Hi everyone!!!
Thanks in advance for your answer, I got a error message when I run this command
qiime feature-classifier classify-sklearn --i-classifier classifier.qza --i-reads ref-seqs.qza --o-classification taxonomy.qza
Plugin error from feature-classifier:
Debug info has been saved to /tmp/qiime2-q2cli-err-gw4i8alk.log
this is the result:
–verbose flag
Traceback (most recent call last):
File “/vault2/soft/miniconda2/envs/qiime2-2017.12/lib/python3.5/site-packages/q2cli/commands.py”, line 224, in call
results = action(**arguments)
File “”, line 2, in classify_sklearn
File “/vault2/soft/miniconda2/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 228, in bound_callable
output_types, provenance)
File “/vault2/soft/miniconda2/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 363, in callable_executor
output_views = self._callable(**view_args)
File “/vault2/soft/miniconda2/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_feature_classifier/classifier.py”, line 214, in classify_sklearn
confidence=confidence)
File “/vault2/soft/miniconda2/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_feature_classifier/_skl.py”, line 45, in predict
for chunk in _chunks(reads, chunk_size)) for m in c)
File “/vault2/soft/miniconda2/envs/qiime2-2017.12/lib/python3.5/site-packages/sklearn/externals/joblib/parallel.py”, line 779, in call
while self.dispatch_one_batch(iterator):
File “/vault2/soft/miniconda2/envs/qiime2-2017.12/lib/python3.5/site-packages/sklearn/externals/joblib/parallel.py”, line 625, in dispatch_one_batch
self._dispatch(tasks)
File “/vault2/soft/miniconda2/envs/qiime2-2017.12/lib/python3.5/site-packages/sklearn/externals/joblib/parallel.py”, line 588, in _dispatch
job = self._backend.apply_async(batch, callback=cb)
File “/vault2/soft/miniconda2/envs/qiime2-2017.12/lib/python3.5/site-packages/sklearn/externals/joblib/_parallel_backends.py”, line 111, in apply_async
result = ImmediateResult(func)
File “/vault2/soft/miniconda2/envs/qiime2-2017.12/lib/python3.5/site-packages/sklearn/externals/joblib/_parallel_backends.py”, line 332, in init
self.results = batch()
File “/vault2/soft/miniconda2/envs/qiime2-2017.12/lib/python3.5/site-packages/sklearn/externals/joblib/parallel.py”, line 131, in call
return [func(*args, **kwargs) for func, args, kwargs in self.items]
File “/vault2/soft/miniconda2/envs/qiime2-2017.12/lib/python3.5/site-packages/sklearn/externals/joblib/parallel.py”, line 131, in
return [func(*args, **kwargs) for func, args, kwargs in self.items]
File “/vault2/soft/miniconda2/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_feature_classifier/_skl.py”, line 52, in _predict_chunk
return _predict_chunk_with_conf(pipeline, separator, confidence, chunk)
File “/vault2/soft/miniconda2/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_feature_classifier/_skl.py”, line 66, in _predict_chunk_with_conf
prob_pos = pipeline.predict_proba(X)
File “/vault2/soft/miniconda2/envs/qiime2-2017.12/lib/python3.5/site-packages/sklearn/utils/metaestimators.py”, line 115, in
out = lambda *args, **kwargs: self.fn(obj, *args, **kwargs)
File “/vault2/soft/miniconda2/envs/qiime2-2017.12/lib/python3.5/site-packages/sklearn/pipeline.py”, line 357, in predict_proba
return self.steps[-1][-1].predict_proba(Xt)
File “/vault2/soft/miniconda2/envs/qiime2-2017.12/lib/python3.5/site-packages/sklearn/naive_bayes.py”, line 104, in predict_proba
return np.exp(self.predict_log_proba(X))
File “/vault2/soft/miniconda2/envs/qiime2-2017.12/lib/python3.5/site-packages/sklearn/naive_bayes.py”, line 84, in predict_log_proba
jll = self._joint_log_likelihood(X)
File “/vault2/soft/miniconda2/envs/qiime2-2017.12/lib/python3.5/site-packages/sklearn/naive_bayes.py”, line 725, in joint_log_likelihood
return (safe_sparse_dot(X, self.feature_log_prob.T) +
File “/vault2/soft/miniconda2/envs/qiime2-2017.12/lib/python3.5/site-packages/sklearn/utils/extmath.py”, line 135, in safe_sparse_dot
ret = a * b
File “/vault2/soft/miniconda2/envs/qiime2-2017.12/lib/python3.5/site-packages/scipy/sparse/base.py”, line 360, in mul
return self._mul_multivector(other)
File “/vault2/soft/miniconda2/envs/qiime2-2017.12/lib/python3.5/site-packages/scipy/sparse/compressed.py”, line 507, in _mul_multivector
other.dtype.char))
MemoryError
before to run this I runned
###Training feature classifiers with q2-feature-classifier con SILVA 128
##Obtaining and importing reference data sets
qiime tools import --type ‘FeatureData[Sequence]’ --input-path SILVA_99_otus_16S.fasta --output-path SILVA_99_otus_16S.qza
qiime tools import --type ‘FeatureData[Taxonomy]’ --source-format HeaderlessTSVTaxonomyFormat --input-path SILVA_consensus_taxonomy_7_levels.txt --output-path SILVA_ref-taxonomy.qza
##Extract reference reads
qiime feature-classifier extract-reads --i-sequences SILVA_99_otus_16S.qza --p-f-primer CCTACGGGNGGCWGCAG --p-r-primer GACTACHVGGGTATCTAATCC --p-trunc-len 300 --o-reads ref-seqs.qza
##Train the classifier
qiime feature-classifier fit-classifier-naive-bayes --i-reference-reads ref-seqs.qza --i-reference-taxonomy SILVA_ref-taxonomy.qza --o-classifier classifier.qza
My Qiime version es 2017.12