Hi @wcm
The error message suggests that non-paired reads were used. It can be accidental submission of files from different samples or reads were trimmed as SE, not PE, or something else.
If you trimmed the reads in PE mode, check job setup of the failed job(s) using info (i) or Re-run icons. If the files are from the same sample, you can share the history and post the link here, so someone can check what is going on.
History sharing: History options (three horizontal bars icon at the top right corner of the history panel) > Share or Publish > Make the history accessible (in the middle window) > Copy and paste the URL in reply.
Kind regards,
Igor