Is there any possibility of adding the GTDB v220 database to Kraken2??? Also the EupathDB 46 would be helpful.

Hi @Jon_Colman Both of these indexes are available at UseGalaxy.org for now. There are some technical reason why these are not at the EU server yet. When possible, all the UseGalaxy servers will host them. GTDB [org-kraken2-gtdb] EuPathDB [org-kraken2-eupathdb] I believe you know how to do t…

Yes, I’ve been transferring over to run them on the main site. Of note, on usegalaxy.eu I would normally only use Kraken2 on the smaller databases, as the Core-nt would take forever. Seems to be working well now.

Thanks for letting is know. And agree, core-nt jobs will take some time. The reference data is very large, then filtering the results takes time. I’m really glad we can host these! They would be unlikely to work on a laptop, or even most desktops. :slight_smile:

It was worse than that on the .eu, even files not very large using the core-nt database, I would start it and it would start running, even after a whole day it wouldn’t complete. Now it runs pretty fast, at least when I was trying it again.

I am guessing that they are sending those jobs over to a larger cluster node now, or larger nodes are simply available now. These “which node” tuning details are modified constantly in response to the runtime metrics from everyone’s jobs and the cluster/nodes that are available. Threading is added …

Galaxy Community Help

Kraken2 Database Addition GTDB v220

usegalaxy.eu support

troubleshooting

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