Hi all,
I've gotten this error with a few Picard tools now (using v1.113), including
CollectWgsMetrics.jar and CollectGcBiasMetrics (below):
INFO 2014-05-27 11:02:55 CollectGcBiasMetrics Processed 34,000,000
records. Elapsed time: 00:02:
28s. Time for last 1,000,000: 4s. Last read position: chr1:121,485,129
[Tue May 27 11:02:58 BST 2014] net.sf.picard.analysis.CollectGcBiasMetrics
done. Elapsed time: 2.54 minutes.
Runtime.totalMemory()=1509883904
To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 142535338
at
net.sf.picard.analysis.CollectGcBiasMetrics.doWork(CollectGcBiasMetrics.java:152)
at
net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:179)
at
net.sf.picard.analysis.CollectGcBiasMetrics.main(CollectGcBiasMetrics.java:95)
It always occurs after chr1:121,000,000 and after Runtime.totalMemory ~ 1.5GB
I've tried increasing the -Xmx2g to 4g and running on the biggest machine we
have (40 cores, 126G) to no avail.
My bams are 55-80GB Illumina WGS.
The only way I got CollectWgsMetrics to complete was to use the STOP_AFTER
option, but this is not available in CollectGcBiasMetrics.
Any recommendations on how to overcome this exception?
If not, could you add the STOP_AFTER option in CollectGcBiasMetrics as well?
Thank you,
Stathis
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