#!/bin/sh
#PBS -N qc
#PBS -j oe
#PBS -l ncpus=10
#PBS -l nodes=1
#PBS -l mem=20G
source  /home/liuxiangqiong/miniconda3/bin/activate base
outputdir=${inputpath}/8Fastqc
#1rawdata_qc
/cgdata/soft/cellar/iTools_Code20170705/iTools  Fqtools stat -InFq ${inputpath}/${sample}_R1.fastq.gz -InFq ${inputpath}/${sample}_R2.fastq.gz -OutStat ${outputdir}/${sample}.stat  -CPU 2
#2fastqc_rawdata
fastqc ${inputpath}/${sample}_R1.fastq.gz  ${inputpath}/${sample}_R2.fastq.gz -o ${outputdir}
#2fastqc_cleandata
fastqc ${inputpath}/${sample}_clean_R1.fq.gz  ${inputpath}/${sample}_clean_R2.fq.gz -o ${outputdir}