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

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

Ok, good to know!  And anyone looking for the same problem will be able to
fix it with what you said.  Thank you!

Hopefully this Sourceforge upgrade that I'm about to hit OK on won't affect
the mailing list though...


On Fri, Dec 7, 2012 at 2:45 AM, Laure QUINTRIC <Lau...@if...>wrote:

> 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:Laure.Quintric@**ifremer.fr<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.
>>
>


-- 
Lee Katz, Ph.D.