scikit version for 2024.10 release downgrades to 0.59 after installing empress

Technical Support
1

Hi.

I'm using the new release qiime2-amplicon-2024.10 with some 16S data from stool samples. I wanted to run phylo-rpca on them, so I pip installed gemelli and empress. After generating the phylo-rpca plots, I wanted to compare this with unifrac and jaccard, so I tried running the basic core-metrics-phylogenetic command, but got the error:

module 'skbio.diversity.alpha' has no attribute 'sobs'

I think this may have to do with the scikit-bio version? I did see an earlier post regarding this from last Jun. I saw @SoilRotifier 's final reply on the topic ([Moving Picture Tutorial] Issues when running the "core-metrics-phylogeny" pipeline in "diversity" plugin - #28 by SoilRotifer) confirm that installing emperess could be downgrading the scikit-bio version. Was this the issue behind the error? Was it fixed?

The only other fix I've seen is some users downgrading to an older qiime version, but I've had issues with artifacts generated from different qiime versions not being compatible with commands written in other qiime environments, so I'm just trying to check first if there is now a work-around for this? Or maybe I'm doing something wrong and its not an issue from installing emperess?

Thanks in advance for your help, community!

2

Hello Deepan,

Yes, this is a known issue: Qiime2-2024.5 and empress - scikit-bio issue · Issue #566 · biocore/empress · GitHub

I'm sorry this is causing you problems. Hopefully this Empress issue will be fixed in a new version of Qiime2!

2 Likes
3

Understood! Thank you for pointing me to this issue.

4

Hi, were you able to run core-metrics-phylogenetic command eventually?

With scikit-bio 0.5.9, you get this error : module 'skbio.diversity.alpha' has no attribute 'sobs'
With scikit-bio 0.6.0, you get this error : Requirement.parse('scikit-bio<0.6.0,>=0.5.0')

So, I am not really sure what to do for my pipeline to run smoothly without these two errors.