Hi all,
When running Picards MarkDuplicates I get the following error:
Exception in thread "main" java.lang.RuntimeException: SAM validation error: ERROR: Record 124760536, Read name B80PDAABXX:1:26
:2364:123720#0, MAPQ should be 0 for unmapped read.
at net.sf.samtools.SAMUtils.processValidationErrors(SAMUtils.java:334)
at net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:469)
at net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:450)
at net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:417)
at net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:629)
at net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:607)
at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:276)
at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:113)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:158)
at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:97)
It says that MAPQ should be 0 for unmapped reads, and this sounds reasonable. But could it be that something went wrong earlier in the analysis? Hope anyone can help!
Nat.
When running Picards MarkDuplicates I get the following error:
Exception in thread "main" java.lang.RuntimeException: SAM validation error: ERROR: Record 124760536, Read name B80PDAABXX:1:26
:2364:123720#0, MAPQ should be 0 for unmapped read.
at net.sf.samtools.SAMUtils.processValidationErrors(SAMUtils.java:334)
at net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:469)
at net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:450)
at net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:417)
at net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:629)
at net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:607)
at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:276)
at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:113)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:158)
at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:97)
It says that MAPQ should be 0 for unmapped reads, and this sounds reasonable. But could it be that something went wrong earlier in the analysis? Hope anyone can help!
Nat.
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