Using humann v3.9 I try to run it on a dummy gene table which looks as follows:
# Gene Family E100002696_L01_1_kneaddata_Abundance-RPKs
UNMAPPED 4887640.0000000000
UniRef50_Q9RCA1 2135.6903965600
UniRef50_D7UV20 2135.6122163071
UniRef50_A0A7X0X377 2135.6122163071
I verified that the file is tab-separated and yet I am getting a following error in the gene_table_humann_temp/gene_table.log :
12/11/2024 12:56:48 PM - humann.humann - INFO: Process the gene table ...
12/11/2024 12:56:48 PM - humann.store - DEBUG: Unable to convert gene table value to float: UNMAPPED 4887640.0000000000
12/11/2024 12:56:48 PM - humann.store - DEBUG: Unable to convert gene table value to float: UniRef50_Q9RCA1 2135.6903965600
12/11/2024 12:56:48 PM - humann.store - DEBUG: Unable to convert gene table value to float: UniRef50_D7UV20 2135.6122163071
12/11/2024 12:56:48 PM - humann.store - DEBUG: Unable to convert gene table value to float: UniRef50_A0A7X0X377 2135.6122163071
12/11/2024 12:56:48 PM - humann.humann - INFO: TIMESTAMP: Completed processing gene table : 0 seconds
The resulting gene_table_pathabundance.tsv file looks as follows:
# Pathway gene_table_Abundance
UNMAPPED 0.0000000000
UNINTEGRATED 0.0000000000
I also tried to use the example data posted in this issue: Example for `File Type 4 (gene table) tsv` as input to HUMAnN? - #2 by w_ceasea with the same result.
What is the correct format of gene table if that’s what I want to use as an input for HUMAnN?