Re: [Aatpackage-users] AAT doesn't work for proteins

[Brian H. <bh...@br...>]

Hi Daniel,

If you want to install this in /usr/local/bin, then you'll also have to
copy the matrices/ directory to /usr/local, because the AAT.pl script is
looking for it as /usr/local/matrices

best,

-b

On Tue, Feb 21, 2012 at 12:45 AM, Daniel Fernandez
<dan...@gm...>wrote:

> Dear Mr.
>
> I'm trying to run AAT program for genomic sequences against proteins but
> it doesn't work
>
> I run the "runMe.sh" script, this run ok
>
> But when I tried to run the command into the "runMe.sh" separately, the
> first command "AAT.pl -N ..." for nucleotide, this run ok but ..
> when I tried run the command
> $ AAT.pl -P -q arab.genomicSeq -s arab.pep --dps '-f 100 -i 30 -a 200'
> --filter '-c 10' --nap '-x 10'
> this doesn't work
>
> After I installed the AAT program, I copied the AAT.pl dds, dps, ext,
> filter, gap2, nap and show in /usr/local/bin
> Sorry but I don't know much about programming
> Could you tell me what is the problem, please?
>
> This is the result.
>
> ###################################################################
> $ AAT.pl -P -q arab.genomicSeq -s arab.pep --dps '-f 100 -i 30 -a 200'
> --filter '-c 10' --nap '-x 10'
> params: arab.pep, arab.genomicSeq, , arab.pep, -f 100 -i 30 -a 200, , -c
> 10, -x 10
>
> ## Processing (AAT-protein) bac_F8G22
> querySeq: bac_F8G22
> CMD: /usr/local/bin/dps bac_F8G22 arab.pep /usr/local/bin/../matrices/BS
> -f 100 -i 30 -a 200 2>&1 > bac_F8G22.arab.pep.dps
> ret(256)
> Error, command failed: /usr/local/bin/dps bac_F8G22 arab.pep
> /usr/local/bin/../matrices/BS -f 100 -i 30 -a 200 2>&1 >
> bac_F8G22.arab.pep.dps, returns(256), response: Cannot open
> /usr/local/bin/../matrices/BS.
>
> ----
> Error encountered while running pipeline:
> CMD: -P -q arab.genomicSeq -s arab.pep --dps -f 100 -i 30 -a 200 --filter
> -c 10 --nap -x 10
> protein (dps/nap) pipeline
> genomic acc: bac_F8G22
> searchDB: arab.pep
> queryDB: arab.genomicSeq
> dps_opts: -f 100 -i 30 -a 200
> ext_opts:
> filter_opts: -c 10
> nap_opts: -x 10
> ERROR running cmd: /usr/local/bin/dps bac_F8G22 arab.pep
> /usr/local/bin/../matrices/BS -f 100 -i 30 -a 200 2>&1 >
> bac_F8G22.arab.pep.dps, returns(256), reponse: Cannot open
> /usr/local/bin/../matrices/BS.
>
> Errors were encountered while running the AAT pipeline.
> Check the file (arab.pep.arab.genomicSeq.21988.AAT.errlog) for details.
> ###################################################################
>
> --
> Daniel Antonio Fernández Ugaz
> Lab. Virology and Molecular Genetics
> Faculty of Veterinary
> Universidad Nacional Mayor de San Marcos - UNMSM
> Av. Circunvalación 2800, San Borja
> Lima 41, Perú
>
>
>
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-- 
-- 
Brian J. Haas
Manager, Genome Annotation and Analysis Research and Development
The Broad Institute
http://broad.mit.edu/~bhaas