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Old 02-10-2012, 02:00 PM   #1
Daniel Fernandez
Member
 
Location: Lima. Perú

Join Date: Nov 2011
Posts: 31
Default AAT (analysis and annotation of genomes) - error

Hi everyone.

I'm trying to analysing a mammalian genome by the AAT package (http://aatpackage.sourceforge.net/), the package comes with examples (only I have to run the script runMe.sh) but don't work, it show me that:

Quote:
*************************************************
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.2702.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.2707.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.
Sorry it's very long, I tried to run only:

Code:
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'
But it show me the same error.

If any people had used this package please tell me what's the problem (or tell me another downloadable program, I want to find some genes in a mammalian genome, proteins and DNA to compare against a genome)

Thanks a lot

Last edited by Daniel Fernandez; 02-15-2012 at 08:17 AM. Reason: SOLVED
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Old 02-15-2012, 08:16 AM   #2
Daniel Fernandez
Member
 
Location: Lima. Perú

Join Date: Nov 2011
Posts: 31
Default Solved

SOLVED ok I write to the author and my error was only write ./configure , I did the exactly building with the --prefix=pwd and when I finished all installation, I copy all executables to /usr/local/bin

Code:
./configure --prefix=`pwd`
make
make install
sudo cp bin/* /usr/local/bin

Last edited by Daniel Fernandez; 02-15-2012 at 08:19 AM.
Daniel Fernandez is offline   Reply With Quote
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aat, analysis, annotation, genome, splicing

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