Hi,
I met error about GenomeStrip2.0 CNVDiscoveryPipeline. Some parts of the error log are as following,
However, I am not able to fix it by myself, could you help? Thanks so much!
SVToolkit version 2.00 (build 1611)
Build date: 2015/10/04 09:22:55
Web site: http://www.broadinstitute.org/software/genomestrip
INFO 14:07:50,796 QScriptManager - Compiling 2 QScripts
INFO 14:07:59,714 QScriptManager - Compilation complete
ERROR ------------------------------------------------------------------------------------ ------
ERROR stack trace
org.broadinstitute.gatk.utils.commandline.MissingArgumentException:
Argument with name '--tilingwindowsize' (-tilingWindowSize) is missing.
Argument with name '--minimumrefinedlength' (-minimumRefinedLength) is missing.
Argument with name '--maximumreferencegaplength' (-maximumReferenceGapLength) is missing.
Argument with name '--tilingwindowoverlap' (-tilingWindowOverlap) is missing.
Argument with name '--boundaryprecision' (-boundaryPrecision) is missing.
at org.broadinstitute.gatk.utils.commandline.ParsingEngine.validate(ParsingEngine.java:2 99)
at org.broadinstitute.gatk.utils.commandline.ParsingEngine.validate(ParsingEngine.java:2 79)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram .java:216)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram .java:155)
at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:62)
at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)
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: Argument with name '--tilingwindowsize' (-tilingWindowSize) is missing.
ERROR Argument with name '--minimumrefinedlength' (-minimumRefinedLength) is missing.
ERROR Argument with name '--maximumreferencegaplength' (-maximumReferenceGapLength) is mis sing.
ERROR Argument with name '--tilingwindowoverlap' (-tilingWindowOverlap) is missing.
ERROR Argument with name '--boundaryprecision' (-boundaryPrecision) is missing.
ERROR ------------------------------------------------------------------------------------ ------
INFO 14:07:59,799 QCommandLine - Shutting down jobs. Please wait...
CNVDiscovery.sh: line 32: -md: command not found
CNVDiscovery.sh: line 35: -tilingWindowSize: command not found
CNVDiscovery.sh: line 37: -tilingWindowOverlap: command not found
Wendy