Dear all, When I try to validate my sam file using ValidateSamFile from picard, I am getting this exception.
[Mon Feb 27 09:01:57 CET 2012] net.sf.picard.sam.ValidateSamFile done. Elapsed time: 0.43 minutes. Runtime.totalMemory()=2144075776 Exception in thread "main" net.sf.picard.PicardException: Requesting earlier reference sequence: 13 < 16 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)
Thinking that my reference sequence files were somehow corrupted I re-indexed them and created a new sam file (using bwa), but the problem seems to be still there, and when I tried to validate a sam file generated earlier using the same parametes on the same reference sequence file, it did not throw any error. Any suggestions ? Thanks
