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  • CABOG: how to merge two genomes?

    I want to merge two assemblies with Cabog 8.2, since Cabog can handle long fragments.

    This is my command line:

    module load cabog/x86_64/8.2
    module load openmpi/x86_64/1.4.3
    module list

    runCA -d merged_assembly -p Artemia_inbred_merged -s CabogSpecfile_default.txt -version genome1.frg genome2.frg


    I left the CabogSpecfile_default.txt completely default and just added the file names in the bottom of the specfile.

    This is the error output I get:

    Currently Loaded Modulefiles:

    1) /perl/x86_64/5.14.1 3) /openmpi/x86_64/1.4.3
    2) /gridengine/x86_64/2011.11 4) /cabog/x86_64/8.2
    ENV: SGE_TASK_ID needs to be unset, done.
    CA version 8.2 ($Id: AS_GKP_main.C 4535 2014-06-10 22:08:29Z skoren $).
    CA version 8.2 ($Id: AS_CGB_unitigger.C 4518 2014-03-31 20:11:04Z brianwalenz $).
    CA version 8.2 ($Id: BuildUnitigs.C 4371 2013-08-01 17:19:47Z brianwalenz $).
    Using up to 64 OpenMP threads.
    CA version 8.2 ($Id: AS_CGW_main.C 4557 2014-08-11 12:24:27Z brianwalenz $).
    CA version 8.2 ($Id: terminator.C 4371 2013-08-01 17:19:47Z brianwalenz $).


    Does anyone know what is the problem? I am also not getting any data output.

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