Re: [svtoolkit-help] SVDiscovery breaks qithout obvious error message; truncated log file

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

It's unlikely that there's some internal processing error in Genome 
STRiP that will cause it to terminate without some error messages (like 
a java exception report).
I would suspect that either (a) the error output is getting lost 
somewhere or (b) the job has been killed externally, if you are running 
in lsf this might be due to
exceeding a resource or runtime limit.  When I see jobs killed due to 
resource limits on our cluster, I often end up with a core file and 
hs_err_*.log file and lsf reports
the reason for termination, which may be in a separate log file.
Hope this helps,
-Bob

On 1/31/12 11:05 AM, Verena Tischler wrote:
> Hi,
>
> running GenomeSTRiP, I run into the problem, that the SVDiscovery step 
> does not work for one chromosome without giving a particularly helpful 
> error message.
> The error is independant from using the released GenomeSTRiP version 
> or the interim version.
>
> Here is what I get:
> <lots of similar lines here>
> #DBG: RC Cache miss    chr7.fa:103685075-104038844    353770    5    
> 31.443630 sec
> INFO  03:53:01,710 SVDiscovery - Clustering: Generating clusters for 
> 285 read pairs.
> INFO  03:53:01,727 SVDiscovery - Clustering: LR split size 285 / 285 
> maximal clique size 228 clique count 1
> INFO  03:53:01,728 SVDiscovery - Clustering: LR split size 57 / 285 
> maximal clique size 22 clique count 1
> INFO  03:53:01,728 SVDiscovery - Clustering: LR split size 35 / 285 
> maximal clique size 17 clique count 1
> INFO  03:53:01,728 SVDiscovery - Clustering: LR split size 18 / 285 
> maximal clique size 9 clique count 1
> INFO  03:53:01,728 SVDiscovery - Clustering: LR split size 9 / 285 
> maximal clique size 6 clique count 1
> INFO  03:53:01,728 SVDiscovery - Clustering: LR split size 3 / 285 
> maximal clique size 2 clique count 1
> INFO  03:53:01,728 SVDiscovery - Processing cluster 
> chr7.fa:103684956-103685204 chr7.fa:104017134-104017254 LR 2
> [GC 1468359K->72359K(1776128K), 0
>
> <truncated>
> INFO  13:54:06,102 QCommandLine - Done with errors
> INFO  13:54:06,113 QGraph - -------
> INFO  13:54:06,126 QGraph - Failed:
>
> The chromosome is far longer than the point where GS breaks and there 
> are also no obvious genomic annotations that might cause trouble
>
> Any ideas what the problem might be?
>
> Thanks a lot in advance for your help
> Verena
>
>
>
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