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Old 08-20-2012, 05:52 AM   #1
Location: Pittsburgh

Join Date: Aug 2011
Posts: 72
Default picard error: Mismatch between read length and quals length writing read

I am getting an error in picard when trying to merge some sam files. I can't find this error posted about anywhere. I am wondering if someone knows what it might mean and how i can go about fixing it. The output for me standard error is:

Exception in thread "main" java.lang.RuntimeException: Mismatch between read length and quals length writing read MWR-PRG-0014:8613KTACXX:4:2203:11277:100870_1:N:0:CTTGTA/1; read length: 54995; quals length: 3
at net.sf.samtools.BAMRecordCodec.encode(
at net.sf.samtools.BAMRecordCodec.encode(
at net.sf.samtools.util.SortingCollection.spillToDisk(
at net.sf.samtools.util.SortingCollection.add(
at net.sf.samtools.SAMFileWriterImpl.addAlignment(
at net.sf.picard.sam.MergeSamFiles.doWork(
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(
at net.sf.picard.sam.MergeSamFiles.main(
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