[Errno 12] Cannot allocate memory (Plugin error from feature-classifier)

[SongkranTh]

I used MicrobiomeHelper for 16s V3-4 analysis. I had a problem in feature-classifier step as problem log show follows:

mh_user@MicrobiomeHelper:~ source activate qiime2-2018.6 (qiime2-2018.6) mh_user@MicrobiomeHelper:~ cd /media
(qiime2-2018.6) mh_user@MicrobiomeHelper:/media$ cd sf_shared_folder
(qiime2-2018.6) mh_user@MicrobiomeHelper:/media/sf_shared_folder$ cd working
(qiime2-2018.6) mh_user@MicrobiomeHelper:/media/sf_shared_folder/working$ qiime feature-classifier classify-sklearn --i-reads dada2_output/rep_seqs_filt.qza --i-classifier database/silva-132-99-515-806-nb-classifier.qza --p-n-jobs 4 --output-dir taxa --verbose
Traceback (most recent call last):
File “/home/mh_user/anaconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/q2cli/commands.py”, line 274, in call
results = action(**arguments)
File “”, line 2, in classify_sklearn
File “/home/mh_user/anaconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 232, in bound_callable
output_types, provenance)
File “/home/mh_user/anaconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 367, in callable_executor
output_views = self._callable(**view_args)
File “/home/mh_user/anaconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/q2_feature_classifier/classifier.py”, line 205, in classify_sklearn
reads_per_batch = _autotune_reads_per_batch(reads, n_jobs)
File “/home/mh_user/anaconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/q2_feature_classifier/classifier.py”, line 191, in _autotune_reads_per_batch
stdout=subprocess.PIPE)
File “/home/mh_user/anaconda2/envs/qiime2-2018.6/lib/python3.5/subprocess.py”, line 383, in run
with Popen(*popenargs, **kwargs) as process:
File “/home/mh_user/anaconda2/envs/qiime2-2018.6/lib/python3.5/subprocess.py”, line 676, in init
restore_signals, start_new_session)
File “/home/mh_user/anaconda2/envs/qiime2-2018.6/lib/python3.5/subprocess.py”, line 1228, in _execute_child
restore_signals, start_new_session, preexec_fn)
OSError: [Errno 12] Cannot allocate memory

Plugin error from feature-classifier:

[Errno 12] Cannot allocate memory

How to resolve this problem (Errno 12) ?

I used Oracle VM Virtual box with ram set to 22gb.

Thank you so much
Songkran Th

[Mehrbod_Estaki]

Hi @SongkranTh,
Welcome to the forum!
The error you are receiving is due to insufficient memory available. The Silva database is huge and can easily eat up more than 22 Gig of RAM. Your options are to a) allocate more memory, b) use the GreenGenes database which uses considerably less memory, or c) try some parameter adjustments as outlined here. Hope that helps!