Align.srun

#!/bin/bash
#SBATCH --account=bgmp
#SBATCH --partition=bgmp
#SBATCH --job-name=STARAlign
#SBATCH --output=STARAlign_%j.out
#SBATCH --nodes=1 
#SBATCH --cpus-per-task=28
#SBATCH --time=2:00:00 

/usr/bin/time -v STAR --runThreadN 8 \
--runMode alignReads --outFilterMultimapNmax 3 \
--outSAMunmapped Within KeepPairs --alignIntronMax 1000000 \
--alignMatesGapMax 1000000 --readFilesCommand zcat \
--readFilesIn Read1Filtered.fastq.gz Read2Filtered.fastq.gz \
--genomeDir /projects/bgmp/shared/2021_projects/Salish/SalishProj/Genome_ref_dir \
--outFileNamePrefix Align_OUTPUT