#!/bin/sh
#PBS -N noUMI_unpair_qc
#PBS -j oe
#PBS -l ncpus=20
#PBS -l nodes=1
#PBS -l mem=40G
source  /home/liuxiangqiong/miniconda3/bin/activate base
cmddir=/cgdata/liuxiangqiong/work62pancancer/Client/v0/script/20220705
starttime="`date '+%Y%m%d%H%M%S'`"
echo "for qc"
#$cmddir/s9_noUMI_qc_unpair_20220606.sh
$cmddir/s9_noUMI_qc_unpair_20220929.sh
#for chemical
echo "for ontarget"
#$cmddir/s10_noUMI_ontarget_unpair_20220606.sh
#$cmddir/s10_noUMI_ontarget_unpair_20220929.sh
#for HLA
echo "for covergae"
#$cmddir/s11_noUMI_coverage_unpair_20220808.sh
$cmddir/s11_noUMI_coverage_unpair_20220929.sh
#计算质控
#python3 /cgdata/liuxiangqiong/work62pancancer/Client/v0/script/20220705/datafile_QC_v0_20220906_finish.py -i ${inputpath} -s ${sample}
python3 /cgdata/liuxiangqiong/work62pancancer/Client/v0/script/20220705/datafile_QC_v0_20230406_finish.py -i ${inputpath} -s ${sample}

##计算测序错误
echo "for seqERROR"
$cmddir/s14_seqError_unpair_20230422.sh
endtime="`date '+%Y%m%d%H%M%S'`"
echo "run " $[$endtime-$starttime]"s">${inputpath}/${sample}_QC_unpair.log1
echo "${sample} QC finish!" >>${inputpath}/${sample}_QC_unpair.log1