Welcome @Laurapbt
The GTDB-Tk Classify genomes tool updated to the 2.6 + versions and we still need to index the reference index for everyone. I’ll create a ticket and link that back here. Update GTDB-Tk indexes to R10-RS226 · Issue #68 · galaxyproject/idc · GitHub
But you don’t need to wait! The original 2.5 + versions are still available and these have the built-in reference index ready to use!
To navigate tool versions in Galaxy, load up the tool form and use the Versions menu at the top of the form.
Screenshot with the choice GTDB-Tk Classify genomes by placement in GTDB reference tree (Galaxy Version 2.5.2+galaxy1)
Please give that a try and let us know if you can find it! 