Urgent! Scikit-bio issue

Technical Support
1

Qiime2.2024.10 v uses Python 3.10 and has scikit-bio 0.6.2v. when I want to run the following code for diversity analysis

qiime diversity core-metrics-phylogenetic \
  --i-table table.qza \
  --i-phylogeny rooted-tree.qza \
  --m-metadata-file metadata.tsv \
  --p-sampling-depth 9768 \
  --output-dir core-metrics-results

I am getting this error code
"pkg_resources.ContextualVersionConflict: (scikit-bio 0.6.2 (/home/mehmet/.conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages), Requirement.parse('scikit-bio<0.6.0,>=0.5.0'), {'iow'})"

It seems like I need to downgrade Python to use other versions of scikit bio. Could you please help me with this issue in an alternative way?

qiime info results:

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
feature-classifier: 2024.10.0
feature-table: 2024.10.0
fragment-insertion: 2024.10.0
greengenes2: 2024.1
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

Thanks for your help in advance

2

Hey @fatihfarabigazali,

Welcome to the :qiime2: forum :wave:

Check out our current environment files for 2024.10 - we aren't using scikit-bio 0.6.2, we're using 0.6.0. Did you try installing skbio separately? If not, I'd recommend either forcing a downgrade of skbio in your current environment (you can run conda install -c conda-forge -c bioconda scikit-bio=0.6.0 to achieve this). Otherwise, I'd start from a clean slate - removing this current environment, running conda clean --all, and then re-installing the 2024.10 amplicon distribution from our install docs.

Hope this helps! Cheers :lizard:

5

Hey Lizgehret,

Thank you so much for replying to my question. I tried them and did not work for me. I solved the issue by using the 2024.5 version.