0s autopkgtest [22:43:42]: starting date and time: 2024-05-05 22:43:42+0000 0s autopkgtest [22:43:42]: git checkout: 699e7f9f ssh-setup/nova: explicitely set 'fqdn' in cloud-init 0s autopkgtest [22:43:42]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.atkxd1z2/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@lcy02-13.secgroup --name adt-oracular-amd64-biobambam2-20240505-221601-juju-7f2275-prod-proposed-migration-environment-3-d1c69820-0799-4297-a135-06ef6dee61b6 --image adt/ubuntu-oracular-amd64-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://ftpmaster.internal/ubuntu/ 322s autopkgtest [22:49:04]: testbed dpkg architecture: amd64 323s autopkgtest [22:49:05]: testbed apt version: 2.7.14build2 323s autopkgtest [22:49:05]: @@@@@@@@@@@@@@@@@@@@ test bed setup 323s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [64.7 kB] 323s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [108 kB] 323s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [2800 B] 323s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [23.5 kB] 323s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [1639 kB] 323s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main i386 Packages [165 kB] 323s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 Packages [192 kB] 323s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 Packages [8572 B] 323s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted i386 Packages [1260 B] 323s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 Packages [1298 kB] 323s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe i386 Packages [635 kB] 323s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse i386 Packages [16.0 kB] 323s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 Packages [52.6 kB] 323s Fetched 4206 kB in 1s (7381 kB/s) 323s Reading package lists... 325s Reading package lists... 325s Building dependency tree... 325s Reading state information... 325s Calculating upgrade... 325s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 325s Reading package lists... 326s Building dependency tree... 326s Reading state information... 326s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 326s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 326s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 326s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 326s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 327s Reading package lists... 327s Reading package lists... 328s Building dependency tree... 328s Reading state information... 328s Calculating upgrade... 328s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 328s Reading package lists... 328s Building dependency tree... 328s Reading state information... 329s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 329s autopkgtest [22:49:11]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 00:40:06 UTC 2024 329s autopkgtest [22:49:11]: @@@@@@@@@@@@@@@@@@@@ apt-source biobambam2 330s Get:1 http://ftpmaster.internal/ubuntu oracular/universe biobambam2 2.0.185+ds-1 (dsc) [2257 B] 330s Get:2 http://ftpmaster.internal/ubuntu oracular/universe biobambam2 2.0.185+ds-1 (tar) [249 kB] 330s Get:3 http://ftpmaster.internal/ubuntu oracular/universe biobambam2 2.0.185+ds-1 (diff) [1032 kB] 330s gpgv: Signature made Mon Jan 2 20:43:59 2023 UTC 330s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 330s gpgv: issuer "emollier@debian.org" 330s gpgv: Can't check signature: No public key 330s dpkg-source: warning: cannot verify inline signature for ./biobambam2_2.0.185+ds-1.dsc: no acceptable signature found 330s autopkgtest [22:49:12]: testing package biobambam2 version 2.0.185+ds-1 330s autopkgtest [22:49:12]: build not needed 330s autopkgtest [22:49:12]: test run-unit-test: preparing testbed 331s Reading package lists... 331s Building dependency tree... 331s Reading state information... 331s Starting pkgProblemResolver with broken count: 0 331s Starting 2 pkgProblemResolver with broken count: 0 331s Done 332s The following additional packages will be installed: 332s biobambam2 libgomp1 libmaus2-2 332s Suggested packages: 332s secrecy 332s The following NEW packages will be installed: 332s autopkgtest-satdep biobambam2 libgomp1 libmaus2-2 332s 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 332s Need to get 11.3 MB/11.3 MB of archives. 332s After this operation, 63.6 MB of additional disk space will be used. 332s Get:1 /tmp/autopkgtest.av4lFi/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [704 B] 332s Get:2 http://ftpmaster.internal/ubuntu oracular/main amd64 libgomp1 amd64 14-20240412-0ubuntu1 [147 kB] 332s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 libmaus2-2 amd64 2.0.813+ds-3 [1564 kB] 332s Get:4 http://ftpmaster.internal/ubuntu oracular/universe amd64 biobambam2 amd64 2.0.185+ds-1 [9634 kB] 332s Fetched 11.3 MB in 0s (37.0 MB/s) 332s Selecting previously unselected package libgomp1:amd64. 333s (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 ... 73894 files and directories currently installed.) 333s Preparing to unpack .../libgomp1_14-20240412-0ubuntu1_amd64.deb ... 333s Unpacking libgomp1:amd64 (14-20240412-0ubuntu1) ... 333s Selecting previously unselected package libmaus2-2:amd64. 333s Preparing to unpack .../libmaus2-2_2.0.813+ds-3_amd64.deb ... 333s Unpacking libmaus2-2:amd64 (2.0.813+ds-3) ... 333s Selecting previously unselected package biobambam2. 333s Preparing to unpack .../biobambam2_2.0.185+ds-1_amd64.deb ... 333s Unpacking biobambam2 (2.0.185+ds-1) ... 333s Selecting previously unselected package autopkgtest-satdep. 333s Preparing to unpack .../1-autopkgtest-satdep.deb ... 333s Unpacking autopkgtest-satdep (0) ... 333s Setting up libgomp1:amd64 (14-20240412-0ubuntu1) ... 333s Setting up libmaus2-2:amd64 (2.0.813+ds-3) ... 333s Setting up biobambam2 (2.0.185+ds-1) ... 333s Setting up autopkgtest-satdep (0) ... 333s Processing triggers for man-db (2.12.0-4build2) ... 334s Processing triggers for libc-bin (2.39-0ubuntu8) ... 335s (Reading database ... 74062 files and directories currently installed.) 335s Removing autopkgtest-satdep (0) ... 335s autopkgtest [22:49:17]: test run-unit-test: [----------------------- 336s Test 1 336s [V] 9997 01151042 MemUsage(size=753.172,rss=15.5,peak=817.172) AutoArrayMemUsage(memusage=593.072,peakmemusage=593.072,maxmem=1.75922e+13) final 338s [V] flushing read ends lists...done. 339s [V] merging read ends lists/computing duplicates...done, time 01:00347445 339s [V] num dups 5373 339s # bamsormadup 339s 339s ##METRICS 339s LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE 339s Unknown Library 7917 0 2080 5373 0 0 0.678666 -1 339s 339s ## HISTOGRAM 339s BIN VALUE 339s [V] temp file id 0 name bamsormadup_autopkgtest_2027_1714949358_algn_frag_000000 count 1 339s [V] temp file id 1 name bamsormadup_autopkgtest_2027_1714949358_algn_frag_000001 count 1 339s [V] blocks generated in time 03:01627965 339s [V] number of blocks to be merged is 1 using 8192 blocks per input with block size 1048576 339s [V] 9997 340s [D] md5 98938f224d078462ba4b3e5019e5f620 340s [V] checksum ok 340s [V] blocks merged in time 01:04858863 340s [V] run time 04:12433517 (4.12435 s) MemUsage(size=8445.25,rss=69.7461,peak=9469.26) 340s Passed 340s 340s Test 2 340s [V] 9997 340s [V] MemUsage(size=17.2383,rss=9.46484,peak=244.891) wall clock time 29265334 340s Passed 340s 340s Test 3 340s [V] output compression level -1 341s [D] excntpairs=0 fincntpairs=0 strcntpairs=0 341s [D] excntfrags=0 fincntfrags=4689 strcntfrags=0 341s [V] fragment and pair data computed in time 0.527876 (52792094) 341s [V] 9997 lines, 9997 als, 4689 mapped frags, 0 mapped pairs, 214480 frags/s MemUsage(size=34.4961,rss=26.7148,peak=467.039) 341s [V] Checking pairs...done, rate 0 341s [V] Checking single fragments...done, rate 0 341s [V] number of alignments marked as duplicates: 4225 time 0.53273 (53273373) 341s # bammarkduplicates2 I=SRR11728641.bam O=SRR11728641.uniq.bam D=SRR11728641.dups.bam rmdup=1 341s 341s ##METRICS 341s LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE 341s Unknown Library 4689 0 5308 4225 0 0 0.901045 -1 341s 341s ## HISTOGRAM 341s BIN VALUE 341s [V] Filtered 9996(0,1) total for marking time 06858775 MemUsage(size=34.4961,rss=26.8398,peak=467.039) 341s [V] MemUsage(size=34.4961,rss=26.8398,peak=467.039) 0.607885 (60788693) 341s Passed 341s 341s Test 4 341s [V] output compression level -1 341s [D] excntpairs=0 fincntpairs=0 strcntpairs=0 341s [D] excntfrags=0 fincntfrags=4689 strcntfrags=0 341s [V] fragment and pair data computed in time 0.543329 (54334976) 341s [V] 9997 lines, 9997 als, 4689 mapped frags, 0 mapped pairs, 225522 frags/s MemUsage(size=34.4961,rss=26.7109,peak=467.039) 341s [V] Checking pairs...done, rate 0 341s [V] Checking single fragments...done, rate 0 341s [V] number of alignments marked as duplicates: 4225 time 0.548371 (54837547) 341s # bammarkduplicates2 I=SRR11728641.bam O=SRR11728641.dupmarked.bam md5=1 md5filename=SRR11728641.dupmarked.bam.md5 341s 341s ##METRICS 341s LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE 341s Unknown Library 4689 0 5308 4225 0 0 0.901045 -1 341s 341s ## HISTOGRAM 341s BIN VALUE 341s [D] using incremental BAM header parser on serial decoder. 341s [V] Marked 1 total for marking time 06937555 MemUsage(size=34.4961,rss=26.8359,peak=467.039) 341s [V] MemUsage(size=34.4961,rss=26.8359,peak=467.039) 0.619499 (61950105) 341s Passed 341s 341s Test 5 341s Keeping flags 1;2;4;8;32;64;128;256;512;1024;2048; 341s Erasing flags 16; 341s Passed 341s 341s Test 6 341s 00009611 0MB, 2.52472MB/s 342s 53476728 2MB, 4.74659MB/s 343s Passed 343s 343s Test 7 343s [V] Reading alignments from source. 343s [V] read 9997 alignments 343s [V] producing sorted output 343s [V] wrote 9997 alignments 343s Passed 343s 343s Test 8 343s Passed 343s 343s [V] 9997 343s [V] MemUsage(size=16.418,rss=8.60938,peak=148.945) wall clock time 16561986 344s autopkgtest [22:49:26]: test run-unit-test: -----------------------] 344s autopkgtest [22:49:26]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 344s run-unit-test PASS 344s autopkgtest [22:49:26]: @@@@@@@@@@@@@@@@@@@@ summary 344s run-unit-test PASS 369s Creating nova instance adt-oracular-amd64-biobambam2-20240505-221601-juju-7f2275-prod-proposed-migration-environment-3-d1c69820-0799-4297-a135-06ef6dee61b6 from image adt/ubuntu-oracular-amd64-server-20240505.img (UUID b7c640bd-0b66-4d87-8d8c-2bf086621bf4)...