Delete postprocessing.sh

#!/bin/bash

jID_launch=$( qstat | grep Lnch_${groupname} | cut -c 1-7 )

if [ -z $postproc ]

then

    waitstring3="#PBS -W depend=afterok:${jID_launch}"

fi

echo "waitstring3 is: ${waitstring3}"

timestamp=$(date +"%s" | cut -c 4-10)

qsub <<- POSTPROCWRAP

#PBS -S /bin/bash

#PBS -q $queue

#PBS -l $walltime

#PBS -l nodes=1:ppn=1:AMD

#PBS -l mem=4gb

#PBS -o ${logdir}/${timestamp}_postproc_wrap_${groupname}.log

#PBS -j oe

#PBS -N PPrWrp${groupname}

${waitstring3}

date +"%Y-%m-%d %H:%M:%S"

jID_hic30=\$(qstat | grep hic30_${groupname} |cut -c 1-7)

if [ -z $postproc ]

then

    waitstring4="#PBS -W depend=afterok:\${jID_hic30}" 

fi

echo "waitstring4 is : ${waitstring4}"

timestamp=\$(date +"%s" | cut -c 4-10)

qsub <<POSTPROCESS

	#PBS -S /bin/bash

	#PBS -q $queue

	#PBS -l $long_walltime

	#PBS -l nodes=1:ppn=1:gpus=1:GPU 

	#PBS -l mem=60gb

	#PBS -o ${logdir}/\${timestamp}_postproc_${groupname}.log

	#PBS -j oe

	#PBS -N PProc_${groupname}

    $waitstring4

    date +"%Y-%m-%d %H:%M:%S"

    $load_java

    $load_cuda

    module list 

    export _JAVA_OPTIONS=-Xmx16384m

    export LC_ALL=en_US.UTF-8

    ${juiceDir}/scripts/juicer_postprocessing.sh -j ${juiceDir}/scripts/juicer_tools -i ${outputdir}/inter_30.hic -m ${juiceDir}/references/motif -g $genomeID

POSTPROCESS

POSTPROCWRAP

jID_postprocwrap=$( qstat |grep PPrWrp${groupname} | cut -c 1-7 )

echo $jID_postprowrap

wait

timestamp=$(date +"%s" | cut -c 4-10)

qsub <<- FINCK

#PBS -S /bin/bash

#PBS -q $queue  

#PBS -l $walltime

#PBS -o ${logdir}/${timestamp}_prep_done_${groupname}.log

#PBS -j oe

#PBS -N Pdone_${groupname}

#PBS -W depend=afterok:${jID_postprocwrap}

date +"%Y-%m-%d %H:%M:%S"    

jID_hic30=\$(qstat | grep hic30_${groupname} |cut -c 1-7)

jID_stats0=\$(qstat | grep stats0${groupname} |cut -c 1-7)

jID_stats30=\$(qstat | grep stats30${groupname} |cut -c 1-7)

jID_hic=\$(qstat | grep hic0_${groupname} |cut -c 1-7)

jID_postproc=\$(qstat | grep PProc_${groupname} |cut -c 1-7)

waitstring5="#PBS -W depend=afterok:\${jID_postproc}"

if [ -z $postproc ]

then

    waitstring5="#PBS -W depend=afterok:\${jID_hic30}:\${jID_stats0}:\${jID_stats30}:\${jID_hic}:\${jID_postproc}"

fi

timestamp=\$(date +"%s" | cut -c 4-10)

qsub <<DONE

	#PBS -S /bin/bash

	#PBS -q $queue

	#PBS -l $walltime

	#PBS -l nodes=1:ppn=1:AMD 

	#PBS -l mem=4gb

	#PBS -o ${logdir}/\${timestamp}_done_${groupname}.log

	#PBS -j oe

	#PBS -N done_${groupname}

	\${waitstring5}

	date +"%Y-%m-%d %H:%M:%S"    

	export splitdir=${splitdir}

	export outputdir=${outputdir}

	${juiceDir}/scripts/check.sh

DONE

FINCK