Re: [svtoolkit-help] SV filtering steph (VariantFiltration) not working

[Thomas Z. <tho...@em...>]

Dear Bob,

thank you very much for your reply!
I now ran it on my local machine instead of the cluster and it works. I 
don't know what the actual problem might have been.

The only thing I noticed is that the calling of the filtering step 
doesn't contain the "-runDirectory" parameter. Could this cause problems?

Kind regards
Thomas




On 20.01.2012 16:21, Bob Handsaker wrote:
> No idea offhand.  Have you looked in the log file produced by queue?
> What I would try is to take the log file from queue, which lists the
> java command that was run, and run this command directly.
> If the behavior persists, then maybe truncate the unfiltered.vcf down to
> just the first record and if the problem still persists, then post the
> short vcf file.
> -Bob
>
> On 1/20/12 3:01 AM, Thomas Zichner wrote:
>> Hi,
>>
>> I am running GenomeSTRiP on individual chromosomes which seems to work
>> very well. In most cases, I get the file discovery.vcf as expected.
>> However, in a few cases I only get discovery.unfiltered.vcf (as well as
>> .discovery.unfiltered.vcf.done).
>> When I rerun GenomeSTRiP, the variant filtration is executed again,
>> however, there is still no output, but also no error message. And as far
>> I can see, also the log file doesn't contain any error message.
>>
>> Any idea what the problem might be?
>>
>> Thank you very much!
>> Kind regards
>> Thomas Zichner
>>