Hi Lina,
I think you might be trying to give your forward reads twice to both the in1 and in2 arguments. Maybe your in2 argument should be:
in2=${R2}
I guess bbmap checks that the F and R reads have different file names and this is why you get an 'assertion' error.
Cheers,
Matt.
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Error encountered when running kmercountexact.sh from bbmap
Hi all,
I am encountering a java.lang.AssertionError when trying to run kmercountexact.sh.
The two input files are 820 Mb each. I also tried running this script with subsetted data of the original datasets (using just the first 250 fastq records) but I got the same error message.
The help documentation says "Last modified August 2, 2017" so it is a fairly recent version.
Any advice is appreciated!
~Lina
Code:$ ~/bbmap/kmercountexact.sh in1=${R1} in2=${R1} khist=${HIST} peaks=${PEAKS} java -ea -Xmx89748m -Xms89748m -cp /home/lina/bbmap/current/ jgi.KmerCountExact in1=7064890_R1.fastq in2=7064890_R1.fastq khist=khist.txt peaks=peaks.txt Executing jgi.KmerCountExact [in1=7064890_R1.fastq, in2=7064890_R1.fastq, khist=khist.txt, peaks=peaks.txt] Initial: Memory: max=90186m, free=88774m, used=1412m Executing kmer.KmerTableSet [in1=7064890_R1.fastq, in2=7064890_R1.fastq, khist=khist.txt, peaks=peaks.txt] Initial: Ways=101, initialSize=128000, prefilter=f, prealloc=f Memory: max=90186m, free=87363m, used=2823m Estimated kmer capacity: 3509022984 After table allocation: Memory: max=90186m, free=86421m, used=3765m Exception in thread "main" java.lang.AssertionError: 7064890_R1.fastq, 7064890_R1.fastq at stream.ConcurrentReadInputStream.getReadInputStream(ConcurrentReadInputStream.java:111) at stream.ConcurrentReadInputStream.getReadInputStream(ConcurrentReadInputStream.java:45) at kmer.KmerTableSet.loadKmers(KmerTableSet.java:381) at kmer.AbstractKmerTableSet.loadKmers(AbstractKmerTableSet.java:288) at kmer.AbstractKmerTableSet.processInput(AbstractKmerTableSet.java:135) at kmer.AbstractKmerTableSet.process(AbstractKmerTableSet.java:80) at jgi.KmerCountExact.process2(KmerCountExact.java:285) at jgi.KmerCountExact.process(KmerCountExact.java:259) at jgi.KmerCountExact.main(KmerCountExact.java:58)
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