[DOCKTESTERS] Amazon account
Miguel Vazquez
mikisvaz at gmail.com
Tue Sep 20 14:55:07 EDT 2016
Just a heads up, the process failed.
The complete log is bellow, but I think this is the culprit:
Error while running job: Error collecting output for parameter
'somatic_cnv_tar_gz': Did not find output file with glob pattern:
'['*.somatic.cnv.tar.gz']'
I wrote something like this in Dockerstore.json
"somatic_cnv_tar_gz": {
"path":
"/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.cnv.tar.gz",
"class": "File"
}
I've replace those entries with this
"somatic_cnv_tar_gz": {
"path":
"/home/ubuntu/DockerTest-Miguel/Sanger/results/DONOR.somatic.cnv.tar.gz",
"class": "File"
}
so that the glob work. I'm trying again. I'll update the documentation
Best
Miguel
------------------
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_25.stderr
-----------------------------------------------------------------------
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_56.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_54
Job ID: 335639174
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_54.e335639174
Updated: Tue Sep 20 03:55:15 UTC 2016
Contents Excerpt:
Command run:
bash -lc
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_54.sh
Command exit code: 0
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_54.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_13
Job ID: 335639178
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_13.e335639178
Updated: Tue Sep 20 12:07:55 UTC 2016
Contents Excerpt:
Command run:
bash -lc
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_13.sh
Command exit code: 0
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_13.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_17
Job ID: 335639179
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_17.e335639179
Updated: Tue Sep 20 12:05:07 UTC 2016
Contents Excerpt:
Command run:
bash -lc
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_17.sh
Command exit code: 0
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_17.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_15
Job ID: 335639180
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_15.e335639180
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_48
Job ID: 335639020
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_48.e335639020
Updated: Tue Sep 20 05:54:57 UTC 2016
Contents Excerpt:
Command run:
bash -lc
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_48.sh
Command exit code: 0
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_48.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_50
Job ID: 335639025
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_50.e335639025
Updated: Tue Sep 20 04:48:39 UTC 2016
Contents Excerpt:
Command run:
bash -lc
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_50.sh
Command exit code: 0
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_50.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_52
Job ID: 335639111
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_52.e335639111
Updated: Tue Sep 20 05:05:25 UTC 2016
Contents Excerpt:
Command run:
bash -lc
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_52.sh
Command exit code: 0
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_52.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_56
Job ID: 335639173
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_56.e335639173
Updated: Tue Sep 20 03:39:33 UTC 2016
Contents Excerpt:
Command run:
bash -lc
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_56.sh
Command exit code: 0
Contents Excerpt:
Command run:
bash -lc
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_34.sh
Command exit code: 0
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_34.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_38
Job ID: 335638783
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_38.e335638783
Updated: Tue Sep 20 06:49:18 UTC 2016
Contents Excerpt:
Command run:
bash -lc
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_38.sh
Command exit code: 0
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_38.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_42
Job ID: 335638805
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_42.e335638805
Updated: Tue Sep 20 06:07:49 UTC 2016
Contents Excerpt:
Command run:
bash -lc
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_42.sh
Command exit code: 0
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_42.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_46
Job ID: 335638826
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_46.e335638826
Updated: Tue Sep 20 05:40:42 UTC 2016
Contents Excerpt:
Command run:
bash -lc
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_46.sh
Command exit code: 0
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_46.stderr
-----------------------------------------------------------------------
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_10.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_22
Job ID: 335638775
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_22.e335638775
Updated: Tue Sep 20 09:32:19 UTC 2016
Contents Excerpt:
Command run:
bash -lc
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_22.sh
Command exit code: 0
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_22.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_28
Job ID: 335638776
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_28.e335638776
Updated: Tue Sep 20 08:57:31 UTC 2016
Contents Excerpt:
Command run:
bash -lc
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_28.sh
Command exit code: 0
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_28.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_32
Job ID: 335638777
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_32.e335638777
Updated: Tue Sep 20 08:12:44 UTC 2016
Contents Excerpt:
Command run:
bash -lc
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_32.sh
Command exit code: 0
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_32.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_34
Job ID: 335638778
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_34.e335638778
Updated: Tue Sep 20 08:24:35 UTC 2016
Job Name: s58_unpackRef_NA_9
Job ID: 331891142
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_9.e331891142
Updated: Tue Sep 20 00:39:16 UTC 2016
Contents Excerpt:
Command run:
bash -lc
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_9.sh
Command exit code: 0
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_9.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_verifyBamHomChk_control_6
Job ID: 331891143
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_verifyBamHomChk_control_6.e331891143
Updated: Tue Sep 20 00:44:52 UTC 2016
Contents Excerpt:
Command run:
bash -lc
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_verifyBamHomChk_control_6.sh
Command exit code: 0
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_verifyBamHomChk_control_6.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_basFileGenerate_control_11
Job ID: 332292910
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_basFileGenerate_control_11.e332292910
Updated: Tue Sep 20 01:20:39 UTC 2016
Contents Excerpt:
Command run:
bash -lc
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_basFileGenerate_control_11.sh
Command exit code: 0
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_basFileGenerate_control_11.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_unpackRef_NA_10
Job ID: 332292911
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_10.e332292911
Updated: Tue Sep 20 00:44:57 UTC 2016
Contents Excerpt:
Command run:
bash -lc
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_10.sh
Command exit code: 0
Command run:
bash -lc
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_start_0.sh
Command exit code: 0
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_start_0.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_mark_start_1
Job ID: 331890603
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_mark_start_1.e331890603
Updated: Tue Sep 20 00:38:10 UTC 2016
Contents Excerpt:
Command run:
bash -lc
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_mark_start_1.sh
Command exit code: 0
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_mark_start_1.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_prepBam_control_3
Job ID: 331890831
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_control_3.e331890831
Updated: Tue Sep 20 00:38:11 UTC 2016
Contents Excerpt:
Command run:
bash -lc
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_control_3.sh
Command exit code: 0
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_control_3.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_prepBam_tumour_2
Job ID: 331890832
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_tumour_2.e331890832
Updated: Tue Sep 20 00:38:11 UTC 2016
Contents Excerpt:
Command run:
bash -lc
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_tumour_2.sh
Command exit code: 0
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_tumour_2.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_61.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_BRASS_input_99
Job ID: 379374477
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_BRASS_input_99.o379374477
Updated: Tue Sep 20 16:49:15 UTC 2016
Contents Excerpt:
[V] 18 0.49745MB/s 1781.56
[V] 19 0.525041MB/s 1879.07
[V] 20 0.552722MB/s 1976.44
[V] 21 0.579942MB/s 2072.21
[V] 22 0.607543MB/s 2169.2
[V] 23 0.635118MB/s 2266.04
[V] 24264262
[V] MemUsage(size=71.1484,rss=10.9336,peak=291.977) wall clock time
02:57:24:31175299
11827.06user 310.09system 2:59:40elapsed 112%CPU (0avgtext+0avgdata
4265632maxresident)k
117507424inputs+14421104outputs (84major+234838minor)pagefaults 0swaps
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_BRASS_input_99.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_merge_59
Job ID: 379374478
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.o379374478
Updated: Tue Sep 20 13:51:15 UTC 2016
Contents Excerpt:
87.14user 5.10system 1:41.25elapsed 91%CPU (0avgtext+0avgdata
66448maxresident)k
2720952inputs+4360560outputs (5major+7600minor)pagefaults 0swaps
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.stdout
-----------------------------------------------------------------------
% Total % Received % Xferd Average Speed Time Time Time
Current
Dload Upload Total Spent Left
Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:--
--:--:-- 0
100 54.9M 100 54.9M 0 0 1016k 0 0:00:55 0:00:55 --:--:--
1047k
% Total % Received % Xferd Average Speed Time Time Time
Current
Dload Upload Total Spent Left
Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:--
--:--:-- 0
100 174k 100 174k 0 0 174k 0 0:00:01 0:00:01 --:--:--
567k
[2016/09/20 16:49:15] | Output for stderr due to workflow run failure:
-----------------------------------------------------------------------
Job Name: s58_start_0
Job ID: 331890362
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_start_0.e331890362
Updated: Tue Sep 20 00:38:10 UTC 2016
Contents Excerpt:
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_renameSampleFile_208.o373317274
Updated: Tue Sep 20 12:08:37 UTC 2016
Contents Excerpt:
Modified command: cp
/var/spool/cwl/b02b4bba-6e66-44fb-a48f-38c309aaaac5.genotype.tar.gz
/var/spool/cwl/b02b4bba-6e66-44fb-a48f-38c309aaaac5.csc_0-0-0.20160920.somatic.genotype.tar.gz
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_renameSampleFile_208.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_57
Job ID: 373317275
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_57.o373317275
Updated: Tue Sep 20 13:29:27 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l
/var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr23.txt
-o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.23.tsv -b
/var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam
4798.51user 50.73system 1:20:50elapsed 99%CPU (0avgtext+0avgdata
3115856maxresident)k
9833328inputs+56328outputs (0major+199552minor)pagefaults 0swaps
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_57.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_ASCAT_allele_count_60
Job ID: 379374473
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_60.o379374473
Updated: Tue Sep 20 15:34:45 UTC 2016
Contents Excerpt:
Errors from command: /opt/wtsi-cgp/bin/alleleCounter -b
/var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam -o
/var/spool/cwl/0/ascat/tmpAscat/allele_count/b02b4bba-6e66-44fb-a48f-38c309aaaac5.allct
-l /var/spool/cwl/reference_files/ascat/SnpLocus.tsv -m 20
5928.09user 101.55system 1:45:10elapsed 95%CPU (0avgtext+0avgdata
2345888maxresident)k
221140208inputs+43144outputs (37major+169349minor)pagefaults 0swaps
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_60.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_ASCAT_allele_count_61
Job ID: 379374475
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_61.o379374475
Updated: Tue Sep 20 14:58:41 UTC 2016
Contents Excerpt:
Errors from command: /opt/wtsi-cgp/bin/alleleCounter -b
/var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam -o
/var/spool/cwl/0/ascat/tmpAscat/allele_count/8c0354eb-6a3e-4a98-b41c-f8add599884c.allct
-l /var/spool/cwl/reference_files/ascat/SnpLocus.tsv -m 20
3864.82user 67.24system 1:09:07elapsed 94%CPU (0avgtext+0avgdata
2350544maxresident)k
157460240inputs+43120outputs (57major+167795minor)pagefaults 0swaps
11476.37user 140.61system 6:48:23elapsed 47%CPU (0avgtext+0avgdata
3035728maxresident)k
7380072inputs+56816outputs (0major+196640minor)pagefaults 0swaps
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_39.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_41
Job ID: 335639489
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_41.o335639489
Updated: Tue Sep 20 07:35:04 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l
/var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr15.txt
-o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.15.tsv -b
/var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam
9429.90user 117.09system 5:54:22elapsed 44%CPU (0avgtext+0avgdata
2739152maxresident)k
5273744inputs+51000outputs (0major+177355minor)pagefaults 0swaps
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_41.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_45
Job ID: 335639845
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_45.o335639845
Updated: Tue Sep 20 07:29:41 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l
/var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr17.txt
-o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.17.tsv -b
/var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam
9231.30user 116.04system 5:49:00elapsed 44%CPU (0avgtext+0avgdata
2540400maxresident)k
5255296inputs+46736outputs (0major+165277minor)pagefaults 0swaps
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_45.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_43
Job ID: 335639853
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_43.o335639853
Updated: Tue Sep 20 08:28:45 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l
/var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr16.txt
-o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.16.tsv -b
/var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam
11465.31user 146.48system 6:48:03elapsed 47%CPU (0avgtext+0avgdata
2945712maxresident)k
6906080inputs+54432outputs (0major+190932minor)pagefaults 0swaps
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_43.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_renameSampleFile_208
Job ID: 373317274
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_33
Job ID: 335639420
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_33.o335639420
Updated: Tue Sep 20 10:42:41 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l
/var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr11.txt
-o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.11.tsv -b
/var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam
18904.62user 233.41system 9:02:00elapsed 58%CPU (0avgtext+0avgdata
4537600maxresident)k
15888800inputs+86400outputs (0major+292553minor)pagefaults 0swaps
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_33.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_35
Job ID: 335639430
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_35.o335639430
Updated: Tue Sep 20 10:03:48 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l
/var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr12.txt
-o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.12.tsv -b
/var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam
16584.76user 210.26system 8:23:07elapsed 55%CPU (0avgtext+0avgdata
4373600maxresident)k
12917040inputs+82896outputs (0major+281480minor)pagefaults 0swaps
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_35.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_37
Job ID: 335639431
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_37.o335639431
Updated: Tue Sep 20 08:26:17 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l
/var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr13.txt
-o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.13.tsv -b
/var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam
11361.18user 138.30system 6:45:36elapsed 47%CPU (0avgtext+0avgdata
3301008maxresident)k
7418080inputs+62192outputs (0major+212951minor)pagefaults 0swaps
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_37.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_39
Job ID: 335639452
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_39.o335639452
Updated: Tue Sep 20 08:29:04 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l
/var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr14.txt
-o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.14.tsv -b
/var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam
Updated: Tue Sep 20 11:02:29 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l
/var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr7.txt
-o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.7.tsv -b
/var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam
20088.69user 242.69system 9:21:48elapsed 60%CPU (0avgtext+0avgdata
5281504maxresident)k
18604808inputs+96776outputs (0major+339332minor)pagefaults 0swaps
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_25.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_27
Job ID: 335639400
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_27.o335639400
Updated: Tue Sep 20 11:02:53 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l
/var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr8.txt
-o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.8.tsv -b
/var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam
20108.48user 243.42system 9:22:11elapsed 60%CPU (0avgtext+0avgdata
5228912maxresident)k
17295080inputs+95440outputs (0major+335764minor)pagefaults 0swaps
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_27.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_29
Job ID: 335639401
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_29.o335639401
Updated: Tue Sep 20 09:18:32 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l
/var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr9.txt
-o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.9.tsv -b
/var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam
13962.23user 175.03system 7:37:51elapsed 51%CPU (0avgtext+0avgdata
3971872maxresident)k
12246072inputs+72144outputs (0major+255173minor)pagefaults 0swaps
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_29.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_31
Job ID: 335639417
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_31.o335639417
Updated: Tue Sep 20 10:11:08 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l
/var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr10.txt
-o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.10.tsv -b
/var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam
17052.42user 207.86system 8:30:26elapsed 56%CPU (0avgtext+0avgdata
4504144maxresident)k
13931760inputs+85488outputs (0major+289717minor)pagefaults 0swaps
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_31.stdout
-----------------------------------------------------------------------
23593416inputs+121608outputs (0major+421477minor)pagefaults 0swaps
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_17.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_15
Job ID: 335639180
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_15.o335639180
Updated: Tue Sep 20 12:08:37 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l
/var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr2.txt
-o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.2.tsv -b
/var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam
24021.20user 275.32system 10:27:56elapsed 64%CPU (0avgtext+0avgdata
7851136maxresident)k
24358016inputs+146264outputs (0major+499924minor)pagefaults 0swaps
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_15.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_19
Job ID: 335639200
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_19.o335639200
Updated: Tue Sep 20 11:57:43 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l
/var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr4.txt
-o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.4.tsv -b
/var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam
23336.68user 273.00system 10:17:02elapsed 63%CPU (0avgtext+0avgdata
6501344maxresident)k
22397816inputs+120192outputs (0major+416448minor)pagefaults 0swaps
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_19.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_23
Job ID: 335639375
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_23.o335639375
Updated: Tue Sep 20 11:14:37 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l
/var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr6.txt
-o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.6.tsv -b
/var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam
20846.11user 251.83system 9:33:55elapsed 61%CPU (0avgtext+0avgdata
5765024maxresident)k
19462064inputs+106080outputs (0major+369701minor)pagefaults 0swaps
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_23.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_25
Job ID: 335639387
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_25.o335639387
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_56
Job ID: 335639173
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_56.o335639173
Updated: Tue Sep 20 03:39:33 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l
/var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr22.txt
-o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.22.tsv -b
/var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam
2810.79user 34.33system 1:58:52elapsed 39%CPU (0avgtext+0avgdata
1250144maxresident)k
1243552inputs+22208outputs (0major+82726minor)pagefaults 0swaps
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_56.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_54
Job ID: 335639174
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_54.o335639174
Updated: Tue Sep 20 03:55:15 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l
/var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr21.txt
-o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.21.tsv -b
/var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam
3187.08user 39.68system 2:14:34elapsed 39%CPU (0avgtext+0avgdata
1302656maxresident)k
1689216inputs+23256outputs (0major+86038minor)pagefaults 0swaps
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_54.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_58
Job ID: 335639178
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_58.o335639178
Updated: Tue Sep 20 04:41:10 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l
/var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr23.txt
-o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.23.tsv -b
/var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam
4375.73user 53.14system 3:00:29elapsed 40%CPU (0avgtext+0avgdata
3123136maxresident)k
4325272inputs+56240outputs (0major+199643minor)pagefaults 0swaps
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_58.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_17
Job ID: 335639179
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_17.o335639179
Updated: Tue Sep 20 12:05:07 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l
/var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr3.txt
-o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.3.tsv -b
/var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam
23819.53user 283.10system 10:24:27elapsed 64%CPU (0avgtext+0avgdata
6576048maxresident)k
Contents Excerpt:
Modified command: alleleCounter -l
/var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr17.txt
-o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.17.tsv -b
/var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam
5945.65user 71.96system 4:00:01elapsed 41%CPU (0avgtext+0avgdata
2544496maxresident)k
5572568inputs+46720outputs (0major+163875minor)pagefaults 0swaps
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_46.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_48
Job ID: 335639020
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_48.o335639020
Updated: Tue Sep 20 05:54:57 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l
/var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr18.txt
-o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.18.tsv -b
/var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam
6337.11user 77.66system 4:14:16elapsed 42%CPU (0avgtext+0avgdata
2647504maxresident)k
5337616inputs+48704outputs (0major+170347minor)pagefaults 0swaps
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_48.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_50
Job ID: 335639025
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_50.o335639025
Updated: Tue Sep 20 04:48:39 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l
/var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr19.txt
-o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.19.tsv -b
/var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam
4542.91user 55.47system 3:07:58elapsed 40%CPU (0avgtext+0avgdata
1995904maxresident)k
3514080inputs+36192outputs (0major+129470minor)pagefaults 0swaps
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_50.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_52
Job ID: 335639111
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_52.o335639111
Updated: Tue Sep 20 05:05:25 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l
/var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr20.txt
-o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.20.tsv -b
/var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam
4979.15user 61.39system 3:24:44elapsed 41%CPU (0avgtext+0avgdata
2102832maxresident)k
3653168inputs+38272outputs (0major+136206minor)pagefaults 0swaps
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_52.stdout
-----------------------------------------------------------------------
-6a3e-4a98-b41c-f8add599884c.11.tsv -b
/var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam
11287.76user 142.04system 6:43:55elapsed 47%CPU (0avgtext+0avgdata
4543376maxresident)k
9747344inputs+86048outputs (0major+289230minor)pagefaults 0swaps
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_34.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_38
Job ID: 335638783
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_38.o335638783
Updated: Tue Sep 20 06:49:18 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l
/var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr13.txt
-o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.13.tsv -b
/var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam
7981.44user 98.27system 5:08:39elapsed 43%CPU (0avgtext+0avgdata
3310512maxresident)k
6948640inputs+62176outputs (7major+211942minor)pagefaults 0swaps
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_38.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_42
Job ID: 335638805
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_42.o335638805
Updated: Tue Sep 20 06:07:49 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l
/var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr15.txt
-o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.15.tsv -b
/var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam
6705.59user 83.09system 4:27:09elapsed 42%CPU (0avgtext+0avgdata
2746816maxresident)k
6146600inputs+50992outputs (0major+176574minor)pagefaults 0swaps
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_42.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_46
Job ID: 379374477
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.e379374477
Updated: Tue Sep 20 13:50:00 UTC 2016
Contents Excerpt:
Command run:
bash -lc
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.sh
Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl -b
/var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam
-o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c
-t 4 -e
/var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz
[SeqWare Pipeline] ERROR [2016/09/20 13:50:00] | The exit value was 25
Command exit code: 1
Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl -b
/var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam
-o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c
-t 4 -e
/var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_merge_59
Job ID: 379374478
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.e379374478
Updated: Tue Sep 20 13:51:15 UTC 2016
Contents Excerpt:
Command run:
bash -lc
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.sh
Command exit code: 0
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.stderr
-----------------------------------------------------------------------
The method 'do_run' exited abnormally so the Runner will terminate here!
Return value was: 15
[WARNING] command: seqware bundle launch --dir
/home/seqware/CGP-Somatic-Docker/target/Workflow_Bundle_CgpSomaticCore_0.0.0_SeqWare_1.1.1/
--engine whitestar-parallel --ini /var/spool/cwl/workflow.ini --no-metadata
exited with code: 15
Error while running job: Error collecting output for parameter
'somatic_cnv_tar_gz': Did not find output file with glob pattern:
'['*.somatic.cnv.tar.gz']'
[job temp319312608049643386.cwl] completed permanentFail
Final process status is permanentFail
Workflow error, try again with --debug for more information:
Process status is ['permanentFail']
stdout :
java.lang.RuntimeException: problems running command: cwltool --enable-dev
--non-strict --enable-net --outdir
/mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/outputs/
--tmpdir-prefix
/mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/working/
/tmp/1474331255066-0/temp319312608049643386.cwl
/mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/workflow_params.json
ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ f
f: command not found
ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ df
Filesystem 1K-blocks Used Available Use% Mounted on
udev 62947280 12 62947268 1% /dev
tmpfs 12590448 364 12590084 1% /run
/dev/xvda1 8115168 6093092 1586800 80% /
none 4 0 4 0% /sys/fs/cgroup
none 5120 0 5120 0% /run/lock
none 62952228 0 62952228 0% /run/shm
none 102400 0 102400 0% /run/user
/dev/xvdb 1031992064 303267080 676279800 31% /mnt/1TB
ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ df -h
Filesystem Size Used Avail Use% Mounted on
udev 61G 12K 61G 1% /dev
tmpfs 13G 364K 13G 1% /run
/dev/xvda1 7.8G 5.9G 1.6G 80% /
none 4.0K 0 4.0K 0% /sys/fs/cgroup
none 5.0M 0 5.0M 0% /run/lock
none 61G 0 61G 0% /run/shm
none 100M 0 100M 0% /run/user
/dev/xvdb 985G 290G 645G 31% /mnt/1TB
ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ vi Dockstore.json
{
"bbFrom": {
"bbFrom": {
"path": "
https://s3-eu-west-1.amazonaws.com/wtsi-pancancer/reference/GRCh37d5_battenberg.tar.gz
",
"class": "File"
},
"refFrom": {
"path": "
https://s3-eu-west-1.amazonaws.com/wtsi-pancancer/reference/GRCh37d5_CGP_refBundle.tar.gz
",
"class": "File"
},
"tumor": {
"path":
"/home/ubuntu/DockerTest-Miguel/data/7875b5196f6b8b52847f99bf370aada0.bam",
"class": "File"
},
"normal": {
"path":
"/home/ubuntu/DockerTest-Miguel/data/fdcb1bd7cffca69d15383ca9566c58e0.bam",
"class": "File"
},
"somatic_sv_tar_gz": {
"path":
"/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.sv.tar.gz",
"class": "File"
},
"somatic_snv_mnv_tar_gz": {
"path":
"/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.snv.mnv.tar.gz",
"class": "File"
},
"somatic_verifyBamId_tar_gz": {
"path":
"/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.verifyBamId.tar.gz",
"class": "File"
},
"somatic_cnv_tar_gz": {
"path":
"/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.cnv.tar.gz",
"class": "File"
},
"somatic_imputeCounts_tar_gz": {
"path":
"/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.imputeCounts.tar.gz",
"class": "File"
},
"somatic_genotype_tar_gz": {
"path":
"/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.genotype.tar.gz",
"class": "File"
},
"somatic_indel_tar_gz": {
"path":
"/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.indel.tar.gz",
"class": "File"
}
}
~
~
~
~
ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ l results/
ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ vi Dockstore.json ^C
Updated: Tue Sep 20 13:51:15 UTC 2016
Contents Excerpt:
Command run:
bash -lc
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.sh
Command exit code: 0
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.stderr
-----------------------------------------------------------------------
The method 'do_run' exited abnormally so the Runner will terminate here!
Return value was: 15
[WARNING] command: seqware bundle launch --dir
/home/seqware/CGP-Somatic-Docker/target/Workflow_Bundle_CgpSomaticCore_0.0.0_SeqWare_1.1.1/
--engine whitestar-parallel --ini /var/spool/cwl/workflow.ini --no-metadata
exited with code: 15
Error while running job: Error collecting output for parameter
'somatic_cnv_tar_gz': Did not find output file with glob pattern:
'['*.somatic.cnv.tar.gz']'
[job temp319312608049643386.cwl] completed permanentFail
Final process status is permanentFail
Workflow error, try again with --debug for more information:
Process status is ['permanentFail']
stdout :
java.lang.RuntimeException: problems running command: cwltool --enable-dev
--non-strict --enable-net --outdir
/mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/outputs/
--tmpdir-prefix
/mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/working/
/tmp/1474331255066-0/temp319312608049643386.cwl
/mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/workflow_params.json
ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ f
f: command not found
ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ df
Filesystem 1K-blocks Used Available Use% Mounted on
udev 62947280 12 62947268 1% /dev
tmpfs 12590448 364 12590084 1% /run
/dev/xvda1 8115168 6093092 1586800 80% /
none 4 0 4 0% /sys/fs/cgroup
none 5120 0 5120 0% /run/lock
none 62952228 0 62952228 0% /run/shm
none 102400 0 102400 0% /run/user
/dev/xvdb 1031992064 303267080 676279800 31% /mnt/1TB
ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ df -h
Filesystem Size Used Avail Use% Mounted on
udev 61G 12K 61G 1% /dev
tmpfs 13G 364K 13G 1% /run
/dev/xvda1 7.8G 5.9G 1.6G 80% /
none 4.0K 0 4.0K 0% /sys/fs/cgroup
none 5.0M 0 5.0M 0% /run/lock
none 61G 0 61G 0% /run/shm
none 100M 0 100M 0% /run/user
/dev/xvdb 985G 290G 645G 31% /mnt/1TB
ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ vi Dockstore.json
{
Output from command: /opt/wtsi-cgp/bin/alleleCounter -b
/var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam -o
/var/spool/cwl/0/ascat/tmpAscat/allele_count/b02b4bba-6e66-44fb-a48f-38c309aaaac5.allct
-l /var/spool/cwl/reference_files/ascat/SnpLocus.tsv -m 20
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_60.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_ASCAT_allele_count_61
Job ID: 379374475
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_61.e379374475
Updated: Tue Sep 20 14:58:41 UTC 2016
Contents Excerpt:
Command run:
bash -lc
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_61.sh
Command exit code: 0
Output from command: /opt/wtsi-cgp/bin/alleleCounter -b
/var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam -o
/var/spool/cwl/0/ascat/tmpAscat/allele_count/8c0354eb-6a3e-4a98-b41c-f8add599884c.allct
-l /var/spool/cwl/reference_files/ascat/SnpLocus.tsv -m 20
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_61.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_cgpPindel_input_70
Job ID: 379374477
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.e379374477
Updated: Tue Sep 20 13:50:00 UTC 2016
Contents Excerpt:
Command run:
bash -lc
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.sh
Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl -b
/var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam
-o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c
-t 4 -e
/var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz
[SeqWare Pipeline] ERROR [2016/09/20 13:50:00] | The exit value was 25
Command exit code: 1
Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl -b
/var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam
-o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c
-t 4 -e
/var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_merge_59
Job ID: 379374478
File:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.e379374478
Updated: Tue Sep 20 13:51:15 UTC 2016
Contents Excerpt:
Command run:
bash -lc
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.sh
Command exit code: 0
Full output:
/datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.stderr
-----------------------------------------------------------------------
The method 'do_run' exited abnormally so the Runner will terminate here!
Return value was: 15
[WARNING] command: seqware bundle launch --dir
/home/seqware/CGP-Somatic-Docker/target/Workflow_Bundle_CgpSomaticCore_0.0.0_SeqWare_1.1.1/
--engine whitestar-parallel --ini /var/spool/cwl/workflow.ini --no-metadata
exited with code: 15
Error while running job: Error collecting output for parameter
'somatic_cnv_tar_gz': Did not find output file with glob pattern:
'['*.somatic.cnv.tar.gz']'
[job temp319312608049643386.cwl] completed permanentFail
Final process status is permanentFail
Workflow error, try again with --debug for more information:
Process status is ['permanentFail']
stdout :
java.lang.RuntimeException: problems running command: cwltool --enable-dev
--non-strict --enable-net --outdir
/mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/outputs/
--tmpdir-prefix
/mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/working/
/tmp/1474331255066-0/temp319312608049643386.cwl
/mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/workflow_params.json
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