Hi @lautaro.rostoll,
It seems you have extraneous spaces in your --p-exclude string. For example, note the space right at the beginning after the first quote:
" d__Bacteria;...
Also, you should not have spaces between the commas of the different strings. That is:
...g__Muribaculaceae;s__uncultured_bacterium , d__Bacteria;p__Bacteroidota;...
should be:
...g__Muribaculaceae;s__uncultured_bacterium,d__Bacteria;p__Bacteroidota;...
etc...
See the example here
It also appears that you are copying the taxonomy from one of the taxonomy QZV visualizations. That is, the actual taxonomy strings do not contain ;__. This only appears in the visualizer as you select different rank depths. This simply conveys that there is no information at that level in the visualizer. More information can be found here:
Finally, why not use --p-mode contains? Then make your --p-exclude line be simply like:
--p-exclude "g__Muribaculaceae,f__Oscillospiraceae,Peptostreptococcales-Tissierellales,g__Howardella,g__Oligella,s__Lachnospiraceae_bacterium,f__Weeksellaceae,f__Aerococcaceae,s__Wohlfahrtiimonas_chitiniclastica,s__Paenalcaligenes_hominis"
or something similar to that. I may have missed a few... but you get the point. 