%] * HMM computations [75%] * HMM computations [76%] * HMM computations [77%] * HMM computations [78%] * HMM computations [79%] * HMM computations [80%] * HMM computations [81%] * HMM computations [82%] * HMM computations [83%] * HMM computations [84%] * HMM computations [85%] * HMM computations [86%] * HMM computations [87%] * HMM computations [88%] * HMM computations [89%] * HMM computations [90%] * HMM computations [91%] * HMM computations [92%] * HMM computations [93%] * HMM computations [94%] * HMM computations [95%] * HMM computations [96%] * HMM computations [97%] * HMM computations [98%] * HMM computations [99%] * HMM computations [100%] * HMM computations [K=233.557+/-14.359 / W=1.00Mb] (2.85s) 352s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 352s * HAP update (0.01s) 352s * H2V transpose (0.00s) 352s 352s Burn-in iteration [5/5] 352s * V2H transpose (0.00s) 352s * PBWT selection [0%] * PBWT selection [1%] * PBWT selection [2%] * PBWT selection [3%] * PBWT selection [4%] * PBWT selection [5%] * PBWT selection [6%] * PBWT selection [7%] * PBWT selection [8%] * PBWT selection [9%] * PBWT selection [10%] * PBWT selection [11%] * PBWT selection [12%] * PBWT selection [13%] * PBWT selection [14%] * PBWT selection [15%] * PBWT selection [16%] * PBWT selection [17%] * PBWT selection [18%] * PBWT selection [19%] * PBWT selection [20%] * PBWT selection [21%] * PBWT selection [22%] * PBWT selection [23%] * PBWT selection [24%] * PBWT selection [25%] * PBWT selection [26%] * PBWT selection [27%] * PBWT selection [28%] * PBWT selection [29%] * PBWT selection [30%] * PBWT selection [31%] * 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) 352s * C2H transpose (0.00s) 355s * 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=228.212+/-13.714 / W=1.00Mb] (2.79s) 355s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 355s * HAP update (0.01s) 355s * H2V transpose (0.00s) 355s 355s Pruning iteration [1/1] 355s * V2H transpose (0.00s) 355s * 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) 355s * C2H transpose (0.00s) 358s * 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=226.039+/-14.317 / W=1.00Mb] (3.10s) 358s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 358s * HAP update (0.01s) 358s * H2V transpose (0.00s) 358s * Trimming [pc=41.23%] 358s 358s Burn-in iteration [1/1] 358s * V2H transpose (0.00s) 358s * 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) 358s * C2H transpose (0.00s) 360s * 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=225.768+/-15.273 / W=1.00Mb] (2.34s) 360s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 360s * HAP update (0.01s) 360s * H2V transpose (0.00s) 360s 360s Pruning iteration [1/1] 360s * V2H transpose (0.00s) 360s * 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) 360s * C2H transpose (0.00s) 363s * 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=220.951+/-15.118 / W=1.00Mb] (2.48s) 363s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 363s * HAP update (0.01s) 363s * H2V transpose (0.00s) 363s * Trimming [pc=64.98%] 363s 363s Burn-in iteration [1/1] 363s * V2H transpose (0.00s) 363s * 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) 363s * C2H transpose (0.00s) 365s * 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=217.675+/-14.848 / W=1.00Mb] (1.99s) 365s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 365s * HAP update (0.01s) 365s * H2V transpose (0.00s) 365s 365s Pruning iteration [1/1] 365s * V2H transpose (0.00s) 365s * 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) 365s * C2H transpose (0.00s) 367s * 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=215.064+/-16.465 / W=1.00Mb] (2.11s) 367s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 367s * HAP update (0.01s) 367s * H2V transpose (0.00s) 367s * Trimming [pc=77.64%] 367s 367s Main iteration [1/5] 367s * V2H transpose (0.00s) 367s * 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) 367s * C2H transpose (0.00s) 369s * 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=208.951+/-16.077 / W=1.00Mb] (1.81s) 369s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 369s * HAP update (0.01s) 369s * H2V transpose (0.00s) 369s 369s Main iteration [2/5] 369s * V2H transpose (0.00s) 369s * 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) 369s * C2H transpose (0.00s) 370s * 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=213.887+/-17.350 / W=1.00Mb] (1.84s) 370s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 371s * HAP update (0.01s) 371s * H2V transpose (0.00s) 371s 371s Main iteration [3/5] 371s * V2H transpose (0.00s) 371s * 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) 371s * C2H transpose (0.00s) 372s * 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=211.300+/-16.244 / W=1.00Mb] (1.82s) 372s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 372s * HAP update (0.01s) 372s * H2V transpose (0.00s) 372s 372s Main iteration [4/5] 372s * V2H transpose (0.00s) 372s * 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) 372s * C2H transpose (0.00s) 374s * 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=208.867+/-16.549 / W=1.00Mb] (1.81s) 374s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 374s * HAP update (0.01s) 374s * H2V transpose (0.00s) 374s 374s Main iteration [5/5] 374s * V2H transpose (0.00s) 374s * 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) 374s * C2H transpose (0.00s) 376s * 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=206.665+/-17.239 / W=1.00Mb] (1.79s) 376s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 376s * HAP update (0.01s) 376s * H2V transpose (0.00s) 376s 376s Finalization: 376s * HAP solving (0.01s) 376s * HAP update (0.01s) 376s * H2V transpose (0.00s) 376s * 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] (0.19s) 376s * Total running time = 37 seconds 376s + 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 376s 376s SHAPEIT 376s * Author : Olivier DELANEAU, University of Lausanne 376s * Contact : olivier.delaneau@gmail.com 376s * Version : 4.2.2 376s * Run date : 24/03/2024 - 13:11:54 376s 376s Files: 376s * Input VCF : [unphased.bcf] 376s * Reference VCF : [reference.bcf] 376s * Scaffold VCF : [scaffold.bcf] 376s * Genetic Map : [chr20.b37.gmap.gz] 376s * Output VCF : [phased.bcf] 376s * Output LOG : [phased.log] 376s 376s Parameters: 376s * Seed : 15052011 376s * Threads : 4 threads 376s * MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m] 376s * PBWT : Depth of PBWT neighbours to condition on: 4 376s * PBWT : Store indexes at variants [MAC>=2 / MDR<=0.5 / Dist=0.02 cM] 376s * HMM : K is variable / min W is 2.50cM / Ne is 15000 376s * HMM : Recombination rates given by genetic map 376s * HMM : Inform phasing using VCF/PS field / Error rate of PS field is 0.0001 376s * HMM : AVX2 optimization inactive / Activating AVX2 substantially improves performance 376s 376s Initialization: 376s * VCF/BCF scanning ... * VCF/BCF scanning [Nm=203 / Nr=300 / L=24990 / Reg=20] (0.09s) 377s * 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%] (0.32s) 377s * GMAP parsing [n=82962] (0.06s) 377s * cM interpolation [s=3296 / i=21694] (0.00s) 377s * Region length [2999624 bp / 6.6 cM] 377s * HMM parameters [Ne=15000 / Error=0.0001 / #rare=9606] 377s * PBWT indexing [l=328] (0.00s) 377s * HAP update (0.04s) 377s * H2V transpose (0.01s) 377s * PBWT phase sweep [0%] * PBWT phase sweep [1%] * PBWT phase sweep [2%] * PBWT phase sweep [3%] * PBWT phase sweep [4%] * PBWT phase sweep [5%] * PBWT phase sweep [6%] * PBWT phase sweep [7%] * PBWT phase sweep [8%] * PBWT phase sweep [9%] * PBWT phase sweep [10%] * PBWT phase sweep [11%] * PBWT phase sweep [12%] * PBWT phase sweep [13%] * PBWT phase sweep [14%] * PBWT phase sweep [15%] * PBWT phase sweep [16%] * PBWT phase sweep [17%] * PBWT phase sweep [18%] * PBWT phase sweep [19%] * PBWT phase sweep [20%] * PBWT phase sweep [21%] * PBWT phase sweep [22%] * PBWT phase sweep [23%] * PBWT phase sweep [24%] * PBWT phase sweep [25%] * PBWT phase sweep [26%] * PBWT phase sweep [27%] * PBWT phase sweep [28%] * PBWT phase sweep [29%] * PBWT phase sweep [30%] * PBWT phase sweep [31%] * PBWT phase sweep [32%] * PBWT phase sweep [33%] * PBWT phase sweep [34%] * PBWT phase sweep [35%] * PBWT phase sweep [36%] * PBWT phase sweep [37%] * PBWT phase sweep [38%] * PBWT phase sweep [39%] * PBWT phase sweep [40%] * PBWT phase sweep [41%] * PBWT phase sweep [42%] * PBWT phase sweep [43%] * PBWT phase sweep [44%] * PBWT phase sweep [45%] * PBWT phase sweep [46%] * PBWT phase sweep [47%] * PBWT phase sweep [48%] * PBWT phase sweep [49%] * PBWT phase sweep [50%] * PBWT phase sweep [51%] * PBWT phase sweep [52%] * PBWT phase sweep [53%] * PBWT phase sweep [54%] * PBWT phase sweep [55%] * PBWT phase sweep [56%] * PBWT phase sweep [57%] * PBWT phase sweep [58%] * PBWT phase sweep [59%] * PBWT phase sweep [60%] * PBWT phase sweep [61%] * PBWT phase sweep [62%] * PBWT phase sweep [63%] * PBWT phase sweep [64%] * PBWT phase sweep [65%] * PBWT phase sweep [66%] * PBWT phase sweep [67%] * PBWT phase sweep [68%] * PBWT phase sweep [69%] * PBWT phase sweep [70%] * PBWT phase sweep [71%] * PBWT phase sweep [72%] * PBWT phase sweep [73%] * PBWT phase sweep [74%] * PBWT phase sweep [75%] * PBWT phase sweep [76%] * PBWT phase sweep [77%] * PBWT phase sweep [78%] * PBWT phase sweep [79%] * PBWT phase sweep [80%] * PBWT phase sweep [81%] * PBWT phase sweep [82%] * PBWT phase sweep [83%] * PBWT phase sweep [84%] * PBWT phase sweep [85%] * PBWT phase sweep [86%] * PBWT phase sweep [87%] * PBWT phase sweep [88%] * PBWT phase sweep [89%] * PBWT phase sweep [90%] * PBWT phase sweep [91%] * PBWT phase sweep [92%] * PBWT phase sweep [93%] * PBWT phase sweep [94%] * PBWT phase sweep [95%] * PBWT phase sweep [96%] * PBWT phase sweep [97%] * PBWT phase sweep [98%] * PBWT phase sweep [99%] * PBWT phase sweep [100%] * PBWT phase sweep (0.25s) 377s * Build genotype graphs [seg=164449] (0.07s) 377s 377s Burn-in iteration [1/5] 377s * V2H transpose (0.00s) 377s * 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) 377s * C2H transpose (0.00s) 395s * 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=578.658+/-109.174 / W=2.26Mb] (18.22s) 395s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 395s * HAP update (0.01s) 395s * H2V transpose (0.00s) 395s 395s Burn-in iteration [2/5] 395s * V2H transpose (0.00s) 395s * 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) 395s * C2H transpose (0.00s) 410s * 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=454.193+/-122.453 / W=2.26Mb] (14.69s) 410s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 410s * HAP update (0.01s) 410s * H2V transpose (0.00s) 410s 410s Burn-in iteration [3/5] 410s * V2H transpose (0.00s) 410s * 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) 410s * C2H transpose (0.00s) 424s * 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=422.514+/-113.339 / W=2.21Mb] (13.72s) 424s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 424s * HAP update (0.01s) 424s * H2V transpose (0.00s) 424s 424s Burn-in iteration [4/5] 424s * V2H transpose (0.00s) 424s * 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) 424s * C2H transpose (0.00s) 438s * 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=420.149+/-114.956 / W=2.21Mb] (13.63s) 438s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 438s * HAP update (0.01s) 438s * H2V transpose (0.00s) 438s 438s Burn-in iteration [5/5] 438s * V2H transpose (0.00s) 438s * 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) 438s * C2H transpose (0.00s) 451s * 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=416.552+/-119.610 / W=2.17Mb] (13.69s) 451s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 451s * HAP update (0.01s) 451s * H2V transpose (0.00s) 451s 451s Pruning iteration [1/1] 451s * V2H transpose (0.00s) 451s * 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) 451s * C2H transpose (0.00s) 466s * 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=430.601+/-118.415 / W=2.23Mb] (14.86s) 466s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 466s * HAP update (0.01s) 466s * H2V transpose (0.00s) 466s * Trimming [pc=42.02%] 466s 466s Burn-in iteration [1/1] 466s * V2H transpose (0.00s) 466s * 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) 466s * C2H transpose (0.00s) 478s * 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=420.495+/-122.348 / W=2.20Mb] (11.60s) 478s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 478s * HAP update (0.01s) 478s * H2V transpose (0.00s) 478s 478s Pruning iteration [1/1] 478s * V2H transpose (0.00s) 478s * 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) 478s * C2H transpose (0.00s) 490s * 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=402.964+/-113.696 / W=2.18Mb] (11.54s) 490s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 490s * HAP update (0.01s) 490s * H2V transpose (0.00s) 490s * Trimming [pc=66.12%] 490s 490s Burn-in iteration [1/1] 490s * V2H transpose (0.00s) 490s * 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) 490s * C2H transpose (0.00s) 499s * 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=400.784+/-116.536 / W=2.19Mb] (9.86s) 499s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 499s * HAP update (0.01s) 499s * H2V transpose (0.00s) 499s 499s Pruning iteration [1/1] 499s * V2H transpose (0.00s) 500s * 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) 500s * C2H transpose (0.00s) 510s * 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=400.487+/-114.905 / W=2.23Mb] (10.06s) 510s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 510s * HAP update (0.01s) 510s * H2V transpose (0.00s) 510s * Trimming [pc=78.13%] 510s 510s Main iteration [1/5] 510s * V2H transpose (0.00s) 510s * 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) 510s * C2H transpose (0.00s) 519s * 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=396.404+/-114.984 / W=2.20Mb] (9.09s) 519s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 519s * HAP update (0.01s) 519s * H2V transpose (0.00s) 519s 519s Main iteration [2/5] 519s * V2H transpose (0.00s) 519s * 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) 519s * C2H transpose (0.00s) 528s * 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=408.590+/-113.337 / W=2.28Mb] (9.34s) 528s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 528s * HAP update (0.01s) 528s * H2V transpose (0.00s) 528s 528s Main iteration [3/5] 528s * V2H transpose (0.00s) 528s * 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) 528s * C2H transpose (0.00s) 537s * 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=394.968+/-115.532 / W=2.19Mb] (9.07s) 537s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 537s * HAP update (0.01s) 537s * H2V transpose (0.00s) 537s 537s Main iteration [4/5] 537s * V2H transpose (0.00s) 537s * 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) 537s * C2H transpose (0.00s) 547s * 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=412.172+/-117.084 / W=2.33Mb] (9.42s) 547s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 547s * HAP update (0.01s) 547s * H2V transpose (0.00s) 547s 547s Main iteration [5/5] 547s * V2H transpose (0.00s) 547s * 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) 547s * C2H transpose (0.00s) 556s * 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=387.644+/-112.996 / W=2.15Mb] (9.00s) 556s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 556s * HAP update (0.01s) 556s * H2V transpose (0.00s) 556s 556s Finalization: 556s * HAP solving (0.03s) 556s * HAP update (0.01s) 556s * H2V transpose (0.00s) 556s * 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] (0.29s) 556s * Total running time = 179 seconds 557s autopkgtest [13:14:55]: test run-sample-analysis: -----------------------] 557s autopkgtest [13:14:55]: test run-sample-analysis: - - - - - - - - - - results - - - - - - - - - - 557s run-sample-analysis PASS 557s autopkgtest [13:14:55]: @@@@@@@@@@@@@@@@@@@@ summary 557s run-sample-analysis PASS 618s Creating nova instance adt-noble-ppc64el-shapeit4-20240324-130538-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240321.img (UUID 024d6af5-fcba-4a84-85f9-01f41e1878d6)...