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

[Laure Q. <Lau...@if...>]

Actually, the issue was glimmer3 and long-orfs options which were not 
recognized, so I modified AKUtils.pm to change $longorfs_opts and 
$glimmer_opts in order to have something like :
long-orfs $longorfs_opts -n -t 1.15
instead of
long-orfs $longorfs_opts --no_header --cutoff 1.15.

maybe my glimmer3 version does not allow using long options...

Regards,
Laure

Le 06/12/2012 17:54, Lee Katz a écrit :
> 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 <http://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... <mailto: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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