Regarding GenderMap file in genomestrip

Hello,
Can someone tell me that what should i define gender for plant sample in gendermap file.
Please explain me??

Thank you in Advance

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @deepika
    Hi,
    I just moved this to GenomeSTRiP where @bhandsaker can help you.
    -Sheila

  • @Sheila

    would you please suggest me that i ran SV discovery and it ran well but in the end it did not generate final output and when i saw the log file it showed -

    INFO 16:45:51,118 QCommandLine - Scripting SVDiscovery
    INFO 16:45:53,204 QCommandLine - Added 10 functions
    INFO 16:45:53,206 QGraph - Generating graph.
    INFO 16:45:53,222 QGraph - Running jobs.
    INFO 16:45:54,775 FunctionEdge - Starting: 'java' '-Xmx4096m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work/dlakhwani/strip/.queue/tmp' '-cp' '/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/SVToolkit.jar:/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVDiscovery '-T' 'SVDiscoveryWalker' '-R' '/work/dlakhwani/mapping/rose-genome.fa' '-I' '/work/dlakhwani/bamdata/DG/DG-markduplicate.bam' '-O' '/work/dlakhwani/strip/P0001.discovery.vcf.gz' '-disableGATKTraversal' 'true' '-md' '/work/dlakhwani/mapping/' '-configFile' '/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/conf/genstrip_parameters.txt' '-genderMapFile' 'gender.txt' '-partitionName' 'P0001' '-runFilePrefix' 'P0001' -L Chr01:1-64770848 -searchLocus Chr01:1-64770848 -searchWindow Chr01:1-64770848
    INFO 16:45:54,775 FunctionEdge - Output written to /work/dlakhwani/strip/SVDiscovery-1.out
    INFO 18:18:13,283 FunctionEdge - Starting: 'java' '-Xmx4096m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work/dlakhwani/strip/.queue/tmp' '-cp' '/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/SVToolkit.jar:/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVDiscovery '-T' 'SVDiscoveryWalker' '-R' '/work/dlakhwani/mapping/rose-genome.fa' '-I' '/work/dlakhwani/bamdata/DG/DG-markduplicate.bam' '-O' '/work/dlakhwani/strip/P0002.discovery.vcf.gz' '-disableGATKTraversal' 'true' '-md' '/work/dlakhwani/mapping/' '-configFile' '/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/conf/genstrip_parameters.txt' '-genderMapFile' 'gender.txt' '-partitionName' 'P0002' '-runFilePrefix' 'P0002' -L Chr00:1-52404850 -searchLocus Chr00:1-52404850 -searchWindow Chr00:1-52404850
    INFO 18:18:13,286 FunctionEdge - Output written to /work/dlakhwani/strip/SVDiscovery-2.out
    INFO 18:35:55,349 FunctionEdge - Starting: 'java' '-Xmx4096m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work/dlakhwani/strip/.queue/tmp' '-cp' '/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/SVToolkit.jar:/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVDiscovery '-T' 'SVDiscoveryWalker' '-R' '/work/dlakhwani/mapping/rose-genome.fa' '-I' '/work/dlakhwani/bamdata/DG/DG-markduplicate.bam' '-O' '/work/dlakhwani/strip/P0003.discovery.vcf.gz' '-disableGATKTraversal' 'true' '-md' '/work/dlakhwani/mapping/' '-configFile' '/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/conf/genstrip_parameters.txt' '-genderMapFile' 'gender.txt' '-partitionName' 'P0003' '-runFilePrefix' 'P0003' -L Chr03:1-46843630 -searchLocus Chr03:1-46843630 -searchWindow Chr03:1-46843630
    INFO 18:35:55,350 FunctionEdge - Output written to /work/dlakhwani/strip/SVDiscovery-3.out
    INFO 19:05:55,603 FunctionEdge - Starting: 'java' '-Xmx4096m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work/dlakhwani/strip/.queue/tmp' '-cp' '/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/SVToolkit.jar:/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVDiscovery '-T' 'SVDiscoveryWalker' '-R' '/work/dlakhwani/mapping/rose-genome.fa' '-I' '/work/dlakhwani/bamdata/DG/DG-markduplicate.bam' '-O' '/work/dlakhwani/strip/P0004.discovery.vcf.gz' '-disableGATKTraversal' 'true' '-md' '/work/dlakhwani/mapping/' '-configFile' '/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/conf/genstrip_parameters.txt' '-genderMapFile' 'gender.txt' '-partitionName' 'P0004' '-runFilePrefix' 'P0004' -L Chr02:1-75129302 -searchLocus Chr02:1-75129302 -searchWindow Chr02:1-75129302
    INFO 19:05:55,604 FunctionEdge - Output written to /work/dlakhwani/strip/SVDiscovery-4.out
    INFO 20:41:27,049 FunctionEdge - Starting: 'java' '-Xmx4096m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work/dlakhwani/strip/.queue/tmp' '-cp' '/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/SVToolkit.jar:/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVDiscovery '-T' 'SVDiscoveryWalker' '-R' '/work/dlakhwani/mapping/rose-genome.fa' '-I' '/work/dlakhwani/bamdata/DG/DG-markduplicate.bam' '-O' '/work/dlakhwani/strip/P0005.discovery.vcf.gz' '-disableGATKTraversal' 'true' '-md' '/work/dlakhwani/mapping/' '-configFile' '/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/conf/genstrip_parameters.txt' '-genderMapFile' 'gender.txt' '-partitionName' 'P0005' '-runFilePrefix' 'P0005' -L Chr05:1-85885663 -searchLocus Chr05:1-85885663 -searchWindow Chr05:1-85885663
    INFO 20:41:27,049 FunctionEdge - Output written to /work/dlakhwani/strip/SVDiscovery-5.out
    INFO 23:04:23,203 FunctionEdge - Starting: 'java' '-Xmx4096m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work/dlakhwani/strip/.queue/tmp' '-cp' '/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/SVToolkit.jar:/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVDiscovery '-T' 'SVDiscoveryWalker' '-R' '/work/dlakhwani/mapping/rose-genome.fa' '-I' '/work/dlakhwani/bamdata/DG/DG-markduplicate.bam' '-O' '/work/dlakhwani/strip/P0006.discovery.vcf.gz' '-disableGATKTraversal' 'true' '-md' '/work/dlakhwani/mapping/' '-configFile' '/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/conf/genstrip_parameters.txt' '-genderMapFile' 'gender.txt' '-partitionName' 'P0006' '-runFilePrefix' 'P0006' -L Chr04:1-59004735 -searchLocus Chr04:1-59004735 -searchWindow Chr04:1-59004735
    INFO 23:04:23,203 FunctionEdge - Output written to /work/dlakhwani/strip/SVDiscovery-6.out
    INFO 00:00:54,474 FunctionEdge - Starting: 'java' '-Xmx4096m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work/dlakhwani/strip/.queue/tmp' '-cp' '/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/SVToolkit.jar:/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVDiscovery '-T' 'SVDiscoveryWalker' '-R' '/work/dlakhwani/mapping/rose-genome.fa' '-I' '/work/dlakhwani/bamdata/DG/DG-markduplicate.bam' '-O' '/work/dlakhwani/strip/P0007.discovery.vcf.gz' '-disableGATKTraversal' 'true' '-md' '/work/dlakhwani/mapping/' '-configFile' '/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/conf/genstrip_parameters.txt' '-genderMapFile' 'gender.txt' '-partitionName' 'P0007' '-runFilePrefix' 'P0007' -L Chr07:1-67081725 -searchLocus Chr07:1-67081725 -searchWindow Chr07:1-67081725
    INFO 00:00:54,474 FunctionEdge - Output written to /work/dlakhwani/strip/SVDiscovery-7.out
    INFO 01:14:47,355 FunctionEdge - Starting: 'java' '-Xmx4096m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work/dlakhwani/strip/.queue/tmp' '-cp' '/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/SVToolkit.jar:/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVDiscovery '-T' 'SVDiscoveryWalker' '-R' '/work/dlakhwani/mapping/rose-genome.fa' '-I' '/work/dlakhwani/bamdata/DG/DG-markduplicate.bam' '-O' '/work/dlakhwani/strip/P0008.discovery.vcf.gz' '-disableGATKTraversal' 'true' '-md' '/work/dlakhwani/mapping/' '-configFile' '/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/conf/genstrip_parameters.txt' '-genderMapFile' 'gender.txt' '-partitionName' 'P0008' '-runFilePrefix' 'P0008' -L Chr06:1-67395200 -searchLocus Chr06:1-67395200 -searchWindow Chr06:1-67395200
    INFO 01:14:47,381 FunctionEdge - Output written to /work/dlakhwani/strip/SVDiscovery-8.out
    INFO 02:28:42,236 QGraph - 2 Pend, 8 Run, 0 Fail, 0 Done
    INFO 02:28:42,247 FunctionEdge - Done: 'java' '-Xmx4096m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work/dlakhwani/strip/.queue/tmp' '-cp' '/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/SVToolkit.jar:/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVDiscovery '-T' 'SVDiscoveryWalker' '-R' '/work/dlakhwani/mapping/rose-genome.fa' '-I' '/work/dlakhwani/bamdata/DG/DG-markduplicate.bam' '-O' '/work/dlakhwani/strip/P0005.discovery.vcf.gz' '-disableGATKTraversal' 'true' '-md' '/work/dlakhwani/mapping/' '-configFile' '/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/conf/genstrip_parameters.txt' '-genderMapFile' 'gender.txt' '-partitionName' 'P0005' '-runFilePrefix' 'P0005' -L Chr05:1-85885663 -searchLocus Chr05:1-85885663 -searchWindow Chr05:1-85885663
    ERROR 02:28:42,250 FunctionEdge - Error: 'java' '-Xmx4096m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work/dlakhwani/strip/.queue/tmp' '-cp' '/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/SVToolkit.jar:/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVDiscovery '-T' 'SVDiscoveryWalker' '-R' '/work/dlakhwani/mapping/rose-genome.fa' '-I' '/work/dlakhwani/bamdata/DG/DG-markduplicate.bam' '-O' '/work/dlakhwani/strip/P0001.discovery.vcf.gz' '-disableGATKTraversal' 'true' '-md' '/work/dlakhwani/mapping/' '-configFile' '/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/conf/genstrip_parameters.txt' '-genderMapFile' 'gender.txt' '-partitionName' 'P0001' '-runFilePrefix' 'P0001' -L Chr01:1-64770848 -searchLocus Chr01:1-64770848 -searchWindow Chr01:1-64770848
    ERROR 02:28:42,370 FunctionEdge - Contents of /work/dlakhwani/strip/SVDiscovery-1.out:
    INFO 18:18:04,937 30-Oct-2017 SVDiscovery - Clustering: LR split size 21 / 21 maximal clique size 17 clique count 1
    INFO 18:18:04,937 30-Oct-2017 SVDiscovery - Clustering: LR split size 4 / 21 maximal clique size 4 clique count 1
    INFO 18:18:04,937 30-Oct-2017 SVDiscovery - Processing cluster Chr01:63633485-63634003 Chr01:63664029-63664331 LR 3
    INFO 18:18:05,075 30-Oct-2017 SVDiscovery - Processing cluster Chr01:63668491-63668698 Chr01:63729896-63730399 LR 8
    INFO 18:18:05,220 30-Oct-2017 SVDiscovery - Processing cluster Chr01:63668474-63670053 Chr01:63735309-63736870 LR 5
    INFO 18:18:05,367 30-Oct-2017 SVDiscovery - Processing cluster Chr01:63671171-63671439 Chr01:63752934-63753519 LR 4
    INFO 18:18:05,512 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 2 read pairs.
    INFO 18:18:05,512 30-Oct-2017 SVDiscovery - Processing cluster Chr01:63672499-63673378 Chr01:63754458-63755076 LR 17
    INFO 18:18:05,661 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 4 read pairs.
    INFO 18:18:05,661 30-Oct-2017 SVDiscovery - Processing cluster Chr01:63677156-63677300 Chr01:63729306-63729461 LR 2
    INFO 18:18:05,803 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 4 read pairs.
    INFO 18:18:05,803 30-Oct-2017 SVDiscovery - Processing cluster Chr01:63682071-63683398 Chr01:63751515-63752608 LR 4
    INFO 18:18:05,946 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 16 read pairs.
    INFO 18:18:05,946 30-Oct-2017 SVDiscovery - Clustering: LR split size 16 / 16 maximal clique size 11 clique count 1
    INFO 18:18:05,946 30-Oct-2017 SVDiscovery - Clustering: LR split size 5 / 16 maximal clique size 4 clique count 1
    INFO 18:18:05,949 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 2 read pairs.
    INFO 18:18:05,949 30-Oct-2017 SVDiscovery - Processing cluster Chr01:63690986-63691657 Chr01:63698537-63699189 LR 4
    INFO 18:18:06,088 30-Oct-2017 SVDiscovery - Processing cluster Chr01:63702315-63702501 Chr01:63751472-63751685 LR 4
    INFO 18:18:06,229 30-Oct-2017 SVDiscovery - Processing cluster Chr01:63702376-63702594 Chr01:63712408-63712578 LR 2
    INFO 18:18:06,365 30-Oct-2017 SVDiscovery - Progress: processed 8400 clusters ...
    INFO 18:18:06,368 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 3 read pairs.
    INFO 18:18:06,368 30-Oct-2017 SVDiscovery - Processing cluster Chr01:63703089-63704589 Chr01:63752414-63753927 LR 11
    INFO 18:18:06,513 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 22 read pairs.
    INFO 18:18:06,513 30-Oct-2017 SVDiscovery - Processing cluster Chr01:63713319-63713496 Chr01:63753576-63753992 LR 3
    INFO 18:18:06,652 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 3 read pairs.
    INFO 18:18:06,657 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 2 read pairs.
    INFO 18:18:06,657 30-Oct-2017 SVDiscovery - Processing cluster Chr01:63716142-63716468 Chr01:63721620-63722565 LR 22
    INFO 18:18:06,807 30-Oct-2017 SVDiscovery - Processing cluster Chr01:63730179-63730379 Chr01:63736354-63736745 LR 3
    INFO 18:18:06,945 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 2 read pairs.
    INFO 18:18:06,945 30-Oct-2017 SVDiscovery - Processing cluster Chr01:63731107-63731216 Chr01:63752433-63752606 LR 2
    INFO 18:18:07,085 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 21 read pairs.
    INFO 18:18:07,086 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 6 read pairs.
    INFO 18:18:07,086 30-Oct-2017 SVDiscovery - Processing cluster Chr01:63736748-63736870 Chr01:63752455-63752639 LR 2
    INFO 18:18:07,226 30-Oct-2017 SVDiscovery - Processing cluster Chr01:63808741-63809342 Chr01:63864164-63864374 LR 21
    INFO 18:18:07,375 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 11 read pairs.
    INFO 18:18:07,376 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 2 read pairs.
    INFO 18:18:07,376 30-Oct-2017 SVDiscovery - Processing cluster Chr01:63809304-63809508 Chr01:63854596-63854777 LR 6
    INFO 18:18:07,517 30-Oct-2017 SVDiscovery - Processing cluster Chr01:63831257-63831560 Chr01:63894259-63895003 LR 11
    INFO 18:18:07,660 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 5 read pairs.
    INFO 18:18:07,662 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 2 read pairs.
    INFO 18:18:07,662 30-Oct-2017 SVDiscovery - Processing cluster Chr01:63831558-63831662 Chr01:63859640-63859806 LR 2
    INFO 18:18:07,807 30-Oct-2017 SVDiscovery - Processing cluster Chr01:63850294-63850387 Chr01:63866098-63866560 LR 5
    INFO 18:18:07,946 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 9 read pairs.
    INFO 18:18:07,946 30-Oct-2017 SVDiscovery - Processing cluster Chr01:63851701-63851962 Chr01:64342702-64342772 LR 2
    INFO 18:18:08,123 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 124 read pairs.
    INFO 18:18:08,123 30-Oct-2017 SVDiscovery - Processing cluster Chr01:63858620-63858834 Chr01:63894331-63895149 LR 9
    INFO 18:18:08,269 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 7 read pairs.
    INFO 18:18:08,269 30-Oct-2017 SVDiscovery - Processing cluster Chr01:63896666-63897717 Chr01:63905898-63906925 LR 124
    INFO 18:18:08,457 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 47 read pairs.
    INFO 18:18:08,458 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 6 read pairs.
    INFO 18:18:08,458 30-Oct-2017 SVDiscovery - Clustering: LR split size 6 / 6 maximal clique size 4 clique count 2
    INFO 18:18:08,458 30-Oct-2017 SVDiscovery - Processing cluster Chr01:64063013-64063245 Chr01:64068001-64068542 LR 7
    INFO 18:18:08,599 30-Oct-2017 SVDiscovery - Processing cluster Chr01:64068106-64069714 Chr01:64083118-64084709 LR 47
    INFO 18:18:08,758 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 20 read pairs.
    INFO 18:18:08,758 30-Oct-2017 SVDiscovery - Processing cluster Chr01:64071372-64072280 Chr01:64090472-64091174 LR 4
    INFO 18:18:08,899 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 3 read pairs.
    INFO 18:18:08,899 30-Oct-2017 SVDiscovery - Processing cluster Chr01:64084069-64085892 Chr01:64089167-64090704 LR 20
    INFO 18:18:09,044 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 9 read pairs.
    INFO 18:18:09,044 30-Oct-2017 SVDiscovery - Processing cluster Chr01:64110638-64110888 Chr01:64118967-64119180 LR 3
    INFO 18:18:09,196 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 50 read pairs.
    INFO 18:18:09,196 30-Oct-2017 SVDiscovery - Clustering: LR split size 50 / 50 maximal clique size 48 clique count 1
    INFO 18:18:09,196 30-Oct-2017 SVDiscovery - Processing cluster Chr01:64223905-64224254 Chr01:64230300-64230616 LR 9
    INFO 18:18:09,342 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 50 read pairs.
    INFO 18:18:09,342 30-Oct-2017 SVDiscovery - Clustering: LR split size 50 / 50 maximal clique size 32 clique count 1
    INFO 18:18:09,342 30-Oct-2017 SVDiscovery - Clustering: LR split size 18 / 50 maximal clique size 17 clique count 1
    INFO 18:18:09,342 30-Oct-2017 SVDiscovery - Processing cluster Chr01:64226958-64227792 Chr01:64255236-64256346 LR 48
    INFO 18:18:09,498 30-Oct-2017 SVDiscovery - Processing cluster Chr01:64248064-64248310 Chr01:64255236-64255717 LR 17
    INFO 18:18:09,648 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 160 read pairs.
    INFO 18:18:09,649 30-Oct-2017 SVDiscovery - Processing cluster Chr01:64248653-64249014 Chr01:64253811-64255327 LR 32
    INFO 18:18:09,799 30-Oct-2017 ProgressMeter - Starting 0.0 92.2 m 9143.8 w 100.0% 92.2 m 0.0 s
    INFO 18:18:09,799 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 109 read pairs.
    INFO 18:18:09,799 30-Oct-2017 SVDiscovery - Processing cluster Chr01:64267820-64268862 Chr01:64279262-64280321 LR 160
    INFO 18:18:10,003 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 88 read pairs.
    INFO 18:18:10,005 30-Oct-2017 SVDiscovery - Clustering: LR split size 88 / 88 maximal clique size 71 clique count 1
    INFO 18:18:10,005 30-Oct-2017 SVDiscovery - Clustering: LR split size 17 / 88 maximal clique size 11 clique count 1
    INFO 18:18:10,005 30-Oct-2017 SVDiscovery - Clustering: LR split size 6 / 88 maximal clique size 6 clique count 1
    INFO 18:18:10,005 30-Oct-2017 SVDiscovery - Processing cluster Chr01:64296035-64296874 Chr01:64304109-64305003 LR 109
    INFO 18:18:10,183 30-Oct-2017 SVDiscovery - Processing cluster Chr01:64307682-64307853 Chr01:64318696-64319106 LR 6
    INFO 18:18:10,322 30-Oct-2017 SVDiscovery - Processing cluster Chr01:64308599-64308905 Chr01:64317833-64318195 LR 11
    INFO 18:18:10,464 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 79 read pairs.
    INFO 18:18:10,464 30-Oct-2017 SVDiscovery - Processing cluster Chr01:64307691-64308906 Chr01:64320449-64321350 LR 71
    INFO 18:18:10,632 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 17 read pairs.
    INFO 18:18:10,632 30-Oct-2017 SVDiscovery - Processing cluster Chr01:64394958-64396034 Chr01:64404435-64405612 LR 79
    INFO 18:18:10,801 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 22 read pairs.
    INFO 18:18:10,801 30-Oct-2017 SVDiscovery - Processing cluster Chr01:64413744-64414228 Chr01:64419406-64420313 LR 17
    INFO 18:18:10,947 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 124 read pairs.
    INFO 18:18:10,948 30-Oct-2017 SVDiscovery - Processing cluster Chr01:64435686-64437432 Chr01:64445460-64446861 LR 22
    INFO 18:18:11,092 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 20 read pairs.
    INFO 18:18:11,094 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 2 read pairs.
    INFO 18:18:11,094 30-Oct-2017 SVDiscovery - Processing cluster Chr01:64512109-64513252 Chr01:64525603-64526602 LR 124
    INFO 18:18:11,279 30-Oct-2017 SVDiscovery - Processing cluster Chr01:64607501-64607629 Chr01:64617373-64617516 LR 2
    INFO 18:18:11,423 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 67 read pairs.
    INFO 18:18:11,423 30-Oct-2017 SVDiscovery - Processing cluster Chr01:64606993-64607962 Chr01:64619172-64619386 LR 20
    INFO 18:18:11,568 30-Oct-2017 SVDiscovery - Clustering: Generating clusters for 5 read pairs.
    INFO 18:18:11,568 30-Oct-2017 SVDiscovery - Processing cluster Chr01:64619216-64619730 Chr01:64635205-64635897 LR 67
    INFO 18:18:11,737 30-Oct-2017 SVDiscovery - Processing cluster Chr01:64638289-64638343 Chr01:64646544-64647176 LR 5
    INFO 18:18:11,876 30-Oct-2017 SVDiscovery - Processed 8436 clusters.
    INFO 18:18:11,893 30-Oct-2017 ProgressMeter - done 0.0 92.2 m 9147.2 w 100.0% 92.2 m 0.0 s
    INFO 18:18:11,893 30-Oct-2017 ProgressMeter - Total runtime 5532.24 secs, 92.20 min, 1.54 hours
    INFO 18:18:13,229 30-Oct-2017 GATKRunReport - Uploaded run statistics report to AWS S3
    INFO 02:28:42,374 FunctionEdge - Done: 'java' '-Xmx4096m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work/dlakhwani/strip/.queue/tmp' '-cp' '/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/SVToolkit.jar:/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVDiscovery '-T' 'SVDiscoveryWalker' '-R' '/work/dlakhwani/mapping/rose-genome.fa' '-I' '/work/dlakhwani/bamdata/DG/DG-markduplicate.bam' '-O' '/work/dlakhwani/strip/P0006.discovery.vcf.gz' '-disableGATKTraversal' 'true' '-md' '/work/dlakhwani/mapping/' '-configFile' '/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/conf/genstrip_parameters.txt' '-genderMapFile' 'gender.txt' '-partitionName' 'P0006' '-runFilePrefix' 'P0006' -L Chr04:1-59004735 -searchLocus Chr04:1-59004735 -searchWindow Chr04:1-59004735
    INFO 02:28:42,376 FunctionEdge - Done: 'java' '-Xmx4096m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work/dlakhwani/strip/.queue/tmp' '-cp' '/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/SVToolkit.jar:/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVDiscovery '-T' 'SVDiscoveryWalker' '-R' '/work/dlakhwani/mapping/rose-genome.fa' '-I' '/work/dlakhwani/bamdata/DG/DG-markduplicate.bam' '-O' '/work/dlakhwani/strip/P0002.discovery.vcf.gz' '-disableGATKTraversal' 'true' '-md' '/work/dlakhwani/mapping/' '-configFile' '/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/conf/genstrip_parameters.txt' '-genderMapFile' 'gender.txt' '-partitionName' 'P0002' '-runFilePrefix' 'P0002' -L Chr00:1-52404850 -searchLocus Chr00:1-52404850 -searchWindow Chr00:1-52404850
    INFO 02:28:42,378 FunctionEdge - Done: 'java' '-Xmx4096m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work/dlakhwani/strip/.queue/tmp' '-cp' '/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/SVToolkit.jar:/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVDiscovery '-T' 'SVDiscoveryWalker' '-R' '/work/dlakhwani/mapping/rose-genome.fa' '-I' '/work/dlakhwani/bamdata/DG/DG-markduplicate.bam' '-O' '/work/dlakhwani/strip/P0007.discovery.vcf.gz' '-disableGATKTraversal' 'true' '-md' '/work/dlakhwani/mapping/' '-configFile' '/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/conf/genstrip_parameters.txt' '-genderMapFile' 'gender.txt' '-partitionName' 'P0007' '-runFilePrefix' 'P0007' -L Chr07:1-67081725 -searchLocus Chr07:1-67081725 -searchWindow Chr07:1-67081725
    INFO 02:28:42,380 FunctionEdge - Done: 'java' '-Xmx4096m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work/dlakhwani/strip/.queue/tmp' '-cp' '/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/SVToolkit.jar:/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVDiscovery '-T' 'SVDiscoveryWalker' '-R' '/work/dlakhwani/mapping/rose-genome.fa' '-I' '/work/dlakhwani/bamdata/DG/DG-markduplicate.bam' '-O' '/work/dlakhwani/strip/P0003.discovery.vcf.gz' '-disableGATKTraversal' 'true' '-md' '/work/dlakhwani/mapping/' '-configFile' '/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/conf/genstrip_parameters.txt' '-genderMapFile' 'gender.txt' '-partitionName' 'P0003' '-runFilePrefix' 'P0003' -L Chr03:1-46843630 -searchLocus Chr03:1-46843630 -searchWindow Chr03:1-46843630
    INFO 02:28:42,381 FunctionEdge - Done: 'java' '-Xmx4096m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work/dlakhwani/strip/.queue/tmp' '-cp' '/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/SVToolkit.jar:/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVDiscovery '-T' 'SVDiscoveryWalker' '-R' '/work/dlakhwani/mapping/rose-genome.fa' '-I' '/work/dlakhwani/bamdata/DG/DG-markduplicate.bam' '-O' '/work/dlakhwani/strip/P0008.discovery.vcf.gz' '-disableGATKTraversal' 'true' '-md' '/work/dlakhwani/mapping/' '-configFile' '/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/conf/genstrip_parameters.txt' '-genderMapFile' 'gender.txt' '-partitionName' 'P0008' '-runFilePrefix' 'P0008' -L Chr06:1-67395200 -searchLocus Chr06:1-67395200 -searchWindow Chr06:1-67395200
    INFO 02:28:42,383 FunctionEdge - Done: 'java' '-Xmx4096m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work/dlakhwani/strip/.queue/tmp' '-cp' '/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/SVToolkit.jar:/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVDiscovery '-T' 'SVDiscoveryWalker' '-R' '/work/dlakhwani/mapping/rose-genome.fa' '-I' '/work/dlakhwani/bamdata/DG/DG-markduplicate.bam' '-O' '/work/dlakhwani/strip/P0004.discovery.vcf.gz' '-disableGATKTraversal' 'true' '-md' '/work/dlakhwani/mapping/' '-configFile' '/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/conf/genstrip_parameters.txt' '-genderMapFile' 'gender.txt' '-partitionName' 'P0004' '-runFilePrefix' 'P0004' -L Chr02:1-75129302 -searchLocus Chr02:1-75129302 -searchWindow Chr02:1-75129302
    INFO 02:28:42,384 QGraph - Writing incremental jobs reports...
    INFO 02:28:42,384 QJobsReporter - Writing JobLogging GATKReport to file /work/dlakhwani/strip/SVDiscovery.jobreport.txt
    INFO 02:28:42,406 QGraph - 2 Pend, 0 Run, 1 Fail, 7 Done
    INFO 02:28:42,406 QCommandLine - Writing final jobs report...
    INFO 02:28:42,407 QJobsReporter - Writing JobLogging GATKReport to file /work/dlakhwani/strip/SVDiscovery.jobreport.txt
    INFO 02:28:42,414 QJobsReporter - Plotting JobLogging GATKReport to file /work/dlakhwani/strip/SVDiscovery.jobreport.pdf
    INFO 02:28:50,653 QCommandLine - Done with errors
    INFO 02:28:50,655 QGraph - -------
    INFO 02:28:50,656 QGraph - Failed: 'java' '-Xmx4096m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work/dlakhwani/strip/.queue/tmp' '-cp' '/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/SVToolkit.jar:/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVDiscovery '-T' 'SVDiscoveryWalker' '-R' '/work/dlakhwani/mapping/rose-genome.fa' '-I' '/work/dlakhwani/bamdata/DG/DG-markduplicate.bam' '-O' '/work/dlakhwani/strip/P0001.discovery.vcf.gz' '-disableGATKTraversal' 'true' '-md' '/work/dlakhwani/mapping/' '-configFile' '/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/conf/genstrip_parameters.txt' '-genderMapFile' 'gender.txt' '-partitionName' 'P0001' '-runFilePrefix' 'P0001' -L Chr01:1-64770848 -searchLocus Chr01:1-64770848 -searchWindow Chr01:1-64770848
    INFO 02:28:50,657 QGraph - Log: /work/dlakhwani/strip/SVDiscovery-1.out
    INFO 02:28:50,657 QCommandLine - Script failed: 2 Pend, 0 Run, 1 Fail, 7 Done

    The command is used for that ----
    java -Xmx8g -cp ${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar:${SV_DIR}/lib/gatk/Queue.jar org.broadinstitute.gatk.queue.QCommandLine -S ${SV_DIR}/qscript/SVDiscovery.q -S ${SV_DIR}/qscript/SVQScript.q -cp /usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/SVToolkit.jar:/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/Queue.jar -gatk /usr/local/bioinfo/src/genomeSTRIP/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -R /work/dlakhwani/mapping/rose-genome.fa -configFile /usr/local/bioinfo/src/genomeSTRIP/svtoolkit/conf/genstrip_parameters.txt -I /work/dlakhwani/bamdata/DG/DG-markduplicate.bam -md /work/dlakhwani/mapping/ -O mark.del.vcf -genderMapFile gender.txt -run

    can you please resolve my problem.

  • bhandsakerbhandsaker Member, Broadie, Moderator

    It looks like you solved the gender map problem (you should not need to supply one).

    The second problem is something that happens with Queue and some cluster management systems: It looks like the job that was run completed successfully, but Queue either lost the job status or thought the job failed for some reason. If you rerun, Queue will retry the failed job and it will likely complete just fine.

  • @bhandsaker ..no i did not solve the gender map problem..would you please tell me what should i use gendermap file for plants ???

  • bhandsakerbhandsaker Member, Broadie, Moderator

    You should not need to supply one. Presumably you are supplying a ploidy map that does not define any regions of sex specific ploidy.

Sign In or Register to comment.