Re: [svtoolkit-help] STRiP Configuration file failed

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

Dear Bob,

Thanks a lot for your rapid response. I have removed the -L 1 argument
as you suggested and now the problem is gone.

However, I have 2 other issues:

1. Pre-processing output empty

I did not get any summary statistics from the pre-processing step even
thought it was error free. For example, the depth.dat is empty with a
header only. "SAMPLE	LIBRARY	READGROUP	COUNT"

2. cannot parse configuration file
I used the downloaded
/svtoolkit/el5/x86_64/svtoolkit-1.03.619/svtoolkit/conf/genstrip_parameters.txt
However I received the following error. Can you please suggest a way
to fix it? Many thanks for your help!!!

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
java.lang.RuntimeException: Cannot parse configuration file:
/share/apps/svtoolkit/el5/x86_64/svtoolkit-1.03.619/svtoolkit/conf/genstrip_parameters
.txt
	at org.broadinstitute.sv.discovery.SVDiscoveryWalker.initialize(SVDiscoveryWalker.java:122)
	at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:49)
	at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:217)
	at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:111)
	at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:110)
	at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:239)
	at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:72)
	at org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21)
##### 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: Cannot parse configuration file:
/share/apps/svtoolkit/el5/x86_64/svtoolkit-1.03.619/svtoolkit/conf/genstrip_parameters.txt
##### ERROR ------------------------------------------------------------------------------------------



On Fri, Oct 28, 2011 at 9:17 AM, Bob Handsaker
<han...@br...> wrote:
> This is usually because you have copied the installation test, which uses
> the argument "-L 1", but your reference genome has not chromosome named "1".
> The -L argument specifies a specific locus to process.  This option is used
> in the installation test just to make it run slightly faster.
> -Bob