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  • FastX tool :: fastq_quality_filter

    Dear All,
    i am doing quality filtering of my fastq file using fastq_quality_filter
    and i am getting this error
    Premature End-Of-File (filename ='-')
    my code is
    nohup fastq_quality_filter ‐v ‐q 20 ‐p 100 -Q33 ‐i GO06_2500_Mate.read2.fastq ‐o Read2.filteredQ20.GO06.fastq > fastq_quality_filterlog &

    my fastq look like
    @GO06_2500_Mate:1_4_72/2
    NGAAGGGTGGGCATGTNATTGNGGGTNATGTNANNTNNNNTNNNNNNNN
    +
    !%(''(%%&/%%%%'&!)'+%!%&+1!%)'(!%!!(!!!!)!!!!!!!!
    @GO06_2500_Mate:1_5_104/2
    NGAAAGGAGGGAGAGGNAAGTNAGTTNAGGTNGNNTNNNNTNNNNNNNN
    +
    !'&(%(*0'&+&%+%%!%*)%!(+%(!'&%(!(!!'!!!!%!!!!!!!!
    @GO06_2500_Mate:1_9_50/2
    NAAATAAAAAGCCGGAAAAGTNGGGTNAATGNANNTNNNNANNNNNNNN
    +
    !%'*'%&&%(*%%)1(%)(**!%&),!)%%%!%!!%!!!!(!!!!!!!!

    can any body help me with this error i
    Last edited by huma Asif; 12-09-2014, 04:43 AM.

  • #2
    I copied your code and had a similar problem.
    But writing it in the same style, it worked:
    Your '-' symbols look on my bash a bit shorter than mine.
    Code:
     -v vs. ‐v
    Try to re-write your code in a plain text editor and run it again.

    Comment


    • #3
      i corrected that but now getting this error
      failed to open input file 'GO06_2500_Mate.read2.fastq': Value too large for defined data type

      Comment


      • #4
        How big is your file?
        Maybe it is really to big for the old fastx tool-kit.
        If that's the case and you need to stick to the program, you can split the file into several smaller ones.

        Alternatively, you may have a look at bbduk. Especially, if you are dealing with paired-end data.

        Comment


        • #5
          thank you for your help
          i will try that

          Comment

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