Metaphlan 4.0.6 and Humann 4.0.0a1
Attempting to make a joint taxonomic profile per GitHub - biobakery/humann: HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network). · GitHub , but humann_join_tables throws this error:
Traceback (most recent call last):
File “/hpc/group/hestonlab/smh114/miniconda3/envs/human_4/bin/humann_join_tables”, line 11, in
sys.exit(main())
^^^^^^
File “/hpc/group/hestonlab/smh114/miniconda3/envs/human_4/lib/python3.12/site-packages/humann/tools/join_tables.py”, line 238, in main
join_gene_tables(gene_tables,args.output,verbose=args.verbose)
File “/hpc/group/hestonlab/smh114/miniconda3/envs/human_4/lib/python3.12/site-packages/humann/tools/join_tables.py”, line 98, in join_gene_tables
sorted_gene_list=util.fsort(list(gene_table_data))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/hpc/group/hestonlab/smh114/miniconda3/envs/human_4/lib/python3.12/site-packages/humann/tools/util.py”, line 403, in fsort
features = sorted( features, key=lambda f: c_topsort.get( fsplit( f )[0], default ) )
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/hpc/group/hestonlab/smh114/miniconda3/envs/human_4/lib/python3.12/site-packages/humann/tools/util.py”, line 403, in
features = sorted( features, key=lambda f: c_topsort.get( fsplit( f )[0], default ) )
^^^^^^^^^^^
File “/hpc/group/hestonlab/smh114/miniconda3/envs/human_4/lib/python3.12/site-packages/humann/tools/util.py”, line 377, in fsplit
sys.exit( “LETHAL ERROR: bad feature name: {}”.format( f ) )
^
NameError: name ‘f’ is not defined
…and if i use metaphlan merge table and then try humann_reduce_table (as was suggested albeit for earlier versions), i get error:
Traceback (most recent call last):
File “/hpc/group/hestonlab/smh114/miniconda3/envs/human_4/bin/humann”, line 11, in
sys.exit(main())
^^^^^^
File “/hpc/group/hestonlab/smh114/miniconda3/envs/human_4/lib/python3.12/site-packages/humann/humann.py”, line 972, in main
custom_database = prescreen.create_custom_database(config.nucleotide_database, bug_file)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/hpc/group/hestonlab/smh114/miniconda3/envs/human_4/lib/python3.12/site-packages/humann/search/prescreen.py”, line 131, in create_custom_database
read_percent, coverage=get_abundance_coverage(line)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/hpc/group/hestonlab/smh114/miniconda3/envs/human_4/lib/python3.12/site-packages/humann/search/prescreen.py”, line 72, in get_abundance_coverage
read_percent=float(data[-3])
~~~~^^^^
IndexError: list index out of range
Any advice on how to get around this? I have a ton of samples and hoping to save time and space by creating one taxonomic profile. Thanks in advance!