0s autopkgtest [17:18:34]: starting date and time: 2024-03-24 17:18:34+0000 0s autopkgtest [17:18:34]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [17:18:34]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.rwroi1e7/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:samtools,src:curl,src:gnutls28,src:htslib,src:libpsl,src:nettle,src:openssl --apt-upgrade berkeley-express --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=samtools/1.19.2-1build1 curl/8.5.0-2ubuntu7 gnutls28/3.8.3-1.1ubuntu2 htslib/1.19+ds-1.1build2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos01-arm64-6.secgroup --name adt-noble-arm64-berkeley-express-20240324-171834-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-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://us.ports.ubuntu.com/ubuntu-ports/ 105s autopkgtest [17:20:19]: testbed dpkg architecture: arm64 105s autopkgtest [17:20:19]: testbed apt version: 2.7.12 105s autopkgtest [17:20:19]: @@@@@@@@@@@@@@@@@@@@ test bed setup 106s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 107s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3986 kB] 107s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 107s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 107s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 107s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [708 kB] 107s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 107s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 107s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 107s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4364 kB] 107s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 107s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [70.1 kB] 107s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 110s Fetched 9850 kB in 2s (5808 kB/s) 110s Reading package lists... 112s Reading package lists... 112s Building dependency tree... 112s Reading state information... 113s Calculating upgrade... 113s The following packages will be REMOVED: 113s libssl3 113s The following NEW packages will be installed: 113s libssl3t64 113s The following packages have been kept back: 113s curl 113s The following packages will be upgraded: 113s openssl 114s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 114s Need to get 2777 kB of archives. 114s After this operation, 139 kB of additional disk space will be used. 114s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu2 [985 kB] 114s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu2 [1793 kB] 114s Fetched 2777 kB in 1s (4028 kB/s) 114s (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.) 114s Preparing to unpack .../openssl_3.0.13-0ubuntu2_arm64.deb ... 114s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 115s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 115s wget depends on libssl3 (>= 3.0.0). 115s u-boot-tools depends on libssl3 (>= 3.0.0). 115s tnftp depends on libssl3 (>= 3.0.0). 115s tcpdump depends on libssl3 (>= 3.0.0). 115s systemd-resolved depends on libssl3 (>= 3.0.0). 115s systemd depends on libssl3 (>= 3.0.0). 115s sudo depends on libssl3 (>= 3.0.0). 115s sbsigntool depends on libssl3 (>= 3.0.0). 115s rsync depends on libssl3 (>= 3.0.0). 115s python3-cryptography depends on libssl3 (>= 3.0.0). 115s openssh-server depends on libssl3 (>= 3.0.10). 115s openssh-client depends on libssl3 (>= 3.0.10). 115s mtd-utils depends on libssl3 (>= 3.0.0). 115s mokutil depends on libssl3 (>= 3.0.0). 115s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 115s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 115s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 115s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 115s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 115s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 115s libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0). 115s libnvme1 depends on libssl3 (>= 3.0.0). 115s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 115s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 115s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 115s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 115s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 115s kmod depends on libssl3 (>= 3.0.0). 115s dhcpcd-base depends on libssl3 (>= 3.0.0). 115s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 115s 115s (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.) 115s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 115s Selecting previously unselected package libssl3t64:arm64. 115s (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 ... 75900 files and directories currently installed.) 115s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_arm64.deb ... 115s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu2) ... 115s Setting up libssl3t64:arm64 (3.0.13-0ubuntu2) ... 115s Setting up openssl (3.0.13-0ubuntu2) ... 115s Processing triggers for man-db (2.12.0-3) ... 115s Processing triggers for libc-bin (2.39-0ubuntu6) ... 115s Reading package lists... 116s Building dependency tree... 116s Reading state information... 116s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 117s sh: Attempting to set up Debian/Ubuntu apt sources automatically 117s sh: Distribution appears to be Ubuntu 118s Reading package lists... 118s Building dependency tree... 118s Reading state information... 118s eatmydata is already the newest version (131-1). 118s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 118s Reading package lists... 119s Building dependency tree... 119s Reading state information... 119s dbus is already the newest version (1.14.10-4ubuntu1). 119s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 119s Reading package lists... 120s Building dependency tree... 120s Reading state information... 120s rng-tools-debian is already the newest version (2.4). 120s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 120s Reading package lists... 120s Building dependency tree... 120s Reading state information... 121s The following packages will be REMOVED: 121s cloud-init* python3-configobj* python3-debconf* 121s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 121s After this operation, 3256 kB disk space will be freed. 121s (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 ... 75913 files and directories currently installed.) 121s Removing cloud-init (24.1.2-0ubuntu1) ... 122s Removing python3-configobj (5.0.8-3) ... 122s Removing python3-debconf (1.5.86) ... 122s Processing triggers for man-db (2.12.0-3) ... 122s (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 ... 75524 files and directories currently installed.) 122s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 123s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 123s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 123s invoke-rc.d: policy-rc.d denied execution of try-restart. 123s Reading package lists... 123s Building dependency tree... 123s Reading state information... 124s linux-generic is already the newest version (6.8.0-11.11+1). 124s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 124s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 124s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 124s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 127s Reading package lists... 127s Reading package lists... 127s Building dependency tree... 127s Reading state information... 127s Calculating upgrade... 128s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 128s Reading package lists... 128s Building dependency tree... 128s Reading state information... 129s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 129s autopkgtest [17:20:43]: rebooting testbed after setup commands that affected boot 283s autopkgtest [17:23:17]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 286s autopkgtest [17:23:20]: @@@@@@@@@@@@@@@@@@@@ apt-source berkeley-express 288s Get:1 http://ftpmaster.internal/ubuntu noble/universe berkeley-express 1.5.3+dfsg-3build3 (dsc) [2571 B] 288s Get:2 http://ftpmaster.internal/ubuntu noble/universe berkeley-express 1.5.3+dfsg-3build3 (tar) [366 kB] 288s Get:3 http://ftpmaster.internal/ubuntu noble/universe berkeley-express 1.5.3+dfsg-3build3 (diff) [10.9 kB] 288s gpgv: Signature made Tue Dec 19 15:00:44 2023 UTC 288s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 288s gpgv: Can't check signature: No public key 288s dpkg-source: warning: cannot verify inline signature for ./berkeley-express_1.5.3+dfsg-3build3.dsc: no acceptable signature found 288s autopkgtest [17:23:22]: testing package berkeley-express version 1.5.3+dfsg-3build3 288s autopkgtest [17:23:22]: build not needed 289s autopkgtest [17:23:23]: test run-tests: preparing testbed 293s Reading package lists... 293s Building dependency tree... 293s Reading state information... 293s Starting pkgProblemResolver with broken count: 0 293s Starting 2 pkgProblemResolver with broken count: 0 293s Done 294s The following additional packages will be installed: 294s berkeley-express berkeley-express-doc bowtie libbamtools2.5.2 294s libboost-filesystem1.83.0 libboost-program-options1.83.0 294s libboost-thread1.83.0 libdeflate0 libhts3 libhtscodecs2 libprotobuf32 294s samtools 294s Suggested packages: 294s bowtie-examples cwltool 294s Recommended packages: 294s med-config 294s The following NEW packages will be installed: 294s autopkgtest-satdep berkeley-express berkeley-express-doc bowtie 294s libbamtools2.5.2 libboost-filesystem1.83.0 libboost-program-options1.83.0 294s libboost-thread1.83.0 libdeflate0 libhts3 libhtscodecs2 libprotobuf32 294s samtools 294s 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. 294s Need to get 5538 kB/5539 kB of archives. 294s After this operation, 23.3 MB of additional disk space will be used. 294s Get:1 /tmp/autopkgtest.9linkk/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [732 B] 294s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 libbamtools2.5.2 arm64 2.5.2+dfsg-4 [134 kB] 295s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libboost-filesystem1.83.0 arm64 1.83.0-2ubuntu1 [366 kB] 295s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libboost-program-options1.83.0 arm64 1.83.0-2ubuntu1 [410 kB] 295s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libboost-thread1.83.0 arm64 1.83.0-2ubuntu1 [358 kB] 295s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libprotobuf32 arm64 3.21.12-8ubuntu5 [860 kB] 295s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 berkeley-express arm64 1.5.3+dfsg-3build3 [213 kB] 295s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 berkeley-express-doc all 1.5.3+dfsg-3build3 [724 kB] 295s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 295s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 295s Get:11 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 295s Get:12 http://ftpmaster.internal/ubuntu noble/universe arm64 samtools arm64 1.19.2-1 [584 kB] 295s Get:13 http://ftpmaster.internal/ubuntu noble/universe arm64 bowtie arm64 1.3.1-3 [1346 kB] 295s Fetched 5538 kB in 1s (7203 kB/s) 295s Selecting previously unselected package libbamtools2.5.2:arm64. 295s (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 ... 75469 files and directories currently installed.) 295s Preparing to unpack .../00-libbamtools2.5.2_2.5.2+dfsg-4_arm64.deb ... 295s Unpacking libbamtools2.5.2:arm64 (2.5.2+dfsg-4) ... 295s Selecting previously unselected package libboost-filesystem1.83.0:arm64. 295s Preparing to unpack .../01-libboost-filesystem1.83.0_1.83.0-2ubuntu1_arm64.deb ... 295s Unpacking libboost-filesystem1.83.0:arm64 (1.83.0-2ubuntu1) ... 295s Selecting previously unselected package libboost-program-options1.83.0:arm64. 295s Preparing to unpack .../02-libboost-program-options1.83.0_1.83.0-2ubuntu1_arm64.deb ... 295s Unpacking libboost-program-options1.83.0:arm64 (1.83.0-2ubuntu1) ... 295s Selecting previously unselected package libboost-thread1.83.0:arm64. 295s Preparing to unpack .../03-libboost-thread1.83.0_1.83.0-2ubuntu1_arm64.deb ... 295s Unpacking libboost-thread1.83.0:arm64 (1.83.0-2ubuntu1) ... 295s Selecting previously unselected package libprotobuf32:arm64. 295s Preparing to unpack .../04-libprotobuf32_3.21.12-8ubuntu5_arm64.deb ... 295s Unpacking libprotobuf32:arm64 (3.21.12-8ubuntu5) ... 295s Selecting previously unselected package berkeley-express. 295s Preparing to unpack .../05-berkeley-express_1.5.3+dfsg-3build3_arm64.deb ... 295s Unpacking berkeley-express (1.5.3+dfsg-3build3) ... 295s Selecting previously unselected package berkeley-express-doc. 295s Preparing to unpack .../06-berkeley-express-doc_1.5.3+dfsg-3build3_all.deb ... 295s Unpacking berkeley-express-doc (1.5.3+dfsg-3build3) ... 296s Selecting previously unselected package libdeflate0:arm64. 296s Preparing to unpack .../07-libdeflate0_1.19-1_arm64.deb ... 296s Unpacking libdeflate0:arm64 (1.19-1) ... 296s Selecting previously unselected package libhtscodecs2:arm64. 296s Preparing to unpack .../08-libhtscodecs2_1.6.0-1_arm64.deb ... 296s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 296s Selecting previously unselected package libhts3:arm64. 296s Preparing to unpack .../09-libhts3_1.18+ds-1_arm64.deb ... 296s Unpacking libhts3:arm64 (1.18+ds-1) ... 296s Selecting previously unselected package samtools. 296s Preparing to unpack .../10-samtools_1.19.2-1_arm64.deb ... 296s Unpacking samtools (1.19.2-1) ... 296s Selecting previously unselected package bowtie. 296s Preparing to unpack .../11-bowtie_1.3.1-3_arm64.deb ... 296s Unpacking bowtie (1.3.1-3) ... 296s Selecting previously unselected package autopkgtest-satdep. 296s Preparing to unpack .../12-1-autopkgtest-satdep.deb ... 296s Unpacking autopkgtest-satdep (0) ... 296s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 296s Setting up libboost-program-options1.83.0:arm64 (1.83.0-2ubuntu1) ... 296s Setting up bowtie (1.3.1-3) ... 296s Setting up berkeley-express-doc (1.5.3+dfsg-3build3) ... 296s Setting up libdeflate0:arm64 (1.19-1) ... 296s Setting up libboost-thread1.83.0:arm64 (1.83.0-2ubuntu1) ... 296s Setting up libboost-filesystem1.83.0:arm64 (1.83.0-2ubuntu1) ... 296s Setting up libbamtools2.5.2:arm64 (2.5.2+dfsg-4) ... 296s Setting up libprotobuf32:arm64 (3.21.12-8ubuntu5) ... 296s Setting up libhts3:arm64 (1.18+ds-1) ... 296s Setting up samtools (1.19.2-1) ... 296s Setting up berkeley-express (1.5.3+dfsg-3build3) ... 296s Setting up autopkgtest-satdep (0) ... 296s Processing triggers for man-db (2.12.0-3) ... 296s Processing triggers for libc-bin (2.39-0ubuntu6) ... 299s (Reading database ... 75703 files and directories currently installed.) 299s Removing autopkgtest-satdep (0) ... 300s autopkgtest [17:23:34]: test run-tests: [----------------------- 300s + pkg=berkeley-express 300s + [ /tmp/autopkgtest.9linkk/autopkgtest_tmp = ] 300s + cd /tmp/autopkgtest.9linkk/autopkgtest_tmp 300s + 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 . 300s + gunzip reads_1.fastq.gz reads_2.fastq.gz transcripts.fasta.gz 300s + bowtie-build --offrate 1 transcripts.fasta transcripts 300s Settings: 300s Output files: "transcripts.*.ebwt" 300s Line rate: 6 (line is 64 bytes) 300s Lines per side: 1 (side is 64 bytes) 300s Offset rate: 1 (one in 2) 300s FTable chars: 10 300s Strings: unpacked 300s Max bucket size: default 300s Max bucket size, sqrt multiplier: default 300s Max bucket size, len divisor: 4 300s Difference-cover sample period: 1024 300s Endianness: little 300s Actual local endianness: little 300s Sanity checking: disabled 300s Assertions: disabled 300s Random seed: 0 300s Sizeofs: void*:8, int:4, long:8, size_t:8 300s Input files DNA, FASTA: 300s transcripts.fasta 300s Reading reference sizes 300s Time reading reference sizes: 00:00:00 300s Calculating joined length 300s Writing header 300s Reserving space for joined string 300s Joining reference sequences 300s Time to join reference sequences: 00:00:00 300s bmax according to bmaxDivN setting: 7140 300s Using parameters --bmax 5355 --dcv 1024 300s Doing ahead-of-time memory usage test 300s Passed! Constructing with these parameters: --bmax 5355 --dcv 1024 300s Constructing suffix-array element generator 300s Building DifferenceCoverSample 300s Building sPrime 300s Building sPrimeOrder 300s V-Sorting samples 300s V-Sorting samples time: 00:00:00 300s Allocating rank array 300s Ranking v-sort output 300s Ranking v-sort output time: 00:00:00 300s Invoking Larsson-Sadakane on ranks 300s Invoking Larsson-Sadakane on ranks time: 00:00:00 300s Sanity-checking and returning 300s Building samples 300s Reserving space for 12 sample suffixes 300s Generating random suffixes 300s QSorting 12 sample offsets, eliminating duplicates 300s Multikey QSorting 12 samples 300s (Using difference cover) 300s Multikey QSorting samples time: 00:00:00 300s QSorting sample offsets, eliminating duplicates time: 00:00:00 300s Calculating bucket sizes 300s Splitting and merging 300s Splitting and merging time: 00:00:00 300s Split 2, merged 6; iterating... 300s Splitting and merging 300s Splitting and merging time: 00:00:00 300s Split 1, merged 2; iterating... 300s Splitting and merging 300s Splitting and merging time: 00:00:00 300s Avg bucket size: 3569.38 (target: 5354) 300s Converting suffix-array elements to index image 300s Allocating ftab, absorbFtab 300s Entering Ebwt loop 300s Getting block 1 of 8 300s Reserving size (5355) for bucket 1 300s Calculating Z arrays for bucket 1 300s Entering block accumulator loop for bucket 1: 300s bucket 1: 10% 300s bucket 1: 20% 300s bucket 1: 30% 300s bucket 1: 40% 300s bucket 1: 50% 300s bucket 1: 60% 300s bucket 1: 70% 300s bucket 1: 80% 300s bucket 1: 90% 300s bucket 1: 100% 300s Sorting block of length 3445 for bucket 1 300s (Using difference cover) 300s Sorting block time: 00:00:00 300s Returning block of 3446 for bucket 1 300s Getting block 2 of 8 300s Reserving size (5355) for bucket 2 300s Calculating Z arrays for bucket 2 300s Entering block accumulator loop for bucket 2: 300s bucket 2: 10% 300s bucket 2: 20% 300s bucket 2: 30% 300s bucket 2: 40% 300s bucket 2: 50% 300s bucket 2: 60% 300s bucket 2: 70% 300s bucket 2: 80% 300s bucket 2: 90% 300s bucket 2: 100% 300s Sorting block of length 5081 for bucket 2 300s (Using difference cover) 300s Sorting block time: 00:00:00 300s Returning block of 5082 for bucket 2 300s Getting block 3 of 8 300s Reserving size (5355) for bucket 3 300s Calculating Z arrays for bucket 3 300s Entering block accumulator loop for bucket 3: 300s bucket 3: 10% 300s bucket 3: 20% 300s bucket 3: 30% 300s bucket 3: 40% 300s bucket 3: 50% 300s bucket 3: 60% 300s bucket 3: 70% 300s bucket 3: 80% 300s bucket 3: 90% 300s bucket 3: 100% 300s Sorting block of length 2382 for bucket 3 300s (Using difference cover) 300s Sorting block time: 00:00:00 300s Returning block of 2383 for bucket 3 300s Getting block 4 of 8 300s Reserving size (5355) for bucket 4 300s Calculating Z arrays for bucket 4 300s Entering block accumulator loop for bucket 4: 300s bucket 4: 10% 300s bucket 4: 20% 300s bucket 4: 30% 300s bucket 4: 40% 300s bucket 4: 50% 300s bucket 4: 60% 300s bucket 4: 70% 300s bucket 4: 80% 300s bucket 4: 90% 300s bucket 4: 100% 300s Sorting block of length 5217 for bucket 4 300s (Using difference cover) 300s Sorting block time: 00:00:00 300s Returning block of 5218 for bucket 4 300s Getting block 5 of 8 300s Reserving size (5355) for bucket 5 300s Calculating Z arrays for bucket 5 300s Entering block accumulator loop for bucket 5: 300s bucket 5: 10% 300s bucket 5: 20% 300s bucket 5: 30% 300s bucket 5: 40% 300s bucket 5: 50% 300s bucket 5: 60% 300s bucket 5: 70% 300s bucket 5: 80% 300s bucket 5: 90% 300s bucket 5: 100% 300s Sorting block of length 3095 for bucket 5 300s (Using difference cover) 300s Sorting block time: 00:00:00 300s Returning block of 3096 for bucket 5 300s Getting block 6 of 8 300s Reserving size (5355) for bucket 6 300s Calculating Z arrays for bucket 6 300s Entering block accumulator loop for bucket 6: 300s bucket 6: 10% 300s bucket 6: 20% 300s bucket 6: 30% 300s bucket 6: 40% 300s bucket 6: 50% 300s bucket 6: 60% 300s bucket 6: 70% 300s bucket 6: 80% 300s bucket 6: 90% 300s bucket 6: 100% 300s Sorting block of length 3727 for bucket 6 300s (Using difference cover) 300s Sorting block time: 00:00:00 300s Returning block of 3728 for bucket 6 300s Getting block 7 of 8 300s Reserving size (5355) for bucket 7 300s Calculating Z arrays for bucket 7 300s Entering block accumulator loop for bucket 7: 300s bucket 7: 10% 300s bucket 7: 20% 300s bucket 7: 30% 300s bucket 7: 40% 300s bucket 7: 50% 300s bucket 7: 60% 300s bucket 7: 70% 300s bucket 7: 80% 300s bucket 7: 90% 300s bucket 7: 100% 300s Sorting block of length 5329 for bucket 7 300s (Using difference cover) 300s Sorting block time: 00:00:00 300s Returning block of 5330 for bucket 7 300s Getting block 8 of 8 300s Reserving size (5355) for bucket 8 300s Calculating Z arrays for bucket 8 300s Entering block accumulator loop for bucket 8: 300s bucket 8: 10% 300s bucket 8: 20% 300s bucket 8: 30% 300s bucket 8: 40% 300s bucket 8: 50% 300s bucket 8: 60% 300s bucket 8: 70% 300s bucket 8: 80% 300s bucket 8: 90% 300s bucket 8: 100% 300s Sorting block of length 279 for bucket 8 300s (Using difference cover) 300s Sorting block time: 00:00:00 300s Returning block of 280 for bucket 8 300s Exited Ebwt loop 300s fchr[A]: 0 300s fchr[C]: 7097 300s fchr[G]: 15029 300s fchr[T]: 22254 300s fchr[$]: 28562 300s Exiting Ebwt::buildToDisk() 300s Returning from initFromVector 300s Wrote 4203034 bytes to primary EBWT file: transcripts.1.ebwt 300s Wrote 57132 bytes to secondary EBWT file: transcripts.2.ebwt 300s Re-opening _in1 and _in2 as input streams 300s Returning from Ebwt constructor 300s Headers: 300s len: 28562 300s bwtLen: 28563 300s sz: 7141 300s bwtSz: 7141 300s lineRate: 6 300s linesPerSide: 1 300s offRate: 1 300s offMask: 0xfffffffe 300s isaRate: -1 300s isaMask: 0xffffffff 300s ftabChars: 10 300s eftabLen: 20 300s eftabSz: 80 300s ftabLen: 1048577 300s ftabSz: 4194308 300s offsLen: 14282 300s offsSz: 57128 300s isaLen: 0 300s isaSz: 0 300s lineSz: 64 300s sideSz: 64 300s sideBwtSz: 56 300s sideBwtLen: 224 300s numSidePairs: 64 300s numSides: 128 300s numLines: 128 300s ebwtTotLen: 8192 300s ebwtTotSz: 8192 300s reverse: 0 300s Total time for call to driver() for forward index: 00:00:00 300s Reading reference sizes 300s Time reading reference sizes: 00:00:00 300s Calculating joined length 300s Writing header 300s Reserving space for joined string 300s Joining reference sequences 300s Time to join reference sequences: 00:00:00 300s bmax according to bmaxDivN setting: 7140 300s Using parameters --bmax 5355 --dcv 1024 300s Doing ahead-of-time memory usage test 300s Passed! Constructing with these parameters: --bmax 5355 --dcv 1024 300s Constructing suffix-array element generator 300s Building DifferenceCoverSample 300s Building sPrime 300s Building sPrimeOrder 300s V-Sorting samples 300s V-Sorting samples time: 00:00:00 300s Allocating rank array 300s Ranking v-sort output 300s Ranking v-sort output time: 00:00:00 300s Invoking Larsson-Sadakane on ranks 300s Invoking Larsson-Sadakane on ranks time: 00:00:00 300s Sanity-checking and returning 300s Building samples 300s Reserving space for 12 sample suffixes 300s Generating random suffixes 300s QSorting 12 sample offsets, eliminating duplicates 300s Multikey QSorting 12 samples 300s (Using difference cover) 300s Multikey QSorting samples time: 00:00:00 300s QSorting sample offsets, eliminating duplicates time: 00:00:00 300s Calculating bucket sizes 300s Splitting and merging 300s Splitting and merging time: 00:00:00 300s Avg bucket size: 4079.43 (target: 5354) 300s Converting suffix-array elements to index image 300s Allocating ftab, absorbFtab 300s Entering Ebwt loop 300s Getting block 1 of 7 300s Reserving size (5355) for bucket 1 300s Calculating Z arrays for bucket 1 300s Entering block accumulator loop for bucket 1: 300s bucket 1: 10% 300s bucket 1: 20% 300s bucket 1: 30% 300s bucket 1: 40% 300s bucket 1: 50% 300s bucket 1: 60% 300s bucket 1: 70% 300s bucket 1: 80% 300s bucket 1: 90% 300s bucket 1: 100% 300s Sorting block of length 1796 for bucket 1 300s (Using difference cover) 300s Sorting block time: 00:00:00 300s Returning block of 1797 for bucket 1 300s Getting block 2 of 7 300s Reserving size (5355) for bucket 2 300s Calculating Z arrays for bucket 2 300s Entering block accumulator loop for bucket 2: 300s bucket 2: 10% 300s bucket 2: 20% 300s bucket 2: 30% 300s bucket 2: 40% 300s bucket 2: 50% 300s bucket 2: 60% 300s bucket 2: 70% 300s bucket 2: 80% 300s bucket 2: 90% 300s bucket 2: 100% 300s Sorting block of length 4275 for bucket 2 300s (Using difference cover) 300s Sorting block time: 00:00:00 300s Returning block of 4276 for bucket 2 300s Getting block 3 of 7 300s Reserving size (5355) for bucket 3 300s Calculating Z arrays for bucket 3 300s Entering block accumulator loop for bucket 3: 300s bucket 3: 10% 300s bucket 3: 20% 300s bucket 3: 30% 300s bucket 3: 40% 300s bucket 3: 50% 300s bucket 3: 60% 300s bucket 3: 70% 300s bucket 3: 80% 300s bucket 3: 90% 300s bucket 3: 100% 300s Sorting block of length 4010 for bucket 3 300s (Using difference cover) 300s Sorting block time: 00:00:00 300s Returning block of 4011 for bucket 3 300s Getting block 4 of 7 300s Reserving size (5355) for bucket 4 300s Calculating Z arrays for bucket 4 300s Entering block accumulator loop for bucket 4: 300s bucket 4: 10% 300s bucket 4: 20% 300s bucket 4: 30% 300s bucket 4: 40% 300s bucket 4: 50% 300s bucket 4: 60% 300s bucket 4: 70% 300s bucket 4: 80% 300s bucket 4: 90% 300s bucket 4: 100% 300s Sorting block of length 3860 for bucket 4 300s (Using difference cover) 300s Sorting block time: 00:00:00 300s Returning block of 3861 for bucket 4 300s Getting block 5 of 7 300s Reserving size (5355) for bucket 5 300s Calculating Z arrays for bucket 5 300s Entering block accumulator loop for bucket 5: 300s bucket 5: 10% 300s bucket 5: 20% 300s bucket 5: 30% 300s bucket 5: 40% 300s bucket 5: 50% 300s bucket 5: 60% 300s bucket 5: 70% 300s bucket 5: 80% 300s bucket 5: 90% 300s bucket 5: 100% 300s Sorting block of length 4188 for bucket 5 300s (Using difference cover) 300s Sorting block time: 00:00:00 300s Returning block of 4189 for bucket 5 300s Getting block 6 of 7 300s Reserving size (5355) for bucket 6 300s Calculating Z arrays for bucket 6 300s Entering block accumulator loop for bucket 6: 300s bucket 6: 10% 300s bucket 6: 20% 300s bucket 6: 30% 300s bucket 6: 40% 300s bucket 6: 50% 300s bucket 6: 60% 300s bucket 6: 70% 300s bucket 6: 80% 300s bucket 6: 90% 300s bucket 6: 100% 300s Sorting block of length 5102 for bucket 6 300s (Using difference cover) 300s Sorting block time: 00:00:00 300s Returning block of 5103 for bucket 6 300s Getting block 7 of 7 300s Reserving size (5355) for bucket 7 300s Calculating Z arrays for bucket 7 300s Entering block accumulator loop for bucket 7: 300s bucket 7: 10% 300s bucket 7: 20% 300s bucket 7: 30% 300s bucket 7: 40% 300s bucket 7: 50% 300s bucket 7: 60% 300s bucket 7: 70% 300s bucket 7: 80% 300s bucket 7: 90% 300s bucket 7: 100% 300s Sorting block of length 5325 for bucket 7 300s (Using difference cover) 300s Sorting block time: 00:00:00 300s Returning block of 5326 for bucket 7 300s Exited Ebwt loop 300s fchr[A]: 0 300s fchr[C]: 7097 300s fchr[G]: 15029 300s fchr[T]: 22254 300s fchr[$]: 28562 300s Exiting Ebwt::buildToDisk() 300s Returning from initFromVector 300s Wrote 4203034 bytes to primary EBWT file: transcripts.rev.1.ebwt 300s Wrote 57132 bytes to secondary EBWT file: transcripts.rev.2.ebwt 300s Re-opening _in1 and _in2 as input streams 300s Returning from Ebwt constructor 300s Headers: 300s len: 28562 300s bwtLen: 28563 300s sz: 7141 300s bwtSz: 7141 300s lineRate: 6 300s linesPerSide: 1 300s offRate: 1 300s offMask: 0xfffffffe 300s isaRate: -1 300s isaMask: 0xffffffff 300s ftabChars: 10 300s eftabLen: 20 300s eftabSz: 80 300s ftabLen: 1048577 300s ftabSz: 4194308 300s offsLen: 14282 300s offsSz: 57128 300s isaLen: 0 300s isaSz: 0 300s lineSz: 64 300s sideSz: 64 300s sideBwtSz: 56 300s sideBwtLen: 224 300s numSidePairs: 64 300s numSides: 128 300s numLines: 128 300s ebwtTotLen: 8192 300s ebwtTotSz: 8192 300s reverse: 0 300s Total time for backward call to driver() for mirror index: 00:00:01 300s + + samtools view -Sb - 300s bowtie -aS -X 800 --offrate 1 transcripts -1 reads_1.fastq -2 reads_2.fastq 300s Setting the index via positional argument will be deprecated in a future release. Please use -x option instead. 301s # reads processed: 10000 301s # reads with at least one alignment: 10000 (100.00%) 301s # reads that failed to align: 0 (0.00%) 301s Reported 14270 paired-end alignments 301s + berkeley-express transcripts.fasta hits.bam 301s 2024-Mar-24 17:23:35 - Attempting to read 'hits.bam' in BAM format... 301s 2024-Mar-24 17:23:35 - Parsing BAM header... 301s 2024-Mar-24 17:23:35 - Loading target sequences and measuring bias background... 301s 2024-Mar-24 17:23:35 - Initialized 15 targets. 301s 2024-Mar-24 17:23:35 - Processing input fragment alignments... 301s 2024-Mar-24 17:23:36 - COMPLETED: Processed 10000 mapped fragments, targets are in 8 bundles. 301s 2024-Mar-24 17:23:36 - 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). 301s 2024-Mar-24 17:23:36 - Writing results to file... 301s 2024-Mar-24 17:23:36 - Done. 302s autopkgtest [17:23:36]: test run-tests: -----------------------] 302s autopkgtest [17:23:36]: test run-tests: - - - - - - - - - - results - - - - - - - - - - 302s run-tests PASS 303s autopkgtest [17:23:37]: @@@@@@@@@@@@@@@@@@@@ summary 303s run-tests PASS 316s Creating nova instance adt-noble-arm64-berkeley-express-20240324-171834-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240324.img (UUID 2df78aec-1bf7-4c70-8bf1-31fba04b7d21)...