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

[Daniel F. <dan...@gm...>]

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