I am trying to create a SILVA classifier, just for my own experience - we already have an up to date one that we use in our research group but I want to see the steps that go into making one first hand so I have a better understanding of it.
I downloaded the SILVA 104 release (yes I know this is an old version) from this page: https://www.arb-silva.de/no_cache/download/archive/qiime/ and was using these files respectively for the database sequences and the reference taxonomy file.
I ran the following (from the Training Feature Classifier Tutorial, I guess I should also note that I have an outdated version of QIIME2 - 2018.8 if that could be driving where this error is arising from) command to train the classifier:
qiime feature-classifier fit-classifier-naive-bayes
–i-reference-reads silva-ref-seqs.qza
–i-reference-taxonomy silva-ref-taxonomy.qza
–o-classifier silva-classifier.qza
It took a surprisingly short time to be honest… I was expecting it to take a while to run but it took less than 5 minutes so I feel like something must be wrong with it. I then tested the classifier and got the plugin error “pop from empty list” (like this question it seems) .
Full print out of the error log:
File “/opt/anaconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/q2cli/commands.py”, line 274, in call
results = action(**arguments)
File “”, line 2, in classify_sklearn
File “/opt/anaconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/opt/anaconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 362, in callable_executor
output_views = self._callable(**view_args)
File “/opt/anaconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_feature_classifier/classifier.py”, line 212, in classify_sklearn
reads, classifier, read_orientation=read_orientation)
File “/opt/anaconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_feature_classifier/classifier.py”, line 169, in _autodetect_orientation
result = list(zip(*predict(first_n_reads, classifier, confidence=0.)))
File “/opt/anaconda3/envs/qiime2-2018.8/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 “/opt/anaconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/sklearn/externals/joblib/parallel.py”, line 779, in call
while self.dispatch_one_batch(iterator):
File “/opt/anaconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/sklearn/externals/joblib/parallel.py”, line 625, in dispatch_one_batch
self._dispatch(tasks)
File “/opt/anaconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/sklearn/externals/joblib/parallel.py”, line 588, in _dispatch
job = self._backend.apply_async(batch, callback=cb)
File “/opt/anaconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/sklearn/externals/joblib/_parallel_backends.py”, line 111, in apply_async
result = ImmediateResult(func)
File “/opt/anaconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/sklearn/externals/joblib/_parallel_backends.py”, line 332, in init
self.results = batch()
File “/opt/anaconda3/envs/qiime2-2018.8/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 “/opt/anaconda3/envs/qiime2-2018.8/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 “/opt/anaconda3/envs/qiime2-2018.8/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 “/opt/anaconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_feature_classifier/_skl.py”, line 79, in _predict_chunk_with_conf
classes = [cls for cls in classes if cls[0].pop(0) == level]
File “/opt/anaconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_feature_classifier/_skl.py”, line 79, in
classes = [cls for cls in classes if cls[0].pop(0) == level]
IndexError: pop from empty list
Is this an error due to the taxonomy or something else? Maybe it’s just time I update my QIIME2 as well… Any input on solving this issue would be great!