Hey man, I'm just here waiting for my fastq.gz to download. Ben
I'm glad my suggestion helped!
And thanks for pointing out what my input files should be, because it was confusing.
I (kind of) know the methods (or rather, the logic behind it) because metagenomic analysis was a part of my PhD thesis, though I worked on 16S libraries preparation rather than bioinformatics. I only mentioned some of the methods in the work and got the logic behind them but never got the chance to use them directly. Now I joined a new post-doc research project and I'm working on performing the analysis directly!