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04a_align_reads_hisat2_JL201.sb
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04a_align_reads_hisat2_JL201.sb
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#!/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_JL201 # 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/JL201_masked_scaffolds \
-1 $DATADIR/filt_trimmed/JL201_S181_1P.fastq.gz \
-2 $DATADIR/filt_trimmed/JL201_S181_2P.fastq.gz \
--summary-file $DATADIR/read_mapping/JL201.hisat2-summary.txt \
--un-gz $DATADIR/read_mapping/JL201.unaligned.fastq.gz \
-p 16 | samtools sort -O bam -o $DATADIR/read_mapping/JL201.aligned.bam
scontrol show job $SLURM_JOB_ID ### write job information to output file