Commit 5b5bd5ef authored by nchernia's avatar nchernia
Browse files

Bug fix for postproc stage; bug fix for when count ligations takes longer than alignment

parent 1da25fb7

SLURM/scripts/juicer.sh

+56 −54
Changes for SLURM/scripts/juicer.sh: 56 added lines, 54 removed lines.
Original line number Diff line number Diff line
@@ -82,11 +82,13 @@ then 
    load_gpu="module load gcccuda/2016a;module load CUDA/8.0.54;" 

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

    # can also be set in options via -D

    juiceDir="/work/ea14/juicer" ### RICE

    juiceDir="/projects/ea14/juicer" ### RICE

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

    queue="commons"

    queue_time="1440"

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

    long_queue="commons"

    long_queue_time="1440"

elif [ $isBCM -eq 1 ]

then    

    # Juicer directory, contains scripts/, references/, and restriction_sites/
@@ -108,8 +110,10 @@ else 
    juiceDir="/gpfs0/juicer/"

    # default queue, can also be set in options

    queue="commons"

    queue_time="1440"

    # default long queue, can also be set in options

    long_queue="long"

    long_queue_time="10080"

fi



# size to split fastqs. adjust to match your needs. 4000000=1M reads per split
@@ -263,6 +267,7 @@ if [ ! -e "${refSeq}.bwt" ]; then 
fi



## Set ligation junction based on restriction enzyme

if [ -z "$ligation" ]; then

    case $site in

	HindIII) ligation="AAGCTAGCTT";;

	DpnII) ligation="GATCGATC";;
@@ -273,6 +278,7 @@ case $site in 
	    echo "$site not listed as recognized enzyme. Using $site_file as site file"

	    echo "Ligation junction is undefined"

    esac

fi



## If DNAse-type experiment, no fragment maps

if [ "$site" == "none" ]
@@ -414,8 +420,8 @@ jid=`sbatch <<- HEADER | egrep -o -e "\b[0-9]+$" 
	#SBATCH -e $debugdir/head-%j.err

	#SBATCH -J "${groupname}_cmd"

	date

	$load_bwa

	$load_java

	${load_bwa}

	${load_java}



	# Experiment description

	if [ -n "${about}" ]
@@ -476,7 +482,7 @@ then 
		    jid=`sbatch <<- SPLITEND | egrep -o -e "\b[0-9]+$"

			#!/bin/bash -l

			#SBATCH -p $queue

			#SBATCH -t 1440

			#SBATCH -t $queue_time

			#SBATCH -c 1

			#SBATCH -o $debugdir/split-%j.out

			#SBATCH -e $debugdir/split-%j.err
@@ -490,7 +496,7 @@ SPLITEND` 
		    jid=`sbatch <<- SPLITEND | egrep -o -e "\b[0-9]+$"

			#!/bin/bash -l

			#SBATCH -p $queue

			#SBATCH -t 1440

			#SBATCH -t $queue_time

			#SBATCH -c 1

			#SBATCH -o $debugdir/split-%j.out

			#SBATCH -e $debugdir/split-%j.err
@@ -557,10 +563,10 @@ SPLITEND` 
	fi



	# count ligations

	jid=`sbatch <<- CNTLIG

	jid=`sbatch <<- CNTLIG |  egrep -o -e "\b[0-9]+$"

		#!/bin/bash -l

		#SBATCH -p $queue

		#SBATCH -t 1440

		#SBATCH -t $queue_time

		#SBATCH -c 1

		#SBATCH -o $debugdir/count_ligation-%j.out

		#SBATCH -e $debugdir/count_ligation-%j.err
@@ -569,7 +575,7 @@ SPLITEND` 
		export usegzip=${usegzip}; export name=${name}; export name1=${name1}; export name2=${name2}; export ext=${ext}; export ligation=${ligation}; ${juiceDir}/scripts/countligations.sh

		date

CNTLIG`



	dependcount="$jid"

	# align read1 fastq

	touchfile1=${tmpdir}/${jname}1
@@ -578,14 +584,14 @@ CNTLIG` 
		#SBATCH -p $queue

		#SBATCH -o $debugdir/align1-%j.out

		#SBATCH -e $debugdir/align1-%j.err

		#SBATCH -t 1440

		#SBATCH -t $queue_time

		#SBATCH -n 1

		#SBATCH -c $threads

		#SBATCH --ntasks=1

		#SBATCH --mem-per-cpu=$alloc_mem

		#SBATCH -J "${groupname}_align1_${jname}"

		#SBATCH --threads-per-core=1		

		$load_bwa

		${load_bwa}

		# Align read1

		date

		if [ -n "$shortread" ] || [ "$shortreadend" -eq 1 ]
@@ -615,8 +621,7 @@ CNTLIG` 
		date

ALGNR1`



	dependalign="afterok:$jid"

	

	dependalign="afterok:$jid:$dependcount"

	# align read2 fastq

	touchfile2=${tmpdir}/${jname}2

	jid=`sbatch <<- ALGNR2 | egrep -o -e "\b[0-9]+$"
@@ -624,14 +629,14 @@ ALGNR1` 
		#SBATCH -p $queue

		#SBATCH -o $debugdir/align2-%j.out

		#SBATCH -e $debugdir/align2-%j.err

		#SBATCH -t 1440

		#SBATCH -t $queue_time

		#SBATCH -n 1

		#SBATCH -c $threads

		#SBATCH --ntasks=1

		#SBATCH --mem-per-cpu=$alloc_mem

		#SBATCH -J "${groupname}_align2_${jname}"

		#SBATCH --threads-per-core=1		

		$load_bwa

		${load_bwa}

		date

		# Align read2

		if [ -n "$shortread" ] || [ "$shortreadend" -eq 2 ]
@@ -671,7 +676,7 @@ ALGNR2` 
		#SBATCH -o $debugdir/merge-%j.out

		#SBATCH -e $debugdir/merge-%j.err

		#SBATCH --mem-per-cpu=14G

		#SBATCH -t 1440

		#SBATCH -t $queue_time

		#SBATCH -c 8 

		#SBATCH --ntasks=1

		#SBATCH -d $dependalign
@@ -802,7 +807,7 @@ MRGALL` 
		#!/usr/bin/bash

		#SBATCH -o $debugdir/aligncheck-%j.out

		#SBATCH -e $debugdir/aligncheck-%j.err

		#SBATCH -t 1440

		#SBATCH -t $queue_time

		#SBATCH -p $queue

		#SBATCH -J "${groupname}_check"

		#SBATCH -d $dependmerge
@@ -861,7 +866,7 @@ then 


		if [ $isRice -eq 1 ]

		then

			if ! /work/ea14/olga-scripts/useful-small-scripts/sort --parallel=48 -S8G -T HIC_tmp -m -k2,2d -k6,6d -k4,4n -k8,8n -k1,1n -k5,5n -k3,3n $splitdir/*.sort.txt > $outputdir/merged_sort.txt

			if ! ${juiceDir}/scripts/sort --parallel=48 -S8G -T ${tmpdir} -m -k2,2d -k6,6d -k4,4n -k8,8n -k1,1n -k5,5n -k3,3n $splitdir/*.sort.txt > $outputdir/merged_sort.txt

			then

				echo "***! Some problems occurred somewhere in creating sorted align files."

				touch $errorfile
@@ -870,7 +875,7 @@ then 
				echo "(-: Finished sorting all sorted files into a single merge."

			fi

		else

			if ! sort --parallel=48 -S8G -T HIC_tmp -m -k2,2d -k6,6d -k4,4n -k8,8n -k1,1n -k5,5n -k3,3n $splitdir/*.sort.txt > $outputdir/merged_sort.txt

			if ! sort --parallel=48 -S8G -T ${tmpdir} -m -k2,2d -k6,6d -k4,4n -k8,8n -k1,1n -k5,5n -k3,3n $splitdir/*.sort.txt > $outputdir/merged_sort.txt

			then

				echo "***! Some problems occurred somewhere in creating sorted align files."

				touch $errorfile
@@ -921,7 +926,7 @@ DEDUPGUARD` 
	#SBATCH --mem-per-cpu=2G

	#SBATCH -o $debugdir/dedup-%j.out

	#SBATCH -e $debugdir/dedup-%j.err

	#SBATCH -t 1440

	#SBATCH -t $queue_time

	#SBATCH -c 1

	#SBATCH --ntasks=1

	#SBATCH -J "${groupname}_dedup"
@@ -978,16 +983,39 @@ then 
fi



# if early exit, we stop here, once the merged_nodups.txt file is created.

if [ -z "$earlyexit" ]

if [ -n "$earlyexit" ]

then

    jid=`sbatch <<- FINCLN1 | egrep -o -e "\b[0-9]+$" 

	#!/bin/bash

	#SBATCH -p $queue

	#SBATCH --mem-per-cpu=2G

	#SBATCH -o $debugdir/fincln1-%j.out

	#SBATCH -e $debugdir/fincln1-%j.err

	#SBATCH -t 1200

	#SBATCH -c 1

	#SBATCH --ntasks=1

	#SBATCH -J "${groupname}_prep_done"     

	${sbatch_wait}

	date

	export splitdir=${splitdir}; export outputdir=${outputdir}; export early=1; ${juiceDir}/scripts/check.sh

	date

FINCLN1`

    echo "(-: Finished adding all jobs... Now is a good time to get that cup of coffee.."

    exit 0

fi



#Skip if post-processing only is required

if [ -z $postproc ]

    then

    # Check that dedupping worked properly

    # in ideal world, we would check this in split_rmdups and not remove before we know they are correct

    awkscript='BEGIN{sscriptname = sprintf("%s/.%s_rmsplit.slurm", debugdir, groupname);}NR==1{if (NF == 2 && $1 == $2 ){print "Sorted and dups/no dups files add up"; printf("#!/bin/bash -l\n#SBATCH -o %s/dup-rm.out\n#SBATCH -e %s/dup-rm.err\n#SBATCH -p %s\n#SBATCH -J %s_msplit0\n#SBATCH -d singleton\n#SBATCH -t 1440\n#SBATCH -c 1\n#SBATCH --ntasks=1\ndate;\nrm %s/*_msplit*_optdups.txt; rm %s/*_msplit*_dups.txt; rm %s/*_msplit*_merged_nodups.txt;rm %s/split*;\ndate\n", debugdir, debugdir, queue, groupname, dir, dir, dir, dir) > sscriptname; sysstring = sprintf("sbatch %s", sscriptname); system(sysstring);close(sscriptname); }else{print "Problem"; print "***! Error! The sorted file and dups/no dups files do not add up, or were empty."}}'

    jid=`sbatch <<- DUPCHECK | egrep -o -e "\b[0-9]+$"

	#!/bin/bash -l

	#SBATCH -p $queue

	#SBATCH -o $debugdir/dupcheck-%j.out

	#SBATCH -e $debugdir/dupcheck-%j.err

	#SBATCH -t 1440

	#SBATCH -t $queue_time

	#SBATCH -c 1

	#SBATCH --ntasks=1

	#SBATCH --mem-per-cpu=1G
@@ -997,20 +1025,16 @@ then 
	date      

	ls -l ${outputdir}/merged_sort.txt | awk '{printf("%s ", \\\$5)}' > $debugdir/dupcheck-${groupname}

	ls -l ${outputdir}/merged_nodups.txt ${outputdir}/dups.txt ${outputdir}/opt_dups.txt | awk '{sum = sum + \\\$5}END{print sum}' >> $debugdir/dupcheck-${groupname}

	awk 'NR==1{if (NF == 2 && \\\$1 == \\\$2){print "Sorted and dups/no dups files add up"}else{print "Problem" >> ${errorfile}; print "***! Error! The sorted file and dups/no dups files do not add up, or were empty."}}' $debugdir/dupcheck-${groupname} 

	awk -v debugdir=$debugdir -v queue=$queue -v groupname=$groupname -v dir=$outputdir '$awkscript' $debugdir/dupcheck-${groupname}

        date                                                                                                           

DUPCHECK`

    sbatch_wait="#SBATCH -d afterok:$jid"



    #Skip if post-processing only is required

    if [ -z $postproc ]

    then

    jid=`sbatch <<- STATS | egrep -o -e "\b[0-9]+$"

		#!/bin/bash -l

		#SBATCH -p $long_queue

		#SBATCH -o $debugdir/stats-%j.out

		#SBATCH -e $debugdir/stats-%j.err

		#SBATCH -t 1440

		#SBATCH -t $long_queue_time

		#SBATCH -c 1

		#SBATCH --ntasks=1

		#SBATCH --mem-per-cpu=6G
@@ -1051,7 +1075,7 @@ STATS` 
	#SBATCH -p $long_queue

	#SBATCH -o $debugdir/hic-%j.out

	#SBATCH -e $debugdir/hic-%j.err	

	#SBATCH -t 1440

	#SBATCH -t $long_queue_time

	#SBATCH -c 1

	#SBATCH --ntasks=1

	#SBATCH --mem-per-cpu=32G
@@ -1081,7 +1105,7 @@ HIC` 
	#SBATCH -p $long_queue

	#SBATCH -o $debugdir/hic30-%j.out

	#SBATCH -e $debugdir/hic30-%j.err

	#SBATCH -t 1440

	#SBATCH -t $long_queue_time

	#SBATCH -c 1

	#SBATCH --ntasks=1

	#SBATCH --mem-per-cpu=32G
@@ -1105,14 +1129,11 @@ HIC` 
HIC30`



    dependhic30="${dependhic}:$jid"

	fi



	if [ -z $postproc ]

	then

    sbatch_wait="#SBATCH -d $dependhic30"

else

    sbatch_wait=""

fi



if [ $isRice -eq 1 ] || [ $isVoltron -eq 1 ]

then

    if [  $isRice -eq 1 ]
@@ -1126,7 +1147,7 @@ HIC30` 
	${sbatch_req}

	#SBATCH -o $debugdir/hiccups_wrap-%j.out

	#SBATCH -e $debugdir/hiccups_wrap-%j.err

	#SBATCH -t 1440

	#SBATCH -t $long_queue_time

	#SBATCH --ntasks=1

	#SBATCH -J "${groupname}_hiccups_wrap"

	${sbatch_wait}
@@ -1154,7 +1175,7 @@ HICCUPS` 
	#SBATCH --mem-per-cpu=8G

	#SBATCH -o $debugdir/arrowhead_wrap-%j.out

	#SBATCH -e $debugdir/arrowhead_wrap-%j.err

	#SBATCH -t 1440

	#SBATCH -t $long_queue_time

	#SBATCH --ntasks=1

	#SBATCH -J "${groupname}_arrowhead_wrap"

	${sbatch_wait}
@@ -1185,24 +1206,5 @@ ARROWS` 
	export splitdir=${splitdir}; export outputdir=${outputdir}; ${juiceDir}/scripts/check.sh

	date

FINCLN1`

else



	jid=`sbatch <<- FINCLN1 | egrep -o -e "\b[0-9]+$" 

	#!/bin/bash

	#SBATCH -p $queue

	#SBATCH --mem-per-cpu=2G

	#SBATCH -o $debugdir/fincln1-%j.out

	#SBATCH -e $debugdir/fincln1-%j.err

	#SBATCH -t 1200

	#SBATCH -c 1

	#SBATCH --ntasks=1

	#SBATCH -J "${groupname}_prep_done"     

	#SBATCH -d $dependarrows

	date

	export splitdir=${splitdir}; export outputdir=${outputdir}; export early=1; ${juiceDir}/scripts/check.sh

	date

FINCLN1`

	dependprepdone="afterok:$jid"



fi

echo "(-: Finished adding all jobs... Now is a good time to get that cup of coffee.."

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