Why isn't alpha-rarefaction using more than 1 core?

Ideas and Suggestions
,
1

Hi all,

Love qiime2 but am struggling with a fairly long rarefaction plot calculation (>1hr). It seems to me that "qiime diversity alpha-rarefaction" should be able to be executed in parallel. Qiime1 seems to have supported that option previously: alpha_rarefaction.py – A workflow script for performing alpha rarefaction — Homepage. Any idea why the parallelization was dropped for Qiime2?

Best,

Stephan

3

Hello @Stephan_Bitterwolf. We basically just didn't have a good way to parallelize it in QIIME 2 when the action was written. We recently added the ability to parallelize actions in a fairly straightforward manner, so there is potential that this action will be parallelized in QIIME 2 (or a different version of the action that is parallelized will be added).

4 Likes
4

I see! Thats awesome about it potentially coming soon!!!!
Thanks for the reply :).

1 Like