CRITICAL ERROR: The directory provided for ChocoPhlAn contains files ( alaS.centroids.v201901_v31.ffn.gz ) that are not of the expected version

Microbial community profiling HUMAnN
1

Hi all,

My humann is v4.0 and metaphlan is version 4.1.0 (23 Aug 2023).
I downloaded the databases using the following link because I still couldn’t use humann_databases --download :
HUMAnN database download - Microbial community profiling / HUMAnN - The bioBakery help forum

And then updated config file as below:

HUMAnN Configuration ( Section : Name = Value )
database_folders : nucleotide = /ibers/ernie/home/yil23/chocophlan/
database_folders : protein = /ibers/ernie/home/yil23/uniref/
database_folders : utility_mapping = /ibers/ernie/home/yil23/metacyc/
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 = 0.5
alignment_settings : average_read_length = 150
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

And I ran humann and got this error:
CRITICAL ERROR: The directory provided for ChocoPhlAn contains files ( alaS.centroids.v201901_v31.ffn.gz ) that are not of the expected version. Please install the latest version of the database: SGB

I check multiple times that I am using the latest version.
If someone can help me this issue. That will be really helpful.
Thank you.

2

Did you pull the HUMAnN 4 source code from the development branch? We haven’t formally released that version yet, so the corresponding databases are not currently provided for download (hence the error message).

3

Hi Franzosa,

Thank you for replying. I already changed my version to v3.9 and fixed this issue. Thank you for your help.