Hello @kindergarten,
Looking into your data, ControlC5 only has one feature that isn't in your list of features to retain. So your command only filter out the occurrences of 1 unique sequence for ControlC5.
I would
- make sure that your list of features to retain is accurate to what you want to retain.
- Think about removing the 349 features that you do not want by using the --p-exclude-ids flag. It might be easier to manage than the list of 1559 features.
side note: You can't really see what unique features make up a sample using the table.qzv so I had to do some finagling in python