0s autopkgtest [08:17:14]: starting date and time: 2024-03-24 08:17:14+0000 0s autopkgtest [08:17:14]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [08:17:14]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.tfqey83s/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-3@bos01-ppc64el-16.secgroup --name adt-noble-ppc64el-shapeit4-20240324-081714-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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/ 288s autopkgtest [08:22:02]: testbed dpkg architecture: ppc64el 288s autopkgtest [08:22:02]: testbed apt version: 2.7.12 288s autopkgtest [08:22:02]: @@@@@@@@@@@@@@@@@@@@ test bed setup 289s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 289s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB] 289s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4004 kB] 290s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [494 kB] 290s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 290s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [698 kB] 290s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 290s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 290s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 290s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4265 kB] 290s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 290s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [60.8 kB] 290s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 293s Fetched 9715 kB in 2s (4111 kB/s) 294s Reading package lists... 296s Reading package lists... 296s Building dependency tree... 296s Reading state information... 297s Calculating upgrade... 297s The following packages will be REMOVED: 297s libssl3 297s The following NEW packages will be installed: 297s libssl3t64 297s The following packages have been kept back: 297s curl 297s The following packages will be upgraded: 297s openssl 297s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 297s Need to get 3151 kB of archives. 297s After this operation, 73.7 kB of additional disk space will be used. 297s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu2 [1026 kB] 297s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu2 [2125 kB] 298s Fetched 3151 kB in 1s (3927 kB/s) 298s (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.) 298s Preparing to unpack .../openssl_3.0.13-0ubuntu2_ppc64el.deb ... 298s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 298s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested: 298s wget depends on libssl3 (>= 3.0.0). 298s tnftp depends on libssl3 (>= 3.0.0). 298s tcpdump depends on libssl3 (>= 3.0.0). 298s systemd-resolved depends on libssl3 (>= 3.0.0). 298s systemd depends on libssl3 (>= 3.0.0). 298s sudo depends on libssl3 (>= 3.0.0). 298s rsync depends on libssl3 (>= 3.0.0). 298s python3-cryptography depends on libssl3 (>= 3.0.0). 298s openssh-server depends on libssl3 (>= 3.0.10). 298s openssh-client depends on libssl3 (>= 3.0.10). 298s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 298s libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0). 298s libssh-4:ppc64el depends on libssl3 (>= 3.0.0). 298s libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0). 298s libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0). 298s libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0). 298s libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0). 298s libnvme1 depends on libssl3 (>= 3.0.0). 298s libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0). 298s libkmod2:ppc64el depends on libssl3 (>= 3.0.0). 298s libfido2-1:ppc64el depends on libssl3 (>= 3.0.0). 298s libcurl4:ppc64el depends on libssl3 (>= 3.0.0). 298s libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0). 298s kmod depends on libssl3 (>= 3.0.0). 298s dhcpcd-base depends on libssl3 (>= 3.0.0). 298s bind9-libs:ppc64el depends on libssl3 (>= 3.0.0). 298s 298s (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.) 298s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ... 298s Selecting previously unselected package libssl3t64:ppc64el. 298s (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.) 298s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_ppc64el.deb ... 298s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 298s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 298s Setting up openssl (3.0.13-0ubuntu2) ... 298s Processing triggers for man-db (2.12.0-3) ... 299s Processing triggers for libc-bin (2.39-0ubuntu2) ... 299s Reading package lists... 299s Building dependency tree... 299s Reading state information... 299s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 300s sh: Attempting to set up Debian/Ubuntu apt sources automatically 300s sh: Distribution appears to be Ubuntu 301s Reading package lists... 301s Building dependency tree... 301s Reading state information... 301s eatmydata is already the newest version (131-1). 301s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 301s Reading package lists... 301s Building dependency tree... 301s Reading state information... 301s dbus is already the newest version (1.14.10-4ubuntu1). 301s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 301s Reading package lists... 301s Building dependency tree... 301s Reading state information... 302s rng-tools-debian is already the newest version (2.4). 302s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 302s Reading package lists... 302s Building dependency tree... 302s Reading state information... 302s The following packages will be REMOVED: 302s cloud-init* python3-configobj* python3-debconf* 302s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 302s After this operation, 3252 kB disk space will be freed. 302s (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 ... 70159 files and directories currently installed.) 302s Removing cloud-init (24.1.1-0ubuntu1) ... 303s Removing python3-configobj (5.0.8-3) ... 303s Removing python3-debconf (1.5.86) ... 303s Processing triggers for man-db (2.12.0-3) ... 303s (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 ... 69770 files and directories currently installed.) 303s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 304s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 304s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 304s invoke-rc.d: policy-rc.d denied execution of try-restart. 304s Reading package lists... 304s Building dependency tree... 304s Reading state information... 304s linux-generic is already the newest version (6.8.0-11.11+1). 304s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 305s Get:1 http://ftpmaster.internal/ubuntu noble InRelease [255 kB] 305s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 305s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 305s Get:4 http://ftpmaster.internal/ubuntu noble/universe Sources [19.8 MB] 306s Get:5 http://ftpmaster.internal/ubuntu noble/main Sources [1375 kB] 306s Get:6 http://ftpmaster.internal/ubuntu noble/multiverse Sources [295 kB] 306s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el Packages [1379 kB] 307s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el Packages [14.9 MB] 307s Get:9 http://ftpmaster.internal/ubuntu noble/multiverse ppc64el Packages [185 kB] 314s Fetched 38.2 MB in 8s (5038 kB/s) 314s Reading package lists... 314s Reading package lists... 314s Building dependency tree... 314s Reading state information... 315s Calculating upgrade... 315s The following packages will be upgraded: 315s fonts-ubuntu-console libbsd0 libc-bin libc6 locales python3-markupsafe 315s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 315s Need to get 8345 kB of archives. 315s After this operation, 67.6 kB disk space will be freed. 315s Get:1 http://ftpmaster.internal/ubuntu noble/main ppc64el libc6 ppc64el 2.39-0ubuntu6 [3274 kB] 315s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libc-bin ppc64el 2.39-0ubuntu6 [751 kB] 315s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libbsd0 ppc64el 0.12.1-1 [56.9 kB] 315s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el locales all 2.39-0ubuntu6 [4232 kB] 316s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-ubuntu-console all 0.869+git20240321-0ubuntu1 [18.7 kB] 316s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-markupsafe ppc64el 2.1.5-1build1 [13.2 kB] 316s Preconfiguring packages ... 316s Fetched 8345 kB in 1s (8732 kB/s) 316s (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 ... 69715 files and directories currently installed.) 316s Preparing to unpack .../libc6_2.39-0ubuntu6_ppc64el.deb ... 316s Unpacking libc6:ppc64el (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 316s Setting up libc6:ppc64el (2.39-0ubuntu6) ... 317s (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 ... 69715 files and directories currently installed.) 317s Preparing to unpack .../libc-bin_2.39-0ubuntu6_ppc64el.deb ... 317s Unpacking libc-bin (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 317s Setting up libc-bin (2.39-0ubuntu6) ... 317s (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 ... 69715 files and directories currently installed.) 317s Preparing to unpack .../libbsd0_0.12.1-1_ppc64el.deb ... 317s Unpacking libbsd0:ppc64el (0.12.1-1) over (0.11.8-1) ... 317s Preparing to unpack .../locales_2.39-0ubuntu6_all.deb ... 317s Unpacking locales (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 318s Preparing to unpack .../fonts-ubuntu-console_0.869+git20240321-0ubuntu1_all.deb ... 318s Unpacking fonts-ubuntu-console (0.869+git20240321-0ubuntu1) over (0.869-0ubuntu1) ... 318s Preparing to unpack .../python3-markupsafe_2.1.5-1build1_ppc64el.deb ... 318s Unpacking python3-markupsafe (2.1.5-1build1) over (2.1.5-1) ... 318s Setting up fonts-ubuntu-console (0.869+git20240321-0ubuntu1) ... 318s Setting up locales (2.39-0ubuntu6) ... 318s Generating locales (this might take a while)... 320s en_US.UTF-8... done 320s Generation complete. 320s Setting up python3-markupsafe (2.1.5-1build1) ... 320s Setting up libbsd0:ppc64el (0.12.1-1) ... 320s Processing triggers for man-db (2.12.0-3) ... 320s Processing triggers for libc-bin (2.39-0ubuntu6) ... 321s Reading package lists... 321s Building dependency tree... 321s Reading state information... 321s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 321s autopkgtest [08:22:35]: rebooting testbed after setup commands that affected boot 505s autopkgtest [08:25:39]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 507s autopkgtest [08:25:41]: @@@@@@@@@@@@@@@@@@@@ apt-source shapeit4 512s Get:1 http://ftpmaster.internal/ubuntu noble/universe shapeit4 4.2.2+dfsg-1build1 (dsc) [2158 B] 512s Get:2 http://ftpmaster.internal/ubuntu noble/universe shapeit4 4.2.2+dfsg-1build1 (tar) [59.0 MB] 512s Get:3 http://ftpmaster.internal/ubuntu noble/universe shapeit4 4.2.2+dfsg-1build1 (diff) [5280 B] 512s gpgv: Signature made Tue Dec 19 15:03:10 2023 UTC 512s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 512s gpgv: Can't check signature: No public key 512s dpkg-source: warning: cannot verify inline signature for ./shapeit4_4.2.2+dfsg-1build1.dsc: no acceptable signature found 513s autopkgtest [08:25:47]: testing package shapeit4 version 4.2.2+dfsg-1build1 513s autopkgtest [08:25:47]: build not needed 519s autopkgtest [08:25:53]: test run-sample-analysis: preparing testbed 523s Reading package lists... 523s Building dependency tree... 523s Reading state information... 523s Starting pkgProblemResolver with broken count: 0 523s Starting 2 pkgProblemResolver with broken count: 0 523s Done 523s The following additional packages will be installed: 523s libboost-iostreams1.83.0 libboost-program-options1.83.0 libdeflate0 libhts3 523s libhtscodecs2 shapeit4 shapeit4-example 523s The following NEW packages will be installed: 523s autopkgtest-satdep libboost-iostreams1.83.0 libboost-program-options1.83.0 523s libdeflate0 libhts3 libhtscodecs2 shapeit4 shapeit4-example 523s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. 523s Need to get 53.9 MB/53.9 MB of archives. 523s After this operation, 59.8 MB of additional disk space will be used. 523s Get:1 /tmp/autopkgtest.9Ep6CJ/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [716 B] 523s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libboost-iostreams1.83.0 ppc64el 1.83.0-2ubuntu1 [340 kB] 524s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libboost-program-options1.83.0 ppc64el 1.83.0-2ubuntu1 [421 kB] 524s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 524s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 524s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB] 524s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el shapeit4 ppc64el 4.2.2+dfsg-1build1 [186 kB] 524s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el shapeit4-example all 4.2.2+dfsg-1build1 [52.3 MB] 527s Fetched 53.9 MB in 3s (17.1 MB/s) 527s Selecting previously unselected package libboost-iostreams1.83.0:ppc64el. 527s (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.) 527s Preparing to unpack .../0-libboost-iostreams1.83.0_1.83.0-2ubuntu1_ppc64el.deb ... 527s Unpacking libboost-iostreams1.83.0:ppc64el (1.83.0-2ubuntu1) ... 527s Selecting previously unselected package libboost-program-options1.83.0:ppc64el. 527s Preparing to unpack .../1-libboost-program-options1.83.0_1.83.0-2ubuntu1_ppc64el.deb ... 527s Unpacking libboost-program-options1.83.0:ppc64el (1.83.0-2ubuntu1) ... 527s Selecting previously unselected package libdeflate0:ppc64el. 527s Preparing to unpack .../2-libdeflate0_1.19-1_ppc64el.deb ... 527s Unpacking libdeflate0:ppc64el (1.19-1) ... 527s Selecting previously unselected package libhtscodecs2:ppc64el. 527s Preparing to unpack .../3-libhtscodecs2_1.6.0-1_ppc64el.deb ... 527s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 527s Selecting previously unselected package libhts3:ppc64el. 527s Preparing to unpack .../4-libhts3_1.18+ds-1_ppc64el.deb ... 527s Unpacking libhts3:ppc64el (1.18+ds-1) ... 527s Selecting previously unselected package shapeit4. 527s Preparing to unpack .../5-shapeit4_4.2.2+dfsg-1build1_ppc64el.deb ... 527s Unpacking shapeit4 (4.2.2+dfsg-1build1) ... 527s Selecting previously unselected package shapeit4-example. 527s Preparing to unpack .../6-shapeit4-example_4.2.2+dfsg-1build1_all.deb ... 527s Unpacking shapeit4-example (4.2.2+dfsg-1build1) ... 527s Selecting previously unselected package autopkgtest-satdep. 527s Preparing to unpack .../7-1-autopkgtest-satdep.deb ... 527s Unpacking autopkgtest-satdep (0) ... 527s Setting up libhtscodecs2:ppc64el (1.6.0-1) ... 527s Setting up libboost-program-options1.83.0:ppc64el (1.83.0-2ubuntu1) ... 527s Setting up libdeflate0:ppc64el (1.19-1) ... 527s Setting up shapeit4-example (4.2.2+dfsg-1build1) ... 527s Setting up libboost-iostreams1.83.0:ppc64el (1.83.0-2ubuntu1) ... 527s Setting up libhts3:ppc64el (1.18+ds-1) ... 527s Setting up shapeit4 (4.2.2+dfsg-1build1) ... 527s Setting up autopkgtest-satdep (0) ... 527s Processing triggers for man-db (2.12.0-3) ... 528s Processing triggers for libc-bin (2.39-0ubuntu6) ... 530s (Reading database ... 69776 files and directories currently installed.) 530s Removing autopkgtest-satdep (0) ... 530s autopkgtest [08:26:04]: test run-sample-analysis: [----------------------- 531s + shapeit4 --input unphased.vcf.gz --map chr20.b37.gmap.gz --region 20:2000000-3000000 --thread 4 --output phased.vcf.gz 531s 531s SHAPEIT 531s * Author : Olivier DELANEAU, University of Lausanne 531s * Contact : olivier.delaneau@gmail.com 531s * Version : 4.2.2 531s * Run date : 24/03/2024 - 08:26:04 531s 531s Files: 531s * Input VCF : [unphased.vcf.gz] 531s * Genetic Map : [chr20.b37.gmap.gz] 531s * Output VCF : [phased.vcf.gz] 531s 531s Parameters: 531s * Seed : 15052011 531s * Threads : 4 threads 531s * MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m] 531s * PBWT : Depth of PBWT neighbours to condition on: 4 531s * PBWT : Store indexes at variants [MAC>=2 / MDR<=0.5 / Dist=0.02 cM] 531s * HMM : K is variable / min W is 2.50cM / Ne is 15000 531s * HMM : Recombination rates given by genetic map 531s * HMM : AVX2 optimization inactive / Activating AVX2 substantially improves performance 531s 531s Initialization: 531s * VCF/BCF scanning ... * VCF/BCF scanning [N=203 / L=8651 / Reg=20:2000000-3000000] (0.12s) 531s * 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%] (0.16s) 531s * GMAP parsing [n=82962] (0.06s) 531s * cM interpolation [s=1236 / i=7415] (0.00s) 531s * Region length [999850 bp / 2.5 cM] 531s * HMM parameters [Ne=15000 / Error=0.0001 / #rare=2243] 531s * PBWT indexing [l=120] (0.00s) 531s * HAP update (0.01s) 531s * H2V transpose (0.00s) 531s * 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) 531s * Build genotype graphs [seg=62841] (0.03s) 531s 531s Burn-in iteration [1/5] 531s * V2H transpose (0.00s) 531s * 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) 531s * C2H transpose (0.00s) 535s * 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] (3.59s) 535s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 535s * HAP update (0.01s) 535s * H2V transpose (0.00s) 535s 535s Burn-in iteration [2/5] 535s * V2H transpose (0.00s) 535s * 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) 535s * C2H transpose (0.00s) 538s * 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=251.719+/-12.988 / W=1.00Mb] (3.11s) 538s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 538s * HAP update (0.01s) 538s * H2V transpose (0.00s) 538s 538s Burn-in iteration [3/5] 538s * V2H transpose (0.00s) 538s * 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) 538s * C2H transpose (0.00s) 541s * 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=238.296+/-13.212 / W=1.00Mb] (2.93s) 541s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 541s * HAP update (0.01s) 541s * H2V transpose (0.00s) 541s 541s Burn-in iteration [4/5] 541s * V2H transpose (0.00s) 541s * 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) 541s * C2H transpose (0.00s) 544s * 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=232.025+/-13.087 / W=1.00Mb] (2.86s) 544s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 544s * HAP update (0.01s) 544s * H2V transpose (0.00s) 544s 544s Burn-in iteration [5/5] 544s * V2H transpose (0.00s) 544s * 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) 544s * C2H transpose (0.00s) 546s * 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=228.365+/-14.057 / W=1.00Mb] (2.81s) 546s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 546s * HAP update (0.01s) 546s * H2V transpose (0.00s) 546s 546s Pruning iteration [1/1] 546s * V2H transpose (0.00s) 546s * 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) 546s * C2H transpose (0.00s) 549s * 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=224.227+/-13.706 / W=1.00Mb] (3.09s) 549s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 549s * HAP update (0.01s) 549s * H2V transpose (0.00s) 549s * Trimming [pc=41.25%] 549s 549s Burn-in iteration [1/1] 549s * V2H transpose (0.00s) 549s * 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) 549s * C2H transpose (0.00s) 552s * 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=225.823+/-14.112 / W=1.00Mb] (2.34s) 552s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 552s * HAP update (0.01s) 552s * H2V transpose (0.00s) 552s 552s Pruning iteration [1/1] 552s * V2H transpose (0.00s) 552s * 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) 552s * C2H transpose (0.00s) 554s * 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=216.980+/-15.601 / W=1.00Mb] (2.45s) 554s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 554s * HAP update (0.01s) 554s * H2V transpose (0.00s) 554s * Trimming [pc=65.05%] 554s 554s Burn-in iteration [1/1] 554s * V2H transpose (0.00s) 554s * 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) 554s * 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=217.108+/-16.365 / W=1.00Mb] (1.98s) 556s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 556s * HAP update (0.01s) 556s * H2V transpose (0.00s) 556s 556s Pruning iteration [1/1] 556s * V2H transpose (0.00s) 556s * 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) 556s * C2H transpose (0.00s) 558s * 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=212.044+/-15.426 / W=1.00Mb] (2.07s) 558s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 558s * HAP update (0.01s) 558s * H2V transpose (0.00s) 558s * Trimming [pc=77.68%] 558s 558s Main iteration [1/5] 558s * V2H transpose (0.00s) 558s * 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) 558s * C2H transpose (0.00s) 560s * 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=210.680+/-15.697 / W=1.00Mb] (1.84s) 560s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 560s * HAP update (0.01s) 560s * H2V transpose (0.00s) 560s 560s Main iteration [2/5] 560s * V2H transpose (0.00s) 560s * 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) 560s * C2H transpose (0.00s) 562s * 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=209.833+/-16.706 / W=1.00Mb] (1.83s) 562s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 562s * HAP update (0.01s) 562s * H2V transpose (0.00s) 562s 562s Main iteration [3/5] 562s * V2H transpose (0.00s) 562s * 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) 562s * C2H transpose (0.00s) 564s * 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=207.882+/-16.845 / W=1.00Mb] (1.81s) 564s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 564s * HAP update (0.01s) 564s * H2V transpose (0.00s) 564s 564s Main iteration [4/5] 564s * V2H transpose (0.00s) 564s * 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) 564s * C2H transpose (0.00s) 566s * 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=208.941+/-17.672 / W=1.00Mb] (1.81s) 566s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 566s * HAP update (0.01s) 566s * H2V transpose (0.00s) 566s 566s Main iteration [5/5] 566s * V2H transpose (0.00s) 566s * 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) 566s * C2H transpose (0.00s) 568s * 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=209.764+/-16.256 / W=1.00Mb] (1.81s) 568s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 568s * HAP update (0.01s) 568s * H2V transpose (0.00s) 568s 568s Finalization: 568s * HAP solving (0.01s) 568s * HAP update (0.01s) 568s * H2V transpose (0.00s) 568s * 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) 568s * Total running time = 37 seconds 568s + 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 568s 568s SHAPEIT 568s * Author : Olivier DELANEAU, University of Lausanne 568s * Contact : olivier.delaneau@gmail.com 568s * Version : 4.2.2 568s * Run date : 24/03/2024 - 08:26:42 568s 568s Files: 568s * Input VCF : [unphased.bcf] 568s * Reference VCF : [reference.bcf] 568s * Scaffold VCF : [scaffold.bcf] 568s * Genetic Map : [chr20.b37.gmap.gz] 568s * Output VCF : [phased.bcf] 568s * Output LOG : [phased.log] 568s 568s Parameters: 568s * Seed : 15052011 568s * Threads : 4 threads 568s * MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m] 568s * PBWT : Depth of PBWT neighbours to condition on: 4 568s * PBWT : Store indexes at variants [MAC>=2 / MDR<=0.5 / Dist=0.02 cM] 568s * HMM : K is variable / min W is 2.50cM / Ne is 15000 568s * HMM : Recombination rates given by genetic map 568s * HMM : Inform phasing using VCF/PS field / Error rate of PS field is 0.0001 568s * HMM : AVX2 optimization inactive / Activating AVX2 substantially improves performance 568s 568s Initialization: 568s * VCF/BCF scanning ... * VCF/BCF scanning [Nm=203 / Nr=300 / L=24990 / Reg=20] (0.09s) 568s * 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) 568s * GMAP parsing [n=82962] (0.06s) 568s * cM interpolation [s=3296 / i=21694] (0.00s) 568s * Region length [2999624 bp / 6.6 cM] 568s * HMM parameters [Ne=15000 / Error=0.0001 / #rare=9606] 568s * PBWT indexing [l=328] (0.00s) 568s * HAP update (0.04s) 568s * H2V transpose (0.01s) 569s * 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) 569s * Build genotype graphs [seg=164449] (0.07s) 569s 569s Burn-in iteration [1/5] 569s * V2H transpose (0.00s) 569s * 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) 569s * C2H transpose (0.00s) 587s * 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=574.414+/-107.998 / W=2.23Mb] (18.27s) 587s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 587s * HAP update (0.01s) 587s * H2V transpose (0.00s) 587s 587s Burn-in iteration [2/5] 587s * V2H transpose (0.00s) 587s * 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) 587s * C2H transpose (0.00s) 602s * 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=451.657+/-124.795 / W=2.22Mb] (14.80s) 602s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 602s * HAP update (0.01s) 602s * H2V transpose (0.00s) 602s 602s Burn-in iteration [3/5] 602s * V2H transpose (0.00s) 602s * 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) 602s * C2H transpose (0.00s) 616s * 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=444.494+/-116.605 / W=2.33Mb] (14.33s) 616s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 616s * HAP update (0.01s) 616s * H2V transpose (0.00s) 616s 616s Burn-in iteration [4/5] 616s * V2H transpose (0.00s) 616s * 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) 616s * C2H transpose (0.00s) 630s * 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=422.735+/-116.006 / W=2.18Mb] (13.81s) 630s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 630s * HAP update (0.01s) 630s * H2V transpose (0.00s) 630s 630s Burn-in iteration [5/5] 630s * V2H transpose (0.00s) 630s * 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) 630s * C2H transpose (0.00s) 644s * 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=432.483+/-116.103 / W=2.28Mb] (13.92s) 644s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 644s * HAP update (0.01s) 644s * H2V transpose (0.00s) 644s 644s Pruning iteration [1/1] 644s * V2H transpose (0.00s) 644s * 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) 644s * C2H transpose (0.00s) 658s * 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=410.153+/-120.299 / W=2.12Mb] (14.31s) 658s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 658s * HAP update (0.01s) 658s * H2V transpose (0.00s) 658s * Trimming [pc=42.04%] 658s 658s Burn-in iteration [1/1] 658s * V2H transpose (0.00s) 659s * 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) 659s * C2H transpose (0.00s) 670s * 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=422.402+/-123.316 / W=2.21Mb] (11.66s) 670s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 670s * HAP update (0.01s) 670s * H2V transpose (0.00s) 670s 670s Pruning iteration [1/1] 670s * V2H transpose (0.00s) 670s * 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) 670s * C2H transpose (0.00s) 682s * 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=408.797+/-114.179 / W=2.21Mb] (11.78s) 682s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 682s * HAP update (0.01s) 682s * H2V transpose (0.00s) 682s * Trimming [pc=66.14%] 682s 682s Burn-in iteration [1/1] 682s * V2H transpose (0.00s) 682s * 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) 682s * C2H transpose (0.00s) 692s * 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=407.699+/-115.009 / W=2.24Mb] (9.90s) 692s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 692s * HAP update (0.01s) 692s * H2V transpose (0.00s) 692s 692s Pruning iteration [1/1] 692s * V2H transpose (0.00s) 692s * 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) 692s * C2H transpose (0.00s) 702s * 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=404.298+/-113.390 / W=2.24Mb] (10.11s) 702s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 702s * HAP update (0.01s) 702s * H2V transpose (0.00s) 702s * Trimming [pc=78.13%] 702s 702s Main iteration [1/5] 702s * V2H transpose (0.00s) 702s * 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) 702s * C2H transpose (0.00s) 711s * 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=393.711+/-113.793 / W=2.18Mb] (9.11s) 711s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 711s * HAP update (0.01s) 711s * H2V transpose (0.00s) 711s 711s Main iteration [2/5] 711s * V2H transpose (0.00s) 711s * 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) 711s * C2H transpose (0.00s) 720s * 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=389.557+/-115.016 / W=2.18Mb] (9.00s) 720s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 720s * HAP update (0.01s) 720s * H2V transpose (0.00s) 720s 720s Main iteration [3/5] 720s * V2H transpose (0.00s) 720s * 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) 720s * C2H transpose (0.00s) 729s * 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=388.806+/-113.558 / W=2.16Mb] (8.95s) 729s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 729s * HAP update (0.01s) 729s * H2V transpose (0.00s) 729s 729s Main iteration [4/5] 729s * V2H transpose (0.00s) 730s * 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) 730s * C2H transpose (0.00s) 739s * 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=402.598+/-114.075 / W=2.25Mb] (9.28s) 739s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 739s * HAP update (0.01s) 739s * H2V transpose (0.00s) 739s 739s Main iteration [5/5] 739s * V2H transpose (0.00s) 739s * 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) 739s * C2H transpose (0.00s) 748s * 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=399.215+/-110.442 / W=2.23Mb] (9.18s) 748s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 748s * HAP update (0.01s) 748s * H2V transpose (0.00s) 748s 748s Finalization: 748s * HAP solving (0.03s) 748s * HAP update (0.01s) 748s * H2V transpose (0.00s) 748s * 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) 748s * Total running time = 180 seconds 749s autopkgtest [08:29:43]: test run-sample-analysis: -----------------------] 749s autopkgtest [08:29:43]: test run-sample-analysis: - - - - - - - - - - results - - - - - - - - - - 749s run-sample-analysis PASS 750s autopkgtest [08:29:44]: @@@@@@@@@@@@@@@@@@@@ summary 750s run-sample-analysis PASS 765s Creating nova instance adt-noble-ppc64el-shapeit4-20240324-081714-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-ppc64el-server-20240321.img (UUID 024d6af5-fcba-4a84-85f9-01f41e1878d6)...