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  • Picard Exception

    When I try to validate my sam file (from bwa) using picard ValidateSamFile I get the following exception.
    HotSpot(TM) 64-Bit Server VM 1.6.0_06-b02; Picard version: 1.62(1113)
    [Wed Feb 29 13:16:32 CET 2012] net.sf.picard.sam.ValidateSamFile done. Elapsed time: 0,11 minutes.
    Runtime.totalMemory()=1135607808
    Exception in thread "main" net.sf.picard.PicardException: Requesting earlier reference sequence: 1 < 17
    at net.sf.picard.reference.ReferenceSequenceFileWalker.get(ReferenceSequenceFileWalker.java:78)
    at net.sf.picard.sam.SamFileValidator.validateNmTag(SamFileValidator.java:379)
    at net.sf.picard.sam.SamFileValidator.validateSamRecords(SamFileValidator.java:247)
    at net.sf.picard.sam.SamFileValidator.validateSamFile(SamFileValidator.java:176)
    at net.sf.picard.sam.SamFileValidator.validateSamFileVerbose(SamFileValidator.java:135)
    at net.sf.picard.sam.ValidateSamFile.doWork(ValidateSamFile.java:156)
    at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
    at net.sf.picard.sam.ValidateSamFile.main(ValidateSamFile.java:92)
    I have tried validating other sam files with the same reference and I didn't have any problems, so I don't know what went wrong, I need some help to understand what is going on
    Thank you all.

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