Hello QIIME2 communit,
As I am new and still learning bioinformatic and QIIME2 , 2019.1 in particular, using Virtualbox, I ran into this problem:
qiime feature-classifier classify-sklearn \
--i-classifier gg-13-8-99-nb-classifier.qza
--i-reads rep-seqs.qza
--o-classification taxonomy.qza
Plugin error from feature-classifier:
Debug info has been saved to /tmp/qiime2-q2cli-err-l9b_6vro.log
and when I run this command
less /tmp/qiime2-q2cli-err-l9b_6vro.log
this happend:
...
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/sklearn/pipeline.py", line 382, in predict_proba
return self.steps[-1][-1].predict_proba(Xt)
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/sklearn/naive_bayes.py", line 104, in predict_proba
return np.exp(self.predict_log_proba(X))
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/sklearn/naive_bayes.py", line 84, in predict_log_proba
jll = self._joint_log_likelihood(X)
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/sklearn/naive_bayes.py", line 731, in joint_log_likelihood
return (safe_sparse_dot(X, self.feature_log_prob.T) +
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/sklearn/utils/extmath.py", line 168, in safe_sparse_dot
ret = a * b
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/scipy/sparse/base.py", line 473, in mul
return self._mul_multivector(other)
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/scipy/sparse/compressed.py", line 482, in _mul_multivector
other.ravel(), result.ravel())
MemoryError
I tried to Train feature classifiers with q2-feature-classifier
this one was successful but did not fix the issue
I hope you can help..