0s autopkgtest [02:38:18]: starting date and time: 2024-03-27 02:38:18+0000 0s autopkgtest [02:38:18]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [02:38:18]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.93dqbzbf/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --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-3@bos02-arm64-9.secgroup --name adt-noble-arm64-berkeley-express-20240327-023818-juju-7f2275-prod-proposed-migration-environment-3-a0f491c2-4fc9-4070-8ea5-6f47d6da0cdc --image adt/ubuntu-noble-arm64-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/ 100s autopkgtest [02:39:58]: testbed dpkg architecture: arm64 100s autopkgtest [02:39:58]: testbed apt version: 2.7.12 100s autopkgtest [02:39:58]: @@@@@@@@@@@@@@@@@@@@ test bed setup 102s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 102s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [55.4 kB] 102s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3984 kB] 103s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [497 kB] 103s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [8504 B] 103s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [717 kB] 103s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 103s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [43.0 kB] 103s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 103s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4303 kB] 103s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 103s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [71.0 kB] 103s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 110s Fetched 9808 kB in 3s (2968 kB/s) 110s Reading package lists... 115s Reading package lists... 116s Building dependency tree... 116s Reading state information... 117s Calculating upgrade... 118s The following packages will be upgraded: 118s psmisc 119s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 119s Need to get 178 kB of archives. 119s After this operation, 28.7 kB disk space will be freed. 119s Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 psmisc arm64 23.7-1 [178 kB] 120s Fetched 178 kB in 1s (304 kB/s) 120s (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 ... 75911 files and directories currently installed.) 120s Preparing to unpack .../psmisc_23.7-1_arm64.deb ... 120s Unpacking psmisc (23.7-1) over (23.6-2) ... 121s Setting up psmisc (23.7-1) ... 121s Processing triggers for man-db (2.12.0-3) ... 122s Reading package lists... 123s Building dependency tree... 123s Reading state information... 124s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 125s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 125s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 125s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 125s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 130s Reading package lists... 130s Reading package lists... 130s Building dependency tree... 130s Reading state information... 132s Calculating upgrade... 133s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 133s Reading package lists... 133s Building dependency tree... 133s Reading state information... 135s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 139s autopkgtest [02:40:37]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 139s autopkgtest [02:40:37]: @@@@@@@@@@@@@@@@@@@@ apt-source berkeley-express 143s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/universe berkeley-express 1.5.3+dfsg-3build4 (dsc) [2600 B] 143s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe berkeley-express 1.5.3+dfsg-3build4 (tar) [366 kB] 143s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe berkeley-express 1.5.3+dfsg-3build4 (diff) [11.0 kB] 143s gpgv: Signature made Fri Mar 22 15:50:13 2024 UTC 143s gpgv: using RSA key 4FB588A84C2DDE79A74C77876FA458DD1DB03F71 143s gpgv: issuer "juliank@ubuntu.com" 143s gpgv: Can't check signature: No public key 143s dpkg-source: warning: cannot verify inline signature for ./berkeley-express_1.5.3+dfsg-3build4.dsc: no acceptable signature found 144s autopkgtest [02:40:42]: testing package berkeley-express version 1.5.3+dfsg-3build4 144s autopkgtest [02:40:42]: build not needed 145s autopkgtest [02:40:43]: test run-tests: preparing testbed 146s Reading package lists... 147s Building dependency tree... 147s Reading state information... 148s Starting pkgProblemResolver with broken count: 0 148s Starting 2 pkgProblemResolver with broken count: 0 148s Done 150s The following additional packages will be installed: 150s berkeley-express berkeley-express-doc bowtie libbamtools2.5.2 150s libboost-filesystem1.83.0 libboost-program-options1.83.0 150s libboost-thread1.83.0 libdeflate0 libhts3 libhtscodecs2 libprotobuf32t64 150s samtools 150s Suggested packages: 150s bowtie-examples cwltool 150s Recommended packages: 150s med-config 150s The following NEW packages will be installed: 150s autopkgtest-satdep berkeley-express berkeley-express-doc bowtie 150s libbamtools2.5.2 libboost-filesystem1.83.0 libboost-program-options1.83.0 150s libboost-thread1.83.0 libdeflate0 libhts3 libhtscodecs2 libprotobuf32t64 150s samtools 150s 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. 150s Need to get 5537 kB/5537 kB of archives. 150s After this operation, 23.3 MB of additional disk space will be used. 150s Get:1 /tmp/autopkgtest.RJoSsP/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [736 B] 150s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 libbamtools2.5.2 arm64 2.5.2+dfsg-4 [134 kB] 151s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libboost-filesystem1.83.0 arm64 1.83.0-2ubuntu1 [366 kB] 151s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libboost-program-options1.83.0 arm64 1.83.0-2ubuntu1 [410 kB] 151s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libboost-thread1.83.0 arm64 1.83.0-2ubuntu1 [358 kB] 151s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libprotobuf32t64 arm64 3.21.12-8.2 [859 kB] 152s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 berkeley-express arm64 1.5.3+dfsg-3build4 [213 kB] 152s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 berkeley-express-doc all 1.5.3+dfsg-3build4 [724 kB] 152s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 152s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 152s Get:11 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 153s Get:12 http://ftpmaster.internal/ubuntu noble/universe arm64 samtools arm64 1.19.2-1 [584 kB] 153s Get:13 http://ftpmaster.internal/ubuntu noble/universe arm64 bowtie arm64 1.3.1-3 [1346 kB] 154s Fetched 5537 kB in 3s (1696 kB/s) 154s Selecting previously unselected package libbamtools2.5.2:arm64. 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 ... 75908 files and directories currently installed.) 154s Preparing to unpack .../00-libbamtools2.5.2_2.5.2+dfsg-4_arm64.deb ... 154s Unpacking libbamtools2.5.2:arm64 (2.5.2+dfsg-4) ... 154s Selecting previously unselected package libboost-filesystem1.83.0:arm64. 154s Preparing to unpack .../01-libboost-filesystem1.83.0_1.83.0-2ubuntu1_arm64.deb ... 154s Unpacking libboost-filesystem1.83.0:arm64 (1.83.0-2ubuntu1) ... 154s Selecting previously unselected package libboost-program-options1.83.0:arm64. 154s Preparing to unpack .../02-libboost-program-options1.83.0_1.83.0-2ubuntu1_arm64.deb ... 154s Unpacking libboost-program-options1.83.0:arm64 (1.83.0-2ubuntu1) ... 155s Selecting previously unselected package libboost-thread1.83.0:arm64. 155s Preparing to unpack .../03-libboost-thread1.83.0_1.83.0-2ubuntu1_arm64.deb ... 155s Unpacking libboost-thread1.83.0:arm64 (1.83.0-2ubuntu1) ... 155s Selecting previously unselected package libprotobuf32t64:arm64. 155s Preparing to unpack .../04-libprotobuf32t64_3.21.12-8.2_arm64.deb ... 155s Unpacking libprotobuf32t64:arm64 (3.21.12-8.2) ... 155s Selecting previously unselected package berkeley-express. 155s Preparing to unpack .../05-berkeley-express_1.5.3+dfsg-3build4_arm64.deb ... 155s Unpacking berkeley-express (1.5.3+dfsg-3build4) ... 155s Selecting previously unselected package berkeley-express-doc. 155s Preparing to unpack .../06-berkeley-express-doc_1.5.3+dfsg-3build4_all.deb ... 155s Unpacking berkeley-express-doc (1.5.3+dfsg-3build4) ... 155s Selecting previously unselected package libdeflate0:arm64. 155s Preparing to unpack .../07-libdeflate0_1.19-1_arm64.deb ... 155s Unpacking libdeflate0:arm64 (1.19-1) ... 155s Selecting previously unselected package libhtscodecs2:arm64. 155s Preparing to unpack .../08-libhtscodecs2_1.6.0-1_arm64.deb ... 155s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 155s Selecting previously unselected package libhts3:arm64. 155s Preparing to unpack .../09-libhts3_1.18+ds-1_arm64.deb ... 155s Unpacking libhts3:arm64 (1.18+ds-1) ... 155s Selecting previously unselected package samtools. 155s Preparing to unpack .../10-samtools_1.19.2-1_arm64.deb ... 155s Unpacking samtools (1.19.2-1) ... 155s Selecting previously unselected package bowtie. 155s Preparing to unpack .../11-bowtie_1.3.1-3_arm64.deb ... 155s Unpacking bowtie (1.3.1-3) ... 156s Selecting previously unselected package autopkgtest-satdep. 156s Preparing to unpack .../12-1-autopkgtest-satdep.deb ... 156s Unpacking autopkgtest-satdep (0) ... 156s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 156s Setting up libboost-program-options1.83.0:arm64 (1.83.0-2ubuntu1) ... 156s Setting up libprotobuf32t64:arm64 (3.21.12-8.2) ... 156s Setting up bowtie (1.3.1-3) ... 156s Setting up berkeley-express-doc (1.5.3+dfsg-3build4) ... 156s Setting up libdeflate0:arm64 (1.19-1) ... 156s Setting up libboost-thread1.83.0:arm64 (1.83.0-2ubuntu1) ... 156s Setting up libboost-filesystem1.83.0:arm64 (1.83.0-2ubuntu1) ... 156s Setting up libbamtools2.5.2:arm64 (2.5.2+dfsg-4) ... 156s Setting up berkeley-express (1.5.3+dfsg-3build4) ... 156s Setting up libhts3:arm64 (1.18+ds-1) ... 156s Setting up samtools (1.19.2-1) ... 156s Setting up autopkgtest-satdep (0) ... 156s Processing triggers for man-db (2.12.0-3) ... 156s Processing triggers for libc-bin (2.39-0ubuntu6) ... 163s (Reading database ... 76143 files and directories currently installed.) 163s Removing autopkgtest-satdep (0) ... 164s autopkgtest [02:41:02]: test run-tests: [----------------------- 165s + pkg=berkeley-express 165s + [ /tmp/autopkgtest.RJoSsP/autopkgtest_tmp = ] 165s + cd /tmp/autopkgtest.RJoSsP/autopkgtest_tmp 165s + 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 . 165s + gunzip reads_1.fastq.gz reads_2.fastq.gz transcripts.fasta.gz 165s + bowtie-build --offrate 1 transcripts.fasta transcripts 165s Settings: 165s Output files: "transcripts.*.ebwt" 165s Line rate: 6 (line is 64 bytes) 165s Lines per side: 1 (side is 64 bytes) 165s Offset rate: 1 (one in 2) 165s FTable chars: 10 165s Strings: unpacked 165s Max bucket size: default 165s Max bucket size, sqrt multiplier: default 165s Max bucket size, len divisor: 4 165s Difference-cover sample period: 1024 165s Endianness: little 165s Actual local endianness: little 165s Sanity checking: disabled 165s Assertions: disabled 165s Random seed: 0 165s Sizeofs: void*:8, int:4, long:8, size_t:8 165s Input files DNA, FASTA: 165s transcripts.fasta 165s Reading reference sizes 165s Time reading reference sizes: 00:00:00 165s Calculating joined length 165s Writing header 165s Reserving space for joined string 165s Joining reference sequences 165s Time to join reference sequences: 00:00:00 165s bmax according to bmaxDivN setting: 7140 165s Using parameters --bmax 5355 --dcv 1024 165s Doing ahead-of-time memory usage test 165s Passed! Constructing with these parameters: --bmax 5355 --dcv 1024 165s Constructing suffix-array element generator 165s Building DifferenceCoverSample 165s Building sPrime 165s Building sPrimeOrder 165s V-Sorting samples 165s V-Sorting samples time: 00:00:00 165s Allocating rank array 165s Ranking v-sort output 165s Ranking v-sort output time: 00:00:00 165s Invoking Larsson-Sadakane on ranks 165s Invoking Larsson-Sadakane on ranks time: 00:00:00 165s Sanity-checking and returning 165s Building samples 165s Reserving space for 12 sample suffixes 165s Generating random suffixes 165s QSorting 12 sample offsets, eliminating duplicates 165s Multikey QSorting 12 samples 165s (Using difference cover) 165s Multikey QSorting samples time: 00:00:00 165s QSorting sample offsets, eliminating duplicates time: 00:00:00 165s Calculating bucket sizes 165s Splitting and merging 165s Splitting and merging time: 00:00:00 165s Split 2, merged 6; iterating... 165s Splitting and merging 165s Splitting and merging time: 00:00:00 165s Split 1, merged 2; iterating... 165s Splitting and merging 165s Splitting and merging time: 00:00:00 165s Avg bucket size: 3569.38 (target: 5354) 165s Converting suffix-array elements to index image 165s Allocating ftab, absorbFtab 165s Entering Ebwt loop 165s Getting block 1 of 8 165s Reserving size (5355) for bucket 1 165s Calculating Z arrays for bucket 1 165s Entering block accumulator loop for bucket 1: 165s bucket 1: 10% 165s bucket 1: 20% 165s bucket 1: 30% 165s bucket 1: 40% 165s bucket 1: 50% 165s bucket 1: 60% 165s bucket 1: 70% 165s bucket 1: 80% 165s bucket 1: 90% 165s bucket 1: 100% 165s Sorting block of length 3445 for bucket 1 165s (Using difference cover) 165s Sorting block time: 00:00:00 165s Returning block of 3446 for bucket 1 165s Getting block 2 of 8 165s Reserving size (5355) for bucket 2 165s Calculating Z arrays for bucket 2 165s Entering block accumulator loop for bucket 2: 165s bucket 2: 10% 165s bucket 2: 20% 165s bucket 2: 30% 165s bucket 2: 40% 165s bucket 2: 50% 165s bucket 2: 60% 165s bucket 2: 70% 165s bucket 2: 80% 165s bucket 2: 90% 165s bucket 2: 100% 165s Sorting block of length 5081 for bucket 2 165s (Using difference cover) 165s Sorting block time: 00:00:00 165s Returning block of 5082 for bucket 2 165s Getting block 3 of 8 165s Reserving size (5355) for bucket 3 165s Calculating Z arrays for bucket 3 165s Entering block accumulator loop for bucket 3: 165s bucket 3: 10% 165s bucket 3: 20% 165s bucket 3: 30% 165s bucket 3: 40% 165s bucket 3: 50% 165s bucket 3: 60% 165s bucket 3: 70% 165s bucket 3: 80% 165s bucket 3: 90% 165s bucket 3: 100% 165s Sorting block of length 2382 for bucket 3 165s (Using difference cover) 165s Sorting block time: 00:00:00 165s Returning block of 2383 for bucket 3 165s Getting block 4 of 8 165s Reserving size (5355) for bucket 4 165s Calculating Z arrays for bucket 4 165s Entering block accumulator loop for bucket 4: 165s bucket 4: 10% 165s bucket 4: 20% 165s bucket 4: 30% 165s bucket 4: 40% 165s bucket 4: 50% 165s bucket 4: 60% 165s bucket 4: 70% 165s bucket 4: 80% 165s bucket 4: 90% 165s bucket 4: 100% 165s Sorting block of length 5217 for bucket 4 165s (Using difference cover) 165s Sorting block time: 00:00:00 165s Returning block of 5218 for bucket 4 165s Getting block 5 of 8 165s Reserving size (5355) for bucket 5 165s Calculating Z arrays for bucket 5 165s Entering block accumulator loop for bucket 5: 165s bucket 5: 10% 165s bucket 5: 20% 165s bucket 5: 30% 165s bucket 5: 40% 165s bucket 5: 50% 165s bucket 5: 60% 165s bucket 5: 70% 165s bucket 5: 80% 165s bucket 5: 90% 165s bucket 5: 100% 165s Sorting block of length 3095 for bucket 5 165s (Using difference cover) 165s Sorting block time: 00:00:00 165s Returning block of 3096 for bucket 5 165s Getting block 6 of 8 165s Reserving size (5355) for bucket 6 165s Calculating Z arrays for bucket 6 165s Entering block accumulator loop for bucket 6: 165s bucket 6: 10% 165s bucket 6: 20% 165s bucket 6: 30% 165s bucket 6: 40% 165s bucket 6: 50% 165s bucket 6: 60% 165s bucket 6: 70% 165s bucket 6: 80% 165s bucket 6: 90% 165s bucket 6: 100% 165s Sorting block of length 3727 for bucket 6 165s (Using difference cover) 165s Sorting block time: 00:00:00 165s Returning block of 3728 for bucket 6 165s Getting block 7 of 8 165s Reserving size (5355) for bucket 7 165s Calculating Z arrays for bucket 7 165s Entering block accumulator loop for bucket 7: 165s bucket 7: 10% 165s bucket 7: 20% 165s bucket 7: 30% 165s bucket 7: 40% 165s bucket 7: 50% 165s bucket 7: 60% 165s bucket 7: 70% 165s bucket 7: 80% 165s bucket 7: 90% 165s bucket 7: 100% 165s Sorting block of length 5329 for bucket 7 165s (Using difference cover) 165s Sorting block time: 00:00:00 165s Returning block of 5330 for bucket 7 165s Getting block 8 of 8 165s Reserving size (5355) for bucket 8 165s Calculating Z arrays for bucket 8 165s Entering block accumulator loop for bucket 8: 165s bucket 8: 10% 165s bucket 8: 20% 165s bucket 8: 30% 165s bucket 8: 40% 165s bucket 8: 50% 165s bucket 8: 60% 165s bucket 8: 70% 165s bucket 8: 80% 165s bucket 8: 90% 165s bucket 8: 100% 165s Sorting block of length 279 for bucket 8 165s (Using difference cover) 165s Sorting block time: 00:00:00 165s Returning block of 280 for bucket 8 165s Exited Ebwt loop 165s fchr[A]: 0 165s fchr[C]: 7097 165s fchr[G]: 15029 165s fchr[T]: 22254 165s fchr[$]: 28562 165s Exiting Ebwt::buildToDisk() 165s Returning from initFromVector 165s Wrote 4203034 bytes to primary EBWT file: transcripts.1.ebwt 165s Wrote 57132 bytes to secondary EBWT file: transcripts.2.ebwt 165s Re-opening _in1 and _in2 as input streams 165s Returning from Ebwt constructor 165s Headers: 165s len: 28562 165s bwtLen: 28563 165s sz: 7141 165s bwtSz: 7141 165s lineRate: 6 165s linesPerSide: 1 165s offRate: 1 165s offMask: 0xfffffffe 165s isaRate: -1 165s isaMask: 0xffffffff 165s ftabChars: 10 165s eftabLen: 20 165s eftabSz: 80 165s ftabLen: 1048577 165s ftabSz: 4194308 165s offsLen: 14282 165s offsSz: 57128 165s isaLen: 0 165s isaSz: 0 165s lineSz: 64 165s sideSz: 64 165s sideBwtSz: 56 165s sideBwtLen: 224 165s numSidePairs: 64 165s numSides: 128 165s numLines: 128 165s ebwtTotLen: 8192 165s ebwtTotSz: 8192 165s reverse: 0 165s Total time for call to driver() for forward index: 00:00:00 165s Reading reference sizes 165s Time reading reference sizes: 00:00:00 165s Calculating joined length 165s Writing header 165s Reserving space for joined string 165s Joining reference sequences 165s Time to join reference sequences: 00:00:00 165s bmax according to bmaxDivN setting: 7140 165s Using parameters --bmax 5355 --dcv 1024 165s Doing ahead-of-time memory usage test 165s Passed! Constructing with these parameters: --bmax 5355 --dcv 1024 165s Constructing suffix-array element generator 165s Building DifferenceCoverSample 165s Building sPrime 165s Building sPrimeOrder 165s V-Sorting samples 165s V-Sorting samples time: 00:00:00 165s Allocating rank array 165s Ranking v-sort output 165s Ranking v-sort output time: 00:00:00 165s Invoking Larsson-Sadakane on ranks 165s Invoking Larsson-Sadakane on ranks time: 00:00:00 165s Sanity-checking and returning 165s Building samples 165s Reserving space for 12 sample suffixes 165s Generating random suffixes 165s QSorting 12 sample offsets, eliminating duplicates 165s Multikey QSorting 12 samples 165s (Using difference cover) 165s Multikey QSorting samples time: 00:00:00 165s QSorting sample offsets, eliminating duplicates time: 00:00:00 165s Calculating bucket sizes 165s Splitting and merging 165s Splitting and merging time: 00:00:00 165s Avg bucket size: 4079.43 (target: 5354) 165s Converting suffix-array elements to index image 165s Allocating ftab, absorbFtab 165s Entering Ebwt loop 165s Getting block 1 of 7 165s Reserving size (5355) for bucket 1 165s Calculating Z arrays for bucket 1 165s Entering block accumulator loop for bucket 1: 165s bucket 1: 10% 165s bucket 1: 20% 165s bucket 1: 30% 165s bucket 1: 40% 165s bucket 1: 50% 165s bucket 1: 60% 165s bucket 1: 70% 165s bucket 1: 80% 165s bucket 1: 90% 165s bucket 1: 100% 165s Sorting block of length 1796 for bucket 1 165s (Using difference cover) 165s Sorting block time: 00:00:00 165s Returning block of 1797 for bucket 1 165s Getting block 2 of 7 165s Reserving size (5355) for bucket 2 165s Calculating Z arrays for bucket 2 165s Entering block accumulator loop for bucket 2: 165s bucket 2: 10% 165s bucket 2: 20% 165s bucket 2: 30% 165s bucket 2: 40% 165s bucket 2: 50% 165s bucket 2: 60% 165s bucket 2: 70% 165s bucket 2: 80% 165s bucket 2: 90% 165s bucket 2: 100% 165s Sorting block of length 4275 for bucket 2 165s (Using difference cover) 165s Sorting block time: 00:00:00 165s Returning block of 4276 for bucket 2 165s Getting block 3 of 7 165s Reserving size (5355) for bucket 3 165s Calculating Z arrays for bucket 3 165s Entering block accumulator loop for bucket 3: 165s bucket 3: 10% 165s bucket 3: 20% 165s bucket 3: 30% 165s bucket 3: 40% 165s bucket 3: 50% 165s bucket 3: 60% 165s bucket 3: 70% 165s bucket 3: 80% 165s bucket 3: 90% 165s bucket 3: 100% 165s Sorting block of length 4010 for bucket 3 165s (Using difference cover) 165s Sorting block time: 00:00:00 165s Returning block of 4011 for bucket 3 165s Getting block 4 of 7 165s Reserving size (5355) for bucket 4 165s Calculating Z arrays for bucket 4 165s Entering block accumulator loop for bucket 4: 165s bucket 4: 10% 165s bucket 4: 20% 165s bucket 4: 30% 165s bucket 4: 40% 165s bucket 4: 50% 165s bucket 4: 60% 165s bucket 4: 70% 165s bucket 4: 80% 165s bucket 4: 90% 165s bucket 4: 100% 165s Sorting block of length 3860 for bucket 4 165s (Using difference cover) 165s Sorting block time: 00:00:00 165s Returning block of 3861 for bucket 4 165s Getting block 5 of 7 165s Reserving size (5355) for bucket 5 165s Calculating Z arrays for bucket 5 165s Entering block accumulator loop for bucket 5: 165s bucket 5: 10% 165s bucket 5: 20% 165s bucket 5: 30% 165s bucket 5: 40% 165s bucket 5: 50% 165s bucket 5: 60% 165s bucket 5: 70% 165s bucket 5: 80% 165s bucket 5: 90% 165s bucket 5: 100% 165s Sorting block of length 4188 for bucket 5 165s (Using difference cover) 165s Sorting block time: 00:00:00 165s Returning block of 4189 for bucket 5 165s Getting block 6 of 7 165s Reserving size (5355) for bucket 6 165s Calculating Z arrays for bucket 6 165s Entering block accumulator loop for bucket 6: 165s bucket 6: 10% 165s bucket 6: 20% 165s bucket 6: 30% 165s bucket 6: 40% 165s bucket 6: 50% 165s bucket 6: 60% 165s bucket 6: 70% 165s bucket 6: 80% 165s bucket 6: 90% 165s bucket 6: 100% 165s Sorting block of length 5102 for bucket 6 165s (Using difference cover) 165s Sorting block time: 00:00:00 165s Returning block of 5103 for bucket 6 165s Getting block 7 of 7 165s Reserving size (5355) for bucket 7 165s Calculating Z arrays for bucket 7 165s Entering block accumulator loop for bucket 7: 165s bucket 7: 10% 165s bucket 7: 20% 165s bucket 7: 30% 165s bucket 7: 40% 165s bucket 7: 50% 165s bucket 7: 60% 165s bucket 7: 70% 165s bucket 7: 80% 165s bucket 7: 90% 165s bucket 7: 100% 165s Sorting block of length 5325 for bucket 7 165s (Using difference cover) 165s Sorting block time: 00:00:00 165s Returning block of 5326 for bucket 7 165s Exited Ebwt loop 165s fchr[A]: 0 165s fchr[C]: 7097 165s fchr[G]: 15029 165s fchr[T]: 22254 165s fchr[$]: 28562 165s Exiting Ebwt::buildToDisk() 165s Returning from initFromVector 165s Wrote 4203034 bytes to primary EBWT file: transcripts.rev.1.ebwt 165s Wrote 57132 bytes to secondary EBWT file: transcripts.rev.2.ebwt 165s Re-opening _in1 and _in2 as input streams 165s Returning from Ebwt constructor 165s Headers: 165s len: 28562 165s bwtLen: 28563 165s sz: 7141 165s bwtSz: 7141 165s lineRate: 6 165s linesPerSide: 1 165s offRate: 1 165s offMask: 0xfffffffe 165s isaRate: -1 165s isaMask: 0xffffffff 165s ftabChars: 10 165s eftabLen: 20 165s eftabSz: 80 165s ftabLen: 1048577 165s ftabSz: 4194308 165s + bowtie -aS -X 800 --offrate 1 transcripts -1 reads_1.fastq -2 reads_2.fastq 165s + samtools view -Sb - 165s offsLen: 14282 165s offsSz: 57128 165s isaLen: 0 165s isaSz: 0 165s lineSz: 64 165s sideSz: 64 165s sideBwtSz: 56 165s sideBwtLen: 224 165s numSidePairs: 64 165s numSides: 128 165s numLines: 128 165s ebwtTotLen: 8192 165s ebwtTotSz: 8192 165s reverse: 0 165s Total time for backward call to driver() for mirror index: 00:00:00 165s Setting the index via positional argument will be deprecated in a future release. Please use -x option instead. 167s # reads processed: 10000 167s # reads with at least one alignment: 10000 (100.00%) 167s # reads that failed to align: 0 (0.00%) 167s Reported 14270 paired-end alignments 167s + berkeley-express transcripts.fasta hits.bam 167s 2024-Mar-27 02:41:05 - Attempting to read 'hits.bam' in BAM format... 167s 2024-Mar-27 02:41:05 - Parsing BAM header... 167s 2024-Mar-27 02:41:05 - Loading target sequences and measuring bias background... 167s 2024-Mar-27 02:41:05 - Initialized 15 targets. 167s 2024-Mar-27 02:41:05 - Processing input fragment alignments... 168s 2024-Mar-27 02:41:06 - COMPLETED: Processed 10000 mapped fragments, targets are in 8 bundles. 168s 2024-Mar-27 02:41:06 - 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). 168s 2024-Mar-27 02:41:06 - Writing results to file... 168s 2024-Mar-27 02:41:06 - Done. 168s autopkgtest [02:41:06]: test run-tests: -----------------------] 169s autopkgtest [02:41:07]: test run-tests: - - - - - - - - - - results - - - - - - - - - - 169s run-tests PASS 170s autopkgtest [02:41:08]: @@@@@@@@@@@@@@@@@@@@ summary 170s run-tests PASS 181s Creating nova instance adt-noble-arm64-berkeley-express-20240327-023818-juju-7f2275-prod-proposed-migration-environment-3-a0f491c2-4fc9-4070-8ea5-6f47d6da0cdc from image adt/ubuntu-noble-arm64-server-20240326.img (UUID 0221ee4c-7186-4bac-9e7d-f1a20b702f58)...