sr320@mox1 ~]$ cat /gscratch/srlab/sr320/jobs/1017_0800.sh #!/bin/bash ## Job Name #SBATCH --job-name=bow64 ## Allocation Definition #SBATCH --account=srlab #SBATCH --partition=srlab ## Resources ## Nodes (We only get 1, so this is fixed) #SBATCH --nodes=1 ## Walltime (days-hours:minutes:seconds format) #SBATCH --time=5-100:00:00 ## Memory per node #SBATCH --mem=100G #SBATCH --mail-type=ALL #SBATCH --mail-user=sr320@uw.edu ## Specify the working directory for this job #SBATCH --workdir=/gscratch/srlab/sr320/analyses/1017 source /gscratch/srlab/programs/scripts/paths.sh for fastq in /gscratch/scrubbed/sr320/Phred64_fqs/*1.fq.gz; do read1=$(echo "$fastq") read1_array+=("$read1") done for fastq in /gscratch/scrubbed/sr320/Phred64_fqs/*2.fq.gz; do read2=$(echo "$fastq") read2_array+=("$read2") done for pair in "${!read1_array[@]}"; do i=${read1_array[$pair]} j=${read2_array[$pair]} filename="${i##*/}" no_ext="${filename%%.*}" /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 \ -x /gscratch/srlab/sr320/data/Chinook_genome_scaffold_masked/chinook_genome_masked \ -1 "$i" \ -2 "$j" \ -X 2000 --sensitive --no-mixed --phred64 --no-discordant --no-unal \ -S /gscratch/scrubbed/sr320/cw/1017/"$no_ext"_bowtie2.sam \ -q \ -p 28 done
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