The bioBakery help forum

Speed up humann3

I am running a 77G input file into humann. It takes about a day to complete the analysis. Is there a way to speed up the process? I am only interested in identifying species og genera.
This is my command:

humann --threads 20 --protein-database uniref/uniref/ --input $FILE.fastq --output $FILE

If you are not interested in unclassified results from translated search you can add --bypass-translated-search to your command. This will probably speed up the process by at least 10x.