StrainPhlan clade "s__Akkermansia_muciniphila" not accepted and should provide in SGB format

Microbial community profiling StrainPhlAn
1

I want to run strainphlan4 on my metagenomics data to get the strains of the “s__Akkermansia_muciniphila”. However, following the tutorial for strainohlan4 pipeline, the clades are specified in SGB format. So I cannot pass “s__Akkermansia_muciniphila” as the option of the extract_marker step:
extract_markers.py -c s__Akkermansia_muciniphila
or at the strainphlan step:
strainphlan.py -c s__Akkermansia_muciniphila

Instead of the “s__Akkermansia_muciniphila”, I have to pass “SGB9228” or “SGB9228” which I found in the " mpa_vJan21_CHOCOPhlAnSGB_202103_species.txt.bz2 file corresponding to the “s__Akkermansia_muciniphila” species. I am wondering how am I supposed to use both of them in my strainphlan and excract_marker run to get all the strains of the “s__Akkermansia_muciniphila”.

2

Hi @raminka
As you can see in the strainphlan tutorial (StrainPhlAn 4 · biobakery/MetaPhlAn Wiki · GitHub) in version 4, the clades (-c) should be specified at the SGB level (as some species might span multiple SGBs). in your case, you should pass -c t__SGB9228 in both extract_markers and strainphlan scripts