I am currently attempting to use Rescript to filter my reference database but have run into some issues with the include parameter. Here is an example of how the reference database is formatted:
To test this out I have used the following command to only keep p__Chordata and p__Echinodermata and received an error:
qiime rescript filter-taxa
Plugin error from rescript:
All features were filtered, resulting in an empty collection of taxonomies.
Debug info has been saved to /tmp/qiime2-q2cli-err-x6mkv0am.log
My other attempts have also resulted in only the one phylum being retained, or nothing being filtered out. I think I am simply inputting the string incorrectly, but I would like to only keep both phyla. Any help would be greatly appreciated!