Empty output files after running METABOLIC-C

[Valentin-Bio]

Hello , I ran METABOLIC-C under a HPC with slurm over my acquatic metagenomic paired end reads data set (93 samples).The program was installed via mamba:

mamba install -c hcc metabolic

I ran the program as following:

comau="/lustre/groups/cbi/Users/ecastron/valentin/comau"


perl ~/miniconda3/envs/metabolic/bin/METABOLIC-C.pl -t 32 -m-cutoff 0.75  -in-gn ${comau}/comau_mags/DATA_MAGs_Comau -kofam-db full -r /lustre/groups/cbi/Users/ecastron/shared_data/Comau/readlist.txt -o ${comau}/comau_annotation

slurm noticed me that the program worked well. I checked the 'METABOLIC_run.log' file and this is the content of it:

METABOLIC-C.pl v4.0
Run Start: 2023-06-23 19:09:26
Run End: 2023-06-23 19:14:23
Input Reads: /lustre/groups/cbi/Users/ecastron/shared_data/Comau/readlist.txt
Reads type: metaG
Input Genome directory (nucleotides): /lustre/groups/cbi/Users/ecastron/valentin/comau/comau_mags/DATA_MAGs_Comau
Number of Threads: 32
Prodigal Method: meta
KOfam DB: full
Module Cutoff Value: 0.75
Output directory: /lustre/groups/cbi/Users/ecastron/valentin/comau/comau_annotation

The program finished really fast for my dataset (runtime: 5 minutes)

So I checked the output files under comau_annotation directory and there were the output directories and files but the files are empty.

this is the content of the stdout message :

[2023-06-23 19:09:26] The Prodigal annotation is running...
[2023-06-23 19:09:26] The Prodigal annotation is finished
[2023-06-23 19:09:26] The hmmsearch is running with 32 cpu threads...
[2023-06-23 19:09:28] The hmmsearch is finished
[2023-06-23 19:09:29] Generating each hmm faa collection...
[2023-06-23 19:09:29] Each hmm faa collection has been made
[2023-06-23 19:09:29] The KEGG module result is calculating...
[2023-06-23 19:09:29] The KEGG identifier (KO id) result is calculating...
[2023-06-23 19:09:29] The KEGG identifier (KO id) seaching result is finished
[2023-06-23 19:09:29] Searching CAZymes by dbCAN2...
[2023-06-23 19:09:29] dbCAN2 searching is done
[2023-06-23 19:09:29] Searching MEROPS peptidase...
[2023-06-23 19:09:33] MEROPS peptidase searching is done
[2023-06-23 19:09:34] METABOLIC table has been generated
[2023-06-23 19:09:34] Drawing element cycling diagrams...
[2023-06-23 19:14:09] Drawing element cycling diagrams finished
[2023-06-23 19:14:09] Drawing metabolic handoff diagrams...
[2023-06-23 19:14:14] Drawing metabolic handoff diagrams finished
[2023-06-23 19:14:14] Drawing energy flow chart...
[2023-06-23 19:14:23] Drawing energy flow chart finished
[2023-06-23 19:14:23] Calculating MN-score ...
[2023-06-23 19:14:23] Calculating MN-score is done

So why do I have empty files ? can it be that some conda dependencies were not installed ? if so I attach here a txt file of my conda environment

metabolic_env.txt

[ChaoLab]

The conda package from https://anaconda.org/HCC/metabolic/files is not checked by me, and it is two years ago, never updated.
I suggest following the installation instructions here: https://github.com/AnantharamanLab/METABOLIC/wiki/Installation#anaconda-environment