How do I get what strains are present in each sample?

I want to know what strains of each species is present in each sample. How do I do that?

Can i get in the .pkl file? If so, how do I unpickle it?

Hi @Bella_Smith
You can unpickle the sample2markers output using the pickle python library, e.g:
sample = pickle.load(open('sample.pkl', 'rb'))

If you load the file this way, the sample variable will be a dictionary containing the information of all the markers the script was able to reconstruct from your sample.
To know to which species each marker belongs to, you can use the latest marker information file mpa_v30_CHOCOPhlAn_201901_marker_info.txt.bz2 , that can be found here: mpa_v30_CHOCOPhlAn_201901_marker_info.txt.bz2