wiki:cypress/Cellranger-ARC

Version 1 (modified by fuji, 9 months ago) (diff)

Run Cellranger-ARC on Cypress

See Generating FASTQs with cellranger-arc mkfastq. This page to show how to run Cellranger-ARC with the cluster mode on Cypress.

Example SLURM script:

#!/bin/bash
#SBATCH --qos=normal		# Quality of Service
#SBATCH --job-name=mkFASTQ # Job Name
#SBATCH --time=24:00:00	# WallTime
#SBATCH --nodes=1 		# Number of Nodes = 1
#SBATCH --ntasks-per-node=1 	# Number of tasks (MPI presseces) = 1
#SBATCH --cpus-per-task=1 	# Number of processors per task OpenMP threads() = 1 
#SBATCH --gres=mic:0  		# Number of Co-Processors
#SBATCH --export=ALL
#SBATCH --mail-type=ALL
#SBATCH --mail-user='USERID'@tulane.edu # SET YOUR EMAIL ADDRESS

module load cellranger-arc/1.0.1

cellranger-arc mkfastq --id=tiny-bcl-atac \
                 --run=./cellranger-arc-tiny-bcl-atac-1.0.0 \
                 --csv=./cellranger-arc-tiny-bcl-atac-simple-1.0.0.csv \
		 --jobmode=slurm \
		 --localmem=120 \
		 --localcores=20 \
          	 --maxjobs=4 \
                 --jobinterval=1000

With this script, 'cellranger-arc' submits at most 4 sub-jobs. You can set the maximum number of jobs by changing:

          	 --maxjobs=18 \