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  • marlivlok
    Junior Member
    • Nov 2012
    • 2
    #1

    Trimmomatic String index error

    I've been using Trimmomatic 0.30 with great success, but today I got an error message for 8 of my 9 libraries and I have no idea how to fix it.

    Exception in thread "main" java.lang.StringIndexOutOfBoundsException: String index out of range: 0
    at java.lang.String.charAt(String.java:658)
    at org.usadellab.trimmomatic.fastq.FastqParser.parseOne(FastqParser.java:47)
    at org.usadellab.trimmomatic.fastq.FastqParser.parse(FastqParser.java:93)
    at org.usadellab.trimmomatic.TrimmomaticPE.process(TrimmomaticPE.java:254)
    at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:347)
    at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:23)

    Any help would be much appreciated.
    Tags: string index out of range, trimmomatic error
  • GenoMax
    Senior Member
    • Feb 2008
    • 7142
    #2
    Do you possibly have a blank line somewhere in your fastq files? You could try and validate them: https://github.com/statgen/fastQValidator

    Comment

    • marlivlok
      Junior Member
      • Nov 2012
      • 2
      #3
      Awesome, thanks. Yeah for some reason my GBS sequence removal script added blank lines to some of the reverse read files. All running smoothly now

      Comment

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