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Commands for ACCESS_pipeline.cwl
Ian edited this page Apr 5, 2021
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Here are the commands used in the ACCESS-Pipeline.
These steps are run in this order on all samples.
Note that different steps might have different sample IDs. These commands are for illustration purposes only.
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/ProcessLoopUMIFastq.cwl' p/P/jobl6qlfI INFO:cwltool:[job ProcessLoopUMIFastq.cwl] $ /opt/common/CentOS_6/java/jdk1.8.0_31/bin/java \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/ProcessLoopUMIFastq.cwl' p/P/jobl6qlfI -server \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/ProcessLoopUMIFastq.cwl' p/P/jobl6qlfI -Xms8g \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/ProcessLoopUMIFastq.cwl' p/P/jobl6qlfI -Xmx8g \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/ProcessLoopUMIFastq.cwl' p/P/jobl6qlfI -cp \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/ProcessLoopUMIFastq.cwl' p/P/jobl6qlfI /home/johnsoni/vendor_tools/Marianas-1.5.jar \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/ProcessLoopUMIFastq.cwl' p/P/jobl6qlfI org.mskcc.marianas.umi.duplex.fastqprocessing.ProcessLoopUMIFastq \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/ProcessLoopUMIFastq.cwl' p/P/jobl6qlfI /out_tmpdirTQXKRm/DH-ntrk-012-pl-T1
8_IGO_05500_ES_42_S42_R1_001.fastq.gz \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/ProcessLoopUMIFastq.cwl' p/P/jobl6qlfI 3 \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/ProcessLoopUMIFastq.cwl' p/P/jobl6qlfI .
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/ProcessLoopUMIFastq.cwl' p/P/jobl6qlfI [job ProcessLoopUMIFastq.cwl] completed success
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/ProcessLoopUMIFastq.cwl' p/P/jobl6qlfI INFO:cwltool:[job ProcessLoopUMIFastq.cwl] completed success
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/trimgalore/trimgalore.cwl' w/n/jobSYo3vi INFO:cwltool:[job trimgalore.cwl] /ES_5-1_yes_md-retry/out_tmpdirS
vjdUc$ /opt/common/CentOS_6/perl/perl-5.20.2/bin/perl \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/trimgalore/trimgalore.cwl' w/n/jobSYo3vi /opt/common/CentOS_6/trim_galore/Trim_Galore_v0.2.5/trim_galore \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/trimgalore/trimgalore.cwl' w/n/jobSYo3vi -a \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/trimgalore/trimgalore.cwl' w/n/jobSYo3vi GATCGGAAGAGC \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/trimgalore/trimgalore.cwl' w/n/jobSYo3vi -a2 \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/trimgalore/trimgalore.cwl' w/n/jobSYo3vi AGATCGGAAGAGC \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/trimgalore/trimgalore.cwl' w/n/jobSYo3vi --gzip \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/trimgalore/trimgalore.cwl' w/n/jobSYo3vi -length \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/trimgalore/trimgalore.cwl' w/n/jobSYo3vi 25 \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/trimgalore/trimgalore.cwl' w/n/jobSYo3vi --paired \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/trimgalore/trimgalore.cwl' w/n/jobSYo3vi -q \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/trimgalore/trimgalore.cwl' w/n/jobSYo3vi 1 \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/trimgalore/trimgalore.cwl' w/n/jobSYo3vi --stringency \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/trimgalore/trimgalore.cwl' w/n/jobSYo3vi 3 \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/trimgalore/trimgalore.cwl' w/n/jobSYo3vi --suppress_warn \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/trimgalore/trimgalore.cwl' w/n/jobSYo3vi /stg0355b382-01c6-48b2-9720-58d3
3f795425/DH-ntrk-012-pl-T18_IGO_05500_ES_42_S42_R1_001.fastq.gz \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/trimgalore/trimgalore.cwl' w/n/jobSYo3vi /stg743d9ddb-d80f-48b6-a31b-1eeb
dbf04288/DH-ntrk-012-pl-T18_IGO_05500_ES_42_S42_R2_001.fastq.gz
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/trimgalore/trimgalore.cwl' w/n/jobSYo3vi [job trimgalore.cwl] completed success
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/trimgalore/trimgalore.cwl' w/n/jobSYo3vi INFO:cwltool:[job trimgalore.cwl] completed success
x32.cbio.private 2019-04-08 23:32:56,800 Thread-403 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/bwa-mem/bwa-mem.cwl' f/J/jobiUV60J [job bwa-mem.cwl] /06302R_06302S/set_4/Project_06302_R/MB-Grail-group_2-2.0.0/out_tmpdirEdRJl9$ /opt/common/CentOS_6/bwa/bwa-0.7.5a/bwa \
x32.cbio.private 2019-04-08 23:32:56,800 Thread-403 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/bwa-mem/bwa-mem.cwl' f/J/jobiUV60J mem \
x32.cbio.private 2019-04-08 23:32:56,800 Thread-403 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/bwa-mem/bwa-mem.cwl' f/J/jobiUV60J -t \
x32.cbio.private 2019-04-08 23:32:56,800 Thread-403 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/bwa-mem/bwa-mem.cwl' f/J/jobiUV60J 4 \
x32.cbio.private 2019-04-08 23:32:56,801 Thread-403 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/bwa-mem/bwa-mem.cwl' f/J/jobiUV60J -PM \
x32.cbio.private 2019-04-08 23:32:56,801 Thread-403 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/bwa-mem/bwa-mem.cwl' f/J/jobiUV60J -R \
x32.cbio.private 2019-04-08 23:32:56,801 Thread-403 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/bwa-mem/bwa-mem.cwl' f/J/jobiUV60J '@RG ID:SM:sample_id LB:1 SM:sample_id PL:Illumina PU:- CN:BergerLab_MSKCC' \
x32.cbio.private 2019-04-08 23:32:56,801 Thread-403 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/bwa-mem/bwa-mem.cwl' f/J/jobiUV60J /hg-fasta/VERSIONS/hg19/Homo_sapiens_assembly19.fasta \
x32.cbio.private 2019-04-08 23:32:56,801 Thread-403 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/bwa-mem/bwa-mem.cwl' f/J/jobiUV60J /06302R_06302S/set_4/Project_06302_R/MB-Grail-group_2-2.0.0/tmpFUuolS/stgb885a90c-99f8-44bf-a12d-35cfcd864d49/MSK-ML-0053-04-5000722C_cl_aln_srt_MD_IR_FX_BR_R1_.fastq.gz \
x32.cbio.private 2019-04-08 23:32:56,801 Thread-403 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/bwa-mem/bwa-mem.cwl' f/J/jobiUV60J /06302R_06302S/set_4/Project_06302_R/MB-Grail-group_2-2.0.0/tmpFUuolS/stgd69b432d-3e83-40be-8fe5-cb1a2aeb092f/MSK-ML-0053-04-5000722C_cl_aln_srt_MD_IR_FX_BR_R2_.fastq.gz > /06302R_06302S/set_4/Project_06302_R/MB-Grail-group_2-2.0.0/out_tmpdirEdRJl9/MSK-ML-0053-04-5000722C_cl_aln_srt_MD_IR_FX_BR__aln.sam
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 6/3/jobDixfv2 INFO:cwltool:[job AddOrReplaceReadGroups.cwl] /ES_5-1_yes_
md-retry/out_tmpdir3oc845$ /opt/common/CentOS_6/java/jdk1.7.0_75/bin/java \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 6/3/jobDixfv2 -Xmx4g \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 6/3/jobDixfv2 -jar \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 6/3/jobDixfv2 /home/johnsoni/vendor_tools/AddOrReplaceReadGroups-1.96.jar \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 6/3/jobDixfv2 RGCN=BergerLab_MSKCC \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 6/3/jobDixfv2 RGID=DH-ntrk-012-pl-T18_IGO_05500_ES_42 \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 6/3/jobDixfv2 RGLB=7 \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 6/3/jobDixfv2 O=DH-ntrk-012-pl-T18_IGO_05500_ES_42_S42_001_aln_srt.bam \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 6/3/jobDixfv2 RGPL=Illumina \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 6/3/jobDixfv2 RGPU=bc418-bc418 \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 6/3/jobDixfv2 RGSM=DH-ntrk-012-pl-T18_IGO_05500_ES_42 \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 6/3/jobDixfv2 COMPRESSION_LEVEL=0 \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 6/3/jobDixfv2 CREATE_INDEX=true \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 6/3/jobDixfv2 I=/ES_5-1_yes_md-retry/tmpjs2RvO/stg4b9621dc-41c9-4902
-b81e-01ca8ca8eeea/DH-ntrk-012-pl-T18_IGO_05500_ES_42_S42_001_aln.sam \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 6/3/jobDixfv2 SO=coordinate \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 6/3/jobDixfv2 TMP_DIR=/scratch \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 6/3/jobDixfv2 VALIDATION_STRINGENCY=LENIENT
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 6/3/jobDixfv2 [Tue May 01 20:39:22 EDT 2018] net.sf.picard.sam.AddOrReplaceReadGroups INPUT=/ES_5-1_yes_md-retry/tmpjs2RvO/stg4b9621dc-41c9-4902-b81e-01ca8ca8eeea/DH-ntrk-012-pl-T18_IGO_05500_ES_42_S42_001_aln.sam OUTPUT=DH-ntrk-012-pl-T18_IGO_05500_ES_42_S42_001_aln_srt.bam
SORT_ORDER=coordinate RGID=DH-ntrk-012-pl-T18_IGO_05500_ES_42 RGLB=7 RGPL=Illumina RGPU=bc418-bc418 RGSM=DH-ntrk-012-pl-T18_IGO_05500_ES_42 RGCN=BergerLab_MSKCC TMP_DIR=[/scratch] VALIDATION_STRINGENCY=LE
NIENT COMPRESSION_LEVEL=0 CREATE_INDEX=true VERBOSITY=INFO QUIET=false MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 6/3/jobDixfv2 [Tue May 01 20:39:22 EDT 2018] Executing as [email protected] on Linux 2.6.32-696.3.2.el6.x
86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_75-b13; Picard version: 1.96(1510)
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 6/3/jobDixfv2 INFO 2018-05-01 20:39:23 AddOrReplaceReadGroups Created read group ID=DH-ntrk-012-pl-T18_IGO
_05500_ES_42 PL=Illumina LB=7 SM=DH-ntrk-012-pl-T18_IGO_05500_ES_42
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 6/3/jobDixfv2
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 6/3/jobDixfv2 INFO 2018-05-01 20:41:03 AddOrReplaceReadGroups Processed 1,000,000 records. Elapsed ti
me: 00:01:38s. Time for last 1,000,000: 98s. Last read position: 20:57,484,440
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 6/3/jobDixfv2 INFO 2018-05-01 20:42:19 AddOrReplaceReadGroups Processed 2,000,000 records. Elapsed ti
me: 00:02:54s. Time for last 1,000,000: 76s. Last read position: 7:6,017,641
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 6/3/jobDixfv2 INFO 2018-05-01 20:43:31 AddOrReplaceReadGroups Processed 3,000,000 records. Elapsed ti
me: 00:04:06s. Time for last 1,000,000: 71s. Last read position: 3:12,632,470
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 6/3/jobDixfv2 INFO 2018-05-01 20:43:41 AddOrReplaceReadGroups Processed 4,000,000 records. Elapsed ti
me: 00:04:16s. Time for last 1,000,000: 10s. Last read position: 4:1,806,984
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 6/3/jobDixfv2 [Tue May 01 20:44:05 EDT 2018] net.sf.picard.sam.AddOrReplaceReadGroups done. Elapsed time: 4.72 mi
nutes.
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 6/3/jobDixfv2 Runtime.totalMemory()=2210398208
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 6/3/jobDixfv2 [job AddOrReplaceReadGroups.cwl] completed success
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 6/3/jobDixfv2 INFO:cwltool:[job AddOrReplaceReadGroups.cwl] completed success
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/MarkDuplicates.cwl' W/d/jobNOyHVr INFO:cwltool:[job MarkDuplicates.cwl] /ES_5-1_yes_md-retry/out_tmp
diraccHsC$ /opt/common/CentOS_6/java/jdk1.8.0_31/bin/java \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/MarkDuplicates.cwl' W/d/jobNOyHVr -Xmx4g \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/MarkDuplicates.cwl' W/d/jobNOyHVr -jar \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/MarkDuplicates.cwl' W/d/jobNOyHVr /home/johnsoni/vendor_tools/picard-2.8.1.jar \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/MarkDuplicates.cwl' W/d/jobNOyHVr MarkDuplicates \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/MarkDuplicates.cwl' W/d/jobNOyHVr M=DH-ntrk-012-pl-T18_IGO_05500_ES_42_S42_001_aln_srt.md_metrics \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/MarkDuplicates.cwl' W/d/jobNOyHVr O=DH-ntrk-012-pl-T18_IGO_05500_ES_42_S42_001_aln_srt_MD.bam \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/MarkDuplicates.cwl' W/d/jobNOyHVr ASSUME_SORTED=true \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/MarkDuplicates.cwl' W/d/jobNOyHVr COMPRESSION_LEVEL=0 \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/MarkDuplicates.cwl' W/d/jobNOyHVr CREATE_INDEX=true \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/MarkDuplicates.cwl' W/d/jobNOyHVr DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/MarkDuplicates.cwl' W/d/jobNOyHVr I=/ES_5-1_yes_md-retry/tmpNhljc8/stg418a652f-01df-4c00-9c72-5e
8d67f8aaa1/DH-ntrk-012-pl-T18_IGO_05500_ES_42_S42_001_aln_srt.bam \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/MarkDuplicates.cwl' W/d/jobNOyHVr TMP_DIR=/scratch \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/MarkDuplicates.cwl' W/d/jobNOyHVr VALIDATION_STRINGENCY=LENIENT
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm INFO:cwltool:[job FindCoveredIntervals.cwl] /ES_5-1_yes_md-ret
ry/out_tmpdiryZbBx6$ /opt/common/CentOS_6/java/jdk1.8.0_31/bin/java \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm -Xmx20g \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm -Djava.io.tmpdir=/scratch \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm -jar \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm /opt/common/CentOS_6/gatk/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm -T \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm FindCoveredIntervals \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm --input_file \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm /ES_5-1_yes_md-retry/tmpZVWx2a/stg37b44f42-c824-4315-92b0-
ed735b362024/DH-ntrk-002-pl-T18_IGO_05500_ES_37_S37_001_aln_srt_MD.bam \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm --read_filter \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm FailsVendorQualityCheck \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm --reference_sequence \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm /hg-fasta/VERSIONS/hg19/Homo_sapiens_assembly19.fasta \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm --read_filter \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm BadMate \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm --read_filter \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm UnmappedRead \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm --read_filter \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm BadCigar \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm --coverage_threshold \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm 20 \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm --minBaseQuality \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm 20 \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm --minMappingQuality \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm 20 \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm --out \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm DH-ntrk-002.fci.list
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm INFO:cwltool:[job list2bed.cwl] /ES_5-1_yes_md-retry/out_tmpdi
rKIMu_V$ list2bed \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm --input_file \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm /ES_5-1_yes_md-retry/tmppPWS0g/stg930c6f31-a965-4e22-a790-
31a845774e88/DH-ntrk-002.fci.list \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm --output_file \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm DH-ntrk-002.fci.bed.srt \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm --sort
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm Sorting...
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm Namespace(input_file='/ES_5-1_yes_md-retry/tmppPWS0g/stg930c6f
31-a965-4e22-a790-31a845774e88/DH-ntrk-002.fci.list', output_file='DH-ntrk-002.fci.bed.srt', sort=True)
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm [job list2bed.cwl] completed success
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' D/1/job7pLmNm INFO:cwltool:[job list2bed.cwl] completed success
w01.cbio.private 2019-02-22 13:34:28,480 Thread-403 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_0.0.57-marianas_1.8.0-Abra_nonpaired/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' D/k/jobriH52g [job abra.cwl] /triple_abra_versions_TEST/nonpaired/TEST_run-marianas-1.8.0-abra-nonpaired-3-g34c7808/out_tmpdir7f8GEN$ /opt/common/CentOS_6/java/jdk1.7.0_75/bin/java \
w01.cbio.private 2019-02-22 13:34:28,480 Thread-403 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_0.0.57-marianas_1.8.0-Abra_nonpaired/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' D/k/jobriH52g -Xmx60g \
w01.cbio.private 2019-02-22 13:34:28,480 Thread-403 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_0.0.57-marianas_1.8.0-Abra_nonpaired/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' D/k/jobriH52g -Djava.io.tmpdir=/scratch/ \
w01.cbio.private 2019-02-22 13:34:28,481 Thread-403 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_0.0.57-marianas_1.8.0-Abra_nonpaired/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' D/k/jobriH52g -jar \
w01.cbio.private 2019-02-22 13:34:28,481 Thread-403 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_0.0.57-marianas_1.8.0-Abra_nonpaired/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' D/k/jobriH52g /home/johnsoni/vendor_tools/abra-0.92-SNAPSHOT-jar-with-dependencies.jar \
w01.cbio.private 2019-02-22 13:34:28,481 Thread-403 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_0.0.57-marianas_1.8.0-Abra_nonpaired/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' D/k/jobriH52g --in \
w01.cbio.private 2019-02-22 13:34:28,482 Thread-403 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_0.0.57-marianas_1.8.0-Abra_nonpaired/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' D/k/jobriH52g /triple_abra_versions_TEST/nonpaired/TEST_run-marianas-1.8.0-abra-nonpaired-3-g34c7808/tmpPm6hey/stgac6796a8-8611-4106-ba64-61733132f743/test_sample_4_T_cl_aln_srt_MD_IR_FX_BR__aln_srt.bam \
w01.cbio.private 2019-02-22 13:34:28,482 Thread-403 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_0.0.57-marianas_1.8.0-Abra_nonpaired/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' D/k/jobriH52g --kmer \
w01.cbio.private 2019-02-22 13:34:28,482 Thread-403 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_0.0.57-marianas_1.8.0-Abra_nonpaired/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' D/k/jobriH52g 43,53,63,83,93 \
w01.cbio.private 2019-02-22 13:34:28,483 Thread-403 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_0.0.57-marianas_1.8.0-Abra_nonpaired/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' D/k/jobriH52g --mad \
w01.cbio.private 2019-02-22 13:34:28,483 Thread-403 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_0.0.57-marianas_1.8.0-Abra_nonpaired/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' D/k/jobriH52g 1000 \
w01.cbio.private 2019-02-22 13:34:28,483 Thread-403 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_0.0.57-marianas_1.8.0-Abra_nonpaired/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' D/k/jobriH52g --out \
w01.cbio.private 2019-02-22 13:34:28,483 Thread-403 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_0.0.57-marianas_1.8.0-Abra_nonpaired/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' D/k/jobriH52g test_sample_4_T_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR.bam \
w01.cbio.private 2019-02-22 13:34:28,484 Thread-403 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_0.0.57-marianas_1.8.0-Abra_nonpaired/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' D/k/jobriH52g --ref \
w01.cbio.private 2019-02-22 13:34:28,484 Thread-403 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_0.0.57-marianas_1.8.0-Abra_nonpaired/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' D/k/jobriH52g /home/johnsoni/test_reference/fasta/chr14_chr16.fasta \
w01.cbio.private 2019-02-22 13:34:28,484 Thread-403 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_0.0.57-marianas_1.8.0-Abra_nonpaired/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' D/k/jobriH52g --targets \
w01.cbio.private 2019-02-22 13:34:28,485 Thread-403 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_0.0.57-marianas_1.8.0-Abra_nonpaired/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' D/k/jobriH52g /triple_abra_versions_TEST/nonpaired/TEST_run-marianas-1.8.0-abra-nonpaired-3-g34c7808/tmpPm6hey/stg3a0682ca-7554-4b6c-81a4-17fed2f18c5b/test_patient_2.fci.bed.srt \
w01.cbio.private 2019-02-22 13:34:28,486 Thread-403 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_0.0.57-marianas_1.8.0-Abra_nonpaired/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' D/k/jobriH52g --threads \
w01.cbio.private 2019-02-22 13:34:28,486 Thread-403 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_0.0.57-marianas_1.8.0-Abra_nonpaired/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' D/k/jobriH52g 12 \
w01.cbio.private 2019-02-22 13:34:28,487 Thread-403 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_0.0.57-marianas_1.8.0-Abra_nonpaired/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' D/k/jobriH52g --working \
w01.cbio.private 2019-02-22 13:34:28,487 Thread-403 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_0.0.57-marianas_1.8.0-Abra_nonpaired/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' D/k/jobriH52g /scratch//Abra_workdir__test_patient_2_1550860458286
[job abra.cwl] /juno/work/bergerm1/Innovation/Ian/06302_S/06302_S-1-1.1.9/tmp/tmp6V3o2y/a/0/out_tmpdiromiCbf$ /opt/common/CentOS_6/java/jdk1.8.0_31/bin/java \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.8/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' J/O/job0ZZZSk -Xmx60g \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.8/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' J/O/job0ZZZSk -Djava.io.tmpdir=/juno/work/bergerm1/Innovation/Ian/06302_S/06302_S-1-1.1.9/tmp/tmpHiUxl7/stgb982dea2-45c3-4c29-99d7-38426af9d555/empty_dir \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.8/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' J/O/job0ZZZSk -jar \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.8/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' J/O/job0ZZZSk /opt/common/CentOS_6/abra2/abra2-2.17/abra2-2.17.jar \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.8/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' J/O/job0ZZZSk --ca \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.8/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' J/O/job0ZZZSk 10,1 \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.8/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' J/O/job0ZZZSk --cons \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.8/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' J/O/job0ZZZSk --index \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.8/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' J/O/job0ZZZSk --in \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.8/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' J/O/job0ZZZSk /juno/work/bergerm1/Innovation/Ian/06302_S/06302_S-1-1.1.9/tmp/tmpHiUxl7/stg6a4f0ea0-081a-4a09-9b84-d76eaab5fa93/C-002078-L007-d_cl_aln_srt_MD.bam \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.8/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' J/O/job0ZZZSk --mad \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.8/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' J/O/job0ZZZSk 1000 \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.8/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' J/O/job0ZZZSk --mmr \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.8/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' J/O/job0ZZZSk 0.1 \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.8/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' J/O/job0ZZZSk --out \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.8/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' J/O/job0ZZZSk C-002078-L007-d_cl_aln_srt_MD_IR.bam \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.8/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' J/O/job0ZZZSk --ref \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.8/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' J/O/job0ZZZSk /hg-fasta/VERSIONS/hg19/Homo_sapiens_assembly19.fasta \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.8/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' J/O/job0ZZZSk --sc \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.8/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' J/O/job0ZZZSk 100,30,80,15 \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.8/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' J/O/job0ZZZSk --sga \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.8/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' J/O/job0ZZZSk 8,32,48,1 \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.8/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' J/O/job0ZZZSk --targets \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.8/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' J/O/job0ZZZSk /juno/work/bergerm1/Innovation/Ian/06302_S/06302_S-1-1.1.9/tmp/tmpHiUxl7/stg09f42956-f2d5-4e4d-9dac-398e5d336d9e/C-002078.fci.bed.srt \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.8/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' J/O/job0ZZZSk --threads \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.8/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' J/O/job0ZZZSk 12 \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.8/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' J/O/job0ZZZSk --tmpdir \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.8/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' J/O/job0ZZZSk /juno/work/bergerm1/Innovation/Ian/06302_S/06302_S-1-1.1.9/tmp/tmpHiUxl7/stgb982dea2-45c3-4c29-99d7-38426af9d555/empty_dir \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.8/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' J/O/job0ZZZSk --ws \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.8/ACCESS-Pipeline/cwl_tools/abra/abra.cwl' J/O/job0ZZZSk 800,700
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/BaseQualityScoreRecalibration.cwl' Q/8/jobhmugKm INFO:cwltool:[job BaseQualityScoreRecalibration.cwl]
/ES_5-1_yes_md-retry/out_tmpdirSzawl4$ /opt/common/CentOS_6/java/jdk1.8.0_31/bin/java \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/BaseQualityScoreRecalibration.cwl' Q/8/jobhmugKm -Xmx30g \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/BaseQualityScoreRecalibration.cwl' Q/8/jobhmugKm -Djava.io.tmpdir=/scratch \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/BaseQualityScoreRecalibration.cwl' Q/8/jobhmugKm -jar \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/BaseQualityScoreRecalibration.cwl' Q/8/jobhmugKm /opt/common/CentOS_6/gatk/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/BaseQualityScoreRecalibration.cwl' Q/8/jobhmugKm -T \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/BaseQualityScoreRecalibration.cwl' Q/8/jobhmugKm BaseRecalibrator \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/BaseQualityScoreRecalibration.cwl' Q/8/jobhmugKm -I \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/BaseQualityScoreRecalibration.cwl' Q/8/jobhmugKm /ES_5-1_yes_md-retry/tmpBBjbcQ/stgbe3abf3f-f959-4
62a-a128-9acc5fc97ab5/DS-fast-037-pl-T02_IGO_05500_ES_1_S1_001_aln_srt_MD_IR_FX.bam \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/BaseQualityScoreRecalibration.cwl' Q/8/jobhmugKm -knownSites \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/BaseQualityScoreRecalibration.cwl' Q/8/jobhmugKm /ES_5-1_yes_md-retry/tmpBBjbcQ/stge2b79468-ee1a-4
f41-a8d1-0bb6e8a819c1/dbsnp_137.b37.vcf \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/BaseQualityScoreRecalibration.cwl' Q/8/jobhmugKm -knownSites \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/BaseQualityScoreRecalibration.cwl' Q/8/jobhmugKm /ES_5-1_yes_md-retry/tmpBBjbcQ/stg546b8584-9ab7-4
22c-aaab-b4ecac1c57cb/Mills_and_1000G_gold_standard.indels.b37.vcf \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/BaseQualityScoreRecalibration.cwl' Q/8/jobhmugKm -nct \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/BaseQualityScoreRecalibration.cwl' Q/8/jobhmugKm 3 \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/BaseQualityScoreRecalibration.cwl' Q/8/jobhmugKm --out \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/BaseQualityScoreRecalibration.cwl' Q/8/jobhmugKm recal.matrix \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/BaseQualityScoreRecalibration.cwl' Q/8/jobhmugKm -R \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/BaseQualityScoreRecalibration.cwl' Q/8/jobhmugKm /hg-fasta/VERSIONS/hg19/Homo_sapiens_assembly19.fasta
\
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/BaseQualityScoreRecalibration.cwl' Q/8/jobhmugKm -rf \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/BaseQualityScoreRecalibration.cwl' Q/8/jobhmugKm BadCigar
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/PrintReads.cwl' 7/k/jobhR8QGT INFO:cwltool:[job PrintReads.cwl] /ES_5-1_yes_md-retry/out_tmpdiro03Vte$
/opt/common/CentOS_6/java/jdk1.8.0_31/bin/java \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/PrintReads.cwl' 7/k/jobhR8QGT -Xmx4g \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/PrintReads.cwl' 7/k/jobhR8QGT -Djava.io.tmpdir=/scratch \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/PrintReads.cwl' 7/k/jobhR8QGT -jar \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/PrintReads.cwl' 7/k/jobhR8QGT /opt/common/CentOS_6/gatk/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/PrintReads.cwl' 7/k/jobhR8QGT -T \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/PrintReads.cwl' 7/k/jobhR8QGT PrintReads \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/PrintReads.cwl' 7/k/jobhR8QGT --BQSR \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/PrintReads.cwl' 7/k/jobhR8QGT /ES_5-1_yes_md-retry/tmpN1DLZs/stgba3a5db4-dfee-4e9b-8e19-521de11fbb
80/recal.matrix \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/PrintReads.cwl' 7/k/jobhR8QGT -EOQ \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/PrintReads.cwl' 7/k/jobhR8QGT --baq \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/PrintReads.cwl' 7/k/jobhR8QGT RECALCULATE \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/PrintReads.cwl' 7/k/jobhR8QGT --input_file \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/PrintReads.cwl' 7/k/jobhR8QGT /ES_5-1_yes_md-retry/tmpN1DLZs/stg74687828-a42d-44b8-9af3-c318d6a70e
0d/Borecl-Norm-021-cf01_IGO_05500_ES_27_S27_001_aln_srt_MD_IR_FX.bam \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/PrintReads.cwl' 7/k/jobhR8QGT -nct \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/PrintReads.cwl' 7/k/jobhR8QGT 8 \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/PrintReads.cwl' 7/k/jobhR8QGT --out \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/PrintReads.cwl' 7/k/jobhR8QGT Borecl-Norm-021-cf01_IGO_05500_ES_27_S27_001_aln_srt_MD_IR_FX_BR.bam \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/PrintReads.cwl' 7/k/jobhR8QGT --reference_sequence \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/PrintReads.cwl' 7/k/jobhR8QGT /hg-fasta/VERSIONS/hg19/Homo_sapiens_assembly19.fasta
To generate the pileup that is used for collapsing
[job PileupMetrics.cwl] /juno/work/bergerm1/MSK-ACCESS/ACCESS-Projects/09831_B/PROSTATE-02-1.1.14/tmp/tmpLdb7iF/1/f/out_tmpdirLDejhS$ /opt/common/CentOS_6/java/jdk1.8.0_31/bin/java \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.14/ACCESS-Pipeline/cwl_tools/waltz/PileupMetrics.cwl' 2/X/jobhu7Ndg -server \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.14/ACCESS-Pipeline/cwl_tools/waltz/PileupMetrics.cwl' 2/X/jobhu7Ndg -Xms4g \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.14/ACCESS-Pipeline/cwl_tools/waltz/PileupMetrics.cwl' 2/X/jobhu7Ndg -Xmx4g \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.14/ACCESS-Pipeline/cwl_tools/waltz/PileupMetrics.cwl' 2/X/jobhu7Ndg -cp \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.14/ACCESS-Pipeline/cwl_tools/waltz/PileupMetrics.cwl' 2/X/jobhu7Ndg /home/johnsoni/vendor_tools/Waltz-2.0.jar \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.14/ACCESS-Pipeline/cwl_tools/waltz/PileupMetrics.cwl' 2/X/jobhu7Ndg org.mskcc.juber.waltz.Waltz \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.14/ACCESS-Pipeline/cwl_tools/waltz/PileupMetrics.cwl' 2/X/jobhu7Ndg PileupMetrics \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.14/ACCESS-Pipeline/cwl_tools/waltz/PileupMetrics.cwl' 2/X/jobhu7Ndg 20 \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.14/ACCESS-Pipeline/cwl_tools/waltz/PileupMetrics.cwl' 2/X/jobhu7Ndg /juno/work/bergerm1/MSK-ACCESS/ACCESS-Projects/09831_B/PROSTATE-02-1.1.14/tmp/tmp6X3lyG/stg88c6d932-0cf3-4fd3-ae27-530aca334aa5/C-UR571K-L002-d_cl_aln_srt_MD_IR_FX_BR.bam \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.14/ACCESS-Pipeline/cwl_tools/waltz/PileupMetrics.cwl' 2/X/jobhu7Ndg /hg-fasta/VERSIONS/hg19/Homo_sapiens_assembly19.fasta \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.14/ACCESS-Pipeline/cwl_tools/waltz/PileupMetrics.cwl' 2/X/jobhu7Ndg /juno/work/bergerm1/MSK-ACCESS/ACCESS-Projects/09831_B/PROSTATE-02-1.1.14/tmp/tmp6X3lyG/stg5d1ad304-86aa-4981-9070-65729ec1c80c/MSK-ACCESS-v1_0-probe-A.sorted.bed
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/UMIBamToCollapsedFastqFirstPass.cwl' F/b/job0r2TNg [job UMIBamToCollapsedFastqFirstPass.cwl] /EF_5
-3_yes-md-retry/out_tmpdirpFgV2c$ /opt/common/CentOS_6/java/jdk1.8.0_31/bin/java \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/UMIBamToCollapsedFastqFirstPass.cwl' F/b/job0r2TNg -server \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/UMIBamToCollapsedFastqFirstPass.cwl' F/b/job0r2TNg -Xms8g \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/UMIBamToCollapsedFastqFirstPass.cwl' F/b/job0r2TNg -Xmx8g \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/UMIBamToCollapsedFastqFirstPass.cwl' F/b/job0r2TNg -cp \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/UMIBamToCollapsedFastqFirstPass.cwl' F/b/job0r2TNg /home/johnsoni/vendor_tools/Marianas-1.5.jar \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/UMIBamToCollapsedFastqFirstPass.cwl' F/b/job0r2TNg org.mskcc.marianas.umi.duplex.DuplexUMIBamToCollapsedFastqFirstPass \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/UMIBamToCollapsedFastqFirstPass.cwl' F/b/job0r2TNg /EF_5-3_yes-md-retry/tmpWjTjip/stgc4c27349-
0b34-4a3d-9256-0e942b5c5508/BL-tdm1-009-bc-N01_IGO_05500_EF_63_S63_001_cl_aln_srt_MD_IR_FX_BR.bam \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/UMIBamToCollapsedFastqFirstPass.cwl' F/b/job0r2TNg /EF_5-3_yes-md-retry/tmpWjTjip/stgbc9d7206-ac27-4bca-8de3-929c75d86af7/BL-tdm1-009-bc-N01_IGO_05500_EF_63_S63_001_cl_aln_srt_MD_IR_FX_BR-pileup.txt \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/UMIBamToCollapsedFastqFirstPass.cwl' F/b/job0r2TNg 1 \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/UMIBamToCollapsedFastqFirstPass.cwl' F/b/job0r2TNg 20 \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/UMIBamToCollapsedFastqFirstPass.cwl' F/b/job0r2TNg 0 \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/UMIBamToCollapsedFastqFirstPass.cwl' F/b/job0r2TNg 2 \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/UMIBamToCollapsedFastqFirstPass.cwl' F/b/job0r2TNg 90 \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/UMIBamToCollapsedFastqFirstPass.cwl' F/b/job0r2TNg /hg-fasta/VERSIONS/hg19/Homo_sapiens_assembly19.fasta \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/UMIBamToCollapsedFastqFirstPass.cwl' F/b/job0r2TNg .
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas-sort/marianas-sort.cwl' sort M/z/jobJmPZX4 INFO:cwltool:[job marianas-sort.cwl] /EF_5-3_yes-md-ret
ry/out_tmpdir2IuJHB$ /bin/sh \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas-sort/marianas-sort.cwl' sort M/z/jobJmPZX4 -c \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas-sort/marianas-sort.cwl' sort M/z/jobJmPZX4 'sort' -S 8G -k 6,6n -k 8,8n /EF_5-3_yes-md-retry/tmpfhXxpM/stg39c8be2d-f3a6-4f54-af3a-59882992a41b/first-pass.txt > first-pass.mate-position-sorted.txt
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas-sort/marianas-sort.cwl' sort M/z/jobJmPZX4 [job marianas-sort.cwl] completed success
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas-sort/marianas-sort.cwl' sort M/z/jobJmPZX4 INFO:cwltool:[job marianas-sort.cwl] completed success
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/UMIBamToCollapsedFastqSecondPass.cwl' W/p/jobuGv5WR INFO:cwltool:[job UMIBamToCollapsedFastqSecondPass.cwl] /s
andbox/ian/EF_5-3_yes-md-retry/out_tmpdirzww4Xm$ /opt/common/CentOS_6/java/jdk1.8.0_31/bin/java \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/UMIBamToCollapsedFastqSecondPass.cwl' W/p/jobuGv5WR -server \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/UMIBamToCollapsedFastqSecondPass.cwl' W/p/jobuGv5WR -Xms8g \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/UMIBamToCollapsedFastqSecondPass.cwl' W/p/jobuGv5WR -Xmx8g \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/UMIBamToCollapsedFastqSecondPass.cwl' W/p/jobuGv5WR -cp \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/UMIBamToCollapsedFastqSecondPass.cwl' W/p/jobuGv5WR /home/johnsoni/vendor_tools/Marianas-1.5.jar \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/UMIBamToCollapsedFastqSecondPass.cwl' W/p/jobuGv5WR org.mskcc.marianas.umi.duplex.DuplexUMIBamToCollapsedFastqSecondPass \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/UMIBamToCollapsedFastqSecondPass.cwl' W/p/jobuGv5WR /EF_5-3_yes-md-retry/tmpP5_XXe/stg6257edac-3dd8-4730-ab6a-bac894d32a75/BL-nsclc-006-bc-N01_IGO_05500_EF_53_S53_001_cl_aln_srt_MD_IR_FX_BR.bam \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/UMIBamToCollapsedFastqSecondPass.cwl' W/p/jobuGv5WR /EF_5-3_yes-md-retry/tmpP5_XXe/stgfbfec1c2-912c-4cf7-914d-2f1ff2bf7cac/BL-nsclc-006-bc-N01_IGO_05500_EF_53_S53_001_cl_aln_srt_MD_IR_FX_BR-pileup.txt \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/UMIBamToCollapsedFastqSecondPass.cwl' W/p/jobuGv5WR 1 \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/UMIBamToCollapsedFastqSecondPass.cwl' W/p/jobuGv5WR 20 \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/UMIBamToCollapsedFastqSecondPass.cwl' W/p/jobuGv5WR 0 \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/UMIBamToCollapsedFastqSecondPass.cwl' W/p/jobuGv5WR 2 \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/UMIBamToCollapsedFastqSecondPass.cwl' W/p/jobuGv5WR 90 \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/UMIBamToCollapsedFastqSecondPass.cwl' W/p/jobuGv5WR /hg-fasta/VERSIONS/hg19/Homo_sapiens_assembly19.fasta \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/UMIBamToCollapsedFastqSecondPass.cwl' W/p/jobuGv5WR .
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/bwa-mem/bwa-mem.cwl' U/G/job4yl05_ INFO:cwltool:[job bwa-mem.cwl] /EF_5-3_yes-md-retry/out_tmpdirwuD03T$ /o
pt/common/CentOS_6/bwa/bwa-0.7.5a/bwa \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/bwa-mem/bwa-mem.cwl' U/G/job4yl05_ mem \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/bwa-mem/bwa-mem.cwl' U/G/job4yl05_ -t \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/bwa-mem/bwa-mem.cwl' U/G/job4yl05_ 4 \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/bwa-mem/bwa-mem.cwl' U/G/job4yl05_ -PM \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/bwa-mem/bwa-mem.cwl' U/G/job4yl05_ -R \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/bwa-mem/bwa-mem.cwl' U/G/job4yl05_ '@RG ID:BL-nsclc-006-bc-N01 LB:5 SM:BL-nsclc-006-bc-N01 PL:Illumina PU:bc411-bc411 CN:BergerLab
_MSKCC' \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/bwa-mem/bwa-mem.cwl' U/G/job4yl05_ /hg-fasta/VERSIONS/hg19/Homo_sapiens_assembly19.fasta \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/bwa-mem/bwa-mem.cwl' U/G/job4yl05_ /EF_5-3_yes-md-retry/tmp8zHil1/stg42e6a771-eebe-4632-a3bf-8506b0d7d1
b9/BL-nsclc-006-bc-N01_IGO_05500_EF_53_S53_001_cl_aln_srt_MD_IR_FX_BR_R1_.fastq.gz \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/bwa-mem/bwa-mem.cwl' U/G/job4yl05_ /EF_5-3_yes-md-retry/tmp8zHil1/stg39ecb8ac-a9cb-49e2-9d38-201e30ff72
41/BL-nsclc-006-bc-N01_IGO_05500_EF_53_S53_001_cl_aln_srt_MD_IR_FX_BR_R2_.fastq.gz > /EF_5-3_yes-md-retry/out_tmpdirwuD03T/BL-nsclc-006-bc-N01_IGO_05500_EF_53_S53_
001_cl_aln_srt_MD_IR_FX_BR__aln.sam
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 1/Y/job4I2T5O INFO:cwltool:[job AddOrReplaceReadGroups.cwl] /EF_5-3_yes-
md-retry/out_tmpdirSdog9a$ /opt/common/CentOS_6/java/jdk1.7.0_75/bin/java \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 1/Y/job4I2T5O -Xmx4g \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 1/Y/job4I2T5O -jar \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 1/Y/job4I2T5O /home/johnsoni/vendor_tools/AddOrReplaceReadGroups-1.96.jar \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 1/Y/job4I2T5O RGCN=BergerLab_MSKCC \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 1/Y/job4I2T5O RGID=BL-tdm1-009-bc-N01 \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 1/Y/job4I2T5O RGLB=6 \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 1/Y/job4I2T5O O=BL-tdm1-009-bc-N01_IGO_05500_EF_63_S63_001_cl_aln_srt_MD_IR_FX_BR__aln_srt.bam \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 1/Y/job4I2T5O RGPL=Illumina \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 1/Y/job4I2T5O RGPU=bc424-bc424 \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 1/Y/job4I2T5O RGSM=BL-tdm1-009-bc-N01 \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 1/Y/job4I2T5O COMPRESSION_LEVEL=0 \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 1/Y/job4I2T5O CREATE_INDEX=true \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 1/Y/job4I2T5O I=/EF_5-3_yes-md-retry/tmp14yM1s/stg799635de-0587-4324
-8696-dfb94a8aa305/BL-tdm1-009-bc-N01_IGO_05500_EF_63_S63_001_cl_aln_srt_MD_IR_FX_BR__aln.sam \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 1/Y/job4I2T5O SO=coordinate \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 1/Y/job4I2T5O TMP_DIR=/scratch \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/picard/AddOrReplaceReadGroups.cwl' 1/Y/job4I2T5O VALIDATION_STRINGENCY=LENIENT
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 INFO:cwltool:[job FindCoveredIntervals.cwl] /EF_5-3_yes-md-ret
ry/out_tmpdirpXmySx$ /opt/common/CentOS_6/java/jdk1.8.0_31/bin/java \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 -Xmx20g \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 -Djava.io.tmpdir=/scratch \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 -jar \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 /opt/common/CentOS_6/gatk/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 -T \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 FindCoveredIntervals \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 --input_file \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 /EF_5-3_yes-md-retry/tmpw7_V1V/stge5ace6b4-491c-4de7-8680-
dd146dc67aba/DS-fast-144-pl-T02_IGO_05500_EF_29_S29_001_cl_aln_srt_MD_IR_FX_BR__aln_srt.bam \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 --read_filter \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 FailsVendorQualityCheck \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 --reference_sequence \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 /hg-fasta/VERSIONS/hg19/Homo_sapiens_assembly19.fasta \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 --input_file \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 /EF_5-3_yes-md-retry/tmpw7_V1V/stg289d1508-95f8-410f-ab6d-
a12acc349e46/DS-fast-147-bc-N01_IGO_05500_EF_36_S36_001_cl_aln_srt_MD_IR_FX_BR__aln_srt.bam \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 --read_filter \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 BadMate \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 --read_filter \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 UnmappedRead \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 --read_filter \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 BadCigar \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 --coverage_threshold \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 20 \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 --allow_potentially_misencoded_quality_scores \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 --minBaseQuality \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 20 \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 --minMappingQuality \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 20 \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 --out \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 DS-fast-144.fci.list
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 [job list2bed.cwl] /EF_5-3_yes-md-retry/out_tmpdirXITNez$ list
2bed \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 --input_file \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 /EF_5-3_yes-md-retry/tmpNIRASW/stg76d74bd9-7417-43e3-b478-
b58365a9b69c/DS-fast-144.fci.list \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 --output_file \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 DS-fast-144.fci.bed.srt \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 --sort
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 INFO:cwltool:[job list2bed.cwl] /EF_5-3_yes-md-retry/out_tmpdi
rXITNez$ list2bed \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 --input_file \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 /EF_5-3_yes-md-retry/tmpNIRASW/stg76d74bd9-7417-43e3-b478-
b58365a9b69c/DS-fast-144.fci.list \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 --output_file \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 DS-fast-144.fci.bed.srt \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 --sort
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 Sorting...
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 Namespace(input_file='/EF_5-3_yes-md-retry/tmpNIRASW/stg76d74b
d9-7417-43e3-b478-b58365a9b69c/DS-fast-144.fci.list', output_file='DS-fast-144.fci.bed.srt', sort=True)
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 [job list2bed.cwl] completed success
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/gatk/FindCoveredIntervals.cwl' p/k/jobtzOOM4 INFO:cwltool:[job list2bed.cwl] completed success
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/SeparateBams.cwl' Q/o/jobryvHaa INFO:cwltool:[job SeparateBams.cwl] /EF_5-3_yes-md-retry/out_tmpdi
rNbLkbN$ /opt/common/CentOS_6/java/jdk1.8.0_31/bin/java \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/SeparateBams.cwl' Q/o/jobryvHaa -server \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/SeparateBams.cwl' Q/o/jobryvHaa -Xms8g \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/SeparateBams.cwl' Q/o/jobryvHaa -Xmx8g \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/SeparateBams.cwl' Q/o/jobryvHaa -cp \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/SeparateBams.cwl' Q/o/jobryvHaa /home/johnsoni/vendor_tools/Marianas-1.5.jar \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/SeparateBams.cwl' Q/o/jobryvHaa org.mskcc.marianas.umi.duplex.postprocessing.SeparateBams \
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/SeparateBams.cwl' Q/o/jobryvHaa /EF_5-3_yes-md-retry/tmpDzO2Db/stg1cce99e1-cc0a-42c1-9482-efd4
c1c45ef6/BL-tdm1-004-bc-N01_IGO_05500_EF_62_S62_001_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX.bam
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/SeparateBams.cwl' Q/o/jobryvHaa [job SeparateBams.cwl] completed success
'file:///home/johnsoni/Innovation-Pipeline/cwl_tools/marianas/SeparateBams.cwl' Q/o/jobryvHaa INFO:cwltool:[job SeparateBams.cwl] completed success
[job CollectMultipleMetrics.cwl] /juno/work/bergerm1/MSK-ACCESS/ACCESS-Projects/5500-FY/5500-FY_TD-dmplib-8-1.1.13/tmp/tmpY3tj4K/5/3/out_tmpdirYxnp4x$ /opt/common/CentOS_6/java/jdk1.8.0_31/bin/java \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.14/ACCESS-Pipeline/cwl_tools/picard/CollectMultipleMetrics.cwl' 3/k/jobq3i0pw -Xmx4g \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.14/ACCESS-Pipeline/cwl_tools/picard/CollectMultipleMetrics.cwl' 3/k/jobq3i0pw -jar \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.14/ACCESS-Pipeline/cwl_tools/picard/CollectMultipleMetrics.cwl' 3/k/jobq3i0pw /home/johnsoni/vendor_tools/picard-2.8.1.jar \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.14/ACCESS-Pipeline/cwl_tools/picard/CollectMultipleMetrics.cwl' 3/k/jobq3i0pw CollectMultipleMetrics \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.14/ACCESS-Pipeline/cwl_tools/picard/CollectMultipleMetrics.cwl' 3/k/jobq3i0pw VALIDATION_STRINGENCY= \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.14/ACCESS-Pipeline/cwl_tools/picard/CollectMultipleMetrics.cwl' 3/k/jobq3i0pw LENIENT \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.14/ACCESS-Pipeline/cwl_tools/picard/CollectMultipleMetrics.cwl' 3/k/jobq3i0pw INPUT= \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.14/ACCESS-Pipeline/cwl_tools/picard/CollectMultipleMetrics.cwl' 3/k/jobq3i0pw /juno/work/bergerm1/MSK-ACCESS/ACCESS-Projects/5500-FY/5500-FY_TD-dmplib-8-1.1.13/tmp/tmp_yQI0d/stg3bc5168c-c634-415c-8c3d-b4a4e04e1b7f/C-7T7MPU-N001-d_cl_aln_srt_MD_IR_FX_BR.bam \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.14/ACCESS-Pipeline/cwl_tools/picard/CollectMultipleMetrics.cwl' 3/k/jobq3i0pw OUTPUT= \
DEBUG:toil.statsAndLogging:'file:///home/johnsoni/pipeline_1.1.14/ACCESS-Pipeline/cwl_tools/picard/CollectMultipleMetrics.cwl' 3/k/jobq3i0pw C-7T7MPU-N001-d_cl_aln_srt_MD_IR_FX_BR.bam
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