PhyloPhlAn version 3.0.60 (27 November 2020) Command line: /home/usr/miniconda3/envs/myenv/bin/phylophlan -i /home/usr/data/input/11assemblies -d phylophlan -t a --databases_folder /home/usr/phylophlan_databases --diversity medium -f supermatrix_aa.cfg --nproc 8 --verbose Automatically setting "input=11assemblies" and "input_folder=/home/usr/data/input" "medium-accurate" preset Setting "sort=True" because "database=phylophlan" Setting "min_num_markers=100" since no value has been specified and the "database=phylophlan" Arguments: {'input': '11assemblies', 'clean': None, 'output': '11assemblies_phylophlan', 'database': 'phylophlan', 'db_type': 'a', 'config_file': 'supermatrix_aa.cfg', 'diversity': 'medium', 'accurate': True, 'fast': False, 'clean_all': False, 'database_list': False, 'submat': 'pfasum60', 'submat_list': False, 'submod_list': False, 'nproc': 8, 'min_num_proteins': 1, 'min_len_protein': 50, 'min_num_markers': 100, 'trim': 'gap_trim', 'gap_perc_threshold': 0.67, 'not_variant_threshold': 0.99, 'subsample': , 'unknown_fraction': 0.3, 'scoring_function': , 'sort': True, 'remove_fragmentary_entries': False, 'fragmentary_threshold': 0.85, 'min_num_entries': 4, 'maas': None, 'remove_only_gaps_entries': False, 'mutation_rates': False, 'force_nucleotides': False, 'input_folder': '/home/usr/data/input/11assemblies', 'data_folder': '11assemblies_phylophlan/tmp', 'databases_folder': '/home/usr/phylophlan_databases', 'submat_folder': '/home/usr/miniconda3/envs/myenv/lib/python3.7/site-packages/phylophlan/phylophlan_substitution_matrices/', 'submod_folder': '/home/usr/miniconda3/envs/myenv/lib/python3.7/site-packages/phylophlan/phylophlan_substitution_models/', 'configs_folder': '/home/usr/miniconda3/envs/myenv/lib/python3.7/site-packages/phylophlan/phylophlan_configs/', 'output_folder': '', 'genome_extension': '.fna', 'proteome_extension': '.faa', 'update': False, 'verbose': True} Loading configuration file "supermatrix_aa.cfg" Checking configuration file Checking "/home/usr/miniconda3/envs/myenv/bin/diamond" Checking "/home/usr/miniconda3/envs/myenv/bin/mafft" Checking "/home/usr/miniconda3/envs/myenv/bin/trimal" Checking "/home/usr/miniconda3/envs/myenv/bin/FastTreeMP" Checking "/home/usr/miniconda3/envs/myenv/bin/raxmlHPC-PTHREADS-SSE3" [e] database format ("/home/usr/phylophlan_databases/phylophlan/phylophlan.faa", "/home/usr/phylophlan_databases/phylophlan/phylophlan.faa.bz2", or "/home/usr/phylophlan_databases/phylophlan") not recognize