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Old 02-29-2012, 03:33 AM   #1
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Location: Germany

Join Date: Feb 2012
Posts: 2
Default 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.
Exception in thread "main" net.sf.picard.PicardException: Requesting earlier reference sequence: 1 < 17
at net.sf.picard.reference.ReferenceSequenceFileWalker.get(
at net.sf.picard.sam.SamFileValidator.validateNmTag(
at net.sf.picard.sam.SamFileValidator.validateSamRecords(
at net.sf.picard.sam.SamFileValidator.validateSamFile(
at net.sf.picard.sam.SamFileValidator.validateSamFileVerbose(
at net.sf.picard.sam.ValidateSamFile.doWork(
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(
at net.sf.picard.sam.ValidateSamFile.main(
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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