Commit 856b1163 authored by Aiden Lab's avatar Aiden Lab Committed by GitHub
Browse files

Merge pull request #34 from mzhibo/master 

bugs fix
parents 44db5df1 688fc4f3

PBS/scripts/juicer.sh

+27 −36
Changes for PBS/scripts/juicer.sh: 27 added lines, 36 removed lines.
Original line number Diff line number Diff line
@@ -85,7 +85,7 @@ load_cuda='module load cuda/7.5.18/gcc/4.4.7' 


# Juicer directory, contains scripts/, references/, and restriction_sites/

# can also be set in options via -D

juiceDir="/lustre1/mzhibo/hic/apps/juicer"

juiceDir=""

# default queue, can also be set in options via -q

queue="batch"

# default queue time, can also be set in options via -Q
@@ -94,25 +94,18 @@ walltime="walltime=24:00:00" 
long_queue="batch"

# default long queue time, can also be set in options via -L

long_walltime="walltime=120:00:00"



###################

#The specific format for cpu/gpu resource request with #PBS -l node=?:ppn=?:AMD header line

#might be different on different cluster. 

#Please adjust this header line according to your cluster setup.

###################

# give your email address to be used in #PBS -M to receive notifications when job error occurs.

EMAIL=""





# size to split fastqs. adjust to match your needs. 4000000=1M reads per split

# can also be changed via the -C flag

# give your email address to be used in #PBS -M to receive notifications when job error occurs.

# Must be either set with an email address or skipped

# This email is not included in the launch stat and postprocessing steps, add manually if needed

EMAIL='#PBS -M mzhibo@gmail.com'

splitsize=90000000

# fastq files should look like filename_R1.fastq and filename_R2.fastq 

# if your fastq files look different, change this value

read1str="_R1"

read2str="_R2"

#resolutions is optional, set if you want resolutions other than the default in .hic

resolutions='1000000,500000,100000,50000,10000,5000,2000'





# unique groupname for jobs submitted in each run. lab initial with an timestamp

# Length of $groupname in this PBS version needs to be no longer than 8 characters.
@@ -404,9 +397,9 @@ then 
                #PBS -S /bin/bash

                #PBS -q $queue

                #PBS -l $walltime

                $RESOURCE

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

                #PBS -l mem=20gb

                #PBS -M ${EMAIL}

                ${EMAIL}

                #PBS -m a

                #PBS -o ${logdir}/${timestamp}_split_${filename}_${groupname}.log

                #PBS -j oe
@@ -432,7 +425,7 @@ SPLITEND 
            #PBS -l $walltime

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

            #PBS -l mem=20gb

            #PBS -M ${EMAIL}

            ${EMAIL}

            #PBS -m a

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

            #PBS -j oe
@@ -470,7 +463,7 @@ SPLITMV 
    #PBS -j oe

    #PBS -N AlnWrp${groupname}

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

    #PBS -M ${EMAIL}

    ${EMAIL}

    #PBS -m a

    for i in ${read1}

    do
@@ -496,7 +489,7 @@ SPLITMV 
        #PBS -l $walltime

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

        #PBS -l mem=4gb

        #PBS -M ${EMAIL}

        ${EMAIL}

        #PBS -m a

        #PBS -o ${logdir}/\${timestamp}_\${jname}_CntLig_\${countjobs}_${groupname}.log

        #PBS -j oe
@@ -541,7 +534,7 @@ CNTLIG 
        #PBS -l $walltime

        #PBS -l nodes=1:ppn=${threads}:AMD

        #PBS -l mem=\${alloc_mem}

        #PBS -M ${EMAIL}

        ${EMAIL}

        #PBS -m a

        #PBS -o ${logdir}/\${timestamp}_\${jname}_align1_\${countjobs}_${groupname}.log

        #PBS -j oe
@@ -592,7 +585,7 @@ ALGNR1 
        #PBS -l $walltime

        #PBS -l nodes=1:ppn=${threads}:AMD

        #PBS -l mem=\$alloc_mem

        #PBS -M ${EMAIL}

        ${EMAIL}

        #PBS -m a

        #PBS -o ${logdir}/\${timestamp}_\${jname}_align2_\${countjobs}_${groupname}.log

        #PBS -j oe
@@ -643,7 +636,7 @@ ALGNR2 
        #PBS -l $long_walltime

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

        #PBS -l mem=24gb

        #PBS -M ${EMAIL}

        ${EMAIL}

        #PBS -m a

        #PBS -o ${logdir}/\${timestamp}_\${jname}_merge_\${countjobs}_${groupname}.log

        #PBS -j oe
@@ -719,7 +712,7 @@ MRGALL 
    #PBS -l $walltime

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

    #PBS -l mem=24gb

    #PBS -M ${EMAIL}

    ${EMAIL}

    #PBS -m a

    #PBS -o ${logdir}/\${timestamp}_\${jname}_chimeric_\${countjobs}_${groupname}.log

    #PBS -j oe
@@ -791,7 +784,7 @@ CHIMERIC 
    #PBS -l nodes=1:ppn=1:AMD

    #PBS -l mem=2gb

    #PBS -l $walltime

    #PBS -M ${EMAIL}

    ${EMAIL}

    #PBS -m a

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

    #PBS -j oe
@@ -809,7 +802,7 @@ CKALIGNFAIL 
    #PBS -l nodes=1:ppn=1:AMD

    #PBS -l mem=4gb

    #PBS -l $walltime

    #PBS -M ${EMAIL}

    ${EMAIL}

    #PBS -m a

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

    #PBS -j oe
@@ -848,7 +841,7 @@ then 
    #PBS -l nodes=1:ppn=1:AMD

    #PBS -l mem=24gb

    #PBS -l $walltime

    #PBS -M ${EMAIL}

    ${EMAIL}

    #PBS -m a

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

    #PBS -j oe
@@ -875,7 +868,7 @@ then 
        #PBS -l nodes=1:ppn=1:AMD

        #PBS -l mem=24gb

        #PBS -l $walltime

        #PBS -M ${EMAIL}

        ${EMAIL}

        #PBS -m a

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

        #PBS -j oe
@@ -906,7 +899,7 @@ MRGSRT 
        #PBS -l nodes=1:ppn=1:AMD

        #PBS -l mem=2gb

        #PBS -l $walltime

        #PBS -M ${EMAIL}

        ${EMAIL}

        #PBS -m a

        #PBS -o ${logdir}/\${timestamp}_clean1_${groupname}.log

        #PBS -j oe
@@ -939,7 +932,7 @@ then 
    #PBS -l nodes=1:ppn=1:AMD

    #PBS -l mem=4gb

    #PBS -l $walltime

    #PBS -M ${EMAIL}

    ${EMAIL}

    #PBS -m a

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

    #PBS -j oe
@@ -961,7 +954,7 @@ then 
        #PBS -l nodes=1:ppn=1:AMD

        #PBS -l mem=4gb

        #PBS -l $walltime

        #PBS -M ${EMAIL}

        ${EMAIL}

        #PBS -m a   

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

        #PBS -j oe
@@ -1008,7 +1001,7 @@ then 
        #PBS -l nodes=1:ppn=1:AMD

        #PBS -l mem=1gb

        #PBS -l $walltime

        #PBS -M ${EMAIL}

        ${EMAIL}

        #PBS -m a

        #PBS -o ${logdir}/${timestamp}_superwrap1_${groupname}.log

        #PBS -j oe
@@ -1027,12 +1020,11 @@ then 
        export splitdir=$splitdir

        export nofrag=$nofrag

        export genomePath=$genomePath

        export resolutions=$resolutions

        export final=$final

        export queue=$queue

        export walltime=$walltime

        export long_walltime=$long_walltime

        export EMAIL=$EMAIL

        export nofrag=$nofrag

        ${juiceDir}/scripts/launch_stats.sh

SUPERWRAP1

    fi
@@ -1055,7 +1047,7 @@ SUPERWRAP1 
    #PBS -o ${logdir}/${timestamp}_super_wrap2_${groupname}.log

    #PBS -j oe

    #PBS -N SpWrp2${groupname}

    #PBS -M ${EMAIL}

    ${EMAIL}

    #PBS -m a

    ${waitstring6}    

    wait
@@ -1071,7 +1063,6 @@ SUPERWRAP1 
    export walltime=$walltime

    export long_walltime=$long_walltime

    export postproc=$postproc

	export EMAIL=$EMAIL

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

    echo \$jID_launch

    echo "waitstring3 is \${waitstring3}"
@@ -1092,7 +1083,7 @@ else 
    #PBS -l mem=1gb

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

    #PBS -j oe

    #PBS -M ${EMAIL}

    ${EMAIL}

    #PBS -m a

    #PBS -N prepd_${groupname}

    #PBS -W depend=afterok:${jID_rmdupwrap}
@@ -1111,7 +1102,7 @@ else 
        #PBS -o ${logdir}/\${timestamp}_done_${groupname}.log

        #PBS -j oe

        #PBS -N ${groupname}_done

        #PBS -M ${EMAIL}

        ${EMAIL}

        #PBS -m a

        #PBS -W depend=afterok:\${jID_osplit}:\${jID_rmsplit}

PBS/scripts/juicer_tools

deleted100644 → 0
+0 −26
Changes for PBS/scripts/juicer_tools: 0 added lines, 26 removed lines.
Original line number Diff line number Diff line 
#!/bin/bash -l

#

# Copyright (c) 2015 Aiden Lab

#

# Permission is hereby granted, free of charge, to any person obtaining a copy

# of this software and associated documentation files (the "Software"), to deal

# in the Software without restriction, including without limitation the rights

# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell

# copies of the Software, and to permit persons to whom the Software is

# furnished to do so, subject to the following conditions:

# 

# The above copyright notice and this permission notice shall be included in

# all copies or substantial portions of the Software.

# 

# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR

# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,

# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE

# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER

# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,

# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN

# THE SOFTWARE.

#

# Juicer version 1.5



java -Djava.awt.headless=true -Djava.library.path=`dirname $0`/lib64 -Xmx16000m -jar `dirname $0`/juicer_tools.jar $*

PBS/scripts/launch_stats.sh

+2 −16
Changes for PBS/scripts/launch_stats.sh: 2 added lines, 16 removed lines.
Original line number Diff line number Diff line
@@ -17,7 +17,6 @@ echo "resolutions: $resolutions" 
echo "walltime: $walltime"

echo "long_walltime: $long_walltime"

echo $load_java

echo "EMAIL: $EMAIL"

jID_osplit=$( qstat | grep osplit${groupname} | cut -c 1-7 )



if [ -z $final ]
@@ -35,8 +34,6 @@ qsub <<DOSTAT 
#PBS -l nodes=1:ppn=1:AMD

#PBS -l mem=1gb

#PBS -l $walltime

#PBS -M ${EMAIL}

#PBS -m a

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

#PBS -j oe

#PBS -N Lnch_${groupname}
@@ -64,8 +61,6 @@ qsub <<STATS0 
	#PBS -l mem=20gb

	#PBS -l $walltime

	\${waitstring22}

	#PBS -M ${EMAIL}

	#PBS -m a 

	#PBS -o ${logdir}/\${timestamp}_stats0_${groupname}.log

	#PBS -j oe

	#PBS -N stats0${groupname}
@@ -89,8 +84,6 @@ qsub <<STATS30 
	#PBS -l nodes=1:ppn=1:AMD

	#PBS -l mem=20gb

	#PBS -l $walltime

	#PBS -M ${EMAIL}

	#PBS -m a 

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

	#PBS -j oe

	#PBS -N stats30${groupname}
@@ -115,8 +108,6 @@ qsub <<- ABNORMAL 
	#PBS -l nodes=1:ppn=1:AMD

	#PBS -l mem=60gb

	#PBS -l $long_walltime

	#PBS -M ${EMAIL}

	#PBS -m ae

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

	#PBS -j oe

	#PBS -N abnorm_${groupname}
@@ -139,8 +130,6 @@ qsub <<- HICWORK 
	#PBS -l nodes=1:ppn=1:AMD

	#PBS -l mem=60gb

	#PBS -l $long_walltime

	#PBS -M ${EMAIL}

	#PBS -m ae

	#PBS -o ${logdir}/\${timestamp}_hic0_${groupname}.log

	#PBS -j oe

	#PBS -N hic0_${groupname}
@@ -154,7 +143,7 @@ qsub <<- HICWORK 
	then 

		${juiceDir}/scripts/juicer_tools pre -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 $outputdir/merged_nodups.txt $outputdir/inter.hic $genomePath

	else 

		${juiceDir}/scripts/juicer_tools pre -r $resolutions -f $site_file -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 $outputdir/merged_nodups.txt $outputdir/inter.hic $genomePath

		${juiceDir}/scripts/juicer_tools pre -f $site_file -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 $outputdir/merged_nodups.txt $outputdir/inter.hic $genomePath

	fi

HICWORK

jID_stats30=\$( qstat | grep stats30${groupname} | cut -c 1-7)
@@ -166,8 +155,6 @@ qsub <<- HIC30WORK 
	#PBS -l nodes=1:ppn=1:AMD

	#PBS -l mem=60gb

	#PBS -l $long_walltime

	#PBS -M ${EMAIL}

	#PBS -m ae

	#PBS -o ${logdir}/\${timestamp}_hic30_${groupname}.log

	#PBS -j oe

	#PBS -N hic30_${groupname}
@@ -185,9 +172,8 @@ qsub <<- HIC30WORK 
	then 

	${juiceDir}/scripts/juicer_tools pre -s $outputdir/inter_30.txt -g $outputdir/inter_30_hists.m -q 30 $outputdir/merged_nodups.txt $outputdir/inter_30.hic $genomePath

	else 

		${juiceDir}/scripts/juicer_tools pre -r $resolutions -f $site_file -s $outputdir/inter_30.txt -g $outputdir/inter_30_hists.m -q 30 $outputdir/merged_nodups.txt $outputdir/inter_30.hic $genomePath

		${juiceDir}/scripts/juicer_tools pre -f $site_file -s $outputdir/inter_30.txt -g $outputdir/inter_30_hists.m -q 30 $outputdir/merged_nodups.txt $outputdir/inter_30.hic $genomePath

	fi

HIC30WORK

sleep 3m



DOSTAT

PBS/scripts/mega.sh

+9 −12
Changes for PBS/scripts/mega.sh: 9 added lines, 12 removed lines.
Original line number Diff line number Diff line
@@ -48,8 +48,7 @@ juiceDir="/lustre1/mzhibo/hic/apps/juicer" 
# unique name for jobs in this run

groupname="C$(date +"%s"|cut -c 6-11)"



#give an email to receive notification when a job exit with error

EMAIL=""



## Default options, overridden by command line arguments



# top level directory, can also be set in options
@@ -59,8 +58,6 @@ site="MboI" 
# genome ID, default to human, can also be set in options

genomeID="hg19"



#the resolution is optional, set only when you want resolution other than the default

resolutions="1M,500K,100K,50K,10K,5K,3K,2K"

## Read arguments

usageHelp="Usage: ${0##*/} -g genomeID [-d topDir] [-s site] [-r resolutions] [-hx]"

genomeHelp="   genomeID must be defined in the script, e.g. \"hg19\" or \"mm10\" (default \"$genomeID\")"
@@ -235,11 +232,11 @@ jid5=$(qsub -o ${logdir}/hic0_${groupname}.log -j oe -q batch -M ${EMAIL} -m ae 
$load_java

if [ -z "$exclude" ]

then

  echo "Launching ${juiceDir}/scripts/juicer_tools pre -f ${site_file} -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID}"

  ${juiceDir}/scripts/juicer_tools pre -f ${site_file} -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID}

  echo "Launching ${juiceDir}/scripts/juicer_tools pre ${resolutions} -f ${site_file} -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID}"

  ${juiceDir}/scripts/juicer_tools pre ${resolutions} -f ${site_file} -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID}

else

  echo "Launching ${juiceDir}/scripts/juicer_tools pre -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID}"

  ${juiceDir}/scripts/juicer_tools pre -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID}

  echo "Launching ${juiceDir}/scripts/juicer_tools pre ${resolutions} -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID}"

  ${juiceDir}/scripts/juicer_tools pre ${resolutions} -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID}

fi

HIC0

)
@@ -249,11 +246,11 @@ jid6=$(qsub -o ${logdir}/hic30_${groupname}.log -j oe -q batch -M ${EMAIL} -m ae 
$load_java

if [ -z "${exclude}" ]

then

    echo "Launching ${juiceDir}/scripts/juicer_tools pre -f ${site_file} -s ${outputdir}/inter_30.txt -g ${outputdir}/inter_30_hists.m -q 30 ${outputdir}/merged_nodups.txt ${outputdir}/inter_30.hic ${genomeID}"

    ${juiceDir}/scripts/juicer_tools pre -f ${site_file} -s ${outputdir}/inter_30.txt -g ${outputdir}/inter_30_hists.m -q 30 ${outputdir}/merged_nodups.txt ${outputdir}/inter_30.hic ${genomeID}

    echo "Launching ${juiceDir}/scripts/juicer_tools pre ${resolutions} -f ${site_file} -s ${outputdir}/inter_30.txt -g ${outputdir}/inter_30_hists.m -q 30 ${outputdir}/merged_nodups.txt ${outputdir}/inter_30.hic ${genomeID}"

    ${juiceDir}/scripts/juicer_tools pre ${resolutions} -f ${site_file} -s ${outputdir}/inter_30.txt -g ${outputdir}/inter_30_hists.m -q 30 ${outputdir}/merged_nodups.txt ${outputdir}/inter_30.hic ${genomeID}

else

   echo "Launching ${juiceDir}/scripts/juicer_tools pre -s ${outputdir}/inter_30.txt -g ${outputdir}/inter_30_hists.m -q 30 ${outputdir}/merged_nodups.txt ${outputdir}/inter_30.hic ${genomeID}"

   ${juiceDir}/scripts/juicer_tools pre -s ${outputdir}/inter_30.txt -g ${outputdir}/inter_30_hists.m -q 30 ${outputdir}/merged_nodups.txt ${outputdir}/inter_30.hic ${genomeID}

   echo "Launching ${juiceDir}/scripts/juicer_tools pre ${resolutions} -s ${outputdir}/inter_30.txt -g ${outputdir}/inter_30_hists.m -q 30 ${outputdir}/merged_nodups.txt ${outputdir}/inter_30.hic ${genomeID}"

   ${juiceDir}/scripts/juicer_tools pre ${resolutions} -s ${outputdir}/inter_30.txt -g ${outputdir}/inter_30_hists.m -q 30 ${outputdir}/merged_nodups.txt ${outputdir}/inter_30.hic ${genomeID}

fi

HIC30

)

PBS/scripts/postprocessing.sh

+0 −8
Changes for PBS/scripts/postprocessing.sh: 0 added lines, 8 removed lines.
Original line number Diff line number Diff line
@@ -16,8 +16,6 @@ qsub <<- POSTPROCWRAP 
#PBS -o ${logdir}/${timestamp}_postproc_wrap_${groupname}.log

#PBS -j oe

#PBS -N PPrWrp${groupname}

#PBS -M ${EMAIL}

#PBS -m a

${waitstring3}



date +"%Y-%m-%d %H:%M:%S"
@@ -40,8 +38,6 @@ qsub <<POSTPROCESS 
	#PBS -o ${logdir}/\${timestamp}_postproc_${groupname}.log

	#PBS -j oe

	#PBS -N PProc_${groupname}

	#PBS -M ${EMAIL}

	#PBS -m a

    $waitstring4



    date +"%Y-%m-%d %H:%M:%S"
@@ -66,8 +62,6 @@ qsub <<- FINCK 
#PBS -l $walltime

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

#PBS -j oe

#PBS -M ${EMAIL}

#PBS -m a

#PBS -N Pdone_${groupname}

#PBS -W depend=afterok:${jID_postprocwrap}
@@ -93,8 +87,6 @@ qsub <<DONE 
	#PBS -o ${logdir}/\${timestamp}_done_${groupname}.log

	#PBS -j oe

	#PBS -N done_${groupname}

	#PBS -M ${EMAIL}

	#PBS -m a

	\${waitstring5}



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

CRA Git | Maintained and supported by SUSTech CRA and CCSE