I’m using HUMAnN3 to analyze shotgun metagenomics sequences from hair microbiome samples. These samples were subset to the lowest read depth out of the pool of samples using seqtk, then concatenated. I received this output on my first sample, and I am concerned about why this has occurred:
Running metaphlan …
Total species selected from prescreen: 0
Selected species explain 0.00% of predicted community composition
No species were selected from the prescreen.
Because of this the custom ChocoPhlAn database is empty.
This will result in zero species-specific gene families and pathways.
I am concerned and wondering what could have caused this issue. Could this be caused by extreme host DNA contamination, or do I just need to make the settings in HUMAnN3 less sensitive? I’ve also attached my log so far (diamond is still running for the alignment to reference database).
log_2_24_2020_troubleshoot.txt (6.3 KB)