Hi, I am trying to use DRAM to annotate and distill MAGs; however, I encountered errors when running DRAM distill. In addition, the results from DRAM annotate appear to be problematic, as they remain unchanged even after switching the reference databases (e.g., UniRef, VOG, and Kofam). I am not sure whether this is due to the databases not being properly installed or configured. My working history is available here: https://usegalaxy.eu/u/chuan1028/h/dram-g1. Could you please have a look and help identify where the problem might be? Thank you very much.
Welcome @chuanzhai
Yes, these tools have licensing requirements that currently prevent us from hosting them on the public Galaxy servers. I’m not sure if anyone has been able to get this working on a local Galaxy server yet, but that seems possible!
Many more detail are in this topic. → Request to enable KEGG and Pfam databases for DRAM Annotate on Galaxy Europe - #2 by jennaj
Thank you for sharing your history! I reviewed your data and it does reflect this same known issue. Notice how column 9 of the annotation output is empty. The distill tools is interpreting this value (and could interpret even more) – but since there wasn’t any meaningful content, the tool was confused and reported a message in the log (using the i-icon to reach the Details view).
The tool reports the fields it could work with but isn’t and then reports what it is working with – but that value is empty.
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What to do
Please review the topic above for ideas about alternative ways to explore your data, including how to access KEGG annotations with HUMAnN in Galaxy at the public servers. I hope this helps to explain what is going on. 