Question: Problem In Merging Two Bam File In Galaxy. Thanks For Help.
0
Binbin You • 50 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
onary.java:62) at net.sf.samtools.SAMSequenceDictionary.<init>(SAMSequ
enceDictionary.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.j
ava: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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modified 7.2 years ago
by
Jennifer Hillman Jackson ♦ 25k
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written
7.2 years ago by
Binbin You • 50
