Commit f8c584a0 authored by nchernia's avatar nchernia
Browse files

fixed bug with nofrag where we were not checking appropriately in hic and hic30 scripts

parent 2992f9d7

AWS/scripts/juicer.sh

+2 −2
Changes for AWS/scripts/juicer.sh: 2 added lines, 2 removed lines.
Original line number Diff line number Diff line
@@ -781,8 +781,8 @@ then 
        echo "(-: Alignment and merge done, launching other jobs."

        $execstring

        bsub -o $topDir/lsf.out -q $long_queue -W $long_queue_time -R "rusage[mem=16000]" $waitstring22 -J "${groupname}_stats" "df -h;_JAVA_OPTIONS=-Xmx16384m; export LC_ALL=en_US.UTF-8; echo -e 'Experiment description: $about' > $outputdir/inter.txt; ${juiceDir}/scripts/statistics.pl -s $site_file -l $ligation -o $outputdir/stats_dups.txt $outputdir/dups.txt; cat $splitdir/*.res.txt | awk -f ${juiceDir}/scripts/stats_sub.awk >> $outputdir/inter.txt; java -cp ${juiceDir}/scripts/ LibraryComplexity $outputdir inter.txt >> $outputdir/inter.txt; ${juiceDir}/scripts/statistics.pl -s $site_file -l $ligation -o $outputdir/inter.txt -q 1 $outputdir/merged_nodups.txt; cat $splitdir/*_abnorm.sam > $outputdir/abnormal.sam; cat $splitdir/*_unmapped.sam > $outputdir/unmapped.sam; awk -f ${juiceDir}/scripts/collisions.awk $outputdir/abnormal.sam > $outputdir/collisions.txt"

        bsub -o $topDir/lsf.out -q $long_queue -W $long_queue_time -R "rusage[mem=16000]" -w "done(${groupname}_stats)" -J "${groupname}_hic" "df -h;export _JAVA_OPTIONS=-Xmx16384m; if [ -n \"$nofrag\" ]; 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 -f $site_file -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 $outputdir/merged_nodups.txt $outputdir/inter.hic $genomePath; fi ;"

        bsub -o $topDir/lsf.out -q $long_queue -W $long_queue_time -R "rusage[mem=16000]" $waitstring22 -J "${groupname}_hic30" "df -h;export _JAVA_OPTIONS=-Xmx16384m; export LC_ALL=en_US.UTF-8; echo -e 'Experiment description: $about' > $outputdir/inter_30.txt; cat $splitdir/*.res.txt | awk -f ${juiceDir}/scripts/stats_sub.awk >> $outputdir/inter_30.txt; java -cp ${juiceDir}/scripts/ LibraryComplexity $outputdir inter_30.txt >> $outputdir/inter_30.txt; ${juiceDir}/scripts/statistics.pl -s $site_file -l $ligation -o $outputdir/inter_30.txt -q 30 $outputdir/merged_nodups.txt; export _JAVA_OPTIONS=-Xmx8192m; if [ -n \"$nofrag\" ]; 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 -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"

        bsub -o $topDir/lsf.out -q $long_queue -W $long_queue_time -R "rusage[mem=16000]" -w "done(${groupname}_stats)" -J "${groupname}_hic" "df -h;export _JAVA_OPTIONS=-Xmx16384m; if [ \"$nofrag\" -eq 1 ]; 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 -f $site_file -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 $outputdir/merged_nodups.txt $outputdir/inter.hic $genomePath; fi ;"

        bsub -o $topDir/lsf.out -q $long_queue -W $long_queue_time -R "rusage[mem=16000]" $waitstring22 -J "${groupname}_hic30" "df -h;export _JAVA_OPTIONS=-Xmx16384m; export LC_ALL=en_US.UTF-8; echo -e 'Experiment description: $about' > $outputdir/inter_30.txt; cat $splitdir/*.res.txt | awk -f ${juiceDir}/scripts/stats_sub.awk >> $outputdir/inter_30.txt; java -cp ${juiceDir}/scripts/ LibraryComplexity $outputdir inter_30.txt >> $outputdir/inter_30.txt; ${juiceDir}/scripts/statistics.pl -s $site_file -l $ligation -o $outputdir/inter_30.txt -q 30 $outputdir/merged_nodups.txt; export _JAVA_OPTIONS=-Xmx8192m; if [ \"$nofrag\" -eq 1 ]; 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 -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"

DOSTAT

	waitstring3="#BSUB -w \" done(${groupname}_launch) \""

	waitstring4="-w \"done(${groupname}_hic30)\""

CPU/juicer.sh

+2 −2
Changes for CPU/juicer.sh: 2 added lines, 2 removed lines.
Original line number Diff line number Diff line
@@ -498,7 +498,7 @@ then 
        cat $splitdir/*_abnorm.sam > $outputdir/abnormal.sam

        cat $splitdir/*_unmapped.sam > $outputdir/unmapped.sam

        awk -f ${juiceDir}/scripts/common/collisions.awk $outputdir/abnormal.sam > $outputdir/collisions.txt

        if [ -n "$nofrag" ]

        if [ "$nofrag" -eq 1 ]

        then 

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

        else
@@ -508,7 +508,7 @@ then 
        cat $splitdir/*.res.txt | awk -f ${juiceDir}/scripts/common/stats_sub.awk >> $outputdir/inter_30.txt

        java -cp ${juiceDir}/scripts/common/ LibraryComplexity $outputdir inter_30.txt >> $outputdir/inter_30.txt

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

        if [ -n "$nofrag" ]

        if [ "$nofrag" -eq 1 ]

        then 

            ${juiceDir}/scripts/common/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

LSF/scripts/juicer.sh

+2 −2
Changes for LSF/scripts/juicer.sh: 2 added lines, 2 removed lines.
Original line number Diff line number Diff line
@@ -803,8 +803,8 @@ then 
        echo "(-: Alignment and merge done, launching other jobs."

        $execstring

        bsub -o $topDir/lsf.out -q $long_queue -W $long_queue_time -R "rusage[mem=16000]" $waitstring22 -J "${groupname}_stats" -g ${groupname} "$load_java; _JAVA_OPTIONS=-Xmx16384m; export LC_ALL=en_US.UTF-8; echo -e 'Experiment description: $about' > $outputdir/inter.txt; ${juiceDir}/scripts/statistics.pl -s $site_file -l $ligation -o $outputdir/stats_dups.txt $outputdir/dups.txt; cat $splitdir/*.res.txt | awk -f ${juiceDir}/scripts/stats_sub.awk >> $outputdir/inter.txt; java -cp ${juiceDir}/scripts/ LibraryComplexity $outputdir inter.txt >> $outputdir/inter.txt; ${juiceDir}/scripts/statistics.pl -s $site_file -l $ligation -o $outputdir/inter.txt -q 1 $outputdir/merged_nodups.txt; cat $splitdir/*_abnorm.sam > $outputdir/abnormal.sam; cat $splitdir/*_unmapped.sam > $outputdir/unmapped.sam; awk -f ${juiceDir}/scripts/collisions.awk $outputdir/abnormal.sam > $outputdir/collisions.txt"

        bsub -o $topDir/lsf.out -q $long_queue -W $long_queue_time -R "rusage[mem=16000]" -w "done(${groupname}_stats)" -g ${groupname} -J "${groupname}_hic" "$load_java; export _JAVA_OPTIONS=-Xmx16384m; if [ -n \"$nofrag\" ]; 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 -f $site_file -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 $outputdir/merged_nodups.txt $outputdir/inter.hic $genomePath; fi ;"

        bsub -o $topDir/lsf.out -g ${groupname} -q $long_queue -W $long_queue_time -R "rusage[mem=16000]" $waitstring22 -J "${groupname}_hic30" "$load_java; export _JAVA_OPTIONS=-Xmx16384m; export LC_ALL=en_US.UTF-8; echo -e 'Experiment description: $about' > $outputdir/inter_30.txt; cat $splitdir/*.res.txt | awk -f ${juiceDir}/scripts/stats_sub.awk >> $outputdir/inter_30.txt; java -cp ${juiceDir}/scripts/ LibraryComplexity $outputdir inter_30.txt >> $outputdir/inter_30.txt; ${juiceDir}/scripts/statistics.pl -s $site_file -l $ligation -o $outputdir/inter_30.txt -q 30 $outputdir/merged_nodups.txt; if [ -n \"$nofrag\" ]; 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 -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"

        bsub -o $topDir/lsf.out -q $long_queue -W $long_queue_time -R "rusage[mem=16000]" -w "done(${groupname}_stats)" -g ${groupname} -J "${groupname}_hic" "$load_java; export _JAVA_OPTIONS=-Xmx16384m; if [ \"$nofrag\" -eq 1 ]; 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 -f $site_file -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 $outputdir/merged_nodups.txt $outputdir/inter.hic $genomePath; fi ;"

        bsub -o $topDir/lsf.out -g ${groupname} -q $long_queue -W $long_queue_time -R "rusage[mem=16000]" $waitstring22 -J "${groupname}_hic30" "$load_java; export _JAVA_OPTIONS=-Xmx16384m; export LC_ALL=en_US.UTF-8; echo -e 'Experiment description: $about' > $outputdir/inter_30.txt; cat $splitdir/*.res.txt | awk -f ${juiceDir}/scripts/stats_sub.awk >> $outputdir/inter_30.txt; java -cp ${juiceDir}/scripts/ LibraryComplexity $outputdir inter_30.txt >> $outputdir/inter_30.txt; ${juiceDir}/scripts/statistics.pl -s $site_file -l $ligation -o $outputdir/inter_30.txt -q 30 $outputdir/merged_nodups.txt; if [  \"$nofrag\" -eq 1 ]; 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 -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"

DOSTAT

	waitstring3="#BSUB -w \" done(${groupname}_launch) \""

	waitstring4="-w \"done(${groupname}_hic30)\""

SLURM/scripts/juicer.sh

+2 −2
Changes for SLURM/scripts/juicer.sh: 2 added lines, 2 removed lines.
Original line number Diff line number Diff line
@@ -851,7 +851,7 @@ then 
	${load_java}

	export IBM_JAVA_OPTIONS="-Xmx48192m -Xgcthreads1"

	date

	if [ -n "$nofrag" ]

	if [ "$nofrag" -eq 1 ]

	then 

	    ${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
@@ -876,7 +876,7 @@ HIC` 
	${load_java}

	export IBM_JAVA_OPTIONS="-Xmx48192m -Xgcthreads1"

	date

	if [ -n "$nofrag" ]

	if [ "$nofrag" -eq 1 ]

	then 

	    ${juiceDir}/scripts/juicer_tools48g pre -s $outputdir/inter_30.txt -g $outputdir/inter_30_hists.m -q 30 $outputdir/merged_nodups.txt $outputdir/inter_30.hic $genomePath 

	else

UGER/scripts/juicer.sh

+224 −103

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