Hello,
I have been having a problem with one of my jobs, every time I submit it, it fails, I get an error about 7 hours after it starts and I would like to ask if maybe I am doing something wrong. The error: NODE_FAIL, ExitCode 0.
The script I am trying to run is to get a VCF from some .bam files, and you can find it below:
#!/bin/bash
#SBATCH --job-name=DemrefVarCallALL
#SBATCH --partition=long
#SBATCH --ntasks-per-node=20
#SBATCH -o varcallDem.out # STDOUT
#SBATCH -e varcallDem.err # STDERR
#SBATCH --mail-user=julie.ramirez@inrae.fr
#SBATCH --mail-type=ALL
Recommended safety settings:
set -o errexit # Make bash exit on any error
set -o nounset # Treat unset variables as errors
##load modules
module load bcftools/1.10.2
input files
REFERENCE=/pathToReferenceGenome/assembly.fa;
bcftools mpileup --threads 20 --max-depth 500 -a DP,AD,INFO/AD -f ${REFERENCE} /pathToFolder1/*bam |
bcftools call --threads 20 -m --ploidy 1 | bgzip | tee /pathToOutput/newVCF.vcf.gz
thank you in advance