Dear All,
I am running qiime2 version 2019.10 via Virtualbox and this is my command
qiime feature-classifier classify-sklearn --i-reads /media/sf_Microbiome_qiime2/NewPublication/Working/RVA_neg_dada2_output/RVA_neg_rep_seqs_filt.qza --i-classifier /media/sf_Microbiome_qiime2/NewPublication/taxa_classifiers2/silva-132-99-nb-classifier.qza --p-n-jobs 4 --output-dir RVA_neg_taxa
After running I got this Error Plugin error from feature-classifier:
Could not pickle the task to send it to the workers.
Debug info has been saved to /tmp/qiime2-q2cli-err-48xz5fdv.log
joblib.externals.loky.process_executor._RemoteTraceback:
Traceback (most recent call last):
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/joblib/externals/loky/backend/queues.py", line 150, in _feed
obj_ = dumps(obj, reducers=reducers)
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/joblib/externals/loky/backend/reduction.py", line 247, in dumps
dump(obj, buf, reducers=reducers, protocol=protocol)
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/joblib/externals/loky/backend/reduction.py", line 240, in dump
_LokyPickler(file, reducers=reducers, protocol=protocol).dump(obj)
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/joblib/externals/cloudpickle/cloudpickle.py", line 482, in dump
return Pickler.dump(self, obj)
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 409, in dump
self.save(obj)
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 521, in save
self.save_reduce(obj=obj, *rv)
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 634, in save_reduce
save(state)
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 476, in save
f(self, obj) # Call unbound method with explicit self
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 821, in save_dict
self._batch_setitems(obj.items())
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 847, in _batch_setitems
save(v)
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 521, in save
self.save_reduce(obj=obj, *rv)
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 634, in save_reduce
save(state)
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 476, in save
f(self, obj) # Call unbound method with explicit self
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 821, in save_dict
self._batch_setitems(obj.items())
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 852, in _batch_setitems
save(v)
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 521, in save
self.save_reduce(obj=obj, *rv)
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 634, in save_reduce
save(state)
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 476, in save
f(self, obj) # Call unbound method with explicit self
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 821, in save_dict
self._batch_setitems(obj.items())
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 847, in _batch_setitems
save(v)
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 476, in save
f(self, obj) # Call unbound method with explicit self
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 781, in save_list
self._batch_appends(obj)
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 808, in _batch_appends
save(tmp[0])
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 476, in save
f(self, obj) # Call unbound method with explicit self
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 736, in save_tuple
save(element)
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 476, in save
f(self, obj) # Call unbound method with explicit self
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 751, in save_tuple
save(element)
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 521, in save
self.save_reduce(obj=obj, *rv)
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 634, in save_reduce
save(state)
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 476, in save
f(self, obj) # Call unbound method with explicit self
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 821, in save_dict
self._batch_setitems(obj.items())
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 847, in _batch_setitems
save(v)
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 476, in save
f(self, obj) # Call unbound method with explicit self
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 781, in save_list
self._batch_appends(obj)
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 805, in _batch_appends
save(x)
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 476, in save
f(self, obj) # Call unbound method with explicit self
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 781, in save_list
self._batch_appends(obj)
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 805, in _batch_appends
save(x)
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 521, in save
self.save_reduce(obj=obj, *rv)
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 634, in save_reduce
save(state)
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 476, in save
f(self, obj) # Call unbound method with explicit self
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 821, in save_dict
self._batch_setitems(obj.items())
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 847, in _batch_setitems
save(v)
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 482, in save
rv = reduce(obj)
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/joblib/_memmapping_reducer.py", line 339, in __call__
for dumped_filename in dump(a, filename):
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/joblib/numpy_pickle.py", line 505, in dump
NumpyPickler(f, protocol=protocol).dump(value)
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/pickle.py", line 409, in dump
self.save(obj)
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/joblib/numpy_pickle.py", line 292, in save
wrapper.write_array(obj, self)
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/joblib/numpy_pickle.py", line 104, in write_array
pickler.file_handle.write(chunk.tostring('C'))
OSError: [Errno 28] No space left on device
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/commands.py", line 328, in __call__
results = action(**arguments)
File "</home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/decorator.py:decorator-gen-347>", line 2, in classify_sklearn
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py", line 240, in bound_callable
output_types, provenance)
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py", line 383, in _callable_executor_
output_views = self._callable(**view_args)
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_feature_classifier/classifier.py", line 218, in classify_sklearn
confidence=confidence)
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_feature_classifier/_skl.py", line 45, in predict
for chunk in _chunks(reads, chunk_size)) for m in c)
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/joblib/parallel.py", line 1016, in __call__
self.retrieve()
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/joblib/parallel.py", line 908, in retrieve
self._output.extend(job.get(timeout=self.timeout))
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/joblib/_parallel_backends.py", line 554, in wrap_future_result
return future.result(timeout=timeout)
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/concurrent/futures/_base.py", line 432, in result
return self.__get_result()
File "/home/mh_user/anaconda2/envs/qiime2-2019.10/lib/python3.6/concurrent/futures/_base.py", line 384, in __get_result
raise self._exception
_pickle.PicklingError: Could not pickle the task to send it to the workers.
Sincerely,
Suwitchaya