Question: Problem In Merging Two Bam File In Galaxy. Thanks For Help.
gravatar for Binbin You
7.2 years ago by
Binbin You50
Binbin You50 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(SAMSequenceDicti at net.sf.samtools.SAMSequenceDictionary.<init>(SAMSequ at net.sf.samtools.SAMTextHeaderCodec.decode( at net.sf.samtools.BAMFileReader.readHeader( at net.sf.samtools.BAMFileReader.<init>( at net.sf.samtools.BAMFileReader.<init>( at net.sf.samtools.SAMFileReader.init( at net.sf.samtools.SAMFileReader.<init>( at net.sf.samtools.SAMFileReader.<init>( at net.sf.picard.sam.MergeSamFiles.doWork( at net. sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.j ava:175) at net.sf.picard.sam.MergeSamFiles.main( Does anybody have the similar problem and thanks for any suggestion in handling this issue. Best wishes, Bin
samtools bam • 1.4k views
ADD COMMENTlink modified 7.2 years ago by Jennifer Hillman Jackson25k • written 7.2 years ago by Binbin You50
gravatar for Jennifer Hillman Jackson
7.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:
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 -- Jennifer Jackson
ADD COMMENTlink written 7.2 years ago by Jennifer Hillman Jackson25k
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