CRITICAL ERROR: The directory provided for ChocoPhlAn does not contain files of the expected format (ie '^[g__][s__]')

Microbial community profiling HUMAnN
1

hi Franzosa,
I downloaded the newest database of ChocoPhlan and installed humann3. When I run humann as following, some error occured:

(py37) [wenping@localhost data]$ humann --input /data/liying_metagenome/clean_data_ly/SRR5130527.fastq --output try_humann --bypass-translated-search
Creating output directory: /data/try_humann
Output files will be written to: /data/try_humann
Removing spaces from identifiers in input file …

CRITICAL ERROR: The directory provided for ChocoPhlAn does not contain files of the expected format (ie ‘^[g__][s__]’).

can you know how to fix the error?

wenping

2

Hi Wenping,

It looks like the location set in your config for the nucleotide database does not contain files of the expected format. Would you run the humann_config command? It will print the folder that you have set to contain the directory for the ChocoPhlAn files (the nucleotide database). Those files should be named something with “g__” (genus) and “s__” (species) in the name. If the folder location needs to change you can also use the humann_config command or set the new folder location when running HUMAnN with --nucleotide-database <NEW_LOCATION>.

# print the current config settings
$ humann_config --print
HUMAnN Configuration ( Section : Name = Value )
output_format : remove_stratified_output = False
output_format : output_max_decimals = 10
alignment_settings : prescreen_threshold = 0.01
alignment_settings : evalue_threshold = 1.0
alignment_settings : identity_threshold = 50.0
database_folders : nucleotide = data/chocophlan_DEMO

# update the config setting
$ humann_config --update database_folders nucleotide $NEW_LOCATION

Thanks!
Lauren

3

Hi Lauren,
It works.
Thank you very much!
Wenping

4

In regards to this error:

CRITICAL ERROR: The directory provided for ChocoPhlAn does not contain files of the expected format (ie '^[g__][s__]').

full_chocophlan.v201901_v31.tar.gz contains the following file: alaS.centroids.v201901_v31.ffn.gz, which in not formatted like all of the other 12772 genome files in the database.

Should alaS.centroids.v201901_v31.ffn.gz be removed from full_chocophlan.v201901_v31.tar.gz, or is the ^[g__][s__] format not actually needed for all genome files?