Bonjour @team.software
Je fais tourner un programme (DILS) via Snakemake, et depuis la dernière maintenance de l’IFB un script c’est cassé au niveau de l’appel du package R “abcrf”
Avec la même version de R en interactif j’arrive à la charger, donc je ne sais pas trop où ça peut poser problème
Le log:
rule modelComparison:
input: tomato_output/ABCstat_global.txt, tomato_output/ABCstat_loci.txt, tomato_output/modelComp/SC_1M_1N_0/ABCstat.txt, tomato_output/modelComp/SC_1M_1N_1/ABCstat.txt, tomato_output/modelComp/SC_1M_1N_2/>
output: tomato_output/modelComp/report_W_D.txt, tomato_output/modelComp/best_model.txt, tomato_output/modelComp/hierarchical_models.txt, tomato_output/sfs_plot.pdf, tomato_output/sfs_table.txt
jobid: 0
threads: 8
#module load conda
#source activate R_env
module load r/4.5.1"
Rscript /shared/home/awojcik/DILS/DILS/bin/ model_comp_2pop_allModels.R nameA=W nameB=D timeStamp=tomato_output nMin=10 sub_dir_sim=modelComp nSubdir=10 ntree=1000 ncores=8 useSFS=1 population_>
Rscript /shared/home/awojcik/DILS/DILS/bin/model_comp_2pop_allModels_solenopsis.R nameA=W nameB=D timeStamp=tomato_output nMin=10 sub_dir_sim=modelComp nSubdir=10 ntree=1000 ncores=8 useSFS=1 >
/shared/software/miniconda_deployment//envs/r-4.5.1/bin/Rscript
Error: package or namespace load failed for ‘Matrix’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/shared/software/miniconda_deployment/envs/r-4.5.1/lib/R/library/Matrix/libs/Matrix.so':
/lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.35' not found (required by /shared/software/miniconda_deployment/envs/r-4.5.1/lib/R/library/Matrix/libs/Matrix.so)
Execution halted
Pour info un problème similaire avait déjà été remonté avec DILS (ici), voilà le fichier lançant le snakemake
#!/usr/bin/bash
## launch DILS for 2 populations
## the provided argument is for --configfile, expecting the yaml file
export TCL_LIBRARY=/shared/ifbstor1/software/miniconda/envs/pypy-2.7-5.10.0/lib/tcl
module load pypy/2.7-5.10.0
module load snakemake/5.3.0
module load r/4.5.1
module load python/3.9
binpath='/shared/home/awojcik/DILS/DILS/bin'
snakemake --snakefile ${binpath}/Snakefile_2pop -p -j 140 --configfile ${1} --cluster-config ${binpath}/cluster_2pop.json --cluster "sbatch --nodes={cluster.node} --ntasks={cluster.n} --cpus-per-task={cluster.cpusPerTask} --time={cluster.time} --mem-per-cpu={cluster.memPerCpu}" --latency-wait 10
Merci beaucoup de votre retour,
Arthur