Hi Stathis,
I don't think the problem is lack of memory. I think you have an alignment
with a coordinate that is off the end of your reference. Try running
ValidateSamFile on your BAM, and make sure to pass your reference sequence to
the program also. You should also confirm that the lengths of the reference
sequences in the header of your BAM agree with the lengths in your reference
fasta. If you haven't already, you can create a sequence dictionary from your
reference fasta using Picard CreateSequenceDictionary, and then compare the @SQ
records in the sequence dictionary and in the header of your BAM.
-Alec
On May 27, 2014, at 6:22 AM, Kanterakis, Efstathios <ekantera...@illumina.com>
wrote:
> 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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