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  • IndexOutOfBoundsException in BBTool's kmercountexact.sh

    I'm trying to use BBTool's kmercountexact.sh (version 37.50) to produce a sketch from a test fasta file:
    kmercountexact.sh in=test1.fasta sketch=test1.sketch mincount=3 -overwrite=true

    and I'm getting an IndexOutOfBoundsException. Does anyone have any idea of what I can do differently or how I may otherwise get help?

    Here is the full output:

    > kmercountexact.sh in=test1.fasta sketch=test1.sketch mincount=3 -overwrite=true
    Max memory cannot be determined. Attempting to use 3200 MB.
    If this fails, please add the -Xmx flag (e.g. -Xmx24g) to your command,
    or run this program qsubbed or from a qlogin session on Genepool, or set ulimit to an appropriate value.
    java -ea -Xmx3200m -Xms3200m -cp /Users/droe/bin/bbmap/current/ jgi.KmerCountExact in=test1.fasta sketch=test1.sketch mincount=3 -overwrite=true
    Executing jgi.KmerCountExact [in=test1.fasta, sketch=test1.sketch, mincount=3, -overwrite=true]

    Initial:
    Memory: max=3215m, free=3182m, used=33m

    Executing kmer.KmerTableSet [in=test1.fasta, sketch=test1.sketch, mincount=3, -overwrite=true]

    Initial:
    Ways=31, initialSize=128000, prefilter=f, prealloc=f
    Memory: max=3215m, free=3182m, used=33m

    Estimated kmer capacity: 121523321
    After table allocation:
    Memory: max=3215m, free=3111m, used=104m

    After loading:
    Memory: max=3215m, free=3060m, used=155m

    Input: 1 reads 1000 bases.

    For K=31
    Unique Kmers: 970
    Load Time: 0.059 seconds.
    Generating sketch.
    Exception in thread "main" java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
    at java.util.ArrayList.rangeCheck(ArrayList.java:653)
    at java.util.ArrayList.get(ArrayList.java:429)
    at sketch.SketchTool.toSketch(SketchTool.java:327)
    at sketch.SketchTool.toSketch_MT(SketchTool.java:225)
    at sketch.SketchTool.toSketch(SketchTool.java:167)
    at jgi.KmerCountExact.makeSketch(KmerCountExact.java:360)
    at jgi.KmerCountExact.process(KmerCountExact.java:264)
    at jgi.KmerCountExact.main(KmerCountExact.java:58)
    Attached Files

  • #2
    I just tested and was able to replicate this... it's due to the "mincount=3" flag. That file has no kmers that occur at least 3 times, so it ends up trying to make a size-0 sketch, which isn't allowed. If you take away "mincount=3" it works fine. I'll clarify that error message.

    Comment


    • #3
      Makes sense. Thank you!

      Comment

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