I am moving from StrainPhlAn2 to StrainPhlAn3, and one question is whether flag --clade in StrainPhlAn3 is mandatory or not? If yes, and I want to investigate all clades without defining specific extracted markers from MetaPhlAn database and reference-genomes, what shoud I do?
strainphlan -s consensus_markers/*.pkl -o output -n 8 -c xxx? --phylophlan_mode accurate --mutation_rates
Hi, may I get the answer to my question as above? Many thanks.
Sorry for the late response. Yes, the
--clade parameter is mandatory when StrainPhlAn3 is executed. If you want to know all the available species StrainPhlAn is able to profile from your samples, you can use the parameter
--print_clades_only as follows:
strainphlan -s consensus_markers/*.pkl -o output --print_clades_only
Then, you can run StrainPhlAn for each of your clades individually.
So is it not possible to run all the clades at one time?
No, in the new version each clade has to be runned independenly.
Okay, many thanks. Best, Wang