Picard MarkDuplicates throws a java.lang.NegativeArraySizeException

[rdeborja]

Hi,

I'm running picard's MarkDuplicates on a large .bam file like this:

/jdk1.6.0_10/bin/java -Xmx8g -jar /picard-tools-1.21/MarkDuplicates.jar TMP_DIR=picardTemp INPUT=inFile.bam OUTPUT=outFile.bam METRICS_FILE=outFile.bam.mmm ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT REMOVE_DUPLICATES=true"

And after processing maybe a third of the file the program throws the following exception and promptly dies:

Exception in thread "main" java.lang.NegativeArraySizeException
        at net.sf.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:304)
        at net.sf.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:292)
        at net.sf.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:100)
        at net.sf.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:169)
        at java.io.DataInputStream.read(DataInputStream.java:132)
        at net.sf.samtools.util.BinaryCodec.readBytesOrFewer(BinaryCodec.java:394)
        at net.sf.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:371)
        at net.sf.samtools.util.BinaryCodec.readByteBuffer(BinaryCodec.java:480)
        at net.sf.samtools.util.BinaryCodec.readInt(BinaryCodec.java:491)
        at net.sf.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:159)
        at net.sf.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:397)
        at net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:373)
        at net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:363)
        at net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:330)
        at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:261)
        at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:112)
        at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:150)
        at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:96)

The versions and command involved work fine on other .bam files, but I haven't determined anything wrong with the .bam file that causes this exception.

Has anyone run into this or have an idea of something I could look for in the input file? Thanks.