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  • neavemj
    replied
    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.

    Leave a comment:


  • 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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