I have seen similar problems with the classifier on here before but couldn’t find any post of exactly I am working on to fix. Here my problem.
I am running qiime2-2017.10 and submitted the command qiime feature-classifier fit-classifier-naive-bayes. I should mention the extraction step involving the primer sequences went well, the feature data sequence was saved. Training the classifier seems to make problems:
(qiime2-2017.10) Steffens-MacBook-Pro:qiime2-2017.10 steff$ qiime feature-classifier fit-classifier-naive-bayes --i-reference-reads Manta_testing/ref-seqs_16SBV51_trunclen100.qza --i-reference-taxonomy ref-taxonomy_SILVA_16S_97_consensus.qza --o-classifier 16S_classifier.qza --verbose
/Users/steff/miniconda3/envs/qiime2-2017.10/lib/python3.5/site-packages/q2_feature_classifier/classifier.py:98: UserWarning: The TaxonomicClassifier artifact that results from this method was trained using scikit-learn version 0.19.0. 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 “/Users/steff/miniconda3/envs/qiime2-2017.10/lib/python3.5/site-packages/q2cli/commands.py”, line 218, in call**
** results = action(arguments)
** File “”, line 2, in fit_classifier_naive_bayes**
** File “/Users/steff/miniconda3/envs/qiime2-2017.10/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 220, in bound_callable**
** output_types, provenance)**
** File “/Users/steff/miniconda3/envs/qiime2-2017.10/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 355, in callable_executor**
_** output_views = self.callable(view_args)
** File “/Users/steff/miniconda3/envs/qiime2-2017.10/lib/python3.5/site-packages/q2_feature_classifier/classifier.py”, line 276, in generic_fitter**
_** File "/Users/steff/miniconda3/envs/qiime2-2017.10/lib/python3.5/site-packages/q2_feature_classifier/skl.py", line 31, in fit_pipeline**
** y, X = list(zip(*data))**
ValueError: not enough values to unpack (expected 2, got 0)
Plugin error from feature-classifier:
** not enough values to unpack (expected 2, got 0)**
See above for debug info.
Does the error come from the reference sequence or the taxonomy file?
Any help would be really great as I am using the qiime2 pipeline for the first time!