Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20170125_175309_926
Start time	2017-01-25 17:53:09
Run time	01:28:38.134
Tasks executed	14
Tasks failed	0
Tasks failed names
Arguments*	[-species, hg38, -tag1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/rep1/ENCFF002AAZ.nodup.tagAlign.gz, -tag2, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/rep2/ENCFF002AAX.nodup.tagAlign.gz, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz, -final_stage, idr, -chrsz, /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes, -no_pseudo_rep, -histone, -out_dir, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3, $]
System*	sge
Cpus*	-1
Exit value	0

Thread ID	Parent	Tasks
thread_Root	None	chipseq.bds.20170125_175309_926/task.callpeak_macs2.macs2_pooled_rep.line_71.id_10 chipseq.bds.20170125_175309_926/task.callpeak_macs2.macs2_ppr1.line_71.id_11 chipseq.bds.20170125_175309_926/task.callpeak_macs2.macs2_ppr2.line_71.id_12 chipseq.bds.20170125_175309_926/task.callpeak_macs2.macs2_rep1.line_71.id_13 chipseq.bds.20170125_175309_926/task.callpeak_macs2.macs2_rep2.line_71.id_14 chipseq.bds.20170125_175309_926/task.callpeak_naive_overlap.naive_overlap_thresh.line_143.id_15 chipseq.bds.20170125_175309_926/task.callpeak_naive_overlap.naive_overlap_thresh.line_143.id_16 chipseq.bds.20170125_175309_926/task.callpeak_naive_overlap.naive_overlap_thresh.line_143.id_17 chipseq.bds.20170125_175309_926/task.callpeak_blacklist_filter.blacklist_filter_peak_pooled.line_27.id_18 chipseq.bds.20170125_175309_926/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_19 chipseq.bds.20170125_175309_926/task.callpeak_blacklist_filter.blacklist_filter_peak_2.line_27.id_20 chipseq.bds.20170125_175309_926/task.report.peak2hammock.line_412.id_21 chipseq.bds.20170125_175309_926/task.report.peak2hammock.line_412.id_22 chipseq.bds.20170125_175309_926/task.graphviz.report.line_97.id_23
thread_43	thread_Root
thread_41	thread_Root
thread_42	thread_Root

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.callpeak_macs2.macs2_pooled_rep.line_71.id_10
Name	macs2 pooled_rep
Thread	thread_Root
PID	35588

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-25 17:53:22
End	2017-01-25 18:38:36
Elapsed	00:45:13
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/signal/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/signal/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw
Dependencies

 
# SYS command. line 73

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 74

 export LC_COLLATE=C

# SYS command. line 79

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 168 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 168 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 110

 if [[ true == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 121

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep -o "ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -g /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/signal/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

# SYS command. line 140

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep -o "ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 143

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -g /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/signal/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 153

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
14939 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Wed, 25 Jan 2017 17:53:44: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 168 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Wed, 25 Jan 2017 17:53:44: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 17:53:44: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 17:53:45:  1000000 
INFO  @ Wed, 25 Jan 2017 17:53:47:  2000000 
INFO  @ Wed, 25 Jan 2017 17:53:48:  3000000 
INFO  @ Wed, 25 Jan 2017 17:53:50:  4000000 
INFO  @ Wed, 25 Jan 2017 17:53:51:  5000000 
INFO  @ Wed, 25 Jan 2017 17:53:53:  6000000 
INFO  @ Wed, 25 Jan 2017 17:53:55:  7000000 
INFO  @ Wed, 25 Jan 2017 17:53:56:  8000000 
INFO  @ Wed, 25 Jan 2017 17:53:58:  9000000 
INFO  @ Wed, 25 Jan 2017 17:53:59:  10000000 
INFO  @ Wed, 25 Jan 2017 17:54:01:  11000000 
INFO  @ Wed, 25 Jan 2017 17:54:02:  12000000 
INFO  @ Wed, 25 Jan 2017 17:54:04:  13000000 
INFO  @ Wed, 25 Jan 2017 17:54:06:  14000000 
INFO  @ Wed, 25 Jan 2017 17:54:07:  15000000 
INFO  @ Wed, 25 Jan 2017 17:54:09:  16000000 
INFO  @ Wed, 25 Jan 2017 17:54:10:  17000000 
INFO  @ Wed, 25 Jan 2017 17:54:12:  18000000 
INFO  @ Wed, 25 Jan 2017 17:54:13:  19000000 
INFO  @ Wed, 25 Jan 2017 17:54:15:  20000000 
INFO  @ Wed, 25 Jan 2017 17:54:16:  21000000 
INFO  @ Wed, 25 Jan 2017 17:54:18:  22000000 
INFO  @ Wed, 25 Jan 2017 17:54:20:  23000000 
INFO  @ Wed, 25 Jan 2017 17:54:21:  24000000 
INFO  @ Wed, 25 Jan 2017 17:54:23:  25000000 
INFO  @ Wed, 25 Jan 2017 17:54:24:  26000000 
INFO  @ Wed, 25 Jan 2017 17:54:26:  27000000 
INFO  @ Wed, 25 Jan 2017 17:54:27:  28000000 
INFO  @ Wed, 25 Jan 2017 17:54:29:  29000000 
INFO  @ Wed, 25 Jan 2017 17:54:30:  30000000 
INFO  @ Wed, 25 Jan 2017 17:54:32:  31000000 
INFO  @ Wed, 25 Jan 2017 17:54:33:  32000000 
INFO  @ Wed, 25 Jan 2017 17:54:35:  33000000 
INFO  @ Wed, 25 Jan 2017 17:54:37:  34000000 
INFO  @ Wed, 25 Jan 2017 17:54:38:  35000000 
INFO  @ Wed, 25 Jan 2017 17:54:40:  36000000 
INFO  @ Wed, 25 Jan 2017 17:54:41:  37000000 
INFO  @ Wed, 25 Jan 2017 17:54:43:  38000000 
INFO  @ Wed, 25 Jan 2017 17:54:44:  39000000 
INFO  @ Wed, 25 Jan 2017 17:54:46:  40000000 
INFO  @ Wed, 25 Jan 2017 17:54:47:  41000000 
INFO  @ Wed, 25 Jan 2017 17:54:49:  42000000 
INFO  @ Wed, 25 Jan 2017 17:54:51:  43000000 
INFO  @ Wed, 25 Jan 2017 17:54:52:  44000000 
INFO  @ Wed, 25 Jan 2017 17:54:54:  45000000 
INFO  @ Wed, 25 Jan 2017 17:54:55:  46000000 
INFO  @ Wed, 25 Jan 2017 17:54:57:  47000000 
INFO  @ Wed, 25 Jan 2017 17:54:59: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 17:55:01:  1000000 
INFO  @ Wed, 25 Jan 2017 17:55:02:  2000000 
INFO  @ Wed, 25 Jan 2017 17:55:03:  3000000 
INFO  @ Wed, 25 Jan 2017 17:55:05:  4000000 
INFO  @ Wed, 25 Jan 2017 17:55:07:  5000000 
INFO  @ Wed, 25 Jan 2017 17:55:08:  6000000 
INFO  @ Wed, 25 Jan 2017 17:55:10:  7000000 
INFO  @ Wed, 25 Jan 2017 17:55:11:  8000000 
INFO  @ Wed, 25 Jan 2017 17:55:13:  9000000 
INFO  @ Wed, 25 Jan 2017 17:55:14:  10000000 
INFO  @ Wed, 25 Jan 2017 17:55:16:  11000000 
INFO  @ Wed, 25 Jan 2017 17:55:17: #1 tag size is determined as 36 bps 
INFO  @ Wed, 25 Jan 2017 17:55:17: #1 tag size = 36 
INFO  @ Wed, 25 Jan 2017 17:55:17: #1  total tags in treatment: 47588485 
INFO  @ Wed, 25 Jan 2017 17:55:17: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 17:55:17: #1 finished! 
INFO  @ Wed, 25 Jan 2017 17:55:17: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 17:55:17: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 17:55:17: #2 Use 168 as fragment length 
INFO  @ Wed, 25 Jan 2017 17:55:17: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 17:55:17: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Wed, 25 Jan 2017 17:55:17: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 17:56:48: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Wed, 25 Jan 2017 17:56:48: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Wed, 25 Jan 2017 17:56:48: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg 
INFO  @ Wed, 25 Jan 2017 17:56:48: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Wed, 25 Jan 2017 17:56:48: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 18:01:26: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 18:01:26: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Wed, 25 Jan 2017 18:01:26: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed 
INFO  @ Wed, 25 Jan 2017 18:01:26: Done! 
INFO  @ Wed, 25 Jan 2017 18:01:29: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 168 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Wed, 25 Jan 2017 18:01:29: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 18:01:29: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 18:01:31:  1000000 
INFO  @ Wed, 25 Jan 2017 18:01:33:  2000000 
INFO  @ Wed, 25 Jan 2017 18:01:35:  3000000 
INFO  @ Wed, 25 Jan 2017 18:01:36:  4000000 
INFO  @ Wed, 25 Jan 2017 18:01:38:  5000000 
INFO  @ Wed, 25 Jan 2017 18:01:41:  6000000 
INFO  @ Wed, 25 Jan 2017 18:01:42:  7000000 
INFO  @ Wed, 25 Jan 2017 18:01:44:  8000000 
INFO  @ Wed, 25 Jan 2017 18:01:46:  9000000 
INFO  @ Wed, 25 Jan 2017 18:01:49:  10000000 
INFO  @ Wed, 25 Jan 2017 18:01:51:  11000000 
INFO  @ Wed, 25 Jan 2017 18:01:53:  12000000 
INFO  @ Wed, 25 Jan 2017 18:01:55:  13000000 
INFO  @ Wed, 25 Jan 2017 18:01:57:  14000000 
INFO  @ Wed, 25 Jan 2017 18:01:59:  15000000 
INFO  @ Wed, 25 Jan 2017 18:02:01:  16000000 
INFO  @ Wed, 25 Jan 2017 18:02:02:  17000000 
INFO  @ Wed, 25 Jan 2017 18:02:04:  18000000 
INFO  @ Wed, 25 Jan 2017 18:02:06:  19000000 
INFO  @ Wed, 25 Jan 2017 18:02:08:  20000000 
INFO  @ Wed, 25 Jan 2017 18:02:10:  21000000 
INFO  @ Wed, 25 Jan 2017 18:02:12:  22000000 
INFO  @ Wed, 25 Jan 2017 18:02:14:  23000000 
INFO  @ Wed, 25 Jan 2017 18:02:16:  24000000 
INFO  @ Wed, 25 Jan 2017 18:02:18:  25000000 
INFO  @ Wed, 25 Jan 2017 18:02:20:  26000000 
INFO  @ Wed, 25 Jan 2017 18:02:21:  27000000 
INFO  @ Wed, 25 Jan 2017 18:02:23:  28000000 
INFO  @ Wed, 25 Jan 2017 18:02:25:  29000000 
INFO  @ Wed, 25 Jan 2017 18:02:27:  30000000 
INFO  @ Wed, 25 Jan 2017 18:02:29:  31000000 
INFO  @ Wed, 25 Jan 2017 18:02:31:  32000000 
INFO  @ Wed, 25 Jan 2017 18:02:33:  33000000 
INFO  @ Wed, 25 Jan 2017 18:02:35:  34000000 
INFO  @ Wed, 25 Jan 2017 18:02:37:  35000000 
INFO  @ Wed, 25 Jan 2017 18:02:39:  36000000 
INFO  @ Wed, 25 Jan 2017 18:02:41:  37000000 
INFO  @ Wed, 25 Jan 2017 18:02:43:  38000000 
INFO  @ Wed, 25 Jan 2017 18:02:45:  39000000 
INFO  @ Wed, 25 Jan 2017 18:02:47:  40000000 
INFO  @ Wed, 25 Jan 2017 18:02:49:  41000000 
INFO  @ Wed, 25 Jan 2017 18:02:51:  42000000 
INFO  @ Wed, 25 Jan 2017 18:02:52:  43000000 
INFO  @ Wed, 25 Jan 2017 18:02:54:  44000000 
INFO  @ Wed, 25 Jan 2017 18:02:56:  45000000 
INFO  @ Wed, 25 Jan 2017 18:02:58:  46000000 
INFO  @ Wed, 25 Jan 2017 18:03:00:  47000000 
INFO  @ Wed, 25 Jan 2017 18:03:02: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 18:03:04:  1000000 
INFO  @ Wed, 25 Jan 2017 18:03:06:  2000000 
INFO  @ Wed, 25 Jan 2017 18:03:08:  3000000 
INFO  @ Wed, 25 Jan 2017 18:03:10:  4000000 
INFO  @ Wed, 25 Jan 2017 18:03:12:  5000000 
INFO  @ Wed, 25 Jan 2017 18:03:14:  6000000 
INFO  @ Wed, 25 Jan 2017 18:03:16:  7000000 
INFO  @ Wed, 25 Jan 2017 18:03:18:  8000000 
INFO  @ Wed, 25 Jan 2017 18:03:20:  9000000 
INFO  @ Wed, 25 Jan 2017 18:03:22:  10000000 
INFO  @ Wed, 25 Jan 2017 18:03:24:  11000000 
INFO  @ Wed, 25 Jan 2017 18:03:25: #1 tag size is determined as 36 bps 
INFO  @ Wed, 25 Jan 2017 18:03:25: #1 tag size = 36 
INFO  @ Wed, 25 Jan 2017 18:03:25: #1  total tags in treatment: 47588485 
INFO  @ Wed, 25 Jan 2017 18:03:25: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 18:03:25: #1 finished! 
INFO  @ Wed, 25 Jan 2017 18:03:25: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 18:03:25: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 18:03:25: #2 Use 168 as fragment length 
INFO  @ Wed, 25 Jan 2017 18:03:25: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 18:03:25: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Wed, 25 Jan 2017 18:03:25: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 18:05:08: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 18:06:19: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 18:06:20: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak 
INFO  @ Wed, 25 Jan 2017 18:06:20: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Wed, 25 Jan 2017 18:06:21: Done! 
INFO  @ Wed, 25 Jan 2017 18:06:26: Read and build treatment bedGraph... 
INFO  @ Wed, 25 Jan 2017 18:08:07: Read and build control bedGraph... 
INFO  @ Wed, 25 Jan 2017 18:08:41: Build scoreTrackII... 
INFO  @ Wed, 25 Jan 2017 18:09:31: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Wed, 25 Jan 2017 18:14:30: Write bedGraph of scores... 
INFO  @ Wed, 25 Jan 2017 18:18:08: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_FE.bdg'! 
INFO  @ Wed, 25 Jan 2017 18:26:13: Read and build treatment bedGraph... 
INFO  @ Wed, 25 Jan 2017 18:27:51: Read and build control bedGraph... 
INFO  @ Wed, 25 Jan 2017 18:28:23: Build scoreTrackII... 
INFO  @ Wed, 25 Jan 2017 18:29:11: Values in your input bedGraph files will be multiplied by 11.467883 ... 
INFO  @ Wed, 25 Jan 2017 18:33:43: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Wed, 25 Jan 2017 18:34:17: Write bedGraph of scores... 
INFO  @ Wed, 25 Jan 2017 18:35:32: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_ppois.bdg'!

Num	2
ID	task.callpeak_macs2.macs2_ppr1.line_71.id_11
Name	macs2 ppr1
Thread	thread_Root
PID	35589

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-25 17:53:23
End	2017-01-25 18:02:08
Elapsed	00:08:45
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
Dependencies

 
# SYS command. line 73

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 74

 export LC_COLLATE=C

# SYS command. line 79

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 168 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 168 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 110

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 121

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1 -o "ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -g /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

# SYS command. line 140

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1 -o "ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 143

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -g /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 153

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
14938 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Wed, 25 Jan 2017 17:53:44: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 168 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Wed, 25 Jan 2017 17:53:44: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 17:53:44: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 17:53:45:  1000000 
INFO  @ Wed, 25 Jan 2017 17:53:47:  2000000 
INFO  @ Wed, 25 Jan 2017 17:53:49:  3000000 
INFO  @ Wed, 25 Jan 2017 17:53:50:  4000000 
INFO  @ Wed, 25 Jan 2017 17:53:52:  5000000 
INFO  @ Wed, 25 Jan 2017 17:53:54:  6000000 
INFO  @ Wed, 25 Jan 2017 17:53:56:  7000000 
INFO  @ Wed, 25 Jan 2017 17:53:57:  8000000 
INFO  @ Wed, 25 Jan 2017 17:53:59:  9000000 
INFO  @ Wed, 25 Jan 2017 17:54:01:  10000000 
INFO  @ Wed, 25 Jan 2017 17:54:02:  11000000 
INFO  @ Wed, 25 Jan 2017 17:54:04:  12000000 
INFO  @ Wed, 25 Jan 2017 17:54:06:  13000000 
INFO  @ Wed, 25 Jan 2017 17:54:07:  14000000 
INFO  @ Wed, 25 Jan 2017 17:54:09:  15000000 
INFO  @ Wed, 25 Jan 2017 17:54:11:  16000000 
INFO  @ Wed, 25 Jan 2017 17:54:12:  17000000 
INFO  @ Wed, 25 Jan 2017 17:54:14:  18000000 
INFO  @ Wed, 25 Jan 2017 17:54:16:  19000000 
INFO  @ Wed, 25 Jan 2017 17:54:18:  20000000 
INFO  @ Wed, 25 Jan 2017 17:54:19:  21000000 
INFO  @ Wed, 25 Jan 2017 17:54:21:  22000000 
INFO  @ Wed, 25 Jan 2017 17:54:23:  23000000 
INFO  @ Wed, 25 Jan 2017 17:54:26: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 17:54:27:  1000000 
INFO  @ Wed, 25 Jan 2017 17:54:29:  2000000 
INFO  @ Wed, 25 Jan 2017 17:54:30:  3000000 
INFO  @ Wed, 25 Jan 2017 17:54:32:  4000000 
INFO  @ Wed, 25 Jan 2017 17:54:34:  5000000 
INFO  @ Wed, 25 Jan 2017 17:54:35:  6000000 
INFO  @ Wed, 25 Jan 2017 17:54:37:  7000000 
INFO  @ Wed, 25 Jan 2017 17:54:38:  8000000 
INFO  @ Wed, 25 Jan 2017 17:54:40:  9000000 
INFO  @ Wed, 25 Jan 2017 17:54:41:  10000000 
INFO  @ Wed, 25 Jan 2017 17:54:43:  11000000 
INFO  @ Wed, 25 Jan 2017 17:54:44: #1 tag size is determined as 36 bps 
INFO  @ Wed, 25 Jan 2017 17:54:44: #1 tag size = 36 
INFO  @ Wed, 25 Jan 2017 17:54:44: #1  total tags in treatment: 23794243 
INFO  @ Wed, 25 Jan 2017 17:54:44: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 17:54:44: #1 finished! 
INFO  @ Wed, 25 Jan 2017 17:54:44: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 17:54:44: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 17:54:44: #2 Use 168 as fragment length 
INFO  @ Wed, 25 Jan 2017 17:54:44: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 17:54:44: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Wed, 25 Jan 2017 17:54:44: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 17:55:50: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Wed, 25 Jan 2017 17:55:50: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Wed, 25 Jan 2017 17:55:50: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg 
INFO  @ Wed, 25 Jan 2017 17:55:50: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Wed, 25 Jan 2017 17:55:50: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 17:58:50: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 17:58:50: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Wed, 25 Jan 2017 17:58:50: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed 
INFO  @ Wed, 25 Jan 2017 17:58:50: Done! 
INFO  @ Wed, 25 Jan 2017 17:58:53: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 168 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Wed, 25 Jan 2017 17:58:53: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 17:58:53: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 17:58:55:  1000000 
INFO  @ Wed, 25 Jan 2017 17:58:56:  2000000 
INFO  @ Wed, 25 Jan 2017 17:58:58:  3000000 
INFO  @ Wed, 25 Jan 2017 17:59:00:  4000000 
INFO  @ Wed, 25 Jan 2017 17:59:01:  5000000 
INFO  @ Wed, 25 Jan 2017 17:59:03:  6000000 
INFO  @ Wed, 25 Jan 2017 17:59:05:  7000000 
INFO  @ Wed, 25 Jan 2017 17:59:06:  8000000 
INFO  @ Wed, 25 Jan 2017 17:59:08:  9000000 
INFO  @ Wed, 25 Jan 2017 17:59:10:  10000000 
INFO  @ Wed, 25 Jan 2017 17:59:11:  11000000 
INFO  @ Wed, 25 Jan 2017 17:59:13:  12000000 
INFO  @ Wed, 25 Jan 2017 17:59:15:  13000000 
INFO  @ Wed, 25 Jan 2017 17:59:17:  14000000 
INFO  @ Wed, 25 Jan 2017 17:59:18:  15000000 
INFO  @ Wed, 25 Jan 2017 17:59:20:  16000000 
INFO  @ Wed, 25 Jan 2017 17:59:22:  17000000 
INFO  @ Wed, 25 Jan 2017 17:59:23:  18000000 
INFO  @ Wed, 25 Jan 2017 17:59:25:  19000000 
INFO  @ Wed, 25 Jan 2017 17:59:27:  20000000 
INFO  @ Wed, 25 Jan 2017 17:59:28:  21000000 
INFO  @ Wed, 25 Jan 2017 17:59:30:  22000000 
INFO  @ Wed, 25 Jan 2017 17:59:32:  23000000 
INFO  @ Wed, 25 Jan 2017 17:59:35: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 17:59:36:  1000000 
INFO  @ Wed, 25 Jan 2017 17:59:38:  2000000 
INFO  @ Wed, 25 Jan 2017 17:59:40:  3000000 
INFO  @ Wed, 25 Jan 2017 17:59:41:  4000000 
INFO  @ Wed, 25 Jan 2017 17:59:43:  5000000 
INFO  @ Wed, 25 Jan 2017 17:59:45:  6000000 
INFO  @ Wed, 25 Jan 2017 17:59:46:  7000000 
INFO  @ Wed, 25 Jan 2017 17:59:48:  8000000 
INFO  @ Wed, 25 Jan 2017 17:59:49:  9000000 
INFO  @ Wed, 25 Jan 2017 17:59:51:  10000000 
INFO  @ Wed, 25 Jan 2017 17:59:53:  11000000 
INFO  @ Wed, 25 Jan 2017 17:59:54: #1 tag size is determined as 36 bps 
INFO  @ Wed, 25 Jan 2017 17:59:54: #1 tag size = 36 
INFO  @ Wed, 25 Jan 2017 17:59:54: #1  total tags in treatment: 23794243 
INFO  @ Wed, 25 Jan 2017 17:59:54: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 17:59:54: #1 finished! 
INFO  @ Wed, 25 Jan 2017 17:59:54: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 17:59:54: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 17:59:54: #2 Use 168 as fragment length 
INFO  @ Wed, 25 Jan 2017 17:59:54: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 17:59:54: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Wed, 25 Jan 2017 17:59:54: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 18:01:06: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 18:01:56: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 18:01:58: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak 
INFO  @ Wed, 25 Jan 2017 18:01:59: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Wed, 25 Jan 2017 18:02:00: Done!

Num	3
ID	task.callpeak_macs2.macs2_ppr2.line_71.id_12
Name	macs2 ppr2
Thread	thread_Root
PID	35590

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-25 17:53:24
End	2017-01-25 18:16:10
Elapsed	00:22:46
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
Dependencies

 
# SYS command. line 73

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 74

 export LC_COLLATE=C

# SYS command. line 79

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 168 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 168 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 110

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 121

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2 -o "ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -g /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

# SYS command. line 140

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2 -o "ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 143

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -g /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 153

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
49764 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Wed, 25 Jan 2017 17:53:56: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 168 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Wed, 25 Jan 2017 17:53:56: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 17:53:56: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 17:54:03:  1000000 
INFO  @ Wed, 25 Jan 2017 17:54:09:  2000000 
INFO  @ Wed, 25 Jan 2017 17:54:15:  3000000 
INFO  @ Wed, 25 Jan 2017 17:54:22:  4000000 
INFO  @ Wed, 25 Jan 2017 17:54:28:  5000000 
INFO  @ Wed, 25 Jan 2017 17:54:34:  6000000 
INFO  @ Wed, 25 Jan 2017 17:54:40:  7000000 
INFO  @ Wed, 25 Jan 2017 17:54:46:  8000000 
INFO  @ Wed, 25 Jan 2017 17:54:53:  9000000 
INFO  @ Wed, 25 Jan 2017 17:54:59:  10000000 
INFO  @ Wed, 25 Jan 2017 17:55:05:  11000000 
INFO  @ Wed, 25 Jan 2017 17:55:11:  12000000 
INFO  @ Wed, 25 Jan 2017 17:55:18:  13000000 
INFO  @ Wed, 25 Jan 2017 17:55:24:  14000000 
INFO  @ Wed, 25 Jan 2017 17:55:30:  15000000 
INFO  @ Wed, 25 Jan 2017 17:55:36:  16000000 
INFO  @ Wed, 25 Jan 2017 17:55:42:  17000000 
INFO  @ Wed, 25 Jan 2017 17:55:49:  18000000 
INFO  @ Wed, 25 Jan 2017 17:55:55:  19000000 
INFO  @ Wed, 25 Jan 2017 17:56:01:  20000000 
INFO  @ Wed, 25 Jan 2017 17:56:07:  21000000 
INFO  @ Wed, 25 Jan 2017 17:56:13:  22000000 
INFO  @ Wed, 25 Jan 2017 17:56:20:  23000000 
INFO  @ Wed, 25 Jan 2017 17:56:27: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 17:56:33:  1000000 
INFO  @ Wed, 25 Jan 2017 17:56:39:  2000000 
INFO  @ Wed, 25 Jan 2017 17:56:45:  3000000 
INFO  @ Wed, 25 Jan 2017 17:56:51:  4000000 
INFO  @ Wed, 25 Jan 2017 17:56:57:  5000000 
INFO  @ Wed, 25 Jan 2017 17:57:03:  6000000 
INFO  @ Wed, 25 Jan 2017 17:57:09:  7000000 
INFO  @ Wed, 25 Jan 2017 17:57:15:  8000000 
INFO  @ Wed, 25 Jan 2017 17:57:22:  9000000 
INFO  @ Wed, 25 Jan 2017 17:57:28:  10000000 
INFO  @ Wed, 25 Jan 2017 17:57:34:  11000000 
INFO  @ Wed, 25 Jan 2017 17:57:37: #1 tag size is determined as 36 bps 
INFO  @ Wed, 25 Jan 2017 17:57:37: #1 tag size = 36 
INFO  @ Wed, 25 Jan 2017 17:57:37: #1  total tags in treatment: 23794242 
INFO  @ Wed, 25 Jan 2017 17:57:37: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 17:57:37: #1 finished! 
INFO  @ Wed, 25 Jan 2017 17:57:37: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 17:57:37: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 17:57:37: #2 Use 168 as fragment length 
INFO  @ Wed, 25 Jan 2017 17:57:37: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 17:57:37: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Wed, 25 Jan 2017 17:57:37: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 18:00:01: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Wed, 25 Jan 2017 18:00:01: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Wed, 25 Jan 2017 18:00:01: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg 
INFO  @ Wed, 25 Jan 2017 18:00:01: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Wed, 25 Jan 2017 18:00:01: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 18:08:17: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 18:08:18: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Wed, 25 Jan 2017 18:08:18: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed 
INFO  @ Wed, 25 Jan 2017 18:08:18: Done! 
INFO  @ Wed, 25 Jan 2017 18:08:23: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 168 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Wed, 25 Jan 2017 18:08:23: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 18:08:23: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 18:08:29:  1000000 
INFO  @ Wed, 25 Jan 2017 18:08:35:  2000000 
INFO  @ Wed, 25 Jan 2017 18:08:41:  3000000 
INFO  @ Wed, 25 Jan 2017 18:08:47:  4000000 
INFO  @ Wed, 25 Jan 2017 18:08:53:  5000000 
INFO  @ Wed, 25 Jan 2017 18:09:00:  6000000 
INFO  @ Wed, 25 Jan 2017 18:09:06:  7000000 
INFO  @ Wed, 25 Jan 2017 18:09:12:  8000000 
INFO  @ Wed, 25 Jan 2017 18:09:18:  9000000 
INFO  @ Wed, 25 Jan 2017 18:09:24:  10000000 
INFO  @ Wed, 25 Jan 2017 18:09:30:  11000000 
INFO  @ Wed, 25 Jan 2017 18:09:36:  12000000 
INFO  @ Wed, 25 Jan 2017 18:09:42:  13000000 
INFO  @ Wed, 25 Jan 2017 18:09:49:  14000000 
INFO  @ Wed, 25 Jan 2017 18:09:55:  15000000 
INFO  @ Wed, 25 Jan 2017 18:10:01:  16000000 
INFO  @ Wed, 25 Jan 2017 18:10:07:  17000000 
INFO  @ Wed, 25 Jan 2017 18:10:13:  18000000 
INFO  @ Wed, 25 Jan 2017 18:10:19:  19000000 
INFO  @ Wed, 25 Jan 2017 18:10:25:  20000000 
INFO  @ Wed, 25 Jan 2017 18:10:31:  21000000 
INFO  @ Wed, 25 Jan 2017 18:10:37:  22000000 
INFO  @ Wed, 25 Jan 2017 18:10:44:  23000000 
INFO  @ Wed, 25 Jan 2017 18:10:51: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 18:10:57:  1000000 
INFO  @ Wed, 25 Jan 2017 18:11:03:  2000000 
INFO  @ Wed, 25 Jan 2017 18:11:09:  3000000 
INFO  @ Wed, 25 Jan 2017 18:11:15:  4000000 
INFO  @ Wed, 25 Jan 2017 18:11:21:  5000000 
INFO  @ Wed, 25 Jan 2017 18:11:27:  6000000 
INFO  @ Wed, 25 Jan 2017 18:11:33:  7000000 
INFO  @ Wed, 25 Jan 2017 18:11:39:  8000000 
INFO  @ Wed, 25 Jan 2017 18:11:45:  9000000 
INFO  @ Wed, 25 Jan 2017 18:11:50:  10000000 
INFO  @ Wed, 25 Jan 2017 18:11:56:  11000000 
INFO  @ Wed, 25 Jan 2017 18:12:00: #1 tag size is determined as 36 bps 
INFO  @ Wed, 25 Jan 2017 18:12:00: #1 tag size = 36 
INFO  @ Wed, 25 Jan 2017 18:12:00: #1  total tags in treatment: 23794242 
INFO  @ Wed, 25 Jan 2017 18:12:00: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 18:12:00: #1 finished! 
INFO  @ Wed, 25 Jan 2017 18:12:00: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 18:12:00: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 18:12:00: #2 Use 168 as fragment length 
INFO  @ Wed, 25 Jan 2017 18:12:00: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 18:12:00: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Wed, 25 Jan 2017 18:12:00: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 18:14:26: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 18:15:50: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 18:15:55: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak 
INFO  @ Wed, 25 Jan 2017 18:15:58: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Wed, 25 Jan 2017 18:16:01: Done!

Num	4
ID	task.callpeak_macs2.macs2_rep1.line_71.id_13
Name	macs2 rep1
Thread	thread_Root
PID	35591

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-25 17:53:25
End	2017-01-25 19:18:49
Elapsed	01:25:24
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/rep1/ENCFF002AAZ.nodup.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/signal/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/signal/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw
Dependencies

 
# SYS command. line 73

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 74

 export LC_COLLATE=C

# SYS command. line 79

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/rep1/ENCFF002AAZ.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/rep1/ENCFF002AAZ.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 110

 if [[ true == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 121

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1 -o "ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -g /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/signal/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/rep1/ENCFF002AAZ.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

# SYS command. line 140

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1 -o "ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 143

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -g /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/signal/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 153

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
49765 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Wed, 25 Jan 2017 17:53:56: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/rep1/ENCFF002AAZ.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/rep1/ENCFF002AAZ.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Wed, 25 Jan 2017 17:53:56: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 17:53:56: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 17:54:03:  1000000 
INFO  @ Wed, 25 Jan 2017 17:54:09:  2000000 
INFO  @ Wed, 25 Jan 2017 17:54:15:  3000000 
INFO  @ Wed, 25 Jan 2017 17:54:21:  4000000 
INFO  @ Wed, 25 Jan 2017 17:54:27:  5000000 
INFO  @ Wed, 25 Jan 2017 17:54:33:  6000000 
INFO  @ Wed, 25 Jan 2017 17:54:39:  7000000 
INFO  @ Wed, 25 Jan 2017 17:54:45:  8000000 
INFO  @ Wed, 25 Jan 2017 17:54:51:  9000000 
INFO  @ Wed, 25 Jan 2017 17:54:57:  10000000 
INFO  @ Wed, 25 Jan 2017 17:55:03:  11000000 
INFO  @ Wed, 25 Jan 2017 17:55:09:  12000000 
INFO  @ Wed, 25 Jan 2017 17:55:15:  13000000 
INFO  @ Wed, 25 Jan 2017 17:55:21:  14000000 
INFO  @ Wed, 25 Jan 2017 17:55:27:  15000000 
INFO  @ Wed, 25 Jan 2017 17:55:33:  16000000 
INFO  @ Wed, 25 Jan 2017 17:55:39:  17000000 
INFO  @ Wed, 25 Jan 2017 17:55:45:  18000000 
INFO  @ Wed, 25 Jan 2017 17:55:51:  19000000 
INFO  @ Wed, 25 Jan 2017 17:55:57:  20000000 
INFO  @ Wed, 25 Jan 2017 17:56:03:  21000000 
INFO  @ Wed, 25 Jan 2017 17:56:09:  22000000 
INFO  @ Wed, 25 Jan 2017 17:56:15:  23000000 
INFO  @ Wed, 25 Jan 2017 17:56:21:  24000000 
INFO  @ Wed, 25 Jan 2017 17:56:27:  25000000 
INFO  @ Wed, 25 Jan 2017 17:56:31: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 17:56:37:  1000000 
INFO  @ Wed, 25 Jan 2017 17:56:43:  2000000 
INFO  @ Wed, 25 Jan 2017 17:56:48:  3000000 
INFO  @ Wed, 25 Jan 2017 17:56:54:  4000000 
INFO  @ Wed, 25 Jan 2017 17:57:00:  5000000 
INFO  @ Wed, 25 Jan 2017 17:57:06:  6000000 
INFO  @ Wed, 25 Jan 2017 17:57:12:  7000000 
INFO  @ Wed, 25 Jan 2017 17:57:18:  8000000 
INFO  @ Wed, 25 Jan 2017 17:57:24:  9000000 
INFO  @ Wed, 25 Jan 2017 17:57:30:  10000000 
INFO  @ Wed, 25 Jan 2017 17:57:36:  11000000 
INFO  @ Wed, 25 Jan 2017 17:57:39: #1 tag size is determined as 36 bps 
INFO  @ Wed, 25 Jan 2017 17:57:39: #1 tag size = 36 
INFO  @ Wed, 25 Jan 2017 17:57:39: #1  total tags in treatment: 25506574 
INFO  @ Wed, 25 Jan 2017 17:57:39: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 17:57:39: #1 finished! 
INFO  @ Wed, 25 Jan 2017 17:57:39: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 17:57:39: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 17:57:39: #2 Use 145 as fragment length 
INFO  @ Wed, 25 Jan 2017 17:57:39: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 17:57:39: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Wed, 25 Jan 2017 17:57:39: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 18:00:12: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Wed, 25 Jan 2017 18:00:12: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Wed, 25 Jan 2017 18:00:12: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg 
INFO  @ Wed, 25 Jan 2017 18:00:12: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Wed, 25 Jan 2017 18:00:12: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 18:08:50: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 18:08:52: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Wed, 25 Jan 2017 18:08:54: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed 
INFO  @ Wed, 25 Jan 2017 18:08:54: Done! 
INFO  @ Wed, 25 Jan 2017 18:08:58: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/rep1/ENCFF002AAZ.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/rep1/ENCFF002AAZ.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Wed, 25 Jan 2017 18:08:58: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 18:08:58: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 18:09:04:  1000000 
INFO  @ Wed, 25 Jan 2017 18:09:10:  2000000 
INFO  @ Wed, 25 Jan 2017 18:09:15:  3000000 
INFO  @ Wed, 25 Jan 2017 18:09:21:  4000000 
INFO  @ Wed, 25 Jan 2017 18:09:27:  5000000 
INFO  @ Wed, 25 Jan 2017 18:09:33:  6000000 
INFO  @ Wed, 25 Jan 2017 18:09:39:  7000000 
INFO  @ Wed, 25 Jan 2017 18:09:45:  8000000 
INFO  @ Wed, 25 Jan 2017 18:09:51:  9000000 
INFO  @ Wed, 25 Jan 2017 18:09:57:  10000000 
INFO  @ Wed, 25 Jan 2017 18:10:03:  11000000 
INFO  @ Wed, 25 Jan 2017 18:10:09:  12000000 
INFO  @ Wed, 25 Jan 2017 18:10:15:  13000000 
INFO  @ Wed, 25 Jan 2017 18:10:21:  14000000 
INFO  @ Wed, 25 Jan 2017 18:10:27:  15000000 
INFO  @ Wed, 25 Jan 2017 18:10:33:  16000000 
INFO  @ Wed, 25 Jan 2017 18:10:39:  17000000 
INFO  @ Wed, 25 Jan 2017 18:10:44:  18000000 
INFO  @ Wed, 25 Jan 2017 18:10:50:  19000000 
INFO  @ Wed, 25 Jan 2017 18:10:56:  20000000 
INFO  @ Wed, 25 Jan 2017 18:11:02:  21000000 
INFO  @ Wed, 25 Jan 2017 18:11:08:  22000000 
INFO  @ Wed, 25 Jan 2017 18:11:14:  23000000 
INFO  @ Wed, 25 Jan 2017 18:11:20:  24000000 
INFO  @ Wed, 25 Jan 2017 18:11:26:  25000000 
INFO  @ Wed, 25 Jan 2017 18:11:30: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 18:11:35:  1000000 
INFO  @ Wed, 25 Jan 2017 18:11:41:  2000000 
INFO  @ Wed, 25 Jan 2017 18:11:47:  3000000 
INFO  @ Wed, 25 Jan 2017 18:11:53:  4000000 
INFO  @ Wed, 25 Jan 2017 18:11:59:  5000000 
INFO  @ Wed, 25 Jan 2017 18:12:05:  6000000 
INFO  @ Wed, 25 Jan 2017 18:12:10:  7000000 
INFO  @ Wed, 25 Jan 2017 18:12:16:  8000000 
INFO  @ Wed, 25 Jan 2017 18:12:22:  9000000 
INFO  @ Wed, 25 Jan 2017 18:12:28:  10000000 
INFO  @ Wed, 25 Jan 2017 18:12:34:  11000000 
INFO  @ Wed, 25 Jan 2017 18:12:37: #1 tag size is determined as 36 bps 
INFO  @ Wed, 25 Jan 2017 18:12:37: #1 tag size = 36 
INFO  @ Wed, 25 Jan 2017 18:12:37: #1  total tags in treatment: 25506574 
INFO  @ Wed, 25 Jan 2017 18:12:37: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 18:12:37: #1 finished! 
INFO  @ Wed, 25 Jan 2017 18:12:37: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 18:12:37: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 18:12:37: #2 Use 145 as fragment length 
INFO  @ Wed, 25 Jan 2017 18:12:37: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 18:12:37: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Wed, 25 Jan 2017 18:12:37: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 18:15:08: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 18:16:35: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 18:16:39: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak 
INFO  @ Wed, 25 Jan 2017 18:16:43: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Wed, 25 Jan 2017 18:16:45: Done! 
INFO  @ Wed, 25 Jan 2017 18:16:54: Read and build treatment bedGraph... 
INFO  @ Wed, 25 Jan 2017 18:19:53: Read and build control bedGraph... 
INFO  @ Wed, 25 Jan 2017 18:21:46: Build scoreTrackII... 
INFO  @ Wed, 25 Jan 2017 18:23:03: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Wed, 25 Jan 2017 18:34:15: Write bedGraph of scores... 
INFO  @ Wed, 25 Jan 2017 18:40:15: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_FE.bdg'! 
INFO  @ Wed, 25 Jan 2017 18:49:43: Read and build treatment bedGraph... 
INFO  @ Wed, 25 Jan 2017 18:52:46: Read and build control bedGraph... 
INFO  @ Wed, 25 Jan 2017 18:54:41: Build scoreTrackII... 
INFO  @ Wed, 25 Jan 2017 18:56:01: Values in your input bedGraph files will be multiplied by 11.467883 ... 
INFO  @ Wed, 25 Jan 2017 19:07:38: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Wed, 25 Jan 2017 19:08:43: Write bedGraph of scores... 
INFO  @ Wed, 25 Jan 2017 19:12:46: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_ppois.bdg'!

Num	5
ID	task.callpeak_macs2.macs2_rep2.line_71.id_14
Name	macs2 rep2
Thread	thread_Root
PID	35596

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-25 18:02:11
End	2017-01-25 18:30:31
Elapsed	00:28:19
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/rep2/ENCFF002AAX.nodup.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/signal/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/signal/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw
Dependencies

 
# SYS command. line 73

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 74

 export LC_COLLATE=C

# SYS command. line 79

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/rep2/ENCFF002AAX.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 190 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/rep2/ENCFF002AAX.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 190 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 110

 if [[ true == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 121

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2 -o "ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -g /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/signal/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/rep2/ENCFF002AAX.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

# SYS command. line 140

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2 -o "ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 143

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -g /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/signal/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 153

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
3431 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Wed, 25 Jan 2017 18:02:25: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/rep2/ENCFF002AAX.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 190 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/rep2/ENCFF002AAX.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Wed, 25 Jan 2017 18:02:25: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 18:02:25: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 18:02:27:  1000000 
INFO  @ Wed, 25 Jan 2017 18:02:29:  2000000 
INFO  @ Wed, 25 Jan 2017 18:02:31:  3000000 
INFO  @ Wed, 25 Jan 2017 18:02:33:  4000000 
INFO  @ Wed, 25 Jan 2017 18:02:35:  5000000 
INFO  @ Wed, 25 Jan 2017 18:02:37:  6000000 
INFO  @ Wed, 25 Jan 2017 18:02:39:  7000000 
INFO  @ Wed, 25 Jan 2017 18:02:40:  8000000 
INFO  @ Wed, 25 Jan 2017 18:02:43:  9000000 
INFO  @ Wed, 25 Jan 2017 18:02:45:  10000000 
INFO  @ Wed, 25 Jan 2017 18:02:47:  11000000 
INFO  @ Wed, 25 Jan 2017 18:02:49:  12000000 
INFO  @ Wed, 25 Jan 2017 18:02:50:  13000000 
INFO  @ Wed, 25 Jan 2017 18:02:52:  14000000 
INFO  @ Wed, 25 Jan 2017 18:02:54:  15000000 
INFO  @ Wed, 25 Jan 2017 18:02:56:  16000000 
INFO  @ Wed, 25 Jan 2017 18:02:58:  17000000 
INFO  @ Wed, 25 Jan 2017 18:03:01:  18000000 
INFO  @ Wed, 25 Jan 2017 18:03:03:  19000000 
INFO  @ Wed, 25 Jan 2017 18:03:04:  20000000 
INFO  @ Wed, 25 Jan 2017 18:03:06:  21000000 
INFO  @ Wed, 25 Jan 2017 18:03:08:  22000000 
INFO  @ Wed, 25 Jan 2017 18:03:08: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 18:03:11:  1000000 
INFO  @ Wed, 25 Jan 2017 18:03:12:  2000000 
INFO  @ Wed, 25 Jan 2017 18:03:14:  3000000 
INFO  @ Wed, 25 Jan 2017 18:03:15:  4000000 
INFO  @ Wed, 25 Jan 2017 18:03:17:  5000000 
INFO  @ Wed, 25 Jan 2017 18:03:18:  6000000 
INFO  @ Wed, 25 Jan 2017 18:03:19:  7000000 
INFO  @ Wed, 25 Jan 2017 18:03:21:  8000000 
INFO  @ Wed, 25 Jan 2017 18:03:23:  9000000 
INFO  @ Wed, 25 Jan 2017 18:03:24:  10000000 
INFO  @ Wed, 25 Jan 2017 18:03:25:  11000000 
INFO  @ Wed, 25 Jan 2017 18:03:26: #1 tag size is determined as 35 bps 
INFO  @ Wed, 25 Jan 2017 18:03:26: #1 tag size = 35 
INFO  @ Wed, 25 Jan 2017 18:03:26: #1  total tags in treatment: 22081911 
INFO  @ Wed, 25 Jan 2017 18:03:26: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 18:03:26: #1 finished! 
INFO  @ Wed, 25 Jan 2017 18:03:26: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 18:03:26: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 18:03:26: #2 Use 190 as fragment length 
INFO  @ Wed, 25 Jan 2017 18:03:26: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 18:03:26: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Wed, 25 Jan 2017 18:03:26: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 18:04:33: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Wed, 25 Jan 2017 18:04:33: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Wed, 25 Jan 2017 18:04:33: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg 
INFO  @ Wed, 25 Jan 2017 18:04:33: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Wed, 25 Jan 2017 18:04:33: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 18:07:08: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 18:07:09: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Wed, 25 Jan 2017 18:07:09: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed 
INFO  @ Wed, 25 Jan 2017 18:07:09: Done! 
INFO  @ Wed, 25 Jan 2017 18:07:12: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/rep2/ENCFF002AAX.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 190 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/rep2/ENCFF002AAX.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Wed, 25 Jan 2017 18:07:12: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 18:07:12: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 18:07:13:  1000000 
INFO  @ Wed, 25 Jan 2017 18:07:15:  2000000 
INFO  @ Wed, 25 Jan 2017 18:07:16:  3000000 
INFO  @ Wed, 25 Jan 2017 18:07:18:  4000000 
INFO  @ Wed, 25 Jan 2017 18:07:19:  5000000 
INFO  @ Wed, 25 Jan 2017 18:07:21:  6000000 
INFO  @ Wed, 25 Jan 2017 18:07:22:  7000000 
INFO  @ Wed, 25 Jan 2017 18:07:24:  8000000 
INFO  @ Wed, 25 Jan 2017 18:07:26:  9000000 
INFO  @ Wed, 25 Jan 2017 18:07:27:  10000000 
INFO  @ Wed, 25 Jan 2017 18:07:29:  11000000 
INFO  @ Wed, 25 Jan 2017 18:07:30:  12000000 
INFO  @ Wed, 25 Jan 2017 18:07:32:  13000000 
INFO  @ Wed, 25 Jan 2017 18:07:33:  14000000 
INFO  @ Wed, 25 Jan 2017 18:07:35:  15000000 
INFO  @ Wed, 25 Jan 2017 18:07:36:  16000000 
INFO  @ Wed, 25 Jan 2017 18:07:38:  17000000 
INFO  @ Wed, 25 Jan 2017 18:07:40:  18000000 
INFO  @ Wed, 25 Jan 2017 18:07:41:  19000000 
INFO  @ Wed, 25 Jan 2017 18:07:43:  20000000 
INFO  @ Wed, 25 Jan 2017 18:07:44:  21000000 
INFO  @ Wed, 25 Jan 2017 18:07:46:  22000000 
INFO  @ Wed, 25 Jan 2017 18:07:46: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 18:07:48:  1000000 
INFO  @ Wed, 25 Jan 2017 18:07:49:  2000000 
INFO  @ Wed, 25 Jan 2017 18:07:51:  3000000 
INFO  @ Wed, 25 Jan 2017 18:07:52:  4000000 
INFO  @ Wed, 25 Jan 2017 18:07:54:  5000000 
INFO  @ Wed, 25 Jan 2017 18:07:55:  6000000 
INFO  @ Wed, 25 Jan 2017 18:07:57:  7000000 
INFO  @ Wed, 25 Jan 2017 18:07:59:  8000000 
INFO  @ Wed, 25 Jan 2017 18:08:01:  9000000 
INFO  @ Wed, 25 Jan 2017 18:08:02:  10000000 
INFO  @ Wed, 25 Jan 2017 18:08:04:  11000000 
INFO  @ Wed, 25 Jan 2017 18:08:05: #1 tag size is determined as 35 bps 
INFO  @ Wed, 25 Jan 2017 18:08:05: #1 tag size = 35 
INFO  @ Wed, 25 Jan 2017 18:08:05: #1  total tags in treatment: 22081911 
INFO  @ Wed, 25 Jan 2017 18:08:05: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 18:08:05: #1 finished! 
INFO  @ Wed, 25 Jan 2017 18:08:05: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 18:08:05: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 18:08:05: #2 Use 190 as fragment length 
INFO  @ Wed, 25 Jan 2017 18:08:05: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 18:08:05: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Wed, 25 Jan 2017 18:08:05: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 18:09:08: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 18:09:55: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 18:09:58: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak 
INFO  @ Wed, 25 Jan 2017 18:10:00: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Wed, 25 Jan 2017 18:10:01: Done! 
INFO  @ Wed, 25 Jan 2017 18:10:11: Read and build treatment bedGraph... 
INFO  @ Wed, 25 Jan 2017 18:10:56: Read and build control bedGraph... 
INFO  @ Wed, 25 Jan 2017 18:11:29: Build scoreTrackII... 
INFO  @ Wed, 25 Jan 2017 18:12:03: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Wed, 25 Jan 2017 18:14:55: Write bedGraph of scores... 
INFO  @ Wed, 25 Jan 2017 18:16:50: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_FE.bdg'! 
INFO  @ Wed, 25 Jan 2017 18:21:16: Read and build treatment bedGraph... 
INFO  @ Wed, 25 Jan 2017 18:21:59: Read and build control bedGraph... 
INFO  @ Wed, 25 Jan 2017 18:22:29: Build scoreTrackII... 
INFO  @ Wed, 25 Jan 2017 18:22:52: Values in your input bedGraph files will be multiplied by 11.467883 ... 
INFO  @ Wed, 25 Jan 2017 18:25:41: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Wed, 25 Jan 2017 18:26:01: Write bedGraph of scores... 
INFO  @ Wed, 25 Jan 2017 18:27:12: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_ppois.bdg'!

Num	6
ID	task.callpeak_naive_overlap.naive_overlap_thresh.line_143.id_15
Name	naive_overlap_thresh
Thread	thread_Root
PID	35615

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-25 19:18:51
End	2017-01-25 19:20:08
Elapsed	00:01:16
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 145

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 148

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz) | awk 'BEGIN{FS="	";OFS="	"} {s1=$3-$2; s2=$13-$12; if (($21/s1 >= 0.5) || ($21/s2 >= 0.5)) {print $0}}' | cut -f 1-10 | sort | uniq | intersectBed  -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz) | awk 'BEGIN{FS="	";OFS="	"} {s1=$3-$2; s2=$13-$12; if (($21/s1 >= 0.5) || ($21/s2 >= 0.5)) {print $0}}' | cut -f 1-10 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.narrowPeak.gz

# SYS command. line 151

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz) | awk 'BEGIN{FS="	";OFS="	"} {s1=$3-$2; s2=$13-$12; if (($21/s1 >= 0.5) || ($21/s2 >= 0.5)) {print $0}}' | cut -f 1-10 | sort | uniq | intersectBed  -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz) |    awk 'BEGIN{FS="	";OFS="	"} {s1=$3-$2; s2=$13-$12; if (($21/s1 >= 0.5) || ($21/s2 >= 0.5)) {print $0}}' | cut -f 1-10 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.narrowPeak.gz

# SYS command. line 154

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.narrowPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.narrowPeak.gz

# SYS command. line 156

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.narrowPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz  | grep -P 'chr[0-9XY]+(?!_)' | awk 'BEGIN{OFS="	"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz

# SYS command. line 158

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.narrowPeak.gz

# SYS command. line 160

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
17188 (process ID) old priority 0, new priority 10
Waiting for 60 seconds.

Num	7
ID	task.callpeak_naive_overlap.naive_overlap_thresh.line_143.id_16
Name	naive_overlap_thresh
Thread	thread_Root
PID	35616

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-25 19:18:52
End	2017-01-25 19:20:08
Elapsed	00:01:15
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz
Dependencies

 
# SYS command. line 145

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 148

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz) | awk 'BEGIN{FS="	";OFS="	"} {s1=$3-$2; s2=$18-$17; if (($31/s1 >= 0.5) || ($31/s2 >= 0.5)) {print $0}}' | cut -f 1-15 | sort | uniq | intersectBed  -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz) | awk 'BEGIN{FS="	";OFS="	"} {s1=$3-$2; s2=$18-$17; if (($31/s1 >= 0.5) || ($31/s2 >= 0.5)) {print $0}}' | cut -f 1-15 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.gappedPeak.gz

# SYS command. line 151

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz) | awk 'BEGIN{FS="	";OFS="	"} {s1=$3-$2; s2=$18-$17; if (($31/s1 >= 0.5) || ($31/s2 >= 0.5)) {print $0}}' | cut -f 1-15 | sort | uniq | intersectBed  -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz) |    awk 'BEGIN{FS="	";OFS="	"} {s1=$3-$2; s2=$18-$17; if (($31/s1 >= 0.5) || ($31/s2 >= 0.5)) {print $0}}' | cut -f 1-15 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.gappedPeak.gz

# SYS command. line 154

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.gappedPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.gappedPeak.gz

# SYS command. line 156

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.gappedPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz  | grep -P 'chr[0-9XY]+(?!_)' | awk 'BEGIN{OFS="	"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz

# SYS command. line 158

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.gappedPeak.gz

# SYS command. line 160

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
12047 (process ID) old priority 0, new priority 10
Waiting for 52 seconds.

Num	8
ID	task.callpeak_naive_overlap.naive_overlap_thresh.line_143.id_17
Name	naive_overlap_thresh
Thread	thread_Root
PID	35617

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-25 19:18:54
End	2017-01-25 19:20:08
Elapsed	00:01:14
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.broadPeak.gz
Dependencies

 
# SYS command. line 145

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 148

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz) | awk 'BEGIN{FS="	";OFS="	"} {s1=$3-$2; s2=$12-$11; if (($19/s1 >= 0.5) || ($19/s2 >= 0.5)) {print $0}}' | cut -f 1-9 | sort | uniq | intersectBed  -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz) | awk 'BEGIN{FS="	";OFS="	"} {s1=$3-$2; s2=$12-$11; if (($19/s1 >= 0.5) || ($19/s2 >= 0.5)) {print $0}}' | cut -f 1-9 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.broadPeak.gz

# SYS command. line 151

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002AAZ.nodup.pr1_ENCFF002AAX.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz) | awk 'BEGIN{FS="	";OFS="	"} {s1=$3-$2; s2=$12-$11; if (($19/s1 >= 0.5) || ($19/s2 >= 0.5)) {print $0}}' | cut -f 1-9 | sort | uniq | intersectBed  -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002AAZ.nodup.pr2_ENCFF002AAX.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz) |    awk 'BEGIN{FS="	";OFS="	"} {s1=$3-$2; s2=$12-$11; if (($19/s1 >= 0.5) || ($19/s2 >= 0.5)) {print $0}}' | cut -f 1-9 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.broadPeak.gz

# SYS command. line 154

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.broadPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.broadPeak.gz

# SYS command. line 156

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.broadPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz  | grep -P 'chr[0-9XY]+(?!_)' | awk 'BEGIN{OFS="	"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.broadPeak.gz

# SYS command. line 158

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.broadPeak.gz

# SYS command. line 160

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
12046 (process ID) old priority 0, new priority 10
Waiting for 54 seconds.

Num	9
ID	task.callpeak_blacklist_filter.blacklist_filter_peak_pooled.line_27.id_18
Name	blacklist_filter peak_pooled
Thread	thread_Root
PID	8899

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-25 19:20:10
End	2017-01-25 19:21:18
Elapsed	00:01:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 29

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 31

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz \
			| awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' \
			| grep -P 'chr[\dXY]+[ \t]' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/pooled_rep/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.filt.narrowPeak.gz

# SYS command. line 35

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
8903 (process ID) old priority 0, new priority 10
Waiting for 60 seconds.

Num	10
ID	task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_19
Name	blacklist_filter peak 1
Thread	thread_Root
PID	8982

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-25 19:20:11
End	2017-01-25 19:21:18
Elapsed	00:01:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 29

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 31

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz \
			| awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' \
			| grep -P 'chr[\dXY]+[ \t]' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep1/ENCFF002AAZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.filt.narrowPeak.gz

# SYS command. line 35

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
8990 (process ID) old priority 0, new priority 10
Waiting for 60 seconds.

Num	11
ID	task.callpeak_blacklist_filter.blacklist_filter_peak_2.line_27.id_20
Name	blacklist_filter peak 2
Thread	thread_Root
PID	9100

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-25 19:20:12
End	2017-01-25 19:21:20
Elapsed	00:01:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 29

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 31

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz \
			| awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' \
			| grep -P 'chr[\dXY]+[ \t]' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/rep2/ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.filt.narrowPeak.gz

# SYS command. line 35

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
9106 (process ID) old priority 0, new priority 10
Waiting for 60 seconds.

Num	12
ID	task.report.peak2hammock.line_412.id_21
Name	peak2hammock
Thread	thread_Root
PID	13077

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-25 19:21:21
End	2017-01-25 19:21:29
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.hammock.gz
Dependencies

 
# SYS command. line 414

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 415

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp

# SYS command. line 417

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp

   
--------------------Stdout--------------------
13081 (process ID) old priority 0, new priority 10

Num	13
ID	task.report.peak2hammock.line_412.id_22
Name	peak2hammock
Thread	thread_Root
PID	13620

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-25 19:21:30
End	2017-01-25 19:21:39
Elapsed	00:00:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.hammock.gz
Dependencies

 
# SYS command. line 414

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 415

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp

# SYS command. line 417

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/gappedpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/peak/macs2/overlap/ENCFF002AAZ.nodup_ENCFF002AAX.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp

   
--------------------Stdout--------------------
13625 (process ID) old priority 0, new priority 10

Num	14
ID	task.graphviz.report.line_97.id_23
Name	report
Thread	thread_Root
PID	14263

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-25 19:21:40
End	2017-01-25 19:21:48
Elapsed	00:00:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files
Output files
Dependencies

 
# SYS command. line 98

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 99

 dot -Tsvg /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/report/H3K9me3_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/report/H3K9me3_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/report/H3K9me3_workflow.svg" # to suppress dot font error (exit code=1)

   
--------------------Stdout--------------------
14267 (process ID) old priority 0, new priority 10

Type	Name	Value
string	_	/usr/bin/bds
string	_LMFILES_	/software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/homer/default:/software/modulefiles/Matlab/MCR2010b:/software/modulefiles/align2rawsignal/2.0:/software/modulefiles/Matlab/R2014b
bool	allowEmpty	false
string[]	args	[-species, hg38, -tag1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/rep1/ENCFF002AAZ.nodup.tagAlign.gz, -tag2, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3/align/rep2/ENCFF002AAX.nodup.tagAlign.gz, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz, -final_stage, idr, -chrsz, /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes, -no_pseudo_rep, -histone, -out_dir, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3, $]
bool	canFail	false
int	cpus	-1
int	cpusLocal	56
int	day	86400
string	DEEPLIFT_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift
string	DERBY_HOME	/usr/lib/jvm/java-8-oracle/db
string	DISPLAY	localhost:13.0
real	E	2.718281828459045
string	ENHANCER_SCRIPTS_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/
int	G	1073741824
string	HOME	/users/imk1/
int	hour	3600
string	J2REDIR	/usr/lib/jvm/java-8-oracle/jre
string	J2SDKDIR	/usr/lib/jvm/java-8-oracle
string	JAVA_HOME	/usr/lib/jvm/java-8-oracle
int	K	1024
string	KERAS_DIR	/users/imk1/.local/lib/python2.7/site-packages/keras/
string	KRB5CCNAME	FILE:/tmp/krb5cc_1048_wplrRU
string	LANG	en_US.UTF-8
string	LOADEDMODULES	modsappsdir/modsappsdir:homer/default:Matlab/MCR2010b:align2rawsignal/2.0:Matlab/R2014b
string	LOGNAME	imk1
int	M	1048576
string	MAIL	/var/mail/imk1
int	mem	-1
int	minute	60
string	MODULE_VERSION	3.2.10
string	MODULE_VERSION_STACK	3.2.10
string	MODULEPATH	/usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles
string	MODULESAPPSDIR	/software
string	MODULESHOME	/software/env_module/3.2.10
string	NLSPATH	/usr/dt/lib/nls/msg/%L/%N.cat
string	node
int	P	1125899906842624
string	PATH	/software/Matlab/R2014b/bin:/software/align2rawsignal/2.0/bin:/software/ucsc_tools/3.0.9:/software/weblogo/2.8.2:/software/homer/default/bin:/users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/rcade/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/users/imk1/edirect:/users/imk1/edirect
string	PERL5LIB	/users/imk1/perl5/lib/perl5
string	PERL_LOCAL_LIB_ROOT	/users/imk1/perl5
string	PERL_MB_OPT	--install_base \"/users/imk1/perl5\"
string	PERL_MM_OPT	INSTALL_BASE=/users/imk1/perl5
real	PI	3.141592653589793
string	ppwd	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3
string	programName	chipseq.bds
string	programPath	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
string	PWD	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K9me3
string	PYTHONPATH	/users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/
string	queue
int	retry	0
string	RULEFITBASE	/srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/
string	SHELL	/bin/bash
string	SHLVL	3
string	SSH_CLIENT	171.65.77.8 42954 22
string	SSH_CONNECTION	171.65.77.8 42954 171.65.76.63 22
string	SSH_TTY	/dev/pts/152
string	STY	57232.H3K9me3.BDS
string	system	sge
int	T	1099511627776
string	TERM	screen
string	TERMCAP	SC\|screen\|VT 100/ANSI X3.64 virtual terminal:\\\n\t:DO=\\E[%dB:LE=\\E[%dD:RI=\\E[%dC:UP=\\E[%dA:bs:bt=\\E[Z:\\\n\t:cd=\\E[J:ce=\\E[K:cl=\\E[H\\E[J:cm=\\E[%i%d;%dH:ct=\\E[3g:\\\n\t:do=^J:nd=\\E[C:pt:rc=\\E8:rs=\\Ec:sc=\\E7:st=\\EH:up=\\EM:\\\n\t:le=^H:bl=^G:cr=^M:it#8:ho=\\E[H:nw=\\EE:ta=^I:is=\\E)0:\\\n\t:li#24:co#80:am:xn:xv:LP:sr=\\EM:al=\\E[L:AL=\\E[%dL:\\\n\t:cs=\\E[%i%d;%dr:dl=\\E[M:DL=\\E[%dM:dc=\\E[P:DC=\\E[%dP:\\\n\t:im=\\E[4h:ei=\\E[4l:mi:IC=\\E[%d@:ks=\\E[?1h\\E=:\\\n\t:ke=\\E[?1l\\E>:vi=\\E[?25l:ve=\\E[34h\\E[?25h:vs=\\E[34l:\\\n\t:ti=\\E[?1049h:te=\\E[?1049l:Km=\\E[M:k0=\\E[10~:k1=\\EOP:\\\n\t:k2=\\EOQ:k3=\\EOR:k4=\\EOS:k5=\\E[15~:k6=\\E[17~:k7=\\E[18~:\\\n\t:k8=\\E[19~:k9=\\E[20~:k;=\\E[21~:F1=\\E[23~:F2=\\E[24~:\\\n\t:kh=\\E[1~:@1=\\E[1~:kH=\\E[4~:@7=\\E[4~:kN=\\E[6~:kP=\\E[5~:\\\n\t:kI=\\E[2~:kD=\\E[3~:ku=\\EOA:kd=\\EOB:kr=\\EOC:kl=\\EOD:
int	timeout	-1
string	USER	imk1
string	UTIL_SCRIPTS_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/av_scripts/
int	walltimeout	8640000
int	week	604800
string	WINDOW	0
string	XAPPLRESDIR	/software/Matlab/MCR2010b/v714/X11/app-defaults
string	XDG_RUNTIME_DIR	/run/user/1048
string	XDG_SESSION_ID	22185
string	XFILESEARCHPATH	/usr/dt/app-defaults/%L/Dt

BigDataScript report: chipseq.bds

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