0s autopkgtest [11:36:47]: starting date and time: 2024-03-24 11:36:47+0000 0s autopkgtest [11:36:47]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [11:36:47]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.8dwdewk1/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-3@bos02-ppc64el-5.secgroup --name adt-noble-ppc64el-shapeit4-20240324-113647-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/ 113s autopkgtest [11:38:40]: testbed dpkg architecture: ppc64el 113s autopkgtest [11:38:40]: testbed apt version: 2.7.12 113s autopkgtest [11:38:40]: @@@@@@@@@@@@@@@@@@@@ test bed setup 114s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 114s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 114s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 114s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [494 kB] 115s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3983 kB] 117s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [696 kB] 117s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 117s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 117s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 117s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4267 kB] 118s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 118s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [60.8 kB] 118s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 120s Fetched 9695 kB in 4s (2231 kB/s) 121s Reading package lists... 123s Reading package lists... 124s Building dependency tree... 124s Reading state information... 124s Calculating upgrade... 124s The following packages will be REMOVED: 124s libssl3 124s The following NEW packages will be installed: 124s libssl3t64 124s The following packages have been kept back: 124s curl 124s The following packages will be upgraded: 124s openssl 124s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 124s Need to get 3151 kB of archives. 124s After this operation, 73.7 kB of additional disk space will be used. 124s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu2 [1026 kB] 125s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu2 [2125 kB] 125s Fetched 3151 kB in 1s (4527 kB/s) 125s (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.) 125s Preparing to unpack .../openssl_3.0.13-0ubuntu2_ppc64el.deb ... 125s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 125s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested: 125s wget depends on libssl3 (>= 3.0.0). 125s tnftp depends on libssl3 (>= 3.0.0). 125s tcpdump depends on libssl3 (>= 3.0.0). 125s systemd-resolved depends on libssl3 (>= 3.0.0). 125s systemd depends on libssl3 (>= 3.0.0). 125s sudo depends on libssl3 (>= 3.0.0). 125s rsync depends on libssl3 (>= 3.0.0). 125s python3-cryptography depends on libssl3 (>= 3.0.0). 125s openssh-server depends on libssl3 (>= 3.0.10). 125s openssh-client depends on libssl3 (>= 3.0.10). 126s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 126s libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0). 126s libssh-4:ppc64el depends on libssl3 (>= 3.0.0). 126s libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0). 126s libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0). 126s libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0). 126s libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0). 126s libnvme1 depends on libssl3 (>= 3.0.0). 126s libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0). 126s libkmod2:ppc64el depends on libssl3 (>= 3.0.0). 126s libfido2-1:ppc64el depends on libssl3 (>= 3.0.0). 126s libcurl4:ppc64el depends on libssl3 (>= 3.0.0). 126s libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0). 126s kmod depends on libssl3 (>= 3.0.0). 126s dhcpcd-base depends on libssl3 (>= 3.0.0). 126s bind9-libs:ppc64el depends on libssl3 (>= 3.0.0). 126s 126s (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.) 126s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ... 126s Selecting previously unselected package libssl3t64:ppc64el. 126s (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.) 126s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_ppc64el.deb ... 126s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 126s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 126s Setting up openssl (3.0.13-0ubuntu2) ... 126s Processing triggers for man-db (2.12.0-3) ... 127s Processing triggers for libc-bin (2.39-0ubuntu6) ... 127s Reading package lists... 127s Building dependency tree... 127s Reading state information... 127s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 128s sh: Attempting to set up Debian/Ubuntu apt sources automatically 128s sh: Distribution appears to be Ubuntu 128s Reading package lists... 128s Building dependency tree... 128s Reading state information... 129s eatmydata is already the newest version (131-1). 129s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 129s Reading package lists... 129s Building dependency tree... 129s Reading state information... 129s dbus is already the newest version (1.14.10-4ubuntu1). 129s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 129s Reading package lists... 129s Building dependency tree... 129s Reading state information... 129s rng-tools-debian is already the newest version (2.4). 129s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 129s Reading package lists... 129s Building dependency tree... 129s Reading state information... 130s The following packages will be REMOVED: 130s cloud-init* python3-configobj* python3-debconf* 130s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 130s After this operation, 3256 kB disk space will be freed. 130s (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.) 130s Removing cloud-init (24.1.2-0ubuntu1) ... 130s Removing python3-configobj (5.0.8-3) ... 130s Removing python3-debconf (1.5.86) ... 130s Processing triggers for man-db (2.12.0-3) ... 131s (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.) 131s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 131s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 131s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 131s invoke-rc.d: policy-rc.d denied execution of try-restart. 132s Reading package lists... 132s Building dependency tree... 132s Reading state information... 132s linux-generic is already the newest version (6.8.0-11.11+1). 132s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 132s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 132s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 132s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 135s Reading package lists... 135s Reading package lists... 135s Building dependency tree... 135s Reading state information... 135s Calculating upgrade... 135s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 135s Reading package lists... 136s Building dependency tree... 136s Reading state information... 136s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 136s autopkgtest [11:39:03]: rebooting testbed after setup commands that affected boot 176s autopkgtest [11:39:43]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 178s autopkgtest [11:39:45]: @@@@@@@@@@@@@@@@@@@@ apt-source shapeit4 182s Get:1 http://ftpmaster.internal/ubuntu noble/universe shapeit4 4.2.2+dfsg-1build1 (dsc) [2158 B] 182s Get:2 http://ftpmaster.internal/ubuntu noble/universe shapeit4 4.2.2+dfsg-1build1 (tar) [59.0 MB] 182s Get:3 http://ftpmaster.internal/ubuntu noble/universe shapeit4 4.2.2+dfsg-1build1 (diff) [5280 B] 182s gpgv: Signature made Tue Dec 19 15:03:10 2023 UTC 182s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 182s gpgv: Can't check signature: No public key 182s dpkg-source: warning: cannot verify inline signature for ./shapeit4_4.2.2+dfsg-1build1.dsc: no acceptable signature found 184s autopkgtest [11:39:51]: testing package shapeit4 version 4.2.2+dfsg-1build1 184s autopkgtest [11:39:51]: build not needed 187s autopkgtest [11:39:54]: test run-sample-analysis: preparing testbed 191s Reading package lists... 191s Building dependency tree... 191s Reading state information... 192s Starting pkgProblemResolver with broken count: 0 192s Starting 2 pkgProblemResolver with broken count: 0 192s Done 192s The following additional packages will be installed: 192s libboost-iostreams1.83.0 libboost-program-options1.83.0 libdeflate0 libhts3 192s libhtscodecs2 shapeit4 shapeit4-example 192s The following NEW packages will be installed: 192s autopkgtest-satdep libboost-iostreams1.83.0 libboost-program-options1.83.0 192s libdeflate0 libhts3 libhtscodecs2 shapeit4 shapeit4-example 192s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. 192s Need to get 53.9 MB/53.9 MB of archives. 192s After this operation, 59.8 MB of additional disk space will be used. 192s Get:1 /tmp/autopkgtest.8oEUm2/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [716 B] 192s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libboost-iostreams1.83.0 ppc64el 1.83.0-2ubuntu1 [340 kB] 192s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libboost-program-options1.83.0 ppc64el 1.83.0-2ubuntu1 [421 kB] 192s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 192s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 192s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB] 192s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el shapeit4 ppc64el 4.2.2+dfsg-1build1 [186 kB] 192s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el shapeit4-example all 4.2.2+dfsg-1build1 [52.3 MB] 195s Fetched 53.9 MB in 3s (21.3 MB/s) 195s Selecting previously unselected package libboost-iostreams1.83.0:ppc64el. 195s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 69714 files and directories currently installed.) 195s Preparing to unpack .../0-libboost-iostreams1.83.0_1.83.0-2ubuntu1_ppc64el.deb ... 195s Unpacking libboost-iostreams1.83.0:ppc64el (1.83.0-2ubuntu1) ... 195s Selecting previously unselected package libboost-program-options1.83.0:ppc64el. 195s Preparing to unpack .../1-libboost-program-options1.83.0_1.83.0-2ubuntu1_ppc64el.deb ... 195s Unpacking libboost-program-options1.83.0:ppc64el (1.83.0-2ubuntu1) ... 195s Selecting previously unselected package libdeflate0:ppc64el. 195s Preparing to unpack .../2-libdeflate0_1.19-1_ppc64el.deb ... 195s Unpacking libdeflate0:ppc64el (1.19-1) ... 195s Selecting previously unselected package libhtscodecs2:ppc64el. 195s Preparing to unpack .../3-libhtscodecs2_1.6.0-1_ppc64el.deb ... 195s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 195s Selecting previously unselected package libhts3:ppc64el. 195s Preparing to unpack .../4-libhts3_1.18+ds-1_ppc64el.deb ... 195s Unpacking libhts3:ppc64el (1.18+ds-1) ... 195s Selecting previously unselected package shapeit4. 195s Preparing to unpack .../5-shapeit4_4.2.2+dfsg-1build1_ppc64el.deb ... 195s Unpacking shapeit4 (4.2.2+dfsg-1build1) ... 195s Selecting previously unselected package shapeit4-example. 195s Preparing to unpack .../6-shapeit4-example_4.2.2+dfsg-1build1_all.deb ... 195s Unpacking shapeit4-example (4.2.2+dfsg-1build1) ... 195s Selecting previously unselected package autopkgtest-satdep. 195s Preparing to unpack .../7-1-autopkgtest-satdep.deb ... 195s Unpacking autopkgtest-satdep (0) ... 195s Setting up libhtscodecs2:ppc64el (1.6.0-1) ... 195s Setting up libboost-program-options1.83.0:ppc64el (1.83.0-2ubuntu1) ... 195s Setting up libdeflate0:ppc64el (1.19-1) ... 195s Setting up shapeit4-example (4.2.2+dfsg-1build1) ... 195s Setting up libboost-iostreams1.83.0:ppc64el (1.83.0-2ubuntu1) ... 195s Setting up libhts3:ppc64el (1.18+ds-1) ... 195s Setting up shapeit4 (4.2.2+dfsg-1build1) ... 195s Setting up autopkgtest-satdep (0) ... 195s Processing triggers for man-db (2.12.0-3) ... 196s Processing triggers for libc-bin (2.39-0ubuntu6) ... 198s (Reading database ... 69776 files and directories currently installed.) 198s Removing autopkgtest-satdep (0) ... 198s autopkgtest [11:40:05]: test run-sample-analysis: [----------------------- 199s 199s + shapeit4 --input unphased.vcf.gz --map chr20.b37.gmap.gz --region 20:2000000-3000000 --thread 4 --output phased.vcf.gz 199s SHAPEIT 199s * Author : Olivier DELANEAU, University of Lausanne 199s * Contact : olivier.delaneau@gmail.com 199s * Version : 4.2.2 199s * Run date : 24/03/2024 - 11:40:05 199s 199s Files: 199s * Input VCF : [unphased.vcf.gz] 199s * Genetic Map : [chr20.b37.gmap.gz] 199s * Output VCF : [phased.vcf.gz] 199s 199s Parameters: 199s * Seed : 15052011 199s * Threads : 4 threads 199s * MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m] 199s * PBWT : Depth of PBWT neighbours to condition on: 4 199s * PBWT : Store indexes at variants [MAC>=2 / MDR<=0.5 / Dist=0.02 cM] 199s * HMM : K is variable / min W is 2.50cM / Ne is 15000 199s * HMM : Recombination rates given by genetic map 199s * HMM : AVX2 optimization inactive / Activating AVX2 substantially improves performance 199s 199s Initialization: 199s * VCF/BCF scanning ... * VCF/BCF scanning [N=203 / L=8651 / Reg=20:2000000-3000000] (0.11s) 199s * 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) 199s * GMAP parsing [n=82962] (0.06s) 199s * cM interpolation [s=1236 / i=7415] (0.00s) 199s * Region length [999850 bp / 2.5 cM] 199s * HMM parameters [Ne=15000 / Error=0.0001 / #rare=2243] 199s * PBWT indexing [l=120] (0.00s) 199s * HAP update (0.01s) 199s * H2V transpose (0.00s) 199s * 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 [53%] * PBWT phase sweep [54%] * PBWT phase sweep [55%] * PBWT phase sweep [56%] * PBWT phase sweep [57%] * PBWT phase sweep [58%] * PBWT phase sweep [59%] * PBWT phase sweep [60%] * PBWT phase sweep [61%] * PBWT phase sweep [62%] * PBWT phase sweep [63%] * PBWT phase sweep [64%] * PBWT phase sweep [65%] * PBWT phase sweep [66%] * PBWT phase sweep [67%] * PBWT phase sweep [68%] * PBWT phase sweep [69%] * PBWT phase sweep [70%] * PBWT phase sweep [71%] * PBWT phase sweep [72%] * PBWT phase sweep [73%] * PBWT phase sweep [74%] * PBWT phase sweep [75%] * PBWT phase sweep [76%] * PBWT phase sweep [77%] * PBWT phase sweep [78%] * PBWT phase sweep [79%] * PBWT phase sweep [80%] * PBWT phase sweep [81%] * PBWT phase sweep [82%] * PBWT phase sweep [83%] * PBWT phase sweep [84%] * PBWT phase sweep [85%] * PBWT phase sweep [86%] * PBWT phase sweep [87%] * PBWT phase sweep [88%] * PBWT phase sweep [89%] * PBWT phase sweep [90%] * PBWT phase sweep [91%] * PBWT phase sweep [92%] * PBWT phase sweep [93%] * PBWT phase sweep [94%] * PBWT phase sweep [95%] * PBWT phase sweep [96%] * PBWT phase sweep [97%] * PBWT phase sweep [98%] * PBWT phase sweep [99%] * PBWT phase sweep [100%] * PBWT phase sweep (0.07s) 199s * Build genotype graphs [seg=62841] (0.03s) 199s 199s Burn-in iteration [1/5] 199s * V2H transpose (0.00s) 199s * 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) 209s * C2H transpose (0.00s) 211s * 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=222.985+/-14.963 / W=1.00Mb] (2.31s) 220s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 220s * HAP update (0.01s) 220s * H2V transpose (0.00s) 220s 220s Pruning iteration [1/1] 220s * V2H transpose (0.00s) 220s * 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] 230s * HAP update (0.01s) 230s * H2V transpose (0.00s) 230s 230s Main iteration [3/5] 230s * V2H transpose (0.00s) 230s * 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) 236s * Total running time = 37 seconds 236s + 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 236s 236s SHAPEIT 236s * Author : Olivier DELANEAU, University of Lausanne 236s * Contact : olivier.delaneau@gmail.com 236s * Version : 4.2.2 236s * Run date : 24/03/2024 - 11:40:43 236s 236s Files: 236s * Input VCF : [unphased.bcf] 236s * Reference VCF : [reference.bcf] 236s * Scaffold VCF : [scaffold.bcf] 236s * Genetic Map : [chr20.b37.gmap.gz] 236s * Output VCF : [phased.bcf] 236s * Output LOG : [phased.log] 236s 236s Parameters: 236s * Seed : 15052011 236s * Threads : 4 threads 236s * MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m] 236s * PBWT : Depth of PBWT neighbours to condition on: 4 236s * PBWT : Store indexes at variants [MAC>=2 / MDR<=0.5 / Dist=0.02 cM] 236s * HMM : K is variable / min W is 2.50cM / Ne is 15000 236s * HMM : Recombination rates given by genetic map 236s * HMM : Inform phasing using VCF/PS field / Error rate of PS field is 0.0001 236s * HMM : AVX2 optimization inactive / Activating AVX2 substantially improves performance 236s 236s Initialization: 236s * VCF/BCF scanning ... * VCF/BCF scanning [Nm=203 / Nr=300 / L=24990 / Reg=20] (0.09s) 236s * 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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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=389.581+/-111.640 / W=2.15Mb] (8.93s) 379s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 379s * HAP update (0.01s) 379s * H2V transpose (0.00s) 379s 379s Main iteration [2/5] 379s * V2H transpose (0.00s) 379s * 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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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) 379s * C2H transpose (0.00s) 388s * 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 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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=402.782+/-113.849 / W=2.25Mb] (9.14s) 388s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 388s * HAP update (0.01s) 388s * H2V transpose (0.00s) 388s 388s Main iteration [3/5] 388s * V2H transpose (0.00s) 388s * 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) 388s * C2H transpose (0.00s) 397s * 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=399.793+/-113.665 / W=2.22Mb] (9.06s) 406s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 406s * HAP update (0.01s) 406s * H2V transpose (0.00s) 406s 406s Main iteration [5/5] 406s * V2H transpose (0.00s) 406s * 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) 406s * C2H transpose (0.00s) 416s * 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=400.169+/-116.200 / W=2.24Mb] (9.07s) 416s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 416s * HAP update (0.01s) 416s * H2V transpose (0.00s) 416s 416s Finalization: 416s * HAP solving (0.03s) 416s * HAP update (0.01s) 416s * H2V transpose (0.00s) 416s * 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] (0.28s) 416s * Total running time = 179 seconds 416s autopkgtest [11:43:43]: test run-sample-analysis: -----------------------] 417s autopkgtest [11:43:44]: test run-sample-analysis: - - - - - - - - - - results - - - - - - - - - - 417s run-sample-analysis PASS 417s autopkgtest [11:43:44]: @@@@@@@@@@@@@@@@@@@@ summary 417s run-sample-analysis PASS 428s Creating nova instance adt-noble-ppc64el-shapeit4-20240324-113647-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-ppc64el-server-20240323.img (UUID ff8abf95-5243-4ea5-b7f5-3bf690534a1d)...