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  • matias_irazoqui
    Junior Member
    • Aug 2012
    • 1
    #1

    Parsing a MEGAN file by command line

    Hi, I have a quite large RMA file (about 40 GBs), and every time I try to open it, my (poor little) PC freezes. I was wondering if there's a way to parse the RMA file by command line and split it into a few parts more "manageable" (I was thinking one file for 'Bacteria', another for 'Archaea', etc, but it can be in any other way posible).
    I have access to a couple of servers (without graphical interface), so I can run big processes.
    Thanks!
    Tags: command line, megan, metagenomics
  • cliffbeall
    Senior Member
    • Jan 2010
    • 144
    #2
    The manual says rma is a binary compressed format - it didn't seem to be recognized by zip, gzip or bzip2 for me although maybe I was doing something wrong.

    The latest MEGAN includes a command-line tool but that requires the full, paid version.

    You did increase the memory as far as possible by editing the MEGAN.vmoptions file?

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