04a_align_reads_hisat2_JL221.sb

#!/bin/bash --login
########## Define Resources Needed with SBATCH Lines ##########

#SBATCH --time=00:10:00             # limit of wall clock time - how long the job will run (same as -t)
#SBATCH --ntasks=1                 # number of tasks - how many tasks (nodes) that you require (same as -n)
#SBATCH --cpus-per-task=16          # number of CPUs (or cores) per task (same as -c)
#SBATCH --mem=10G                   # memory required per node - amount of memory (in bytes)
#SBATCH --job-name=hisat2_align_JL221        # you can give your job a name for easier identification (same as -J)
#SBATCH --output=%x-%j.SLURMout

########## Command Lines to Run ##########

module load GCC/9.3.0
module load GCCcore/9.3.0
module load SAMtools/1.11
module load hisat2/2.1.0

cd ~/He_Lab/Yeast_genomes/scripts
DATADIR=~/He_Lab/Yeast_genomes/data

hisat2 \
  -x $DATADIR/read_mapping/JL221_masked_scaffolds \
  -1 $DATADIR/filt_trimmed/JL221_S55_1P.fastq.gz \
  -2 $DATADIR/filt_trimmed/JL221_S55_2P.fastq.gz  \
  --summary-file $DATADIR/read_mapping/JL221.hisat2-summary.txt \
  --un-gz $DATADIR/read_mapping/JL221.unaligned.fastq.gz \
  -p 16 | samtools sort -O bam -o $DATADIR/read_mapping/JL221.aligned.bam

scontrol show job $SLURM_JOB_ID     ### write job information to output file