I'm brand new to glimmer and gene assembly and prediction. I'm having a hiccup with the "build the model" step. I write the following command:
$ build-icm –r glm_ref.icm < glm_ref.long.seq
At this point I think I'm on track. My understanding is the model information is saved to a binary file named glm_ref.icm. Given this model, I can now use glimmer to predict genes in the reference genome.
USAGE: build-icm [options] output_file < input-file
Read sequences from standard input and output to output-file
the interpolated context model built from them.
Input also can be piped into the program, e.g.,
cat abc.in | build-icm xyz.icm
If <output-file> is "-", then output goes to standard output
Set depth of model to <num>
Ignore input strings with in-frame stop codons
Print this message
Set period of model to <num>
Use the reverse of input strings to build the model
Output model as text (for debugging only)
Set verbose level; higher is more diagnostic printouts
Set length of model window to <num>
Next, I write the following command:
$ glimmer3 EC.fasta glm_ref.icm glm_ref
But then I keep receiving the following error:
Starting at Tue Feb 6 19:09:00 2018
ERROR: Could not open file glm_ref.icm
errno = 2
I've looked in my directory and do not see a glm_ref.icm file (should I)? I've also looked in my glimmer folder and although I see a folder named ICM,, there is no specific file named glm_ref.icm?