0s autopkgtest [14:31:38]: starting date and time: 2024-03-23 14:31:38+0000 0s autopkgtest [14:31:38]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [14:31:38]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.9t084fga/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/8.5.0-2ubuntu7 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-ppc64el-14.secgroup --name adt-noble-ppc64el-shapeit4-20240323-143138-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 129s autopkgtest [14:33:47]: testbed dpkg architecture: ppc64el 130s autopkgtest [14:33:48]: testbed apt version: 2.7.12 130s autopkgtest [14:33:48]: @@@@@@@@@@@@@@@@@@@@ test bed setup 131s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 131s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3994 kB] 132s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB] 132s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 132s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [494 kB] 132s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [659 kB] 132s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 132s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 132s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 132s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4247 kB] 132s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 132s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [60.8 kB] 132s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 135s Fetched 9650 kB in 2s (3925 kB/s) 135s Reading package lists... 138s Reading package lists... 138s Building dependency tree... 138s Reading state information... 138s Calculating upgrade... 139s The following packages will be REMOVED: 139s libssl3 139s The following NEW packages will be installed: 139s libssl3t64 139s The following packages have been kept back: 139s curl 139s The following packages will be upgraded: 139s openssl 139s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 139s Need to get 3151 kB of archives. 139s After this operation, 73.7 kB of additional disk space will be used. 139s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu2 [1026 kB] 139s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu2 [2125 kB] 140s Fetched 3151 kB in 1s (4589 kB/s) 140s (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 ... 70156 files and directories currently installed.) 140s Preparing to unpack .../openssl_3.0.13-0ubuntu2_ppc64el.deb ... 140s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 140s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested: 140s wget depends on libssl3 (>= 3.0.0). 140s tnftp depends on libssl3 (>= 3.0.0). 140s tcpdump depends on libssl3 (>= 3.0.0). 140s systemd-resolved depends on libssl3 (>= 3.0.0). 140s systemd depends on libssl3 (>= 3.0.0). 140s sudo depends on libssl3 (>= 3.0.0). 140s rsync depends on libssl3 (>= 3.0.0). 140s python3-cryptography depends on libssl3 (>= 3.0.0). 140s openssh-server depends on libssl3 (>= 3.0.10). 140s openssh-client depends on libssl3 (>= 3.0.10). 140s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 140s libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0). 140s libssh-4:ppc64el depends on libssl3 (>= 3.0.0). 140s libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0). 140s libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0). 140s libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0). 140s libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0). 140s libnvme1 depends on libssl3 (>= 3.0.0). 140s libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0). 140s libkmod2:ppc64el depends on libssl3 (>= 3.0.0). 140s libfido2-1:ppc64el depends on libssl3 (>= 3.0.0). 140s libcurl4:ppc64el depends on libssl3 (>= 3.0.0). 140s libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0). 140s kmod depends on libssl3 (>= 3.0.0). 140s dhcpcd-base depends on libssl3 (>= 3.0.0). 140s bind9-libs:ppc64el depends on libssl3 (>= 3.0.0). 140s 140s (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 ... 70156 files and directories currently installed.) 140s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ... 140s Selecting previously unselected package libssl3t64:ppc64el. 140s (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 ... 70145 files and directories currently installed.) 140s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_ppc64el.deb ... 140s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 140s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 140s Setting up openssl (3.0.13-0ubuntu2) ... 140s Processing triggers for man-db (2.12.0-3) ... 141s Processing triggers for libc-bin (2.39-0ubuntu6) ... 141s Reading package lists... 141s Building dependency tree... 141s Reading state information... 141s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 142s sh: Attempting to set up Debian/Ubuntu apt sources automatically 142s sh: Distribution appears to be Ubuntu 143s Reading package lists... 143s Building dependency tree... 143s Reading state information... 143s eatmydata is already the newest version (131-1). 143s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 143s Reading package lists... 143s Building dependency tree... 143s Reading state information... 143s dbus is already the newest version (1.14.10-4ubuntu1). 143s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 143s Reading package lists... 143s Building dependency tree... 143s Reading state information... 144s rng-tools-debian is already the newest version (2.4). 144s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 144s Reading package lists... 144s Building dependency tree... 144s Reading state information... 144s The following packages will be REMOVED: 144s cloud-init* python3-configobj* python3-debconf* 144s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 144s After this operation, 3256 kB disk space will be freed. 144s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70158 files and directories currently installed.) 144s Removing cloud-init (24.1.2-0ubuntu1) ... 145s Removing python3-configobj (5.0.8-3) ... 145s Removing python3-debconf (1.5.86) ... 145s Processing triggers for man-db (2.12.0-3) ... 145s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 69769 files and directories currently installed.) 145s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 146s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 146s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 146s invoke-rc.d: policy-rc.d denied execution of try-restart. 146s Reading package lists... 146s Building dependency tree... 146s Reading state information... 146s linux-generic is already the newest version (6.8.0-11.11+1). 146s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 146s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 147s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 147s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 149s Reading package lists... 149s Reading package lists... 149s Building dependency tree... 149s Reading state information... 149s Calculating upgrade... 149s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 149s Reading package lists... 150s Building dependency tree... 150s Reading state information... 150s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 150s autopkgtest [14:34:08]: rebooting testbed after setup commands that affected boot 314s autopkgtest [14:36:52]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 319s autopkgtest [14:36:57]: @@@@@@@@@@@@@@@@@@@@ apt-source shapeit4 326s Get:1 http://ftpmaster.internal/ubuntu noble/universe shapeit4 4.2.2+dfsg-1build1 (dsc) [2158 B] 326s Get:2 http://ftpmaster.internal/ubuntu noble/universe shapeit4 4.2.2+dfsg-1build1 (tar) [59.0 MB] 326s Get:3 http://ftpmaster.internal/ubuntu noble/universe shapeit4 4.2.2+dfsg-1build1 (diff) [5280 B] 326s gpgv: Signature made Tue Dec 19 15:03:10 2023 UTC 326s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 326s gpgv: Can't check signature: No public key 326s dpkg-source: warning: cannot verify inline signature for ./shapeit4_4.2.2+dfsg-1build1.dsc: no acceptable signature found 327s autopkgtest [14:37:05]: testing package shapeit4 version 4.2.2+dfsg-1build1 328s autopkgtest [14:37:06]: build not needed 338s autopkgtest [14:37:16]: test run-sample-analysis: preparing testbed 342s Reading package lists... 342s Building dependency tree... 342s Reading state information... 342s Starting pkgProblemResolver with broken count: 0 342s Starting 2 pkgProblemResolver with broken count: 0 342s Done 342s The following additional packages will be installed: 342s libboost-iostreams1.83.0 libboost-program-options1.83.0 libdeflate0 libhts3 342s libhtscodecs2 shapeit4 shapeit4-example 342s The following NEW packages will be installed: 342s autopkgtest-satdep libboost-iostreams1.83.0 libboost-program-options1.83.0 342s libdeflate0 libhts3 libhtscodecs2 shapeit4 shapeit4-example 342s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. 342s Need to get 53.9 MB/53.9 MB of archives. 342s After this operation, 59.8 MB of additional disk space will be used. 342s Get:1 /tmp/autopkgtest.Ft8T9r/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [716 B] 342s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libboost-iostreams1.83.0 ppc64el 1.83.0-2ubuntu1 [340 kB] 343s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libboost-program-options1.83.0 ppc64el 1.83.0-2ubuntu1 [421 kB] 343s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 343s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 343s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB] 343s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el shapeit4 ppc64el 4.2.2+dfsg-1build1 [186 kB] 343s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el shapeit4-example all 4.2.2+dfsg-1build1 [52.3 MB] 345s Fetched 53.9 MB in 2s (25.3 MB/s) 345s Selecting previously unselected package libboost-iostreams1.83.0:ppc64el. 345s (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.) 345s Preparing to unpack .../0-libboost-iostreams1.83.0_1.83.0-2ubuntu1_ppc64el.deb ... 345s Unpacking libboost-iostreams1.83.0:ppc64el (1.83.0-2ubuntu1) ... 345s Selecting previously unselected package libboost-program-options1.83.0:ppc64el. 345s Preparing to unpack .../1-libboost-program-options1.83.0_1.83.0-2ubuntu1_ppc64el.deb ... 345s Unpacking libboost-program-options1.83.0:ppc64el (1.83.0-2ubuntu1) ... 345s Selecting previously unselected package libdeflate0:ppc64el. 345s Preparing to unpack .../2-libdeflate0_1.19-1_ppc64el.deb ... 345s Unpacking libdeflate0:ppc64el (1.19-1) ... 345s Selecting previously unselected package libhtscodecs2:ppc64el. 345s Preparing to unpack .../3-libhtscodecs2_1.6.0-1_ppc64el.deb ... 345s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 345s Selecting previously unselected package libhts3:ppc64el. 345s Preparing to unpack .../4-libhts3_1.18+ds-1_ppc64el.deb ... 345s Unpacking libhts3:ppc64el (1.18+ds-1) ... 345s Selecting previously unselected package shapeit4. 345s Preparing to unpack .../5-shapeit4_4.2.2+dfsg-1build1_ppc64el.deb ... 345s Unpacking shapeit4 (4.2.2+dfsg-1build1) ... 345s Selecting previously unselected package shapeit4-example. 345s Preparing to unpack .../6-shapeit4-example_4.2.2+dfsg-1build1_all.deb ... 345s Unpacking shapeit4-example (4.2.2+dfsg-1build1) ... 345s Selecting previously unselected package autopkgtest-satdep. 345s Preparing to unpack .../7-1-autopkgtest-satdep.deb ... 345s Unpacking autopkgtest-satdep (0) ... 345s Setting up libhtscodecs2:ppc64el (1.6.0-1) ... 345s Setting up libboost-program-options1.83.0:ppc64el (1.83.0-2ubuntu1) ... 345s Setting up libdeflate0:ppc64el (1.19-1) ... 345s Setting up shapeit4-example (4.2.2+dfsg-1build1) ... 345s Setting up libboost-iostreams1.83.0:ppc64el (1.83.0-2ubuntu1) ... 345s Setting up libhts3:ppc64el (1.18+ds-1) ... 345s Setting up shapeit4 (4.2.2+dfsg-1build1) ... 345s Setting up autopkgtest-satdep (0) ... 345s Processing triggers for man-db (2.12.0-3) ... 346s Processing triggers for libc-bin (2.39-0ubuntu6) ... 348s (Reading database ... 69776 files and directories currently installed.) 348s Removing autopkgtest-satdep (0) ... 349s autopkgtest [14:37:27]: test run-sample-analysis: [----------------------- 349s 349s SHAPEIT 349s * Author : Olivier DELANEAU, University of Lausanne 349s * Contact : olivier.delaneau@gmail.com 349s + shapeit4 --input unphased.vcf.gz --map chr20.b37.gmap.gz --region 20:2000000-3000000 --thread 4 --output phased.vcf.gz 349s * Version : 4.2.2 349s * Run date : 23/03/2024 - 14:37:27 349s 349s Files: 349s * Input VCF : [unphased.vcf.gz] 349s * Genetic Map : [chr20.b37.gmap.gz] 349s * Output VCF : [phased.vcf.gz] 349s 349s Parameters: 349s * Seed : 15052011 349s * Threads : 4 threads 349s * MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m] 349s * PBWT : Depth of PBWT neighbours to condition on: 4 349s * PBWT : Store indexes at variants [MAC>=2 / MDR<=0.5 / Dist=0.02 cM] 349s * HMM : K is variable / min W is 2.50cM / Ne is 15000 349s * HMM : Recombination rates given by genetic map 349s * HMM : AVX2 optimization inactive / Activating AVX2 substantially improves performance 349s 349s Initialization: 349s * VCF/BCF scanning ... * VCF/BCF scanning [N=203 / L=8651 / Reg=20:2000000-3000000] (0.12s) 349s * VCF/BCF parsing [0%] * VCF/BCF parsing [1%] * VCF/BCF parsing [2%] * VCF/BCF parsing [3%] * VCF/BCF 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[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) 349s * GMAP parsing [n=82962] (0.06s) 349s * cM interpolation [s=1236 / i=7415] (0.00s) 349s * Region length [999850 bp / 2.5 cM] 349s * HMM parameters [Ne=15000 / Error=0.0001 / #rare=2243] 349s * PBWT indexing [l=120] (0.00s) 349s * HAP update (0.01s) 349s * H2V transpose (0.00s) 349s * 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 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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) 349s * Build genotype graphs [seg=62841] (0.03s) 349s 349s Burn-in iteration [1/5] 349s * V2H transpose (0.00s) 349s * PBWT selection [0%] * PBWT selection [1%] * PBWT selection [2%] * PBWT selection [3%] * PBWT selection [4%] * PBWT selection [5%] * PBWT selection [6%] * PBWT selection [7%] * PBWT selection [8%] * PBWT selection [9%] * PBWT selection [10%] * PBWT selection [11%] * PBWT selection [12%] * PBWT selection [13%] * PBWT selection [14%] * PBWT selection [15%] * PBWT selection [16%] * PBWT selection [17%] * PBWT selection [18%] * PBWT selection [19%] * PBWT selection [20%] * PBWT selection [21%] * PBWT selection [22%] * PBWT selection [23%] * PBWT selection [24%] * PBWT selection [25%] * PBWT selection [26%] * PBWT selection [27%] * PBWT selection [28%] * PBWT 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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 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PBWT selection [97%] * PBWT selection [98%] * PBWT selection [99%] * PBWT selection [100%] * PBWT selection (0.01s) 359s * C2H transpose (0.00s) 362s * 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 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HMM computations [95%] * HMM computations [96%] * HMM computations [97%] * HMM computations [98%] * HMM computations [99%] * HMM computations [100%] * HMM computations [K=226.616+/-14.038 / W=1.00Mb] (2.34s) 370s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 370s * HAP update (0.01s) 370s * H2V transpose (0.00s) 370s 370s Pruning iteration [1/1] 370s * V2H transpose (0.00s) 370s * 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 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constraints [#inds=0 / #contraints=0 / #merged = 0] 383s * HAP update (0.01s) 383s * H2V transpose (0.00s) 383s 383s Main iteration [3/5] 383s * V2H transpose (0.00s) 383s * 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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[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) 386s * Total running time = 37 seconds 386s + 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 386s 386s SHAPEIT 386s * Author : Olivier DELANEAU, University of Lausanne 386s * Contact : olivier.delaneau@gmail.com 386s * Version : 4.2.2 386s * Run date : 23/03/2024 - 14:38:04 386s 386s Files: 386s * Input VCF : [unphased.bcf] 386s * Reference VCF : [reference.bcf] 386s * Scaffold VCF : [scaffold.bcf] 386s * Genetic Map : [chr20.b37.gmap.gz] 386s * Output VCF : [phased.bcf] 386s * Output LOG : [phased.log] 386s 386s Parameters: 386s * Seed : 15052011 386s * Threads : 4 threads 386s * MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m] 386s * PBWT : Depth of PBWT neighbours to condition on: 4 386s * PBWT : Store indexes at variants [MAC>=2 / MDR<=0.5 / Dist=0.02 cM] 386s * HMM : K is variable / min W is 2.50cM / Ne is 15000 386s * HMM : Recombination rates given by genetic map 386s * HMM : Inform phasing using VCF/PS field / Error rate of PS field is 0.0001 386s * HMM : AVX2 optimization inactive / Activating AVX2 substantially improves performance 386s 386s Initialization: 386s * VCF/BCF scanning ... * VCF/BCF scanning [Nm=203 / Nr=300 / L=24990 / Reg=20] (0.09s) 386s * 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%] * 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* H2V transpose (0.00s) 449s 449s Burn-in iteration [5/5] 449s * V2H transpose (0.00s) 449s * 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 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computations [K=426.247+/-119.300 / W=2.22Mb] (13.93s) 463s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 463s * HAP update (0.01s) 463s * H2V transpose (0.00s) 463s 463s Pruning iteration [1/1] 463s * V2H transpose (0.00s) 463s * 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 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[K=409.955+/-111.396 / W=2.29Mb] (9.36s) 530s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 530s * HAP update (0.01s) 530s * H2V transpose (0.00s) 530s 530s Main iteration [2/5] 530s * V2H transpose (0.00s) 530s * 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%] * 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computations [96%] * HMM computations [97%] * HMM computations [98%] * HMM computations [99%] * HMM computations [100%] * HMM computations [K=383.403+/-110.849 / W=2.12Mb] (8.84s) 539s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 539s * HAP update (0.01s) 539s * H2V transpose (0.00s) 539s 539s Main iteration [3/5] 539s * V2H transpose (0.00s) 539s * 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%] * 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(0.04s) 557s * 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 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[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=381.266+/-112.213 / W=2.11Mb] (9.01s) 566s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 566s * HAP update (0.01s) 566s * H2V transpose (0.00s) 566s 566s Finalization: 566s * HAP solving (0.04s) 566s * HAP update (0.01s) 566s * H2V transpose (0.00s) 566s * 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) 566s * Total running time = 180 seconds 567s autopkgtest [14:41:05]: test run-sample-analysis: -----------------------] 567s run-sample-analysis PASS 567s autopkgtest [14:41:05]: test run-sample-analysis: - - - - - - - - - - results - - - - - - - - - - 567s autopkgtest [14:41:05]: @@@@@@@@@@@@@@@@@@@@ summary 567s run-sample-analysis PASS 579s Creating nova instance adt-noble-ppc64el-shapeit4-20240323-143138-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240323.img (UUID ff8abf95-5243-4ea5-b7f5-3bf690534a1d)...