0s autopkgtest [00:24:55]: starting date and time: 2024-04-19 00:24:55+0000 0s autopkgtest [00:24:55]: git checkout: 43bc6cdf gitlab-ci: do not include the salsa pipeline 0s autopkgtest [00:24:55]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.rgdjfvmg/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:gsl --apt-upgrade art-nextgen-simulation-tools --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=gsl/2.7.1+dfsg-6ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos01-s390x-15.secgroup --name adt-noble-s390x-art-nextgen-simulation-tools-20240419-002455-juju-7f2275-prod-proposed-migration-environment-2-52189609-da47-4e46-a2b2-d2e7f27a932a --image adt/ubuntu-noble-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://us.ports.ubuntu.com/ubuntu-ports/ 141s autopkgtest [00:27:16]: testbed dpkg architecture: s390x 141s autopkgtest [00:27:16]: testbed apt version: 2.7.14build2 141s autopkgtest [00:27:16]: @@@@@@@@@@@@@@@@@@@@ test bed setup 142s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 142s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [2340 B] 142s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [54.2 kB] 142s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [376 kB] 143s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [12.2 kB] 143s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [95.6 kB] 143s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 143s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [976 B] 143s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 143s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [497 kB] 143s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 143s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 144s Fetched 1166 kB in 1s (825 kB/s) 144s Reading package lists... 146s sh: 4: dhclient: not found 147s Reading package lists... 147s Building dependency tree... 147s Reading state information... 147s Calculating upgrade... 148s The following packages will be upgraded: 148s apport apport-core-dump-handler libkeyutils1 libnuma1 make man-db 148s netcat-openbsd numactl python3-apport python3-problem-report 148s 10 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 148s Need to get 1783 kB of archives. 148s After this operation, 3072 B disk space will be freed. 148s Get:1 http://ftpmaster.internal/ubuntu noble/main s390x python3-problem-report all 2.28.1-0ubuntu1 [23.8 kB] 148s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x python3-apport all 2.28.1-0ubuntu1 [92.1 kB] 148s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x apport-core-dump-handler all 2.28.1-0ubuntu1 [16.8 kB] 148s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x apport all 2.28.1-0ubuntu1 [83.5 kB] 148s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x libkeyutils1 s390x 1.6.3-3build1 [9556 B] 148s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x netcat-openbsd s390x 1.226-1ubuntu2 [44.0 kB] 148s Get:7 http://ftpmaster.internal/ubuntu noble/main s390x libnuma1 s390x 2.0.18-1build1 [25.1 kB] 148s Get:8 http://ftpmaster.internal/ubuntu noble/main s390x man-db s390x 2.12.0-4build2 [1253 kB] 149s Get:9 http://ftpmaster.internal/ubuntu noble/main s390x make s390x 4.3-4.1build2 [196 kB] 149s Get:10 http://ftpmaster.internal/ubuntu noble/main s390x numactl s390x 2.0.18-1build1 [40.0 kB] 149s Preconfiguring packages ... 149s Fetched 1783 kB in 1s (1268 kB/s) 150s (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 ... 78323 files and directories currently installed.) 150s Preparing to unpack .../0-python3-problem-report_2.28.1-0ubuntu1_all.deb ... 150s Unpacking python3-problem-report (2.28.1-0ubuntu1) over (2.28.0-0ubuntu1) ... 150s Preparing to unpack .../1-python3-apport_2.28.1-0ubuntu1_all.deb ... 150s Unpacking python3-apport (2.28.1-0ubuntu1) over (2.28.0-0ubuntu1) ... 150s Preparing to unpack .../2-apport-core-dump-handler_2.28.1-0ubuntu1_all.deb ... 150s Unpacking apport-core-dump-handler (2.28.1-0ubuntu1) over (2.28.0-0ubuntu1) ... 150s Preparing to unpack .../3-apport_2.28.1-0ubuntu1_all.deb ... 150s Unpacking apport (2.28.1-0ubuntu1) over (2.28.0-0ubuntu1) ... 150s Preparing to unpack .../4-libkeyutils1_1.6.3-3build1_s390x.deb ... 150s Unpacking libkeyutils1:s390x (1.6.3-3build1) over (1.6.3-3) ... 150s Preparing to unpack .../5-netcat-openbsd_1.226-1ubuntu2_s390x.deb ... 150s Unpacking netcat-openbsd (1.226-1ubuntu2) over (1.226-1ubuntu1) ... 150s Preparing to unpack .../6-libnuma1_2.0.18-1build1_s390x.deb ... 150s Unpacking libnuma1:s390x (2.0.18-1build1) over (2.0.18-1) ... 150s Preparing to unpack .../7-man-db_2.12.0-4build2_s390x.deb ... 150s Unpacking man-db (2.12.0-4build2) over (2.12.0-4build1) ... 150s Preparing to unpack .../8-make_4.3-4.1build2_s390x.deb ... 150s Unpacking make (4.3-4.1build2) over (4.3-4.1build1) ... 150s Preparing to unpack .../9-numactl_2.0.18-1build1_s390x.deb ... 150s Unpacking numactl (2.0.18-1build1) over (2.0.18-1) ... 150s Setting up libkeyutils1:s390x (1.6.3-3build1) ... 150s Setting up python3-problem-report (2.28.1-0ubuntu1) ... 150s Setting up netcat-openbsd (1.226-1ubuntu2) ... 150s Setting up man-db (2.12.0-4build2) ... 150s Updating database of manual pages ... 152s man-db.service is a disabled or a static unit not running, not starting it. 152s Setting up python3-apport (2.28.1-0ubuntu1) ... 153s Setting up make (4.3-4.1build2) ... 153s Setting up libnuma1:s390x (2.0.18-1build1) ... 153s Setting up numactl (2.0.18-1build1) ... 153s Setting up apport-core-dump-handler (2.28.1-0ubuntu1) ... 154s Setting up apport (2.28.1-0ubuntu1) ... 154s Installing new version of config file /etc/apport/crashdb.conf ... 155s apport-autoreport.service is a disabled or a static unit not running, not starting it. 155s Processing triggers for libc-bin (2.39-0ubuntu8) ... 155s Reading package lists... 155s Building dependency tree... 155s Reading state information... 156s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 157s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 157s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 157s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 157s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 158s Reading package lists... 158s Reading package lists... 158s Building dependency tree... 158s Reading state information... 159s Calculating upgrade... 159s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 159s Reading package lists... 159s Building dependency tree... 159s Reading state information... 160s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 160s autopkgtest [00:27:35]: rebooting testbed after setup commands that affected boot 200s autopkgtest [00:28:15]: testbed running kernel: Linux 6.8.0-22-generic #22-Ubuntu SMP Thu Apr 4 21:54:17 UTC 2024 203s autopkgtest [00:28:18]: @@@@@@@@@@@@@@@@@@@@ apt-source art-nextgen-simulation-tools 207s Get:1 http://ftpmaster.internal/ubuntu noble/universe art-nextgen-simulation-tools 20160605+dfsg-5 (dsc) [2400 B] 207s Get:2 http://ftpmaster.internal/ubuntu noble/universe art-nextgen-simulation-tools 20160605+dfsg-5 (tar) [2229 kB] 207s Get:3 http://ftpmaster.internal/ubuntu noble/universe art-nextgen-simulation-tools 20160605+dfsg-5 (diff) [9420 B] 207s gpgv: Signature made Mon Dec 18 18:32:54 2023 UTC 207s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 207s gpgv: issuer "tille@debian.org" 207s gpgv: Can't check signature: No public key 207s dpkg-source: warning: cannot verify inline signature for ./art-nextgen-simulation-tools_20160605+dfsg-5.dsc: no acceptable signature found 208s autopkgtest [00:28:23]: testing package art-nextgen-simulation-tools version 20160605+dfsg-5 208s autopkgtest [00:28:23]: build not needed 209s autopkgtest [00:28:24]: test run-unit-test: preparing testbed 211s Reading package lists... 211s Building dependency tree... 211s Reading state information... 211s Starting pkgProblemResolver with broken count: 0 211s Starting 2 pkgProblemResolver with broken count: 0 211s Done 211s The following additional packages will be installed: 211s art-nextgen-simulation-tools art-nextgen-simulation-tools-profiles libgsl27 211s libgslcblas0 211s Suggested packages: 211s gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html 211s The following NEW packages will be installed: 211s art-nextgen-simulation-tools art-nextgen-simulation-tools-profiles 211s autopkgtest-satdep libgsl27 libgslcblas0 211s 0 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. 211s Need to get 4937 kB/4937 kB of archives. 211s After this operation, 19.4 MB of additional disk space will be used. 211s Get:1 /tmp/autopkgtest.SnDCC2/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [732 B] 212s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libgslcblas0 s390x 2.7.1+dfsg-6ubuntu2 [150 kB] 212s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libgsl27 s390x 2.7.1+dfsg-6ubuntu2 [1084 kB] 213s Get:4 http://ftpmaster.internal/ubuntu noble/universe s390x art-nextgen-simulation-tools s390x 20160605+dfsg-5 [1747 kB] 213s Get:5 http://ftpmaster.internal/ubuntu noble/universe s390x art-nextgen-simulation-tools-profiles all 20160605+dfsg-5 [1956 kB] 214s Fetched 4937 kB in 2s (2147 kB/s) 214s Selecting previously unselected package libgslcblas0:s390x. 214s (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 ... 78322 files and directories currently installed.) 214s Preparing to unpack .../libgslcblas0_2.7.1+dfsg-6ubuntu2_s390x.deb ... 214s Unpacking libgslcblas0:s390x (2.7.1+dfsg-6ubuntu2) ... 214s Selecting previously unselected package libgsl27:s390x. 214s Preparing to unpack .../libgsl27_2.7.1+dfsg-6ubuntu2_s390x.deb ... 214s Unpacking libgsl27:s390x (2.7.1+dfsg-6ubuntu2) ... 214s Selecting previously unselected package art-nextgen-simulation-tools. 214s Preparing to unpack .../art-nextgen-simulation-tools_20160605+dfsg-5_s390x.deb ... 214s Unpacking art-nextgen-simulation-tools (20160605+dfsg-5) ... 214s Selecting previously unselected package art-nextgen-simulation-tools-profiles. 214s Preparing to unpack .../art-nextgen-simulation-tools-profiles_20160605+dfsg-5_all.deb ... 214s Unpacking art-nextgen-simulation-tools-profiles (20160605+dfsg-5) ... 215s Selecting previously unselected package autopkgtest-satdep. 215s Preparing to unpack .../1-autopkgtest-satdep.deb ... 215s Unpacking autopkgtest-satdep (0) ... 215s Setting up libgslcblas0:s390x (2.7.1+dfsg-6ubuntu2) ... 215s Setting up libgsl27:s390x (2.7.1+dfsg-6ubuntu2) ... 215s Setting up art-nextgen-simulation-tools (20160605+dfsg-5) ... 215s Setting up art-nextgen-simulation-tools-profiles (20160605+dfsg-5) ... 215s Setting up autopkgtest-satdep (0) ... 215s Processing triggers for man-db (2.12.0-4build2) ... 215s Processing triggers for libc-bin (2.39-0ubuntu8) ... 218s (Reading database ... 78442 files and directories currently installed.) 218s Removing autopkgtest-satdep (0) ... 219s autopkgtest [00:28:34]: test run-unit-test: [----------------------- 219s =================================================================== 219s ART_454 (Version 2.6.0) 219s Simulation of 454 Pyrosequencing 219s Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. 219s =================================================================== 219s 219s Single-end simulation 219s 219s Total CPU time used: 0.043775 219s 219s The random seed for the run: 1713486513 219s 219s Parameters Settings 219s number of flow cycles: 100 219s fold of read coverage: 10X 219s 219s 454 Profile for Simulation 219s the built-in GS-FLX profile 219s 219s Output Files 219s 219s FASTQ Sequence File: 219s ./single_454_flx.fq 219s 219s ALN Alignment File: 219s ./single_454_flx.aln 219s 219s SAM Alignment File: 219s ./single_454_flx.sam 219s 219s Read Coverage File: 219s ./single_454_flx.stat 219s 219s =================================================================== 219s ART_454 (Version 2.6.0) 219s Simulation of 454 Pyrosequencing 219s Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. 219s =================================================================== 219s 219s Paired-end simulation 219s 219s Total CPU time used: 0.033377 219s 219s The random seed for the run: 1713486513 219s 219s Parameters Settings 219s number of flow cycles: 100 219s fold of read coverage: 5X 219s fragment length 219s mean: 500 219s std: 20 219s 219s 454 Profile for Simulation 219s the built-in GS-FLX profile 219s 219s Output Files 219s 219s FASTQ Sequence Files: 219s the 1st reads: ./paired_454_flx1.fq 219s the 2nd reads: ./paired_454_flx2.fq 219s 219s ALN Alignment Files: 219s the 1st reads: ./paired_454_flx1.aln 219s the 2nd reads: ./paired_454_flx2.aln 219s 219s SAM Alignment File: 219s ./paired_454_flx.sam 219s 219s Read Coverage File: 219s ./paired_454_flx.stat 219s 219s =================================================================== 219s ART_454 (Version 2.6.0) 219s Simulation of 454 Pyrosequencing 219s Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. 219s =================================================================== 219s 219s Paired-end simulation 219s 219s Total CPU time used: 0.034809 219s 219s The random seed for the run: 1713486513 219s 219s Parameters Settings 219s number of flow cycles: 200 219s fold of read coverage: 6X 219s fragment length 219s mean: 500 219s std: 20 219s 219s 454 Profile for Simulation 219s the built-in GS-FLX Titanium profile 219s 219s Output Files 219s 219s FASTQ Sequence Files: 219s the 1st reads: ./paired_454_flxTitan1.fq 219s the 2nd reads: ./paired_454_flxTitan2.fq 219s 219s ALN Alignment Files: 219s the 1st reads: ./paired_454_flxTitan1.aln 219s the 2nd reads: ./paired_454_flxTitan2.aln 219s 219s SAM Alignment File: 219s ./paired_454_flxTitan.sam 219s 219s Read Coverage File: 219s ./paired_454_flxTitan.stat 219s 219s =================================================================== 219s ART_454 (Version 2.6.0) 219s Simulation of 454 Pyrosequencing 219s Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. 219s =================================================================== 219s 227s Amplicon 5'-end sequencing with single-end reads 227s 227s Total CPU time used: 7.54066 227s 227s The random seed for the run: 1713486513 227s 227s Parameters Settings 227s number of flow cycles: 100 227s # reads per amplion: 10 227s 227s 454 Profile for Simulation 227s the built-in GS-FLX profile 227s 227s Output Files 227s 227s FASTQ Sequence File: 227s ./amp_single_454.fq 227s 227s ALN Alignment File: 227s ./amp_single_454.aln 227s 227s SAM Alignment File: 227s ./amp_single_454.sam 227s 227s Read Coverage File: 227s ./amp_single_454.stat 227s 227s =================================================================== 227s ART_454 (Version 2.6.0) 227s Simulation of 454 Pyrosequencing 227s Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. 227s =================================================================== 227s 233s Amplicon two-end sequencing with paired-end reads 233s 233s Total CPU time used: 6.24977 233s 233s The random seed for the run: 1713486522 233s 233s Parameters Settings 233s number of flow cycles: 100 233s # read pairs per amplion: 5 233s 233s 454 Profile for Simulation 234s the built-in GS-FLX profile 234s 234s Output Files 234s 234s FASTQ Sequence Files: 234s the 1st reads: ./amp_paired_454.fq 234s the 2nd reads: ./amp_paired_4542.fq 234s 234s ALN Alignment Files: 234s the 1st reads: ./amp_paired_454.aln 234s the 2nd reads: ./amp_paired_4542.aln 234s 234s SAM Alignment File: 234s ./amp_paired_454.sam 234s 234s Read Coverage File: 234s ./amp_paired_454.stat 234s 234s =================================================================== 234s ART_454 (Version 2.6.0) 234s Simulation of 454 Pyrosequencing 234s Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. 234s =================================================================== 234s 234s Single-end simulation 234s 234s Total CPU time used: 0.04891 234s 234s The random seed for the run: 777 234s 234s Parameters Settings 234s number of flow cycles: 100 234s fold of read coverage: 10X 234s 234s 454 Profile for Simulation 234s the built-in GS-FLX profile 234s 234s Output Files 234s 234s FASTQ Sequence File: 234s ./single_454_t1.fq 234s 234s ALN Alignment File: 234s ./single_454_t1.aln 234s 234s SAM Alignment File: 234s ./single_454_t1.sam 234s 234s Read Coverage File: 234s ./single_454_t1.stat 234s 234s =================================================================== 234s ART_454 (Version 2.6.0) 234s Simulation of 454 Pyrosequencing 234s Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. 234s =================================================================== 234s 234s Single-end simulation 234s 234s Total CPU time used: 0.051054 234s 234s The random seed for the run: 777 234s 234s Parameters Settings 234s number of flow cycles: 100 234s fold of read coverage: 10X 234s 234s 454 Profile for Simulation 234s the built-in GS-FLX profile 234s 234s Output Files 234s 234s FASTQ Sequence File: 234s ./single_454_t2.fq 234s 234s ALN Alignment File: 234s ./single_454_t2.aln 234s 234s SAM Alignment File: 234s ./single_454_t2.sam 234s 234s Read Coverage File: 234s ./single_454_t2.stat 234s 234s compare difference of two simulation datasets after normalising known difference 234s ================================================================= 234s ART_SOLiD (Version 1.3.3) 234s Simulation of Applied Biosystems' SOLiD Sequencing 234s Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. 234s ================================================================= 234s 234s Single-end simulation 234s 234s Total CPU time used: 0.068022 234s 234s The random seed for the run: 1713486529 234s 234s Parameters Settings 234s fold of read coverage: 10X 234s read length: 25 234s 234s SOLiD Error Profile for Simulation 234s the built-in 35bp error profile 234s 234s Output Files 234s 234s FASTQ Sequence File: 234s ./single_dat.fq 234s 234s MAP Alignment File: 234s ./single_dat.map 234s 234s SAM Alignment File: 234s ./single_dat.sam 234s 234s convert a map file to a UCSC BED file 234s /usr/bin/map2bed.pl single_dat.bed single_dat.map 234s run_test_examples_SOLiD.sh: 12: /usr/bin/map2bed.pl: not found 234s ================================================================= 234s ART_SOLiD (Version 1.3.3) 234s Simulation of Applied Biosystems' SOLiD Sequencing 234s Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. 234s ================================================================= 234s 234s ================================================================= 234s ART_SOLiD (Version 1.3.3) 234s Simulation of Applied Biosystems' SOLiD Sequencing 234s Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. 234s ================================================================= 234s 234s can not open error profile file: ../SOLiD_profiles/profile_pseudo 234s Mate-Pair (F3-R3) simulation 234s run_test_examples_SOLiD.sh: 20: /usr/bin/map2bed.pl: not found 234s 234s Total CPU time used: 0.116706 234s 234s The random seed for the run: 1713486529 234s 234s Parameters Settings 234s fold of read coverage: 20X 234s F3 read length: 35 234s R3 read length: 35 234s fragment length 234s mean: 2000 234s std: 50 234s 234s SOLiD Error Profile for Simulation 234s the built-in 35bp error profile 234s 234s Output Files 234s 234s FASTQ Sequence Files: 234s the 1st reads: ./matepair_dat_R3.fq 234s the 2nd reads: ./matepair_dat_F3.fq 234s 234s MAP Alignment Files: 234s the 1st reads: ./matepair_dat_R3.map 234s the 2nd reads: ./matepair_dat_F3.map 234s 234s SAM Alignment File: 234s ./matepair_dat.sam 234s 234s convert two map files to a UCSC BED file 234s /usr/bin/map2bed.pl maptepair.bed matepair_dat1.map matepair_dat2.map 234s ================================================================= 234s ART_SOLiD (Version 1.3.3) 234s Simulation of Applied Biosystems' SOLiD Sequencing 234s Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. 234s ================================================================= 234s 234s Warning: you are using the 75bp error profile for testing only. 234s 234s Mate-Pair (F3-R3) simulation 234s 234s Total CPU time used: 0.056219 234s 234s The random seed for the run: 777 234s 234s Parameters Settings 234s fold of read coverage: 10X 234s F3 read length: 50 234s R3 read length: 50 234s fragment length 234s mean: 1500 234s Warning: you are using the 75bp error profile for testing only. 234s 234s std: 50 234s 234s SOLiD Error Profile for Simulation 234s the 75bp error profile for testing only 234s 234s Output Files 234s 234s FASTQ Sequence Files: 234s the 1st reads: ./matepair_fs1_R3.fq 234s the 2nd reads: ./matepair_fs1_F3.fq 234s 234s MAP Alignment Files: 234s the 1st reads: ./matepair_fs1_R3.map 234s the 2nd reads: ./matepair_fs1_F3.map 234s 234s SAM Alignment File: 234s ./matepair_fs1.sam 234s 234s ================================================================= 234s ART_SOLiD (Version 1.3.3) 234s Simulation of Applied Biosystems' SOLiD Sequencing 234s Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. 234s ================================================================= 234s 234s Mate-Pair (F3-R3) simulation 234s 234s Total CPU time used: 0.054484 234s 234s The random seed for the run: 777 234s 234s Parameters Settings 234s fold of read coverage: 10X 234s F3 read length: 50 234s R3 read length: 50 234s fragment length 234s mean: 1500 234s std: 50 234s 234s SOLiD Error Profile for Simulation 234s the 75bp error profile for testing only 234s 234s Output Files 234s 234s FASTQ Sequence Files: 234s the 1st reads: ./matepair_fs2_R3.fq 234s the 2nd reads: ./matepair_fs2_F3.fq 234s 234s MAP Alignment Files: 234s the 1st reads: ./matepair_fs2_R3.map 234s the 2nd reads: ./matepair_fs2_F3.map 234s 234s SAM Alignment File: 234s ./matepair_fs2.sam 234s 234s compare two simulation datasets 234s 4c4 234s < @PG ID:03 PN:ART_SOLiD CL:/usr/bin/art_SOLiD -r 777 -s testSeq.fa ./matepair_fs1 50 10 1500 50 234s --- 234s > @PG ID:03 PN:ART_SOLiD CL:/usr/bin/art_SOLiD -r 777 -s testSeq.fa ./matepair_fs2 50 10 1500 50 234s ================================================================= 234s ART_SOLiD (Version 1.3.3) 234s Simulation of Applied Biosystems' SOLiD Sequencing 234s Warning: you are using the 75bp error profile for testing only. 234s 234s Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. 234s ================================================================= 234s 234s Paired-end (F3-F5) simulation 234s 234s Total CPU time used: 0.197412 234s 234s The random seed for the run: 1713486529 234s 234s Parameters Settings 234s fold of read coverage: 50X 234s F3 read length: 75 234s F5 read length: 35 234s fragment length 234s mean: 250 234s std: 10 234s 234s SOLiD Error Profile for Simulation 234s the 75bp error profile for testing only 234s 234s Output Files 234s 234s FASTQ Sequence Files: 234s the 1st reads: ./paired_dat_F5.fq 234s the 2nd reads: ./paired_dat_F3.fq 234s 234s MAP Alignment Files: 234s the 1st reads: ./paired_dat_F5.map 234s the 2nd reads: ./paired_dat_F3.map 234s 234s SAM Alignment File: 234s ./paired_dat.sam 234s 234s ================================================================= 234s ART_SOLiD (Version 1.3.3) 234s Simulation of Applied Biosystems' SOLiD Sequencing 234s Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. 234s ================================================================= 234s 424s Amplicon single-end sequencing simulation 424s 424s Total CPU time used: 188.417 424s 424s The random seed for the run: 1713486529 424s 424s Parameters Settings 424s # reads per amplion: 100 424s read length: 25 424s 424s SOLiD Error Profile for Simulation 424s the built-in 35bp error profile 424s 424s Output Files 424s 424s FASTQ Sequence File: 424s ./amp_single.fq 424s 424s MAP Alignment File: 424s ./amp_single.map 424s 424s SAM Alignment File: 424s ./amp_single.sam 424s 424s ================================================================= 424s ART_SOLiD (Version 1.3.3) 424s Simulation of Applied Biosystems' SOLiD Sequencing 424s Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. 424s ================================================================= 424s 424s Warning: you are using the 75bp error profile for testing only. 424s 544s Amplicon matepair sequencing simulation 544s 544s Total CPU time used: 118.808 544s 544s The random seed for the run: 1713486719 544s 544s Parameters Settings 544s # read pairs per amplion: 80 544s F3 read length: 50 544s R3 read length: 50 544s 544s SOLiD Error Profile for Simulation 544s the 75bp error profile for testing only 544s 544s Output Files 544s 544s FASTQ Sequence Files: 544s the 1st reads: ./amp_matepair_R3.fq 544s the 2nd reads: ./amp_matepair_F3.fq 544s 544s MAP Alignment Files: 544s the 1st reads: ./amp_matepair_R3.map 544s the 2nd reads: ./amp_matepair_F3.map 544s 544s SAM Alignment File: 544s ./amp_matepair.sam 544s 544s ================================================================= 544s ART_SOLiD (Version 1.3.3) 544s Simulation of Applied Biosystems' SOLiD Sequencing 544s Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. 544s ================================================================= 544s 617s Amplicon paired-end sequencing simulation 617s 617s Total CPU time used: 72.026 617s 617s The random seed for the run: 1713486839 617s 617s Parameters Settings 617s # read pairs per amplion: 50 617s F3 read length: 35 617s F5 read length: 25 617s 617s SOLiD Error Profile for Simulation 617s the built-in 35bp error profile 617s 617s Output Files 617s 617s FASTQ Sequence Files: 617s the 1st reads: ./amp_paired_F5.fq 617s the 2nd reads: ./amp_paired_F3.fq 617s 617s MAP Alignment Files: 617s the 1st reads: ./amp_paired_F5.map 617s the 2nd reads: ./amp_paired_F3.map 617s 617s SAM Alignment File: 617s ./amp_paired.sam 617s 617s 617s ====================ART==================== 617s ART_Illumina (2008-2016) 617s Q Version 2.5.8 (June 6, 2016) 617s Contact: Weichun Huang 617s ------------------------------------------- 617s 617s Single-end Simulation 617s 617s Total CPU time used: 0.037984 617s 617s The random seed for the run: 1713486912 617s 617s Parameters used during run 617s Read Length: 35 617s Genome masking 'N' cutoff frequency: 1 in 35 617s Fold Coverage: 10X 617s Profile Type: Combined 617s ID Tag: 617s 617s Quality Profile(s) 617s First Read: Genome Analyzer I Length 36 R1 (built-in profile) 617s 617s Output files 617s 617s FASTQ Sequence File: 617s ./single_end_com.fq 617s 617s ALN Alignment File: 617s ./single_end_com.aln 617s 617s SAM Alignment File: 617s ./single_end_com.sam 617s 617s 617s ====================ART==================== 617s ART_Illumina (2008-2016) 617s Q Version 2.5.8 (June 6, 2016) 617s Contact: Weichun Huang 617s ------------------------------------------- 617s 617s Single-end Simulation 617s 617s Total CPU time used: 0.030142 617s 617s The random seed for the run: 1713486912 617s 617s Parameters used during run 617s Read Length: 50 617s Genome masking 'N' cutoff frequency: 1 in 50 617s Fold Coverage: 10X 617s Profile Type: Separated 617s ID Tag: 617s 617s Quality Profile(s) 617s First Read: MiniSeq TruSeq Length 51 R1 (built-in profile) 617s 617s Output files 617s 617s FASTQ Sequence File: 617s ./single_end_sep.fq 617s 617s ALN Alignment File: 617s ./single_end_sep.aln 617s 617s SAM Alignment File: 617s ./single_end_sep.sam 617s 617s 617s ====================ART==================== 617s ART_Illumina (2008-2016) 617s Q Version 2.5.8 (June 6, 2016) 617s Contact: Weichun Huang 617s ------------------------------------------- 617s 617s Paired-end sequencing simulation 617s 617s Total CPU time used: 0.02229 617s 617s The random seed for the run: 1713486912 617s 617s Parameters used during run 617s Read Length: 150 617s Genome masking 'N' cutoff frequency: 1 in 150 617s Fold Coverage: 10X 617s Mean Fragment Length: 500 617s Standard Deviation: 10 617s Profile Type: Combined 617s ID Tag: 617s 617s Quality Profile(s) 617s First Read: HiSeq 2500 Length 150 R1 (built-in profile) 617s First Read: HiSeq 2500 Length 150 R2 (built-in profile) 617s 617s Output files 617s 617s FASTQ Sequence Files: 617s the 1st reads: ./paired_end_com1.fq 617s the 2nd reads: ./paired_end_com2.fq 617s 617s ALN Alignment Files: 617s the 1st reads: ./paired_end_com1.aln 617s the 2nd reads: ./paired_end_com2.aln 617s 617s SAM Alignment File: 617s ./paired_end_com.sam 617s 617s 617s ====================ART==================== 617s ART_Illumina (2008-2016) 617s Q Version 2.5.8 (June 6, 2016) 617s Contact: Weichun Huang 617s ------------------------------------------- 617s 617s Paired-end sequencing simulation 617s 617s Total CPU time used: 0.036214 617s 617s The random seed for the run: 1713486912 617s 617s Parameters used during run 617s Read Length: 100 617s Genome masking 'N' cutoff frequency: 1 in 100 617s Fold Coverage: 10X 617s Mean Fragment Length: 500 617s Standard Deviation: 10 617s Profile Type: Separated 617s ID Tag: 617s 617s Quality Profile(s) 617s First Read: HiSeq 2000 Length 100 R1 (built-in profile) 617s First Read: HiSeq 2000 Length 100 R2 (built-in profile) 617s 617s Output files 617s 617s FASTQ Sequence Files: 617s the 1st reads: ./paired_end_sep1.fq 617s the 2nd reads: ./paired_end_sep2.fq 617s 617s ALN Alignment Files: 617s the 1st reads: ./paired_end_sep1.aln 617s the 2nd reads: ./paired_end_sep2.aln 617s 617s SAM Alignment File: 617s ./paired_end_sep.sam 617s 617s 617s ====================ART==================== 617s ART_Illumina (2008-2016) 617s Q Version 2.5.8 (June 6, 2016) 617s Contact: Weichun Huang 617s ------------------------------------------- 617s 617s Matepair-end sequencing simulation 617s 617s Total CPU time used: 0.022626 617s 617s The random seed for the run: 1713486912 617s 617s Parameters used during run 617s Read Length: 100 617s Genome masking 'N' cutoff frequency: 1 in 100 617s Fold Coverage: 10X 617s Mean Fragment Length: 2500 617s Standard Deviation: 50 617s Profile Type: Combined 617s ID Tag: 617s 617s Quality Profile(s) 617s First Read: HiSeq 2500 Length 126 R1 (built-in profile) 617s First Read: HiSeq 2500 Length 126 R2 (built-in profile) 617s 617s Output files 617s 617s FASTQ Sequence Files: 617s the 1st reads: ./matepair_com1.fq 617s the 2nd reads: ./matepair_com2.fq 617s 617s ALN Alignment Files: 617s the 1st reads: ./matepair_com1.aln 617s the 2nd reads: ./matepair_com2.aln 617s 617s SAM Alignment File: 617s ./matepair_com.sam 617s 617s 617s ====================ART==================== 617s ART_Illumina (2008-2016) 617s Q Version 2.5.8 (June 6, 2016) 617s Contact: Weichun Huang 617s ------------------------------------------- 617s 617s Amplicon 5'-end sequencing simulation 617s 617s Total CPU time used: 0.24302 617s 617s The random seed for the run: 1713486912 617s 617s Parameters used during run 617s Read Length: 100 617s Genome masking 'N' cutoff frequency: 1 in 100 617s # Reads per Amplion: 2 617s Profile Type: Combined 617s ID Tag: 617s 617s Quality Profile(s) 617s First Read: HiSeqX v2.5 TruSeq Length 151 R1 (built-in profile) 617s 617s Output files 617s 617s FASTQ Sequence File: 617s ./amp_5_end_com.fq 617s 617s ALN Alignment File: 617s ./amp_5_end_com.aln 617s 617s SAM Alignment File: 617s ./amp_5_end_com.sam 617s 617s 617s ====================ART==================== 617s ART_Illumina (2008-2016) 617s Q Version 2.5.8 (June 6, 2016) 617s Contact: Weichun Huang 617s ------------------------------------------- 617s 617s Amplicon paired-end sequencing simulation 617s 617s Total CPU time used: 0.291935 617s 617s The random seed for the run: 1713486912 617s 617s Parameters used during run 617s Read Length: 100 617s Genome masking 'N' cutoff frequency: 1 in 100 617s # Read Pairs per Amplion: 1 617s Profile Type: Combined 617s ID Tag: 617s 617s Quality Profile(s) 617s First Read: MiSeq v1 Length 250 R1 (built-in profile) 617s First Read: MiSeq v1 Length 250 R2 (built-in profile) 617s 617s Output files 617s 617s FASTQ Sequence Files: 617s the 1st reads: ./amp_pair1.fq 617s the 2nd reads: ./amp_pair2.fq 617s 617s ALN Alignment Files: 617s the 1st reads: ./amp_pair1.aln 617s the 2nd reads: ./amp_pair2.aln 617s 617s SAM Alignment File: 617s ./amp_pair.sam 617s 617s 617s ====================ART==================== 617s ART_Illumina (2008-2016) 617s Q Version 2.5.8 (June 6, 2016) 617s Contact: Weichun Huang 617s ------------------------------------------- 617s 618s Amplicon matepair sequencing simulation 618s 618s Total CPU time used: 0.365577 618s 618s The random seed for the run: 1713486912 618s 618s Parameters used during run 618s Read Length: 100 618s Genome masking 'N' cutoff frequency: 1 in 100 618s # Read Pairs per Amplion: 1 618s Profile Type: Combined 618s ID Tag: 618s 618s Quality Profile(s) 618s First Read: MiSeq v3 Length 251 R1 (built-in profile) 618s First Read: MiSeq v3 Length 251 R2 (built-in profile) 618s 618s Output files 618s 618s FASTQ Sequence Files: 618s the 1st reads: ./amp_matepair1.fq 618s the 2nd reads: ./amp_matepair2.fq 618s 618s ALN Alignment Files: 618s the 1st reads: ./amp_matepair1.aln 618s the 2nd reads: ./amp_matepair2.aln 618s 618s SAM Alignment File: 618s ./amp_matepair.sam 618s 618s 618s ====================ART==================== 618s ART_Illumina (2008-2016) 618s Q Version 2.5.8 (June 6, 2016) 618s Contact: Weichun Huang 618s ------------------------------------------- 618s 618s Paired-end sequencing simulation 618s 618s Total CPU time used: 0.026125 618s 618s The random seed for the run: 777 618s 618s Parameters used during run 618s Read Length: 100 618s Genome masking 'N' cutoff frequency: 1 in 100 618s Fold Coverage: 10X 618s Mean Fragment Length: 500 618s Standard Deviation: 10 618s Profile Type: Combined 618s ID Tag: 618s 618s Quality Profile(s) 618s First Read: HiSeqX v2.5 PCR free Length 151 R1 (built-in profile) 618s First Read: HiSeqX v2.5 PCR free Length 151 R2 (built-in profile) 618s 618s Output files 618s 618s FASTQ Sequence Files: 618s the 1st reads: ./paired_end_com_f11.fq 618s the 2nd reads: ./paired_end_com_f12.fq 618s 618s ALN Alignment Files: 618s the 1st reads: ./paired_end_com_f11.aln 618s the 2nd reads: ./paired_end_com_f12.aln 618s 618s SAM Alignment File: 618s ./paired_end_com_f1.sam 618s 618s 618s ====================ART==================== 618s ART_Illumina (2008-2016) 618s Q Version 2.5.8 (June 6, 2016) 618s Contact: Weichun Huang 618s ------------------------------------------- 618s 618s Paired-end sequencing simulation 618s 618s Total CPU time used: 0.022877 618s 618s The random seed for the run: 777 618s 618s Parameters used during run 618s Read Length: 100 618s Genome masking 'N' cutoff frequency: 1 in 100 618s Fold Coverage: 10X 618s Mean Fragment Length: 500 618s Standard Deviation: 10 618s Profile Type: Combined 618s ID Tag: 618s 618s Quality Profile(s) 618s First Read: HiSeqX v2.5 PCR free Length 151 R1 (built-in profile) 618s First Read: HiSeqX v2.5 PCR free Length 151 R2 (built-in profile) 618s 618s Output files 618s 618s FASTQ Sequence Files: 618s the 1st reads: ./paired_end_com_f21.fq 618s the 2nd reads: ./paired_end_com_f22.fq 618s 618s ALN Alignment Files: 618s the 1st reads: ./paired_end_com_f21.aln 618s the 2nd reads: ./paired_end_com_f22.aln 618s 618s SAM Alignment File: 618s ./paired_end_com_f2.sam 618s 618s 618s ====================ART==================== 618s ART_Illumina (2008-2016) 618s Q Version 2.5.8 (June 6, 2016) 618s Contact: Weichun Huang 618s ------------------------------------------- 618s 618s Paired-end sequencing simulation 618s 618s Total CPU time used: 0.027682 618s 618s The random seed for the run: 1713486913 618s 618s Parameters used during run 618s Read Length: 100 618s Genome masking 'N' cutoff frequency: 1 in 100 618s Fold Coverage: 10X 618s Mean Fragment Length: 500 618s Standard Deviation: 10 618s First quality shift: 10 618s Second quality shift: 10 618s Profile Type: Combined 618s ID Tag: 618s 618s Quality Profile(s) 618s First Read: HiSeq 2000 Length 100 R1 (built-in profile) 618s First Read: HiSeq 2000 Length 100 R2 (built-in profile) 618s 618s Output files 618s 618s FASTQ Sequence Files: 618s the 1st reads: ./paired_end_com_f11.fq 618s the 2nd reads: ./paired_end_com_f12.fq 618s 618s ALN Alignment Files: 618s the 1st reads: ./paired_end_com_f11.aln 618s the 2nd reads: ./paired_end_com_f12.aln 618s 618s SAM Alignment File: 618s ./paired_end_com_f1.sam 618s 618s 618s ====================ART==================== 618s ART_Illumina (2008-2016) 618s Q Version 2.5.8 (June 6, 2016) 618s Contact: Weichun Huang 618s ------------------------------------------- 618s 618s Paired-end sequencing simulation 618s 618s Total CPU time used: 0.028725 618s 618s The random seed for the run: 1713486913 618s 618s Parameters used during run 618s Read Length: 75 618s 'N' genomic regions masking turned off 618s Fold Coverage: 10X 618s Mean Fragment Length: 500 618s Standard Deviation: 10 618s Profile Type: Combined 618s ID Tag: 618s 618s Quality Profile(s) 618s First Read: NextSeq 500 v2 Length 76 R1 (built-in profile) 618s First Read: NextSeq 500 v2 Length 76 R2 (built-in profile) 618s 618s Output files 618s 618s FASTQ Sequence Files: 618s the 1st reads: ./paired_nomask1.fq 618s the 2nd reads: ./paired_nomask2.fq 618s 618s ALN Alignment Files: 618s the 1st reads: ./paired_nomask1.aln 618s the 2nd reads: ./paired_nomask2.aln 618s 618s SAM Alignment File: 618s ./paired_nomask.sam 618s 618s autopkgtest [00:35:13]: test run-unit-test: -----------------------] 619s autopkgtest [00:35:14]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 619s run-unit-test PASS 620s autopkgtest [00:35:15]: @@@@@@@@@@@@@@@@@@@@ summary 620s run-unit-test PASS 638s Creating nova instance adt-noble-s390x-art-nextgen-simulation-tools-20240419-002455-juju-7f2275-prod-proposed-migration-environment-2-52189609-da47-4e46-a2b2-d2e7f27a932a from image adt/ubuntu-noble-s390x-server-20240418.img (UUID 85e53509-ea4e-4742-afdb-a30c7e328507)...