Empty output files after running METABOLIC-C

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

AnantharamanLab / METABOLIC

Empty output files after running METABOLIC-C #153