Error "The directory provided for ChocoPhlAn does not contain files of the expected format" exists after checking the location of the databases

Microbial community profiling HUMAnN
1

Hi,
I was running humann v3.9 and it reported the error:
My code:

/home/ruchenyao/anaconda3/envs/bioBakery/bin/humann \
--input /home/ruchenyao/project/smoke/data/clean_data/${j%.*}.fastq --output \
/home/ruchenyao/project/smoke/output/humann/${j%.fastq}/ \
--taxonomic-profile /home/ruchenyao/project/smoke/output/metaphlan/metaphlan_abundance/${j%.*}.tsv \
--threads 20

the ERROR:

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

I run the humann_config command and it seems that the directory and location for the ChocoPhlAn files is correct.

(bioBakery) [ruchenyao@ln01 ~]$ humann_config --print
HUMAnN Configuration ( Section : Name = Value )
database_folders : nucleotide = /home/ruchenyao/database/humann/chocophlan
database_folders : protein = /home/ruchenyao/database/humann/uniref90
database_folders : utility_mapping = /home/ruchenyao/database/humann/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

My directory for the ChocoPhlAn files (downloaded from Index of /biobakery4/metaphlan_databases) shows the files exist:

ls /home/ruchenyao/database/humann/chocophlan
DEMO_chocophlan.v201901_v31.tar.gz  full_chocophlan.v201901_v31.tar.gz

My software version is humann v3.9, MetaPhlAn version 4.1.1 (11 Mar 2024)
After trying the method in critical-error, the error still occurs.
Could you help with this error? Should I remove and re-download the databases? Thank you for your guidance.

2

This problem has been solved. I did not decompress those tar.gz files of humann databases. All the files shoud be decompressed in related directory.

3

Hello, I am glad you were able to solve the issue. Thank you for posting the solution. You are correct that the software expects the files in the tar archive.

Thanks,
Lauren