0s autopkgtest [22:25:44]: starting date and time: 2024-05-03 22:25:44+0000 0s autopkgtest [22:25:44]: git checkout: 699e7f9f ssh-setup/nova: explicitely set 'fqdn' in cloud-init 0s autopkgtest [22:25:44]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.pllesp0q/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:libmaus2 --apt-upgrade biobambam2 --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=libmaus2/2.0.813+ds-3 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos01-ppc64el-9.secgroup --name adt-oracular-ppc64el-biobambam2-20240503-222544-juju-7f2275-prod-proposed-migration-environment-3-88982b65-237d-477e-926b-b30b80782b91 --image adt/ubuntu-oracular-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,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://us.ports.ubuntu.com/ubuntu-ports/ 102s autopkgtest [22:27:26]: testbed dpkg architecture: ppc64el 102s autopkgtest [22:27:26]: testbed apt version: 2.7.14build2 102s autopkgtest [22:27:26]: @@@@@@@@@@@@@@@@@@@@ test bed setup 103s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [64.7 kB] 103s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [35.7 kB] 103s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [2800 B] 103s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [150 kB] 103s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [2016 kB] 105s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el Packages [206 kB] 105s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/restricted ppc64el Packages [1260 B] 105s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/universe ppc64el Packages [1449 kB] 105s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse ppc64el Packages [28.3 kB] 106s Fetched 3953 kB in 3s (1373 kB/s) 106s Reading package lists... 109s Reading package lists... 109s Building dependency tree... 109s Reading state information... 109s Calculating upgrade... 109s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 109s Reading package lists... 109s Building dependency tree... 109s Reading state information... 109s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 110s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 110s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 110s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 110s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 111s Reading package lists... 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s Calculating upgrade... 111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 111s Reading package lists... 112s Building dependency tree... 112s Reading state information... 112s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 115s autopkgtest [22:27:39]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP Sat Apr 20 00:05:55 UTC 2024 115s autopkgtest [22:27:39]: @@@@@@@@@@@@@@@@@@@@ apt-source biobambam2 118s Get:1 http://ftpmaster.internal/ubuntu oracular/universe biobambam2 2.0.185+ds-1 (dsc) [2257 B] 118s Get:2 http://ftpmaster.internal/ubuntu oracular/universe biobambam2 2.0.185+ds-1 (tar) [249 kB] 118s Get:3 http://ftpmaster.internal/ubuntu oracular/universe biobambam2 2.0.185+ds-1 (diff) [1032 kB] 118s gpgv: Signature made Mon Jan 2 20:43:59 2023 UTC 118s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 118s gpgv: issuer "emollier@debian.org" 118s gpgv: Can't check signature: No public key 118s dpkg-source: warning: cannot verify inline signature for ./biobambam2_2.0.185+ds-1.dsc: no acceptable signature found 118s autopkgtest [22:27:42]: testing package biobambam2 version 2.0.185+ds-1 119s autopkgtest [22:27:43]: build not needed 119s autopkgtest [22:27:43]: test run-unit-test: preparing testbed 120s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s Starting pkgProblemResolver with broken count: 0 121s Starting 2 pkgProblemResolver with broken count: 0 121s Done 121s The following additional packages will be installed: 121s biobambam2 libgomp1 libmaus2-2 121s Suggested packages: 121s secrecy 121s The following NEW packages will be installed: 121s autopkgtest-satdep biobambam2 libgomp1 libmaus2-2 121s 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 121s Need to get 11.4 MB/11.4 MB of archives. 121s After this operation, 78.2 MB of additional disk space will be used. 121s Get:1 /tmp/autopkgtest.LYoGcR/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [712 B] 121s Get:2 http://ftpmaster.internal/ubuntu oracular/main ppc64el libgomp1 ppc64el 14-20240412-0ubuntu1 [161 kB] 122s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/universe ppc64el libmaus2-2 ppc64el 2.0.813+ds-3 [2039 kB] 122s Get:4 http://ftpmaster.internal/ubuntu oracular/universe ppc64el biobambam2 ppc64el 2.0.185+ds-1 [9182 kB] 124s Fetched 11.4 MB in 3s (3961 kB/s) 124s Selecting previously unselected package libgomp1:ppc64el. 124s (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 ... 72135 files and directories currently installed.) 124s Preparing to unpack .../libgomp1_14-20240412-0ubuntu1_ppc64el.deb ... 124s Unpacking libgomp1:ppc64el (14-20240412-0ubuntu1) ... 124s Selecting previously unselected package libmaus2-2:ppc64el. 124s Preparing to unpack .../libmaus2-2_2.0.813+ds-3_ppc64el.deb ... 124s Unpacking libmaus2-2:ppc64el (2.0.813+ds-3) ... 124s Selecting previously unselected package biobambam2. 124s Preparing to unpack .../biobambam2_2.0.185+ds-1_ppc64el.deb ... 124s Unpacking biobambam2 (2.0.185+ds-1) ... 125s Selecting previously unselected package autopkgtest-satdep. 125s Preparing to unpack .../1-autopkgtest-satdep.deb ... 125s Unpacking autopkgtest-satdep (0) ... 125s Setting up libgomp1:ppc64el (14-20240412-0ubuntu1) ... 125s Setting up libmaus2-2:ppc64el (2.0.813+ds-3) ... 125s Setting up biobambam2 (2.0.185+ds-1) ... 125s Setting up autopkgtest-satdep (0) ... 125s Processing triggers for man-db (2.12.0-4build2) ... 125s Processing triggers for libc-bin (2.39-0ubuntu8) ... 128s (Reading database ... 72303 files and directories currently installed.) 128s Removing autopkgtest-satdep (0) ... 128s autopkgtest [22:27:52]: test run-unit-test: [----------------------- 129s Test 1 129s [V] 9997 01739470 MemUsage(size=436.312,rss=50.4375,peak=500.312) AutoArrayMemUsage(memusage=336.845,peakmemusage=0,maxmem=1.75922e+13) final 131s [V] flushing read ends lists...done. 132s [V] merging read ends lists/computing duplicates...done, time 01:00218740 132s [V] num dups 5373 132s # bamsormadup 132s 132s ##METRICS 132s LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE 132s Unknown Library 7917 0 2080 5373 0 0 0.678666 -1 132s 132s ## HISTOGRAM 132s BIN VALUE 132s [V] temp file id 0 name bamsormadup_autopkgtest_2076_1714775273_algn_frag_000000 count 1 132s [V] temp file id 1 name bamsormadup_autopkgtest_2076_1714775273_algn_frag_000001 count 1 132s [V] blocks generated in time 03:01221067 132s [V] number of blocks to be merged is 1 using 8192 blocks per input with block size 1048576 132s [V] 9997 133s [D] md5 b2a238aa684719383cc98af29a9a8ba0 133s [V] checksum ok 133s [V] blocks merged in time 01:08741158 133s [V] run time 04:24457132 (4.24458 s) MemUsage(size=8312.12,rss=554,peak=9336.38) 133s Passed 133s 133s Test 2 133s [V] 9997 133s [V] MemUsage(size=27.9375,rss=13.5,peak=256) wall clock time 45430310 133s Passed 133s 133s Test 3 133s [V] output compression level -1 134s [D] excntpairs=0 fincntpairs=0 strcntpairs=0 134s [D] excntfrags=0 fincntfrags=4689 strcntfrags=0 134s [V] fragment and pair data computed in time 1.11541 (01:11547455) 135s [V] 9997 lines, 9997 als, 4689 mapped frags, 0 mapped pairs, 210936 frags/s MemUsage(size=45.25,rss=30.5625,peak=478.438) 135s [V] Checking pairs...done, rate 0 135s [V] Checking single fragments...done, rate 0 135s [V] number of alignments marked as duplicates: 4225 time 1.12076 (01:12084000) 135s # bammarkduplicates2 I=SRR11728641.bam O=SRR11728641.uniq.bam D=SRR11728641.dups.bam rmdup=1 135s 135s ##METRICS 135s LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE 135s Unknown Library 4689 0 5308 4225 0 0 0.901045 -1 135s 135s ## HISTOGRAM 135s BIN VALUE 135s [V] Filtered 9996(0,1) total for marking time 08997294 MemUsage(size=45.25,rss=30.5625,peak=478.438)Passed 135s 135s Test 4 135s 135s [V] MemUsage(size=45.25,rss=30.5625,peak=478.438) 1.21609 (01:21608931) 135s [V] output compression level -1 136s [D] excntpairs=0 fincntpairs=0 strcntpairs=0 136s [D] excntfrags=0 fincntfrags=4689 strcntfrags=0 136s [V] fragment and pair data computed in time 1.11083 (01:11084305) 136s [V] 9997 lines, 9997 als, 4689 mapped frags, 0 mapped pairs, 216724 frags/s MemUsage(size=45.25,rss=30.5625,peak=478.438) 136s [V] Checking pairs...done, rate 0 136s [V] Checking single fragments...done, rate 0 136s [V] number of alignments marked as duplicates: 4225 time 1.11447 (01:11447388) 136s # bammarkduplicates2 I=SRR11728641.bam O=SRR11728641.dupmarked.bam md5=1 md5filename=SRR11728641.dupmarked.bam.md5 136s 136s ##METRICS 136s LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE 136s Unknown Library 4689 0 5308 4225 0 0 0.901045 -1 136s 136s ## HISTOGRAM 136s BIN VALUE 136s [D] using incremental BAM header parser on serial decoder. 136s [V] Marked 1 total for marking time 08787956 MemUsage(size=45.25,rss=30.5625,peak=478.438) 136s [V] MemUsage(size=Passed 136s 136s Test 5 136s 45.25,rss=30.5625,peak=478.438) 1.20532 (01:20531818) 136s Keeping flags 1;2;4;8;32;64;128;256;512;1024;2048; 136s Erasing flags 16; 136s Passed 136s 136s Test 6 136s 00075534 0MB, 0.372484MB/s 137s 83624539 2MB, 3.03508MB/s 138s Passed 138s 138s Test 7 138s [V] Reading alignments from source. 138s [V] read 9997 alignments 138s [V] producing sorted output 138s [V] wrote 9997 alignments 138s Passed 138s 138s Test 8 138s [V] 9997 138s [V] MemUsage(size=27.125,rss=12.5,peak=160.062) wall clock time 29078561 138s Passed 138s 139s autopkgtest [22:28:03]: test run-unit-test: -----------------------] 139s autopkgtest [22:28:03]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 139s run-unit-test PASS 140s autopkgtest [22:28:04]: @@@@@@@@@@@@@@@@@@@@ summary 140s run-unit-test PASS 154s Creating nova instance adt-oracular-ppc64el-biobambam2-20240503-222544-juju-7f2275-prod-proposed-migration-environment-3-88982b65-237d-477e-926b-b30b80782b91 from image adt/ubuntu-oracular-ppc64el-server-20240503.img (UUID 60999710-d97e-47d3-8cca-85ddcf19ebc0)...