Issue with Metagenomic OTU picking

[djcabral92]

Hello,

I am trying to analyze my metagenomic dataset with BugBase but I am having issues with the OTU picking against the IMG database. I followed the instructions on https://github.com/knights-lab/BugBase but after I run the shogun_bugbase command I get an empty taxa_counts.txt file. The command runs for less than a minute and I don't receive any kind of error message so I'm not sure exactly what is going wrong or how to fix it. Do you have any suggestions of how to diagnose the problem? Thanks in advance!

[bhillmann]

It is hard for use to diagnose the issue without the exact commands that you ran.

It sounds like shogun_bugbase isn't finding any hits to the database, and this could be a plethora of issues. Can you send over the exact command history that you ran?