jflucier
commented
12 months ago je viens de tester et ca fonctionne pour moi:
bash $ILL_PIPELINES/generateslurm_assembly_bin_refinement.metawrap.sh \
--sample_tsv /net/nfs-ip34/home/def-ilafores/analysis/20230216_metagenome_test/testset-projet_PROVID19-saliva/preprocess/preprocessed_reads.sample.tsv \
--out /net/nfs-ip34/home/def-ilafores/analysis/20230216_metagenome_test/testset-projet_PROVID19-saliva \
--slurm_email "jean-francois.lucier@calculs.ca" --slurm_threads 48 --slurm_mem 240G \
--refinement_min_compl 30 --refinement_max_cont 2l'output:
15:19:46|jflucier@ip34-rockylinux8:[analysis]> cat /net/nfs-ip34/home/def-ilafores/analysis/20230216_me
tagenome_test/testset-projet_PROVID19-saliva/assembly_bin_refinement.metawrap.slurm.sh
#!/bin/bash
#SBATCH --mail-type=END,FAIL
#SBATCH -D /net/nfs-ip34/home/def-ilafores/analysis/20230216_metagenome_test/testset-projet_PROVID19-sal
iva
#SBATCH -o /net/nfs-ip34/home/def-ilafores/analysis/20230216_metagenome_test/testset-projet_PROVID19-sal
iva/logs/assembly_bin_refinement-%A_%a.slurm.out
#SBATCH --time=24:00:00
#SBATCH --mem=240G
#SBATCH -n 48
#SBATCH -N 1
#SBATCH -A def-ilafores
#SBATCH -J assembly_bin_refinement
#SBATCH --mail-user=jean-francois.lucier@calculs.ca
echo "loading env"
...
La variable $ILL_PIPELINES doit etre setter a /net/nfs-ip34/home/def-ilafores/programs/ILL_pipelines/
Si je change --slurm_threads et --slurm_mem, ex: bash $ILL_PIPELINES/generateslurm_assembly_bin_refinement.metawrap.sh --sample_tsv $tsv --out ${PARENT_DIR}/coassembly --slurm_email "ronj2303@usherbrooke.ca" --refinement_min_compl 50 --refinement_max_cont 10 --slurm_walltime 72:00:00 --slurm_thread 48 --slurm_mem 240
le script généré demeure 125G et 24 threads, tant dans le header SLURM que dans la commande en tant que tel.