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Old 04-17-2011, 01:07 PM   #1
mrfox
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Location: USA

Join Date: Aug 2010
Posts: 103
Default picard: "No enum const clas" error

Hi all,
I am trying to use Picard to remove duplicate reads in the SAM/BAM files. The command I use was (java 1.6 was installed on our linux nodes):
java -jar picard-tools-1.43/MarkDuplicates.jar I=my.bam O=out.bam M=m.txt REMOVE_DUPLICATES=true
Every time I got the error message:
"Exception in thread "main" net.sf.picard.PicardException: AS_DU145-1_4_1_sequence/out.sam is not coordinate sorted.
at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:264)
at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:113)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:157)
at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:97)
"
I wonder if I missed something when I installed Picard.

Thank you.
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Old 04-17-2011, 02:36 PM   #2
upendra_35
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Location: USA

Join Date: Apr 2010
Posts: 102
Default

I do get the same error and i couldn't fix it till now. Could somebody please advise on this.
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