I'm using qiime2 in conda and the size of the memory allocated is 7.7gb with 6.5gb free memory. During the training of sklearn classifier with the naive bayes model, i into some issues i cannot handle. Here are the code, db files and error messages.
Code:
qiime feature-classifier fit-classifier-sklearn
--i-reference-reads silva_ref_seqs.qza
--i-reference-taxonomy taxonomy.qza
--o-classifier classifier_silva_naive_bayes.qza
--p-classifier-specification "naive-bayes"
DB files:
SILVA_138.2_SSURef_NR99_tax_silva.fasta
tax_slv_ssu_138.2.txt
Error messages:
Plugin error from feature-classifier:
Expecting value: line 1 column 1 (char 0)
See above for debug info.
Detailed error:
/home/jaesik/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_feature_classifier/classifier.py:106: UserWarning: The TaxonomicClassifier artifact that results from this method was trained using scikit-learn version 1.5.2. It cannot be used with other versions of scikit-learn. (While the classifier may complete successfully, the results will be unreliable.)
warnings.warn(warning, UserWarning)
Traceback (most recent call last):
File "/home/jaesik/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2cli/commands.py", line 520, in call
results = self._execute_action(
File "/home/jaesik/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2cli/commands.py", line 581, in _execute_action
results = action(**arguments)
File "", line 2, in fit_classifier_sklearn
File "/home/jaesik/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 "/home/jaesik/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/action.py", line 576, in callable_executor
output_views = self._callable(**view_args)
File "/home/jaesik/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_feature_classifier/classifier.py", line 135, in fit_classifier_sklearn
spec = json.loads(classifier_specification)
File "/home/jaesik/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/json/init.py", line 346, in loads
return _default_decoder.decode(s)
File "/home/jaesik/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File "/home/jaesik/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/json/decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)