So i am trying to run the rna/dna biobackery workflow and run into the following issue - this seems to be commen - however i cannot figure out how to solve it. THANKS
humann v3.9
MetaPhlAn version 4.1.1 (11 Mar 2024)
humann_regroup_UniRef2EC____IN01V7_DNA.gz : Failed! Error message : Error executing action 0. Original Exception:
humann_regroup_table: error: argument -g/–groups: invalid choice: ‘uniref90_level4ec’ (choose from ‘uniref90_rxn’, ‘uniref50_rxn’)
2025-02-04 18:27:21,456 LoggerReporter task_failed ERROR: task 33, humann_regroup_UniRef2EC____IN01V7_RNA.gz : Failed! Error message : Error executing action 0. Original Exception:
humann_regroup_table: error: argument -g/–groups: invalid choice: ‘uniref90_level4ec’ (choose from ‘uniref90_rxn’, ‘uniref50_rxn’)
this is what i have in my utility_mapping:
map_ec_name.txt.gz map_eggnog_uniref90.txt.gz map_go_uniref90.txt.gz map_ko_uniref90.txt.gz map_pfam_name.txt.gz map_uniref50_name.txt.bz2 uniref50-tol-lca.dat.bz2
map_eggnog_name.txt.gz map_go_name.txt.gz map_ko_name.txt.gz map_level4ec_uniref50.txt.gz map_pfam_uniref50.txt.gz map_uniref50_uniref90.txt.gz uniref90-tol-lca.dat.bz2
map_eggnog_uniref50.txt.gz map_go_uniref50.txt.gz map_ko_uniref50.txt.gz map_level4ec_uniref90.txt.gz map_pfam_uniref90.txt.gz map_uniref90_name.txt.bz2
HUMAnN Configuration
database_folders : nucleotide = metaphlan_databases/chocophlan
database_folders : protein = metaphlan_databases/uniref
database_folders : utility_mapping =metaphlan_databases/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