htsjdk.samtools.SAMFormatException: SAM validation error: ERROR: Record 40060, Read name ERR001301.6170436, bin field of BAM record does not equal value computed based on alignment start and end, and length of sequence to which read is aligned

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via GitHub by jpdna
, 1 year ago
SAM validation error: ERROR: Record 40060, Read name ERR001301.6170436, bin field of BAM record does not equal value computed based on alignment start and end, and length of sequence to which read is aligned
via GitHub by sicotte
, 2 years ago
SAM validation error: ERROR: Record 78218867, Read name R0251321:126:H7NGRADXX:2:1101:1537:1996, Mapped mate should have mate reference name
via broadinstitute.org by Unknown author, 7 months ago
SAM validation error: ERROR: Record 100838398, Read name HWUSI-EAS1691_0002:1:16:4292:16941#0, MAPQ should be 0 for unmapped read.
via GitHub by Madelinehazel
, 1 year ago
SAM validation er ror: ERROR: Record 922317609, Read name HS5_408:1:2204:5314:102757, MAPQ should be 0 for unmapped read.
via GitHub by timodonnell
, 1 year ago
SAM validation error: ERROR: Record 80, Read name HSQ1004:134:C0D8DACXX:3:1302:16380:148845, Mate Alignment start should be 0 because reference name = *.
via GitHub by apelin20
, 2 years ago
SAM validation error: ERROR: Record 9505, Read name HWI-D00104:87:D1GYYACXX:5:1112:13918:71031, MAPQ should be 0 for unmapped read.
htsjdk.samtools.SAMFormatException: SAM validation error: ERROR: Record 40060, Read name ERR001301.6170436, bin field of BAM record does not equal value computed based on alignment start and end, and length of sequence to which read is aligned
at htsjdk.samtools.SAMUtils.processValidationErrors(SAMUtils.java:441)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:652)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:637)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:607)
at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:545)
at picard.sam.SamToFastq.doWork(SamToFastq.java:174)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:209)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)

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