0s autopkgtest [15:44:55]: starting date and time: 2024-03-23 15:44:55+0000 0s autopkgtest [15:44:55]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [15:44:55]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.uclgra3i/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-3@bos02-ppc64el-25.secgroup --name adt-noble-ppc64el-berkeley-express-20240323-154455-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-ppc64el-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/ 126s autopkgtest [15:47:01]: testbed dpkg architecture: ppc64el 126s autopkgtest [15:47:01]: testbed apt version: 2.7.12 126s autopkgtest [15:47:01]: @@@@@@@@@@@@@@@@@@@@ test bed setup 127s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 127s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB] 127s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 127s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3969 kB] 128s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [493 kB] 128s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [659 kB] 128s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 128s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 128s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 128s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4248 kB] 128s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 128s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [60.8 kB] 128s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 131s Fetched 9623 kB in 3s (3835 kB/s) 132s Reading package lists... 134s Reading package lists... 134s Building dependency tree... 134s Reading state information... 135s Calculating upgrade... 135s The following packages will be REMOVED: 135s libssl3 135s The following NEW packages will be installed: 135s libssl3t64 135s The following packages have been kept back: 135s curl 135s The following packages will be upgraded: 135s openssl 135s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 135s Need to get 3151 kB of archives. 135s After this operation, 73.7 kB of additional disk space will be used. 135s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu2 [1026 kB] 135s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu2 [2125 kB] 136s Fetched 3151 kB in 1s (4545 kB/s) 136s (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.) 136s Preparing to unpack .../openssl_3.0.13-0ubuntu2_ppc64el.deb ... 136s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 136s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested: 136s wget depends on libssl3 (>= 3.0.0). 136s tnftp depends on libssl3 (>= 3.0.0). 136s tcpdump depends on libssl3 (>= 3.0.0). 136s systemd-resolved depends on libssl3 (>= 3.0.0). 136s systemd depends on libssl3 (>= 3.0.0). 136s sudo depends on libssl3 (>= 3.0.0). 136s rsync depends on libssl3 (>= 3.0.0). 136s python3-cryptography depends on libssl3 (>= 3.0.0). 136s openssh-server depends on libssl3 (>= 3.0.10). 136s openssh-client depends on libssl3 (>= 3.0.10). 136s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 136s libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0). 136s libssh-4:ppc64el depends on libssl3 (>= 3.0.0). 136s libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0). 136s libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0). 136s libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0). 136s libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0). 136s libnvme1 depends on libssl3 (>= 3.0.0). 136s libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0). 136s libkmod2:ppc64el depends on libssl3 (>= 3.0.0). 136s libfido2-1:ppc64el depends on libssl3 (>= 3.0.0). 136s libcurl4:ppc64el depends on libssl3 (>= 3.0.0). 136s libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0). 136s kmod depends on libssl3 (>= 3.0.0). 136s dhcpcd-base depends on libssl3 (>= 3.0.0). 136s bind9-libs:ppc64el depends on libssl3 (>= 3.0.0). 136s 136s (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.) 136s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ... 136s Selecting previously unselected package libssl3t64:ppc64el. 136s (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 ... 70145 files and directories currently installed.) 136s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_ppc64el.deb ... 136s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 136s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 136s Setting up openssl (3.0.13-0ubuntu2) ... 136s Processing triggers for man-db (2.12.0-3) ... 137s Processing triggers for libc-bin (2.39-0ubuntu6) ... 137s Reading package lists... 137s Building dependency tree... 137s Reading state information... 137s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 138s sh: Attempting to set up Debian/Ubuntu apt sources automatically 138s sh: Distribution appears to be Ubuntu 139s Reading package lists... 139s Building dependency tree... 139s Reading state information... 139s eatmydata is already the newest version (131-1). 139s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 139s Reading package lists... 139s Building dependency tree... 139s Reading state information... 140s dbus is already the newest version (1.14.10-4ubuntu1). 140s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 140s Reading package lists... 140s Building dependency tree... 140s Reading state information... 140s rng-tools-debian is already the newest version (2.4). 140s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 140s Reading package lists... 140s Building dependency tree... 140s Reading state information... 140s The following packages will be REMOVED: 140s cloud-init* python3-configobj* python3-debconf* 140s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 140s After this operation, 3256 kB disk space will be freed. 140s (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 ... 70158 files and directories currently installed.) 140s Removing cloud-init (24.1.2-0ubuntu1) ... 141s Removing python3-configobj (5.0.8-3) ... 141s Removing python3-debconf (1.5.86) ... 141s Processing triggers for man-db (2.12.0-3) ... 141s (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 ... 69769 files and directories currently installed.) 141s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 142s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 142s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 142s invoke-rc.d: policy-rc.d denied execution of try-restart. 142s Reading package lists... 142s Building dependency tree... 142s Reading state information... 142s linux-generic is already the newest version (6.8.0-11.11+1). 142s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 143s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 143s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 143s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 145s Reading package lists... 145s Reading package lists... 145s Building dependency tree... 145s Reading state information... 146s Calculating upgrade... 146s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 146s Reading package lists... 146s Building dependency tree... 146s Reading state information... 146s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 146s autopkgtest [15:47:21]: rebooting testbed after setup commands that affected boot 185s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 191s autopkgtest [15:48:06]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 194s autopkgtest [15:48:09]: @@@@@@@@@@@@@@@@@@@@ apt-source berkeley-express 196s Get:1 http://ftpmaster.internal/ubuntu noble/universe berkeley-express 1.5.3+dfsg-3build3 (dsc) [2571 B] 196s Get:2 http://ftpmaster.internal/ubuntu noble/universe berkeley-express 1.5.3+dfsg-3build3 (tar) [366 kB] 196s Get:3 http://ftpmaster.internal/ubuntu noble/universe berkeley-express 1.5.3+dfsg-3build3 (diff) [10.9 kB] 196s gpgv: Signature made Tue Dec 19 15:00:44 2023 UTC 196s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 196s gpgv: Can't check signature: No public key 196s dpkg-source: warning: cannot verify inline signature for ./berkeley-express_1.5.3+dfsg-3build3.dsc: no acceptable signature found 196s autopkgtest [15:48:11]: testing package berkeley-express version 1.5.3+dfsg-3build3 197s autopkgtest [15:48:12]: build not needed 197s autopkgtest [15:48:12]: test run-tests: preparing testbed 198s Reading package lists... 198s Building dependency tree... 198s Reading state information... 198s Starting pkgProblemResolver with broken count: 0 199s Starting 2 pkgProblemResolver with broken count: 0 199s Done 199s The following additional packages will be installed: 199s berkeley-express berkeley-express-doc bowtie libbamtools2.5.2 199s libboost-filesystem1.83.0 libboost-program-options1.83.0 199s libboost-thread1.83.0 libdeflate0 libhts3 libhtscodecs2 libprotobuf32 199s samtools 199s Suggested packages: 199s bowtie-examples cwltool 199s Recommended packages: 199s med-config 199s The following NEW packages will be installed: 199s autopkgtest-satdep berkeley-express berkeley-express-doc bowtie 199s libbamtools2.5.2 libboost-filesystem1.83.0 libboost-program-options1.83.0 199s libboost-thread1.83.0 libdeflate0 libhts3 libhtscodecs2 libprotobuf32 199s samtools 199s 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. 199s Need to get 6341 kB/6341 kB of archives. 199s After this operation, 27.5 MB of additional disk space will be used. 199s Get:1 /tmp/autopkgtest.V4I4CJ/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [736 B] 199s Get:2 http://ftpmaster.internal/ubuntu noble/universe ppc64el libbamtools2.5.2 ppc64el 2.5.2+dfsg-4 [161 kB] 199s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libboost-filesystem1.83.0 ppc64el 1.83.0-2ubuntu1 [373 kB] 199s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el libboost-program-options1.83.0 ppc64el 1.83.0-2ubuntu1 [421 kB] 199s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el libboost-thread1.83.0 ppc64el 1.83.0-2ubuntu1 [363 kB] 199s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el libprotobuf32 ppc64el 3.21.12-8ubuntu5 [982 kB] 199s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el berkeley-express ppc64el 1.5.3+dfsg-3build3 [226 kB] 199s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el berkeley-express-doc all 1.5.3+dfsg-3build3 [724 kB] 199s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 199s Get:10 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 199s Get:11 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB] 199s Get:12 http://ftpmaster.internal/ubuntu noble/universe ppc64el samtools ppc64el 1.19.2-1 [669 kB] 200s Get:13 http://ftpmaster.internal/ubuntu noble/universe ppc64el bowtie ppc64el 1.3.1-3 [1698 kB] 200s Fetched 6341 kB in 1s (8053 kB/s) 200s Selecting previously unselected package libbamtools2.5.2:ppc64el. 200s (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 ... 69714 files and directories currently installed.) 200s Preparing to unpack .../00-libbamtools2.5.2_2.5.2+dfsg-4_ppc64el.deb ... 200s Unpacking libbamtools2.5.2:ppc64el (2.5.2+dfsg-4) ... 200s Selecting previously unselected package libboost-filesystem1.83.0:ppc64el. 200s Preparing to unpack .../01-libboost-filesystem1.83.0_1.83.0-2ubuntu1_ppc64el.deb ... 200s Unpacking libboost-filesystem1.83.0:ppc64el (1.83.0-2ubuntu1) ... 200s Selecting previously unselected package libboost-program-options1.83.0:ppc64el. 200s Preparing to unpack .../02-libboost-program-options1.83.0_1.83.0-2ubuntu1_ppc64el.deb ... 200s Unpacking libboost-program-options1.83.0:ppc64el (1.83.0-2ubuntu1) ... 200s Selecting previously unselected package libboost-thread1.83.0:ppc64el. 200s Preparing to unpack .../03-libboost-thread1.83.0_1.83.0-2ubuntu1_ppc64el.deb ... 200s Unpacking libboost-thread1.83.0:ppc64el (1.83.0-2ubuntu1) ... 200s Selecting previously unselected package libprotobuf32:ppc64el. 200s Preparing to unpack .../04-libprotobuf32_3.21.12-8ubuntu5_ppc64el.deb ... 200s Unpacking libprotobuf32:ppc64el (3.21.12-8ubuntu5) ... 200s Selecting previously unselected package berkeley-express. 200s Preparing to unpack .../05-berkeley-express_1.5.3+dfsg-3build3_ppc64el.deb ... 200s Unpacking berkeley-express (1.5.3+dfsg-3build3) ... 200s Selecting previously unselected package berkeley-express-doc. 200s Preparing to unpack .../06-berkeley-express-doc_1.5.3+dfsg-3build3_all.deb ... 200s Unpacking berkeley-express-doc (1.5.3+dfsg-3build3) ... 200s Selecting previously unselected package libdeflate0:ppc64el. 200s Preparing to unpack .../07-libdeflate0_1.19-1_ppc64el.deb ... 200s Unpacking libdeflate0:ppc64el (1.19-1) ... 200s Selecting previously unselected package libhtscodecs2:ppc64el. 200s Preparing to unpack .../08-libhtscodecs2_1.6.0-1_ppc64el.deb ... 200s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 200s Selecting previously unselected package libhts3:ppc64el. 200s Preparing to unpack .../09-libhts3_1.18+ds-1_ppc64el.deb ... 200s Unpacking libhts3:ppc64el (1.18+ds-1) ... 200s Selecting previously unselected package samtools. 200s Preparing to unpack .../10-samtools_1.19.2-1_ppc64el.deb ... 200s Unpacking samtools (1.19.2-1) ... 200s Selecting previously unselected package bowtie. 200s Preparing to unpack .../11-bowtie_1.3.1-3_ppc64el.deb ... 200s Unpacking bowtie (1.3.1-3) ... 200s Selecting previously unselected package autopkgtest-satdep. 200s Preparing to unpack .../12-1-autopkgtest-satdep.deb ... 200s Unpacking autopkgtest-satdep (0) ... 200s Setting up libhtscodecs2:ppc64el (1.6.0-1) ... 200s Setting up libboost-program-options1.83.0:ppc64el (1.83.0-2ubuntu1) ... 200s Setting up bowtie (1.3.1-3) ... 200s Setting up berkeley-express-doc (1.5.3+dfsg-3build3) ... 200s Setting up libdeflate0:ppc64el (1.19-1) ... 200s Setting up libboost-thread1.83.0:ppc64el (1.83.0-2ubuntu1) ... 200s Setting up libboost-filesystem1.83.0:ppc64el (1.83.0-2ubuntu1) ... 200s Setting up libbamtools2.5.2:ppc64el (2.5.2+dfsg-4) ... 200s Setting up libprotobuf32:ppc64el (3.21.12-8ubuntu5) ... 200s Setting up libhts3:ppc64el (1.18+ds-1) ... 200s Setting up samtools (1.19.2-1) ... 200s Setting up berkeley-express (1.5.3+dfsg-3build3) ... 200s Setting up autopkgtest-satdep (0) ... 200s Processing triggers for man-db (2.12.0-3) ... 201s Processing triggers for libc-bin (2.39-0ubuntu6) ... 203s (Reading database ... 69948 files and directories currently installed.) 203s Removing autopkgtest-satdep (0) ... 204s autopkgtest [15:48:19]: test run-tests: [----------------------- 204s + pkg=berkeley-express 204s + [ /tmp/autopkgtest.V4I4CJ/autopkgtest_tmp = ] 204s + cd /tmp/autopkgtest.V4I4CJ/autopkgtest_tmp 204s + 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 . 204s + gunzip reads_1.fastq.gz reads_2.fastq.gz transcripts.fasta.gz 204s + bowtie-build --offrate 1 transcripts.fasta transcripts 204s Settings: 204s Output files: "transcripts.*.ebwt" 204s Line rate: 6 (line is 64 bytes) 204s Lines per side: 1 (side is 64 bytes) 204s Offset rate: 1 (one in 2) 204s FTable chars: 10 204s Strings: unpacked 204s Max bucket size: default 204s Max bucket size, sqrt multiplier: default 204s Max bucket size, len divisor: 4 204s Difference-cover sample period: 1024 204s Endianness: little 204s Actual local endianness: little 204s Sanity checking: disabled 204s Assertions: disabled 204s Random seed: 0 204s Sizeofs: void*:8, int:4, long:8, size_t:8 204s Input files DNA, FASTA: 204s transcripts.fasta 204s Reading reference sizes 204s Time reading reference sizes: 00:00:00 204s Calculating joined length 204s Writing header 204s Reserving space for joined string 204s Joining reference sequences 204s Time to join reference sequences: 00:00:00 204s bmax according to bmaxDivN setting: 7140 204s Using parameters --bmax 5355 --dcv 1024 204s Doing ahead-of-time memory usage test 204s Passed! Constructing with these parameters: --bmax 5355 --dcv 1024 204s Constructing suffix-array element generator 204s Building DifferenceCoverSample 204s Building sPrime 204s Building sPrimeOrder 204s V-Sorting samples 204s V-Sorting samples time: 00:00:00 204s Allocating rank array 204s Ranking v-sort output 204s Ranking v-sort output time: 00:00:00 204s Invoking Larsson-Sadakane on ranks 204s Invoking Larsson-Sadakane on ranks time: 00:00:00 204s Sanity-checking and returning 204s Building samples 204s Reserving space for 12 sample suffixes 204s Generating random suffixes 204s QSorting 12 sample offsets, eliminating duplicates 204s Multikey QSorting 12 samples 204s (Using difference cover) 204s Multikey QSorting samples time: 00:00:00 204s QSorting sample offsets, eliminating duplicates time: 00:00:00 204s Calculating bucket sizes 204s Splitting and merging 204s Splitting and merging time: 00:00:00 204s Split 2, merged 6; iterating... 204s Splitting and merging 204s Splitting and merging time: 00:00:00 204s Split 1, merged 2; iterating... 204s Splitting and merging 204s Splitting and merging time: 00:00:00 204s Avg bucket size: 3569.38 (target: 5354) 204s Converting suffix-array elements to index image 204s Allocating ftab, absorbFtab 204s Entering Ebwt loop 204s Getting block 1 of 8 204s Reserving size (5355) for bucket 1 204s Calculating Z arrays for bucket 1 204s Entering block accumulator loop for bucket 1: 204s bucket 1: 10% 204s bucket 1: 20% 204s bucket 1: 30% 204s bucket 1: 40% 204s bucket 1: 50% 204s bucket 1: 60% 204s bucket 1: 70% 204s bucket 1: 80% 204s bucket 1: 90% 204s bucket 1: 100% 204s Sorting block of length 3445 for bucket 1 204s (Using difference cover) 204s Sorting block time: 00:00:00 204s Returning block of 3446 for bucket 1 204s Getting block 2 of 8 204s Reserving size (5355) for bucket 2 204s Calculating Z arrays for bucket 2 204s Entering block accumulator loop for bucket 2: 204s bucket 2: 10% 204s bucket 2: 20% 204s bucket 2: 30% 204s bucket 2: 40% 204s bucket 2: 50% 204s bucket 2: 60% 204s bucket 2: 70% 204s bucket 2: 80% 204s bucket 2: 90% 204s bucket 2: 100% 204s Sorting block of length 5081 for bucket 2 204s (Using difference cover) 204s Sorting block time: 00:00:00 204s Returning block of 5082 for bucket 2 204s Getting block 3 of 8 204s Reserving size (5355) for bucket 3 204s Calculating Z arrays for bucket 3 204s Entering block accumulator loop for bucket 3: 204s bucket 3: 10% 204s bucket 3: 20% 204s bucket 3: 30% 204s bucket 3: 40% 204s bucket 3: 50% 204s bucket 3: 60% 204s bucket 3: 70% 204s bucket 3: 80% 204s bucket 3: 90% 204s bucket 3: 100% 204s Sorting block of length 2382 for bucket 3 204s (Using difference cover) 204s Sorting block time: 00:00:00 204s Returning block of 2383 for bucket 3 204s Getting block 4 of 8 204s Reserving size (5355) for bucket 4 204s Calculating Z arrays for bucket 4 204s Entering block accumulator loop for bucket 4: 204s bucket 4: 10% 204s bucket 4: 20% 204s bucket 4: 30% 204s bucket 4: 40% 204s bucket 4: 50% 204s bucket 4: 60% 204s bucket 4: 70% 204s bucket 4: 80% 204s bucket 4: 90% 204s bucket 4: 100% 204s Sorting block of length 5217 for bucket 4 204s (Using difference cover) 204s Sorting block time: 00:00:00 204s Returning block of 5218 for bucket 4 204s Getting block 5 of 8 204s Reserving size (5355) for bucket 5 204s Calculating Z arrays for bucket 5 204s Entering block accumulator loop for bucket 5: 204s bucket 5: 10% 204s bucket 5: 20% 204s bucket 5: 30% 204s bucket 5: 40% 204s bucket 5: 50% 204s bucket 5: 60% 204s bucket 5: 70% 204s bucket 5: 80% 204s bucket 5: 90% 204s bucket 5: 100% 204s Sorting block of length 3095 for bucket 5 204s (Using difference cover) 204s Sorting block time: 00:00:00 204s Returning block of 3096 for bucket 5 204s Getting block 6 of 8 204s Reserving size (5355) for bucket 6 204s Calculating Z arrays for bucket 6 204s Entering block accumulator loop for bucket 6: 204s bucket 6: 10% 204s bucket 6: 20% 204s bucket 6: 30% 204s bucket 6: 40% 204s bucket 6: 50% 204s bucket 6: 60% 204s bucket 6: 70% 204s bucket 6: 80% 204s bucket 6: 90% 204s bucket 6: 100% 204s Sorting block of length 3727 for bucket 6 204s (Using difference cover) 204s Sorting block time: 00:00:00 204s Returning block of 3728 for bucket 6 204s Getting block 7 of 8 204s Reserving size (5355) for bucket 7 204s Calculating Z arrays for bucket 7 204s Entering block accumulator loop for bucket 7: 204s bucket 7: 10% 204s bucket 7: 20% 204s bucket 7: 30% 204s bucket 7: 40% 204s bucket 7: 50% 204s bucket 7: 60% 204s bucket 7: 70% 204s bucket 7: 80% 204s bucket 7: 90% 204s bucket 7: 100% 204s Sorting block of length 5329 for bucket 7 204s (Using difference cover) 204s Sorting block time: 00:00:00 204s Returning block of 5330 for bucket 7 204s Getting block 8 of 8 204s Reserving size (5355) for bucket 8 204s Calculating Z arrays for bucket 8 204s Entering block accumulator loop for bucket 8: 204s bucket 8: 10% 204s bucket 8: 20% 204s bucket 8: 30% 204s bucket 8: 40% 204s bucket 8: 50% 204s bucket 8: 60% 204s bucket 8: 70% 204s bucket 8: 80% 204s bucket 8: 90% 204s bucket 8: 100% 204s Sorting block of length 279 for bucket 8 204s (Using difference cover) 204s Sorting block time: 00:00:00 204s Returning block of 280 for bucket 8 204s Exited Ebwt loop 204s fchr[A]: 0 204s fchr[C]: 7097 204s fchr[G]: 15029 204s fchr[T]: 22254 204s fchr[$]: 28562 204s Exiting Ebwt::buildToDisk() 204s Returning from initFromVector 204s Wrote 4203034 bytes to primary EBWT file: transcripts.1.ebwt 204s Wrote 57132 bytes to secondary EBWT file: transcripts.2.ebwt 204s Re-opening _in1 and _in2 as input streams 204s Returning from Ebwt constructor 204s Headers: 204s len: 28562 204s bwtLen: 28563 204s sz: 7141 204s bwtSz: 7141 204s lineRate: 6 204s linesPerSide: 1 204s offRate: 1 204s offMask: 0xfffffffe 204s isaRate: -1 204s isaMask: 0xffffffff 204s ftabChars: 10 204s eftabLen: 20 204s eftabSz: 80 204s ftabLen: 1048577 204s ftabSz: 4194308 204s offsLen: 14282 204s offsSz: 57128 204s isaLen: 0 204s isaSz: 0 204s lineSz: 64 204s sideSz: 64 204s sideBwtSz: 56 204s sideBwtLen: 224 204s numSidePairs: 64 204s numSides: 128 204s numLines: 128 204s ebwtTotLen: 8192 204s ebwtTotSz: 8192 204s reverse: 0 204s Total time for call to driver() for forward index: 00:00:00 204s Reading reference sizes 204s Time reading reference sizes: 00:00:00 204s Calculating joined length 204s Writing header 204s Reserving space for joined string 204s Joining reference sequences 204s Time to join reference sequences: 00:00:00 204s bmax according to bmaxDivN setting: 7140 204s Using parameters --bmax 5355 --dcv 1024 204s Doing ahead-of-time memory usage test 204s Passed! Constructing with these parameters: --bmax 5355 --dcv 1024 204s Constructing suffix-array element generator 204s Building DifferenceCoverSample 204s Building sPrime 204s Building sPrimeOrder 204s V-Sorting samples 204s V-Sorting samples time: 00:00:00 204s Allocating rank array 204s Ranking v-sort output 204s Ranking v-sort output time: 00:00:00 204s Invoking Larsson-Sadakane on ranks 204s Invoking Larsson-Sadakane on ranks time: 00:00:00 204s Sanity-checking and returning 204s Building samples 204s Reserving space for 12 sample suffixes 204s Generating random suffixes 204s QSorting 12 sample offsets, eliminating duplicates 204s Multikey QSorting 12 samples 204s (Using difference cover) 204s Multikey QSorting samples time: 00:00:00 204s QSorting sample offsets, eliminating duplicates time: 00:00:00 204s Calculating bucket sizes 204s Splitting and merging 204s Splitting and merging time: 00:00:00 204s Avg bucket size: 4079.43 (target: 5354) 204s Converting suffix-array elements to index image 204s Allocating ftab, absorbFtab 204s Entering Ebwt loop 204s Getting block 1 of 7 204s Reserving size (5355) for bucket 1 204s Calculating Z arrays for bucket 1 204s Entering block accumulator loop for bucket 1: 204s bucket 1: 10% 204s bucket 1: 20% 204s bucket 1: 30% 204s bucket 1: 40% 204s bucket 1: 50% 204s bucket 1: 60% 204s bucket 1: 70% 204s bucket 1: 80% 204s bucket 1: 90% 204s bucket 1: 100% 204s Sorting block of length 1796 for bucket 1 204s (Using difference cover) 204s Sorting block time: 00:00:00 204s Returning block of 1797 for bucket 1 204s Getting block 2 of 7 204s Reserving size (5355) for bucket 2 204s Calculating Z arrays for bucket 2 204s Entering block accumulator loop for bucket 2: 204s bucket 2: 10% 204s bucket 2: 20% 204s bucket 2: 30% 204s bucket 2: 40% 204s bucket 2: 50% 204s bucket 2: 60% 204s bucket 2: 70% 204s bucket 2: 80% 204s bucket 2: 90% 204s bucket 2: 100% 204s Sorting block of length 4275 for bucket 2 204s (Using difference cover) 204s Sorting block time: 00:00:00 204s Returning block of 4276 for bucket 2 204s Getting block 3 of 7 204s Reserving size (5355) for bucket 3 204s Calculating Z arrays for bucket 3 204s Entering block accumulator loop for bucket 3: 204s bucket 3: 10% 204s bucket 3: 20% 204s bucket 3: 30% 204s bucket 3: 40% 204s bucket 3: 50% 204s bucket 3: 60% 204s bucket 3: 70% 204s bucket 3: 80% 204s bucket 3: 90% 204s bucket 3: 100% 204s Sorting block of length 4010 for bucket 3 204s (Using difference cover) 204s Sorting block time: 00:00:00 204s Returning block of 4011 for bucket 3 204s Getting block 4 of 7 204s Reserving size (5355) for bucket 4 204s Calculating Z arrays for bucket 4 204s Entering block accumulator loop for bucket 4: 204s bucket 4: 10% 204s bucket 4: 20% 204s bucket 4: 30% 204s bucket 4: 40% 204s bucket 4: 50% 204s bucket 4: 60% 204s bucket 4: 70% 204s bucket 4: 80% 204s bucket 4: 90% 204s bucket 4: 100% 204s Sorting block of length 3860 for bucket 4 204s (Using difference cover) 204s Sorting block time: 00:00:00 204s Returning block of 3861 for bucket 4 204s Getting block 5 of 7 204s Reserving size (5355) for bucket 5 204s Calculating Z arrays for bucket 5 204s Entering block accumulator loop for bucket 5: 204s bucket 5: 10% 204s bucket 5: 20% 204s bucket 5: 30% 204s bucket 5: 40% 204s bucket 5: 50% 204s bucket 5: 60% 204s bucket 5: 70% 204s bucket 5: 80% 204s bucket 5: 90% 204s bucket 5: 100% 204s Sorting block of length 4188 for bucket 5 204s (Using difference cover) 204s Sorting block time: 00:00:00 204s Returning block of 4189 for bucket 5 204s Getting block 6 of 7 204s Reserving size (5355) for bucket 6 204s Calculating Z arrays for bucket 6 204s Entering block accumulator loop for bucket 6: 204s bucket 6: 10% 204s bucket 6: 20% 204s bucket 6: 30% 204s bucket 6: 40% 204s bucket 6: 50% 204s bucket 6: 60% 204s bucket 6: 70% 204s bucket 6: 80% 204s bucket 6: 90% 204s bucket 6: 100% 204s Sorting block of length 5102 for bucket 6 204s (Using difference cover) 204s Sorting block time: 00:00:00 204s Returning block of 5103 for bucket 6 204s Getting block 7 of 7 204s Reserving size (5355) for bucket 7 204s Calculating Z arrays for bucket 7 204s Entering block accumulator loop for bucket 7: 204s bucket 7: 10% 204s bucket 7: 20% 204s bucket 7: 30% 204s bucket 7: 40% 204s bucket 7: 50% 204s bucket 7: 60% 204s bucket 7: 70% 204s bucket 7: 80% 204s bucket 7: 90% 204s bucket 7: 100% 204s Sorting block of length 5325 for bucket 7 204s (Using difference cover) 204s Sorting block time: 00:00:00 204s Returning block of 5326 for bucket 7 204s Exited Ebwt loop 204s fchr[A]: 0 204s fchr[C]: 7097 204s fchr[G]: 15029 204s fchr[T]: 22254 204s fchr[$]: 28562 204s Exiting Ebwt::buildToDisk() 204s Returning from initFromVector 204s Wrote 4203034 bytes to primary EBWT file: transcripts.rev.1.ebwt 204s Wrote 57132 bytes to secondary EBWT file: transcripts.rev.2.ebwt 204s Re-opening _in1 and _in2 as input streams 204s Returning from Ebwt constructor 204s Headers: 204s len: 28562 204s bwtLen: 28563 204s sz: 7141 204s + bowtie -aS -X 800 --offrate 1 transcripts -1 reads_1.fastq -2 reads_2.fastq 204s + samtools view -Sb - 204s bwtSz: 7141 204s lineRate: 6 204s linesPerSide: 1 204s offRate: 1 204s offMask: 0xfffffffe 204s isaRate: -1 204s isaMask: 0xffffffff 204s ftabChars: 10 204s eftabLen: 20 204s eftabSz: 80 204s ftabLen: 1048577 204s ftabSz: 4194308 204s offsLen: 14282 204s offsSz: 57128 204s isaLen: 0 204s isaSz: 0 204s lineSz: 64 204s sideSz: 64 204s sideBwtSz: 56 204s sideBwtLen: 224 204s numSidePairs: 64 204s numSides: 128 204s numLines: 128 204s ebwtTotLen: 8192 204s ebwtTotSz: 8192 204s reverse: 0 204s Total time for backward call to driver() for mirror index: 00:00:01 204s Setting the index via positional argument will be deprecated in a future release. Please use -x option instead. 205s # reads processed: 10000 205s # reads with at least one alignment: 10000 (100.00%) 205s # reads that failed to align: 0 (0.00%) 205s Reported 14270 paired-end alignments 205s + berkeley-express transcripts.fasta hits.bam 205s 2024-Mar-23 15:48:20 - Attempting to read 'hits.bam' in BAM format... 205s 2024-Mar-23 15:48:20 - Parsing BAM header... 205s 2024-Mar-23 15:48:20 - Loading target sequences and measuring bias background... 205s 2024-Mar-23 15:48:20 - Initialized 15 targets. 205s 2024-Mar-23 15:48:20 - Processing input fragment alignments... 206s 2024-Mar-23 15:48:20 - COMPLETED: Processed 10000 mapped fragments, targets are in 8 bundles. 206s 2024-Mar-23 15:48:20 - 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). 206s 2024-Mar-23 15:48:20 - Writing results to file... 206s 2024-Mar-23 15:48:20 - Done. 206s autopkgtest [15:48:21]: test run-tests: -----------------------] 207s run-tests PASS 207s autopkgtest [15:48:22]: test run-tests: - - - - - - - - - - results - - - - - - - - - - 207s autopkgtest [15:48:22]: @@@@@@@@@@@@@@@@@@@@ summary 207s run-tests PASS 218s Creating nova instance adt-noble-ppc64el-berkeley-express-20240323-154455-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-ppc64el-server-20240323.img (UUID ff8abf95-5243-4ea5-b7f5-3bf690534a1d)...