I am trying to do gene prediction using GlimmerHMM. Training model was successfully completed but during prediction its giving "segmentation fault".

command : glimmerhmm_linux_x86_64 input.fasta -d Directory -o glimmer_results.gff -g

I am not familiar with this particular program, but perhaps this post will help you...

I assume you are referring to this program glimmerhmm download page.

If so... did you compile the program from source or did you manage to get a pre-compiled 64 bit version?

When I run the compiled program, without any options, on my machine I get the options menu like this:

USAGE:  ./glimmerhmm <genome1-file> <training-dir-for-genome1> [options] 
-p file_name     If protein domain searches are available, read them from file file_name
-d dir_name      Training directory is specified by dir_name (introduced for compatibility with earlier versions)
-o file_name     Print output in file_name; if n>1 for top best predictions, output is in file_name.1, file_name.2, ... , file_name.n f
-n n             Print top n best predictions
-g               Print output in gff format
-v               Don't use svm splice site predictions
-f               Don't make partial gene predictions
-h               Display the options of the program

The program's usage menu indicates seems to match your command line option list.

So there are a few possibilities:

  1. Somehow the build of the program went awry and doesn't function... missing library or something.
  2. There is no directory named Directory and instead you will need to specify something like ~/my_training_directory
  3. You are attempting to run a 64 bit program on a 32 bit machine.

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