Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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

                Latest Articles

                Collapse

                • seqadmin
                  Strategies for Sequencing Challenging Samples
                  by seqadmin


                  Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
                  03-22-2024, 06:39 AM
                • seqadmin
                  Techniques and Challenges in Conservation Genomics
                  by seqadmin



                  The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

                  Avian Conservation
                  Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
                  03-08-2024, 10:41 AM

                ad_right_rmr

                Collapse

                News

                Collapse

                Topics Statistics Last Post
                Started by seqadmin, Yesterday, 06:37 PM
                0 responses
                12 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, Yesterday, 06:07 PM
                0 responses
                10 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 03-22-2024, 10:03 AM
                0 responses
                51 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 03-21-2024, 07:32 AM
                0 responses
                68 views
                0 likes
                Last Post seqadmin  
                Working...
                X