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  • Trouble running CEGMA sample data

    Hello,

    I am installing cegma for the first time and I am having trouble running sample data. I googled it, I could not able to find a solution. I followed steps exactly as described in http://korflab.ucdavis.edu/Datasets/...ructions_2.txt

    Any suggestions will be greatly appreciated!



    user:~/cegma_v2.4.010312/bin$ ./cegma -g /home/src/cegma_v2.4.010312/sample/sample.dna -p /home/src/cegma_v2.4.010312/sample/sample.prot


    ********************************************************************************
    ** MAPPING PROTEINS TO GENOME (TBLASTN) **
    ********************************************************************************

    RUNNING: genome_map -n genome -p 6 -o 5000 -c 2000 -t 1 /home/src/cegma_v2.4.010312/sample/sample.prot /home/src/cegma_v2.4.010312/sample/sample.dna 2>output.cegma.errors


    Building a new DB, current time: 08/28/2014 11:41:29
    New DB name: /tmp/genome12011.blastdb
    New DB title: /home/src/cegma_v2.4.010312/sample/sample.dna
    Sequence type: Nucleotide
    Keep Linkouts: T
    Keep MBits: T
    Maximum file size: 1000000000B
    Adding sequences from FASTA; added 1 sequences in 0.167003 seconds.
    Found 86 candidate regions in /home/src/cegma_v2.4.010312/sample/sample.dna


    ********************************************************************************
    ** MAKING INITIAL GENE PREDICTIONS FOR CORE GENES (GENEWISE + GENEID) **
    ********************************************************************************

    RUNNING: local_map -n local -f -h ./data/hmm_profiles -i KOG genome.chunks.fa 2>output.cegma.errors
    FATAL ERROR when running local map 6400: "No such file or directory"

    ---------------------------------------------------------

    less output.cegma.errors

    Warning Error
    Could not open ./data/hmm_profiles/KOG0292.hmm for HMM reading
    Warning Error
    Could not read hmm from ./data/hmm_profiles/KOG0292.hmm

    Fatal Error
    Could not build objects!
    Can't run genewise -splice_gtag -quiet -gff -pretty -alb -hmmer ./data/hmm_profiles/KOG0292.hmm /tmp/genomic13567.fa > /tmp/genewise13567

  • #2
    You may have followed the steps in the link you included but did you get any errors along the way?

    Is there a local "bin" directory in the cegma base directory and are there several files in there including "local_map"?

    Comment


    • #3
      I made an amazon machine image for CEGMA - search CEGMA on AWS and you should find it. It is ami-18935a70. It's preconfigured, just upload your data and run.

      Comment


      • #4
        From the location where you ran CEGMA, is there a valid path to ./data/hmm_profiles?

        Comment

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