Hi @Isa
Both your data and the index appear to be Yeast R64 with the accession GCF_000146045.2.
See this in the metadata for all the files, including Snpeff’'s and in yours. These appear to all be based on the same genome. So, you could try out both ways, and decide which works best.
For the error, I think the SnpEff tool itself has a problem on the UseGalaxy.org server!! I follow up about that, but you don’t need to wait. Update: found my outstanding ticket about this. The fix is still pending Resolved! Snpeff build galaxy6 failures at Jetstream2 ORG · Issue #731 · galaxyproject/usegalaxy-tools · GitHub
The earlier version works fine.
If you rerun your original jobs, but switch to using 4.3+T.galaxy5, both runs will be successful. FAQ: Changing the tool version
SnpEff build: database from Genbank or GFF record (Galaxy Version 4.3+T.galaxy5)
Please also give that a try and let us know if it works!