At second glance, @Ricardo_Ramiro, it looks like you have an ID mismatch here - your command is trying to filter the features in your rep-seqs using the sample ids from your metadata file. Your sample and feature IDs are different, so the query finds no matches.
Try using your --p-where query to filter samples from your FeatureTable[Frequency].
Filtering out the samples that match your query will produce a FeatureTable[frequency] file you can then pass into filter-seqs without a --p-where query. Features that exist in your filtered table will be retained, features that don't exist in those samples will be dropped.
Lots of good information on filtering in the Filtering Data Tutorial
Hope this helps!
Chris