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03-hisat2.srun
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03-hisat2.srun
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#!/bin/bash
#SBATCH --partition=ficklin
#SBATCH --account=ficklin
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --time=8:00:00
#SBATCH --job-name=KGEM03
#SBATCH --output=logs/03-hisat2.%a.log
#SBATCH --array=0-999
factor=0
basename='all'
module add hisat2
IDs=(`cat SRA_IDs.txt`)
ID=${IDs[$SLURM_ARRAY_TASK_ID + $factor]}
forward="${ID}_1.trim.fastq"
reverse="${ID}_2.trim.fastq"
done=`tail -n 1 logs/03-hisat2.${SLURM_ARRAY_TASK_ID}.out | grep -c "Overall time:"`
if [ $done != 1 ]; then
cd ${ID}
splice_file=`ls ../reference/${basename}.Splice_Sites.txt`
export HISAT2_INDEXES=`pwd`/../reference
if [ -e $reverse ]; then
hisat2 \
-x ${basename} \
--no-temp-splicesite \
--known-splicesite-infile $splice_file \
-q \
-1 ${ID}_1.trim.fastq \
-2 ${ID}_2.trim.fastq \
-U ${ID}_1s.trim.fastq,${ID}_2s.trim.fastq \
-S ${ID}_vs_${basename}.sam \
-t \
-p 1 \
--dta-cufflinks > ../logs/03-hisat2.${SLURM_ARRAY_TASK_ID}.out 2>&1
else
hisat2 \
-x ${basename} \
--no-temp-splicesite \
--known-splicesite-infile $splice_file \
-q \
-U ${ID}_1.trim.fastq \
-S ${ID}_vs_${basename}.sam \
-t \
-p 1 \
--dta-cufflinks > ../logs/03-hisat2.${SLURM_ARRAY_TASK_ID}.out 2>&1
fi
else
echo "$ID Completed"
fi