I still got this error. I checked the dash that is correct now. Any idea?
thanks,
Gary
$ qiime feature-classifier extract-reads --i-sequences 99_otus.qza --p-r-primer TCCTCCGCTTATTGATATGC --p-f-primer GCATCGATGAAGAACGCAGC --p-trunc-len 500 --o-reads 99_ref-seqs_500.qza
Plugin error from feature-classifier:
Invalid characters in sequence: [‘a’, ‘c’].
Valid characters: [‘M’, ‘C’, ‘G’, ‘R’, ‘.’, ‘V’, ‘A’, ‘Y’, ‘D’, ‘H’, ‘T’, ‘B’, ‘S’, ‘W’, ‘K’, ‘N’, ‘-’]
Note: Use lowercase
if your sequence contains lowercase characters not in the sequence’s alphabet.
Debug info has been saved to /tmp/qiime2-q2cli-err-t7_oxus7.log
$ more /tmp/qiime2-q2cli-err-t7_oxus7.log
Traceback (most recent call last):
File “/opt/apps/Miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2cli/commands.py”, line 224, in call
results = action(**arguments)
File “”, line 2, in extract_reads
File “/opt/apps/Miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 228, in bound_callable
output_types, provenance)
File “/opt/apps/Miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 391, in callable_executor
spec.qiime_type, output_view, spec.view_type, prov)
File “/opt/apps/Miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/result.py”, line 239, in _from_view
result = transformation(view)
File “/opt/apps/Miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/core/transform.py”, line 59, in transformation
new_view = transformer(view)
File “/opt/apps/Miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/core/transform.py”, line 207, in wrapped
file_view = transformer(view)
File “/opt/apps/Miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_types/feature_data/_transformer.py”, line 271, in _10
skbio.io.write(iter(data), format=‘fasta’, into=str(ff))
File “/opt/apps/Miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/skbio/io/registry.py”, line 1166, in write
return io_registry.write(obj, format, into, **kwargs)
File “/opt/apps/Miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/skbio/io/registry.py”, line 619, in write
writer(obj, into, **kwargs)
File “/opt/apps/Miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/skbio/io/registry.py”, line 1082, in wrapped_writer
writer_function(obj, fhs[-1], **kwargs)
File “/opt/apps/Miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/skbio/io/format/fasta.py”, line 774, in _generator_to_fasta
for header, seq_str, qual_scores in formatted_records:
File “/opt/apps/Miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/skbio/io/format/_base.py”, line 146, in _format_fasta_like_records
for idx, seq in enumerate(generator):
File “/opt/apps/Miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_types/feature_data/_transformer.py”, line 228, in iter
yield from self.generator
File “/opt/apps/Miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_feature_classifier/_cutter.py”, line 104, in _gen_reads
for seq in sequences:
File “/opt/apps/Miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_types/feature_data/_transformer.py”, line 228, in iter
yield from self.generator
File “/opt/apps/Miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/skbio/io/registry.py”, line 506, in
return (x for x in itertools.chain([next(gen)], gen))
File “/opt/apps/Miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/skbio/io/registry.py”, line 531, in _read_gen
yield from reader(file, **kwargs)
File “/opt/apps/Miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/skbio/io/registry.py”, line 1008, in wrapped_reader
yield from reader_function(fhs[-1], **kwargs)
File “/opt/apps/Miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/skbio/io/format/fasta.py”, line 677, in _fasta_to_generator
**kwargs)
File “/opt/apps/Miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/skbio/sequence/_grammared_sequence.py”, line 338, in init
self._validate()
File “/opt/apps/Miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/skbio/sequence/_grammared_sequence.py”, line 362, in _validate
list(self.alphabet)))
ValueError: Invalid characters in sequence: [‘a’, ‘c’].
Valid characters: [‘M’, ‘C’, ‘G’, ‘R’, ‘.’, ‘V’, ‘A’, ‘Y’, ‘D’, ‘H’, ‘T’, ‘B’, ‘S’, ‘W’, ‘K’, ‘N’, ‘-’]
Note: Use lowercase
if your sequence contains lowercase characters not in the sequence’s alphabet.