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
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