V3V4 classifier no matches found


I am trying to assign taxonomy using the training feature classifiers tutorial for the V3V4 region, and I keep getting errors that there are no matches found. Any suggestions?

I’ve tried it with and without --p-length 465, and get the same errors:

(qiime2-2017.4) [[email protected] training-feature-classifiers]$ qiime feature-classifier extract-reads --i-sequences 85_otus.qza --p-f-primer TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG --p-r-primer GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC  --o-reads ref-seqs.qza --verbose

Traceback (most recent call last):
  File "/home/ec2-user/miniconda3/envs/qiime2-2017.4/lib/python3.5/site-packages/q2cli/commands.py", line 218, in __call__
    results = action(**arguments)
  File "<decorator-gen-221>", line 2, in extract_reads
  File "/home/ec2-user/miniconda3/envs/qiime2-2017.4/lib/python3.5/site-packages/qiime2/sdk/action.py", line 171, in callable_wrapper
    output_types, provenance)
  File "/home/ec2-user/miniconda3/envs/qiime2-2017.4/lib/python3.5/site-packages/qiime2/sdk/action.py", line 248, in _callable_executor_
    output_views = callable(**view_args)
  File "/home/ec2-user/miniconda3/envs/qiime2-2017.4/lib/python3.5/site-packages/q2_feature_classifier/_cutter.py", line 148, in extract_reads
    raise RuntimeError('No matches found') from None
RuntimeError: No matches found

Plugin error from feature-classifier:

  No matches found

See above for debug info.



Hi @akknight216,
The primer sequences that you’re providing are very long (much longer than any 16S primers that I’m familiar with). Are you sure you don’t have sequencing adapter or barcode sequence in those? Note that the primers you provide here should only be the region that pairs with the 16S sequence. You shouldn’t need to use the --p-length parameter for this (that’s only if you want to trim the resulting reads).


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