Plugin error from diversity: module 'skbio.diversity.alpha' has no attribute 'sobs'

Technical Support
,
1

I have Qiime2 installed on a virtual machine (see version below) and I am working on a Snakemake pipeline. So far everything has been functioning with no issues until I reached the core_metrics step which is giving the following error :

Plugin error from diversity: module 'skbio.diversity.alpha' has no attribute 'sobs'

There could be a conflict of versions but I can't really figure it out. This issue was previously posted but unsolved.

P.S. I tried scikit-bio v0.5.9 as well as scikit-bio v0.6.0

System versions
Python version: 3.10.14
QIIME 2 release: 2024.10
QIIME 2 version: 2024.10.1
q2cli version: 2024.10.1

Installed plugins
alignment: 2024.10.0
composition: 2024.10.0
cutadapt: 2024.10.0
dada2: 2024.10.0
deblur: 2024.10.0
demux: 2024.10.0
diversity: 2024.10.0
diversity-lib: 2024.10.0
emperor: 2024.10.0
empress: 1.2.0
feature-classifier: 2024.10.0
feature-table: 2024.10.0
fragment-insertion: 2024.10.0
longitudinal: 2024.10.0
metadata: 2024.10.0
phylogeny: 2024.10.0
quality-control: 2024.10.0
quality-filter: 2024.10.0
rescript: 2024.10.0
sample-classifier: 2024.10.0
stats: 0+unknown
taxa: 2024.10.0
types: 2024.10.0
vizard: 0.0.1.dev0
vsearch: 2024.10.0

2

Hello Linda,

Welcome to the forums! :qiime2:

I'm glad you found that other thread about this 'sobs' error.

(I've removed the duplicate post from the old thread, so we can work on your issue without bothering other forum members. We read every post, so there's no reason to post twice.)

While using Qiime2 2024.10, does the workaround here help you?

3

Hello! Thank you, the forum is very helpful and active.

The confirm that the workaround in the github solved my issue while using Qiime2 2024.10. I appreciate it, thanks!

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