Rescript filter-taxa error

Hi there!

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
–i-taxonomy midori-ref-taxa.qza
–p-include ‘p__Chordata_7711’,‘p__Echinodermata_7586’
–o-filtered-taxonomy test.qza

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!

Hi @Newt,

Thank you for using RESCRIPt!

Try using:
–p-include p__Chordata_7711 p__Echinodermata_7586

Note that the --p-include and --p-exclude flags are set up as List[Str], which means you do not use commas to separate the taxonomies you’d like to filter. Just add a space in between each :slight_smile:

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Ah, that worked! I had a feeling a was doing something silly. Thank you so much. :slightly_smiling_face:

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