Qiime feature-classifier extract-reads

I ran this command qiime feature-classifier extract-reads --i-sequences 85_otus.qza --p-f-primer CCTACGGGNGGCWGCAG --p-r-primer GACTACHVGGGTATCTAATCC --p-trunc-len 466 --o-reads ref-seqs.qza

and I got this error

Traceback (most recent call last):
File “/scratch/sysusers/kedibone/.conda/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 “/scratch/sysusers/kedibone/.conda/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 228, in bound_callable
output_types, provenance)
File “/scratch/sysusers/kedibone/.conda/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 363, in callable_executor
output_views = self._callable(**view_args)
File “/scratch/sysusers/kedibone/.conda/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_feature_classifier/_cutter.py”, line 157, in extract_reads
raise RuntimeError(‘No matches found’) from None
RuntimeError: No matches found

/tmp/qiime2-q2cli-err-f00w7pu3.log (END)
Please help

@kedi, The error that you're seeing will occur if the primers you're providing didn't match any of the sequences in that input file. I tested your command with the 85_otus.qza file that is used in the Training feature classifiers tutorial, and the command completed successfully. (The resulting file is attached here.) The command that I ran was as follows, and I'm using QIIME 2 2017.12.

$ qiime feature-classifier extract-reads --i-sequences 85_otus.qza --p-f-primer CCTACGGGNGGCWGCAG --p-r-primer GACTACHVGGGTATCTAATCC --p-trunc-len 466 --o-reads ref-seqs.qza

Can you provide some details about the 85_otus.qza file that you're providing as input? Is that a different file from the one in the tutorial that I linked to above? If so, are you sure that the sequences you're providing are 16S? Can you confirm the version of QIIME 2 that you're using (you can find this information by running qiime info).

ref-seqs.qza (479.1 KB)

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@gregcaporaso thanks for your response, I downloaded the fast file from the Training feature classifiers tutorial and ran the script qiime tools import --type FeatureData[Sequence] --input-path aligned_85_otu_sequences.fasta --output-path 85_otus.qza, to get the qza file. I didn’t extract the reads from the qza file on the tutorial.

Hi @kedi, It sounds like you have this working now, and the original error was because you accidentally imported aligned sequences as FeatureData[Sequence] instead of as FeatureData[AlignedSequence]. Glad it’s working!

One important note: the 85% OTUs that are used in that tutorial should be considered for testing purposes only. When training the classifier that you’ll apply in your analysis, you should train on the Greengenes 99% OTUs. You can find the corresponding files in the GG 13_8 OTUs resource, which is linked from the QIIME 2 resources page. You can then follow the import instructions in the Training feature classifiers… tutorial to import the required files.

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