I have run into an issue with Rescript that I cannot see reported after searching the forum. When attempting to run 'qiime rescript evaluate-fit-classifier' I get the following:
Plugin error from rescript: Passing a set as an indexer is not supported. Use a list instead. The generation of ref-seqs and taxonomy all appears fine up to here.
Last entry in the debug log is:
File "/opt/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/pandas/core/indexing.py", line 2774, in check_dict_or_set_indexers
raise TypeError(
TypeError: Passing a set as an indexer is not supported. Use a list instead.
I am running Rescript via qiime2-amplicon-2024.5 in a conda environment via a Mac Terminal.
Any help or insights as to how to solve this would be hugely appreciated.
Thanks so much for the quick reply. Here is the whole command with the --verbose flag:
qiime rescript evaluate-fit-classifier \
--i-sequences spike-path-only-refseqs.qza \
--i-taxonomy spike-path-only-taxonomy.qza \
--o-classifier spike-path-only-refseqs-classifier.qza \
--o-evaluation spike-path-only-refseqs-classifier-evaluation.qzv \
--o-observed-taxonomy spike-path-only-refseqs-predicted-taxonomy.qza \
--verbose
Traceback (most recent call last):
File "/opt/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2cli/commands.py", line 520, in __call__
results = self._execute_action(
File "/opt/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2cli/commands.py", line 586, in _execute_action
results = action(**arguments)
File "<decorator-gen-720>", line 2, in evaluate_fit_classifier
File "/opt/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self._callable_executor_(
File "/opt/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/action.py", line 657, in _callable_executor_
outputs = self._callable(scope.ctx, **view_args)
File "/opt/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/rescript/cross_validate.py", line 34, in evaluate_fit_classifier
taxa = taxa.loc[seq_ids]
File "/opt/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/pandas/core/indexing.py", line 1178, in __getitem__
check_dict_or_set_indexers(key)
File "/opt/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/pandas/core/indexing.py", line 2774, in check_dict_or_set_indexers
raise TypeError(
TypeError: Passing a set as an indexer is not supported. Use a list instead.
Plugin error from rescript:
Passing a set as an indexer is not supported. Use a list instead.
See above for debug info.
Acknowledging I am at the limit of my understanding, some googling suggests that a python function in Rescript has been updated and now needs a list as an input?
and recovered the same error (last line of error log only)
File "/anaconda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/pandas/core/indexing.py", line 2774, in check_dict_or_set_indexers
raise TypeError(
TypeError: Passing a set as an indexer is not supported. Use a list instead.
Plugin error from rescript:
Passing a set as an indexer is not supported. Use a list instead.
Plugin error from rescript:
Passing a set as an indexer is not supported. Use a list instead.
Debug info has been saved to /tmp/qiime2-q2cli-err-l0g956ta.log
Hi @John_Strisler and @Mat_Goddard,
Looks like this was a bug in our q2-2024.5 release but we just released a patch. Uninstall this env and reinstall a new q2-2024.5 release, and you should be golden!
Just a note to all that any ref-seq or taxomony objects built prior to the patch will need to be re-built after the patch to avoid this error when creating a classifier.
Where is the updated distribution located when I call qiime --version on the redownloaded environment it reads q2cli version 2024.5.0. I also tried to create another environment with qiime2-amplicon-ubuntu-latest-conda.yml. But is appears to likely just be an update file
You won't see an updated version for q2cli - you'll only see updated versions for the packages that were patched. When running qiime info you should see q2-diversity and rescript at 2024.5.1, as those were the packages that received patch updates. If you're not seeing those versions, you are likely still working with the original release version of the amplicon distribution.
Here's a direct install command you can use to ensure you're installing the latest version (without needing to download a file to your local machine):
