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