Re: [svtoolkit-help] STRiP Configuration file failed

[Bob H. <han...@br...>]

On 10/28/11 10:06 AM, Jingerbread wrote:
> 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"
If you post the SAM header from one of your input files, perhaps that 
will help.
I suspect some problem with the @RG header (and make sure your bam 
records have RG tags).
>
> 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!!!
Hmm. Unfortunately the code is swallowing the error message.
It is quite possibly a syntax error on one line in the file.
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.

-Bob
>
> ##### 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