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Old 07-26-2016, 05:06 AM   #1
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Location: Rafaela, Argenitna

Join Date: Aug 2012
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Default 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.
matias_irazoqui is offline   Reply With Quote
Old 08-02-2016, 02:18 PM   #2
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Location: Ohio

Join Date: Jan 2010
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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?
cliffbeall is offline   Reply With Quote

command line, megan, metagenomics

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