training GlimmerHMM

[pageskipro]

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!

[ckuanglim]

Do you know about the parameter on running glimmerhmm?

[pageskipro]

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.

[ckuanglim]

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?

[pageskipro]

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.

http://www.cbcb.umd.edu/software/glimmerhmm/man.shtml

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.

[ckuanglim]

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".

[pageskipro]

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.

[sagarutturkar]

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

[sagarutturkar]

Error 69

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?

[ersgupta]

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

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?