[Samtools-help] collectGCBiasMetrics Error

[Richard C. <rco...@bc...>]

Hi Picard developers.

I'm trying to get the pretty GC bias plot for some bisulfite treated 
data that has been aligned with bismark:

java  -Xms4g -Xmx4g -jar picard-tools-1.71/CollectGcBiasMetrics.jar 
I=D1KEUACXX_1.bam.downsampled.bam.newDups 
O=D1KEUACXX_1.bam.downsampled.bam.newDups.gcmets   R=GRCh37-lite.fa 
CHART=D1KEUACXX_1.bam.downsampled.bam.newDups.pdf 
S=D1KEUACXX_1.bam.downsampled.bam.newDups.summ VALIDATION_STRINGENCY=LENIENT

It looks like everything is going well but after iterating over the 
chromosomes I get this error:
...
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 
59373644
         at 
net.sf.picard.analysis.CollectGcBiasMetrics.doWork(CollectGcBiasMetrics.java:154)
         at 
net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
         at 
net.sf.picard.analysis.CollectGcBiasMetrics.main(CollectGcBiasMetrics.java:99)

I am attaching the stout/stderr output.

I suspect the problem is something to do with the bisulfite conversion 
creating lots and lots of matches with respect to the "reference".   Any 
ideas out there about how to get around this? I'm just interested in the 
coverage and not concerned about mismatch rates (if that is the issue).

thanks,
RIchard