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

[Verena T. <tis...@go...>]

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