Re: [Cg-pipeline-users] cg-pipeline trying to run prediction

[Lee K. <ls...@gm...>]

Let's see... this is older code so I am feeling my way here.  I'll give a
few points to look into, and hopefully one will address your issue.

First, the `run_pipeline predict` command will look for the file
myproject/assembly.fasta.  Does myseq.fasta match myproject/assembly.fasta?
 You could simply copy myseq.fasta to assembly.fasta, or another thing you
could do is use `run_prediction myseq.fasta -o myproject/prediction.gb`

Second, is glimmer installed properly on your machine?  Did you install it
using Linux repositories?

Third if all else fails, could you give us the CG-Pipeline where it matches
this error reporting line?
Error running long-orfs with command\n  long-orfs $longorfs_opts
--no_header --cutoff 1.15 '$longorfs_infile' '$longorfs_infile.longorfs'
2>'$$settings{tempdir}/glimmer3.log'\nError was $!

Thanks for letting us know about the problem!  Let us know if one of these
avenues fixes the problem.




On Thu, Dec 6, 2012 at 10:39 AM, Laure QUINTRIC
<Lau...@if...>wrote:

> Hello,
> I'm currently trying to use the cg-pipeline, and I have some troubles
> using the prediction part to calculate long-orfs :
>
> when I run run_pipeline predict -p myproject -i myseq.fasta
>
> in the myproject/build/prediction/glimmer3.log is written :
>
> ---
> Starting at Thu Dec  6 16:18:59 2012
>
> long-orfs: invalid option -- '-'
> Unrecognized option --
> USAGE:  long-orfs [options] <sequence-file> <output-file>
> ---
>
> is there a way to go through this ? maybe by launching manually the
> command?
> thanks.
>
> Laure
> IFREMER - France
>
>
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-- 
Lee Katz, Ph.D.