You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
After sorting the golden bam I encounter this message:
Exception in thread "main" htsjdk.samtools.SAMFormatException: SAM validation error: WARNING: Read name A.tha_01-1-35477/2, No M or N operator between pair of I 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$AssertingIterator.next(SamReader.java:548) at picard.sam.AddOrReplaceReadGroups.doWork(AddOrReplaceReadGroups.java:182) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:282) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)
This is the read:
Exception in thread "main" htsjdk.samtools.SAMFormatException: SAM validation error: ERROR: Record 9111, Read name A.tha_02-1-6417/1, CIGAR covers 148 bases but the sequence is 150 read bases at htsjdk.samtools.SAMUtils.processValidationErrors(SAMUtils.java:454) at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:812) 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.sam.AddOrReplaceReadGroups.doWork(AddOrReplaceReadGroups.java:182) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:282) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)
The text was updated successfully, but these errors were encountered:
After sorting the golden bam I encounter this message:
Exception in thread "main" htsjdk.samtools.SAMFormatException: SAM validation error: WARNING: Read name A.tha_01-1-35477/2, No M or N operator between pair of I 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$AssertingIterator.next(SamReader.java:548) at picard.sam.AddOrReplaceReadGroups.doWork(AddOrReplaceReadGroups.java:182) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:282) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)
This is the read:
A.tha_01-1-35477/2 147 1 24491 70 85M2I1D6I57M = 24142 -499 AAAATTGGTTACCTATTGGTTTTGGTTGGTTGATTTATCTTACGTTATCAGCAAGCAGAAGTGATCCGTAATCAAACTTGTTTTCAATTGGACATTATTGTCCGAGGGGCGGTGAGATGGGACAGGACTTTTGGGATTCTCGAAGGTGGC 06FFFE>FC>F?FF?@FFFF9GAEGGGEGGGGD5FD)5FFGFGEFE@DGGFG3@FAGFGFGA>GG3GGGEFBFGG4G><;GG>G:F&GGGGBGGE2GFF6F9*B85GE6?FCEEBFG@GGGFE@3DCDGG;E<;FEDG:GEFA-3GG<FD
Also:
Exception in thread "main" htsjdk.samtools.SAMFormatException: SAM validation error: ERROR: Record 9111, Read name A.tha_02-1-6417/1, CIGAR covers 148 bases but the sequence is 150 read bases at htsjdk.samtools.SAMUtils.processValidationErrors(SAMUtils.java:454) at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:812) 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.sam.AddOrReplaceReadGroups.doWork(AddOrReplaceReadGroups.java:182) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:282) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)
The text was updated successfully, but these errors were encountered: