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Old 02-29-2012, 03:33 AM   #1
sudeep
Junior Member
 
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.
Quote:
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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