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  • 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:

    *************************************************
    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, 09:17 AM. Reason: SOLVED

  • #2
    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, 09:19 AM.

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