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Old 05-24-2018, 01:08 PM   #1
Junior Member
Location: Boston, MA

Join Date: Jul 2017
Posts: 4
Default Error encountered when running from bbmap

Hi all,

I am encountering a java.lang.AssertionError when trying to run

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!

$ ~/bbmap/ 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]

Memory: max=90186m, free=88774m, used=1412m

Executing kmer.KmerTableSet [in1=7064890_R1.fastq, in2=7064890_R1.fastq, khist=khist.txt, peaks=peaks.txt]

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(
        at stream.ConcurrentReadInputStream.getReadInputStream(
        at kmer.KmerTableSet.loadKmers(
        at kmer.AbstractKmerTableSet.loadKmers(
        at kmer.AbstractKmerTableSet.processInput(
        at kmer.AbstractKmerTableSet.process(
        at jgi.KmerCountExact.process2(
        at jgi.KmerCountExact.process(
        at jgi.KmerCountExact.main(
lfaller is offline   Reply With Quote
Old 06-11-2018, 04:59 PM   #2
Location: MA, USA

Join Date: Feb 2014
Posts: 58

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:


I guess bbmap checks that the F and R reads have different file names and this is why you get an 'assertion' error.


neavemj is offline   Reply With Quote

bbmap, error, kmer

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