Question: picard CollectInsertSizeMetrics error
0
gravatar for sunnykevin97
4 months ago by
sunnykevin9710
sunnykevin9710 wrote:

Hi, why Im getting the error message using picard insert-metrics only on some bam files ?

**Error**
xception in thread "main" htsjdk.samtools.SAMFormatException: **SAM validation error: WARNING: Read name D00360:95:H2YWMBCXX:1:2113:8832:19449, No M or N operator between pair of D operators in CIGAR**
    at htsjdk.samtools.SAMUtils.processValidationErrors(SAMUtils.java:454)
    at htsjdk.samtools.BAMRecord.getCigar(BAMRecord.java:253)
    at htsjdk.samtools.SAMRecord.getAlignmentEnd(SAMRecord.java:606)
    at htsjdk.samtools.SAMRecord.computeIndexingBin(SAMRecord.java:1575)
    at htsjdk.samtools.SAMRecord.isValid(SAMRecord.java:2087)
    at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:811)
    at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:797)
    at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:765)
    at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:576)
    at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:548)
    at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:136)
    at picard.analysis.SinglePassSamProgram.doWork(SinglePassSamProgram.java:84)
    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:282)
    at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:98)
    at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:108)
alignment assembly genome • 200 views
ADD COMMENTlink modified 3 months ago by Biostar ♦♦ 20 • written 4 months ago by sunnykevin9710
2
gravatar for Pierre Lindenbaum
4 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum116k wrote:

use VALIDATION_STRINGENCY=LENIENT

ADD COMMENTlink modified 4 months ago by RamRS20k • written 4 months ago by Pierre Lindenbaum116k
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