hi all, after i run the following in the linux server (16GB, 16 cores):
qiime feature-classifier fit-classifier-naive-bayes
–i-reference-reads ref-seqs.qza
–i-reference-taxonomy ref-taxonomy.qza
–o-classifier classifier.qza
the debug info coming out like:
qiime2-q2cli-err-1p9e05ge.log
/opt/conda/envs/qiime2-2018.2/lib/python3.5/site-packages/q2_feature_classifier/classifier.py:101: UserWarning: The TaxonomicClassifier artifact that results from this method was trained using scikit-learn version 0.19.1. 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 “/opt/conda/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/commands.py”, line 246, in call
results = action(**arguments)
File “”, line 2, in fit_classifier_naive_bayes
File “/opt/conda/envs/qiime2-2018.2/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 228, in bound_callable
output_types, provenance)
File “/opt/conda/envs/qiime2-2018.2/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 363, in callable_executor
output_views = self._callable(**view_args)
File “/opt/conda/envs/qiime2-2018.2/lib/python3.5/site-packages/q2_feature_classifier/classifier.py”, line 310, in generic_fitter
pipeline)
File “/opt/conda/envs/qiime2-2018.2/lib/python3.5/site-packages/q2_feature_classifier/_skl.py”, line 32, in fit_pipeline
pipeline.fit(X, y)
File “/opt/conda/envs/qiime2-2018.2/lib/python3.5/site-packages/sklearn/pipeline.py”, line 250, in fit
self._final_estimator.fit(Xt, y, **fit_params)
File “/opt/conda/envs/qiime2-2018.2/lib/python3.5/site-packages/q2_feature_classifier/custom.py”, line 41, in fit
classes=classes)
File “/opt/conda/envs/qiime2-2018.2/lib/python3.5/site-packages/sklearn/naive_bayes.py”, line 555, in partial_fit
self._update_feature_log_prob(alpha)
File “/opt/conda/envs/qiime2-2018.2/lib/python3.5/site-packages/sklearn/naive_bayes.py”, line 718, in _update_feature_log_prob
np.log(smoothed_cc.reshape(-1, 1)))
MemoryError
I would like to know my input data is wrong or memory not enough? Thx a lot.