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  • bbduk memory error

    Hello everyone,

    I've installed bbmap throw 'sudo apt-get install bbmap' and also by downloading the package, untaring it and adding the path to the directory in the .bashrc file. However, when running "bbduk.sh --version" or a script "bbduk.sh -Xmx ..." I get the following error:

    /usr/bin/bbduk.sh: línea 344: /usr/share/bbmap/calcmem: No existe el archivo o el directorio
    /usr/bin/bbduk.sh: línea 345: setEnvironment: orden no encontrada
    /usr/bin/bbduk.sh: línea 346: parseXmx: orden no encontrada
    /usr/bin/bbduk.sh: línea 350: freeRam: orden no encontrada
    java -Xmxm -Xmsm -cp /usr/share/java/bbmap.jar jgi.BBDuk --version
    Invalid maximum heap size: -Xmxm
    Error: Could not create the Java Virtual Machine.
    Error: A fatal exception has occurred. Program will exit.

    I've tried -Xmx with different amounts of memory and receive the same error. Also, the folder /calcmem does indeed do not exist. Any ideas on how to solve this problem?

    Thank you!

  • #2
    Cross-posted and answered here: https://www.biostars.org/p/9469494/#9469500

    Please use that answer.

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