0s autopkgtest [21:26:54]: starting date and time: 2024-03-25 21:26:54+0000 0s autopkgtest [21:26:54]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [21:26:54]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work._byev6jt/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:shapeit4,src:curl,src:gnutls28,src:htslib,src:libpsl,src:nettle,src:openssl --apt-upgrade shapeit4 --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=shapeit4/4.2.2+dfsg-1build2 curl/8.5.0-2ubuntu8 gnutls28/3.8.3-1.1ubuntu2 htslib/1.19+ds-1.1build2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-s390x-12.secgroup --name adt-noble-s390x-shapeit4-20240325-212654-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 94s autopkgtest [21:28:28]: testbed dpkg architecture: s390x 94s autopkgtest [21:28:28]: testbed apt version: 2.7.12 94s autopkgtest [21:28:28]: @@@@@@@@@@@@@@@@@@@@ test bed setup 95s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 95s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [497 kB] 95s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.0 kB] 95s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4038 kB] 97s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [7608 B] 97s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [692 kB] 97s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 97s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 97s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 97s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4136 kB] 99s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 99s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [47.8 kB] 99s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 100s Fetched 9603 kB in 5s (2082 kB/s) 100s Reading package lists... 103s Reading package lists... 103s Building dependency tree... 103s Reading state information... 103s Calculating upgrade... 103s The following packages will be REMOVED: 103s libssl3 103s The following NEW packages will be installed: 103s libssl3t64 103s The following packages have been kept back: 103s curl 103s The following packages will be upgraded: 103s openssl 103s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 103s Need to get 2685 kB of archives. 103s After this operation, 239 kB of additional disk space will be used. 103s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main s390x openssl s390x 3.0.13-0ubuntu2 [1010 kB] 104s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libssl3t64 s390x 3.0.13-0ubuntu2 [1675 kB] 105s Fetched 2685 kB in 1s (2310 kB/s) 105s (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 ... 52170 files and directories currently installed.) 105s Preparing to unpack .../openssl_3.0.13-0ubuntu2_s390x.deb ... 105s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 105s dpkg: libssl3:s390x: dependency problems, but removing anyway as you requested: 105s wget depends on libssl3 (>= 3.0.0). 105s tnftp depends on libssl3 (>= 3.0.0). 105s tcpdump depends on libssl3 (>= 3.0.0). 105s systemd-resolved depends on libssl3 (>= 3.0.0). 105s systemd depends on libssl3 (>= 3.0.0). 105s sudo depends on libssl3 (>= 3.0.0). 105s s390-tools depends on libssl3 (>= 3.0.0). 105s rsync depends on libssl3 (>= 3.0.0). 105s python3-cryptography depends on libssl3 (>= 3.0.0). 105s openssh-server depends on libssl3 (>= 3.0.10). 105s openssh-client depends on libssl3 (>= 3.0.10). 105s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 105s libsystemd-shared:s390x depends on libssl3 (>= 3.0.0). 105s libssh-4:s390x depends on libssl3 (>= 3.0.0). 105s libsasl2-modules:s390x depends on libssl3 (>= 3.0.0). 105s libsasl2-2:s390x depends on libssl3 (>= 3.0.0). 105s libpython3.12-minimal:s390x depends on libssl3 (>= 3.0.0). 105s libpython3.11-minimal:s390x depends on libssl3 (>= 3.0.0). 105s libnvme1 depends on libssl3 (>= 3.0.0). 105s libkrb5-3:s390x depends on libssl3 (>= 3.0.0). 105s libkmod2:s390x depends on libssl3 (>= 3.0.0). 105s libfido2-1:s390x depends on libssl3 (>= 3.0.0). 105s libcurl4:s390x depends on libssl3 (>= 3.0.0). 105s libcryptsetup12:s390x depends on libssl3 (>= 3.0.0). 105s kmod depends on libssl3 (>= 3.0.0). 105s dhcpcd-base depends on libssl3 (>= 3.0.0). 105s bind9-libs:s390x depends on libssl3 (>= 3.0.0). 105s 105s (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 ... 52170 files and directories currently installed.) 105s Removing libssl3:s390x (3.0.10-1ubuntu4) ... 105s Selecting previously unselected package libssl3t64:s390x. 105s (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 ... 52159 files and directories currently installed.) 105s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_s390x.deb ... 105s Unpacking libssl3t64:s390x (3.0.13-0ubuntu2) ... 105s Setting up libssl3t64:s390x (3.0.13-0ubuntu2) ... 105s Setting up openssl (3.0.13-0ubuntu2) ... 105s Processing triggers for man-db (2.12.0-3) ... 105s Processing triggers for libc-bin (2.39-0ubuntu6) ... 106s Reading package lists... 106s Building dependency tree... 106s Reading state information... 106s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 106s Unknown architecture, assuming PC-style ttyS0 106s sh: Attempting to set up Debian/Ubuntu apt sources automatically 106s sh: Distribution appears to be Ubuntu 107s Reading package lists... 107s Building dependency tree... 107s Reading state information... 108s eatmydata is already the newest version (131-1). 108s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 108s dbus is already the newest version (1.14.10-4ubuntu1). 108s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 108s rng-tools-debian is already the newest version (2.4). 108s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 109s The following packages will be REMOVED: 109s cloud-init* python3-configobj* python3-debconf* 109s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 109s After this operation, 3256 kB disk space will be freed. 109s (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 ... 52172 files and directories currently installed.) 109s Removing cloud-init (24.1.2-0ubuntu1) ... 109s Removing python3-configobj (5.0.8-3) ... 109s Removing python3-debconf (1.5.86) ... 109s Processing triggers for man-db (2.12.0-3) ... 110s (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 ... 51783 files and directories currently installed.) 110s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 110s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 110s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 110s invoke-rc.d: policy-rc.d denied execution of try-restart. 110s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s linux-generic is already the newest version (6.8.0-11.11+1). 111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 111s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 111s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 111s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 113s Reading package lists... 113s Reading package lists... 113s Building dependency tree... 113s Reading state information... 113s Calculating upgrade... 113s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 113s Reading package lists... 113s Building dependency tree... 113s Reading state information... 114s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 114s autopkgtest [21:28:48]: rebooting testbed after setup commands that affected boot 130s autopkgtest [21:29:04]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 133s autopkgtest [21:29:07]: @@@@@@@@@@@@@@@@@@@@ apt-source shapeit4 157s Get:1 http://ftpmaster.internal/ubuntu noble/universe shapeit4 4.2.2+dfsg-1build1 (dsc) [2158 B] 157s Get:2 http://ftpmaster.internal/ubuntu noble/universe shapeit4 4.2.2+dfsg-1build1 (tar) [59.0 MB] 157s Get:3 http://ftpmaster.internal/ubuntu noble/universe shapeit4 4.2.2+dfsg-1build1 (diff) [5280 B] 157s gpgv: Signature made Tue Dec 19 15:03:10 2023 UTC 157s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 157s gpgv: Can't check signature: No public key 157s dpkg-source: warning: cannot verify inline signature for ./shapeit4_4.2.2+dfsg-1build1.dsc: no acceptable signature found 158s autopkgtest [21:29:32]: testing package shapeit4 version 4.2.2+dfsg-1build1 159s autopkgtest [21:29:33]: build not needed 177s autopkgtest [21:29:51]: test run-sample-analysis: preparing testbed 183s Reading package lists... 183s Building dependency tree... 183s Reading state information... 183s Starting pkgProblemResolver with broken count: 0 184s Starting 2 pkgProblemResolver with broken count: 0 184s Done 184s The following additional packages will be installed: 184s libboost-iostreams1.83.0 libboost-program-options1.83.0 libdeflate0 libhts3 184s libhtscodecs2 shapeit4 shapeit4-example 184s The following NEW packages will be installed: 184s autopkgtest-satdep libboost-iostreams1.83.0 libboost-program-options1.83.0 184s libdeflate0 libhts3 libhtscodecs2 shapeit4 shapeit4-example 184s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. 184s Need to get 53.8 MB/53.8 MB of archives. 184s After this operation, 59.0 MB of additional disk space will be used. 184s Get:1 /tmp/autopkgtest.Wg9nYt/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [712 B] 184s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libboost-iostreams1.83.0 s390x 1.83.0-2ubuntu1 [340 kB] 184s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x libboost-program-options1.83.0 s390x 1.83.0-2ubuntu1 [418 kB] 185s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x libdeflate0 s390x 1.19-1 [46.0 kB] 185s Get:5 http://ftpmaster.internal/ubuntu noble/universe s390x libhtscodecs2 s390x 1.6.0-1 [87.2 kB] 185s Get:6 http://ftpmaster.internal/ubuntu noble/universe s390x libhts3 s390x 1.18+ds-1 [463 kB] 185s Get:7 http://ftpmaster.internal/ubuntu noble/universe s390x shapeit4 s390x 4.2.2+dfsg-1build1 [230 kB] 185s Get:8 http://ftpmaster.internal/ubuntu noble/universe s390x shapeit4-example all 4.2.2+dfsg-1build1 [52.3 MB] 193s Fetched 53.8 MB in 9s (6292 kB/s) 193s Selecting previously unselected package libboost-iostreams1.83.0:s390x. 193s (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 ... 51728 files and directories currently installed.) 193s Preparing to unpack .../0-libboost-iostreams1.83.0_1.83.0-2ubuntu1_s390x.deb ... 193s Unpacking libboost-iostreams1.83.0:s390x (1.83.0-2ubuntu1) ... 193s Selecting previously unselected package libboost-program-options1.83.0:s390x. 193s Preparing to unpack .../1-libboost-program-options1.83.0_1.83.0-2ubuntu1_s390x.deb ... 193s Unpacking libboost-program-options1.83.0:s390x (1.83.0-2ubuntu1) ... 193s Selecting previously unselected package libdeflate0:s390x. 193s Preparing to unpack .../2-libdeflate0_1.19-1_s390x.deb ... 193s Unpacking libdeflate0:s390x (1.19-1) ... 193s Selecting previously unselected package libhtscodecs2:s390x. 193s Preparing to unpack .../3-libhtscodecs2_1.6.0-1_s390x.deb ... 193s Unpacking libhtscodecs2:s390x (1.6.0-1) ... 193s Selecting previously unselected package libhts3:s390x. 193s Preparing to unpack .../4-libhts3_1.18+ds-1_s390x.deb ... 193s Unpacking libhts3:s390x (1.18+ds-1) ... 193s Selecting previously unselected package shapeit4. 193s Preparing to unpack .../5-shapeit4_4.2.2+dfsg-1build1_s390x.deb ... 193s Unpacking shapeit4 (4.2.2+dfsg-1build1) ... 193s Selecting previously unselected package shapeit4-example. 193s Preparing to unpack .../6-shapeit4-example_4.2.2+dfsg-1build1_all.deb ... 193s Unpacking shapeit4-example (4.2.2+dfsg-1build1) ... 193s Selecting previously unselected package autopkgtest-satdep. 193s Preparing to unpack .../7-1-autopkgtest-satdep.deb ... 193s Unpacking autopkgtest-satdep (0) ... 193s Setting up libhtscodecs2:s390x (1.6.0-1) ... 193s Setting up libboost-program-options1.83.0:s390x (1.83.0-2ubuntu1) ... 193s Setting up libdeflate0:s390x (1.19-1) ... 193s Setting up shapeit4-example (4.2.2+dfsg-1build1) ... 193s Setting up libboost-iostreams1.83.0:s390x (1.83.0-2ubuntu1) ... 193s Setting up libhts3:s390x (1.18+ds-1) ... 193s Setting up shapeit4 (4.2.2+dfsg-1build1) ... 193s Setting up autopkgtest-satdep (0) ... 193s Processing triggers for man-db (2.12.0-3) ... 193s Processing triggers for libc-bin (2.39-0ubuntu6) ... 196s (Reading database ... 51790 files and directories currently installed.) 196s Removing autopkgtest-satdep (0) ... 196s autopkgtest [21:30:10]: test run-sample-analysis: [----------------------- 197s 197s SHAPEIT 197s * Author : Olivier DELANEAU, University of Lausanne 197s * Contact : olivier.delaneau@gmail.com 197s * Version : 4.2.2 197s * Run date : 25/03/2024 - 21:30:11 197s 197s Files: 197s * Input VCF : [unphased.vcf.gz] 197s * Genetic Map : [chr20.b37.gmap.gz] 197s * Output VCF : [phased.vcf.gz] 197s 197s Parameters: 197s * Seed : 15052011 197s * Threads : 4 threads 197s * MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m] 197s * PBWT : Depth of PBWT neighbours to condition on: 4 197s * PBWT : Store indexes at variants [MAC>=2 / MDR<=0.5 / Dist=0.02 cM] 197s * HMM : K is variable / min W is 2.50cM / Ne is 15000 197s * HMM : Recombination rates given by genetic map 197s * HMM : AVX2 optimization inactive / Activating AVX2 substantially improves performance 197s 197s Initialization: 197s * VCF/BCF scanning ... + shapeit4 --input unphased.vcf.gz --map chr20.b37.gmap.gz --region 20:2000000-3000000 --thread 4 --output phased.vcf.gz 197s * VCF/BCF scanning [N=203 / L=8651 / Reg=20:2000000-3000000] (0.12s) 197s * VCF/BCF parsing [0%] * VCF/BCF parsing [1%] * VCF/BCF parsing [2%] * VCF/BCF parsing [3%] * VCF/BCF parsing [4%] * VCF/BCF parsing 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VCF/BCF parsing [89%] * VCF/BCF parsing [90%] * VCF/BCF parsing [91%] * VCF/BCF parsing [92%] * VCF/BCF parsing [93%] * VCF/BCF parsing [94%] * VCF/BCF parsing [95%] * VCF/BCF parsing [96%] * VCF/BCF parsing [97%] * VCF/BCF parsing [98%] * VCF/BCF parsing [99%] * VCF/BCF parsing [100%] * VCF/BCF parsing [Hom=89.3% / Het=10.7% / Mis=0.0%] (0.15s) 197s * GMAP parsing [n=82962] (0.06s) 197s * cM interpolation [s=1236 / i=7415] (0.00s) 197s * Region length [999850 bp / 2.5 cM] 197s * HMM parameters [Ne=15000 / Error=0.0001 / #rare=2243] 197s * PBWT indexing [l=120] (0.00s) 197s * HAP update (0.04s) 197s * H2V transpose (0.00s) 197s * 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%] 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* 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) 197s * Build genotype graphs [seg=62841] (0.03s) 197s 197s Burn-in iteration [1/5] 197s * V2H transpose (0.00s) 197s * 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%] * 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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) 197s * C2H transpose (0.00s) 202s * 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 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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=318.030+/-8.855 / W=1.00Mb] (5.21s) 202s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 202s * HAP update (0.01s) 202s * H2V transpose (0.00s) 202s 202s Burn-in iteration [2/5] 202s * V2H transpose (0.00s) 202s * 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 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selection [98%] * PBWT selection [99%] * PBWT selection [100%] * PBWT selection (0.01s) 213s * C2H transpose (0.00s) 218s * 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 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HMM computations [97%] * HMM computations [98%] * HMM computations [99%] * HMM computations [100%] * HMM computations [K=326.680+/-8.702 / W=1.00Mb] (4.69s) 234s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 234s * HAP update (0.01s) 234s * H2V transpose (0.00s) 234s 234s Pruning iteration [1/1] 234s * V2H transpose (0.00s) 234s * 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%] 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* 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] (0.38s) 267s * Total running time = 70 seconds 267s + 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 267s 267s SHAPEIT 267s * Author : Olivier DELANEAU, University of Lausanne 267s * Contact : olivier.delaneau@gmail.com 267s * Version : 4.2.2 267s * Run date : 25/03/2024 - 21:31:21 267s 267s Files: 267s * Input VCF : [unphased.bcf] 267s * Reference VCF : [reference.bcf] 267s * Scaffold VCF : [scaffold.bcf] 267s * Genetic Map : [chr20.b37.gmap.gz] 267s * Output VCF : [phased.bcf] 267s * Output LOG : [phased.log] 267s 267s Parameters: 267s * Seed : 15052011 267s * Threads : 4 threads 267s * MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m] 267s * PBWT : Depth of PBWT neighbours to condition on: 4 267s * PBWT : Store indexes at variants [MAC>=2 / MDR<=0.5 / Dist=0.02 cM] 267s * HMM : K is variable / min W is 2.50cM / Ne is 15000 267s * HMM : Recombination rates given by genetic map 267s * HMM : Inform phasing using VCF/PS field / Error rate of PS field is 0.0001 267s * HMM : AVX2 optimization inactive / Activating AVX2 substantially improves performance 267s 267s Initialization: 267s * VCF/BCF scanning ... * VCF/BCF scanning [Nm=203 / Nr=300 / L=24990 / Reg=20] (0.13s) 267s * VCF/BCF parsing [0%] * VCF/BCF parsing [1%] * 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#contraints=0 / #merged = 0] 396s * HAP update (0.01s) 396s * H2V transpose (0.01s) 396s 396s Pruning iteration [1/1] 396s * V2H transpose (0.01s) 396s * 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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PBWT selection [96%] * PBWT selection [97%] * PBWT selection [98%] * PBWT selection [99%] * PBWT selection [100%] * PBWT selection (0.06s) 484s * C2H transpose (0.00s) 500s * 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 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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=580.1+/-99.5 / W=2.21Mb / U=2] (17.86s) 518s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 518s * HAP update (0.01s) 518s * H2V transpose (0.01s) 518s 518s Main iteration [2/5] 518s * V2H transpose (0.01s) 518s * 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 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computations [100%] * HMM computations [K=478.344+/-69.482 / W=2.19Mb] (15.35s) 534s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 534s * HAP update (0.01s) 534s * H2V transpose (0.01s) 534s 534s Main iteration [3/5] 534s * V2H transpose (0.01s) 534s * 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 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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=572.1+/-96.9 / W=2.17Mb / U=4] (17.93s) 586s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 586s * HAP update (0.01s) 586s * H2V transpose (0.01s) 586s 586s Finalization: 586s * HAP solving (0.04s) 586s * HAP update (0.01s) 586s * H2V transpose (0.01s) 586s * 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] (0.70s) 586s * Total running time = 319 seconds 587s autopkgtest [21:36:41]: test run-sample-analysis: -----------------------] 587s run-sample-analysis PASS 587s autopkgtest [21:36:41]: test run-sample-analysis: - - - - - - - - - - results - - - - - - - - - - 588s autopkgtest [21:36:42]: @@@@@@@@@@@@@@@@@@@@ summary 588s run-sample-analysis PASS 599s Creating nova instance adt-noble-s390x-shapeit4-20240325-212654-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-s390x-server-20240325.img (UUID 9f25d9bc-613c-4979-9452-2ea8e4d84cd0)...