Re: [svtoolkit-help] STRiP Configuration file failed

[Jingerbread <ae4...@gm...>]

Hi Bob,

As you suggested, I have run the interim release; however the same
error persisted (below). I also attach the entire error message
(jindiscovery.sh.o11699) in case you need to see. Can you please offer
some guidance in order to trouble-shoot or get around this problem?

Many thanks,

Jin


##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
java.lang.RuntimeException: Cannot parse configuration file:
/share/apps/svtoolkit/el5/x86_64/svtoolkit-1.04.797/svtoolkit/conf/genstrip_parameters.txt
	at org.broadinstitute.sv.discovery.SVDiscoveryWalker.initialize(SVDiscoveryWalker.java:135)
	at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:49)
	at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:234)
	at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
	at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:105)
	at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221)
	at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:67)
	at org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21)
Caused by: java.io.FileNotFoundException:
/share/apps/svtoolkit/el5/x86_64/svtoolkit-1.04.797/svtoolkit/conf/genstrip_parameters.txt
(No such file or directory)
	at java.io.FileInputStream.open(Native Method)
	at java.io.FileInputStream.<init>(FileInputStream.java:120)
	at java.io.FileReader.<init>(FileReader.java:55)
	at org.broadinstitute.sv.util.ParameterParser.parseParameterFile(ParameterParser.java:30)
	at org.broadinstitute.sv.discovery.SVDiscoveryWalker.initialize(SVDiscoveryWalker.java:133)
	... 7 more
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0-6121-g40e3165):
##### ERROR
##### ERROR Please visit the 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: Cannot parse configuration file:
/share/apps/svtoolkit/el5/x86_64/svtoolkit-1.04.797/svtoolkit/conf/genstrip_parameters.txt
##### ERROR ------------------------------------------------------------------------------------------



> If you run the interim release from
> ftp://ftp.broadinstitute.org/pub/svtoolkit/releases/interim/svtoolkit_1.04.797.tar.gz
> then you should hopefully get a more explanatory message / stack trace.
> You can decide whether to run the interim release for your processing or
> just to debug this problem - there is no documentation of any new features
> or potential incompatibilities in the interim releases.