Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Latest Developments in Precision Medicine
      by seqadmin



      Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

      Somatic Genomics
      “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
      Yesterday, 01:16 PM
    • seqadmin
      Recent Advances in Sequencing Analysis Tools
      by seqadmin


      The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
      05-06-2024, 07:48 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, Yesterday, 07:15 AM
    0 responses
    13 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-23-2024, 10:28 AM
    0 responses
    17 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-23-2024, 07:35 AM
    0 responses
    20 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-22-2024, 02:06 PM
    0 responses
    10 views
    0 likes
    Last Post seqadmin  
    Working...
    X