Bonjour,
J'essaie de faire tourner kofamscan, mais à chaque fois il crée une grande quantité de fichiers core. Avez vous une idée de ce qui pourrait être la raison ? Je crains que mon script ne cause le problème mais je suis bloquée ...
Voici mon script sbatch :
#SBATCH --mem=80G
#SBATCH --cpus-per-task=8
module load kofamscan/1.3.0
/shared/ifbstor1/software/miniconda/envs/kofamscan-1.3.0/bin/exec_annotation -o kofamscan_result.txt PROKKA_07112022.fasta -c config_kofamscan.yml --cpu=8
Et mon fichier de configuration :
# Path to your KO-HMM database
# A database can be a .hmm file, a .hal file or a directory in which
# .hmm files are. Omit the extension if it is .hal or .hmm file
# profile: /path/to/your/profile/db
profile: /shared/ifbstor1/home/rpopall/Kofam-db/profiles
# Path to the KO list file
# ko_list: /path/to/your/kolist/file
ko_list: /shared/ifbstor1/home/rpopall/Kofam-db/ko_list
# Path to an executable file of hmmsearch
# You do not have to set this if it is in your $PATH
# hmmsearch: /usr/local/bin/hmmsearch
# Path to an executable file of GNU parallel
# You do not have to set this if it is in your $PATH
# parallel: /usr/local/bin/parallel
# Number of hmmsearch processes to be run parallelly
cpu: 8
Merci beaucoup d'avance !