I just did a fresh install of qiime2-metagenome-2024.5. After activating the environment, I ran quast-download-busco and received errors that the bacteria, fungi, and eukaryota databases cannot be found at their URLs (example below). Sure enough, the https://busco-archive.ezlab.org webpage comes back as 403 Forbidden for me.
ERROR! Failed downloading bacteria database (url: https://busco-archive.ezlab.org/v3/datasets/bacteria_odb9.tar.gz), QUAST functionality will be limited! Exception caught: HTTP Error 404: Not Found
Sorry to hear you've stumbled upon this annoying issue! There seems to be an open GitHub issue on the QUAST issue tracker which claims that the fix to this may come in the future... Since this is something supported by QUAST directly (and not QIIME) we cannot really do much about it - also, I am not sure whether the new databases would work with the way that QUAST is using BUSCO internally... So, I think I would follow the QUAST developers suggestion and just use it without it until they fix it...
We do have a dedicated action in q2-moshpit to fetch BUSCO databases and a corresponding action to estimate the quality of MAGs using BUSCO, but since you mentioned QUAST, I'm guessing you wanted to use it on contigs?
Thanks for reporting this. FYI, I am re-categorizing this topic as "other bioinformatics tools" as this is an error with a QUAST command, unrelated to q2-moshpit.
