Hello HUMAnN3 team,
I recently encountered an issue with the humann_infer_taxonomy function and I was not able to find similar posts in the forum. When I ran humann_infer_taxonomy -h, I received the following error: This tool requires the HUMAnN utility data files. To add these to your installation, please execute: $ humann_databases --download utility_mapping full $DIR Replacing, $DIR with the directory to install the databases.
Here is my humann configuration file and I am using humann3 v3.0.0.alpha.3 on a computing cluster.
HUMAnN Configuration ( Section : Name = Value ) database_folders : nucleotide = /projects/pxxxxx/chocophlan database_folders : protein = /projects/pxxxxx/uniref database_folders : utility_mapping = /projects/pxxxxx/utility_mapping run_modes : resume = False run_modes : verbose = False run_modes : bypass_prescreen = False run_modes : bypass_nucleotide_index = False run_modes : bypass_nucleotide_search = False run_modes : bypass_translated_search = False run_modes : threads = 1 alignment_settings : evalue_threshold = 1.0 alignment_settings : prescreen_threshold = 0.01 alignment_settings : translated_subject_coverage_threshold = 50.0 alignment_settings : translated_query_coverage_threshold = 90.0 alignment_settings : nucleotide_subject_coverage_threshold = 50.0 alignment_settings : nucleotide_query_coverage_threshold = 90.0 output_format : output_max_decimals = 10 output_format : remove_stratified_output = False output_format : remove_column_description_output = False
My utility folder (/projects/pxxxxx/utility_mapping) contains several gz files including map_ec_name.txt.gz
It seems like that I did successfully downloaded the database and updated the configuration file but humann_infer_taxonomy does not recognize the path. Am I missing something important? Thank you so much for your help!