HiC_scripts/runQth.pbs at master · epigen-UCSD/HiC_scripts · GitHub

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#!/bin/bash
#PBS -q home-epigen
#PBS -N juicer
#PBS -l nodes=1:ppn=28
#PBS -l mem=96g
#PBS -l walltime=24:00:00
#PBS -V
#PBS -m abe
#PBS -A epigen-group

# -v sample=,mpq

set -x
PS4='+\d+\t '

source activate hic
module load cuda/8.0.44
export _JAVA_OPTIONS="-Xmx64g"

cd /home/zhc268/scratch/juicer/work/${sample}

../../scripts/common/statistics.pl -s ../..//restriction_sites/hg19_MboI.txt \
                                    -l GATCGATC -o /home/zhc268/scratch/juicer/work/${sample}/aligned/inter_${mpq}.txt \
                                    -q ${mpq} /home/zhc268/scratch/juicer/work/${sample}/aligned/merged_nodups.txt

../../scripts/common/juicer_tools pre -s /home/zhc268/scratch/juicer/work/${sample}/aligned/inter_${mpq}.txt \
                                   -g /home/zhc268/scratch/juicer/work/${sample}/aligned/inter_${mpq}_hists.m \
                                   -q ${mpq} /home/zhc268/scratch/juicer/work/${sample}/aligned/merged_nodups.txt \
                                   /home/zhc268/scratch/juicer/work/${sample}/aligned/inter_${mpq}.hic hg19