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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