CAMI format output

To print the result in CAMI format you need to use the -C option, which is explained more in details here.

There are two additional parameters that you can use with the -C option:

1. --remove_cami_comments, to remove the information about the parameters used for the computation.
2. -not_renormalise_cami, to keep the relative abundances as they are calculated by the mOTUs profiler. The mOTUs profiler is able to measure known and unknown species. As a result, the relative abundance of the species (and at other taxonomic level) do not necessarily sum up to 100% (see also here). If you use -not_renormalise_cami the relative abundance will not sum up to 100%, while by default (hence not using -not_renormalise_cami) it will be normalised (hence, summing up to 100%). See also link where it says "How can Metaphlan2, the overall best-performing tool in Fig. 3A of..."