Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Error adding read groups to golden bam file #44

Open
afzm opened this issue Jun 6, 2018 · 0 comments
Open

Error adding read groups to golden bam file #44

afzm opened this issue Jun 6, 2018 · 0 comments

Comments

@afzm
Copy link

afzm commented Jun 6, 2018

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)

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant