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No gender data for sample

February 11, 2015, 7:30 am
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Hi!
I am trying to run the SVToolkit.2.00.1533 on rice ,which is a self-pollinated pants and has no genders.I got an error for" No gender data for sample".

Because my samples ,rice, a self-pollinated pants and has no genders. I edit the related files like this.

input_bam_files_gender.map:

LGW1.reheader 1
LGW2.reheader 1
LGW3.reheader 1

............

rice7_reference.ploidymap.txt:

* * * * 2

rice7_reference_rdmask.bed:

chr01 1 43270923
chr02 1 35937250
chr03 1 36413819
chr04 1 35502694
chr05 1 29958434
chr06 1 31248787
chr07 1 29697621
chr08 1 28443022
chr09 1 23012720
chr10 1 23207287
chr11 1 29021106

chr12 1 27531856

There is a part of my log files.

INFO 22:22:30,326 SVDiscovery - Initializing SVDiscovery ...
INFO 22:22:30,327 SVDiscovery - Reading configuration file ...
INFO 22:22:30,336 SVDiscovery - Read configuration file.
INFO 22:22:30,336 SVDiscovery - Opening reference sequence ...
INFO 22:22:30,338 SVDiscovery - Opened reference sequence.
INFO 22:22:30,339 SVDiscovery - Opening genome mask ...
INFO 22:22:30,341 SVDiscovery - Opened genome mask.
INFO 22:22:30,341 SVDiscovery - Initializing input data set ...
INFO 22:22:30,393 SVDiscovery - Initialized data set: 3 files, 66 read groups, 3 samples.
INFO 22:22:30,395 MetaData - Opening metadata ...
INFO 22:22:30,396 MetaData - Adding metadata directory rice_discovery/metadata ...
INFO 22:22:30,398 MetaData - Opened metadata.
INFO 22:22:30,402 SVDiscovery - Opened metadata.
INFO 22:22:30,415 MetaData - Loading insert size distributions ...
INFO 22:22:30,447 SVDiscovery - Discovery alt home filtering is disabled.
INFO 22:22:30,503 SVDiscovery - Processing locus: chr01:0-0:100-1000000
INFO 22:22:30,504 SVDiscovery - Locus search window: chr01:0-0
INFO 22:23:00,334 ProgressMeter - Starting 0.0 30.0 s 49.6 w 100.0% 30.0 s 0.0 s
INFO 22:23:30,336 ProgressMeter - Starting 0.0 60.0 s 99.2 w 100.0% 60.0 s 0.0 s
INFO 22:24:00,338 ProgressMeter - Starting 0.0 90.0 s 148.8 w 100.0% 90.0 s 0.0 s
INFO 22:24:30,340 ProgressMeter - Starting 0.0 120.0 s 198.4 w 100.0% 120.0 s 0.0 s
INFO 22:25:00,341 ProgressMeter - Starting 0.0 2.5 m 248.0 w 100.0% 2.5 m 0.0 s
INFO 22:25:30,343 ProgressMeter - Starting 0.0 3.0 m 297.6 w 100.0% 3.0 m 0.0 s
INFO 22:26:00,344 ProgressMeter - Starting 0.0 3.5 m 347.3 w 100.0% 3.5 m 0.0 s
INFO 22:26:30,346 ProgressMeter - Starting 0.0 4.0 m 396.9 w 100.0% 4.0 m 0.0 s
INFO 22:27:00,354 ProgressMeter - Starting 0.0 4.5 m 446.5 w 100.0% 4.5 m 0.0 s
INFO 22:27:30,356 ProgressMeter - Starting 0.0 5.0 m 496.1 w 100.0% 5.0 m 0.0 s
INFO 22:28:00,372 ProgressMeter - Starting 0.0 5.5 m 545.7 w 100.0% 5.5 m 0.0 s

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.RuntimeException: No gender data for sample: LGW1
at org.broadinstitute.sv.discovery.ClusterMembershipModule.init(ClusterMembershipModule.java:180)
at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.createMembershipModule(DeletionDiscoveryAlgorithm.java:
1047)
at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.initClusterModules(DeletionDiscoveryAlgorithm.java:992)
at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processClusters(DeletionDiscoveryAlgorithm.java:325)
at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.runDiscovery(DeletionDiscoveryAlgorithm.java:192)
at org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:109)
at org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:42)
at org.broadinstitute.gatk.engine.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:116)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:319)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:125)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:79)
at org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version ):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: No gender data for sample: LGW1
ERROR ------------------------------------------------------------------------------------------

INFO 22:28:39,463 QGraph - Writing incremental jobs reports...
INFO 22:28:39,464 QGraph - 1 Pend, 0 Run, 1 Fail, 0 Done
INFO 22:28:39,467 QCommandLine - Writing final jobs report...
INFO 22:28:39,468 QCommandLine - Done with errors
INFO 22:28:39,471 QGraph - -------
INFO 22:28:39,474 QGraph - Failed: 'java' '-Xmx4096m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/home/ligw/tools/svtoolkit2.1553/svtoolkit/worktest/tmpdir.rice' '-cp' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/SVToolkit.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVDiscovery '-T' 'SVDiscoveryWalker' '-R' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/worktest/data/rice7_reference.fasta' '-I' 'data/input_bam_files.list' '-O' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/worktest/rice_discovery/rice1.discovery.unfiltered.vcf' '-disableGATKTraversal' 'true' '-md' 'rice_discovery/metadata' '-configFile' 'conf/genstrip_installtest_parameters.txt' '-P' 'select.validateReadPairs:false' '-runDirectory' 'rice_discovery' '-genderMapFile' 'data/input_bam_files_gender.map' '-genomeMaskFile' 'data/rice7_reference_svmask.fasta' '-L' 'chr01' '-runFilePrefix' 'rice1' '-searchLocus' 'chr01' '-searchWindow' 'chr01' '-searchMinimumSize' '100' '-searchMaximumSize' '1000000'
INFO 22:28:39,475 QGraph - Log: /home/ligw/tools/svtoolkit2.1553/svtoolkit/worktest/rice_discovery/logs/SVDiscovery-1.out

INFO 22:28:39,476 QCommandLine - Script failed: 1 Pend, 0 Run, 1 Fail, 0 Done

My script is based on installtest/discovery.sh as below

java -cp ${classpath} ${mx} \
org.broadinstitute.gatk.queue.QCommandLine \
-S ${SV_DIR}/qscript/SVPreprocess.q \
-S ${SV_DIR}/qscript/SVQScript.q \
-gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
--disableJobReport \
-cp ${classpath} \
-configFile conf/genstrip_installtest_parameters.txt \
-tempDir ${SV_TMPDIR} \
-R data/rice7_reference.fasta \
-genomeMaskFile data/rice7_reference_svmask.fasta \
-readDepthMaskFile data/rice7_reference_rdmask.bed \
-genderMapFile data/input_bam_files_gender.map \
-runDirectory ${runDir} \
-md ${runDir}/metadata \
-disableGATKTraversal \
-useMultiStep \
-L chr01 \
-reduceInsertSizeDistributions true \
-computeReadCounts true \
-computeGCProfiles true \
-jobLogDir ${runDir}/logs \
-I ${bam} \
-run \
|| exit 1

Run discovery.

java -cp ${classpath} ${mx} \
org.broadinstitute.gatk.queue.QCommandLine \
-S ${SV_DIR}/qscript/SVDiscovery.q \
-S ${SV_DIR}/qscript/SVQScript.q \
-gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
--disableJobReport \
-cp ${classpath} \
-configFile conf/genstrip_installtest_parameters.txt \
-tempDir ${SV_TMPDIR} \
-R data/rice7_reference.fasta \
-genomeMaskFile data/rice7_reference_svmask.fasta \
-genderMapFile data/input_bam_files_gender.map \
-runDirectory ${runDir} \
-P select.validateReadPairs:false \
-md ${runDir}/metadata \
-disableGATKTraversal \
-L chr01 \
-jobLogDir ${runDir}/logs \
-minimumSize 100 \
-maximumSize 1000000 \
-suppressVCFCommandLines \
-I ${bam} \
-O ${sites} \
-run \
|| exit 1

(grep -v ^##fileDate= ${sites} | grep -v ^##source= | grep -v ^##reference= | diff -q - benchmark/${sites}) \
|| { echo "Error: test results do not match benchmark data"; exit 1; }

Run genotyping on the discovered sites.

java -cp ${classpath} ${mx} \
org.broadinstitute.gatk.queue.QCommandLine \
-S ${SV_DIR}/qscript/SVGenotyper.q \
-S ${SV_DIR}/qscript/SVQScript.q \
-gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
--disableJobReport \
-cp ${classpath} \
-configFile conf/genstrip_installtest_parameters.txt \
-tempDir ${SV_TMPDIR} \
-R data/rice7_reference.fasta \
-genomeMaskFile data/rice7_reference_svmask.fasta \
-genderMapFile data/input_bam_files_gender.map \
-runDirectory ${runDir} \
-md ${runDir}/metadata \
-disableGATKTraversal \
-jobLogDir ${runDir}/logs \
-I ${bam} \
-vcf ${sites} \
-O ${genotypes} \
-run \
|| exit 1

How can I do with the no gender organism? Many thanks!

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