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  • bair
    Member
    • Jan 2010
    • 65
    #1

    Picard

    Hello all,

    I merged two ELAND export files by using samtools, but samtools flagstat shows that

    191134982 in total
    0 QC failure
    0 duplicates
    139825529 mapped (73.16%)
    191134982 paired in sequencing
    95567491 read1
    95567491 read2
    0 properly paired (0.00%)
    115989136 with itself and mate mapped
    23836393 singletons (12.47%)
    0 with mate mapped to a different chr
    0 with mate mapped to a different chr (mapQ>=5)

    Why it shows 0 properly paired?

    Couldn't run picard MarkDuplicates, thread exception:

    Exception in thread "main" java.lang.NullPointerException
    at net.sf.picard.sam.DiskReadEndsMap.remove(DiskReadEndsMap.java:87)
    at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:289)
    at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:126)
    at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:143)
    at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:105)

    Any help? Many thanks.
    Tags: None
    • nilshomer
      Nils Homer
      • Nov 2008
      • 1283
      #2
      Originally posted by bair View Post
      Hello all,

      I merged two ELAND export files by using samtools, but samtools flagstat shows that

      191134982 in total
      0 QC failure
      0 duplicates
      139825529 mapped (73.16%)
      191134982 paired in sequencing
      95567491 read1
      95567491 read2
      0 properly paired (0.00%)
      115989136 with itself and mate mapped
      23836393 singletons (12.47%)
      0 with mate mapped to a different chr
      0 with mate mapped to a different chr (mapQ>=5)

      Why it shows 0 properly paired?
      It looks like the converter did not set the "properly paired" bit in the FLAG field.

      Originally posted by bair View Post
      Couldn't run picard MarkDuplicates, thread exception:

      Exception in thread "main" java.lang.NullPointerException
      at net.sf.picard.sam.DiskReadEndsMap.remove(DiskReadEndsMap.java:87)
      at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:289)
      at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:126)
      at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:143)
      at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:105)

      Any help? Many thanks.
      Looks like a bug to me.

      Send both to [email protected]

        Comment

        • Lv Ray
          Member
          • Jun 2014
          • 42
          #3
          I got the same error. Have you solved your problem, bair or nilshomer?

            Comment

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