feature-table filter-samples can't read metadata categories with dashes

Hi! I’m not sure I think there is a bug with the “feature-table filter-x” command on metadata categories with “-”.

For example, here is my command:

qiime feature-table filter-samples
–i-table 16S_ec_filtered_table.qza
–m-metadata-file PMF_metadata.txt
–p-where “location-id=‘cleland’”
–o-filtered-table no-cleland-filtered-table.qza

On previous runs, not using this same dataset I did something similar where it was something like

–p-where “sample-or-control=‘control’” \

and it worked just fine in filtering out the control samples. I had to go into the metadata file and change the location-id to something like LocationID for it to work. Will this be fixed, if it needs fixing?


Hi there @sarah_i, no, this isn't a bug, this is within the specification for SQLite. Check out this very similar post for a detailed explanation, as well as a instructions for moving forward.

Thanks! :t_rex: :qiime2:

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