In order to run MISO (http://genes.mit.edu/burgelab/miso/docs/) on a SLURM (https://computing.llnl.gov/linux/slurm/) operated cluster any tips facilitating multiple CPU usage would be awesome! At the moment I can't motivate MISO to use all of the "booked" node CPUs.
job script:
Available MISO options are:
--use-cluster
--chunk-jobs N
and some for SGEarray
(http://genes.mit.edu/burgelab/miso/d...s-to-a-cluster)
Thanks for any idea!
Ben
job script:
Code:
#!/bin/bash #SBATCH --ntasks=1 #SBATCH --cpus-per-task=24 #SBATCH --error=miso_err.log #SBATCH --output=miso_out.log #SBATCH --job-name=miso_laczA #SBATCH --mem-per-cpu=3000 #SBATCH --partition=test #SBATCH --time=00:59:59 # export OMP_NUM_THREADS=24 module load python/2.7.3 python -c "import numpy" python -c "import scipy" python -c "import pysam" srun python $HOME/programs/MISO/misopy/run_events_analysis.py --compute-genes-psi /MISO/hg19/indexed/indexedSE /bam/laczA/Aligned.out.sorted.bam --output-dir laczA_MISO_output/ --read-len 100 --paired-end 186 16 --use-cluster --chunk-jobs 200
--use-cluster
--chunk-jobs N
and some for SGEarray
(http://genes.mit.edu/burgelab/miso/d...s-to-a-cluster)
Thanks for any idea!
Ben
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