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  • mrfox
    Senior Member
    • Aug 2010
    • 103

    #1

    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.
  • upendra_35
    Senior Member
    • Apr 2010
    • 102

    #2
    I do get the same error and i couldn't fix it till now. Could somebody please advise on this.

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