Hello all,
I am using this command phylophlan -i /mnt/bigdata/nikhil/Bradyrhizobium_genomes -d phylophlan --databases_folder /mnt/bigdata/nikhil/Bradyrhizobium_genomes/database --diversity medium --configs_folder /mnt/bigdata/nikhil/Bradyrhizobium_genomes/phylophlan_configs -f supermatrix_aa.cfg --nproc 80 --verbose to do phylogenetic analysis on my 156 bacterial genomes. However, it’s been around more than 138 hrs and analysis is still going on. I checked the steps, there is no error in the analysis. Kindly provide guidance.