Commit d1c95feb authored by nchernia's avatar nchernia
Browse files

fixing bug in SLURM juicer when ligation flag -b sent in; updating mega in... 

fixing bug in SLURM juicer when ligation flag -b sent in; updating mega in SLURM; updating cleanup script
parent e3a0483b

SLURM/scripts/cleanup.sh

+4 −0
Changes for SLURM/scripts/cleanup.sh: 4 added lines, 0 removed lines.
Original line number Diff line number Diff line
@@ -31,10 +31,14 @@ if [ $total -eq $total2 ] 
then 

    rm aligned/merged_sort.txt 

    rm -r splits 

    testname=$(ls -l fastq | awk 'NR==1{print $9}')

    if [ "${testname: -5}" == ".fastq" ]

    then

	for i in fastq/*.fastq

	do

            gzip $i

	done

    fi

    gzip aligned/merged_nodups.txt

    gzip aligned/dups.txt

    gzip aligned/opt_dups.txt

SLURM/scripts/juicer.sh

+22 −24
Changes for SLURM/scripts/juicer.sh: 22 added lines, 24 removed lines.
Original line number Diff line number Diff line
@@ -85,8 +85,10 @@ then 
    juiceDir="/work/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 [ "$site" == "none" ]
@@ -476,7 +482,7 @@ then 
		    jid=`sbatch <<- SPLITEND | egrep -o -e "\b[0-9]+$"

			#!/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
@@ -560,7 +566,7 @@ SPLITEND` 
	jid=`sbatch <<- CNTLIG

		#!/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
@@ -578,7 +584,7 @@ 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
@@ -624,7 +630,7 @@ 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
@@ -671,7 +677,7 @@ ALGNR2` 
		#SBATCH -o $debugdir/merge-%j.out

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

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

		#SBATCH -t 1440

		#SBATCH -t $long_queue_time

		#SBATCH -c 8 

		#SBATCH --ntasks=1

		#SBATCH -d $dependalign
@@ -802,7 +808,7 @@ 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
@@ -832,21 +838,12 @@ then 
    

    # merge the sorted files into one giant file that is also sorted.      jid=`sbatch <<- MRGSRT | egrep -o -e "\b[0-9]+$"



    if [ $isVoltron -eq 1 ]

    then  

	sbatch_time="#SBATCH -t 10080"

    else

	sbatch_time="#SBATCH -t 1440"

    fi







    jid=`sbatch <<- EOF

		#!/usr/bin/bash

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

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

		#SBATCH --mem 256000

		${sbatch_time}

		#SBATCH -t $long_queue_time

		#SBATCH -p $long_queue

		#SBATCH -c 8

		#SBATCH -J "${groupname}_fragmerge"
@@ -921,7 +918,7 @@ 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"
@@ -987,7 +984,7 @@ then 
	#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
@@ -1010,7 +1007,7 @@ DUPCHECK` 
		#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 +1048,7 @@ 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
@@ -1070,6 +1067,7 @@ STATS` 
		${juiceDir}/scripts/juicer_tools48g pre -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 $outputdir/merged_nodups.txt $outputdir/inter.hic $genomePath

	else

		${juiceDir}/scripts/juicer_tools48g pre -f $site_file -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 $outputdir/merged_nodups.txt $outputdir/inter.hic $genomePath

echo "${juiceDir}/scripts/juicer_tools48g pre -f $site_file -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 $outputdir/merged_nodups.txt $outputdir/inter.hic $genomePath "

	fi

	date

HIC`
@@ -1081,7 +1079,7 @@ 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
@@ -1126,7 +1124,7 @@ HIC30` 
	${sbatch_req}

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

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

	#SBATCH -t 1440

	#SBATCH -t $queue_time

	#SBATCH --ntasks=1

	#SBATCH -J "${groupname}_hiccups_wrap"

	${sbatch_wait}
@@ -1154,7 +1152,7 @@ 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 $queue_time

	#SBATCH --ntasks=1

	#SBATCH -J "${groupname}_arrowhead_wrap"

	${sbatch_wait}

SLURM/scripts/mega.sh

+84 −51
Changes for SLURM/scripts/mega.sh: 84 added lines, 51 removed lines.
Original line number Diff line number Diff line
@@ -32,21 +32,54 @@ 
# [topDir]/mega     - Location of result of processing the mega map

#

# Juicer version 1.5

juicer_version="1.5" 

juicer_version="1.5.6" 

## Set the following variables to work with your system



## use cluster load commands:

#usePath=""

load_java="module load Java/7.1.2.0"

#load_cluster=""

#load_coreutils=""

load_gpu="module load gcccuda/2.6.10;export PATH=\$PATH:/usr/local/cuda/bin/;"

# Juicer directory, contains scripts/ and restriction_sites/

juiceDir="/poscratch/aidenlab/juicer"

# Aiden Lab specific check

isRice=$(hostname | awk '{if ($1~/rice/){print 1}else {print 0}}')

isBCM=$(hostname | awk '{if ($1~/bcm/){print 1}else {print 0}}')

isVoltron=0

## path additionals, make sure paths are correct for your system

## use cluster load commands

if [ $isRice -eq 1 ] 

then

    myPath=/bin:$PATH 

    load_bwa="module load BioBuilds/2015.04" 

    load_java="module load Java/8.0.3.22" 

    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

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

    queue="commons"

    # 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/

    # can also be set in options via -D

    juiceDir="/storage/aiden/juicer/"

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

    queue="mhgcp"

    queue_time="1200"

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

    long_queue="mhgcp"

    long_queue_time="3600"

else

    isVoltron=1

    export PATH=/gpfs0/biobuild/biobuilds-2016.11/bin:$PATH 

    unset MALLOC_ARENA_MAX

    load_gpu="CUDA_VISIBLE_DEVICES=0,1,2,3"

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

    # can also be set in options via -D

    juiceDir="/gpfs0/juicer/"

    # default queue, can also be set in options

    queue="commons"

    # default long queue, can also be set in options

long_queue="commons"

    long_queue="long"

    long_queue_time="10080"

fi



# unique name for jobs in this run

groupname="a$(date +%s)"
@@ -56,7 +89,7 @@ groupname="a$(date +%s)" 
# top level directory, can also be set in options

topDir=$(pwd)

# restriction enzyme, can also be set in options

site="DpnII"

site="MboI"

# genome ID, default to human, can also be set in options

genomeID="hg19"
@@ -192,7 +225,7 @@ touchfile2=${megadir}/touch2 
jid2=`sbatch <<- MRGSRT | egrep -o -e "\b[0-9]+$"

#!/bin/bash -l

#SBATCH -p ${long_queue}

#SBATCH -t 1440

#SBATCH -t ${long_queue_time}

#SBATCH -c 1

#SBATCH --ntasks=1

#SBATCH --mem-per-cpu=16384
@@ -203,7 +236,7 @@ jid2=`sbatch <<- MRGSRT | egrep -o -e "\b[0-9]+$" 
if [ ! -f "${touchfile1}" ]

then

    echo "***! Top stats job failed, type \"scontrol show job $jid1\" to see what happened."

    exit 100;

    exit 1

fi

if ! sort -T ${tmpdir} -m -k2,2d -k6,6d ${merged_names} > ${outputdir}/merged_nodups.txt

then
@@ -222,7 +255,7 @@ touchfile3=${megadir}/touch3 
jid3=`sbatch <<- INTER0 | egrep -o -e "\b[0-9]+$"

#!/bin/bash -l

#SBATCH -p ${long_queue}

#SBATCH -t 1440

#SBATCH -t ${long_queue_time}

#SBATCH -c 1

#SBATCH --ntasks=1

#SBATCH -o $logdir/inter0-%j.out
@@ -232,7 +265,7 @@ jid3=`sbatch <<- INTER0 | egrep -o -e "\b[0-9]+$" 
if [ ! -f "${touchfile2}" ]

then

   echo "***! Sort job failed."

   exit 100;

   exit 1

fi

${juiceDir}/scripts/statistics.pl -q 1 -o${outputdir}/inter.txt -s $site_file -l $ligation ${outputdir}/merged_nodups.txt

touch $touchfile3
@@ -244,7 +277,7 @@ touchfile4=${megadir}/touch4 
jid4=`sbatch <<- INTER30 | egrep -o -e "\b[0-9]+$"

#!/bin/bash -l

#SBATCH -p ${long_queue}

#SBATCH -t 1440

#SBATCH -t ${long_queue_time}

#SBATCH -c 1

#SBATCH --ntasks=1

#SBATCH -o $logdir/inter30-%j.out
@@ -254,7 +287,7 @@ jid4=`sbatch <<- INTER30 | egrep -o -e "\b[0-9]+$" 
if [ ! -f "${touchfile2}" ]

then

   echo "***! Sort job failed."

   exit 100;

   exit 1

fi

${juiceDir}/scripts/statistics.pl -q 30 -o${outputdir}/inter_30.txt -s $site_file -l $ligation ${outputdir}/merged_nodups.txt 

touch $touchfile4
@@ -266,7 +299,7 @@ touchfile5=${megadir}/touch5 
jid5=`sbatch <<- HIC0 | egrep -o -e "\b[0-9]+$"

#!/bin/bash -l

#SBATCH -p ${long_queue}

#SBATCH -t 1440

#SBATCH -t ${long_queue_time}

#SBATCH -c 1

#SBATCH --ntasks=1

#SBATCH -o $logdir/hic0-%j.out
@@ -279,17 +312,12 @@ $load_java 
if [ ! -f "${touchfile3}" ]

then

   echo "***! Statistics q=1 job failed."

   exit 100;

   exit 1

fi

if [ -z "$exclude" ]

if [ -z "$exclude" ] &&  ${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} 

then

	${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}

    exitcode=\$?

else

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

    exitcode=\$?

fi

if [ "\${exitcode}" -eq 0 ]

   touch $touchfile5

elif [ -n "$exclude" ] &&  ${juiceDir}/scripts/juicer_tools pre -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID} 

then

   touch $touchfile5 

fi
@@ -301,7 +329,7 @@ touchfile6=${megadir}/touch6 
jid6=`sbatch <<- HIC30 | egrep -o -e "\b[0-9]+$"

#!/bin/bash -l

#SBATCH -p ${long_queue}

#SBATCH -t 1440

#SBATCH -t ${long_queue_time}

#SBATCH -c 1

#SBATCH --ntasks=1

#SBATCH -o $logdir/hic30-%j.out
@@ -314,17 +342,12 @@ $load_java 
if [ ! -f "${touchfile4}" ]

then

   echo "***! Statistics q=30 job failed."

   exit 100;

   exit 1

fi

if [ -z "${exclude}" ]

if [ -z "${exclude}" ] &&  ${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} 

then

	${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}

   exitcode=\$?

else

	${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}

   exitcode=\$?

fi

if [ "\${exitcode}" -eq 0 ]

   touch $touchfile6

elif [ -n "${exclude}" ] && ${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} 

then

   touch $touchfile6

fi
@@ -334,6 +357,12 @@ dependhic30only="afterok:$jid6" 


# Create loop lists file for MQ > 30

touchfile7=${megadir}/touch7

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

then

    if [  $isRice -eq 1 ]

    then

	sbatch_req="#SBATCH --gres=gpu:kepler:1"

    fi

    jid7=`sbatch <<- HICCUPS | egrep -o -e "\b[0-9]+$"

	#!/bin/bash -l

	#SBATCH -p ${long_queue}
@@ -341,30 +370,33 @@ jid7=`sbatch <<- HICCUPS | egrep -o -e "\b[0-9]+$" 
	#SBATCH -c 2

	#SBATCH --ntasks=1

	#SBATCH --mem-per-cpu=4G 

#SBATCH --gres=gpu:kepler:1

	#SBATCH -o $logdir/hiccups-%j.out

	#SBATCH -e $logdir/hiccups-%j.err

	#SBATCH -J "${groupname}_hiccups"

	#SBATCH -d "${dependhic30only}"

#source $usePath

	${sbatch_req}

	$load_java

	if [ ! -f "${touchfile6}" ]

	then

	   echo "***! HIC maps q=30 job failed."

   exit 100;

	   exit 1

	fi

	${load_gpu}

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

	touch $touchfile7

	HICCUPS`

    dependhiccups="afterok:$jid7"

else

    dependhiccups="afterok"

    touch $touchfile7

fi



touchfile8=${megadir}/touch8

# Create domain lists for MQ > 30

jid8=`sbatch <<- ARROWHEAD | egrep -o -e "\b[0-9]+$"

#!/bin/bash -l

#SBATCH -p ${long_queue}

#SBATCH -t 1440

#SBATCH -t ${long_queue_time}

#SBATCH -c 2

#SBATCH --ntasks=1

#SBATCH --mem-per-cpu=4G
@@ -377,13 +409,12 @@ $load_java 
if [ ! -f "${touchfile6}" ]

then

   echo "***! HIC maps q=30 job failed."

   exit 100;

   exit 1

fi

${juiceDir}/scripts/juicer_arrowhead.sh -j ${juiceDir}/scripts/juicer_tools -i $outputdir/inter_30.hic

touch $touchfile8

ARROWHEAD`

dependarrows="${dependhic0}:$jid8"

dependarrowsonly="afterok:$jid8"

dependarrows="${dependhiccups}:$jid8"



# Final checks

jid9=`sbatch <<- FINAL | egrep -o -e "\b[0-9]+$"
@@ -400,27 +431,29 @@ jid9=`sbatch <<- FINAL | egrep -o -e "\b[0-9]+$" 
if [ ! -f "${touchfile5}" ]

then

   echo "***! Failed to make inter.hic."   

   exit 100;

   exit 1

fi

if [ ! -f "${touchfile6}" ]

then

   echo "***! Failed to make inter_30.hic."   

   exit 100;

   exit 1

fi

if [ ! -f "${touchfile7}" ]

then

   echo "***! Failed to create loop lists."   

   exit 100;

   exit 1

fi

if [ ! -f "${touchfile8}" ]

then

   echo "***! Failed to create domain lists."   

   exit 100;

   exit 1

fi

rmdir ${tmpdir}

rm -r ${tmpdir}

rm $touchfile1 $touchfile2 $touchfile3 $touchfile4 $touchfile5 $touchfile6 $touchfile7 $touchfile8

echo "(-: Successfully completed making mega map. Done. :-)"

echo $topDir, $site, $genomeID, $genomePath | mail -r MegaJuicer@rice.edu -s \"Mega Juicer pipeline finished successfully @ Rice" -t $USER@rice.edu;

if [ $isRice -eq 1 ]

then

   echo $topDir, $site, $genomeID, $genomePath | mail -r MegaJuicer@rice.edu -s \"Mega Juicer pipeline finished successfully @ Rice\" -t $USER@rice.edu;

fi

FINAL`

dependfinal="afterok:$jid9"

echo "(-: Finished adding all jobs... please wait while processing."

SLURM/scripts/relaunch_prep.sh

+3 −8
Changes for SLURM/scripts/relaunch_prep.sh: 3 added lines, 8 removed lines.
Original line number Diff line number Diff line
@@ -22,19 +22,14 @@ 
#  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN

#  THE SOFTWARE.

##########

# Helper script for finding what files successfully aligned and preparing the 

# directory for rerunning juicer.sh



# Helper script for finding what files successfully aligned and preparing the directory for

# rerunning juicer.sh

# Juicer version 1.5

ls -l splits > ls_splits



awk '($9 ~/_R1/ && $9 ~/fastq$/) || ($9 ~/_R1/ && $9 ~/gz$/) {split($9, a, "_R1");  print a[1]a[2], $9}($9 ~/_R2/ && $9 ~/fastq$/) || ($9 ~/_R2/ && $9 ~/gz$/){split($9,a,"_R2");print a[1]a[2], $9}' ls_splits > fastq.txt

awk '{name="splits/"$1"_norm.txt.res.txt"; if ((getline line < name) > 0){ split(line, a); if (length(a)<6 || a[2] != a[3]+a[4]+a[5]+a[6] || a[2] == 0){print "mv splits/"$2, "not_done; rm -f splits/"$1"*; rm -f splits/"$2"*;"} close(name);}else {print "mv splits/"$2, "not_done; rm -f splits/"$1"*; rm -f splits/"$2"*;"}}' fastq.txt > mv_me.sh

#for i in splits/*_linecount.txt

#do 

#    j=${i%_*} 

#    paste $i ${j}_norm.txt.res.txt | awk -v fname=$j '{if ($3 != $1/4){print "mv", fname, "not_done"}}'; >> mv_me.sh

#done



mkdir not_done

chmod 755 mv_me.sh

./mv_me.sh

UGER/scripts/cleanup.sh

+4 −0
Changes for UGER/scripts/cleanup.sh: 4 added lines, 0 removed lines.
Original line number Diff line number Diff line
@@ -31,10 +31,14 @@ if [ $total -eq $total2 ] 
then 

    rm aligned/merged_sort.txt 

    rm -r splits 

    testname=$(ls -l fastq | awk 'NR==1{print $9}')

    if [ "${testname: -5}" == ".fastq" ]

    then

	for i in fastq/*.fastq

	do

            gzip $i

	done

    fi

    gzip aligned/merged_nodups.txt

    gzip aligned/dups.txt

    gzip aligned/opt_dups.txt

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