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)
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)
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