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- #!/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
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