0s autopkgtest [18:33:25]: starting date and time: 2024-03-25 18:33:25+0000 0s autopkgtest [18:33:25]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [18:33:25]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.2ug4aowi/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:berkeley-express,src:protobuf --apt-upgrade berkeley-express --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=berkeley-express/1.5.3+dfsg-3build4 protobuf/3.21.12-8.2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-s390x-4.secgroup --name adt-noble-s390x-berkeley-express-20240325-183325-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 105s autopkgtest [18:35:10]: testbed dpkg architecture: s390x 105s autopkgtest [18:35:10]: testbed apt version: 2.7.12 105s autopkgtest [18:35:10]: @@@@@@@@@@@@@@@@@@@@ test bed setup 107s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 107s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3989 kB] 108s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [498 kB] 109s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.0 kB] 109s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [7608 B] 109s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [694 kB] 109s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 109s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 109s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 109s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4189 kB] 109s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 109s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [47.8 kB] 109s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 110s Fetched 9611 kB in 3s (3209 kB/s) 110s Reading package lists... 113s Reading package lists... 114s Building dependency tree... 114s Reading state information... 114s Calculating upgrade... 114s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 114s Reading package lists... 114s Building dependency tree... 114s Reading state information... 114s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 115s Unknown architecture, assuming PC-style ttyS0 115s sh: Attempting to set up Debian/Ubuntu apt sources automatically 115s sh: Distribution appears to be Ubuntu 115s Reading package lists... 116s Building dependency tree... 116s Reading state information... 116s eatmydata is already the newest version (131-1). 116s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 116s Reading package lists... 116s Building dependency tree... 116s Reading state information... 116s dbus is already the newest version (1.14.10-4ubuntu1). 116s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 116s Reading package lists... 116s Building dependency tree... 116s Reading state information... 116s rng-tools-debian is already the newest version (2.4). 116s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 116s Reading package lists... 117s Building dependency tree... 117s Reading state information... 117s The following packages will be REMOVED: 117s cloud-init* python3-configobj* python3-debconf* 117s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 117s After this operation, 3256 kB disk space will be freed. 117s (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 ... 52170 files and directories currently installed.) 117s Removing cloud-init (24.1.2-0ubuntu1) ... 117s Removing python3-configobj (5.0.8-3) ... 117s Removing python3-debconf (1.5.86) ... 118s Processing triggers for man-db (2.12.0-3) ... 118s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 51781 files and directories currently installed.) 118s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 118s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 118s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 118s invoke-rc.d: policy-rc.d denied execution of try-restart. 119s Reading package lists... 119s Building dependency tree... 119s Reading state information... 119s linux-generic is already the newest version (6.8.0-11.11+1). 119s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 119s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 120s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 120s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 121s Reading package lists... 121s Reading package lists... 121s Building dependency tree... 121s Reading state information... 122s Calculating upgrade... 122s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 122s Reading package lists... 122s Building dependency tree... 122s Reading state information... 122s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 122s autopkgtest [18:35:27]: rebooting testbed after setup commands that affected boot 141s autopkgtest [18:35:46]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 144s autopkgtest [18:35:49]: @@@@@@@@@@@@@@@@@@@@ apt-source berkeley-express 146s Get:1 http://ftpmaster.internal/ubuntu noble/universe berkeley-express 1.5.3+dfsg-3build3 (dsc) [2571 B] 146s Get:2 http://ftpmaster.internal/ubuntu noble/universe berkeley-express 1.5.3+dfsg-3build3 (tar) [366 kB] 146s Get:3 http://ftpmaster.internal/ubuntu noble/universe berkeley-express 1.5.3+dfsg-3build3 (diff) [10.9 kB] 147s gpgv: Signature made Tue Dec 19 15:00:44 2023 UTC 147s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 147s gpgv: Can't check signature: No public key 147s dpkg-source: warning: cannot verify inline signature for ./berkeley-express_1.5.3+dfsg-3build3.dsc: no acceptable signature found 147s autopkgtest [18:35:52]: testing package berkeley-express version 1.5.3+dfsg-3build3 147s autopkgtest [18:35:52]: build not needed 149s autopkgtest [18:35:53]: test run-tests: preparing testbed 151s Reading package lists... 151s Building dependency tree... 151s Reading state information... 151s Starting pkgProblemResolver with broken count: 0 151s Starting 2 pkgProblemResolver with broken count: 0 151s Done 151s The following additional packages will be installed: 151s berkeley-express berkeley-express-doc bowtie libbamtools2.5.2 151s libboost-filesystem1.83.0 libboost-program-options1.83.0 151s libboost-thread1.83.0 libdeflate0 libhts3 libhtscodecs2 libprotobuf32 151s samtools 151s Suggested packages: 151s bowtie-examples cwltool 151s Recommended packages: 151s med-config 151s The following NEW packages will be installed: 151s autopkgtest-satdep berkeley-express berkeley-express-doc bowtie 151s libbamtools2.5.2 libboost-filesystem1.83.0 libboost-program-options1.83.0 151s libboost-thread1.83.0 libdeflate0 libhts3 libhtscodecs2 libprotobuf32 151s samtools 151s 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. 151s Need to get 6076 kB/6076 kB of archives. 151s After this operation, 23.5 MB of additional disk space will be used. 151s Get:1 /tmp/autopkgtest.Ft59Kq/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [736 B] 151s Get:2 http://ftpmaster.internal/ubuntu noble/universe s390x libbamtools2.5.2 s390x 2.5.2+dfsg-4 [134 kB] 152s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x libboost-filesystem1.83.0 s390x 1.83.0-2ubuntu1 [372 kB] 152s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x libboost-program-options1.83.0 s390x 1.83.0-2ubuntu1 [418 kB] 152s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x libboost-thread1.83.0 s390x 1.83.0-2ubuntu1 [362 kB] 152s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x libprotobuf32 s390x 3.21.12-8ubuntu5 [954 kB] 152s Get:7 http://ftpmaster.internal/ubuntu noble/universe s390x berkeley-express s390x 1.5.3+dfsg-3build3 [232 kB] 153s Get:8 http://ftpmaster.internal/ubuntu noble/universe s390x berkeley-express-doc all 1.5.3+dfsg-3build3 [724 kB] 153s Get:9 http://ftpmaster.internal/ubuntu noble/main s390x libdeflate0 s390x 1.19-1 [46.0 kB] 153s Get:10 http://ftpmaster.internal/ubuntu noble/universe s390x libhtscodecs2 s390x 1.6.0-1 [87.2 kB] 153s Get:11 http://ftpmaster.internal/ubuntu noble/universe s390x libhts3 s390x 1.18+ds-1 [463 kB] 153s Get:12 http://ftpmaster.internal/ubuntu noble/universe s390x samtools s390x 1.19.2-1 [613 kB] 153s Get:13 http://ftpmaster.internal/ubuntu noble/universe s390x bowtie s390x 1.3.1-3 [1671 kB] 154s Fetched 6076 kB in 3s (2341 kB/s) 154s Selecting previously unselected package libbamtools2.5.2:s390x. 154s (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 ... 51726 files and directories currently installed.) 154s Preparing to unpack .../00-libbamtools2.5.2_2.5.2+dfsg-4_s390x.deb ... 154s Unpacking libbamtools2.5.2:s390x (2.5.2+dfsg-4) ... 154s Selecting previously unselected package libboost-filesystem1.83.0:s390x. 154s Preparing to unpack .../01-libboost-filesystem1.83.0_1.83.0-2ubuntu1_s390x.deb ... 154s Unpacking libboost-filesystem1.83.0:s390x (1.83.0-2ubuntu1) ... 154s Selecting previously unselected package libboost-program-options1.83.0:s390x. 154s Preparing to unpack .../02-libboost-program-options1.83.0_1.83.0-2ubuntu1_s390x.deb ... 154s Unpacking libboost-program-options1.83.0:s390x (1.83.0-2ubuntu1) ... 154s Selecting previously unselected package libboost-thread1.83.0:s390x. 154s Preparing to unpack .../03-libboost-thread1.83.0_1.83.0-2ubuntu1_s390x.deb ... 154s Unpacking libboost-thread1.83.0:s390x (1.83.0-2ubuntu1) ... 154s Selecting previously unselected package libprotobuf32:s390x. 154s Preparing to unpack .../04-libprotobuf32_3.21.12-8ubuntu5_s390x.deb ... 154s Unpacking libprotobuf32:s390x (3.21.12-8ubuntu5) ... 154s Selecting previously unselected package berkeley-express. 154s Preparing to unpack .../05-berkeley-express_1.5.3+dfsg-3build3_s390x.deb ... 154s Unpacking berkeley-express (1.5.3+dfsg-3build3) ... 154s Selecting previously unselected package berkeley-express-doc. 154s Preparing to unpack .../06-berkeley-express-doc_1.5.3+dfsg-3build3_all.deb ... 154s Unpacking berkeley-express-doc (1.5.3+dfsg-3build3) ... 154s Selecting previously unselected package libdeflate0:s390x. 154s Preparing to unpack .../07-libdeflate0_1.19-1_s390x.deb ... 154s Unpacking libdeflate0:s390x (1.19-1) ... 154s Selecting previously unselected package libhtscodecs2:s390x. 154s Preparing to unpack .../08-libhtscodecs2_1.6.0-1_s390x.deb ... 154s Unpacking libhtscodecs2:s390x (1.6.0-1) ... 154s Selecting previously unselected package libhts3:s390x. 154s Preparing to unpack .../09-libhts3_1.18+ds-1_s390x.deb ... 154s Unpacking libhts3:s390x (1.18+ds-1) ... 154s Selecting previously unselected package samtools. 154s Preparing to unpack .../10-samtools_1.19.2-1_s390x.deb ... 154s Unpacking samtools (1.19.2-1) ... 154s Selecting previously unselected package bowtie. 154s Preparing to unpack .../11-bowtie_1.3.1-3_s390x.deb ... 154s Unpacking bowtie (1.3.1-3) ... 154s Selecting previously unselected package autopkgtest-satdep. 154s Preparing to unpack .../12-1-autopkgtest-satdep.deb ... 154s Unpacking autopkgtest-satdep (0) ... 154s Setting up libhtscodecs2:s390x (1.6.0-1) ... 154s Setting up libboost-program-options1.83.0:s390x (1.83.0-2ubuntu1) ... 154s Setting up bowtie (1.3.1-3) ... 154s Setting up berkeley-express-doc (1.5.3+dfsg-3build3) ... 154s Setting up libdeflate0:s390x (1.19-1) ... 154s Setting up libboost-thread1.83.0:s390x (1.83.0-2ubuntu1) ... 154s Setting up libboost-filesystem1.83.0:s390x (1.83.0-2ubuntu1) ... 154s Setting up libbamtools2.5.2:s390x (2.5.2+dfsg-4) ... 154s Setting up libprotobuf32:s390x (3.21.12-8ubuntu5) ... 154s Setting up libhts3:s390x (1.18+ds-1) ... 154s Setting up samtools (1.19.2-1) ... 154s Setting up berkeley-express (1.5.3+dfsg-3build3) ... 154s Setting up autopkgtest-satdep (0) ... 154s Processing triggers for man-db (2.12.0-3) ... 155s Processing triggers for libc-bin (2.39-0ubuntu6) ... 157s (Reading database ... 51960 files and directories currently installed.) 157s Removing autopkgtest-satdep (0) ... 158s autopkgtest [18:36:03]: test run-tests: [----------------------- 158s + pkg=berkeley-express 158s + [ /tmp/autopkgtest.Ft59Kq/autopkgtest_tmp = ] 158s + cd /tmp/autopkgtest.Ft59Kq/autopkgtest_tmp 158s + cp /usr/share/doc/berkeley-express/sample_data/reads_1.fastq.gz /usr/share/doc/berkeley-express/sample_data/reads_2.fastq.gz /usr/share/doc/berkeley-express/sample_data/transcripts.fasta.gz . 158s + gunzip reads_1.fastq.gz reads_2.fastq.gz transcripts.fasta.gz 158s + bowtie-build --offrate 1 transcripts.fasta transcripts 158s Settings: 158s Output files: "transcripts.*.ebwt" 158s Line rate: 6 (line is 64 bytes) 158s Lines per side: 1 (side is 64 bytes) 158s Offset rate: 1 (one in 2) 158s FTable chars: 10 158s Strings: unpacked 158s Max bucket size: default 158s Max bucket size, sqrt multiplier: default 158s Max bucket size, len divisor: 4 158s Difference-cover sample period: 1024 158s Endianness: little 158s Actual local endianness: big 158s Sanity checking: disabled 158s Assertions: disabled 158s Random seed: 0 158s Sizeofs: void*:8, int:4, long:8, size_t:8 158s Input files DNA, FASTA: 158s transcripts.fasta 158s Reading reference sizes 158s Time reading reference sizes: 00:00:00 158s Calculating joined length 158s Writing header 158s Reserving space for joined string 158s Joining reference sequences 158s Time to join reference sequences: 00:00:00 158s bmax according to bmaxDivN setting: 7140 158s Using parameters --bmax 5355 --dcv 1024 158s Doing ahead-of-time memory usage test 158s Passed! Constructing with these parameters: --bmax 5355 --dcv 1024 158s Constructing suffix-array element generator 158s Building DifferenceCoverSample 158s Building sPrime 158s Building sPrimeOrder 158s V-Sorting samples 158s V-Sorting samples time: 00:00:00 158s Allocating rank array 158s Ranking v-sort output 158s Ranking v-sort output time: 00:00:00 158s Invoking Larsson-Sadakane on ranks 158s Invoking Larsson-Sadakane on ranks time: 00:00:00 158s Sanity-checking and returning 158s Building samples 158s Reserving space for 12 sample suffixes 158s Generating random suffixes 158s QSorting 12 sample offsets, eliminating duplicates 158s Multikey QSorting 12 samples 158s (Using difference cover) 158s Multikey QSorting samples time: 00:00:00 158s QSorting sample offsets, eliminating duplicates time: 00:00:00 158s Calculating bucket sizes 158s Splitting and merging 158s Splitting and merging time: 00:00:00 158s Split 2, merged 6; iterating... 158s Splitting and merging 158s Splitting and merging time: 00:00:00 158s Split 1, merged 2; iterating... 158s Splitting and merging 158s Splitting and merging time: 00:00:00 158s Avg bucket size: 3569.38 (target: 5354) 158s Converting suffix-array elements to index image 158s Allocating ftab, absorbFtab 158s Entering Ebwt loop 158s Getting block 1 of 8 158s Reserving size (5355) for bucket 1 158s Calculating Z arrays for bucket 1 158s Entering block accumulator loop for bucket 1: 158s bucket 1: 10% 158s bucket 1: 20% 158s bucket 1: 30% 158s bucket 1: 40% 158s bucket 1: 50% 158s bucket 1: 60% 158s bucket 1: 70% 158s bucket 1: 80% 158s bucket 1: 90% 158s bucket 1: 100% 158s Sorting block of length 3445 for bucket 1 158s (Using difference cover) 158s Sorting block time: 00:00:00 158s Returning block of 3446 for bucket 1 158s Getting block 2 of 8 158s Reserving size (5355) for bucket 2 158s Calculating Z arrays for bucket 2 158s Entering block accumulator loop for bucket 2: 158s bucket 2: 10% 158s bucket 2: 20% 158s bucket 2: 30% 158s bucket 2: 40% 158s bucket 2: 50% 158s bucket 2: 60% 158s bucket 2: 70% 158s bucket 2: 80% 158s bucket 2: 90% 158s bucket 2: 100% 158s Sorting block of length 5081 for bucket 2 158s (Using difference cover) 158s Sorting block time: 00:00:00 158s Returning block of 5082 for bucket 2 158s Getting block 3 of 8 158s Reserving size (5355) for bucket 3 158s Calculating Z arrays for bucket 3 158s Entering block accumulator loop for bucket 3: 158s bucket 3: 10% 158s bucket 3: 20% 158s bucket 3: 30% 158s bucket 3: 40% 158s bucket 3: 50% 158s bucket 3: 60% 158s bucket 3: 70% 158s bucket 3: 80% 158s bucket 3: 90% 158s bucket 3: 100% 158s Sorting block of length 2382 for bucket 3 158s (Using difference cover) 158s Sorting block time: 00:00:00 158s Returning block of 2383 for bucket 3 158s Getting block 4 of 8 158s Reserving size (5355) for bucket 4 158s Calculating Z arrays for bucket 4 158s Entering block accumulator loop for bucket 4: 158s bucket 4: 10% 158s bucket 4: 20% 158s bucket 4: 30% 158s bucket 4: 40% 158s bucket 4: 50% 158s bucket 4: 60% 158s bucket 4: 70% 158s bucket 4: 80% 158s bucket 4: 90% 158s bucket 4: 100% 158s Sorting block of length 5217 for bucket 4 158s (Using difference cover) 158s Sorting block time: 00:00:00 158s Returning block of 5218 for bucket 4 158s Getting block 5 of 8 158s Reserving size (5355) for bucket 5 158s Calculating Z arrays for bucket 5 158s Entering block accumulator loop for bucket 5: 158s bucket 5: 10% 158s bucket 5: 20% 158s bucket 5: 30% 158s bucket 5: 40% 158s bucket 5: 50% 158s bucket 5: 60% 158s bucket 5: 70% 158s bucket 5: 80% 158s bucket 5: 90% 158s bucket 5: 100% 158s Sorting block of length 3095 for bucket 5 158s (Using difference cover) 158s Sorting block time: 00:00:00 158s Returning block of 3096 for bucket 5 158s Getting block 6 of 8 158s Reserving size (5355) for bucket 6 158s Calculating Z arrays for bucket 6 158s Entering block accumulator loop for bucket 6: 158s bucket 6: 10% 158s bucket 6: 20% 158s bucket 6: 30% 158s bucket 6: 40% 158s bucket 6: 50% 158s bucket 6: 60% 158s bucket 6: 70% 158s bucket 6: 80% 158s bucket 6: 90% 158s bucket 6: 100% 158s Sorting block of length 3727 for bucket 6 158s (Using difference cover) 158s Sorting block time: 00:00:00 158s Returning block of 3728 for bucket 6 158s Getting block 7 of 8 158s Reserving size (5355) for bucket 7 158s Calculating Z arrays for bucket 7 158s Entering block accumulator loop for bucket 7: 158s bucket 7: 10% 158s bucket 7: 20% 158s bucket 7: 30% 158s bucket 7: 40% 158s bucket 7: 50% 158s bucket 7: 60% 158s bucket 7: 70% 158s bucket 7: 80% 158s bucket 7: 90% 158s bucket 7: 100% 158s Sorting block of length 5329 for bucket 7 158s (Using difference cover) 158s Sorting block time: 00:00:00 158s Returning block of 5330 for bucket 7 158s Getting block 8 of 8 158s Reserving size (5355) for bucket 8 158s Calculating Z arrays for bucket 8 158s Entering block accumulator loop for bucket 8: 158s bucket 8: 10% 158s bucket 8: 20% 158s bucket 8: 30% 158s bucket 8: 40% 158s bucket 8: 50% 158s bucket 8: 60% 158s bucket 8: 70% 158s bucket 8: 80% 158s bucket 8: 90% 158s bucket 8: 100% 158s Sorting block of length 279 for bucket 8 158s (Using difference cover) 158s Sorting block time: 00:00:00 158s Returning block of 280 for bucket 8 158s Exited Ebwt loop 158s fchr[A]: 0 158s fchr[C]: 7097 158s fchr[G]: 15029 158s fchr[T]: 22254 158s fchr[$]: 28562 158s Exiting Ebwt::buildToDisk() 158s Returning from initFromVector 158s Wrote 4203034 bytes to primary EBWT file: transcripts.1.ebwt 158s Wrote 57132 bytes to secondary EBWT file: transcripts.2.ebwt 158s Re-opening _in1 and _in2 as input streams 158s Returning from Ebwt constructor 158s Headers: 158s len: 28562 158s bwtLen: 28563 158s sz: 7141 158s bwtSz: 7141 158s lineRate: 6 158s linesPerSide: 1 158s offRate: 1 158s offMask: 0xfffffffe 158s isaRate: -1 158s isaMask: 0xffffffff 158s ftabChars: 10 158s eftabLen: 20 158s eftabSz: 80 158s ftabLen: 1048577 158s ftabSz: 4194308 158s offsLen: 14282 158s offsSz: 57128 158s isaLen: 0 158s isaSz: 0 158s lineSz: 64 158s sideSz: 64 158s sideBwtSz: 56 158s sideBwtLen: 224 158s numSidePairs: 64 158s numSides: 128 158s numLines: 128 158s ebwtTotLen: 8192 158s ebwtTotSz: 8192 158s reverse: 0 158s Total time for call to driver() for forward index: 00:00:01 158s Reading reference sizes 158s Time reading reference sizes: 00:00:00 158s Calculating joined length 158s Writing header 158s Reserving space for joined string 158s Joining reference sequences 158s Time to join reference sequences: 00:00:00 158s bmax according to bmaxDivN setting: 7140 158s Using parameters --bmax 5355 --dcv 1024 158s Doing ahead-of-time memory usage test 158s Passed! Constructing with these parameters: --bmax 5355 --dcv 1024 158s Constructing suffix-array element generator 158s Building DifferenceCoverSample 158s Building sPrime 158s Building sPrimeOrder 158s V-Sorting samples 158s V-Sorting samples time: 00:00:00 158s Allocating rank array 158s Ranking v-sort output 158s Ranking v-sort output time: 00:00:00 158s Invoking Larsson-Sadakane on ranks 158s Invoking Larsson-Sadakane on ranks time: 00:00:00 158s Sanity-checking and returning 158s Building samples 158s Reserving space for 12 sample suffixes 158s Generating random suffixes 158s QSorting 12 sample offsets, eliminating duplicates 158s Multikey QSorting 12 samples 158s (Using difference cover) 158s Multikey QSorting samples time: 00:00:00 158s QSorting sample offsets, eliminating duplicates time: 00:00:00 158s Calculating bucket sizes 158s Splitting and merging 158s Splitting and merging time: 00:00:00 158s Avg bucket size: 4079.43 (target: 5354) 158s Converting suffix-array elements to index image 158s Allocating ftab, absorbFtab 158s Entering Ebwt loop 158s Getting block 1 of 7 158s Reserving size (5355) for bucket 1 158s Calculating Z arrays for bucket 1 158s Entering block accumulator loop for bucket 1: 158s bucket 1: 10% 158s bucket 1: 20% 158s bucket 1: 30% 158s bucket 1: 40% 158s bucket 1: 50% 158s bucket 1: 60% 158s bucket 1: 70% 158s bucket 1: 80% 158s bucket 1: 90% 158s bucket 1: 100% 158s Sorting block of length 1796 for bucket 1 158s (Using difference cover) 158s Sorting block time: 00:00:00 158s Returning block of 1797 for bucket 1 158s Getting block 2 of 7 158s Reserving size (5355) for bucket 2 158s Calculating Z arrays for bucket 2 158s Entering block accumulator loop for bucket 2: 158s bucket 2: 10% 158s bucket 2: 20% 158s bucket 2: 30% 158s bucket 2: 40% 158s bucket 2: 50% 158s bucket 2: 60% 158s bucket 2: 70% 158s bucket 2: 80% 158s bucket 2: 90% 158s bucket 2: 100% 158s Sorting block of length 4275 for bucket 2 158s (Using difference cover) 158s Sorting block time: 00:00:00 158s Returning block of 4276 for bucket 2 158s Getting block 3 of 7 158s Reserving size (5355) for bucket 3 158s Calculating Z arrays for bucket 3 158s Entering block accumulator loop for bucket 3: 158s bucket 3: 10% 158s bucket 3: 20% 158s bucket 3: 30% 158s bucket 3: 40% 158s bucket 3: 50% 158s bucket 3: 60% 158s bucket 3: 70% 158s bucket 3: 80% 158s bucket 3: 90% 158s bucket 3: 100% 158s Sorting block of length 4010 for bucket 3 158s (Using difference cover) 158s Sorting block time: 00:00:00 158s Returning block of 4011 for bucket 3 158s Getting block 4 of 7 158s Reserving size (5355) for bucket 4 158s Calculating Z arrays for bucket 4 158s Entering block accumulator loop for bucket 4: 158s bucket 4: 10% 158s bucket 4: 20% 158s bucket 4: 30% 158s bucket 4: 40% 158s bucket 4: 50% 158s bucket 4: 60% 158s bucket 4: 70% 158s bucket 4: 80% 158s bucket 4: 90% 158s bucket 4: 100% 158s Sorting block of length 3860 for bucket 4 158s (Using difference cover) 158s Sorting block time: 00:00:00 158s Returning block of 3861 for bucket 4 158s Getting block 5 of 7 158s Reserving size (5355) for bucket 5 158s Calculating Z arrays for bucket 5 158s Entering block accumulator loop for bucket 5: 158s bucket 5: 10% 158s bucket 5: 20% 158s bucket 5: 30% 158s bucket 5: 40% 158s bucket 5: 50% 158s bucket 5: 60% 158s bucket 5: 70% 158s bucket 5: 80% 158s bucket 5: 90% 158s bucket 5: 100% 158s Sorting block of length 4188 for bucket 5 158s (Using difference cover) 158s Sorting block time: 00:00:00 158s Returning block of 4189 for bucket 5 158s Getting block 6 of 7 158s Reserving size (5355) for bucket 6 158s Calculating Z arrays for bucket 6 158s Entering block accumulator loop for bucket 6: 158s bucket 6: 10% 158s bucket 6: 20% 158s bucket 6: 30% 158s bucket 6: 40% 158s bucket 6: 50% 158s bucket 6: 60% 158s bucket 6: 70% 158s bucket 6: 80% 158s bucket 6: 90% 158s bucket 6: 100% 158s Sorting block of length 5102 for bucket 6 158s (Using difference cover) 158s Sorting block time: 00:00:00 158s Returning block of 5103 for bucket 6 158s Getting block 7 of 7 158s Reserving size (5355) for bucket 7 158s Calculating Z arrays for bucket 7 158s Entering block accumulator loop for bucket 7: 158s bucket 7: 10% 158s bucket 7: 20% 158s bucket 7: 30% 158s bucket 7: 40% 158s bucket 7: 50% 158s bucket 7: 60% 158s bucket 7: 70% 158s bucket 7: 80% 158s bucket 7: 90% 158s bucket 7: 100% 158s Sorting block of length 5325 for bucket 7 158s (Using difference cover) 158s Sorting block time: 00:00:00 158s Returning block of 5326 for bucket 7 158s Exited Ebwt loop 158s fchr[A]: 0 158s fchr[C]: 7097 158s fchr[G]: 15029 158s fchr[T]: 22254 158s fchr[$]: 28562 158s Exiting Ebwt::buildToDisk() 158s Returning from initFromVector 158s Wrote 4203034 bytes to primary EBWT file: transcripts.rev.1.ebwt 158s Wrote 57132 bytes to secondary EBWT file: transcripts.rev.2.ebwt 158s Re-opening _in1 and _in2 as input streams 158s Returning from Ebwt constructor 158s Headers: 158s len: 28562 158s bwtLen: 28563 158s sz: 7141 158s bwtSz: 7141 158s lineRate: 6 158s linesPerSide: 1 158s offRate: 1 158s offMask: 0xfffffffe 158s isaRate: -1 158s isaMask: 0xffffffff 158s ftabChars: 10 158s eftabLen: 20 158s eftabSz: 80 158s ftabLen: 1048577 158s ftabSz: 4194308 158s offsLen: 14282 158s offsSz: 57128 158s isaLen: 0 158s isaSz: 0 158s lineSz: 64 158s sideSz: 64 158s sideBwtSz: 56 158s sideBwtLen: 224 158s numSidePairs: 64 158s numSides: 128 158s numLines: 128 158s ebwtTotLen: 8192 158s ebwtTotSz: 8192 158s reverse: 0 158s Total time for backward call to driver() for mirror index: 00:00:00 158s + bowtie -aS -X 800 --offrate 1 transcripts -1 reads_1.fastq -2 reads_2.fastq 158s + samtools view -Sb - 158s Setting the index via positional argument will be deprecated in a future release. Please use -x option instead. 159s # reads processed: 10000 159s # reads with at least one alignment: 10000 (100.00%) 159s # reads that failed to align: 0 (0.00%) 159s Reported 14270 paired-end alignments 159s + berkeley-express transcripts.fasta hits.bam 159s 2024-Mar-25 18:36:03 - Attempting to read 'hits.bam' in BAM format... 159s 2024-Mar-25 18:36:03 - Parsing BAM header... 159s 2024-Mar-25 18:36:03 - Loading target sequences and measuring bias background... 159s 2024-Mar-25 18:36:03 - Initialized 15 targets. 159s 2024-Mar-25 18:36:03 - Processing input fragment alignments... 160s 2024-Mar-25 18:36:03 - COMPLETED: Processed 10000 mapped fragments, targets are in 8 bundles. 160s 2024-Mar-25 18:36:03 - WARNING: Not enough fragments observed to accurately learn bias parameters. Either disable bias correction (--no-bias-correct) or provide a file containing auxiliary parameters (--aux-param-file). 160s 2024-Mar-25 18:36:03 - Writing results to file... 160s 2024-Mar-25 18:36:03 - Done. 160s autopkgtest [18:36:05]: test run-tests: -----------------------] 161s run-tests PASS 161s autopkgtest [18:36:06]: test run-tests: - - - - - - - - - - results - - - - - - - - - - 161s autopkgtest [18:36:06]: @@@@@@@@@@@@@@@@@@@@ summary 161s run-tests PASS 183s Creating nova instance adt-noble-s390x-berkeley-express-20240325-183325-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-s390x-server-20240325.img (UUID 9f25d9bc-613c-4979-9452-2ea8e4d84cd0)...