[svtoolkit-help] SVdiscovery "truncated" error

[John B. <jo...@we...>]

This happened during SVdiscovery.  I've seen 'truncated' twice in two attempts with these 
data (153 samples from 1000Genomes, selected for chr14).  The first time had no "-L" 
argument and happened while "Processing cluster 14:82555551-82555838 14:82556031-82556335 
LR 2"
The second has the same input data but I'd specified "-L 14" and the error was thrown 
while "Processing cluster 14:85768136-85768422"

Try 1:
...
#DBG: RC Cache fill     14:85750104-85860103    110000  153     8.480425 sec
INFO  03:39:35,613 SVDiscovery - Clustering: Generating clusters for 2 read pairs.
INFO  03:39:35,613 SVDiscovery - Processing cluster 14:85762691-85762973 
14:85763261-85763496 LR 2
INFO  03:39:36,280 SVDiscovery - Clustering: Generating clusters for 2 read pairs.
INFO  03:39:36,280 SVDiscovery - Processing cluster 14:85768136-85768422 
14:85768594-85768960 LR 2
INFO  03:39:36,974 SVDiscovery - Clustering: Generating clusters for 3 read pairs.
INFO  03:39:36,974 SVDiscovery - Clustering: LR split size 3 / 3 maximal clique size 2 c

<truncated>
         at org.broadinstitute.sting.queue.util.ShellJob.run(ShellJob.scala:24)
         at 
org.broadinstitute.sting.queue.engine.shell.ShellJobRunner.start(ShellJobRunner.scala:54)
         at org.broadinstitute.sting.queue.engine.FunctionEdge.start(FunctionEdge.scala:56)
         at org.broadinstitute.sting.queue.engine.QGraph.runJobs(QGraph.scala:383)
         at org.broadinstitute.sting.queue.engine.QGraph.run(QGraph.scala:123)
         at org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scala:111)
         at 
org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221)
         at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:57)
         at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala)
INFO  04:47:49,290 QGraph - 1 Pend, 1 Run, 0 Fail, 0 Done
INFO  04:47:49,294 QGraph - 1 Pend, 0 Run, 1 Fail, 0 Done
INFO  04:47:49,294 QCommandLine - Done with errors
INFO  04:47:49,295 QGraph - -------
INFO  04:47:49,317 QGraph - Failed:
...

Try 2:
...
INFO  18:19:17,401 SVDiscovery - Clustering: Generating clusters for 2 read pairs.
INFO  18:19:17,403 SVDiscovery - Clustering: Generating clusters for 2 read pairs.
INFO  18:19:17,403 SVDiscovery - Processing cluster 14:82555551-82555838 
14:82556031-82556335 LR 2
[GC 369154K->321806K(386752K), 0.0043100 secs]
[GC 368014K->322288K(386048K), 0.0028780 secs]
[GC 368112K->322455K(386048K), 0.0023780 secs]
[GC 367895K->322378K(385280K), 0.0087230 secs]
[GC 367498K->322576K(385344K), 0.0021090 secs]
[GC 367376K->322712K(384832K), 0.0030720 secs]
[GC 367192K->322559K(384576K), 0.0019880 secs]
[GC 366719K->322632K(384000K), 0.0029070 secs]
[GC 366472K->322642K(383936K), 0.0039400 secs]
[GC 366162K->321695K(382272K), 0.0027450 se

<truncated>

Any suggestions as to what's 'truncated', what might have caused it and how to fix it?  I 
have definitely not run out of disk space.

Thanks
John

-- 
John Broxholme
Wellcome Trust Centre for Human Genetics
Oxford