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broadinstitute / pilon

Pilon is an automated genome assembly improvement and variant detection tool
GNU General Public License v2.0
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Memory usage relation to file size? #149

Open snail123815 opened 2 years ago

snail123815 commented 2 years ago

Dear Pilon team,

I now know that pilon needs larger memory when processing larger data. Could you please give a rough estimation about how it is correlated to the file size?

Specifically, how should I set -Xmx{}g when it comes with a MB of fasta and b MB of bam file.

I know it is simpler to set a large enough memory for all possible runs, however, when I put it into our pipeline, I might need to ask for more resources from HPC and increase waiting time. Thus, knowing this relationship will be good to reduce waiting time.

Thank you very much!

Nkosinathi15 commented 1 year ago

hi Snail,

were you assisted on this,

I have the same problem.