There is 100% a chance that I'm missing something I should have found. I want keep sequences that were clustered in my original ASV table. So, I'm clustering my data closed reference, and then using the discard sequences as a negative filter for my data
# Clusters the sequences closed reference at a low percent identity qiime vsearch cluster-features-closed-reference \ --i-sequences $seqs_in_fp \ --i-table $table_in_fp \ --i-reference-sequences $ref_seq_fp \ --p-perc-identity 0.85 \ --output-dir $cluster_out_dir # Filters the table against the discarded sequences qiime feature-table filter-features \ --i-table $table_in_fp \ --m-metadata-file $seq_discard_fp \ --p-exclude-ids \ --o-filtered-table $table_dir_fp
I get an error message:
Saved FeatureData[Sequence] to: data/output/mock/3.split_orientation/closed-ref-clustering-fwd/unmatched_sequences.qza There was an issue with loading the file data/output/mock/3.split_orientation/closed-ref-clustering-fwd/unmatched-sequences.qza as metadata: Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): data/output/mock/3.split_orientation/closed-ref-clustering-fwd/unmatched-sequences.qza There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2021.8/tutorials/metadata/
So, clearly, I can't transform my sequences into a metadata semantic type.
So, I guess, am I missing something that's hiding in plain sight, or is this one of things that I should open an issue to fix?