Picard MarkDuplicates error. It seems MarkDupllicates can't process BWA (aln + sampe & mem) output.

Hey guys,

I was running MarkDuplicates with BWA output, and I got a error "java.lang.NoClassDefFoundError: java/lang/ref/Finalizer$2". To get around it, I tried the following:

1) Used different versions of Picard. I tried 1.90, 1.119, 1.228. None of them worked.
2) I built picard.jar from source code. Still didn't work.
3) Used -M in BWA mem, no luck. When I used aln and sampe, I still got the same error.
4) So I tried MarkDuplicates on RNA-Seq data, it worked perfectly on TopHat output!

So the conclusion I've reached is that MarkDuplicats doesn't work well with BWA output. Anyone knows how to deal with this situation? Thank you in advance!

More information:
I'm using openjdk version "1.6.0-internal", Linux system.

The error message:
Exception in thread "main" java.lang.NoClassDefFoundError: java/lang/ref/Finalizer$2
at java.lang.ref.Finalizer.runFinalization(Finalizer.java:144)
at java.lang.Runtime.runFinalization0(Native Method)
at java.lang.Runtime.runFinalization(Runtime.java:705)
at java.lang.System.runFinalization(System.java:967)
at htsjdk.samtools.util.FileAppendStreamLRUCache$Functor.makeValue(FileAppendStreamLRUCache.java:58)
at htsjdk.samtools.util.FileAppendStreamLRUCache$Functor.makeValue(FileAppendStreamLRUCache.java:49)
at htsjdk.samtools.util.ResourceLimitedMap.get(ResourceLimitedMap.java:76)
at htsjdk.samtools.CoordinateSortedPairInfoMap.getOutputStreamForSequence(CoordinateSortedPairInfoMap.java:180)
at htsjdk.samtools.CoordinateSortedPairInfoMap.put(CoordinateSortedPairInfoMap.java:164)
at picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap.put(DiskBasedReadEndsForMarkDuplicatesMap.java:65)
at picard.sam.markduplicates.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:290)
at picard.sam.markduplicates.MarkDuplicates.doWork(MarkDuplicates.java:114)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:187)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)

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