The bioBakery help forum

Time of analysis questions

Hi, I am able to get humann3 up and running, however, our fastq files are quite large (10-12 GB each), and we have 24 samples. Would you know if this would take hours or days using 40 cores (threads)? Thank you!

Best wishes,

Carla Uranga

That’s pretty similar to the size of the files we used in benchmarking HUMAnN 3 (30M 150 nt reads). Depending on the settings, those ran for 8-16 hours using 5 cores, almost all of which is spent during translated search. I have found that performance doesn’t necessarily scale linearly with the number of cores per sample, such that you’re probably better off running e.g. 8 samples in parallel with 5 cores each vs. 1 sample at a time with 40 cores.