Hi,
I’m having difficulties with the feature-classifier plugin, in qiime 2019.7. When I run the following command:
qiime feature-classifier classify-sklearn
–i-classifier silva-132-99-nb-classifier.qza
–i-reads rep-seqs.qza
–p-pre-dispatch ‘n_jobs’
–o-classification taxonomy.qza
–verbose
I receive this error:
Traceback (most recent call last):
File “/home/qiime2/miniconda/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/commands.py”, line 327, in call
results = action(**arguments)
File “</home/qiime2/miniconda/envs/qiime2-2019.7/lib/python3.6/site-packages/decorator.py:decorator-gen-347>”, line 2, in classify_sklearn
File “/home/qiime2/miniconda/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 229, in bound_callable
spec.view_type, recorder)
File “/home/qiime2/miniconda/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/result.py”, line 289, in _view
result = transformation(self._archiver.data_dir)
File “/home/qiime2/miniconda/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/core/transform.py”, line 70, in transformation
new_view = transformer(view)
File “/home/qiime2/miniconda/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_feature_classifier/_taxonomic_classifier.py”, line 72, in _1
pipeline = joblib.load(os.path.join(dirname, ‘sklearn_pipeline.pkl’))
File “/home/qiime2/miniconda/envs/qiime2-2019.7/lib/python3.6/site-packages/joblib/numpy_pickle.py”, line 598, in load
obj = _unpickle(fobj, filename, mmap_mode)
File “/home/qiime2/miniconda/envs/qiime2-2019.7/lib/python3.6/site-packages/joblib/numpy_pickle.py”, line 526, in _unpickle
obj = unpickler.load()
File “/home/qiime2/miniconda/envs/qiime2-2019.7/lib/python3.6/pickle.py”, line 1050, in load
dispatchkey[0]
File “/home/qiime2/miniconda/envs/qiime2-2019.7/lib/python3.6/site-packages/joblib/numpy_pickle.py”, line 352, in load_build
self.stack.append(array_wrapper.read(self))
File “/home/qiime2/miniconda/envs/qiime2-2019.7/lib/python3.6/site-packages/joblib/numpy_pickle.py”, line 195, in read
array = self.read_array(unpickler)
File “/home/qiime2/miniconda/envs/qiime2-2019.7/lib/python3.6/site-packages/joblib/numpy_pickle.py”, line 141, in read_array
array = unpickler.np.empty(count, dtype=self.dtype)
numpy.core._exceptions.MemoryError: Unable to allocate array with shape (895606784,) and data type float64
Plugin error from feature-classifier:
Unable to allocate array with shape (895606784,) and data type float64
I’ve tried this with and without the --p-pre-dispatch ‘n_jobs’ \ but the result is always the same. The VM currently has around 8gb ram allocated to it, and is on a dynamic disk, with the host having around 100gb storage on the drive
Thanks!