Commit 9b10bc6c authored by nchernia's avatar nchernia
Browse files

adding in tmpdir for sort call in the collisions dedup

parent 57900218

CPU/juicer.sh

+1 −1
Changes for CPU/juicer.sh: 1 added line, 1 removed line.
Original line number Diff line number Diff line
@@ -457,7 +457,7 @@ then 
    cat $splitdir/*_unmapped.sam > $outputdir/unmapped.sam

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

    # Collisions dedupping: two pass algorithm, ideally would make one pass

    gawk -v fname=$outputdir/collisions.txt -f ${juiceDir}/scripts/common/collisions_dedup_rearrange_cols.awk $outputdir/collisions.txt | sort -k3,3n -k4,4n -k10,10n -k11,11n -k17,17n -k18,18n -k24,24n -k25,25n -k31,31n -k32,32n | awk -v name=$outputdir/ -f ${juiceDir}/scripts/common/collisions_dups.awk

    gawk -v fname=$outputdir/collisions.txt -f ${juiceDir}/scripts/common/collisions_dedup_rearrange_cols.awk $outputdir/collisions.txt | sort -T $tmpdir -k3,3n -k4,4n -k10,10n -k11,11n -k17,17n -k18,18n -k24,24n -k25,25n -k31,31n -k32,32n | awk -v name=$outputdir/ -f ${juiceDir}/scripts/common/collisions_dups.awk

fi



if [ -z "$genomePath" ]

SLURM/scripts/juicer.sh

+1 −1
Changes for SLURM/scripts/juicer.sh: 1 added line, 1 removed line.
Original line number Diff line number Diff line
@@ -1090,7 +1090,7 @@ STATS30` 
		# collect collisions and dedup them

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

		# dedup: two pass algorithm, ideally would make one pass

		gawk -v fname=$outputdir/collisions.txt -f ${juiceDir}/scripts/collisions_dedup_rearrange_cols.awk $outputdir/collisions.txt | sort -k3,3n -k4,4n -k10,10n -k11,11n -k17,17n -k18,18n -k24,24n -k25,25n -k31,31n -k32,32n | awk -v name=$outputdir/ -f ${juiceDir}/scripts/collisions_dups.awk

		gawk -v fname=$outputdir/collisions.txt -f ${juiceDir}/scripts/collisions_dedup_rearrange_cols.awk $outputdir/collisions.txt | sort -T $tmpdir -k3,3n -k4,4n -k10,10n -k11,11n -k17,17n -k18,18n -k24,24n -k25,25n -k31,31n -k32,32n | awk -v name=$outputdir/ -f ${juiceDir}/scripts/collisions_dups.awk

		date

CONCATFILES`

UGER/scripts/juicer.sh

+1 −1
Changes for UGER/scripts/juicer.sh: 1 added line, 1 removed line.
Original line number Diff line number Diff line
@@ -751,7 +751,7 @@ EOF 
        if [ ! -f $touchfile5 ]; then touch $errorfile; exit 1; fi; if [ -s ${debugdir}/dedup-${groupname}.err ]; then touch $errorfile; exit 1; fi; source $usePath; date; $load_java; export _JAVA_OPTIONS=-Xmx16384m; export LC_ALL=en_US.UTF-8;${juiceDir}/scripts/statistics.pl -s $site_file -l $ligation -o $outputdir/inter.txt -q 1 $outputdir/merged_nodups.txt; date

EOF

        qsub -o ${debugdir}/abnormal-${groupname}.out -e ${debugdir}/abnormal-${groupname}.err -q $long_queue -l h_vmem=1g -l m_mem_free=1g -N ${groupname}_abnormal -r y -l h_rt=${long_queue_time} $holdjobs <<-EOF 

        if [ ! -f $touchfile5 ]; then touch $errorfile; exit 1; fi; if [ -s ${debugdir}/dedup-${groupname}.err ]; then touch $errorfile; exit 1; fi; date; cat $splitdir/*_abnorm.sam > $outputdir/abnormal.sam; cat $splitdir/*_unmapped.sam > $outputdir/unmapped.sam; awk -f ${juiceDir}/scripts/collisions.awk $outputdir/abnormal.sam > $outputdir/collisions.txt; gawk -v fname=$outputdir/collisions.txt -f ${juiceDir}/scripts/collisions_dedup_rearrange_cols.awk $outputdir/collisions.txt | sort -k3,3n -k4,4n -k10,10n -k11,11n -k17,17n -k18,18n -k24,24n -k25,25n -k31,31n -k32,32n | awk -v name=$outputdir/ -f ${juiceDir}/scripts/collisions_dups.awk; date

        if [ ! -f $touchfile5 ]; then touch $errorfile; exit 1; fi; if [ -s ${debugdir}/dedup-${groupname}.err ]; then touch $errorfile; exit 1; fi; date; cat $splitdir/*_abnorm.sam > $outputdir/abnormal.sam; cat $splitdir/*_unmapped.sam > $outputdir/unmapped.sam; awk -f ${juiceDir}/scripts/collisions.awk $outputdir/abnormal.sam > $outputdir/collisions.txt; gawk -v fname=$outputdir/collisions.txt -f ${juiceDir}/scripts/collisions_dedup_rearrange_cols.awk $outputdir/collisions.txt | sort -T $tmpdir -k3,3n -k4,4n -k10,10n -k11,11n -k17,17n -k18,18n -k24,24n -k25,25n -k31,31n -k32,32n | awk -v name=$outputdir/ -f ${juiceDir}/scripts/collisions_dups.awk; date

EOF

     qsub -o ${debugdir}/stats30-${groupname}.out -e ${debugdir}/stats30-${groupname}.err -q $long_queue -l h_vmem=16g -l m_mem_free=16g -N ${groupname}_stats30 -r y -l h_rt=${long_queue_time} $holdjobs <<-EOF

     if [ ! -f $touchfile5 ]; then touch $errorfile; exit 1; fi; if [ -s ${debugdir}/dedup-${groupname}.err ]; then touch $errorfile; exit 1; fi; source $usePath; date; $load_java; export _JAVA_OPTIONS=-Xmx16384m; export LC_ALL=en_US.UTF-8; ${juiceDir}/scripts/statistics.pl -s $site_file -l $ligation -o $outputdir/inter_30.txt -q 30 $outputdir/merged_nodups.txt; date

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