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GAT_K562_ReRun2019_opOQS.sh
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GAT_K562_ReRun2019_opOQS.sh
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#!/bin/sh
#SBATCH --partition general
#SBATCH --mem 64GB
#SBATCH --job-name K562GAT_opOQS
#SBATCH --output /scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/Logs/GAT_K562_Rerun_opOQS.%j.log
/home/spiege01/python/bin/gat-run.py \
--segments=/scratchb/sblab/spiege01/ENCODE_K562/reference_data/Quadruplex/20180108_K562_async_rep1-3.mult.5of8.bed \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CEK.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CEL.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CEM.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CLR.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CMA.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CMJ.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CMK.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CMM.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CMN.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CMO.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CMP.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CMY.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CVM.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CVN.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CVP.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CVR.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CVS.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CVU.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CVW.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CVX.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CWC.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CWI.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CWK.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CWM.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CWN.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CWR.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CWT.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CXE.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CXG.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CXH.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CXK.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CXR.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CXT.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CXU.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CXW.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CXX.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CXZ.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002CYL.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002DBC.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002DBD.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002DBE.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002DDJ.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002DDU.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002DDV.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002DDY.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF002DDZ.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF004WYV.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF007DKB.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF009DUY.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF010MMQ.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF010STZ.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF010UHD.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF011KRN.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF012VES.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF019ALY.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF019PEL.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF030HWZ.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF030QEM.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF033EBX.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF033KXY.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF034CQR.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF034PQD.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF036YVI.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF041YQC.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF042RAK.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF043YZF.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF044JNJ.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF048OBR.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF048OIZ.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF049CRW.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF057ZUY.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF059ONJ.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF059WVE.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF062ARS.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF067LIW.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF074EZL.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF076IFG.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF076MSV.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF076YZO.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF077UYM.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF080NBZ.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF083YCQ.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF085HTY.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF085JHT.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF096XMD.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF099LMD.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF099SDW.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF106DAY.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF113PMT.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF114IWY.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF114PTZ.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF116DIO.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF117EWO.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF120IDE.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF120WOF.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF122QSN.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF126BCK.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF126QYP.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF127XXD.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF134CUM.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF134NMW.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF137IBM.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF139CKE.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF142CPK.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF144PPR.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF150VTD.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF152VMJ.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF156WRH.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF157UUF.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF163VUK.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF164HLQ.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF165BCW.cut.bed.gz \
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--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF738WCE.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF744SVC.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF757ODD.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF768TJI.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF769GYG.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF769WZF.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF772HOY.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF772QPO.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF774QKS.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF776YPS.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF777CWV.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF778RMG.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF782GWS.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF784FIE.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF785ACI.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF785HXY.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF786WZD.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF788EBS.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF798URE.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF799HIG.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF801YZV.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF802XZN.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF803COK.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF803LEC.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF806BDC.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF809OEX.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF809YFY.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF812QPN.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF815TTY.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF820EVZ.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF821VBM.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF822FWM.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF823SYE.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF828JWK.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF833FCO.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF833KXP.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF834WGJ.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF835KAT.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF835YLR.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF836LBG.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF836VRV.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF838COI.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF841YFF.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF844HBQ.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF849ZUF.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF853TZC.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF853ZMA.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF858QMI.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF859FVX.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF859NPS.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF861YKK.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF868QLL.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF872JJJ.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF872YNU.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF874QUM.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF877ANE.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF881QBT.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF881XQF.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF883POK.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF883TOD.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF883WYX.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF886VSU.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF891MVM.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF894VEM.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF895QLA.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF898FAQ.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF901AHW.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF905VXX.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF906PGD.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF908UIY.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF909LKK.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF911VSD.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF914RFS.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF917COW.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF920RYJ.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF921WMN.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF922TDM.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF925ANU.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF925DJG.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF925MHB.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF926FUM.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF927JBT.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF929YBC.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF932UEC.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF937VZI.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF938IOJ.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF939ZFS.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF941RVL.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF944GJH.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF944GZI.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF947KPB.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF948TXN.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF948YVM.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF954NAJ.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF958KNK.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF962FQM.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF962VSZ.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF966MVC.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF967IKR.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF968EAL.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF968JVX.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF968KBN.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF970LCB.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF971VJZ.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF972LPT.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF973LDQ.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF973OME.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF975IRM.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF985TSH.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF986MHU.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF987VNY.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF990CFV.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF992QZV.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF993GXU.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF995IAC.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF995NIE.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF996CUX.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF996IVU.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF996ZGL.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF998HOR.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF998KKJ.cut.bed.gz \
--annotations=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/K562_Cut_Bed_Jan2019/ENCFF998YJY.cut.bed.gz \
--workspace=/scratchb/sblab/spiege01/ENCODE_K562/reference_data/Mod_ChrM/openOQs_chrM.bed \
–-ignore-segment-tracks \
--num-samples=10000 \
--log=/scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/Logs/GAT_K562_Rerun2019_opOQS_LOG.txt \
--num-threads=16 > /scratchb/sblab/spiege01/ENCODE_K562/GAT_Rerun_Jan2019/GAT_Rerun2019_output/GAT.K562.Rerun_2019.opOQS.tsv