[Aatpackage-users] About ATT package - error

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

Dear sr.

I have some problems when I try to run the script runMe.sh in the AAT
package, it show me that:


> *************************************************
> running AAT nucleotide spliced alignment pipeline
> *************************************************
>
> ../bin/AAT.pl -N -q arab.genomicSeq -s arab.cdna --dds '-f 100 -i 20 -o 75
> -p 70 -a 2000' --filter '-c 10' --gap2 '-x 1'
> ## Processing (AAT-transcript) bac_F8G22
> CMD: /home/ubigem/PROGRAMAS/AAT/AAT/bin/dds bac_F8G22 arab.cdna -f 100 -i
> 20 -o 75 -p 70 -a 2000 2>&1 > bac_F8G22.arab.cdna.dds
> ret(512)
> Error, command failed: /home/ubigem/PROGRAMAS/AAT/AAT/bin/dds bac_F8G22
> arab.cdna -f 100 -i 20 -o 75 -p 70 -a 2000 2>&1 > bac_F8G22.arab.cdna.dds,
> returns(512), response: /home/ubigem/PROGRAMAS/AAT/AAT/bin/dds: 1: Syntax
> error: word unexpected (expecting ")")
> ----
> Error encountered while running pipeline:
> CMD: -N -q arab.genomicSeq -s arab.cdna --dds -f 100 -i 20 -o 75 -p 70 -a
> 2000 --filter -c 10 --gap2 -x 1
> transcript (dds/gap2) pipeline
> genomic acc: bac_F8G22
> searchDB: arab.cdna
> queryDB: arab.genomicSeq
> dds_opts: -f 100 -i 20 -o 75 -p 70 -a 2000
> ext_opts:
> filter_opts: -c 10
> gap2_opts: -x 1
> ERROR running cmd: /home/ubigem/PROGRAMAS/AAT/AAT/bin/dds bac_F8G22
> arab.cdna -f 100 -i 20 -o 75 -p 70 -a 2000 2>&1 > bac_F8G22.arab.cdna.dds,
> returns(512), reponse: /home/ubigem/PROGRAMAS/AAT/AAT/bin/dds: 1: Syntax
> error: word unexpected (expecting ")")
> Errors were encountered while running the AAT pipeline.
> Check the file (arab.cdna.arab.genomicSeq.1374.AAT.errlog) for details.
> **********************************************
> running AAT protein spliced alignment pipeline
> **********************************************
>
> ../bin/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: /home/ubigem/PROGRAMAS/AAT/AAT/bin/dps bac_F8G22 arab.pep
> /home/ubigem/PROGRAMAS/AAT/AAT/bin/../matrices/BS -f 100 -i 30 -a 200 2>&1
> > bac_F8G22.arab.pep.dps
> ret(512)
> Error, command failed: /home/ubigem/PROGRAMAS/AAT/AAT/bin/dps bac_F8G22
> arab.pep /home/ubigem/PROGRAMAS/AAT/AAT/bin/../matrices/BS -f 100 -i 30 -a
> 200 2>&1 > bac_F8G22.arab.pep.dps, returns(512), response:
> /home/ubigem/PROGRAMAS/AAT/AAT/bin/dps: 2: Syntax error: word unexpected
> (expecting ")")
> ----
> 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: /home/ubigem/PROGRAMAS/AAT/AAT/bin/dps bac_F8G22
> arab.pep /home/ubigem/PROGRAMAS/AAT/AAT/bin/../matrices/BS -f 100 -i 30 -a
> 200 2>&1 > bac_F8G22.arab.pep.dps, returns(512), reponse:
> /home/ubigem/PROGRAMAS/AAT/AAT/bin/dps: 2: Syntax error: word unexpected
> (expecting ")")
> Errors were encountered while running the AAT pipeline.
> Check the file (arab.pep.arab.genomicSeq.1379.AAT.errlog) for details.
> ************************************************
> combining results into a multiple alignment file
> ************************************************
>
> ../bin/show *gap2 *nap > multalignment.show.txt
> ./runMe.sh: línea 38: ../bin/show: no se puede ejecutar el fichero binario
>
> done.  See 'multalignment.show.txt' to examine all spliced alignments.
>


Can you tell me what is the solution, please?

Thanks for your time.

-- 
*Daniel Antonio Fernández Ugaz*
*Lab. Genetics of South American Camelids*
*Faculty of Veterinary*
*Universidad Nacional Mayor de San Marcos - UNMSM*
*Av. Circunvalación 2800, San Borja*
*Lima 41, Perú*