Hi @zschong and @Jon_Colman
Does this help? → How to see the UseGalaxy.eu job queue statistics
The server is processing work but it is very busy. Be sure to leave your work queued or you will lose your place! New jobs are always added back to the end of the queue.
UseGalaxy.org is also very busy! We don’t have the server statistics posted publicly but I just looked and it is about the same.
More details are in this topic from yesterday. → waiting for a long time
And, if I am understanding correctly, we need to populate some more indexes! Let me know if I have this correct and I’ll help to make the request. It probably won’t be immediate but we can at least get it started. 
- Tool → Kraken2
- Add EuPathDB-46 to UseGalaxy.eu (currently at UseGalaxy.org)
- Add Mycobacterium V1 to UseGalaxy.org (currently at UseGalaxy.eu)