Humann_infer_taxonomy not recognizing utility_mapping folder

Microbial community profiling HUMAnN
1

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
map_go_uniref50.txt.gz
map_level4ec_uniref50.txt.gz
map_uniref50_name.txt.bz2
map_eggnog_name.txt.gz
map_go_uniref90.txt.gz
map_level4ec_uniref90.txt.gz
map_uniref50_uniref90.txt.gz
map_eggnog_uniref50.txt.gz
map_ko_name.txt.gz
map_pfam_name.txt.gz
map_uniref90_name.txt.bz2
map_eggnog_uniref90.txt.gz
map_ko_uniref50.txt.gz
map_pfam_uniref50.txt.gz
uniref50-tol-lca.dat.bz2
map_go_name.txt.gz
map_ko_uniref90.txt.gz
map_pfam_uniref90.txt.gz
uniref90-tol-lca.dat.bz2

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!

3

I believe this tool is still not implemented yet for humann3. I received an answer on this in this subject earlier in November in this biobakery message thread.

4

Hello! Thanks a lot for sharing the post! I came across the thread but was confused by the error message I received. Problem solved! Thank you

5

And just to follow up here - the updates to infer_taxonomy will be made in the next HUMAnN v3 release. This (along with a few improves) will require folks to update their utility mapping databases, so we wanted to coordinate the change to avoid folks having to update the databases multiple times.

6

Hi, just curious if there are updates to this? Thanks.