To start off, I’m pretty new to all of this!
After successfully running through the tutorial, I’m attempting to analyze my own data using HUMAnN3. However, I’ve been getting the message that 0 species are selected from the prescreen and I can’t figure out what’s going on. Here’s the command I used and the output:
humann --input d6.fastq --output Outputs --nucleotide-database ./chocoplan --protein-database ./uniref
I’ve tried a lot of troubleshooting on my own (redownloading databases, etc.) but I’m not sure if I’m even on the right track with what’s causing the issue. I’m using a remote server through my workplace so I do not have permissions to change settings like I would normally–I’m not sure if that complicates things. I believe that could be the reason for the bowtie2 error but I’m not sure, although I ran the tutorial fine even with the warning there.
I would really appreciate any guidance on what could be causing this problem. Even getting a general idea of where to start would be very helpful. Thank you!