Summarized reads not included in command line mode

While running megan in command line mode, performing:

    extract what=reads outdir='some dir' outfile='some file' data=Taxonomy ids= 2 allBelow=true;

Summarized reads are not extracted to file.

This problem does not happens while using MEGAN via the GUI.

MEGAN Ultimate Edition (version 6.8.18, built 21 Jul 2017)

Exact command line file I supplied:
open file='a file’
extract what=reads outdir=‘some dir’ outfile=‘some file’ data=Taxonomy ids= 2 allBelow=true;

Command line used:

xvfb-run --auto-servernum --server-num=1 $shot/software/megan6/MEGAN -g -c extract_reads.megan

After playing with java’s VM parameter and amount to memory given to the process, the command ran successfully.


I had to give the process 12G of memory though.

Yes, MEGAN requires a lot of memory, especially when processing a DAA file.