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
      Strategies for Sequencing Challenging Samples
      by seqadmin


      Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
      03-22-2024, 06:39 AM
    • seqadmin
      Techniques and Challenges in Conservation Genomics
      by seqadmin



      The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

      Avian Conservation
      Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
      03-08-2024, 10:41 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, Yesterday, 06:37 PM
    0 responses
    7 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 06:07 PM
    0 responses
    7 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    49 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    66 views
    0 likes
    Last Post seqadmin  
    Working...
    X