[svtoolkit-help] found the syntax error, please ignore this particular question Re: STRiP Configuration file failed

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

Dear Bob, I have located the syntax error. Thanks a lot for your
guidance. best, -Jin

On Fri, Oct 28, 2011 at 3:50 PM, Jingerbread <ae4...@gm...> wrote:
> 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.
>