0s autopkgtest [19:39:54]: starting date and time: 2024-03-25 19:39:54+0000 0s autopkgtest [19:39:54]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [19:39:54]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ru62bz8r/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-ppc64el-8.secgroup --name adt-noble-ppc64el-berkeley-express-20240325-193954-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-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/ 124s autopkgtest [19:41:58]: testbed dpkg architecture: ppc64el 124s autopkgtest [19:41:58]: testbed apt version: 2.7.12 124s autopkgtest [19:41:58]: @@@@@@@@@@@@@@@@@@@@ test bed setup 125s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 126s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [7608 B] 126s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3992 kB] 126s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.0 kB] 126s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [497 kB] 126s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [700 kB] 126s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 126s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 126s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 126s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4231 kB] 127s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 127s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [61.7 kB] 127s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 130s Fetched 9677 kB in 3s (3333 kB/s) 130s Reading package lists... 133s Reading package lists... 133s Building dependency tree... 133s Reading state information... 134s Calculating upgrade... 134s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 134s Reading package lists... 134s Building dependency tree... 134s Reading state information... 134s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 135s sh: Attempting to set up Debian/Ubuntu apt sources automatically 135s sh: Distribution appears to be Ubuntu 136s Reading package lists... 136s Building dependency tree... 136s Reading state information... 136s eatmydata is already the newest version (131-1). 136s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 136s Reading package lists... 136s Building dependency tree... 136s Reading state information... 136s dbus is already the newest version (1.14.10-4ubuntu1). 136s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 136s Reading package lists... 137s Building dependency tree... 137s Reading state information... 137s rng-tools-debian is already the newest version (2.4). 137s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 137s Reading package lists... 137s Building dependency tree... 137s Reading state information... 137s The following packages will be REMOVED: 137s cloud-init* python3-configobj* python3-debconf* 137s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 137s After this operation, 3256 kB disk space will be freed. 137s (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.) 137s Removing cloud-init (24.1.2-0ubuntu1) ... 138s Removing python3-configobj (5.0.8-3) ... 138s Removing python3-debconf (1.5.86) ... 138s Processing triggers for man-db (2.12.0-3) ... 139s (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 ... 69767 files and directories currently installed.) 139s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 139s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 139s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 139s invoke-rc.d: policy-rc.d denied execution of try-restart. 139s Reading package lists... 140s Building dependency tree... 140s Reading state information... 140s linux-generic is already the newest version (6.8.0-11.11+1). 140s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 140s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 140s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 140s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 143s Reading package lists... 143s Reading package lists... 143s Building dependency tree... 143s Reading state information... 143s Calculating upgrade... 143s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 143s Reading package lists... 144s Building dependency tree... 144s Reading state information... 144s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 144s autopkgtest [19:42:18]: rebooting testbed after setup commands that affected boot 309s autopkgtest [19:45:03]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 312s autopkgtest [19:45:06]: @@@@@@@@@@@@@@@@@@@@ apt-source berkeley-express 315s Get:1 http://ftpmaster.internal/ubuntu noble/universe berkeley-express 1.5.3+dfsg-3build3 (dsc) [2571 B] 315s Get:2 http://ftpmaster.internal/ubuntu noble/universe berkeley-express 1.5.3+dfsg-3build3 (tar) [366 kB] 315s Get:3 http://ftpmaster.internal/ubuntu noble/universe berkeley-express 1.5.3+dfsg-3build3 (diff) [10.9 kB] 315s gpgv: Signature made Tue Dec 19 15:00:44 2023 UTC 315s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 315s gpgv: Can't check signature: No public key 315s dpkg-source: warning: cannot verify inline signature for ./berkeley-express_1.5.3+dfsg-3build3.dsc: no acceptable signature found 315s autopkgtest [19:45:09]: testing package berkeley-express version 1.5.3+dfsg-3build3 315s autopkgtest [19:45:09]: build not needed 316s autopkgtest [19:45:10]: test run-tests: preparing testbed 322s Reading package lists... 322s Building dependency tree... 322s Reading state information... 323s Starting pkgProblemResolver with broken count: 0 323s Starting 2 pkgProblemResolver with broken count: 0 323s Done 323s The following additional packages will be installed: 323s berkeley-express berkeley-express-doc bowtie libbamtools2.5.2 323s libboost-filesystem1.83.0 libboost-program-options1.83.0 323s libboost-thread1.83.0 libdeflate0 libhts3 libhtscodecs2 libprotobuf32 323s samtools 323s Suggested packages: 323s bowtie-examples cwltool 323s Recommended packages: 323s med-config 323s The following NEW packages will be installed: 323s autopkgtest-satdep berkeley-express berkeley-express-doc bowtie 323s libbamtools2.5.2 libboost-filesystem1.83.0 libboost-program-options1.83.0 323s libboost-thread1.83.0 libdeflate0 libhts3 libhtscodecs2 libprotobuf32 323s samtools 323s 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. 323s Need to get 6341 kB/6341 kB of archives. 323s After this operation, 27.5 MB of additional disk space will be used. 323s Get:1 /tmp/autopkgtest.cmLBfH/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [736 B] 323s Get:2 http://ftpmaster.internal/ubuntu noble/universe ppc64el libbamtools2.5.2 ppc64el 2.5.2+dfsg-4 [161 kB] 324s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libboost-filesystem1.83.0 ppc64el 1.83.0-2ubuntu1 [373 kB] 324s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el libboost-program-options1.83.0 ppc64el 1.83.0-2ubuntu1 [421 kB] 324s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el libboost-thread1.83.0 ppc64el 1.83.0-2ubuntu1 [363 kB] 324s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el libprotobuf32 ppc64el 3.21.12-8ubuntu5 [982 kB] 325s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el berkeley-express ppc64el 1.5.3+dfsg-3build3 [226 kB] 325s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el berkeley-express-doc all 1.5.3+dfsg-3build3 [724 kB] 325s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 325s Get:10 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 325s Get:11 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB] 325s Get:12 http://ftpmaster.internal/ubuntu noble/universe ppc64el samtools ppc64el 1.19.2-1 [669 kB] 325s Get:13 http://ftpmaster.internal/ubuntu noble/universe ppc64el bowtie ppc64el 1.3.1-3 [1698 kB] 326s Fetched 6341 kB in 3s (2293 kB/s) 326s Selecting previously unselected package libbamtools2.5.2:ppc64el. 326s (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 ... 69712 files and directories currently installed.) 326s Preparing to unpack .../00-libbamtools2.5.2_2.5.2+dfsg-4_ppc64el.deb ... 326s Unpacking libbamtools2.5.2:ppc64el (2.5.2+dfsg-4) ... 326s Selecting previously unselected package libboost-filesystem1.83.0:ppc64el. 326s Preparing to unpack .../01-libboost-filesystem1.83.0_1.83.0-2ubuntu1_ppc64el.deb ... 326s Unpacking libboost-filesystem1.83.0:ppc64el (1.83.0-2ubuntu1) ... 326s Selecting previously unselected package libboost-program-options1.83.0:ppc64el. 326s Preparing to unpack .../02-libboost-program-options1.83.0_1.83.0-2ubuntu1_ppc64el.deb ... 326s Unpacking libboost-program-options1.83.0:ppc64el (1.83.0-2ubuntu1) ... 326s Selecting previously unselected package libboost-thread1.83.0:ppc64el. 326s Preparing to unpack .../03-libboost-thread1.83.0_1.83.0-2ubuntu1_ppc64el.deb ... 326s Unpacking libboost-thread1.83.0:ppc64el (1.83.0-2ubuntu1) ... 326s Selecting previously unselected package libprotobuf32:ppc64el. 326s Preparing to unpack .../04-libprotobuf32_3.21.12-8ubuntu5_ppc64el.deb ... 326s Unpacking libprotobuf32:ppc64el (3.21.12-8ubuntu5) ... 326s Selecting previously unselected package berkeley-express. 326s Preparing to unpack .../05-berkeley-express_1.5.3+dfsg-3build3_ppc64el.deb ... 326s Unpacking berkeley-express (1.5.3+dfsg-3build3) ... 326s Selecting previously unselected package berkeley-express-doc. 326s Preparing to unpack .../06-berkeley-express-doc_1.5.3+dfsg-3build3_all.deb ... 326s Unpacking berkeley-express-doc (1.5.3+dfsg-3build3) ... 327s Selecting previously unselected package libdeflate0:ppc64el. 327s Preparing to unpack .../07-libdeflate0_1.19-1_ppc64el.deb ... 327s Unpacking libdeflate0:ppc64el (1.19-1) ... 327s Selecting previously unselected package libhtscodecs2:ppc64el. 327s Preparing to unpack .../08-libhtscodecs2_1.6.0-1_ppc64el.deb ... 327s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 327s Selecting previously unselected package libhts3:ppc64el. 327s Preparing to unpack .../09-libhts3_1.18+ds-1_ppc64el.deb ... 327s Unpacking libhts3:ppc64el (1.18+ds-1) ... 327s Selecting previously unselected package samtools. 327s Preparing to unpack .../10-samtools_1.19.2-1_ppc64el.deb ... 327s Unpacking samtools (1.19.2-1) ... 327s Selecting previously unselected package bowtie. 327s Preparing to unpack .../11-bowtie_1.3.1-3_ppc64el.deb ... 327s Unpacking bowtie (1.3.1-3) ... 327s Selecting previously unselected package autopkgtest-satdep. 327s Preparing to unpack .../12-1-autopkgtest-satdep.deb ... 327s Unpacking autopkgtest-satdep (0) ... 327s Setting up libhtscodecs2:ppc64el (1.6.0-1) ... 327s Setting up libboost-program-options1.83.0:ppc64el (1.83.0-2ubuntu1) ... 327s Setting up bowtie (1.3.1-3) ... 327s Setting up berkeley-express-doc (1.5.3+dfsg-3build3) ... 327s Setting up libdeflate0:ppc64el (1.19-1) ... 327s Setting up libboost-thread1.83.0:ppc64el (1.83.0-2ubuntu1) ... 327s Setting up libboost-filesystem1.83.0:ppc64el (1.83.0-2ubuntu1) ... 327s Setting up libbamtools2.5.2:ppc64el (2.5.2+dfsg-4) ... 327s Setting up libprotobuf32:ppc64el (3.21.12-8ubuntu5) ... 327s Setting up libhts3:ppc64el (1.18+ds-1) ... 327s Setting up samtools (1.19.2-1) ... 327s Setting up berkeley-express (1.5.3+dfsg-3build3) ... 327s Setting up autopkgtest-satdep (0) ... 327s Processing triggers for man-db (2.12.0-3) ... 327s Processing triggers for libc-bin (2.39-0ubuntu6) ... 330s (Reading database ... 69946 files and directories currently installed.) 330s Removing autopkgtest-satdep (0) ... 331s autopkgtest [19:45:25]: test run-tests: [----------------------- 331s + pkg=berkeley-express 331s + [ /tmp/autopkgtest.cmLBfH/autopkgtest_tmp = ] 331s + cd /tmp/autopkgtest.cmLBfH/autopkgtest_tmp 331s + 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 . 331s + gunzip reads_1.fastq.gz reads_2.fastq.gz transcripts.fasta.gz 331s + bowtie-build --offrate 1 transcripts.fasta transcripts 331s Settings: 331s Output files: "transcripts.*.ebwt" 331s Line rate: 6 (line is 64 bytes) 331s Lines per side: 1 (side is 64 bytes) 331s Offset rate: 1 (one in 2) 331s FTable chars: 10 331s Strings: unpacked 331s Max bucket size: default 331s Max bucket size, sqrt multiplier: default 331s Max bucket size, len divisor: 4 331s Difference-cover sample period: 1024 331s Endianness: little 331s Actual local endianness: little 331s Sanity checking: disabled 331s Assertions: disabled 331s Random seed: 0 331s Sizeofs: void*:8, int:4, long:8, size_t:8 331s Input files DNA, FASTA: 331s transcripts.fasta 331s Reading reference sizes 331s Time reading reference sizes: 00:00:00 331s Calculating joined length 331s Writing header 331s Reserving space for joined string 331s Joining reference sequences 331s Time to join reference sequences: 00:00:00 331s bmax according to bmaxDivN setting: 7140 331s Using parameters --bmax 5355 --dcv 1024 331s Doing ahead-of-time memory usage test 331s Passed! Constructing with these parameters: --bmax 5355 --dcv 1024 331s Constructing suffix-array element generator 331s Building DifferenceCoverSample 331s Building sPrime 331s Building sPrimeOrder 331s V-Sorting samples 331s V-Sorting samples time: 00:00:00 331s Allocating rank array 331s Ranking v-sort output 331s Ranking v-sort output time: 00:00:00 331s Invoking Larsson-Sadakane on ranks 331s Invoking Larsson-Sadakane on ranks time: 00:00:00 331s Sanity-checking and returning 331s Building samples 331s Reserving space for 12 sample suffixes 331s Generating random suffixes 331s QSorting 12 sample offsets, eliminating duplicates 331s Multikey QSorting 12 samples 331s (Using difference cover) 331s Multikey QSorting samples time: 00:00:00 331s QSorting sample offsets, eliminating duplicates time: 00:00:00 331s Calculating bucket sizes 331s Splitting and merging 331s Splitting and merging time: 00:00:00 331s Split 2, merged 6; iterating... 331s Splitting and merging 331s Splitting and merging time: 00:00:00 331s Split 1, merged 2; iterating... 331s Splitting and merging 331s Splitting and merging time: 00:00:00 331s Avg bucket size: 3569.38 (target: 5354) 331s Converting suffix-array elements to index image 331s Allocating ftab, absorbFtab 331s Entering Ebwt loop 331s Getting block 1 of 8 331s Reserving size (5355) for bucket 1 331s Calculating Z arrays for bucket 1 331s Entering block accumulator loop for bucket 1: 331s bucket 1: 10% 331s bucket 1: 20% 331s bucket 1: 30% 331s bucket 1: 40% 331s bucket 1: 50% 331s bucket 1: 60% 331s bucket 1: 70% 331s bucket 1: 80% 331s bucket 1: 90% 331s bucket 1: 100% 331s Sorting block of length 3445 for bucket 1 331s (Using difference cover) 331s Sorting block time: 00:00:00 331s Returning block of 3446 for bucket 1 331s Getting block 2 of 8 331s Reserving size (5355) for bucket 2 331s Calculating Z arrays for bucket 2 331s Entering block accumulator loop for bucket 2: 331s bucket 2: 10% 331s bucket 2: 20% 331s bucket 2: 30% 331s bucket 2: 40% 331s bucket 2: 50% 331s bucket 2: 60% 331s bucket 2: 70% 331s bucket 2: 80% 331s bucket 2: 90% 331s bucket 2: 100% 331s Sorting block of length 5081 for bucket 2 331s (Using difference cover) 331s Sorting block time: 00:00:00 331s Returning block of 5082 for bucket 2 331s Getting block 3 of 8 331s Reserving size (5355) for bucket 3 331s Calculating Z arrays for bucket 3 331s Entering block accumulator loop for bucket 3: 331s bucket 3: 10% 331s bucket 3: 20% 331s bucket 3: 30% 331s bucket 3: 40% 331s bucket 3: 50% 331s bucket 3: 60% 331s bucket 3: 70% 331s bucket 3: 80% 331s bucket 3: 90% 331s bucket 3: 100% 331s Sorting block of length 2382 for bucket 3 331s (Using difference cover) 331s Sorting block time: 00:00:00 331s Returning block of 2383 for bucket 3 331s Getting block 4 of 8 331s Reserving size (5355) for bucket 4 331s Calculating Z arrays for bucket 4 331s Entering block accumulator loop for bucket 4: 331s bucket 4: 10% 331s bucket 4: 20% 331s bucket 4: 30% 331s bucket 4: 40% 331s bucket 4: 50% 331s bucket 4: 60% 331s bucket 4: 70% 331s bucket 4: 80% 331s bucket 4: 90% 331s bucket 4: 100% 331s Sorting block of length 5217 for bucket 4 331s (Using difference cover) 331s Sorting block time: 00:00:00 331s Returning block of 5218 for bucket 4 331s Getting block 5 of 8 331s Reserving size (5355) for bucket 5 331s Calculating Z arrays for bucket 5 331s Entering block accumulator loop for bucket 5: 331s bucket 5: 10% 331s bucket 5: 20% 331s bucket 5: 30% 331s bucket 5: 40% 331s bucket 5: 50% 331s bucket 5: 60% 331s bucket 5: 70% 331s bucket 5: 80% 331s bucket 5: 90% 331s bucket 5: 100% 331s Sorting block of length 3095 for bucket 5 331s (Using difference cover) 331s Sorting block time: 00:00:00 331s Returning block of 3096 for bucket 5 331s Getting block 6 of 8 331s Reserving size (5355) for bucket 6 331s Calculating Z arrays for bucket 6 331s Entering block accumulator loop for bucket 6: 331s bucket 6: 10% 331s bucket 6: 20% 331s bucket 6: 30% 331s bucket 6: 40% 331s bucket 6: 50% 331s bucket 6: 60% 331s bucket 6: 70% 331s bucket 6: 80% 331s bucket 6: 90% 331s bucket 6: 100% 331s Sorting block of length 3727 for bucket 6 331s (Using difference cover) 331s Sorting block time: 00:00:00 331s Returning block of 3728 for bucket 6 331s Getting block 7 of 8 331s Reserving size (5355) for bucket 7 331s Calculating Z arrays for bucket 7 331s Entering block accumulator loop for bucket 7: 331s bucket 7: 10% 331s bucket 7: 20% 331s bucket 7: 30% 331s bucket 7: 40% 331s bucket 7: 50% 331s bucket 7: 60% 331s bucket 7: 70% 331s bucket 7: 80% 331s bucket 7: 90% 331s bucket 7: 100% 331s Sorting block of length 5329 for bucket 7 331s (Using difference cover) 331s Sorting block time: 00:00:00 331s Returning block of 5330 for bucket 7 331s Getting block 8 of 8 331s Reserving size (5355) for bucket 8 331s Calculating Z arrays for bucket 8 331s Entering block accumulator loop for bucket 8: 331s bucket 8: 10% 331s bucket 8: 20% 331s bucket 8: 30% 331s bucket 8: 40% 331s bucket 8: 50% 331s bucket 8: 60% 331s bucket 8: 70% 331s bucket 8: 80% 331s bucket 8: 90% 331s bucket 8: 100% 331s Sorting block of length 279 for bucket 8 331s (Using difference cover) 331s Sorting block time: 00:00:00 331s Returning block of 280 for bucket 8 331s Exited Ebwt loop 331s fchr[A]: 0 331s fchr[C]: 7097 331s fchr[G]: 15029 331s fchr[T]: 22254 331s fchr[$]: 28562 331s Exiting Ebwt::buildToDisk() 331s Returning from initFromVector 331s Wrote 4203034 bytes to primary EBWT file: transcripts.1.ebwt 331s Wrote 57132 bytes to secondary EBWT file: transcripts.2.ebwt 331s Re-opening _in1 and _in2 as input streams 331s Returning from Ebwt constructor 331s Headers: 331s len: 28562 331s bwtLen: 28563 331s sz: 7141 331s bwtSz: 7141 331s lineRate: 6 331s linesPerSide: 1 331s offRate: 1 331s offMask: 0xfffffffe 331s isaRate: -1 331s isaMask: 0xffffffff 331s ftabChars: 10 331s eftabLen: 20 331s eftabSz: 80 331s ftabLen: 1048577 331s ftabSz: 4194308 331s offsLen: 14282 331s offsSz: 57128 331s isaLen: 0 331s isaSz: 0 331s lineSz: 64 331s sideSz: 64 331s sideBwtSz: 56 331s sideBwtLen: 224 331s numSidePairs: 64 331s numSides: 128 331s numLines: 128 331s ebwtTotLen: 8192 331s ebwtTotSz: 8192 331s reverse: 0 331s Total time for call to driver() for forward index: 00:00:00 331s Reading reference sizes 331s Time reading reference sizes: 00:00:00 331s Calculating joined length 331s Writing header 331s Reserving space for joined string 331s Joining reference sequences 331s Time to join reference sequences: 00:00:00 331s bmax according to bmaxDivN setting: 7140 331s Using parameters --bmax 5355 --dcv 1024 331s Doing ahead-of-time memory usage test 331s Passed! Constructing with these parameters: --bmax 5355 --dcv 1024 331s Constructing suffix-array element generator 331s Building DifferenceCoverSample 331s Building sPrime 331s Building sPrimeOrder 331s V-Sorting samples 331s V-Sorting samples time: 00:00:00 331s Allocating rank array 331s Ranking v-sort output 331s Ranking v-sort output time: 00:00:00 331s Invoking Larsson-Sadakane on ranks 331s Invoking Larsson-Sadakane on ranks time: 00:00:00 331s Sanity-checking and returning 331s Building samples 331s Reserving space for 12 sample suffixes 331s Generating random suffixes 331s QSorting 12 sample offsets, eliminating duplicates 331s Multikey QSorting 12 samples 331s (Using difference cover) 331s Multikey QSorting samples time: 00:00:00 331s QSorting sample offsets, eliminating duplicates time: 00:00:00 331s Calculating bucket sizes 331s Splitting and merging 331s Splitting and merging time: 00:00:00 331s Avg bucket size: 4079.43 (target: 5354) 331s Converting suffix-array elements to index image 331s Allocating ftab, absorbFtab 331s Entering Ebwt loop 331s Getting block 1 of 7 331s Reserving size (5355) for bucket 1 331s Calculating Z arrays for bucket 1 331s Entering block accumulator loop for bucket 1: 331s bucket 1: 10% 331s bucket 1: 20% 331s bucket 1: 30% 331s bucket 1: 40% 331s bucket 1: 50% 331s bucket 1: 60% 331s bucket 1: 70% 331s bucket 1: 80% 331s bucket 1: 90% 331s bucket 1: 100% 331s Sorting block of length 1796 for bucket 1 331s (Using difference cover) 331s Sorting block time: 00:00:00 331s Returning block of 1797 for bucket 1 331s Getting block 2 of 7 331s Reserving size (5355) for bucket 2 331s Calculating Z arrays for bucket 2 331s Entering block accumulator loop for bucket 2: 331s bucket 2: 10% 331s bucket 2: 20% 331s bucket 2: 30% 331s bucket 2: 40% 331s bucket 2: 50% 331s bucket 2: 60% 331s bucket 2: 70% 331s bucket 2: 80% 331s bucket 2: 90% 331s bucket 2: 100% 331s Sorting block of length 4275 for bucket 2 331s (Using difference cover) 331s Sorting block time: 00:00:00 331s Returning block of 4276 for bucket 2 331s Getting block 3 of 7 331s Reserving size (5355) for bucket 3 331s Calculating Z arrays for bucket 3 331s Entering block accumulator loop for bucket 3: 331s bucket 3: 10% 331s bucket 3: 20% 331s bucket 3: 30% 331s bucket 3: 40% 331s bucket 3: 50% 331s bucket 3: 60% 331s bucket 3: 70% 331s bucket 3: 80% 331s bucket 3: 90% 331s bucket 3: 100% 331s Sorting block of length 4010 for bucket 3 331s (Using difference cover) 331s Sorting block time: 00:00:00 331s Returning block of 4011 for bucket 3 331s Getting block 4 of 7 331s Reserving size (5355) for bucket 4 331s Calculating Z arrays for bucket 4 331s Entering block accumulator loop for bucket 4: 331s bucket 4: 10% 331s bucket 4: 20% 331s bucket 4: 30% 331s bucket 4: 40% 331s bucket 4: 50% 331s bucket 4: 60% 331s bucket 4: 70% 331s bucket 4: 80% 331s bucket 4: 90% 331s bucket 4: 100% 331s Sorting block of length 3860 for bucket 4 331s (Using difference cover) 331s Sorting block time: 00:00:00 331s Returning block of 3861 for bucket 4 331s Getting block 5 of 7 331s Reserving size (5355) for bucket 5 331s Calculating Z arrays for bucket 5 331s Entering block accumulator loop for bucket 5: 331s bucket 5: 10% 331s bucket 5: 20% 331s bucket 5: 30% 331s bucket 5: 40% 331s bucket 5: 50% 331s bucket 5: 60% 331s bucket 5: 70% 331s bucket 5: 80% 331s bucket 5: 90% 331s bucket 5: 100% 331s Sorting block of length 4188 for bucket 5 331s (Using difference cover) 331s Sorting block time: 00:00:00 331s Returning block of 4189 for bucket 5 331s Getting block 6 of 7 331s Reserving size (5355) for bucket 6 331s Calculating Z arrays for bucket 6 331s Entering block accumulator loop for bucket 6: 331s bucket 6: 10% 331s bucket 6: 20% 331s bucket 6: 30% 331s bucket 6: 40% 331s bucket 6: 50% 331s bucket 6: 60% 331s bucket 6: 70% 331s bucket 6: 80% 331s bucket 6: 90% 331s bucket 6: 100% 331s Sorting block of length 5102 for bucket 6 331s (Using difference cover) 331s Sorting block time: 00:00:00 331s Returning block of 5103 for bucket 6 331s Getting block 7 of 7 331s Reserving size (5355) for bucket 7 331s Calculating Z arrays for bucket 7 331s Entering block accumulator loop for bucket 7: 331s bucket 7: 10% 331s bucket 7: 20% 331s bucket 7: 30% 331s bucket 7: 40% 331s bucket 7: 50% 331s bucket 7: 60% 331s bucket 7: 70% 331s bucket 7: 80% 331s bucket 7: 90% 331s bucket 7: 100% 331s Sorting block of length 5325 for bucket 7 331s (Using difference cover) 331s Sorting block time: 00:00:00 331s Returning block of 5326 for bucket 7 331s Exited Ebwt loop 331s fchr[A]: 0 331s fchr[C]: 7097 331s fchr[G]: 15029 331s fchr[T]: 22254 331s fchr[$]: 28562 331s Exiting Ebwt::buildToDisk() 331s + bowtie -aS -X 800 --offrate 1 transcripts -1 reads_1.fastq -2 reads_2.fastq 331s + samtools view -Sb - 331s Returning from initFromVector 331s Wrote 4203034 bytes to primary EBWT file: transcripts.rev.1.ebwt 331s Wrote 57132 bytes to secondary EBWT file: transcripts.rev.2.ebwt 331s Re-opening _in1 and _in2 as input streams 331s Returning from Ebwt constructor 331s Headers: 331s len: 28562 331s bwtLen: 28563 331s sz: 7141 331s bwtSz: 7141 331s lineRate: 6 331s linesPerSide: 1 331s offRate: 1 331s offMask: 0xfffffffe 331s isaRate: -1 331s isaMask: 0xffffffff 331s ftabChars: 10 331s eftabLen: 20 331s eftabSz: 80 331s ftabLen: 1048577 331s ftabSz: 4194308 331s offsLen: 14282 331s offsSz: 57128 331s isaLen: 0 331s isaSz: 0 331s lineSz: 64 331s sideSz: 64 331s sideBwtSz: 56 331s sideBwtLen: 224 331s numSidePairs: 64 331s numSides: 128 331s numLines: 128 331s ebwtTotLen: 8192 331s ebwtTotSz: 8192 331s reverse: 0 331s Total time for backward call to driver() for mirror index: 00:00:00 331s Setting the index via positional argument will be deprecated in a future release. Please use -x option instead. 332s # reads processed: 10000 332s # reads with at least one alignment: 10000 (100.00%) 332s # reads that failed to align: 0 (0.00%) 332s Reported 14270 paired-end alignments 332s + berkeley-express transcripts.fasta hits.bam 332s 2024-Mar-25 19:45:26 - Attempting to read 'hits.bam' in BAM format... 332s 2024-Mar-25 19:45:26 - Parsing BAM header... 332s 2024-Mar-25 19:45:26 - Loading target sequences and measuring bias background... 332s 2024-Mar-25 19:45:26 - Initialized 15 targets. 332s 2024-Mar-25 19:45:26 - Processing input fragment alignments... 333s 2024-Mar-25 19:45:27 - COMPLETED: Processed 10000 mapped fragments, targets are in 8 bundles. 333s 2024-Mar-25 19:45:27 - 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). 333s 2024-Mar-25 19:45:27 - Writing results to file... 333s 2024-Mar-25 19:45:27 - Done. 333s autopkgtest [19:45:27]: test run-tests: -----------------------] 334s autopkgtest [19:45:28]: test run-tests: - - - - - - - - - - results - - - - - - - - - - 334s run-tests PASS 334s autopkgtest [19:45:28]: @@@@@@@@@@@@@@@@@@@@ summary 334s run-tests PASS 347s Creating nova instance adt-noble-ppc64el-berkeley-express-20240325-193954-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240325.img (UUID ce50e202-ac12-4562-879d-419903f0141e)...