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  • prs321
    Member
    • Jun 2013
    • 96

    #1

    Is FastX Trimmer supposed to take a long time to trim the fastq file?

    I'm not sure whether or not the terminal is frozen or the file is still processing through the software...
  • GenoMax
    Senior Member
    • Feb 2008
    • 7142

    #2
    Originally posted by prs321 View Post
    I'm not sure whether or not the terminal is frozen or the file is still processing through the software...
    If you can't tell by looking at your system, how can we

    On a more serious note: Do you have a reference for how long it took for a similar size file to finish processing or is this the first one?

    Comment

    • prs321
      Member
      • Jun 2013
      • 96

      #3
      Originally posted by GenoMax View Post
      If you can't tell by looking at your system, how can we

      On a more serious note: Do you have a reference for how long it took for a similar size file to finish processing or is this the first one?
      For sure, I got it to work, thank you.

      Comment

      • balsampoplar
        Member
        • Mar 2014
        • 14

        #4
        If the terminal is not showing any signs of progress, you can always check for the size of the output file. This size will continually get updated as more data is trimmed and added to the output file. You can also check 'top' to see if the trimmer is occupying processor and memory.

        Comment

        • Brian Bushnell
          Super Moderator
          • Jan 2014
          • 2709

          #5
          Fastx is very slow; there are other trimmers that are better and faster (see graph).
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