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Can't run GenomeSTRiP with "ploidyMapFile", "copyNumberMaskFile", "bamFilesAreDisjoint" etc.

Command line:

java -cp ${classpath} \
org.broadinstitute.sting.queue.QCommandLine \
-S ${SV_DIR}/qscript/SVPreprocess.q \
-S ${SV_DIR}/qscript/SVQScript.q \
-gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
-cp ${classpath} \
-configFile ${SV_DIR}/conf/genstrip_parameters.txt \
-tempDir ${SV_TMPDIR} \
-R /home/list/work/g1kv37/human_g1k_v37.fasta \
-genomeMaskFile ../raw_data/human_g1k_v37.mask.36.fasta \
-ploidyMapFile ../raw_data/humgen_g1k_v37_ploidy.map \
-copyNumberMaskFile ../raw_data/cn2_mask_g1k_v37.fasta \
-genderMapFile ../raw_data/gender.map \
-runDirectory ${runDir} \
-md ${runDir}/metadata \
-reduceInsertSizeDistributions \
-bamFilesAreDisjoint \
-computeGCProfiles \
-jobLogDir ${runDir}/logs \
-I ${bam} \
-run

Shows errors like this:

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

org.broadinstitute.sting.commandline.InvalidArgumentException:
Argument with name 'ploidyMapFile' isn't defined.
at org.broadinstitute.sting.commandline.ParsingEngine.validate(ParsingEngine.java:199)
at org.broadinstitute.sting.commandline.ParsingEngine.validate(ParsingEngine.java:172)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:199)
at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:117)
at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 1.0.5039M):
ERROR
ERROR Please visit to wiki to see if this is a known problem
ERROR If not, please post the error, with stack trace, to the GATK forum
ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
ERROR
ERROR MESSAGE: Argument with name 'ploidyMapFile' isn't defined.
ERROR ------------------------------------------------------------------------------------------

Could you help me? Thanks!

Best Answer

Answers

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