deeptools
multiple instances of bamcoverage
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Hi,
I am trying to run multiple instances of bamcoverage on our hpc at the same time (as array job) to convert alignments from RNAseq to bigwigs. Always, the first 3 finish, and the others simply sit ideling. I tried playing around with 'OMP_NUM_THREADS' but it had no effect.
The HPC has 3 nodes with with 128Cores and 1T Ram each.
` #! /bin/bash
#SBATCH --array=1-42 #SBATCH --job-name=BamCov #SBATCH --cpus-per-task=12 #SBATCH --time=02:00:00 #SBATCH --output=Bamcov_%A_%a.log
modules
module load deepTools/3.5.1
run
awk -v expNo=$SLURM_ARRAY_TASK_ID 'NR==expNo' Samplesheet.failed.csv | while read ID NAME do bamCoverage -b ./Bam/$ID.bam -o ./BamCoverage/$NAME.\bw -p 12 --minMappingQuality 20 -v done `