how to get prodigal to use more threads

nf-core / mag

Assembly and binning of metagenomes

https://nf-co.re/mag

MIT License

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how to get prodigal to use more threads #711

Closed Drob84761 closed 1 week ago

Drob84761 commented 1 week ago

I am very new to the nf-core. I have modified the base config to use more threads, but it does not seem that prodigal is actually using them. Any suggestions?

prototaxites commented 1 week ago

As far as I am aware, Prodigal doesn't currently support multi-threading, and nor does the more modern replacement Pyrodigal. So I don't think there's currently a way to speed up this step, sorry!

jfy133 commented 1 week ago

I confirm there is no wait to multihread this: you can see this in the prodigal options - https://github.com/hyattpd/prodigal/wiki/cheat-sheet sorry @Drob84761 !

jfy133 commented 1 week ago

Althougugh Pyrodigal does seem to have (some) form of multi-threading support, so we coudl consider replacing it: https://pyrodigal.readthedocs.io/en/stable/guide/parallel.html if requested again