Plugin error from phylogeny: unexpected keyword argument 'reset'

[pau]

Dear Qiimers,

I’ve encountered an error on qiime2-amplicon-2025.10 when running the following command:

qiime phylogeny align-to-tree-mafft-fasttree
--i-sequences rep-seqs.qza
--o-alignment aligned-rep-seqs.qza
--o-masked-alignment masked-aligned-rep-seqs.qza
--o-tree unrooted-tree.qza
--o-rooted-tree rooted-tree.qza

That corresponds to the final command of the pipeline, this one:

qiime phylogeny midpoint-root
--i-tree unrooted-tree.qza
--o-rooted-tree rooted-tree.qza

The error is this one:

Plugin error from phylogeny:

TreeNode.root_at_midpoint() got an unexpected keyword argument 'reset'

Debug info has been saved to /tmp/qiime2-q2cli-err-lewofvhy.log

And the log file says:
Traceback (most recent call last):
File "/home/pau/miniconda3/envs/qiime2-amplicon-2025.10/lib/python3.10/site-packages/q2cli/commands.py", line 567, in call
results = self._execute_action(
File "/home/pau/miniconda3/envs/qiime2-amplicon-2025.10/lib/python3.10/site-packages/q2cli/commands.py", line 639, in _execute_action
results = action(**arguments)
File "", line 2, in midpoint_root
File "/home/pau/miniconda3/envs/qiime2-amplicon-2025.10/lib/python3.10/site-packages/qiime2/sdk/action.py", line 265, in bound_callable
outputs = self.callable_executor(
File "/home/pau/miniconda3/envs/qiime2-amplicon-2025.10/lib/python3.10/site-packages/qiime2/sdk/action.py", line 434, in callable_executor
output_views = self._callable(**view_args)
File "/home/pau/miniconda3/envs/qiime2-amplicon-2025.10/lib/python3.10/site-packages/q2_phylogeny/_util.py", line 13, in midpoint_root
return tree.root_at_midpoint(reset=True, branch_attrs , root_name=None)
TypeError: TreeNode.root_at_midpoint() got an unexpected keyword argument 'reset'

I’ve manually tried to edit this line in util.py, but I get other errors, so I preferred not to edit further…

return tree.root_at_midpoint(reset=True, branch_attrs=, root_name=None)

Any idea on what could be going on?

Thanks!!!

[gregcaporaso]

Hi @pau, I just tried to reproduce this error locally and I wasn't able to do it. Did you make any changes to your conda environment after creating it? Specifically I'm wondering if you somehow have a scikit-bio version < 0.6.2 installed. That wouldn't be supported. You can figure this out by running:

python -c "import skbio; print(skbio.__version__)"

If you do have a different version, I recommend re-installing QIIME 2 2025.10 and trying again.

If you're still stuck after checking for this, can you run qiime info and share the results?

[pau]

Dear @gregcaporaso ,

thanks a lot for your time and quick answer, and apologies for not being able to try it earlier,

Indeed it was related with the scikit-bio version, which was below the pointed one.

Just updated and reinstalled everything and now works perfectly!

Thanks again!