0s autopkgtest [23:45:11]: starting date and time: 2024-04-18 23:45:11+0000 0s autopkgtest [23:45:11]: git checkout: 43bc6cdf gitlab-ci: do not include the salsa pipeline 0s autopkgtest [23:45:11]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.tgubjmyh/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@bos02-ppc64el-16.secgroup --name adt-noble-ppc64el-art-nextgen-simulation-tools-20240418-234511-juju-7f2275-prod-proposed-migration-environment-2-4fe1e158-2352-4998-b9cb-6bff8abf1be2 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 95s autopkgtest [23:46:46]: testbed dpkg architecture: ppc64el 95s autopkgtest [23:46:46]: testbed apt version: 2.7.14build2 95s autopkgtest [23:46:46]: @@@@@@@@@@@@@@@@@@@@ test bed setup 96s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 96s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [12.2 kB] 96s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [2340 B] 96s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [57.5 kB] 96s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [381 kB] 96s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [112 kB] 96s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 96s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [976 B] 96s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 96s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [587 kB] 96s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 96s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [1004 B] 96s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 99s Fetched 1282 kB in 1s (1252 kB/s) 99s Reading package lists... 101s sh: 4: dhclient: not found 102s Reading package lists... 102s Building dependency tree... 102s Reading state information... 102s Calculating upgrade... 102s The following packages will be upgraded: 102s libkeyutils1 libnuma1 make netcat-openbsd numactl 102s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 102s Need to get 343 kB of archives. 102s After this operation, 16.4 kB disk space will be freed. 102s Get:1 http://ftpmaster.internal/ubuntu noble/main ppc64el libkeyutils1 ppc64el 1.6.3-3build1 [11.0 kB] 102s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el netcat-openbsd ppc64el 1.226-1ubuntu2 [46.2 kB] 102s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libnuma1 ppc64el 2.0.18-1build1 [28.2 kB] 103s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el make ppc64el 4.3-4.1build2 [214 kB] 103s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el numactl ppc64el 2.0.18-1build1 [43.9 kB] 103s Fetched 343 kB in 1s (648 kB/s) 103s (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 ... 71981 files and directories currently installed.) 103s Preparing to unpack .../libkeyutils1_1.6.3-3build1_ppc64el.deb ... 103s Unpacking libkeyutils1:ppc64el (1.6.3-3build1) over (1.6.3-3) ... 103s Preparing to unpack .../netcat-openbsd_1.226-1ubuntu2_ppc64el.deb ... 103s Unpacking netcat-openbsd (1.226-1ubuntu2) over (1.226-1ubuntu1) ... 103s Preparing to unpack .../libnuma1_2.0.18-1build1_ppc64el.deb ... 103s Unpacking libnuma1:ppc64el (2.0.18-1build1) over (2.0.18-1) ... 103s Preparing to unpack .../make_4.3-4.1build2_ppc64el.deb ... 103s Unpacking make (4.3-4.1build2) over (4.3-4.1build1) ... 103s Preparing to unpack .../numactl_2.0.18-1build1_ppc64el.deb ... 103s Unpacking numactl (2.0.18-1build1) over (2.0.18-1) ... 103s Setting up libkeyutils1:ppc64el (1.6.3-3build1) ... 103s Setting up netcat-openbsd (1.226-1ubuntu2) ... 103s Setting up make (4.3-4.1build2) ... 103s Setting up libnuma1:ppc64el (2.0.18-1build1) ... 103s Setting up numactl (2.0.18-1build1) ... 103s Processing triggers for man-db (2.12.0-4build1) ... 104s Processing triggers for libc-bin (2.39-0ubuntu8) ... 104s Reading package lists... 105s Building dependency tree... 105s Reading state information... 105s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 105s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 105s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 105s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 105s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 106s Reading package lists... 107s Reading package lists... 107s Building dependency tree... 107s Reading state information... 107s Calculating upgrade... 107s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 107s Reading package lists... 107s Building dependency tree... 107s Reading state information... 107s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 110s autopkgtest [23:47:01]: testbed running kernel: Linux 6.8.0-22-generic #22-Ubuntu SMP Thu Apr 4 22:47:57 UTC 2024 110s autopkgtest [23:47:01]: @@@@@@@@@@@@@@@@@@@@ apt-source art-nextgen-simulation-tools 114s Get:1 http://ftpmaster.internal/ubuntu noble/universe art-nextgen-simulation-tools 20160605+dfsg-5 (dsc) [2400 B] 114s Get:2 http://ftpmaster.internal/ubuntu noble/universe art-nextgen-simulation-tools 20160605+dfsg-5 (tar) [2229 kB] 114s Get:3 http://ftpmaster.internal/ubuntu noble/universe art-nextgen-simulation-tools 20160605+dfsg-5 (diff) [9420 B] 114s gpgv: Signature made Mon Dec 18 18:32:54 2023 UTC 114s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 114s gpgv: issuer "tille@debian.org" 114s gpgv: Can't check signature: No public key 114s dpkg-source: warning: cannot verify inline signature for ./art-nextgen-simulation-tools_20160605+dfsg-5.dsc: no acceptable signature found 114s autopkgtest [23:47:05]: testing package art-nextgen-simulation-tools version 20160605+dfsg-5 114s autopkgtest [23:47:05]: build not needed 116s autopkgtest [23:47:07]: test run-unit-test: preparing testbed 117s Reading package lists... 117s Building dependency tree... 117s Reading state information... 117s Starting pkgProblemResolver with broken count: 0 118s Starting 2 pkgProblemResolver with broken count: 0 118s Done 118s The following additional packages will be installed: 118s art-nextgen-simulation-tools art-nextgen-simulation-tools-profiles libgsl27 118s libgslcblas0 118s Suggested packages: 118s gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html 118s The following NEW packages will be installed: 118s art-nextgen-simulation-tools art-nextgen-simulation-tools-profiles 118s autopkgtest-satdep libgsl27 libgslcblas0 118s 0 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. 118s Need to get 4884 kB/4885 kB of archives. 118s After this operation, 20.0 MB of additional disk space will be used. 118s Get:1 /tmp/autopkgtest.FFH4Dh/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [736 B] 118s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libgslcblas0 ppc64el 2.7.1+dfsg-6ubuntu2 [86.6 kB] 118s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libgsl27 ppc64el 2.7.1+dfsg-6ubuntu2 [1090 kB] 119s Get:4 http://ftpmaster.internal/ubuntu noble/universe ppc64el art-nextgen-simulation-tools ppc64el 20160605+dfsg-5 [1752 kB] 119s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el art-nextgen-simulation-tools-profiles all 20160605+dfsg-5 [1956 kB] 120s Fetched 4884 kB in 2s (2825 kB/s) 120s Selecting previously unselected package libgslcblas0:ppc64el. 120s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 71981 files and directories currently installed.) 120s Preparing to unpack .../libgslcblas0_2.7.1+dfsg-6ubuntu2_ppc64el.deb ... 120s Unpacking libgslcblas0:ppc64el (2.7.1+dfsg-6ubuntu2) ... 120s Selecting previously unselected package libgsl27:ppc64el. 120s Preparing to unpack .../libgsl27_2.7.1+dfsg-6ubuntu2_ppc64el.deb ... 120s Unpacking libgsl27:ppc64el (2.7.1+dfsg-6ubuntu2) ... 120s Selecting previously unselected package art-nextgen-simulation-tools. 120s Preparing to unpack .../art-nextgen-simulation-tools_20160605+dfsg-5_ppc64el.deb ... 120s Unpacking art-nextgen-simulation-tools (20160605+dfsg-5) ... 120s Selecting previously unselected package art-nextgen-simulation-tools-profiles. 120s Preparing to unpack .../art-nextgen-simulation-tools-profiles_20160605+dfsg-5_all.deb ... 120s Unpacking art-nextgen-simulation-tools-profiles (20160605+dfsg-5) ... 120s Selecting previously unselected package autopkgtest-satdep. 120s Preparing to unpack .../1-autopkgtest-satdep.deb ... 120s Unpacking autopkgtest-satdep (0) ... 120s Setting up libgslcblas0:ppc64el (2.7.1+dfsg-6ubuntu2) ... 120s Setting up libgsl27:ppc64el (2.7.1+dfsg-6ubuntu2) ... 120s Setting up art-nextgen-simulation-tools (20160605+dfsg-5) ... 120s Setting up art-nextgen-simulation-tools-profiles (20160605+dfsg-5) ... 120s Setting up autopkgtest-satdep (0) ... 120s Processing triggers for man-db (2.12.0-4build1) ... 120s Processing triggers for libc-bin (2.39-0ubuntu8) ... 123s (Reading database ... 72101 files and directories currently installed.) 123s Removing autopkgtest-satdep (0) ... 123s autopkgtest [23:47:14]: test run-unit-test: [----------------------- 124s =================================================================== 124s ART_454 (Version 2.6.0) 124s Simulation of 454 Pyrosequencing 124s Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. 124s =================================================================== 124s 124s Single-end simulation 124s 124s Total CPU time used: 0.065126 124s 124s The random seed for the run: 1713484034 124s 124s Parameters Settings 124s number of flow cycles: 100 124s fold of read coverage: 10X 124s 124s 454 Profile for Simulation 124s the built-in GS-FLX profile 124s 124s Output Files 124s 124s FASTQ Sequence File: 124s ./single_454_flx.fq 124s 124s ALN Alignment File: 124s ./single_454_flx.aln 124s 124s SAM Alignment File: 124s ./single_454_flx.sam 124s 124s Read Coverage File: 124s ./single_454_flx.stat 124s 124s =================================================================== 124s ART_454 (Version 2.6.0) 124s Simulation of 454 Pyrosequencing 124s Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. 124s =================================================================== 124s 124s Paired-end simulation 124s 124s Total CPU time used: 0.050204 124s 124s The random seed for the run: 1713484035 124s 124s Parameters Settings 124s number of flow cycles: 100 124s fold of read coverage: 5X 124s fragment length 124s mean: 500 124s std: 20 124s 124s 454 Profile for Simulation 124s the built-in GS-FLX profile 124s 124s Output Files 124s 124s FASTQ Sequence Files: 124s the 1st reads: ./paired_454_flx1.fq 124s the 2nd reads: ./paired_454_flx2.fq 124s 124s ALN Alignment Files: 124s the 1st reads: ./paired_454_flx1.aln 124s the 2nd reads: ./paired_454_flx2.aln 124s 124s SAM Alignment File: 124s ./paired_454_flx.sam 124s 124s Read Coverage File: 124s ./paired_454_flx.stat 124s 124s =================================================================== 124s ART_454 (Version 2.6.0) 124s Simulation of 454 Pyrosequencing 124s Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. 124s =================================================================== 124s 124s Paired-end simulation 124s 124s Total CPU time used: 0.052923 124s 124s The random seed for the run: 1713484035 124s 124s Parameters Settings 124s number of flow cycles: 200 124s fold of read coverage: 6X 124s fragment length 124s mean: 500 124s std: 20 124s 124s 454 Profile for Simulation 124s the built-in GS-FLX Titanium profile 124s 124s Output Files 124s 124s FASTQ Sequence Files: 124s the 1st reads: ./paired_454_flxTitan1.fq 124s the 2nd reads: ./paired_454_flxTitan2.fq 124s 124s ALN Alignment Files: 124s the 1st reads: ./paired_454_flxTitan1.aln 124s the 2nd reads: ./paired_454_flxTitan2.aln 124s 124s SAM Alignment File: 124s ./paired_454_flxTitan.sam 124s 124s Read Coverage File: 124s ./paired_454_flxTitan.stat 124s 124s =================================================================== 124s ART_454 (Version 2.6.0) 124s Simulation of 454 Pyrosequencing 124s Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. 124s =================================================================== 124s 134s Amplicon 5'-end sequencing with single-end reads 134s 134s Total CPU time used: 10.1847 134s 134s The random seed for the run: 1713484035 134s 134s Parameters Settings 134s number of flow cycles: 100 134s # reads per amplion: 10 134s 134s 454 Profile for Simulation 134s the built-in GS-FLX profile 134s 134s Output Files 134s 134s FASTQ Sequence File: 134s ./amp_single_454.fq 134s 134s ALN Alignment File: 134s ./amp_single_454.aln 134s 134s SAM Alignment File: 134s ./amp_single_454.sam 134s 134s Read Coverage File: 134s ./amp_single_454.stat 134s 134s =================================================================== 134s ART_454 (Version 2.6.0) 134s Simulation of 454 Pyrosequencing 134s Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. 134s =================================================================== 134s 142s Amplicon two-end sequencing with paired-end reads 142s 142s Total CPU time used: 8.11391 142s 142s The random seed for the run: 1713484045 142s 142s Parameters Settings 142s number of flow cycles: 100 142s # read pairs per amplion: 5 142s 142s 454 Profile for Simulation 142s the built-in GS-FLX profile 142s 142s Output Files 142s 142s FASTQ Sequence Files: 142s the 1st reads: ./amp_paired_454.fq 142s the 2nd reads: ./amp_paired_4542.fq 142s 142s ALN Alignment Files: 142s the 1st reads: ./amp_paired_454.aln 142s the 2nd reads: ./amp_paired_4542.aln 142s 142s SAM Alignment File: 142s ./amp_paired_454.sam 142s 142s Read Coverage File: 142s ./amp_paired_454.stat 142s 142s =================================================================== 142s ART_454 (Version 2.6.0) 142s Simulation of 454 Pyrosequencing 142s Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. 142s =================================================================== 142s 142s Single-end simulation 142s 142s Total CPU time used: 0.056945 142s 142s The random seed for the run: 777 142s 142s Parameters Settings 142s number of flow cycles: 100 142s fold of read coverage: 10X 142s 142s 454 Profile for Simulation 142s the built-in GS-FLX profile 142s 142s Output Files 142s 142s FASTQ Sequence File: 142s ./single_454_t1.fq 142s 142s ALN Alignment File: 142s ./single_454_t1.aln 142s 142s SAM Alignment File: 142s ./single_454_t1.sam 142s 142s Read Coverage File: 142s ./single_454_t1.stat 142s 142s =================================================================== 142s ART_454 (Version 2.6.0) 142s Simulation of 454 Pyrosequencing 142s Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. 142s =================================================================== 142s 142s Single-end simulation 142s 142s Total CPU time used: 0.060027 142s 142s The random seed for the run: 777 142s 142s Parameters Settings 142s number of flow cycles: 100 142s fold of read coverage: 10X 142s 142s 454 Profile for Simulation 142s the built-in GS-FLX profile 142s 142s Output Files 142s 142s FASTQ Sequence File: 142s ./single_454_t2.fq 142s 142s ALN Alignment File: 142s ./single_454_t2.aln 142s 142s SAM Alignment File: 142s ./single_454_t2.sam 142s 142s Read Coverage File: 142s ./single_454_t2.stat 142s 142s compare difference of two simulation datasets after normalising known difference 142s ================================================================= 142s ART_SOLiD (Version 1.3.3) 142s Simulation of Applied Biosystems' SOLiD Sequencing 142s Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. 142s ================================================================= 142s 143s Single-end simulation 143s 143s Total CPU time used: 0.094162 143s 143s The random seed for the run: 1713484053 143s 143s Parameters Settings 143s fold of read coverage: 10X 143s read length: 25 143s 143s SOLiD Error Profile for Simulation 143s the built-in 35bp error profile 143s 143s Output Files 143s 143s FASTQ Sequence File: 143s ./single_dat.fq 143s 143s MAP Alignment File: 143s ./single_dat.map 143s 143s SAM Alignment File: 143s ./single_dat.sam 143s 143s convert a map file to a UCSC BED file 143s /usr/bin/map2bed.pl single_dat.bed single_dat.map 143s run_test_examples_SOLiD.sh: 12: /usr/bin/map2bed.pl: not found 143s ================================================================= 143s ART_SOLiD (Version 1.3.3) 143s Simulation of Applied Biosystems' SOLiD Sequencing 143s Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. 143s ================================================================= 143s 143s can not open error profile file: ../SOLiD_profiles/profile_pseudo 143s ================================================================= 143s ART_SOLiD (Version 1.3.3) 143s Simulation of Applied Biosystems' SOLiD Sequencing 143s Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. 143s ================================================================= 143s 143s Mate-Pair (F3-R3) simulation 143s run_test_examples_SOLiD.sh: 20: /usr/bin/map2bed.pl: not found 143s Warning: you are using the 75bp error profile for testing only. 143s 143s 143s Total CPU time used: 0.155972 143s 143s The random seed for the run: 1713484054 143s 143s Parameters Settings 143s fold of read coverage: 20X 143s F3 read length: 35 143s R3 read length: 35 143s fragment length 143s mean: 2000 143s std: 50 143s 143s SOLiD Error Profile for Simulation 143s the built-in 35bp error profile 143s 143s Output Files 143s 143s FASTQ Sequence Files: 143s the 1st reads: ./matepair_dat_R3.fq 143s the 2nd reads: ./matepair_dat_F3.fq 143s 143s MAP Alignment Files: 143s the 1st reads: ./matepair_dat_R3.map 143s the 2nd reads: ./matepair_dat_F3.map 143s 143s SAM Alignment File: 143s ./matepair_dat.sam 143s 143s convert two map files to a UCSC BED file 143s /usr/bin/map2bed.pl maptepair.bed matepair_dat1.map matepair_dat2.map 143s ================================================================= 143s ART_SOLiD (Version 1.3.3) 143s Simulation of Applied Biosystems' SOLiD Sequencing 143s Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. 143s ================================================================= 143s 143s Mate-Pair (F3-R3) simulation 143s 143s Total CPU time used: 0.070659 143s 143s The random seed for the run: 777 143s 143s Parameters Settings 143s fold of read coverage: 10X 143s F3 read length: 50 143s R3 read length: 50 143s fragment length 143s mean: 1500 143s std: 50 143s 143s SOLiD Error Profile for Simulation 143s the 75bp error profile for testing only 143s 143s Output Files 143s 143s FASTQ Sequence Files: 143s the 1st reads: ./matepair_fs1_R3.fq 143s the 2nd reads: ./matepair_fs1_F3.fq 143s 143s MAP Alignment Files: 143s the 1st reads: ./matepair_fs1_R3.map 143s the 2nd reads: ./matepair_fs1_F3.map 143s 143s SAM Alignment File: 143s ./matepair_fs1.sam 143s 143s ================================================================= 143s ART_SOLiD (Version 1.3.3) 143s Simulation of Applied Biosystems' SOLiD Sequencing 143s Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. 143s ================================================================= 143s 143s Warning: you are using the 75bp error profile for testing only. 143s 143s Mate-Pair (F3-R3) simulation 143s 143s Total CPU time used: 0.072296 143s 143s The random seed for the run: 777 143s 143s Parameters Settings 143s fold of read coverage: 10X 143s F3 read length: 50 143s R3 read length: 50 143s fragment length 143s mean: 1500 143s std: 50 143s 143s SOLiD Error Profile for Simulation 143s the 75bp error profile for testing only 143s 143s Output Files 143s 143s FASTQ Sequence Files: 143s the 1st reads: ./matepair_fs2_R3.fq 143s the 2nd reads: ./matepair_fs2_F3.fq 143s 143s MAP Alignment Files: 143s the 1st reads: ./matepair_fs2_R3.map 143s the 2nd reads: ./matepair_fs2_F3.map 143s 143s SAM Alignment File: 143s ./matepair_fs2.sam 143s 143s compare two simulation datasets 143s 4c4 143s < @PG ID:03 PN:ART_SOLiD CL:/usr/bin/art_SOLiD -r 777 -s testSeq.fa ./matepair_fs1 50 10 1500 50 143s --- 143s > @PG ID:03 PN:ART_SOLiD CL:/usr/bin/art_SOLiD -r 777 -s testSeq.fa ./matepair_fs2 50 10 1500 50 143s ================================================================= 143s ART_SOLiD (Version 1.3.3) 143s Simulation of Applied Biosystems' SOLiD Sequencing 143s Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. 143s ================================================================= 143s 143s Warning: you are using the 75bp error profile for testing only. 143s 143s Paired-end (F3-F5) simulation 143s 143s Total CPU time used: 0.237758 143s 143s The random seed for the run: 1713484054 143s 143s Parameters Settings 143s fold of read coverage: 50X 143s F3 read length: 75 143s F5 read length: 35 143s fragment length 143s mean: 250 143s std: 10 143s 143s SOLiD Error Profile for Simulation 143s the 75bp error profile for testing only 143s 143s Output Files 143s 143s FASTQ Sequence Files: 143s the 1st reads: ./paired_dat_F5.fq 143s the 2nd reads: ./paired_dat_F3.fq 143s 143s MAP Alignment Files: 143s the 1st reads: ./paired_dat_F5.map 143s the 2nd reads: ./paired_dat_F3.map 143s 143s SAM Alignment File: 143s ./paired_dat.sam 143s 143s ================================================================= 143s ART_SOLiD (Version 1.3.3) 143s Simulation of Applied Biosystems' SOLiD Sequencing 143s Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. 143s ================================================================= 143s 376s Amplicon single-end sequencing simulation 376s 376s Total CPU time used: 231.91 376s 376s The random seed for the run: 1713484054 376s 376s Parameters Settings 376s # reads per amplion: 100 376s read length: 25 376s 376s SOLiD Error Profile for Simulation 376s the built-in 35bp error profile 376s 376s Output Files 376s 376s FASTQ Sequence File: 376s ./amp_single.fq 376s 376s MAP Alignment File: 376s ./amp_single.map 376s 376s SAM Alignment File: 376s ./amp_single.sam 376s 376s Warning: you are using the 75bp error profile for testing only. 376s 376s ================================================================= 376s ART_SOLiD (Version 1.3.3) 376s Simulation of Applied Biosystems' SOLiD Sequencing 376s Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. 376s ================================================================= 376s 506s Amplicon matepair sequencing simulation 506s 506s Total CPU time used: 130.597 506s 506s The random seed for the run: 1713484287 506s 506s Parameters Settings 506s # read pairs per amplion: 80 506s F3 read length: 50 506s R3 read length: 50 506s 506s SOLiD Error Profile for Simulation 506s the 75bp error profile for testing only 506s 506s Output Files 506s 506s FASTQ Sequence Files: 506s the 1st reads: ./amp_matepair_R3.fq 506s the 2nd reads: ./amp_matepair_F3.fq 506s 506s MAP Alignment Files: 506s the 1st reads: ./amp_matepair_R3.map 506s the 2nd reads: ./amp_matepair_F3.map 506s 506s SAM Alignment File: 506s ./amp_matepair.sam 506s 506s ================================================================= 506s ART_SOLiD (Version 1.3.3) 506s Simulation of Applied Biosystems' SOLiD Sequencing 506s Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. 506s ================================================================= 506s 597s Amplicon paired-end sequencing simulation 597s 597s Total CPU time used: 90.5754 597s 597s The random seed for the run: 1713484417 597s 597s Parameters Settings 597s # read pairs per amplion: 50 597s F3 read length: 35 597s F5 read length: 25 597s 597s SOLiD Error Profile for Simulation 597s the built-in 35bp error profile 597s 597s Output Files 597s 597s FASTQ Sequence Files: 597s the 1st reads: ./amp_paired_F5.fq 597s the 2nd reads: ./amp_paired_F3.fq 597s 597s MAP Alignment Files: 597s the 1st reads: ./amp_paired_F5.map 597s the 2nd reads: ./amp_paired_F3.map 597s 597s SAM Alignment File: 597s ./amp_paired.sam 597s 597s 597s ====================ART==================== 597s ART_Illumina (2008-2016) 597s Q Version 2.5.8 (June 6, 2016) 597s Contact: Weichun Huang 597s ------------------------------------------- 597s 597s Single-end Simulation 597s 597s Total CPU time used: 0.055986 597s 597s The random seed for the run: 1713484508 597s 597s Parameters used during run 597s Read Length: 35 597s Genome masking 'N' cutoff frequency: 1 in 35 597s Fold Coverage: 10X 597s Profile Type: Combined 597s ID Tag: 597s 597s Quality Profile(s) 597s First Read: Genome Analyzer I Length 36 R1 (built-in profile) 597s 597s Output files 597s 597s FASTQ Sequence File: 597s ./single_end_com.fq 597s 597s ALN Alignment File: 597s ./single_end_com.aln 597s 597s SAM Alignment File: 597s ./single_end_com.sam 597s 597s 597s ====================ART==================== 597s ART_Illumina (2008-2016) 597s Q Version 2.5.8 (June 6, 2016) 597s Contact: Weichun Huang 597s ------------------------------------------- 597s 597s Single-end Simulation 597s 597s Total CPU time used: 0.05223 597s 597s The random seed for the run: 1713484508 597s 597s Parameters used during run 597s Read Length: 50 597s Genome masking 'N' cutoff frequency: 1 in 50 597s Fold Coverage: 10X 597s Profile Type: Separated 597s ID Tag: 597s 597s Quality Profile(s) 597s First Read: MiniSeq TruSeq Length 51 R1 (built-in profile) 597s 597s Output files 597s 597s FASTQ Sequence File: 597s ./single_end_sep.fq 597s 597s ALN Alignment File: 597s ./single_end_sep.aln 597s 597s SAM Alignment File: 597s ./single_end_sep.sam 597s 597s 597s ====================ART==================== 597s ART_Illumina (2008-2016) 597s Q Version 2.5.8 (June 6, 2016) 597s Contact: Weichun Huang 597s ------------------------------------------- 597s 597s Paired-end sequencing simulation 597s 597s Total CPU time used: 0.035018 597s 597s The random seed for the run: 1713484508 597s 597s Parameters used during run 597s Read Length: 150 597s Genome masking 'N' cutoff frequency: 1 in 150 597s Fold Coverage: 10X 597s Mean Fragment Length: 500 597s Standard Deviation: 10 597s Profile Type: Combined 597s ID Tag: 597s 597s Quality Profile(s) 597s First Read: HiSeq 2500 Length 150 R1 (built-in profile) 597s First Read: HiSeq 2500 Length 150 R2 (built-in profile) 597s 597s Output files 597s 597s FASTQ Sequence Files: 597s the 1st reads: ./paired_end_com1.fq 597s the 2nd reads: ./paired_end_com2.fq 597s 597s ALN Alignment Files: 597s the 1st reads: ./paired_end_com1.aln 597s the 2nd reads: ./paired_end_com2.aln 597s 597s SAM Alignment File: 597s ./paired_end_com.sam 597s 597s 597s ====================ART==================== 597s ART_Illumina (2008-2016) 597s Q Version 2.5.8 (June 6, 2016) 597s Contact: Weichun Huang 597s ------------------------------------------- 597s 597s Paired-end sequencing simulation 597s 597s Total CPU time used: 0.050549 597s 597s The random seed for the run: 1713484508 597s 597s Parameters used during run 597s Read Length: 100 597s Genome masking 'N' cutoff frequency: 1 in 100 597s Fold Coverage: 10X 597s Mean Fragment Length: 500 597s Standard Deviation: 10 597s Profile Type: Separated 597s ID Tag: 597s 597s Quality Profile(s) 597s First Read: HiSeq 2000 Length 100 R1 (built-in profile) 597s First Read: HiSeq 2000 Length 100 R2 (built-in profile) 597s 597s Output files 597s 597s FASTQ Sequence Files: 597s the 1st reads: ./paired_end_sep1.fq 597s the 2nd reads: ./paired_end_sep2.fq 597s 597s ALN Alignment Files: 597s the 1st reads: ./paired_end_sep1.aln 597s the 2nd reads: ./paired_end_sep2.aln 597s 597s SAM Alignment File: 597s ./paired_end_sep.sam 597s 597s 597s ====================ART==================== 597s ART_Illumina (2008-2016) 597s Q Version 2.5.8 (June 6, 2016) 597s Contact: Weichun Huang 597s ------------------------------------------- 597s 597s Matepair-end sequencing simulation 597s 597s Total CPU time used: 0.041077 597s 597s The random seed for the run: 1713484508 597s 597s Parameters used during run 597s Read Length: 100 597s Genome masking 'N' cutoff frequency: 1 in 100 597s Fold Coverage: 10X 597s Mean Fragment Length: 2500 597s Standard Deviation: 50 597s Profile Type: Combined 597s ID Tag: 597s 597s Quality Profile(s) 597s First Read: HiSeq 2500 Length 126 R1 (built-in profile) 597s First Read: HiSeq 2500 Length 126 R2 (built-in profile) 597s 597s Output files 597s 597s FASTQ Sequence Files: 597s the 1st reads: ./matepair_com1.fq 597s the 2nd reads: ./matepair_com2.fq 597s 597s ALN Alignment Files: 597s the 1st reads: ./matepair_com1.aln 597s the 2nd reads: ./matepair_com2.aln 597s 597s SAM Alignment File: 597s ./matepair_com.sam 597s 597s 597s ====================ART==================== 597s ART_Illumina (2008-2016) 597s Q Version 2.5.8 (June 6, 2016) 597s Contact: Weichun Huang 597s ------------------------------------------- 597s 598s Amplicon 5'-end sequencing simulation 598s 598s Total CPU time used: 0.450116 598s 598s The random seed for the run: 1713484508 598s 598s Parameters used during run 598s Read Length: 100 598s Genome masking 'N' cutoff frequency: 1 in 100 598s # Reads per Amplion: 2 598s Profile Type: Combined 598s ID Tag: 598s 598s Quality Profile(s) 598s First Read: HiSeqX v2.5 TruSeq Length 151 R1 (built-in profile) 598s 598s Output files 598s 598s FASTQ Sequence File: 598s ./amp_5_end_com.fq 598s 598s ALN Alignment File: 598s ./amp_5_end_com.aln 598s 598s SAM Alignment File: 598s ./amp_5_end_com.sam 598s 598s 598s ====================ART==================== 598s ART_Illumina (2008-2016) 598s Q Version 2.5.8 (June 6, 2016) 598s Contact: Weichun Huang 598s ------------------------------------------- 598s 598s Amplicon paired-end sequencing simulation 598s 598s Total CPU time used: 0.499027 598s 598s The random seed for the run: 1713484509 598s 598s Parameters used during run 598s Read Length: 100 598s Genome masking 'N' cutoff frequency: 1 in 100 598s # Read Pairs per Amplion: 1 598s Profile Type: Combined 598s ID Tag: 598s 598s Quality Profile(s) 598s First Read: MiSeq v1 Length 250 R1 (built-in profile) 598s First Read: MiSeq v1 Length 250 R2 (built-in profile) 598s 598s Output files 598s 598s FASTQ Sequence Files: 598s the 1st reads: ./amp_pair1.fq 598s the 2nd reads: ./amp_pair2.fq 598s 598s ALN Alignment Files: 598s the 1st reads: ./amp_pair1.aln 598s the 2nd reads: ./amp_pair2.aln 598s 598s SAM Alignment File: 598s ./amp_pair.sam 598s 599s 599s ====================ART==================== 599s ART_Illumina (2008-2016) 599s Q Version 2.5.8 (June 6, 2016) 599s Contact: Weichun Huang 599s ------------------------------------------- 599s 599s Amplicon matepair sequencing simulation 599s 599s Total CPU time used: 0.532455 599s 599s The random seed for the run: 1713484510 599s 599s Parameters used during run 599s Read Length: 100 599s Genome masking 'N' cutoff frequency: 1 in 100 599s # Read Pairs per Amplion: 1 599s Profile Type: Combined 599s ID Tag: 599s 599s Quality Profile(s) 599s First Read: MiSeq v3 Length 251 R1 (built-in profile) 599s First Read: MiSeq v3 Length 251 R2 (built-in profile) 599s 599s Output files 599s 599s FASTQ Sequence Files: 599s the 1st reads: ./amp_matepair1.fq 599s the 2nd reads: ./amp_matepair2.fq 599s 599s ALN Alignment Files: 599s the 1st reads: ./amp_matepair1.aln 599s the 2nd reads: ./amp_matepair2.aln 599s 599s SAM Alignment File: 599s ./amp_matepair.sam 599s 599s 599s ====================ART==================== 599s ART_Illumina (2008-2016) 599s Q Version 2.5.8 (June 6, 2016) 599s Contact: Weichun Huang 599s ------------------------------------------- 599s 599s Paired-end sequencing simulation 599s 599s Total CPU time used: 0.040178 599s 599s The random seed for the run: 777 599s 599s Parameters used during run 599s Read Length: 100 599s Genome masking 'N' cutoff frequency: 1 in 100 599s Fold Coverage: 10X 599s Mean Fragment Length: 500 599s Standard Deviation: 10 599s Profile Type: Combined 599s ID Tag: 599s 599s Quality Profile(s) 599s First Read: HiSeqX v2.5 PCR free Length 151 R1 (built-in profile) 599s First Read: HiSeqX v2.5 PCR free Length 151 R2 (built-in profile) 599s 599s Output files 599s 599s FASTQ Sequence Files: 599s the 1st reads: ./paired_end_com_f11.fq 599s the 2nd reads: ./paired_end_com_f12.fq 599s 599s ALN Alignment Files: 599s the 1st reads: ./paired_end_com_f11.aln 599s the 2nd reads: ./paired_end_com_f12.aln 599s 599s SAM Alignment File: 599s ./paired_end_com_f1.sam 599s 599s 599s ====================ART==================== 599s ART_Illumina (2008-2016) 599s Q Version 2.5.8 (June 6, 2016) 599s Contact: Weichun Huang 599s ------------------------------------------- 599s 599s Paired-end sequencing simulation 599s 599s Total CPU time used: 0.040771 599s 599s The random seed for the run: 777 599s 599s Parameters used during run 599s Read Length: 100 599s Genome masking 'N' cutoff frequency: 1 in 100 599s Fold Coverage: 10X 599s Mean Fragment Length: 500 599s Standard Deviation: 10 599s Profile Type: Combined 599s ID Tag: 599s 599s Quality Profile(s) 599s First Read: HiSeqX v2.5 PCR free Length 151 R1 (built-in profile) 599s First Read: HiSeqX v2.5 PCR free Length 151 R2 (built-in profile) 599s 599s Output files 599s 599s FASTQ Sequence Files: 599s the 1st reads: ./paired_end_com_f21.fq 599s the 2nd reads: ./paired_end_com_f22.fq 599s 599s ALN Alignment Files: 599s the 1st reads: ./paired_end_com_f21.aln 599s the 2nd reads: ./paired_end_com_f22.aln 599s 599s SAM Alignment File: 599s ./paired_end_com_f2.sam 599s 599s 599s ====================ART==================== 599s ART_Illumina (2008-2016) 599s Q Version 2.5.8 (June 6, 2016) 599s Contact: Weichun Huang 599s ------------------------------------------- 599s 599s Paired-end sequencing simulation 599s 599s Total CPU time used: 0.043596 599s 599s The random seed for the run: 1713484510 599s 599s Parameters used during run 599s Read Length: 100 599s Genome masking 'N' cutoff frequency: 1 in 100 599s Fold Coverage: 10X 599s Mean Fragment Length: 500 599s Standard Deviation: 10 599s First quality shift: 10 599s Second quality shift: 10 599s Profile Type: Combined 599s ID Tag: 599s 599s Quality Profile(s) 599s First Read: HiSeq 2000 Length 100 R1 (built-in profile) 599s First Read: HiSeq 2000 Length 100 R2 (built-in profile) 599s 599s Output files 599s 599s FASTQ Sequence Files: 599s the 1st reads: ./paired_end_com_f11.fq 599s the 2nd reads: ./paired_end_com_f12.fq 599s 599s ALN Alignment Files: 599s the 1st reads: ./paired_end_com_f11.aln 599s the 2nd reads: ./paired_end_com_f12.aln 599s 599s SAM Alignment File: 599s ./paired_end_com_f1.sam 599s 599s 599s ====================ART==================== 599s ART_Illumina (2008-2016) 599s Q Version 2.5.8 (June 6, 2016) 599s Contact: Weichun Huang 599s ------------------------------------------- 599s 599s Paired-end sequencing simulation 599s 599s Total CPU time used: 0.043604 599s 599s The random seed for the run: 1713484510 599s 599s Parameters used during run 599s Read Length: 75 599s 'N' genomic regions masking turned off 599s Fold Coverage: 10X 599s Mean Fragment Length: 500 599s Standard Deviation: 10 599s Profile Type: Combined 599s ID Tag: 599s 599s Quality Profile(s) 599s First Read: NextSeq 500 v2 Length 76 R1 (built-in profile) 599s First Read: NextSeq 500 v2 Length 76 R2 (built-in profile) 599s 599s Output files 599s 599s FASTQ Sequence Files: 599s the 1st reads: ./paired_nomask1.fq 599s the 2nd reads: ./paired_nomask2.fq 599s 599s ALN Alignment Files: 599s the 1st reads: ./paired_nomask1.aln 599s the 2nd reads: ./paired_nomask2.aln 599s 599s SAM Alignment File: 599s ./paired_nomask.sam 599s 600s autopkgtest [23:55:11]: test run-unit-test: -----------------------] 600s run-unit-test PASS 600s autopkgtest [23:55:11]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 601s autopkgtest [23:55:12]: @@@@@@@@@@@@@@@@@@@@ summary 601s run-unit-test PASS 612s Creating nova instance adt-noble-ppc64el-art-nextgen-simulation-tools-20240418-234511-juju-7f2275-prod-proposed-migration-environment-2-4fe1e158-2352-4998-b9cb-6bff8abf1be2 from image adt/ubuntu-noble-ppc64el-server-20240418.img (UUID eb57e9e5-70fe-4878-ae85-dd88e864cb24)...