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Old 09-11-2017, 04:54 PM   #1
ArtVandelay
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Location: United States

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Default 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
File Type: txt test1.txt (1,007 Bytes, 2 views)
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Old 09-12-2017, 12:53 PM   #2
Brian Bushnell
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Default

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.
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Old 09-12-2017, 05:15 PM   #3
ArtVandelay
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Makes sense. Thank you!
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