0s autopkgtest [16:43:58]: starting date and time: 2025-03-15 16:43:58+0000 0s autopkgtest [16:43:58]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [16:43:58]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.t7qm9maz/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade shapeit4 --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-20.secgroup --name adt-plucky-arm64-shapeit4-20250315-164358-juju-7f2275-prod-proposed-migration-environment-2-2ed5a99e-4290-4c3e-9599-541dbe323299 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 164s autopkgtest [16:46:42]: testbed dpkg architecture: arm64 165s autopkgtest [16:46:43]: testbed apt version: 2.9.33 165s autopkgtest [16:46:43]: @@@@@@@@@@@@@@@@@@@@ test bed setup 165s autopkgtest [16:46:43]: testbed release detected to be: None 166s autopkgtest [16:46:44]: updating testbed package index (apt update) 166s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 167s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 167s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 167s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 167s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 167s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 167s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 167s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [111 kB] 167s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1856 B] 167s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 168s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [324 kB] 168s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [14.7 kB] 168s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 168s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [268 B] 168s Fetched 1078 kB in 2s (642 kB/s) 169s Reading package lists... 170s Reading package lists... 170s Building dependency tree... 170s Reading state information... 170s Calculating upgrade... 171s Calculating upgrade... 171s The following packages will be upgraded: 171s pinentry-curses python3-jinja2 strace 171s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 171s Need to get 647 kB of archives. 171s After this operation, 11.3 kB of additional disk space will be used. 171s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 172s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pinentry-curses arm64 1.3.1-2ubuntu3 [39.2 kB] 172s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 172s Fetched 647 kB in 1s (636 kB/s) 173s (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 ... 117701 files and directories currently installed.) 173s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 173s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 173s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_arm64.deb ... 173s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 173s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 173s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 173s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 173s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 173s Setting up strace (6.13+ds-1ubuntu1) ... 173s Processing triggers for man-db (2.13.0-1) ... 174s Reading package lists... 174s Building dependency tree... 174s Reading state information... 175s Solving dependencies... 175s The following packages will be REMOVED: 175s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 175s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 175s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 175s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 175s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 175s After this operation, 267 MB disk space will be freed. 175s (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 ... 117701 files and directories currently installed.) 175s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 175s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 175s Removing libpython3.12t64:arm64 (3.12.9-1) ... 175s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 175s Removing libnsl2:arm64 (1.3.0-3build3) ... 175s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 176s Removing libunwind8:arm64 (1.6.2-3.1) ... 176s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 176s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 178s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 178s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 178s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 178s /etc/kernel/postrm.d/initramfs-tools: 178s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 178s /etc/kernel/postrm.d/zz-flash-kernel: 178s flash-kernel: Kernel 6.11.0-8-generic has been removed. 178s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 178s /etc/kernel/postrm.d/zz-update-grub: 178s Sourcing file `/etc/default/grub' 178s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 178s Generating grub configuration file ... 179s Found linux image: /boot/vmlinuz-6.14.0-10-generic 179s Found initrd image: /boot/initrd.img-6.14.0-10-generic 179s Warning: os-prober will not be executed to detect other bootable partitions. 179s Systems on them will not be added to the GRUB boot configuration. 179s Check GRUB_DISABLE_OS_PROBER documentation entry. 179s Adding boot menu entry for UEFI Firmware Settings ... 179s done 179s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 180s Processing triggers for libc-bin (2.41-1ubuntu1) ... 180s (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 ... 81650 files and directories currently installed.) 180s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 180s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 180s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 180s autopkgtest [16:46:58]: upgrading testbed (apt dist-upgrade and autopurge) 180s Reading package lists... 180s Building dependency tree... 180s Reading state information... 181s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 181s Starting 2 pkgProblemResolver with broken count: 0 181s Done 182s Entering ResolveByKeep 182s 182s Calculating upgrade... 183s The following packages will be upgraded: 183s libc-bin libc-dev-bin libc6 libc6-dev locales 183s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 183s Need to get 9530 kB of archives. 183s After this operation, 0 B of additional disk space will be used. 183s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 185s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 185s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 189s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 189s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 195s Preconfiguring packages ... 195s Fetched 9530 kB in 12s (791 kB/s) 195s (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 ... 81647 files and directories currently installed.) 195s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 195s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 195s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 195s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 196s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 196s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 196s Setting up libc6:arm64 (2.41-1ubuntu2) ... 196s (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 ... 81647 files and directories currently installed.) 196s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 196s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 196s Setting up libc-bin (2.41-1ubuntu2) ... 196s (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 ... 81647 files and directories currently installed.) 196s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 196s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 196s Setting up locales (2.41-1ubuntu2) ... 197s Generating locales (this might take a while)... 199s en_US.UTF-8... done 199s Generation complete. 199s Setting up libc-dev-bin (2.41-1ubuntu2) ... 199s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 199s Processing triggers for man-db (2.13.0-1) ... 200s Processing triggers for systemd (257.3-1ubuntu3) ... 201s Reading package lists... 201s Building dependency tree... 201s Reading state information... 202s Starting pkgProblemResolver with broken count: 0 202s Starting 2 pkgProblemResolver with broken count: 0 202s Done 202s Solving dependencies... 203s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 203s autopkgtest [16:47:21]: rebooting testbed after setup commands that affected boot 226s autopkgtest [16:47:44]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 229s autopkgtest [16:47:47]: @@@@@@@@@@@@@@@@@@@@ apt-source shapeit4 287s Get:1 http://ftpmaster.internal/ubuntu plucky/universe shapeit4 4.2.2+dfsg-1build3 (dsc) [2237 B] 287s Get:2 http://ftpmaster.internal/ubuntu plucky/universe shapeit4 4.2.2+dfsg-1build3 (tar) [59.0 MB] 287s Get:3 http://ftpmaster.internal/ubuntu plucky/universe shapeit4 4.2.2+dfsg-1build3 (diff) [5424 B] 287s gpgv: Signature made Mon Apr 1 08:00:11 2024 UTC 287s gpgv: using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984 287s gpgv: Can't check signature: No public key 287s dpkg-source: warning: cannot verify inline signature for ./shapeit4_4.2.2+dfsg-1build3.dsc: no acceptable signature found 288s autopkgtest [16:48:46]: testing package shapeit4 version 4.2.2+dfsg-1build3 288s autopkgtest [16:48:46]: build not needed 292s autopkgtest [16:48:50]: test run-sample-analysis: preparing testbed 293s Reading package lists... 293s Building dependency tree... 293s Reading state information... 294s Starting pkgProblemResolver with broken count: 0 294s Starting 2 pkgProblemResolver with broken count: 0 294s Done 295s The following NEW packages will be installed: 295s libboost-iostreams1.83.0 libboost-program-options1.83.0 libdeflate0 295s libhts3t64 libhtscodecs2 shapeit4 shapeit4-example 295s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 295s Need to get 53.6 MB of archives. 295s After this operation, 59.3 MB of additional disk space will be used. 295s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libboost-iostreams1.83.0 arm64 1.83.0-4.1ubuntu2 [259 kB] 295s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libboost-program-options1.83.0 arm64 1.83.0-4.1ubuntu2 [319 kB] 296s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 296s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.1-2 [82.7 kB] 296s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts3t64 arm64 1.21+ds-1 [441 kB] 296s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 shapeit4 arm64 4.2.2+dfsg-1build3 [169 kB] 297s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 shapeit4-example all 4.2.2+dfsg-1build3 [52.3 MB] 356s Fetched 53.6 MB in 1min 1s (882 kB/s) 356s Selecting previously unselected package libboost-iostreams1.83.0:arm64. 356s (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 ... 81647 files and directories currently installed.) 356s Preparing to unpack .../0-libboost-iostreams1.83.0_1.83.0-4.1ubuntu2_arm64.deb ... 356s Unpacking libboost-iostreams1.83.0:arm64 (1.83.0-4.1ubuntu2) ... 356s Selecting previously unselected package libboost-program-options1.83.0:arm64. 356s Preparing to unpack .../1-libboost-program-options1.83.0_1.83.0-4.1ubuntu2_arm64.deb ... 356s Unpacking libboost-program-options1.83.0:arm64 (1.83.0-4.1ubuntu2) ... 356s Selecting previously unselected package libdeflate0:arm64. 356s Preparing to unpack .../2-libdeflate0_1.23-1_arm64.deb ... 356s Unpacking libdeflate0:arm64 (1.23-1) ... 356s Selecting previously unselected package libhtscodecs2:arm64. 356s Preparing to unpack .../3-libhtscodecs2_1.6.1-2_arm64.deb ... 356s Unpacking libhtscodecs2:arm64 (1.6.1-2) ... 356s Selecting previously unselected package libhts3t64:arm64. 356s Preparing to unpack .../4-libhts3t64_1.21+ds-1_arm64.deb ... 356s Unpacking libhts3t64:arm64 (1.21+ds-1) ... 356s Selecting previously unselected package shapeit4. 356s Preparing to unpack .../5-shapeit4_4.2.2+dfsg-1build3_arm64.deb ... 356s Unpacking shapeit4 (4.2.2+dfsg-1build3) ... 356s Selecting previously unselected package shapeit4-example. 356s Preparing to unpack .../6-shapeit4-example_4.2.2+dfsg-1build3_all.deb ... 356s Unpacking shapeit4-example (4.2.2+dfsg-1build3) ... 357s Setting up libhtscodecs2:arm64 (1.6.1-2) ... 357s Setting up libboost-program-options1.83.0:arm64 (1.83.0-4.1ubuntu2) ... 357s Setting up libdeflate0:arm64 (1.23-1) ... 357s Setting up shapeit4-example (4.2.2+dfsg-1build3) ... 357s Setting up libboost-iostreams1.83.0:arm64 (1.83.0-4.1ubuntu2) ... 357s Setting up libhts3t64:arm64 (1.21+ds-1) ... 357s Setting up shapeit4 (4.2.2+dfsg-1build3) ... 357s Processing triggers for man-db (2.13.0-1) ... 357s Processing triggers for libc-bin (2.41-1ubuntu2) ... 359s autopkgtest [16:49:57]: test run-sample-analysis: [----------------------- 359s + shapeit4 --input unphased.vcf.gz --map chr20.b37.gmap.gz --region 20:2000000-3000000 --thread 4 --output phased.vcf.gz 359s 359s SHAPEIT 359s * Author : Olivier DELANEAU, University of Lausanne 359s * Contact : olivier.delaneau@gmail.com 359s * Version : 4.2.2 359s * Run date : 15/03/2025 - 16:49:57 359s 359s Files: 359s * Input VCF : [unphased.vcf.gz] 359s * Genetic Map : [chr20.b37.gmap.gz] 359s * Output VCF : [phased.vcf.gz] 359s 359s Parameters: 359s * Seed : 15052011 359s * Threads : 4 threads 359s * MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m] 359s * PBWT : Depth of PBWT neighbours to condition on: 4 359s * PBWT : Store indexes at variants [MAC>=2 / MDR<=0.5 / Dist=0.02 cM] 359s * HMM : K is variable / min W is 2.50cM / Ne is 15000 359s * HMM : Recombination rates given by genetic map 359s * HMM : AVX2 optimization inactive / Activating AVX2 substantially improves performance 359s 359s Initialization: 359s * VCF/BCF scanning ... * VCF/BCF scanning [N=203 / L=8651 / Reg=20:2000000-3000000] (0.06s) 359s * 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%] (0.10s) 359s * GMAP parsing [n=82962] (0.04s) 359s * cM interpolation [s=1236 / i=7415] (0.00s) 359s * Region length [999850 bp / 2.5 cM] 359s * HMM parameters [Ne=15000 / Error=0.0001 / #rare=2243] 359s * PBWT indexing [l=120] (0.00s) 359s * HAP update (0.01s) 359s * H2V transpose (0.00s) 359s * 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%] * 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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 (0.05s) 359s * Build genotype graphs [seg=62841] (0.01s) 359s 359s Burn-in iteration [1/5] 359s * V2H transpose (0.00s) 359s * 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) 359s * C2H transpose (0.00s) 361s * 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 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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] (1.52s) 361s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 361s * HAP update (0.01s) 361s * H2V transpose (0.00s) 361s 361s Burn-in iteration [2/5] 361s * V2H transpose (0.00s) 361s * 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 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computations [99%] * HMM computations [100%] * HMM computations [K=252.931+/-12.315 / W=1.00Mb] (1.24s) 362s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 362s * HAP update (0.01s) 362s * H2V transpose (0.00s) 362s 362s Burn-in iteration [3/5] 362s * V2H transpose (0.00s) 362s * 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 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[100%] * HMM computations [K=210.995+/-17.151 / W=1.00Mb] (0.69s) 374s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 374s * HAP update (0.01s) 374s * H2V transpose (0.00s) 374s 374s Finalization: 374s * HAP solving (0.01s) 374s * HAP update (0.01s) 374s * H2V transpose (0.00s) 374s * 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 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[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] (0.10s) 374s * Total running time = 15 seconds 374s 374s SHAPEIT 374s * Author : Olivier DELANEAU, University of Lausanne 374s * Contact : olivier.delaneau@gmail.com 374s * Version : 4.2.2 374s * Run date : 15/03/2025 - 16:50:12 374s 374s Files: 374s * Input VCF : [unphased.bcf] 374s * Reference VCF : [reference.bcf] 374s * Scaffold VCF : [scaffold.bcf] 374s * Genetic Map : [chr20.b37.gmap.gz] 374s * Output VCF : [phased.bcf] 374s * Output LOG : [phased.log] 374s 374s Parameters: 374s * Seed : 15052011 374s * Threads : 4 threads 374s * MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m] 374s * PBWT : Depth of PBWT neighbours to condition on: 4 374s * PBWT : Store indexes at variants [MAC>=2 / MDR<=0.5 / Dist=0.02 cM] 374s * HMM : K is variable / min W is 2.50cM / Ne is 15000 374s * HMM : Recombination rates given by genetic map 374s * HMM : Inform phasing using VCF/PS field / Error rate of PS field is 0.0001 374s * HMM : AVX2 optimization inactive / Activating AVX2 substantially improves performance 374s 374s Initialization: 374s * VCF/BCF scanning ... + 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 374s * VCF/BCF scanning [Nm=203 / Nr=300 / L=24990 / Reg=20] (0.04s) 375s * 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 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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%] (0.29s) 375s * GMAP parsing [n=82962] (0.04s) 375s * cM interpolation [s=3296 / i=21694] (0.01s) 375s * Region length [2999624 bp / 6.6 cM] 375s * HMM parameters [Ne=15000 / Error=0.0001 / #rare=9606] 375s * PBWT indexing [l=328] (0.00s) 375s * HAP update (0.02s) 375s * H2V transpose (0.02s) 375s * 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 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sweep (0.23s) 375s * Build genotype graphs [seg=164449] (0.04s) 375s 375s Burn-in iteration [1/5] 375s * V2H transpose (0.01s) 375s * 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%] * 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415s * V2H transpose (0.01s) 415s * 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 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constraints [#inds=0 / #contraints=0 / #merged = 0] 420s * HAP update (0.01s) 420s * H2V transpose (0.01s) 420s 420s Pruning iteration [1/1] 420s * V2H transpose (0.01s) 420s * 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 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computations [98%] * HMM computations [99%] * HMM computations [100%] * HMM computations [K=419.508+/-118.663 / W=2.31Mb] (5.20s) 425s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 426s * HAP update (0.01s) 426s * H2V transpose (0.01s) 426s * Trimming [pc=66.13%] 426s 426s Burn-in iteration [1/1] 426s * V2H transpose (0.01s) 426s * 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 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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) 426s * C2H transpose (0.00s) 430s * 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 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computations [78%] * HMM computations [79%] * HMM computations [80%] * HMM computations [81%] * HMM computations [82%] * HMM computations [83%] * HMM computations [84%] * HMM computations [85%] * HMM computations [86%] * HMM computations [87%] * HMM computations [88%] * HMM computations [89%] * HMM computations [90%] * HMM computations [91%] * HMM computations [92%] * HMM computations [93%] * HMM computations [94%] * HMM computations [95%] * HMM computations [96%] * HMM computations [97%] * HMM computations [98%] * HMM computations [99%] * HMM computations [100%] * HMM computations [K=400.000+/-114.137 / W=2.22Mb] (3.85s) 438s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 438s * HAP update (0.01s) 438s * H2V transpose (0.01s) 438s 438s Main iteration [2/5] 438s * V2H transpose (0.01s) 438s * PBWT selection [0%] * PBWT selection [1%] * PBWT selection [2%] * PBWT selection [3%] * PBWT selection [4%] * PBWT selection [5%] * PBWT selection [6%] * PBWT selection [7%] * PBWT 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PBWT selection [95%] * PBWT selection [96%] * PBWT selection [97%] * PBWT selection [98%] * PBWT selection [99%] * PBWT selection [100%] * PBWT selection (0.04s) 438s * C2H transpose (0.00s) 442s * HMM computations [0%] * HMM computations [1%] * HMM computations [2%] * HMM computations [3%] * HMM computations [4%] * HMM computations [5%] * HMM computations [6%] * HMM computations [7%] * HMM computations [8%] * HMM computations [9%] * HMM computations [10%] * HMM computations [11%] * HMM computations [12%] * HMM computations [13%] * HMM computations [14%] * HMM computations [15%] * HMM computations [16%] * HMM computations [17%] * HMM computations [18%] * HMM computations [19%] * HMM computations [20%] * HMM computations [21%] * HMM computations [22%] * HMM computations [23%] * HMM computations [24%] * HMM computations [25%] * HMM computations [26%] * HMM computations [27%] * HMM computations [28%] * HMM computations [29%] * HMM computations [30%] * HMM computations [31%] * HMM 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computations [72%] * HMM computations [73%] * HMM computations [74%] * HMM computations [75%] * HMM computations [76%] * HMM computations [77%] * HMM computations [78%] * HMM computations [79%] * HMM computations [80%] * HMM computations [81%] * HMM computations [82%] * HMM computations [83%] * HMM computations [84%] * HMM computations [85%] * HMM computations [86%] * HMM computations [87%] * HMM computations [88%] * HMM computations [89%] * HMM computations [90%] * HMM computations [91%] * HMM computations [92%] * HMM computations [93%] * HMM computations [94%] * HMM computations [95%] * HMM computations [96%] * HMM computations [97%] * HMM computations [98%] * HMM computations [99%] * HMM computations [100%] * HMM computations [K=386.194+/-112.654 / W=2.15Mb] (3.73s) 442s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 442s * HAP update (0.01s) 442s * H2V transpose (0.01s) 442s 442s Main iteration [3/5] 442s * V2H transpose (0.01s) 442s * PBWT selection [0%] * PBWT 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HAP update (0.01s) 446s * H2V transpose (0.01s) 446s 446s Main iteration [4/5] 446s * V2H transpose (0.01s) 446s * PBWT selection [0%] * PBWT selection [1%] * PBWT selection [2%] * PBWT selection [3%] * PBWT selection [4%] * PBWT selection [5%] * PBWT selection [6%] * PBWT selection [7%] * PBWT selection [8%] * PBWT selection [9%] * PBWT selection [10%] * PBWT selection [11%] * PBWT selection [12%] * PBWT selection [13%] * PBWT selection [14%] * PBWT selection [15%] * PBWT selection [16%] * PBWT selection [17%] * PBWT selection [18%] * PBWT selection [19%] * PBWT selection [20%] * PBWT selection [21%] * PBWT selection [22%] * PBWT selection [23%] * PBWT selection [24%] * PBWT selection [25%] * PBWT selection [26%] * PBWT selection [27%] * PBWT selection [28%] * PBWT selection [29%] * PBWT selection [30%] * PBWT selection [31%] * PBWT selection [32%] * PBWT selection [33%] * PBWT selection [34%] * PBWT selection [35%] * PBWT selection [36%] * PBWT selection [37%] * PBWT selection [38%] 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[100%] * HMM computations [K=395.487+/-111.068 / W=2.23Mb] (3.81s) 450s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 450s * HAP update (0.02s) 450s * H2V transpose (0.01s) 450s 450s Main iteration [5/5] 450s * V2H transpose (0.01s) 450s * 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%] 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computations [95%] * HMM computations [96%] * HMM computations [97%] * HMM computations [98%] * HMM computations [99%] * HMM computations [100%] * HMM computations [K=392.331+/-115.658 / W=2.22Mb] (3.78s) 454s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 454s * HAP update (0.01s) 454s * H2V transpose (0.01s) 454s 454s Finalization: 454s * HAP solving (0.03s) 454s * HAP update (0.01s) 454s * H2V transpose (0.01s) 454s * 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] (0.13s) 454s * Total running time = 79 seconds 454s autopkgtest [16:51:32]: test run-sample-analysis: -----------------------] 455s autopkgtest [16:51:33]: test run-sample-analysis: - - - - - - - - - - results - - - - - - - - - - 455s run-sample-analysis PASS 455s autopkgtest [16:51:33]: @@@@@@@@@@@@@@@@@@@@ summary 455s run-sample-analysis PASS 475s nova [W] Using flock in prodstack6-arm64 475s Creating nova instance adt-plucky-arm64-shapeit4-20250315-164358-juju-7f2275-prod-proposed-migration-environment-2-2ed5a99e-4290-4c3e-9599-541dbe323299 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 475s nova [W] Timed out waiting for b827b603-efe8-4c86-b842-c692a7558f39 to get deleted.