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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