Hi Adriana,
featureCounts has a little bug affecting built-in genomes
It should work with collections.
The error log points on issue with the annotation file. Maybe paste one gene annotation in reply and I’ll check it.
Alternatively, you can share the history with me, I can have a look. In History Option (small triangle icon at the top right corner of the history panel) select Share or Publish, in the middle window make history accessible, copy the URL link and paste it into reply. Ideally, it should be a small history. You can copy relevant datasets into a new history and share it.
Kind regards,
Igor