0s autopkgtest [12:08:00]: starting date and time: 2024-03-23 12:08:00+0000 0s autopkgtest [12:08:00]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [12:08:00]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.r5r8rjld/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-3@bos02-ppc64el-25.secgroup --name adt-noble-ppc64el-shapeit4-20240323-120421-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 171s autopkgtest [12:10:51]: testbed dpkg architecture: ppc64el 171s autopkgtest [12:10:51]: testbed apt version: 2.7.12 171s autopkgtest [12:10:51]: @@@@@@@@@@@@@@@@@@@@ test bed setup 172s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 172s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [494 kB] 172s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3975 kB] 172s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 172s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB] 172s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [659 kB] 172s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 172s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 172s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 172s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4247 kB] 173s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 173s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [60.8 kB] 173s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 176s Fetched 9630 kB in 2s (3871 kB/s) 177s Reading package lists... 179s Reading package lists... 180s Building dependency tree... 180s Reading state information... 180s Calculating upgrade... 180s The following packages will be REMOVED: 180s libssl3 180s The following NEW packages will be installed: 180s libssl3t64 180s The following packages have been kept back: 180s curl 180s The following packages will be upgraded: 180s libbsd0 libc-bin libc6 locales openssl 180s 5 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 180s Need to get 11.5 MB of archives. 180s After this operation, 75.8 kB of additional disk space will be used. 180s Get:1 http://ftpmaster.internal/ubuntu noble/main ppc64el libc6 ppc64el 2.39-0ubuntu6 [3274 kB] 181s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libc-bin ppc64el 2.39-0ubuntu6 [751 kB] 181s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu2 [1026 kB] 181s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu2 [2125 kB] 181s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el libbsd0 ppc64el 0.12.1-1 [56.9 kB] 181s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el locales all 2.39-0ubuntu6 [4232 kB] 182s Preconfiguring packages ... 182s Fetched 11.5 MB in 2s (6445 kB/s) 182s (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.) 182s Preparing to unpack .../libc6_2.39-0ubuntu6_ppc64el.deb ... 182s Unpacking libc6:ppc64el (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 183s Setting up libc6:ppc64el (2.39-0ubuntu6) ... 183s (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.) 183s Preparing to unpack .../libc-bin_2.39-0ubuntu6_ppc64el.deb ... 183s Unpacking libc-bin (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 183s Setting up libc-bin (2.39-0ubuntu6) ... 183s (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.) 183s Preparing to unpack .../openssl_3.0.13-0ubuntu2_ppc64el.deb ... 183s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 184s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested: 184s wget depends on libssl3 (>= 3.0.0). 184s tnftp depends on libssl3 (>= 3.0.0). 184s tcpdump depends on libssl3 (>= 3.0.0). 184s systemd-resolved depends on libssl3 (>= 3.0.0). 184s systemd depends on libssl3 (>= 3.0.0). 184s sudo depends on libssl3 (>= 3.0.0). 184s rsync depends on libssl3 (>= 3.0.0). 184s python3-cryptography depends on libssl3 (>= 3.0.0). 184s openssh-server depends on libssl3 (>= 3.0.10). 184s openssh-client depends on libssl3 (>= 3.0.10). 184s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 184s libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0). 184s libssh-4:ppc64el depends on libssl3 (>= 3.0.0). 184s libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0). 184s libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0). 184s libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0). 184s libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0). 184s libnvme1 depends on libssl3 (>= 3.0.0). 184s libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0). 184s libkmod2:ppc64el depends on libssl3 (>= 3.0.0). 184s libfido2-1:ppc64el depends on libssl3 (>= 3.0.0). 184s libcurl4:ppc64el depends on libssl3 (>= 3.0.0). 184s libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0). 184s kmod depends on libssl3 (>= 3.0.0). 184s dhcpcd-base depends on libssl3 (>= 3.0.0). 184s bind9-libs:ppc64el depends on libssl3 (>= 3.0.0). 184s 184s (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.) 184s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ... 184s Selecting previously unselected package libssl3t64:ppc64el. 184s (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.) 184s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_ppc64el.deb ... 184s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 184s Preparing to unpack .../libbsd0_0.12.1-1_ppc64el.deb ... 184s Unpacking libbsd0:ppc64el (0.12.1-1) over (0.11.8-1) ... 184s Preparing to unpack .../locales_2.39-0ubuntu6_all.deb ... 184s Unpacking locales (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 184s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 184s Setting up locales (2.39-0ubuntu6) ... 184s Generating locales (this might take a while)... 186s en_US.UTF-8... done 186s Generation complete. 186s Setting up openssl (3.0.13-0ubuntu2) ... 186s Setting up libbsd0:ppc64el (0.12.1-1) ... 186s Processing triggers for man-db (2.12.0-3) ... 187s Processing triggers for libc-bin (2.39-0ubuntu6) ... 187s Reading package lists... 188s Building dependency tree... 188s Reading state information... 188s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 188s sh: Attempting to set up Debian/Ubuntu apt sources automatically 188s sh: Distribution appears to be Ubuntu 189s Reading package lists... 189s Building dependency tree... 189s Reading state information... 190s eatmydata is already the newest version (131-1). 190s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 190s Reading package lists... 190s Building dependency tree... 190s Reading state information... 190s dbus is already the newest version (1.14.10-4ubuntu1). 190s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 190s Reading package lists... 190s Building dependency tree... 190s Reading state information... 190s rng-tools-debian is already the newest version (2.4). 190s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 190s Reading package lists... 190s Building dependency tree... 190s Reading state information... 191s The following packages will be REMOVED: 191s cloud-init* python3-configobj* python3-debconf* 191s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 191s After this operation, 3256 kB disk space will be freed. 191s (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.) 191s Removing cloud-init (24.1.2-0ubuntu1) ... 191s Removing python3-configobj (5.0.8-3) ... 192s Removing python3-debconf (1.5.86) ... 192s Processing triggers for man-db (2.12.0-3) ... 192s (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.) 192s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 193s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 193s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 193s invoke-rc.d: policy-rc.d denied execution of try-restart. 193s Reading package lists... 193s Building dependency tree... 193s Reading state information... 193s linux-generic is already the newest version (6.8.0-11.11+1). 193s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 193s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 194s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 194s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 196s Reading package lists... 196s Reading package lists... 197s Building dependency tree... 197s Reading state information... 197s Calculating upgrade... 197s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 197s Reading package lists... 197s Building dependency tree... 197s Reading state information... 197s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 197s autopkgtest [12:11:17]: rebooting testbed after setup commands that affected boot 236s autopkgtest [12:11:56]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 240s autopkgtest [12:12:00]: @@@@@@@@@@@@@@@@@@@@ apt-source shapeit4 277s Get:1 http://ftpmaster.internal/ubuntu noble/universe shapeit4 4.2.2+dfsg-1build1 (dsc) [2158 B] 277s Get:2 http://ftpmaster.internal/ubuntu noble/universe shapeit4 4.2.2+dfsg-1build1 (tar) [59.0 MB] 277s Get:3 http://ftpmaster.internal/ubuntu noble/universe shapeit4 4.2.2+dfsg-1build1 (diff) [5280 B] 277s gpgv: Signature made Tue Dec 19 15:03:10 2023 UTC 277s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 277s gpgv: Can't check signature: No public key 277s dpkg-source: warning: cannot verify inline signature for ./shapeit4_4.2.2+dfsg-1build1.dsc: no acceptable signature found 279s autopkgtest [12:12:39]: testing package shapeit4 version 4.2.2+dfsg-1build1 279s autopkgtest [12:12:39]: build not needed 286s autopkgtest [12:12:46]: test run-sample-analysis: preparing testbed 288s Reading package lists... 288s Building dependency tree... 288s Reading state information... 288s Starting pkgProblemResolver with broken count: 0 289s Starting 2 pkgProblemResolver with broken count: 0 289s Done 289s The following additional packages will be installed: 289s libboost-iostreams1.83.0 libboost-program-options1.83.0 libdeflate0 libhts3 289s libhtscodecs2 shapeit4 shapeit4-example 289s The following NEW packages will be installed: 289s autopkgtest-satdep libboost-iostreams1.83.0 libboost-program-options1.83.0 289s libdeflate0 libhts3 libhtscodecs2 shapeit4 shapeit4-example 289s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. 289s Need to get 53.9 MB/53.9 MB of archives. 289s After this operation, 59.8 MB of additional disk space will be used. 289s Get:1 /tmp/autopkgtest.vpr2vn/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [720 B] 289s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libboost-iostreams1.83.0 ppc64el 1.83.0-2ubuntu1 [340 kB] 289s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libboost-program-options1.83.0 ppc64el 1.83.0-2ubuntu1 [421 kB] 289s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 289s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 289s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB] 290s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el shapeit4 ppc64el 4.2.2+dfsg-1build1 [186 kB] 290s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el shapeit4-example all 4.2.2+dfsg-1build1 [52.3 MB] 293s Fetched 53.9 MB in 4s (14.3 MB/s) 293s Selecting previously unselected package libboost-iostreams1.83.0:ppc64el. 293s (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.) 293s Preparing to unpack .../0-libboost-iostreams1.83.0_1.83.0-2ubuntu1_ppc64el.deb ... 293s Unpacking libboost-iostreams1.83.0:ppc64el (1.83.0-2ubuntu1) ... 293s Selecting previously unselected package libboost-program-options1.83.0:ppc64el. 293s Preparing to unpack .../1-libboost-program-options1.83.0_1.83.0-2ubuntu1_ppc64el.deb ... 293s Unpacking libboost-program-options1.83.0:ppc64el (1.83.0-2ubuntu1) ... 293s Selecting previously unselected package libdeflate0:ppc64el. 293s Preparing to unpack .../2-libdeflate0_1.19-1_ppc64el.deb ... 293s Unpacking libdeflate0:ppc64el (1.19-1) ... 293s Selecting previously unselected package libhtscodecs2:ppc64el. 293s Preparing to unpack .../3-libhtscodecs2_1.6.0-1_ppc64el.deb ... 293s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 293s Selecting previously unselected package libhts3:ppc64el. 293s Preparing to unpack .../4-libhts3_1.18+ds-1_ppc64el.deb ... 293s Unpacking libhts3:ppc64el (1.18+ds-1) ... 293s Selecting previously unselected package shapeit4. 293s Preparing to unpack .../5-shapeit4_4.2.2+dfsg-1build1_ppc64el.deb ... 293s Unpacking shapeit4 (4.2.2+dfsg-1build1) ... 293s Selecting previously unselected package shapeit4-example. 293s Preparing to unpack .../6-shapeit4-example_4.2.2+dfsg-1build1_all.deb ... 293s Unpacking shapeit4-example (4.2.2+dfsg-1build1) ... 293s Selecting previously unselected package autopkgtest-satdep. 293s Preparing to unpack .../7-1-autopkgtest-satdep.deb ... 293s Unpacking autopkgtest-satdep (0) ... 293s Setting up libhtscodecs2:ppc64el (1.6.0-1) ... 293s Setting up libboost-program-options1.83.0:ppc64el (1.83.0-2ubuntu1) ... 293s Setting up libdeflate0:ppc64el (1.19-1) ... 293s Setting up shapeit4-example (4.2.2+dfsg-1build1) ... 293s Setting up libboost-iostreams1.83.0:ppc64el (1.83.0-2ubuntu1) ... 293s Setting up libhts3:ppc64el (1.18+ds-1) ... 293s Setting up shapeit4 (4.2.2+dfsg-1build1) ... 293s Setting up autopkgtest-satdep (0) ... 293s Processing triggers for man-db (2.12.0-3) ... 294s Processing triggers for libc-bin (2.39-0ubuntu6) ... 296s (Reading database ... 69776 files and directories currently installed.) 296s Removing autopkgtest-satdep (0) ... 297s autopkgtest [12:12:57]: test run-sample-analysis: [----------------------- 297s + shapeit4 --input unphased.vcf.gz --map chr20.b37.gmap.gz --region 20:2000000-3000000 --thread 4 --output phased.vcf.gz 297s 297s SHAPEIT 297s * Author : Olivier DELANEAU, University of Lausanne 297s * Contact : olivier.delaneau@gmail.com 297s * Version : 4.2.2 297s * Run date : 23/03/2024 - 12:12:57 297s 297s Files: 297s * Input VCF : [unphased.vcf.gz] 297s * Genetic Map : [chr20.b37.gmap.gz] 297s * Output VCF : [phased.vcf.gz] 297s 297s Parameters: 297s * Seed : 15052011 297s * Threads : 4 threads 297s * MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m] 297s * PBWT : Depth of PBWT neighbours to condition on: 4 297s * PBWT : Store indexes at variants [MAC>=2 / MDR<=0.5 / Dist=0.02 cM] 297s * HMM : K is variable / min W is 2.50cM / Ne is 15000 297s * HMM : Recombination rates given by genetic map 297s * HMM : AVX2 optimization inactive / Activating AVX2 substantially improves performance 297s 297s Initialization: 297s * VCF/BCF scanning ... * VCF/BCF scanning [N=203 / L=8651 / Reg=20:2000000-3000000] (0.13s) 297s * VCF/BCF parsing [0%] * VCF/BCF parsing [1%] * VCF/BCF parsing [2%] * VCF/BCF parsing [3%] * VCF/BCF 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PBWT selection [97%] * PBWT selection [98%] * PBWT selection [99%] * PBWT selection [100%] * PBWT selection (0.01s) 308s * C2H transpose (0.00s) 312s * 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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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) 318s * C2H transpose (0.00s) 321s * 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%] * 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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=223.783+/-13.766 / W=1.00Mb] (2.58s) 321s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 321s * HAP update (0.01s) 321s * H2V transpose (0.00s) 321s 321s Pruning iteration [1/1] 321s * V2H transpose (0.00s) 321s * 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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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) 328s * C2H transpose (0.00s) 330s * 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 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V2H transpose (0.00s) 330s * 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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constraints [#inds=0 / #contraints=0 / #merged = 0] 332s * HAP update (0.01s) 332s * H2V transpose (0.00s) 332s 332s Main iteration [3/5] 332s * V2H transpose (0.00s) 332s * PBWT selection [0%] * PBWT selection [1%] * PBWT selection [2%] * PBWT selection [3%] * PBWT selection [4%] * PBWT selection [5%] * PBWT selection [6%] * PBWT selection [7%] * PBWT selection [8%] * PBWT selection [9%] * PBWT selection [10%] * PBWT selection [11%] * PBWT selection [12%] * PBWT selection [13%] * PBWT selection [14%] * PBWT selection [15%] * PBWT selection [16%] * PBWT selection [17%] * PBWT selection [18%] * PBWT selection [19%] * PBWT selection [20%] * PBWT selection [21%] * PBWT selection [22%] * PBWT selection [23%] * PBWT selection [24%] * PBWT selection [25%] * PBWT selection [26%] * PBWT selection [27%] * PBWT selection [28%] * PBWT selection [29%] * PBWT selection [30%] * PBWT selection [31%] * PBWT selection [32%] * PBWT selection [33%] * PBWT selection [34%] * PBWT selection [35%] * PBWT 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computations [87%] * HMM computations [88%] * HMM computations [89%] * HMM computations [90%] * HMM computations [91%] * HMM computations [92%] * HMM computations [93%] * HMM computations [94%] * HMM computations [95%] * HMM computations [96%] * HMM computations [97%] * HMM computations [98%] * HMM computations [99%] * HMM computations [100%] * HMM computations [K=210.9+/-16.0 / W=1.00Mb / U=2] (2.01s) 338s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 338s * HAP update (0.01s) 338s * H2V transpose (0.00s) 338s 338s Finalization: 338s * HAP solving (0.02s) 338s * HAP update (0.01s) 338s * H2V transpose (0.00s) 338s * VCF writing [0%] * VCF writing [1%] * VCF writing [2%] * VCF writing [3%] * VCF writing [4%] * VCF writing [5%] * VCF writing [6%] * VCF writing [7%] * VCF writing [8%] * VCF writing [9%] * VCF writing [10%] * VCF writing [11%] * VCF writing [12%] * VCF writing [13%] * VCF writing [14%] * VCF writing [15%] * VCF writing [16%] * VCF writing [17%] * VCF writing [18%] * VCF writing [19%] * VCF writing [20%] * VCF writing [21%] * VCF writing [22%] * VCF writing [23%] * VCF writing [24%] * VCF writing [25%] * VCF writing [26%] * VCF writing [27%] * VCF writing [28%] * VCF writing [29%] * VCF writing [30%] * VCF writing [31%] * VCF writing [32%] * VCF writing [33%] * VCF writing [34%] * VCF writing [35%] * VCF writing [36%] * VCF writing [37%] * VCF writing [38%] * VCF writing [39%] * VCF writing [40%] * VCF writing [41%] * VCF writing [42%] * VCF writing [43%] * VCF writing [44%] * VCF writing [45%] * VCF writing [46%] * VCF writing [47%] * VCF writing [48%] * VCF writing [49%] * VCF writing [50%] * VCF writing [51%] * VCF writing [52%] * VCF writing [53%] * VCF writing [54%] * VCF writing [55%] * VCF writing [56%] * VCF writing [57%] * VCF writing [58%] * VCF writing [59%] * VCF writing [60%] * VCF writing [61%] * VCF writing [62%] * VCF writing [63%] * VCF writing [64%] * VCF writing [65%] * VCF writing [66%] * VCF writing [67%] * VCF writing [68%] * VCF writing [69%] * VCF writing [70%] * VCF writing [71%] * VCF writing [72%] * VCF writing [73%] * VCF writing [74%] * VCF writing [75%] * VCF writing [76%] * VCF writing [77%] * VCF writing [78%] * VCF writing [79%] * VCF writing [80%] * VCF writing [81%] * VCF writing [82%] * VCF writing [83%] * VCF writing [84%] * VCF writing [85%] * VCF writing [86%] * VCF writing [87%] * VCF writing [88%] * VCF writing [89%] * VCF writing [90%] * VCF writing [91%] * VCF writing [92%] * VCF writing [93%] * VCF writing [94%] * VCF writing [95%] * VCF writing [96%] * VCF writing [97%] * VCF writing [98%] * VCF writing [99%] * VCF writing [100%] * VCF writing [Compressed / N=203 / L=8651] (0.22s) 338s * Total running time = 41 seconds 338s + 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 338s 338s SHAPEIT 338s * Author : Olivier DELANEAU, University of Lausanne 338s * Contact : olivier.delaneau@gmail.com 338s * Version : 4.2.2 338s * Run date : 23/03/2024 - 12:13:38 338s 338s Files: 338s * Input VCF : [unphased.bcf] 338s * Reference VCF : [reference.bcf] 338s * Scaffold VCF : [scaffold.bcf] 338s * Genetic Map : [chr20.b37.gmap.gz] 338s * Output VCF : [phased.bcf] 338s * Output LOG : [phased.log] 338s 338s Parameters: 338s * Seed : 15052011 338s * Threads : 4 threads 338s * MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m] 338s * PBWT : Depth of PBWT neighbours to condition on: 4 338s * PBWT : Store indexes at variants [MAC>=2 / MDR<=0.5 / Dist=0.02 cM] 338s * HMM : K is variable / min W is 2.50cM / Ne is 15000 338s * HMM : Recombination rates given by genetic map 338s * HMM : Inform phasing using VCF/PS field / Error rate of PS field is 0.0001 338s * HMM : AVX2 optimization inactive / Activating AVX2 substantially improves performance 338s 338s Initialization: 339s * VCF/BCF scanning ... * VCF/BCF scanning [Nm=203 / Nr=300 / L=24990 / Reg=20] (0.10s) 339s * 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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[K=398.440+/-113.874 / W=2.20Mb] (10.21s) 500s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 500s * HAP update (0.01s) 500s * H2V transpose (0.00s) 500s 500s Main iteration [2/5] 500s * V2H transpose (0.00s) 500s * 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=386.095+/-114.190 / W=2.15Mb] (9.91s) 512s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 512s * HAP update (0.01s) 512s * H2V transpose (0.00s) 512s 512s Main iteration [3/5] 512s * V2H transpose (0.00s) 512s * 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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(0.05s) 530s * C2H transpose (0.00s) 540s * HMM computations [0%] * HMM computations [1%] * HMM computations [2%] * HMM computations [3%] * HMM computations [4%] * HMM computations [5%] * HMM computations [6%] * HMM computations [7%] * HMM computations [8%] * HMM computations [9%] * HMM computations [10%] * HMM computations [11%] * HMM computations [12%] * HMM computations [13%] * HMM computations [14%] * HMM computations [15%] * HMM computations [16%] * HMM computations [17%] * HMM computations [18%] * HMM computations [19%] * HMM computations [20%] * HMM computations [21%] * HMM computations [22%] * HMM computations [23%] * HMM computations [24%] * HMM computations [25%] * HMM computations [26%] * HMM computations [27%] * HMM computations [28%] * HMM computations [29%] * HMM computations [30%] * HMM computations [31%] * HMM computations [32%] * HMM computations [33%] * HMM computations [34%] * HMM computations [35%] * HMM computations [36%] * HMM computations [37%] * HMM computations [38%] * HMM computations [39%] * HMM computations [40%] * HMM computations [41%] * HMM computations [42%] * HMM computations [43%] * HMM computations [44%] * HMM computations [45%] * HMM computations [46%] * HMM computations [47%] * HMM computations [48%] * HMM computations [49%] * HMM computations [50%] * HMM computations [51%] * HMM computations [52%] * HMM computations [53%] * HMM computations [54%] * HMM computations [55%] * HMM computations [56%] * HMM computations [57%] * HMM computations [58%] * HMM computations [59%] * HMM computations [60%] * HMM computations [61%] * HMM computations [62%] * HMM computations [63%] * HMM computations [64%] * HMM computations [65%] * HMM computations [66%] * HMM computations [67%] * HMM computations [68%] * HMM computations [69%] * HMM computations [70%] * HMM computations [71%] * HMM computations [72%] * HMM computations [73%] * HMM computations [74%] * HMM computations [75%] * HMM computations [76%] * HMM computations [77%] * HMM computations [78%] * HMM computations [79%] * HMM computations [80%] * HMM computations [81%] * HMM computations [82%] * HMM computations [83%] * HMM computations [84%] * HMM computations [85%] * HMM computations [86%] * HMM computations [87%] * HMM computations [88%] * HMM computations [89%] * HMM computations [90%] * HMM computations [91%] * HMM computations [92%] * HMM computations [93%] * HMM computations [94%] * HMM computations [95%] * HMM computations [96%] * HMM computations [97%] * HMM computations [98%] * HMM computations [99%] * HMM computations [100%] * HMM computations [K=388.943+/-110.313 / W=2.17Mb] (9.95s) 540s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 540s * HAP update (0.01s) 540s * H2V transpose (0.00s) 540s 540s Finalization: 540s * HAP solving (0.04s) 540s * HAP update (0.03s) 540s * H2V transpose (0.00s) 540s * 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] (0.33s) 540s * Total running time = 201 seconds 540s autopkgtest [12:17:00]: test run-sample-analysis: -----------------------] 541s autopkgtest [12:17:01]: test run-sample-analysis: - - - - - - - - - - results - - - - - - - - - - 541s run-sample-analysis PASS 542s autopkgtest [12:17:02]: @@@@@@@@@@@@@@@@@@@@ summary 542s run-sample-analysis PASS 570s Creating nova instance adt-noble-ppc64el-shapeit4-20240323-120421-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-ppc64el-server-20240322.img (UUID 8499323f-6fcd-4f77-8a53-77410adea6d3)...