[sr320@mox1 1013]$ cat /gscratch/srlab/sr320/jobs/1013_1200.sh
#!/bin/bash
## Job Name
#SBATCH --job-name=bow33
## 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=500G
#SBATCH --mail-type=ALL
#SBATCH --mail-user=sr320@uw.edu
## Specify the working directory for this job
#SBATCH --workdir=/gscratch/srlab/sr320/analyses/1013
source /gscratch/srlab/programs/scripts/paths.sh
for fastq in /gscratch/scrubbed/sr320/Phred33_fqs/*1.fq.gz; do
read1=$(echo "$fastq")
read1_array+=("$read1")
done
for fastq in /gscratch/scrubbed/sr320/Phred33_fqs/*2.fq.gz; do
read2=$(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 "$j" \
-X 2000 --sensitive --no-mixed --phred33 --no-discordant --no-unal \
-S /gscratch/scrubbed/sr320/cw/"$no_ext"_bowtie2.sam \
-q \
-p 28
done
Daily Archives: October 13
[code]#!/bin/bash ## Job Name #SBATCH...
#!/bin/bash
## Job Name
#SBATCH --job-name=bow33
## 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=500G
#SBATCH --mail-type=ALL
#SBATCH --mail-user=sr320@uw.edu
## Specify the working directory for this job
#SBATCH --workdir=/gscratch/srlab/sr320/analyses/1013
source /gscratch/srlab/programs/scripts/paths.sh
for fastq in /gscratch/scrubbed/sr320/Phred33_fqs/*1.fq.gz; do
read1=$(echo "$fastq")
read1_array+=("$read1")
done
for fastq in /gscratch/scrubbed/sr320/Phred33_fqs/*2.fq.gz; do
read2=$(echo "$fastq")
read2_array+=("$read2")
done
for pair in "${!read1_array[@]}"; do
i=${read1_array[$pair]}
j=${read2_array[$pair]}
filename="${i##*/}"
no_ext="${filename%%.*}"
/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 -x \
/gscratch/srlab/sr320/data/Chinook_genome_scaffold_masked \
-1 "$i" \
-2 "$j" \
-X 2000 --sensitive --no-mixed --phred33 --no-discordant --no-unal \
-S /gscratch/scrubbed/sr320/cw/"$no_ext"_bowtie2.sam \
-q \
-p 28
done
Roberts Lab 