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  • training GlimmerHMM

    Can anyone advise me on training on GlimmerHMM. I have the manual and have executed the command for trainGlimmerHMM.

    I get an "error 34 no acceptor for training"

    Does anyone know how to resolve this error?

    Thanks!

  • #2
    Do you know about the parameter on running glimmerhmm?

    Comment


    • #3
      Thanks for your reply.

      I actually got this problem worked out. It has been a while so I can't remember the exact solution but if memory serves me I had a problem with my exon file that was used for the training. Once fixed the training was successful.

      Comment


      • #4
        In my case, I able to run trainGlimmerHMM successfully. Then use the trained directory with glimmerhmm. It has no problem on gene predicting.

        But I don't understand some of the parameter of glimmerhmm (such as -o -v -f). Can you explain the meaning?

        Comment


        • #5
          Check out this link which explains Glimmer training options. I don't know the -o option and I don't see it in the table at the link below.
          glimmer,glimmerhmm, genefinder,genome,genomics,mummer,DNA, signatures, xhtml


          However the -v option explains that this the number of nucleotides that surround the gene coding regions ie, I assume this means at the 5' and 3' ends of the coding region for a gene and the -f option is a number for the average upstream UTR (untranslated region length) for a gene. I assume this means the 5' region of the gene.

          Comment


          • #6
            Thanks for your reply. But the link only show the option for "trainGlimmerHMM".
            My question is actually on "glimmerhmm". The -o -v -f in "glimmerhmm" is different with "trainGlimmerHMM".

            Comment


            • #7
              I used -v, -f and -g(creates a gff file) all with default values while running glimmer, so again I assume the options to train and to run are the same.

              Comment


              • #8
                GlimmerHMM training

                I get the same error! Do you remember what was wrong with your exon file? My exon file looks like:

                contig_1 1299 1430
                contig_1 1773 1886

                contig_2 1263 1376

                contig_3 839 961

                Comment


                • #9
                  Error 69

                  Originally posted by sagarutturkar View Post
                  I get the same error! Do you remember what was wrong with your exon file? My exon file looks like:

                  contig_1 1299 1430
                  contig_1 1773 1886

                  contig_2 1263 1376

                  contig_3 839 961
                  Well I was able to resolve the error. See details here: http://seqanswers.com/forums/showthread.php?t=4643

                  However, I am getting error 69 which says /GlimmerHMM/train/score exited funny: 35584. Does anybody get same error and know how to resolve this?

                  Comment


                  • #10
                    were you able to resolve the "score exited funny" error?

                    Originally posted by sagarutturkar View Post
                    Well I was able to resolve the error. See details here: http://seqanswers.com/forums/showthread.php?t=4643

                    However, I am getting error 69 which says /GlimmerHMM/train/score exited funny: 35584. Does anybody get same error and know how to resolve this?

                    Comment

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