HUMANN 3.0 function downstream analysis

Hi, I’m sorry for asking such a rudimentary question, but I’m really new to this. Basically, I’ve run my samples through HUMANN 3.0, and I’d like to do further analysis on the functional data; specifically the pathway abundances, and I’m completely lost on what to do next and what tools to use. Maybe I’m overthinking it but reading the descriptions of all the tools have confused me more. I have joined all my samples together in one table, and I tried to put it through MaAsLin 2 and I get this output:

Error in FUN(newX[, i], ...) : invalid 'type' (character) of argument
In addition: Warning message:
In vegan::decostand(features_norm, method = "total", MARGIN = 1,  :
  input data contains negative entries: result may be non-sense

I made sure that the sample columns lined up for both the function file and the metadata file, so not sure what exactly is wrong.

Honestly, I’m so lost and I don’t know what I’m doing wrong or where to go. Would really appreciate the help. Thank you in advance.

I’m not sure if that’s what’s causing the negative entries (I don’t see how!) but I think for input into MaAsLin we need to normalize the tables differently using the –units relab option. From the humann readme: Prior to nomalization, select the scheme to use (copies per million or relative abundance). For example, if using MaAsLin, select relative abundance.