Aat (Analysis And Annotation Of Genomes) - Error

Question

[Daniel Fernandez]

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:

*************************************************
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:

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

Answer 1

[Hamish]

Well I get the same errors if I use try to use binaries supplied in the AAT distribution on a Linux x86_64 system. Building the binaries from source solves the problem. So in a terminal change to the directory produced when the distribution was unpacked and enter the following commands (from Building AAT):

./configure --prefix=`pwd`
make
make install

While this produces a number of compiler warnings, none of them appear to be serious and the provided samples run without producing errors.

Checking the binaries supplied in the AAT distribution, they appear to be for MacOS X:

$ file bin/dds 
bin/dds: Mach-O 64-bit executable

Linux binaries (in this case an x86 binary) give something like:

$ file bin/dds 
bin/dds: ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.15, not stripped

Given that the documentation does not mention that binaries are supplied, I suspect that these binaries were included in error and that the authors expect that AAT will always be built from source during installation. You may want to contact the authors and let them know about this, and suggest they have a look the compile on Linux systems.

[Daniel Fernández]

Sorry but I don't know much about programming, my machine is not MacOS X, it's GNU/Linux Ubuntu, so how I can solve this?.

[Hamish]

Answer edited to include details of how to build AAT. If you have problems with the compile I suggest you contact the authors of AAT for additional assistance, this will allow them to take your feedback into account in any future releases.

Answer 2

[Daniel Fernández]

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

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

Thanks to all