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  • MaSuRCA Assembler runCA Error

    Successfuly install MaSuRCA

    HTML Code:
    tar xfz MaSuRCA-3.2.1.tar.gz
    HTML Code:
    cd MaSuRCA-3.2.1
    HTML Code:
    sudo ./install.sh
    Configure and run config.txt

    Code:
    MaSuRCA-3.2.1/bin/masurca MaSuRCA-3.2.1/bin/config.txt
    Verifying PATHS...
    jellyfish OK
    Error: runCA not found or failed to run
    Help me to get through this error.

  • #2
    Please do not crosspost to Biostars if you want help here ..

    jellyfish is in your PATH, runCA is not.

    You could either use --path /PATH/TO/runCA with masurca or add the corresponding path to your PATH variable.

    There is a bin folder in masurca installation directory which holds the common binaries. runCA and other programs are in one of the "neighbor" folders, in CA/bin or CA8/bin.

    best,
    Sven

    Comment


    • #3
      Thank you Sven, its work

      PATH=~/tools/MaSuRCA-3.2.1_12062016/CA/Linux-i686/bin:$PATH
      PATH=$PATH:~/tools/MaSuRCA-3.2.1_12062016/CA/Linux-i686/bin

      sudo env "PATH=$PATH" ~/tools/MaSuRCA-3.2.1_12062016/bin/masurca ~/tools/MaSuRCA-3.2.1_12062016/bin/config.txt

      Comment


      • #4
        I also have a runCA issue, I installed MaSuRCA-3.2.1_01202017 successfully. I use CA8/bin in my PATH. During Assembly, MsSuRCA threw a runCA error:
        "ERROR: the runCA option ovlHashBlockSize is not recognized.
        This runCA functionality changed in CABOG version 7.
        Try using ovlHashBlockLength instead."

        I found masurca generated "assemble.sh" based on runCA6 command, but installed runCA version is 8.2. So how to fix this issue ?

        best,
        mjx

        Comment

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