Hello,
I had trouble with my in-house curated database as it was in aligned format, and thanks to @colinbrislawn I re-formatted it to not-aligned format.
My new problem has arisen when I attempted to perform training of my database. As the primer pair sequences could not be supplied from the sequencing facility, I have tried (up to now) three universal primer sequences (the last one shown below), but all resulted in getting error message ('No matches found').
qiime feature-classifier extract-reads --i-sequences unaligned.qza --p-f-primer CCTACGGGNGGCWGCAG --p-r-primer GACTACHVGGGTATCTAATCC --p-trunc-len 120 --p-min-length 300 --p-max-length 470 --o-reads unaligned-refseqs.qza
I am still not sure whether the problem is resulted from a possible fault in the .fasta file that I submitted for qza conversion (I am enclosing three entries from the file).
The text within the error log file is;
Traceback (most recent call last):
File "/home/tools/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/commands.py", line 327, in call
results = action(**arguments)
File "</home/tools/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/decorator.py:decorator-gen-351>", line 2, in extract_reads
File "/home/tools/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py", line 240, in bound_callable
output_types, provenance)
File "/home/tools/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py", line 383, in callable_executor
output_views = self._callable(**view_args)
File "/home/tools/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_feature_classifier/_cutter.py", line 168, in extract_reads
raise RuntimeError('No matches found') from None
RuntimeError: No matches found
Thank you,
Eray
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