Hello Bin,

The tools under "NGS: Picard (beta) -> BAM/SAM Cleaning" can help to label the reads with the same identifier in the two SAM files appropriately so that they do not trigger this type of error. Specifically, the reads need to be assigned to different run groups.


Hopefully this helps,

Jen
Galaxy team

On 9/27/11 8:52 AM, Binbin You wrote:
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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