Vsearch Feature Classifier Error - IndexError: list index out of range


(Simran S.) #1

Hi Everyone,

Foremost - I want to thank this community. Countless times when I have had errors using Qiime2, this forum has been my saving grace.

Most recently Ive been trying to use Vsearch for my taxonomical classification, and its has previously always worked fine - but now when I run the command:

qiime feature-classifier classify-consensus-vsearch

and use the green genes and/or silva ref seqs and taxonomy I keep getting this error:

"Traceback (most recent call last):
File “/Users/guccciii/miniconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/q2cli/commands.py”, line 274, in call
results = action(**arguments)
File “”, line 2, in classify_consensus_vsearch
File “/Users/guccciii/miniconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/Users/guccciii/miniconda3/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 “/Users/guccciii/miniconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_feature_classifier/_vsearch.py”, line 35, in classify_consensus_vsearch
unassignable_label=unassignable_label)
File “/Users/guccciii/miniconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_feature_classifier/_consensus_assignment.py”, line 29, in _consensus_assignments
output.name, ref_taxa, unassignable_label=unassignable_label)
File “/Users/guccciii/miniconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_feature_classifier/_consensus_assignment.py”, line 98, in _import_blast_format_assignments
if fields[1] == ‘*’:
IndexError: list index out of range

Plugin error from feature-classifier:

list index out of range"

I have no issues when using the qiime feature-classifier classify-sklearn and was hoping someone could provide insight to why the vsearch classifier is doing this all of a sudden.

Thank you so much!

  • Simran

(Nicholas Bokulich) #2

Hi @youngsimbaa32,
Could you please post the commands that you are using and give us some more details on the reference sequences and taxonomy files (e.g., are these downloaded from the QIIME 2 resources page or did you get them directly from SILVA/greengenes).

Thanks!


(system) #3

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