The issue was reported in qiime2 2022.2: slow alpha-rarefaction , Alpha-rarefaction not finishing with Qiime 2021.11 sometimes , and 'qiime diversity alpha-rarefaction' consume too much cpus and run weird slow . I am currently updating qiime2 in my workflows and I was wondering whether I should update the Rarefaction step as well, which I had previously pinned to an older version.
Colin said:
”Turns out that the implementation of faith_pd in q2-diversity changed under-the-hood and may be slowing things down. We need to update the back-end and resolve this performance regression.
Once we have an issue open, we can post it here.”
Was this fixed or at least is there an open issue for it? I looked at the qiime2 release notes since then and saw no mention of a fix for it.