That individual step shouldn't require -runDirectory (the input and
output files are passed explicitly).
It sounds like some transient problem in your cluster environment, but
it's hard to tell what it might be.
-Bob
On 1/29/12 3:41 PM, Thomas Zichner wrote:
> 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
>>>
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