I’m trying to profile some metatranscriptomic stool samples with MetaphlAn 3.0 and getting some strange results. If I run metaphlan3 with default settings, I get a profile that is 100% k__Bacteria. However, when I use the --add_viruses option I get a profile that is 99.9% Virus (Cucumber green mottle mosaic virus, to be specific) and 0.1% Bacteria. If I run Kraken + Bracken on this sample, it only reports 0.7% of reads belonging to this virus, which seems a lot more realistic for stool. BLASTX-ing the sample against this virus is also not resulting in a lot of convincing hits.
I’ve made sure to filter out adapters and low complexity regions (bbduk), and I’m also filtering out human DNA, RNA, and 16S rRNA with kneaddata. Is there something else that could be causing this huge discrepancy between the two methods?
Thank you for your time.