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  • problem of LTRdigest in GenomeTools

    Hi, I'm a genometools user, I'm here to report a problem (or maybe bug) when I was using ltrdigest on Ubuntu 10.04
    I invoked command as follow:
    $ gt ltrdigest -aaout yes -hmms ltrhmm/*.hmm test.gff test > gff3result.txt
    and it returned error as follow:
    gt ltrdigest: error: missing argument
    Usage: gt ltrdigest [option ...] gff3_file indexname
    I checked every directory and find nothing unusual. Would someone please help me find out what was wrong.
    Thank you

  • #2
    You need to specify a prefix for the output filenames with the "-outfileprefix" option. I also see that you are not specifying a file of tRNAs for PBS prediction, though I think that may be optional.

    Comment


    • #3
      Hello,
      I am using genometools and yesterday when using suffixerator I was provided an error message of illegal characters. When I opened my fasta file in Textwrangler and checked for the invisibles to be shown this is what I saw:
      >ˇ˛C?o?n?t?i?g?2?_?c?1?6?6?6?
      ?T?T?G?T?G?T?T?T?T?T?A?G?T?T?T?A?T?T?G?C?A?T?T?T?T?A?G?A?A?A
      ?A?A?G?T?C?A?T?T?T?T?T?G?T?G?T?T?T?T?T?G?T?C?C?A?T?T?A?C?G?T
      ?T?T?T?A?C?G?T?A?T?T?T?G?A?G?T?T?T?T?C?G?A?T?

      looks like the file is corrupt? And it continues this way everytime I download.

      Is there a program or something I can do to fix the file?

      Comment


      • #4
        Originally posted by htetre View Post
        Hello,
        I am using genometools and yesterday when using suffixerator I was provided an error message of illegal characters. When I opened my fasta file in Textwrangler and checked for the invisibles to be shown this is what I saw:
        >ˇ˛C?o?n?t?i?g?2?_?c?1?6?6?6?
        ?T?T?G?T?G?T?T?T?T?T?A?G?T?T?T?A?T?T?G?C?A?T?T?T?T?A?G?A?A?A
        ?A?A?G?T?C?A?T?T?T?T?T?G?T?G?T?T?T?T?T?G?T?C?C?A?T?T?A?C?G?T
        ?T?T?T?A?C?G?T?A?T?T?T?G?A?G?T?T?T?T?C?G?A?T?

        looks like the file is corrupt? And it continues this way everytime I download.

        Is there a program or something I can do to fix the file?
        Are you sure the file was finished downloading? If so, it could be a corrupted file but I've never seen that from likes of NCBI or EMBL, though I suppose it's possible. I would check the file size on the server with that of the download and see if anything looks off.

        Comment


        • #5
          Originally posted by hugh_hang View Post
          Hi, I'm a genometools user, I'm here to report a problem (or maybe bug) when I was using ltrdigest on Ubuntu 10.04
          I invoked command as follow:
          $ gt ltrdigest -aaout yes -hmms ltrhmm/*.hmm test.gff test > gff3result.txt
          and it returned error as follow:
          gt ltrdigest: error: missing argument
          Usage: gt ltrdigest [option ...] gff3_file indexname
          I checked every directory and find nothing unusual. Would someone please help me find out what was wrong.
          Thank you
          You need to terminate your list of HMMs with two minus signs ('--') to separate them from the GFF input:

          $ gt ltrdigest -aaout yes -hmms ltrhmm/*.hmm -- test.gff test > gff3result.txt

          Adding an additional option afterthe HMM list should be fine as well -- just make sure the GFF file and HMMs do not immediately follow each other.

          Comment


          • #6
            Originally posted by sst View Post
            You need to terminate your list of HMMs with two minus signs ('--') to separate them from the GFF input:

            $ gt ltrdigest -aaout yes -hmms ltrhmm/*.hmm -- test.gff test > gff3result.txt

            Adding an additional option afterthe HMM list should be fine as well -- just make sure the GFF file and HMMs do not immediately follow each other.
            thank you, but what does the '--' means? just make the bash know the GFF file as stdin?

            Comment


            • #7
              Originally posted by hugh_hang View Post
              thank you, but what does the '--' means? just make the bash know the GFF file as stdin?
              It is just an empty placeholder option to make the option parser aware that what follows is no longer an argument to the '-hmms' option, but rather the two arguments of the tool itself -- a terminator of sorts.

              Comment


              • #8
                Originally posted by sst View Post
                It is just an empty placeholder option to make the option parser aware that what follows is no longer an argument to the '-hmms' option, but rather the two arguments of the tool itself -- a terminator of sorts.
                I see, thank you!

                Comment

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