Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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)

  • #2
    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.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Multiomics Techniques Advancing Disease Research
      by seqadmin


      New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

      A major leap in the field has
      ...
      02-08-2024, 06:33 AM
    • seqadmin
      The 3D Genome: New Technologies and Emerging Insights
      by seqadmin


      The study of three-dimensional (3D) genomics explores the spatial structure of genomes and their role in processes like gene expression and DNA replication. By employing innovative technologies, researchers can study these arrangements to discover their role in various biological processes. Scientists continue to find new ways in which the organization of DNA is involved in processes like development1 and disease2.

      Basic Organization and Structure
      Understanding...
      01-22-2024, 03:25 PM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, Today, 08:52 AM
    0 responses
    10 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 08:57 AM
    0 responses
    12 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 02-14-2024, 09:19 AM
    0 responses
    48 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 02-12-2024, 03:37 PM
    0 responses
    422 views
    0 likes
    Last Post seqadmin  
    Working...
    X