svtoolkit-help

Re: [svtoolkit-help] SVtoolkit Error: Exception processing cluster: Permitted to write any record upstream of position...

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

[I'm not sure how to reply in a thread, so I'll just send this]

I have version 1.04.797 from the interim folder already.

Regards,
John

-- 
John Broxholme
Wellcome Trust Centre for Human Genetics
Roosevelt Drive, Oxford, OX3 7BN, UK
Tel: (+44 1865) 287611 FAX: 287697

[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

Re: [svtoolkit-help] SVdiscovery "truncated" error

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

I don't have a good theory offhand.  One thing to do is to try to 
eliminate Queue from the equation.
Rather than running the java process through Queue, try copying the 
command line from the Queue output and running it directly.
-Bob

On 11/25/11 8:15 AM, John Broxholme wrote:
> 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
>