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PICARD - Alignment start should != 0 because reference name != *

TSNTSN BrazilMember

The problem start with CleanSam but it runs and creates the output, besides the error! After that AddOrReplaceReadGroups gives the same error but also runs! But in MarkDuplicates the error is fatal!!

Exception in thread "main" htsjdk.samtools.SAMFormatException: SAM validation error: ERROR: Record 1, Read name HISEQ:201:C783JANXX:8:1301:18266:70980, Alignment start should != 0 because reference name != *.
at htsjdk.samtools.SAMUtils.processValidationErrors(SAMUtils.java:441)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:665)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.(BAMFileReader.java:638)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.(BAMFileReader.java:626)
at htsjdk.samtools.BAMFileReader.getIterator(BAMFileReader.java:334)
at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.iterator(SamReader.java:449)
at picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram.openInputs(AbstractMarkDuplicatesCommandLineProgram.java:229)
at picard.sam.markduplicates.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:394)
at picard.sam.markduplicates.MarkDuplicates.doWork(MarkDuplicates.java:193)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:209)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)

Can you tell me about this error? What the problem with my data?


Issue · Github
by Sheila

Issue Number
Last Updated
Closed By


  • deklingdekling Broad InstituteMember admin

    Hi @TSN: Please run your sam/bam file through ValidateSamFile to find out what is going on. In addition, please make sure you are using the latest version of Picard. Keep me posted on your results. Thank you, -David

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