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Old 05-24-2018, 12:08 PM   #1
lfaller
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Location: Boston, MA

Join Date: Jul 2017
Posts: 4
Default 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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Old 06-11-2018, 03:59 PM   #2
neavemj
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Location: MA, USA

Join Date: Feb 2014
Posts: 56
Default

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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