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  • How to run KmerFreq

    Have anyone tried Correction package of SOAPdenovo? I input the fq file, but it alway said that fail to open file?

  • #2
    Dear Elisa,

    you have to provide KmerFreq with a text file containing the names of the sequence file(s), otherwise it will try to open every line as a file name.

    So like

    Code:
    KmerFreq -i filenames.txt -o kmer_table
    Enjoy!

    Comment


    • #3
      I have put the name of file in the txt file like this:

      /diag/home/jjin/oil_palm/raw/DNA1.fastq
      /diag/home/jjin/oil_palm/raw/DNA2.fastq

      However, it still display error for the second file:

      quality cutoff: 5
      seed length: 17
      output kmer index?: no
      file format: fq
      >>>>>>>>>>hash initializing<<<<<<<<<<

      in /diag/home/jjin/oil_palm/raw/DNA1.fastq
      file of the reads - /diag/home/jjin/oil_palm/raw/DNA2.fast - opening failed.
      spend total time 3919

      Can anyone give me some suggestions?

      Thanks!

      Jingjing

      Comment


      • #4
        I met the same problem as yours. Just add an 'return' at the end of second line of the input list file. It will be fine! Hope this will help you!

        Originally posted by jjjscuedu View Post
        I have put the name of file in the txt file like this:

        /diag/home/jjin/oil_palm/raw/DNA1.fastq
        /diag/home/jjin/oil_palm/raw/DNA2.fastq

        However, it still display error for the second file:

        quality cutoff: 5
        seed length: 17
        output kmer index?: no
        file format: fq
        >>>>>>>>>>hash initializing<<<<<<<<<<

        in /diag/home/jjin/oil_palm/raw/DNA1.fastq
        file of the reads - /diag/home/jjin/oil_palm/raw/DNA2.fast - opening failed.
        spend total time 3919

        Can anyone give me some suggestions?

        Thanks!

        Jingjing

        Comment


        • #5
          I don't want to sound like a jerk, but did you make sure the path and permissions were correct?

          Originally posted by jjjscuedu View Post
          I have put the name of file in the txt file like this:

          /diag/home/jjin/oil_palm/raw/DNA1.fastq
          /diag/home/jjin/oil_palm/raw/DNA2.fastq

          However, it still display error for the second file:

          quality cutoff: 5
          seed length: 17
          output kmer index?: no
          file format: fq
          >>>>>>>>>>hash initializing<<<<<<<<<<

          in /diag/home/jjin/oil_palm/raw/DNA1.fastq
          file of the reads - /diag/home/jjin/oil_palm/raw/DNA2.fast - opening failed.
          spend total time 3919

          Can anyone give me some suggestions?

          Thanks!

          Jingjing

          Comment

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