Hi All,

I tried many times to merge two BAM files (3.3 GB and 7.7MB) using different versions of Galaxy. But every time I only  got an empty file and it showed some info like this:

[Wed Sep 14 08:56:06 EDT 2011] net.sf.picard.sam.MergeSamFiles done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=310116352
Exception in thread "main" java.lang.IllegalArgumentException: Cannot add sequence that already exists in SAMSequenceDictionary: contig00311
	at net.sf.samtools.SAMSequenceDictionary.setSequences(SAMSequenceDictionary.java:62)
	at net.sf.samtools.SAMSequenceDictionary.<init>(SAMSequenceDictionary.java:40)
	at net.sf.samtools.SAMTextHeaderCodec.decode(SAMTextHeaderCodec.java:106)
	at net.sf.samtools.BAMFileReader.readHeader(BAMFileReader.java:364)
	at net.sf.samtools.BAMFileReader.<init>(BAMFileReader.java:118)
	at net.sf.samtools.BAMFileReader.<init>(BAMFileReader.java:97)
	at net.sf.samtools.SAMFileReader.init(SAMFileReader.java:504)
	at net.sf.samtools.SAMFileReader.<init>(SAMFileReader.java:165)
	at net.sf.samtools.SAMFileReader.<init>(SAMFileReader.java:120)
	at net.sf.picard.sam.MergeSamFiles.doWork(MergeSamFiles.java:100)
	at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:175)
	at net.sf.picard.sam.MergeSamFiles.main(MergeSamFiles.java:84)
Does anybody have the similar problem and thanks for any suggestion in handling this issue.

Best wishes,
Bin