0s autopkgtest [20:46:29]: starting date and time: 2024-03-24 20:46:29+0000 0s autopkgtest [20:46:29]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [20:46:29]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.s3v28kqb/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-ppc64el-14.secgroup --name adt-noble-ppc64el-shapeit4-20240324-204629-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/ 104s autopkgtest [20:48:13]: testbed dpkg architecture: ppc64el 104s autopkgtest [20:48:13]: testbed apt version: 2.7.12 104s autopkgtest [20:48:13]: @@@@@@@@@@@@@@@@@@@@ test bed setup 106s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 106s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 106s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3984 kB] 106s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 106s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [58.0 kB] 106s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [700 kB] 106s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 106s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 106s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 106s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4266 kB] 106s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 106s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [61.1 kB] 106s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 109s Fetched 9701 kB in 2s (4012 kB/s) 109s Reading package lists... 112s Reading package lists... 112s Building dependency tree... 112s Reading state information... 112s Calculating upgrade... 113s The following packages will be REMOVED: 113s libssl3 113s The following NEW packages will be installed: 113s libssl3t64 113s The following packages have been kept back: 113s curl 113s The following packages will be upgraded: 113s openssl 113s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 113s Need to get 3151 kB of archives. 113s After this operation, 73.7 kB of additional disk space will be used. 113s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu2 [1026 kB] 113s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu2 [2125 kB] 114s Fetched 3151 kB in 1s (4524 kB/s) 114s (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.) 114s Preparing to unpack .../openssl_3.0.13-0ubuntu2_ppc64el.deb ... 114s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 114s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested: 114s wget depends on libssl3 (>= 3.0.0). 114s tnftp depends on libssl3 (>= 3.0.0). 114s tcpdump depends on libssl3 (>= 3.0.0). 114s systemd-resolved depends on libssl3 (>= 3.0.0). 114s systemd depends on libssl3 (>= 3.0.0). 114s sudo depends on libssl3 (>= 3.0.0). 114s rsync depends on libssl3 (>= 3.0.0). 114s python3-cryptography depends on libssl3 (>= 3.0.0). 114s openssh-server depends on libssl3 (>= 3.0.10). 114s openssh-client depends on libssl3 (>= 3.0.10). 114s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 114s libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0). 114s libssh-4:ppc64el depends on libssl3 (>= 3.0.0). 114s libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0). 114s libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0). 114s libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0). 114s libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0). 114s libnvme1 depends on libssl3 (>= 3.0.0). 114s libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0). 114s libkmod2:ppc64el depends on libssl3 (>= 3.0.0). 114s libfido2-1:ppc64el depends on libssl3 (>= 3.0.0). 114s libcurl4:ppc64el depends on libssl3 (>= 3.0.0). 114s libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0). 114s kmod depends on libssl3 (>= 3.0.0). 114s dhcpcd-base depends on libssl3 (>= 3.0.0). 114s bind9-libs:ppc64el depends on libssl3 (>= 3.0.0). 114s 114s (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.) 114s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ... 114s Selecting previously unselected package libssl3t64:ppc64el. 114s (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.) 114s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_ppc64el.deb ... 114s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 114s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 114s Setting up openssl (3.0.13-0ubuntu2) ... 114s Processing triggers for man-db (2.12.0-3) ... 115s Processing triggers for libc-bin (2.39-0ubuntu6) ... 115s Reading package lists... 115s Building dependency tree... 115s Reading state information... 115s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 116s sh: Attempting to set up Debian/Ubuntu apt sources automatically 116s sh: Distribution appears to be Ubuntu 117s Reading package lists... 117s Building dependency tree... 117s Reading state information... 117s eatmydata is already the newest version (131-1). 117s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 117s Reading package lists... 117s Building dependency tree... 117s Reading state information... 117s dbus is already the newest version (1.14.10-4ubuntu1). 117s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 117s Reading package lists... 117s Building dependency tree... 117s Reading state information... 118s rng-tools-debian is already the newest version (2.4). 118s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 118s Reading package lists... 118s Building dependency tree... 118s Reading state information... 118s The following packages will be REMOVED: 118s cloud-init* python3-configobj* python3-debconf* 118s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 118s After this operation, 3256 kB disk space will be freed. 118s (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.) 118s Removing cloud-init (24.1.2-0ubuntu1) ... 119s Removing python3-configobj (5.0.8-3) ... 119s Removing python3-debconf (1.5.86) ... 119s Processing triggers for man-db (2.12.0-3) ... 119s (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.) 119s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 120s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 120s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 120s invoke-rc.d: policy-rc.d denied execution of try-restart. 120s Reading package lists... 120s Building dependency tree... 120s Reading state information... 120s linux-generic is already the newest version (6.8.0-11.11+1). 120s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 121s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 121s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 121s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 123s Reading package lists... 123s Reading package lists... 124s Building dependency tree... 124s Reading state information... 124s Calculating upgrade... 124s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 124s Reading package lists... 124s Building dependency tree... 124s Reading state information... 124s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 124s autopkgtest [20:48:33]: rebooting testbed after setup commands that affected boot 298s autopkgtest [20:51:27]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 300s autopkgtest [20:51:29]: @@@@@@@@@@@@@@@@@@@@ apt-source shapeit4 305s Get:1 http://ftpmaster.internal/ubuntu noble/universe shapeit4 4.2.2+dfsg-1build1 (dsc) [2158 B] 305s Get:2 http://ftpmaster.internal/ubuntu noble/universe shapeit4 4.2.2+dfsg-1build1 (tar) [59.0 MB] 305s Get:3 http://ftpmaster.internal/ubuntu noble/universe shapeit4 4.2.2+dfsg-1build1 (diff) [5280 B] 305s gpgv: Signature made Tue Dec 19 15:03:10 2023 UTC 305s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 305s gpgv: Can't check signature: No public key 305s dpkg-source: warning: cannot verify inline signature for ./shapeit4_4.2.2+dfsg-1build1.dsc: no acceptable signature found 306s autopkgtest [20:51:35]: testing package shapeit4 version 4.2.2+dfsg-1build1 306s autopkgtest [20:51:35]: build not needed 310s autopkgtest [20:51:39]: test run-sample-analysis: preparing testbed 315s Reading package lists... 315s Building dependency tree... 315s Reading state information... 316s Starting pkgProblemResolver with broken count: 0 316s Starting 2 pkgProblemResolver with broken count: 0 316s Done 316s The following additional packages will be installed: 316s libboost-iostreams1.83.0 libboost-program-options1.83.0 libdeflate0 libhts3 316s libhtscodecs2 shapeit4 shapeit4-example 316s The following NEW packages will be installed: 316s autopkgtest-satdep libboost-iostreams1.83.0 libboost-program-options1.83.0 316s libdeflate0 libhts3 libhtscodecs2 shapeit4 shapeit4-example 316s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. 316s Need to get 53.9 MB/53.9 MB of archives. 316s After this operation, 59.8 MB of additional disk space will be used. 316s Get:1 /tmp/autopkgtest.HAhLmz/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [712 B] 316s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libboost-iostreams1.83.0 ppc64el 1.83.0-2ubuntu1 [340 kB] 316s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libboost-program-options1.83.0 ppc64el 1.83.0-2ubuntu1 [421 kB] 316s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 316s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 316s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB] 316s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el shapeit4 ppc64el 4.2.2+dfsg-1build1 [186 kB] 316s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el shapeit4-example all 4.2.2+dfsg-1build1 [52.3 MB] 318s Fetched 53.9 MB in 2s (24.7 MB/s) 318s Selecting previously unselected package libboost-iostreams1.83.0:ppc64el. 318s (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.) 318s Preparing to unpack .../0-libboost-iostreams1.83.0_1.83.0-2ubuntu1_ppc64el.deb ... 318s Unpacking libboost-iostreams1.83.0:ppc64el (1.83.0-2ubuntu1) ... 318s Selecting previously unselected package libboost-program-options1.83.0:ppc64el. 318s Preparing to unpack .../1-libboost-program-options1.83.0_1.83.0-2ubuntu1_ppc64el.deb ... 318s Unpacking libboost-program-options1.83.0:ppc64el (1.83.0-2ubuntu1) ... 318s Selecting previously unselected package libdeflate0:ppc64el. 318s Preparing to unpack .../2-libdeflate0_1.19-1_ppc64el.deb ... 318s Unpacking libdeflate0:ppc64el (1.19-1) ... 318s Selecting previously unselected package libhtscodecs2:ppc64el. 318s Preparing to unpack .../3-libhtscodecs2_1.6.0-1_ppc64el.deb ... 318s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 318s Selecting previously unselected package libhts3:ppc64el. 318s Preparing to unpack .../4-libhts3_1.18+ds-1_ppc64el.deb ... 318s Unpacking libhts3:ppc64el (1.18+ds-1) ... 318s Selecting previously unselected package shapeit4. 318s Preparing to unpack .../5-shapeit4_4.2.2+dfsg-1build1_ppc64el.deb ... 318s Unpacking shapeit4 (4.2.2+dfsg-1build1) ... 318s Selecting previously unselected package shapeit4-example. 318s Preparing to unpack .../6-shapeit4-example_4.2.2+dfsg-1build1_all.deb ... 318s Unpacking shapeit4-example (4.2.2+dfsg-1build1) ... 318s Selecting previously unselected package autopkgtest-satdep. 318s Preparing to unpack .../7-1-autopkgtest-satdep.deb ... 318s Unpacking autopkgtest-satdep (0) ... 318s Setting up libhtscodecs2:ppc64el (1.6.0-1) ... 318s Setting up libboost-program-options1.83.0:ppc64el (1.83.0-2ubuntu1) ... 318s Setting up libdeflate0:ppc64el (1.19-1) ... 318s Setting up shapeit4-example (4.2.2+dfsg-1build1) ... 318s Setting up libboost-iostreams1.83.0:ppc64el (1.83.0-2ubuntu1) ... 318s Setting up libhts3:ppc64el (1.18+ds-1) ... 318s Setting up shapeit4 (4.2.2+dfsg-1build1) ... 318s Setting up autopkgtest-satdep (0) ... 318s Processing triggers for man-db (2.12.0-3) ... 319s Processing triggers for libc-bin (2.39-0ubuntu6) ... 321s (Reading database ... 69776 files and directories currently installed.) 321s Removing autopkgtest-satdep (0) ... 322s autopkgtest [20:51:51]: test run-sample-analysis: [----------------------- 322s 322s SHAPEIT 322s * Author : Olivier DELANEAU, University of Lausanne 322s * Contact : olivier.delaneau@gmail.com 322s + shapeit4 --input unphased.vcf.gz --map chr20.b37.gmap.gz --region 20:2000000-3000000 --thread 4 --output phased.vcf.gz 322s * Version : 4.2.2 322s * Run date : 24/03/2024 - 20:51:51 322s 322s Files: 322s * Input VCF : [unphased.vcf.gz] 322s * Genetic Map : [chr20.b37.gmap.gz] 322s * Output VCF : [phased.vcf.gz] 322s 322s Parameters: 322s * Seed : 15052011 322s * Threads : 4 threads 322s * MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m] 322s * PBWT : Depth of PBWT neighbours to condition on: 4 322s * PBWT : Store indexes at variants [MAC>=2 / MDR<=0.5 / Dist=0.02 cM] 322s * HMM : K is variable / min W is 2.50cM / Ne is 15000 322s * HMM : Recombination rates given by genetic map 322s * HMM : AVX2 optimization inactive / Activating AVX2 substantially improves performance 322s 322s Initialization: 322s * VCF/BCF scanning ... * VCF/BCF scanning [N=203 / L=8651 / Reg=20:2000000-3000000] (0.12s) 322s * 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%] (0.15s) 322s * GMAP parsing [n=82962] (0.06s) 322s * cM interpolation [s=1236 / i=7415] (0.00s) 322s * Region length [999850 bp / 2.5 cM] 322s * HMM parameters [Ne=15000 / Error=0.0001 / #rare=2243] 322s * PBWT indexing [l=120] (0.00s) 322s * HAP update (0.01s) 322s * H2V transpose (0.00s) 322s * 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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PBWT selection [97%] * PBWT selection [98%] * PBWT selection [99%] * PBWT selection [100%] * PBWT selection (0.01s) 332s * C2H transpose (0.00s) 335s * 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=226.877+/-13.794 / W=1.00Mb] (2.33s) 343s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 343s * HAP update (0.01s) 343s * H2V transpose (0.00s) 343s 343s Pruning iteration [1/1] 343s * V2H transpose (0.00s) 343s * PBWT selection [0%] * PBWT selection [1%] * PBWT selection [2%] * PBWT selection [3%] * PBWT selection [4%] * PBWT selection [5%] * PBWT selection [6%] * PBWT selection [7%] * PBWT selection [8%] * PBWT selection [9%] * PBWT selection [10%] * PBWT selection [11%] * PBWT selection [12%] * PBWT selection [13%] * PBWT selection [14%] * PBWT selection [15%] * PBWT selection [16%] * PBWT selection [17%] * PBWT selection [18%] * PBWT selection [19%] * PBWT selection [20%] * PBWT selection [21%] * PBWT selection [22%] * PBWT selection [23%] * PBWT selection [24%] * PBWT selection [25%] * PBWT selection 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V2H transpose (0.00s) 351s * 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 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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) 351s * C2H transpose (0.00s) 353s * 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 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constraints [#inds=0 / #contraints=0 / #merged = 0] 353s * HAP update (0.01s) 353s * H2V transpose (0.00s) 353s 353s Main iteration [3/5] 353s * V2H transpose (0.00s) 353s * 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] (0.20s) 359s * Total running time = 36 seconds 359s + 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 359s 359s SHAPEIT 359s * Author : Olivier DELANEAU, University of Lausanne 359s * Contact : olivier.delaneau@gmail.com 359s * Version : 4.2.2 359s * Run date : 24/03/2024 - 20:52:28 359s 359s Files: 359s * Input VCF : [unphased.bcf] 359s * Reference VCF : [reference.bcf] 359s * Scaffold VCF : [scaffold.bcf] 359s * Genetic Map : [chr20.b37.gmap.gz] 359s * Output VCF : [phased.bcf] 359s * Output LOG : [phased.log] 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 : Inform phasing using VCF/PS field / Error rate of PS field is 0.0001 359s * HMM : AVX2 optimization inactive / Activating AVX2 substantially improves performance 359s 359s Initialization: 359s * VCF/BCF scanning ... * VCF/BCF scanning [Nm=203 / Nr=300 / L=24990 / Reg=20] (0.09s) 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%] * 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PBWT selection [98%] * PBWT selection [99%] * PBWT selection [100%] * PBWT selection (0.04s) 472s * C2H transpose (0.00s) 482s * 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 [62%] * HMM computations [63%] * HMM computations [64%] * HMM computations [65%] * HMM computations [66%] * HMM computations [67%] * HMM computations [68%] * HMM computations [69%] * HMM computations [70%] * HMM computations [71%] * HMM computations [72%] * HMM computations [73%] * HMM computations [74%] * HMM computations [75%] * HMM computations [76%] * HMM computations [77%] * HMM computations [78%] * HMM computations [79%] * HMM computations [80%] * HMM computations [81%] * HMM computations [82%] * HMM computations [83%] * HMM computations [84%] * HMM computations [85%] * HMM computations [86%] * HMM computations [87%] * HMM computations [88%] * HMM computations [89%] * HMM computations [90%] * HMM computations [91%] * HMM computations [92%] * HMM computations [93%] * HMM computations [94%] * HMM computations [95%] * HMM computations [96%] * HMM computations [97%] * HMM computations [98%] * HMM computations [99%] * HMM computations [100%] * HMM computations [K=408.903+/-113.786 / W=2.28Mb] (9.26s) 502s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 502s * HAP update (0.01s) 502s * H2V transpose (0.00s) 502s 502s Main iteration [2/5] 502s * V2H transpose (0.00s) 502s * 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 [56%] * HMM computations [57%] * HMM computations [58%] * HMM computations [59%] * HMM computations [60%] * HMM computations [61%] * HMM computations [62%] * HMM computations [63%] * HMM computations [64%] * HMM computations [65%] * HMM computations [66%] * HMM computations [67%] * HMM computations [68%] * HMM computations [69%] * HMM computations [70%] * HMM computations [71%] * HMM computations [72%] * HMM computations [73%] * HMM computations [74%] * HMM computations [75%] * HMM computations [76%] * HMM computations [77%] * HMM computations [78%] * HMM computations [79%] * HMM computations [80%] * HMM computations [81%] * HMM computations [82%] * HMM computations [83%] * HMM computations [84%] * HMM computations [85%] * HMM computations [86%] * HMM computations [87%] * HMM computations [88%] * HMM computations [89%] * HMM computations [90%] * HMM computations [91%] * HMM computations [92%] * HMM computations [93%] * HMM computations [94%] * HMM computations [95%] * HMM computations [96%] * HMM computations [97%] * HMM computations [98%] * HMM computations [99%] * HMM computations [100%] * HMM computations [K=393.123+/-113.223 / W=2.20Mb] (8.88s) 511s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 511s * HAP update (0.01s) 511s * H2V transpose (0.00s) 511s 511s Main iteration [3/5] 511s * V2H transpose (0.00s) 511s * 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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selection [71%] * PBWT selection [72%] * PBWT selection [73%] * PBWT selection [74%] * PBWT selection [75%] * PBWT selection [76%] * PBWT selection [77%] * PBWT selection [78%] * PBWT selection [79%] * PBWT selection [80%] * PBWT selection [81%] * PBWT selection [82%] * PBWT selection [83%] * PBWT selection [84%] * PBWT selection [85%] * PBWT selection [86%] * PBWT selection [87%] * PBWT selection [88%] * PBWT selection [89%] * PBWT selection [90%] * PBWT selection [91%] * PBWT selection [92%] * PBWT selection [93%] * PBWT selection [94%] * PBWT selection [95%] * PBWT selection [96%] * PBWT selection [97%] * PBWT selection [98%] * PBWT selection [99%] * PBWT selection [100%] * PBWT selection (0.04s) 511s * C2H transpose (0.00s) 519s * HMM computations [0%] * HMM computations [1%] * HMM computations [2%] * HMM computations [3%] * HMM computations [4%] * HMM computations [5%] * HMM computations [6%] * HMM computations [7%] * HMM computations [8%] * HMM computations [9%] * HMM 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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=395.771+/-111.507 / W=2.22Mb] (8.97s) 528s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 528s * HAP update (0.01s) 529s * H2V transpose (0.00s) 529s 529s Main iteration [5/5] 529s * V2H transpose (0.00s) 529s * 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 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(0.04s) 529s * C2H transpose (0.00s) 537s * HMM computations [0%] * HMM computations [1%] * HMM computations [2%] * HMM computations [3%] * HMM computations [4%] * HMM computations [5%] * HMM computations [6%] * HMM computations [7%] * HMM computations [8%] * HMM computations [9%] * HMM computations [10%] * HMM computations [11%] * HMM computations [12%] * HMM computations [13%] * HMM computations [14%] * HMM computations [15%] * HMM computations [16%] * HMM computations [17%] * HMM computations [18%] * HMM computations [19%] * HMM computations [20%] * HMM computations [21%] * HMM computations [22%] * HMM computations [23%] * HMM computations [24%] * HMM computations [25%] * HMM computations [26%] * HMM computations [27%] * HMM computations [28%] * HMM computations [29%] * HMM computations [30%] * HMM computations [31%] * HMM computations [32%] * HMM computations [33%] * HMM computations [34%] * HMM computations [35%] * HMM computations [36%] * HMM computations [37%] * HMM computations 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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=390.190+/-110.510 / W=2.19Mb] (8.84s) 537s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 537s * HAP update (0.01s) 537s * H2V transpose (0.00s) 537s 537s Finalization: 537s * HAP solving (0.03s) 537s * HAP update (0.01s) 537s * H2V transpose (0.00s) 538s * 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] (0.30s) 538s * Total running time = 178 seconds 538s autopkgtest [20:55:27]: test run-sample-analysis: -----------------------] 539s autopkgtest [20:55:28]: test run-sample-analysis: - - - - - - - - - - results - - - - - - - - - - 539s run-sample-analysis PASS 539s autopkgtest [20:55:28]: @@@@@@@@@@@@@@@@@@@@ summary 539s run-sample-analysis PASS 550s Creating nova instance adt-noble-ppc64el-shapeit4-20240324-204629-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240324.img (UUID 456c38b1-f024-4aa9-9fc9-7cea731b220e)...