This PR addresses the memory issues with --metagenome-mode from #2228 with the solutions proposed therein, namely:
by adding a flag variable to the estimate_for_contigs_db_for_metagenome() so that it doesn't store the per-contig estimation data unless we really have to (it is necessary only for storing output in matrix or JSON format)
by updating the program's help menu to make it clear that --metagenome-mode does contig-level estimates, and to clarify that using the -M flag turns this mode on
by adding a warning to the user about potential high memory usage when they request --metagenome-mode with matrix- or JSON-formatted output
I have tested the fix as described in #2228, and it enables the program to run in --metagenome-mode without being killed for excessive memory usage on a large metagenome with 20Gb of memory.
This PR addresses the memory issues with
--metagenome-modefrom #2228 with the solutions proposed therein, namely:estimate_for_contigs_db_for_metagenome()so that it doesn't store the per-contig estimation data unless we really have to (it is necessary only for storing output in matrix or JSON format)--metagenome-modedoes contig-level estimates, and to clarify that using the-Mflag turns this mode on--metagenome-modewith matrix- or JSON-formatted outputI have tested the fix as described in #2228, and it enables the program to run in
--metagenome-modewithout being killed for excessive memory usage on a large metagenome with 20Gb of memory.