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  • CEGMA Error genome_map 6400

    Hi,

    I am trying to get CEGMA to run on our cluster. After the horrors of genewise installation I thought i had everything complete but now I recieve:


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

    RUNNING: genome_map -n genome -p 6 -o 5000 -c 2000 -t 1 ../sample/sample.prot ../sample/sample.dna 2>../test_run/sample.cegma.errors


    Building a new DB, current time: 01/04/2016 14:59:37
    New DB name: /tmp/genome13761.blastdb
    New DB title: ../sample/sample.dna
    Sequence type: Nucleotide
    Keep Linkouts: T
    Keep MBits: T
    Maximum file size: 1000000000B
    Adding sequences from FASTA; added 1 sequences in 0.065515 seconds.
    FATAL ERROR when running genome_map 6400: ""


    Ending CEGMA


    when I try to run CEGMA with: /project/molgen/Bio/CEGMA_v2.5/bin$ ./cegma --genome ../sample/sample.dna --protein ../sample/sample.prot -o ../test_run/sample


    I have installed genewise (wise2.4.1), geneid (1.4.4) and hmmer (3.1b2 and also tried 3.0).

    I have them all added to my path:

    /project/molgen/Bio/hmmer-3.0/src/:
    /project/molgen/Bio/geneid_1.4.4/bin/:
    /project/molgen/Bio/hmmer-3.1b2/bin/:
    /project/molgen/Bio/wise2.4.1/src/bin/:
    ...

    I can run them all from my terminal (tblastn also). And they all produce no Errors.

    I can run cegma -h and it works fine.

    But when I try to run cegma with the sample data set I get Error 6400.

    I googled/searched and it seems 6400 indicates some missing dependency but I have no idea whats missing.


    cat sample.cegma.errors gives me:

    BLAST query/options error: Compressed alphabet lookup table requires word size 6 or 7
    Please refer to the BLAST+ user manual.
    Can't run tblastn


    So is cegma using wrong parameters for tblastn?

    Can anybody help?
    Last edited by voidnyx; 01-04-2016, 06:12 AM.

  • #2
    I managed to get it working.

    Just in case someone stumbles across the same problem:

    Turns out I had only exported the Variables CEGMA and CEGMATMP once by hand and not added to my bashrc so they were gone when I restarted.

    Comment

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