The bioBakery help forum

Configuration file error

I am trying to run phylophlan 3 and I am running into error with config file. I used the “phylophlan_write_config_file” command to generate config files in a folder I called “phylophlan_configs” . However when I tried to run phylophlan , it generates the error below

(phylophlan) D-MGN-05669:~ weisslab$ phylophlan -i /Users/weisslab/input_genomes -d /Users/weisslab/Documents/phylophlan/Phylophlanrefdatabase --diversity high -f /Users/weisslab/phylophlan_configs --nproc 12
[e] configuration file “/Users/weisslab/phylophlan_configs” not found
Available configuration files in “phylophlan_configs/”:
phylophlan_configs/supermatrix_aa.cfg
phylophlan_configs/supermatrix_nt.cfg
phylophlan_configs/supertree_aa.cfg
phylophlan_configs/supertree_nt.cfg

Can you help ?

Hi,
with the -f parameter you should specify which configuration file to use and not the folder.

The configuration file can be specified like this -f supermatrix_aa.cfg and PhyloPhlAn will search for this config file inside the phylophlan_configs folder, or alternatively you can provide the full (absolute or relative, it doesn’t matter) path to the file like -f /Users/weisslab/phylophlan_configs/supermatrix_aa.cfg

I hope this helps.
Francesco