Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20170106_142908_823
Start time	2017-01-06 14:29:08
Run time	01:07:07.041
Tasks executed	10
Tasks failed	0
Tasks failed names
Arguments*	[-title, ZNF136, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF136/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/align/rep1/SRR1370900_1.bam, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz, -final_stage, idr, $]
System*	sge
Cpus*	-1
Exit value	0

Thread ID	Parent	Tasks
thread_Root	None	chipseq.bds.20170106_142908_823/task.callpeak_macs2.macs2_rep1.line_71.id_10 chipseq.bds.20170106_142908_823/task.callpeak_macs2.macs2_rep1_pr1.line_71.id_11 chipseq.bds.20170106_142908_823/task.callpeak_macs2.macs2_rep1_pr2.line_71.id_12 chipseq.bds.20170106_142908_823/task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_13 chipseq.bds.20170106_142908_823/task.callpeak_idr.idr2_rep1_pr.line_73.id_14 chipseq.bds.20170106_142908_823/task.callpeak_idr.idr_final_qc.line_219.id_17 chipseq.bds.20170106_142908_823/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_18 chipseq.bds.20170106_142908_823/task.report.peak2hammock.line_412.id_19 chipseq.bds.20170106_142908_823/task.report.peak2hammock.line_412.id_20 chipseq.bds.20170106_142908_823/task.graphviz.report.line_97.id_21
thread_42	thread_Root
thread_41	thread_Root

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.callpeak_macs2.macs2_rep1.line_71.id_10
Name	macs2 rep1
Thread	thread_Root
PID	24239

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

Start	2017-01-06 14:29:17
End	2017-01-06 15:28:18
Elapsed	00:59:01
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/align/rep1/SRR1370900_1.nodup.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/signal/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/signal/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.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/Najafabadi2015Data/hg38Mapping/ZNF136/out/align/rep1/SRR1370900_1.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 105 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/align/rep1/SRR1370900_1.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 105 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 110

 if [[ true == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.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/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1 -o "SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/signal/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/align/rep1/SRR1370900_1.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.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/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1 -o "SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 143

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/signal/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.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--------------------
3854 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 14:29:39: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/align/rep1/SRR1370900_1.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 105 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/align/rep1/SRR1370900_1.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.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  @ Fri, 06 Jan 2017 14:29:39: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 14:29:39: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 14:29:41:  1000000 
INFO  @ Fri, 06 Jan 2017 14:29:43:  2000000 
INFO  @ Fri, 06 Jan 2017 14:29:46:  3000000 
INFO  @ Fri, 06 Jan 2017 14:29:48:  4000000 
INFO  @ Fri, 06 Jan 2017 14:29:49:  5000000 
INFO  @ Fri, 06 Jan 2017 14:29:51:  6000000 
INFO  @ Fri, 06 Jan 2017 14:29:53:  7000000 
INFO  @ Fri, 06 Jan 2017 14:29:55:  8000000 
INFO  @ Fri, 06 Jan 2017 14:29:57:  9000000 
INFO  @ Fri, 06 Jan 2017 14:29:59:  10000000 
INFO  @ Fri, 06 Jan 2017 14:30:01:  11000000 
INFO  @ Fri, 06 Jan 2017 14:30:03: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 14:30:05:  1000000 
INFO  @ Fri, 06 Jan 2017 14:30:07:  2000000 
INFO  @ Fri, 06 Jan 2017 14:30:09:  3000000 
INFO  @ Fri, 06 Jan 2017 14:30:11:  4000000 
INFO  @ Fri, 06 Jan 2017 14:30:13:  5000000 
INFO  @ Fri, 06 Jan 2017 14:30:15:  6000000 
INFO  @ Fri, 06 Jan 2017 14:30:16:  7000000 
INFO  @ Fri, 06 Jan 2017 14:30:18:  8000000 
INFO  @ Fri, 06 Jan 2017 14:30:20:  9000000 
INFO  @ Fri, 06 Jan 2017 14:30:22:  10000000 
INFO  @ Fri, 06 Jan 2017 14:30:24:  11000000 
INFO  @ Fri, 06 Jan 2017 14:30:26:  12000000 
INFO  @ Fri, 06 Jan 2017 14:30:28:  13000000 
INFO  @ Fri, 06 Jan 2017 14:30:30:  14000000 
INFO  @ Fri, 06 Jan 2017 14:30:32:  15000000 
INFO  @ Fri, 06 Jan 2017 14:30:33:  16000000 
INFO  @ Fri, 06 Jan 2017 14:30:35:  17000000 
INFO  @ Fri, 06 Jan 2017 14:30:37:  18000000 
INFO  @ Fri, 06 Jan 2017 14:30:39:  19000000 
INFO  @ Fri, 06 Jan 2017 14:30:41:  20000000 
INFO  @ Fri, 06 Jan 2017 14:30:43:  21000000 
INFO  @ Fri, 06 Jan 2017 14:30:45:  22000000 
INFO  @ Fri, 06 Jan 2017 14:30:47:  23000000 
INFO  @ Fri, 06 Jan 2017 14:30:48:  24000000 
INFO  @ Fri, 06 Jan 2017 14:30:50:  25000000 
INFO  @ Fri, 06 Jan 2017 14:30:52:  26000000 
INFO  @ Fri, 06 Jan 2017 14:30:54:  27000000 
INFO  @ Fri, 06 Jan 2017 14:30:56:  28000000 
INFO  @ Fri, 06 Jan 2017 14:30:58:  29000000 
INFO  @ Fri, 06 Jan 2017 14:31:00:  30000000 
INFO  @ Fri, 06 Jan 2017 14:31:02:  31000000 
INFO  @ Fri, 06 Jan 2017 14:31:04:  32000000 
INFO  @ Fri, 06 Jan 2017 14:31:06:  33000000 
INFO  @ Fri, 06 Jan 2017 14:31:08:  34000000 
INFO  @ Fri, 06 Jan 2017 14:31:11:  35000000 
INFO  @ Fri, 06 Jan 2017 14:31:13:  36000000 
INFO  @ Fri, 06 Jan 2017 14:31:15:  37000000 
INFO  @ Fri, 06 Jan 2017 14:31:17:  38000000 
INFO  @ Fri, 06 Jan 2017 14:31:19:  39000000 
INFO  @ Fri, 06 Jan 2017 14:31:21:  40000000 
INFO  @ Fri, 06 Jan 2017 14:31:22:  41000000 
INFO  @ Fri, 06 Jan 2017 14:31:24:  42000000 
INFO  @ Fri, 06 Jan 2017 14:31:26:  43000000 
INFO  @ Fri, 06 Jan 2017 14:31:28:  44000000 
INFO  @ Fri, 06 Jan 2017 14:31:30:  45000000 
INFO  @ Fri, 06 Jan 2017 14:31:32:  46000000 
INFO  @ Fri, 06 Jan 2017 14:31:33:  47000000 
INFO  @ Fri, 06 Jan 2017 14:31:35:  48000000 
INFO  @ Fri, 06 Jan 2017 14:31:37:  49000000 
INFO  @ Fri, 06 Jan 2017 14:31:40:  50000000 
INFO  @ Fri, 06 Jan 2017 14:31:42: #1 tag size is determined as 64 bps 
INFO  @ Fri, 06 Jan 2017 14:31:42: #1 tag size = 64 
INFO  @ Fri, 06 Jan 2017 14:31:42: #1  total tags in treatment: 11960123 
INFO  @ Fri, 06 Jan 2017 14:31:42: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 14:31:42: #1 finished! 
INFO  @ Fri, 06 Jan 2017 14:31:42: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 14:31:42: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 14:31:42: #2 Use 105 as fragment length 
INFO  @ Fri, 06 Jan 2017 14:31:42: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 14:31:42: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 14:31:42: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 14:34:52: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 14:34:52: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 14:34:52: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 14:34:52: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 14:34:52: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 14:40:11: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 14:40:13: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 14:40:14: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 14:40:15: Done! 
INFO  @ Fri, 06 Jan 2017 14:40:19: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/align/rep1/SRR1370900_1.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 105 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/align/rep1/SRR1370900_1.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.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  @ Fri, 06 Jan 2017 14:40:19: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 14:40:19: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 14:40:21:  1000000 
INFO  @ Fri, 06 Jan 2017 14:40:23:  2000000 
INFO  @ Fri, 06 Jan 2017 14:40:24:  3000000 
INFO  @ Fri, 06 Jan 2017 14:40:26:  4000000 
INFO  @ Fri, 06 Jan 2017 14:40:27:  5000000 
INFO  @ Fri, 06 Jan 2017 14:40:29:  6000000 
INFO  @ Fri, 06 Jan 2017 14:40:30:  7000000 
INFO  @ Fri, 06 Jan 2017 14:40:32:  8000000 
INFO  @ Fri, 06 Jan 2017 14:40:33:  9000000 
INFO  @ Fri, 06 Jan 2017 14:40:35:  10000000 
INFO  @ Fri, 06 Jan 2017 14:40:36:  11000000 
INFO  @ Fri, 06 Jan 2017 14:40:38: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 14:40:39:  1000000 
INFO  @ Fri, 06 Jan 2017 14:40:41:  2000000 
INFO  @ Fri, 06 Jan 2017 14:40:43:  3000000 
INFO  @ Fri, 06 Jan 2017 14:40:44:  4000000 
INFO  @ Fri, 06 Jan 2017 14:40:45:  5000000 
INFO  @ Fri, 06 Jan 2017 14:40:47:  6000000 
INFO  @ Fri, 06 Jan 2017 14:40:48:  7000000 
INFO  @ Fri, 06 Jan 2017 14:40:50:  8000000 
INFO  @ Fri, 06 Jan 2017 14:40:52:  9000000 
INFO  @ Fri, 06 Jan 2017 14:40:53:  10000000 
INFO  @ Fri, 06 Jan 2017 14:40:55:  11000000 
INFO  @ Fri, 06 Jan 2017 14:40:56:  12000000 
INFO  @ Fri, 06 Jan 2017 14:40:58:  13000000 
INFO  @ Fri, 06 Jan 2017 14:40:59:  14000000 
INFO  @ Fri, 06 Jan 2017 14:41:01:  15000000 
INFO  @ Fri, 06 Jan 2017 14:41:02:  16000000 
INFO  @ Fri, 06 Jan 2017 14:41:04:  17000000 
INFO  @ Fri, 06 Jan 2017 14:41:05:  18000000 
INFO  @ Fri, 06 Jan 2017 14:41:07:  19000000 
INFO  @ Fri, 06 Jan 2017 14:41:08:  20000000 
INFO  @ Fri, 06 Jan 2017 14:41:10:  21000000 
INFO  @ Fri, 06 Jan 2017 14:41:11:  22000000 
INFO  @ Fri, 06 Jan 2017 14:41:13:  23000000 
INFO  @ Fri, 06 Jan 2017 14:41:14:  24000000 
INFO  @ Fri, 06 Jan 2017 14:41:16:  25000000 
INFO  @ Fri, 06 Jan 2017 14:41:17:  26000000 
INFO  @ Fri, 06 Jan 2017 14:41:19:  27000000 
INFO  @ Fri, 06 Jan 2017 14:41:20:  28000000 
INFO  @ Fri, 06 Jan 2017 14:41:22:  29000000 
INFO  @ Fri, 06 Jan 2017 14:41:23:  30000000 
INFO  @ Fri, 06 Jan 2017 14:41:25:  31000000 
INFO  @ Fri, 06 Jan 2017 14:41:26:  32000000 
INFO  @ Fri, 06 Jan 2017 14:41:28:  33000000 
INFO  @ Fri, 06 Jan 2017 14:41:29:  34000000 
INFO  @ Fri, 06 Jan 2017 14:41:31:  35000000 
INFO  @ Fri, 06 Jan 2017 14:41:33:  36000000 
INFO  @ Fri, 06 Jan 2017 14:41:34:  37000000 
INFO  @ Fri, 06 Jan 2017 14:41:36:  38000000 
INFO  @ Fri, 06 Jan 2017 14:41:37:  39000000 
INFO  @ Fri, 06 Jan 2017 14:41:39:  40000000 
INFO  @ Fri, 06 Jan 2017 14:41:40:  41000000 
INFO  @ Fri, 06 Jan 2017 14:41:42:  42000000 
INFO  @ Fri, 06 Jan 2017 14:41:43:  43000000 
INFO  @ Fri, 06 Jan 2017 14:41:45:  44000000 
INFO  @ Fri, 06 Jan 2017 14:41:47:  45000000 
INFO  @ Fri, 06 Jan 2017 14:41:48:  46000000 
INFO  @ Fri, 06 Jan 2017 14:41:50:  47000000 
INFO  @ Fri, 06 Jan 2017 14:41:51:  48000000 
INFO  @ Fri, 06 Jan 2017 14:41:53:  49000000 
INFO  @ Fri, 06 Jan 2017 14:41:54:  50000000 
INFO  @ Fri, 06 Jan 2017 14:41:56: #1 tag size is determined as 64 bps 
INFO  @ Fri, 06 Jan 2017 14:41:56: #1 tag size = 64 
INFO  @ Fri, 06 Jan 2017 14:41:56: #1  total tags in treatment: 11960123 
INFO  @ Fri, 06 Jan 2017 14:41:56: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 14:41:56: #1 finished! 
INFO  @ Fri, 06 Jan 2017 14:41:56: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 14:41:56: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 14:41:56: #2 Use 105 as fragment length 
INFO  @ Fri, 06 Jan 2017 14:41:56: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 14:41:56: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 14:41:56: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 14:44:55: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 14:48:10: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 14:48:21: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 14:48:28: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 14:48:35: Done! 
INFO  @ Fri, 06 Jan 2017 14:48:56: Read and build treatment bedGraph... 
INFO  @ Fri, 06 Jan 2017 14:49:31: Read and build control bedGraph... 
INFO  @ Fri, 06 Jan 2017 14:51:36: Build scoreTrackII... 
INFO  @ Fri, 06 Jan 2017 14:52:23: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Fri, 06 Jan 2017 14:57:47: Write bedGraph of scores... 
INFO  @ Fri, 06 Jan 2017 15:00:17: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_FE.bdg'! 
INFO  @ Fri, 06 Jan 2017 15:05:48: Read and build treatment bedGraph... 
INFO  @ Fri, 06 Jan 2017 15:06:18: Read and build control bedGraph... 
INFO  @ Fri, 06 Jan 2017 15:08:28: Build scoreTrackII... 
INFO  @ Fri, 06 Jan 2017 15:09:12: Values in your input bedGraph files will be multiplied by 11.960123 ... 
INFO  @ Fri, 06 Jan 2017 15:15:07: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Fri, 06 Jan 2017 15:15:45: Write bedGraph of scores... 
INFO  @ Fri, 06 Jan 2017 15:18:44: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_ppois.bdg'!

Num	2
ID	task.callpeak_macs2.macs2_rep1_pr1.line_71.id_11
Name	macs2 rep1-pr1
Thread	thread_Root
PID	24240

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

Start	2017-01-06 14:29:20
End	2017-01-06 14:46:04
Elapsed	00:16:44
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/align/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.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/Najafabadi2015Data/hg38Mapping/ZNF136/out/align/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 105 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/align/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 105 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 110

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.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/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/align/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.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/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 143

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.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--------------------
29322 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 14:29:38: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/align/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 105 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/align/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.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  @ Fri, 06 Jan 2017 14:29:38: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 14:29:38: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 14:29:40:  1000000 
INFO  @ Fri, 06 Jan 2017 14:29:42:  2000000 
INFO  @ Fri, 06 Jan 2017 14:29:43:  3000000 
INFO  @ Fri, 06 Jan 2017 14:29:45:  4000000 
INFO  @ Fri, 06 Jan 2017 14:29:46:  5000000 
INFO  @ Fri, 06 Jan 2017 14:29:48: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 14:29:50:  1000000 
INFO  @ Fri, 06 Jan 2017 14:29:51:  2000000 
INFO  @ Fri, 06 Jan 2017 14:29:52:  3000000 
INFO  @ Fri, 06 Jan 2017 14:29:54:  4000000 
INFO  @ Fri, 06 Jan 2017 14:29:55:  5000000 
INFO  @ Fri, 06 Jan 2017 14:29:57:  6000000 
INFO  @ Fri, 06 Jan 2017 14:29:58:  7000000 
INFO  @ Fri, 06 Jan 2017 14:29:59:  8000000 
INFO  @ Fri, 06 Jan 2017 14:30:01:  9000000 
INFO  @ Fri, 06 Jan 2017 14:30:02:  10000000 
INFO  @ Fri, 06 Jan 2017 14:30:04:  11000000 
INFO  @ Fri, 06 Jan 2017 14:30:05:  12000000 
INFO  @ Fri, 06 Jan 2017 14:30:06:  13000000 
INFO  @ Fri, 06 Jan 2017 14:30:08:  14000000 
INFO  @ Fri, 06 Jan 2017 14:30:09:  15000000 
INFO  @ Fri, 06 Jan 2017 14:30:10:  16000000 
INFO  @ Fri, 06 Jan 2017 14:30:12:  17000000 
INFO  @ Fri, 06 Jan 2017 14:30:13:  18000000 
INFO  @ Fri, 06 Jan 2017 14:30:14:  19000000 
INFO  @ Fri, 06 Jan 2017 14:30:16:  20000000 
INFO  @ Fri, 06 Jan 2017 14:30:17:  21000000 
INFO  @ Fri, 06 Jan 2017 14:30:18:  22000000 
INFO  @ Fri, 06 Jan 2017 14:30:20:  23000000 
INFO  @ Fri, 06 Jan 2017 14:30:21:  24000000 
INFO  @ Fri, 06 Jan 2017 14:30:23:  25000000 
INFO  @ Fri, 06 Jan 2017 14:30:24:  26000000 
INFO  @ Fri, 06 Jan 2017 14:30:25:  27000000 
INFO  @ Fri, 06 Jan 2017 14:30:27:  28000000 
INFO  @ Fri, 06 Jan 2017 14:30:28:  29000000 
INFO  @ Fri, 06 Jan 2017 14:30:29:  30000000 
INFO  @ Fri, 06 Jan 2017 14:30:30:  31000000 
INFO  @ Fri, 06 Jan 2017 14:30:32:  32000000 
INFO  @ Fri, 06 Jan 2017 14:30:33:  33000000 
INFO  @ Fri, 06 Jan 2017 14:30:34:  34000000 
INFO  @ Fri, 06 Jan 2017 14:30:36:  35000000 
INFO  @ Fri, 06 Jan 2017 14:30:37:  36000000 
INFO  @ Fri, 06 Jan 2017 14:30:39:  37000000 
INFO  @ Fri, 06 Jan 2017 14:30:40:  38000000 
INFO  @ Fri, 06 Jan 2017 14:30:41:  39000000 
INFO  @ Fri, 06 Jan 2017 14:30:43:  40000000 
INFO  @ Fri, 06 Jan 2017 14:30:44:  41000000 
INFO  @ Fri, 06 Jan 2017 14:30:45:  42000000 
INFO  @ Fri, 06 Jan 2017 14:30:47:  43000000 
INFO  @ Fri, 06 Jan 2017 14:30:48:  44000000 
INFO  @ Fri, 06 Jan 2017 14:30:50:  45000000 
INFO  @ Fri, 06 Jan 2017 14:30:51:  46000000 
INFO  @ Fri, 06 Jan 2017 14:30:52:  47000000 
INFO  @ Fri, 06 Jan 2017 14:30:54:  48000000 
INFO  @ Fri, 06 Jan 2017 14:30:55:  49000000 
INFO  @ Fri, 06 Jan 2017 14:30:56:  50000000 
INFO  @ Fri, 06 Jan 2017 14:30:58: #1 tag size is determined as 59 bps 
INFO  @ Fri, 06 Jan 2017 14:30:58: #1 tag size = 59 
INFO  @ Fri, 06 Jan 2017 14:30:58: #1  total tags in treatment: 5980062 
INFO  @ Fri, 06 Jan 2017 14:30:58: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 14:30:58: #1 finished! 
INFO  @ Fri, 06 Jan 2017 14:30:58: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 14:30:58: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 14:30:58: #2 Use 105 as fragment length 
INFO  @ Fri, 06 Jan 2017 14:30:58: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 14:30:58: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 14:30:58: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 14:33:19: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 14:33:19: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 14:33:19: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 14:33:19: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 14:33:19: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 14:37:58: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 14:38:00: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 14:38:01: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 14:38:02: Done! 
INFO  @ Fri, 06 Jan 2017 14:38:06: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/align/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 105 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/align/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.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  @ Fri, 06 Jan 2017 14:38:06: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 14:38:06: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 14:38:08:  1000000 
INFO  @ Fri, 06 Jan 2017 14:38:10:  2000000 
INFO  @ Fri, 06 Jan 2017 14:38:12:  3000000 
INFO  @ Fri, 06 Jan 2017 14:38:14:  4000000 
INFO  @ Fri, 06 Jan 2017 14:38:16:  5000000 
INFO  @ Fri, 06 Jan 2017 14:38:18: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 14:38:20:  1000000 
INFO  @ Fri, 06 Jan 2017 14:38:22:  2000000 
INFO  @ Fri, 06 Jan 2017 14:38:24:  3000000 
INFO  @ Fri, 06 Jan 2017 14:38:26:  4000000 
INFO  @ Fri, 06 Jan 2017 14:38:28:  5000000 
INFO  @ Fri, 06 Jan 2017 14:38:30:  6000000 
INFO  @ Fri, 06 Jan 2017 14:38:31:  7000000 
INFO  @ Fri, 06 Jan 2017 14:38:33:  8000000 
INFO  @ Fri, 06 Jan 2017 14:38:35:  9000000 
INFO  @ Fri, 06 Jan 2017 14:38:37:  10000000 
INFO  @ Fri, 06 Jan 2017 14:38:39:  11000000 
INFO  @ Fri, 06 Jan 2017 14:38:41:  12000000 
INFO  @ Fri, 06 Jan 2017 14:38:43:  13000000 
INFO  @ Fri, 06 Jan 2017 14:38:44:  14000000 
INFO  @ Fri, 06 Jan 2017 14:38:46:  15000000 
INFO  @ Fri, 06 Jan 2017 14:38:48:  16000000 
INFO  @ Fri, 06 Jan 2017 14:38:50:  17000000 
INFO  @ Fri, 06 Jan 2017 14:38:52:  18000000 
INFO  @ Fri, 06 Jan 2017 14:38:54:  19000000 
INFO  @ Fri, 06 Jan 2017 14:38:55:  20000000 
INFO  @ Fri, 06 Jan 2017 14:38:57:  21000000 
INFO  @ Fri, 06 Jan 2017 14:38:59:  22000000 
INFO  @ Fri, 06 Jan 2017 14:39:01:  23000000 
INFO  @ Fri, 06 Jan 2017 14:39:03:  24000000 
INFO  @ Fri, 06 Jan 2017 14:39:05:  25000000 
INFO  @ Fri, 06 Jan 2017 14:39:06:  26000000 
INFO  @ Fri, 06 Jan 2017 14:39:08:  27000000 
INFO  @ Fri, 06 Jan 2017 14:39:10:  28000000 
INFO  @ Fri, 06 Jan 2017 14:39:12:  29000000 
INFO  @ Fri, 06 Jan 2017 14:39:14:  30000000 
INFO  @ Fri, 06 Jan 2017 14:39:16:  31000000 
INFO  @ Fri, 06 Jan 2017 14:39:17:  32000000 
INFO  @ Fri, 06 Jan 2017 14:39:19:  33000000 
INFO  @ Fri, 06 Jan 2017 14:39:21:  34000000 
INFO  @ Fri, 06 Jan 2017 14:39:23:  35000000 
INFO  @ Fri, 06 Jan 2017 14:39:25:  36000000 
INFO  @ Fri, 06 Jan 2017 14:39:27:  37000000 
INFO  @ Fri, 06 Jan 2017 14:39:28:  38000000 
INFO  @ Fri, 06 Jan 2017 14:39:30:  39000000 
INFO  @ Fri, 06 Jan 2017 14:39:32:  40000000 
INFO  @ Fri, 06 Jan 2017 14:39:34:  41000000 
INFO  @ Fri, 06 Jan 2017 14:39:36:  42000000 
INFO  @ Fri, 06 Jan 2017 14:39:38:  43000000 
INFO  @ Fri, 06 Jan 2017 14:39:39:  44000000 
INFO  @ Fri, 06 Jan 2017 14:39:41:  45000000 
INFO  @ Fri, 06 Jan 2017 14:39:43:  46000000 
INFO  @ Fri, 06 Jan 2017 14:39:45:  47000000 
INFO  @ Fri, 06 Jan 2017 14:39:47:  48000000 
INFO  @ Fri, 06 Jan 2017 14:39:49:  49000000 
INFO  @ Fri, 06 Jan 2017 14:39:50:  50000000 
INFO  @ Fri, 06 Jan 2017 14:39:52: #1 tag size is determined as 59 bps 
INFO  @ Fri, 06 Jan 2017 14:39:52: #1 tag size = 59 
INFO  @ Fri, 06 Jan 2017 14:39:52: #1  total tags in treatment: 5980062 
INFO  @ Fri, 06 Jan 2017 14:39:52: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 14:39:52: #1 finished! 
INFO  @ Fri, 06 Jan 2017 14:39:52: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 14:39:52: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 14:39:52: #2 Use 105 as fragment length 
INFO  @ Fri, 06 Jan 2017 14:39:52: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 14:39:52: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 14:39:52: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 14:42:17: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 14:45:08: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 14:45:20: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 14:45:30: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 14:45:38: Done!

Num	3
ID	task.callpeak_macs2.macs2_rep1_pr2.line_71.id_12
Name	macs2 rep1-pr2
Thread	thread_Root
PID	24241

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

Start	2017-01-06 14:29:21
End	2017-01-06 14:47:54
Elapsed	00:18:33
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/align/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.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/Najafabadi2015Data/hg38Mapping/ZNF136/out/align/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 105 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/align/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 105 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 110

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.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/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/align/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.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/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 143

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.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--------------------
3855 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 14:29:39: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/align/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 105 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/align/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.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  @ Fri, 06 Jan 2017 14:29:39: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 14:29:39: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 14:29:41:  1000000 
INFO  @ Fri, 06 Jan 2017 14:29:44:  2000000 
INFO  @ Fri, 06 Jan 2017 14:29:46:  3000000 
INFO  @ Fri, 06 Jan 2017 14:29:48:  4000000 
INFO  @ Fri, 06 Jan 2017 14:29:50:  5000000 
INFO  @ Fri, 06 Jan 2017 14:29:53: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 14:29:55:  1000000 
INFO  @ Fri, 06 Jan 2017 14:29:57:  2000000 
INFO  @ Fri, 06 Jan 2017 14:29:59:  3000000 
INFO  @ Fri, 06 Jan 2017 14:30:00:  4000000 
INFO  @ Fri, 06 Jan 2017 14:30:02:  5000000 
INFO  @ Fri, 06 Jan 2017 14:30:04:  6000000 
INFO  @ Fri, 06 Jan 2017 14:30:06:  7000000 
INFO  @ Fri, 06 Jan 2017 14:30:08:  8000000 
INFO  @ Fri, 06 Jan 2017 14:30:09:  9000000 
INFO  @ Fri, 06 Jan 2017 14:30:11:  10000000 
INFO  @ Fri, 06 Jan 2017 14:30:13:  11000000 
INFO  @ Fri, 06 Jan 2017 14:30:14:  12000000 
INFO  @ Fri, 06 Jan 2017 14:30:16:  13000000 
INFO  @ Fri, 06 Jan 2017 14:30:18:  14000000 
INFO  @ Fri, 06 Jan 2017 14:30:19:  15000000 
INFO  @ Fri, 06 Jan 2017 14:30:21:  16000000 
INFO  @ Fri, 06 Jan 2017 14:30:23:  17000000 
INFO  @ Fri, 06 Jan 2017 14:30:25:  18000000 
INFO  @ Fri, 06 Jan 2017 14:30:27:  19000000 
INFO  @ Fri, 06 Jan 2017 14:30:28:  20000000 
INFO  @ Fri, 06 Jan 2017 14:30:30:  21000000 
INFO  @ Fri, 06 Jan 2017 14:30:32:  22000000 
INFO  @ Fri, 06 Jan 2017 14:30:33:  23000000 
INFO  @ Fri, 06 Jan 2017 14:30:35:  24000000 
INFO  @ Fri, 06 Jan 2017 14:30:36:  25000000 
INFO  @ Fri, 06 Jan 2017 14:30:38:  26000000 
INFO  @ Fri, 06 Jan 2017 14:30:39:  27000000 
INFO  @ Fri, 06 Jan 2017 14:30:41:  28000000 
INFO  @ Fri, 06 Jan 2017 14:30:42:  29000000 
INFO  @ Fri, 06 Jan 2017 14:30:44:  30000000 
INFO  @ Fri, 06 Jan 2017 14:30:45:  31000000 
INFO  @ Fri, 06 Jan 2017 14:30:47:  32000000 
INFO  @ Fri, 06 Jan 2017 14:30:48:  33000000 
INFO  @ Fri, 06 Jan 2017 14:30:50:  34000000 
INFO  @ Fri, 06 Jan 2017 14:30:51:  35000000 
INFO  @ Fri, 06 Jan 2017 14:30:53:  36000000 
INFO  @ Fri, 06 Jan 2017 14:30:54:  37000000 
INFO  @ Fri, 06 Jan 2017 14:30:56:  38000000 
INFO  @ Fri, 06 Jan 2017 14:30:57:  39000000 
INFO  @ Fri, 06 Jan 2017 14:30:59:  40000000 
INFO  @ Fri, 06 Jan 2017 14:31:01:  41000000 
INFO  @ Fri, 06 Jan 2017 14:31:02:  42000000 
INFO  @ Fri, 06 Jan 2017 14:31:04:  43000000 
INFO  @ Fri, 06 Jan 2017 14:31:05:  44000000 
INFO  @ Fri, 06 Jan 2017 14:31:07:  45000000 
INFO  @ Fri, 06 Jan 2017 14:31:08:  46000000 
INFO  @ Fri, 06 Jan 2017 14:31:10:  47000000 
INFO  @ Fri, 06 Jan 2017 14:31:12:  48000000 
INFO  @ Fri, 06 Jan 2017 14:31:15:  49000000 
INFO  @ Fri, 06 Jan 2017 14:31:16:  50000000 
INFO  @ Fri, 06 Jan 2017 14:31:18: #1 tag size is determined as 65 bps 
INFO  @ Fri, 06 Jan 2017 14:31:18: #1 tag size = 65 
INFO  @ Fri, 06 Jan 2017 14:31:18: #1  total tags in treatment: 5980061 
INFO  @ Fri, 06 Jan 2017 14:31:18: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 14:31:18: #1 finished! 
INFO  @ Fri, 06 Jan 2017 14:31:18: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 14:31:18: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 14:31:18: #2 Use 105 as fragment length 
INFO  @ Fri, 06 Jan 2017 14:31:18: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 14:31:18: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 14:31:18: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 14:34:18: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 14:34:18: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 14:34:18: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 14:34:18: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 14:34:18: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 14:39:04: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 14:39:07: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 14:39:09: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 14:39:10: Done! 
INFO  @ Fri, 06 Jan 2017 14:39:15: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/align/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 105 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/align/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.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  @ Fri, 06 Jan 2017 14:39:15: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 14:39:15: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 14:39:18:  1000000 
INFO  @ Fri, 06 Jan 2017 14:39:20:  2000000 
INFO  @ Fri, 06 Jan 2017 14:39:22:  3000000 
INFO  @ Fri, 06 Jan 2017 14:39:23:  4000000 
INFO  @ Fri, 06 Jan 2017 14:39:25:  5000000 
INFO  @ Fri, 06 Jan 2017 14:39:27: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 14:39:30:  1000000 
INFO  @ Fri, 06 Jan 2017 14:39:32:  2000000 
INFO  @ Fri, 06 Jan 2017 14:39:33:  3000000 
INFO  @ Fri, 06 Jan 2017 14:39:35:  4000000 
INFO  @ Fri, 06 Jan 2017 14:39:37:  5000000 
INFO  @ Fri, 06 Jan 2017 14:39:38:  6000000 
INFO  @ Fri, 06 Jan 2017 14:39:40:  7000000 
INFO  @ Fri, 06 Jan 2017 14:39:41:  8000000 
INFO  @ Fri, 06 Jan 2017 14:39:43:  9000000 
INFO  @ Fri, 06 Jan 2017 14:39:44:  10000000 
INFO  @ Fri, 06 Jan 2017 14:39:46:  11000000 
INFO  @ Fri, 06 Jan 2017 14:39:48:  12000000 
INFO  @ Fri, 06 Jan 2017 14:39:49:  13000000 
INFO  @ Fri, 06 Jan 2017 14:39:51:  14000000 
INFO  @ Fri, 06 Jan 2017 14:39:52:  15000000 
INFO  @ Fri, 06 Jan 2017 14:39:54:  16000000 
INFO  @ Fri, 06 Jan 2017 14:39:56:  17000000 
INFO  @ Fri, 06 Jan 2017 14:39:57:  18000000 
INFO  @ Fri, 06 Jan 2017 14:39:59:  19000000 
INFO  @ Fri, 06 Jan 2017 14:40:00:  20000000 
INFO  @ Fri, 06 Jan 2017 14:40:02:  21000000 
INFO  @ Fri, 06 Jan 2017 14:40:03:  22000000 
INFO  @ Fri, 06 Jan 2017 14:40:05:  23000000 
INFO  @ Fri, 06 Jan 2017 14:40:07:  24000000 
INFO  @ Fri, 06 Jan 2017 14:40:08:  25000000 
INFO  @ Fri, 06 Jan 2017 14:40:10:  26000000 
INFO  @ Fri, 06 Jan 2017 14:40:11:  27000000 
INFO  @ Fri, 06 Jan 2017 14:40:13:  28000000 
INFO  @ Fri, 06 Jan 2017 14:40:14:  29000000 
INFO  @ Fri, 06 Jan 2017 14:40:16:  30000000 
INFO  @ Fri, 06 Jan 2017 14:40:17:  31000000 
INFO  @ Fri, 06 Jan 2017 14:40:19:  32000000 
INFO  @ Fri, 06 Jan 2017 14:40:20:  33000000 
INFO  @ Fri, 06 Jan 2017 14:40:22:  34000000 
INFO  @ Fri, 06 Jan 2017 14:40:24:  35000000 
INFO  @ Fri, 06 Jan 2017 14:40:25:  36000000 
INFO  @ Fri, 06 Jan 2017 14:40:27:  37000000 
INFO  @ Fri, 06 Jan 2017 14:40:28:  38000000 
INFO  @ Fri, 06 Jan 2017 14:40:30:  39000000 
INFO  @ Fri, 06 Jan 2017 14:40:31:  40000000 
INFO  @ Fri, 06 Jan 2017 14:40:33:  41000000 
INFO  @ Fri, 06 Jan 2017 14:40:34:  42000000 
INFO  @ Fri, 06 Jan 2017 14:40:36:  43000000 
INFO  @ Fri, 06 Jan 2017 14:40:37:  44000000 
INFO  @ Fri, 06 Jan 2017 14:40:39:  45000000 
INFO  @ Fri, 06 Jan 2017 14:40:41:  46000000 
INFO  @ Fri, 06 Jan 2017 14:40:43:  47000000 
INFO  @ Fri, 06 Jan 2017 14:40:44:  48000000 
INFO  @ Fri, 06 Jan 2017 14:40:46:  49000000 
INFO  @ Fri, 06 Jan 2017 14:40:47:  50000000 
INFO  @ Fri, 06 Jan 2017 14:40:49: #1 tag size is determined as 65 bps 
INFO  @ Fri, 06 Jan 2017 14:40:49: #1 tag size = 65 
INFO  @ Fri, 06 Jan 2017 14:40:49: #1  total tags in treatment: 5980061 
INFO  @ Fri, 06 Jan 2017 14:40:49: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 14:40:49: #1 finished! 
INFO  @ Fri, 06 Jan 2017 14:40:49: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 14:40:49: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 14:40:49: #2 Use 105 as fragment length 
INFO  @ Fri, 06 Jan 2017 14:40:49: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 14:40:49: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 14:40:49: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 14:43:44: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 14:46:54: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 14:47:07: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 14:47:17: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 14:47:27: Done!

Num	4
ID	task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_13
Name	naive_overlap_thresh
Thread	thread_Root
PID	24325

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

Start	2017-01-06 15:28:20
End	2017-01-06 15:31:08
Elapsed	00:02:47
Timeout	01:00:00
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/spp/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/spp/overlap/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.gz
Dependencies

 
# SYS command. line 61

 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 64

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/spp/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz) | \
			awk 'BEGIN{FS="\t";OFS="\t"} {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/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz) | \
			awk 'BEGIN{FS="\t";OFS="\t"} {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/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/spp/overlap/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/spp/overlap/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/spp/overlap/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz

# SYS command. line 72

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/spp/overlap/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz  | grep -P 'chr[dXY]+[ 	]' | awk 'BEGIN{OFS="	"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/spp/overlap/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/spp/overlap/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz

# SYS command. line 76

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

   
--------------------Stdout--------------------
32513 (process ID) old priority 0, new priority 10
Waiting for 57 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270857.1	1315162	1315386	.	0	.	18.6766223098195	-1	4.24990732993592	112

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270857.1	1315162	1315386	.	0	.	18.6766223098195	-1	4.24990732993592	112

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270857.1	1315158	1315378	.	0	.	21.8036621509929	-1	4.02428037604708	110

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270857.1	1315158	1315378	.	0	.	21.8036621509929	-1	4.02428037604708	110

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/spp/overlap/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
GL000216.2	158585	158805	.	0	.	7.67072263465156	-1	4.37819797044592	110

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/spp/overlap/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
GL000216.2	158585	158805	.	0	.	7.67072263465156	-1	4.37819797044592	110

Num	5
ID	task.callpeak_idr.idr2_rep1_pr.line_73.id_14
Name	idr2 rep1-pr
Thread	thread_Root
PID	24328

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

Start	2017-01-06 15:31:09
End	2017-01-06 15:33:11
Elapsed	00:02:02
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/spp/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/idr/pseudo_reps/rep1/ZNF136_rep1-pr.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/idr/pseudo_reps/rep1/ZNF136_rep1-pr.unthresholded-peaks.txt.png /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/idr/pseudo_reps/rep1/ZNF136_rep1-pr.unthresholded-peaks.txt.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/idr/pseudo_reps/rep1/ZNF136_rep1-pr.IDR0.05.filt.12-col.bed.gz
Dependencies

 
# SYS command. line 75

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq_py3 | wc -l) != "0" ]]; then source activate aquas_chipseq_py3; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 77

 idr --samples /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370900_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370900_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/spp/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/idr/pseudo_reps/rep1/ZNF136_rep1-pr.unthresholded-peaks.txt --rank signal.value --soft-idr-threshold 0.05 \
			--plot --use-best-multisummit-IDR

# SYS command. line 81

 idr_thresh_transformed=$(awk -v p=0.05 'BEGIN{print -log(p)/log(10)}')

# SYS command. line 84

 awk 'BEGIN{OFS="\t"} $12>='"${idr_thresh_transformed}"' {if ($2<0) $2=0; print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,"0"}' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/idr/pseudo_reps/rep1/ZNF136_rep1-pr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/idr/pseudo_reps/rep1/ZNF136_rep1-pr.IDR0.05.13-col.bed.gz

# SYS command. line 87

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/idr/pseudo_reps/rep1/ZNF136_rep1-pr.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/idr/pseudo_reps/rep1/ZNF136_rep1-pr.IDR0.05.narrowPeak.gz

# SYS command. line 88

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/idr/pseudo_reps/rep1/ZNF136_rep1-pr.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/idr/pseudo_reps/rep1/ZNF136_rep1-pr.IDR0.05.12-col.bed.gz

# SYS command. line 90

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/idr/pseudo_reps/rep1/ZNF136_rep1-pr.IDR0.05.13-col.bed.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz | grep -P 'chr[dXY]+[ 	]' | awk 'BEGIN{OFS="	"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/idr/pseudo_reps/rep1/ZNF136_rep1-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 91

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/idr/pseudo_reps/rep1/ZNF136_rep1-pr.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="	"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/idr/pseudo_reps/rep1/ZNF136_rep1-pr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 92

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/idr/pseudo_reps/rep1/ZNF136_rep1-pr.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="	"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/idr/pseudo_reps/rep1/ZNF136_rep1-pr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 94

 gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/idr/pseudo_reps/rep1/ZNF136_rep1-pr.unthresholded-peaks.txt

# SYS command. line 95

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/idr/pseudo_reps/rep1/ZNF136_rep1-pr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/idr/pseudo_reps/rep1/ZNF136_rep1-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 97

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

   
--------------------Stdout--------------------
32617 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Initial parameter values: [0.10 1.00 0.20 0.50]
Final parameter values: [2.37 1.60 0.93 0.48]
Number of reported peaks - 18691/18691 (100.0%)

Number of peaks passing IDR cutoff of 0.05 - 7317/18691 (39.1%)

Num	6
ID	task.callpeak_idr.idr_final_qc.line_219.id_17
Name	idr final qc
Thread	thread_Root
PID	24330

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

Start	2017-01-06 15:33:13
End	2017-01-06 15:34:36
Elapsed	00:01:23
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/idr/pseudo_reps/rep1/ZNF136_rep1-pr.IDR0.05.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/qc/ZNF136_IDR_final.qc
Dependencies

 
# SYS command. line 221

 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 223

 echo -e "Nt\tN1	N2	""Np\tconservative_set\toptimal_set\trescue_ratio\tself_consistency_ratio\treproducibility" > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/qc/ZNF136_IDR_final.qc

# SYS command. line 224

 echo -e "0\t485	0	""0\tN/A\tN/A\tNaN\t1.0\t1" >> /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/qc/ZNF136_IDR_final.qc

# SYS command. line 226

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

   
--------------------Stdout--------------------
9478 (process ID) old priority 0, new priority 10
Waiting for 60 seconds.

Num	7
ID	task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_18
Name	blacklist_filter peak 1
Thread	thread_Root
PID	31222

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

Start	2017-01-06 15:34:38
End	2017-01-06 15:35:46
Elapsed	00:01:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/spp/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/spp/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.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/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/spp/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.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/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/spp/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.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--------------------
31226 (process ID) old priority 0, new priority 10
Waiting for 59 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/spp/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270857.1	1315164	1315384	.	0	.	40.6821764054698	-1	4.37819797044592	110

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/spp/rep1/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270857.1	1315164	1315384	.	0	.	40.6821764054698	-1	4.37819797044592	110

Num	8
ID	task.report.peak2hammock.line_412.id_19
Name	peak2hammock
Thread	thread_Root
PID	35400

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

Start	2017-01-06 15:35:47
End	2017-01-06 15:35:56
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/spp/overlap/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/spp/overlap/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.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/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/spp/overlap/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/spp/overlap/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp

# SYS command. line 417

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/spp/overlap/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/spp/overlap/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/spp/overlap/SRR1370900_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp

   
--------------------Stdout--------------------
35404 (process ID) old priority 0, new priority 10

Num	9
ID	task.report.peak2hammock.line_412.id_20
Name	peak2hammock
Thread	thread_Root
PID	36020

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

Start	2017-01-06 15:35:57
End	2017-01-06 15:36:06
Elapsed	00:00:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/idr/pseudo_reps/rep1/ZNF136_rep1-pr.IDR0.05.filt.12-col.bed.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/idr/pseudo_reps/rep1/ZNF136_rep1-pr.IDR0.05.filt.12-col.bed.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/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/idr/pseudo_reps/rep1/ZNF136_rep1-pr.IDR0.05.filt.12-col.bed.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/idr/pseudo_reps/rep1/ZNF136_rep1-pr.IDR0.05.filt.12-col.bed.tmp

# SYS command. line 417

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/idr/pseudo_reps/rep1/ZNF136_rep1-pr.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/idr/pseudo_reps/rep1/ZNF136_rep1-pr.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/peak/idr/pseudo_reps/rep1/ZNF136_rep1-pr.IDR0.05.filt.12-col.bed.tmp

   
--------------------Stdout--------------------
36024 (process ID) old priority 0, new priority 10

Num	10
ID	task.graphviz.report.line_97.id_21
Name	report
Thread	thread_Root
PID	36607

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

Start	2017-01-06 15:36:07
End	2017-01-06 15:36:15
Elapsed	00:00:08
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/Najafabadi2015Data/hg38Mapping/ZNF136/out/report/ZNF136_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/report/ZNF136_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/report/ZNF136_workflow.svg" # to suppress dot font error (exit code=1)

   
--------------------Stdout--------------------
36611 (process ID) old priority 0, new priority 10

Type	Name	Value
string	_	/usr/bin/bds
string	_LMFILES_	/software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/ascp/3.5.6:/software/modulefiles/sratoolkit/2.5.2:/software/modulefiles/homer/default
bool	allowEmpty	false
string[]	args	[-title, ZNF136, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF136/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF136/out/align/rep1/SRR1370900_1.bam, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz, -final_stage, idr, $]
string	ASCPKEY	/software/ascp/etc/asperaweb_id_dsa.openssh
bool	canFail	false
int	cpus	-1
int	cpusLocal	56
int	day	86400
string	DEEPLIFT_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift
string	DERBY_HOME	/usr/lib/jvm/java-8-oracle/db
string	DISPLAY	localhost:10.0
real	E	2.718281828459045
string	ENHANCER_SCRIPTS_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/
int	G	1073741824
string	HOME	/users/imk1/
int	hour	3600
string	J2REDIR	/usr/lib/jvm/java-8-oracle/jre
string	J2SDKDIR	/usr/lib/jvm/java-8-oracle
string	JAVA_HOME	/usr/lib/jvm/java-8-oracle
int	K	1024
string	KERAS_DIR	/users/imk1/.local/lib/python2.7/site-packages/keras/
string	KRB5CCNAME	FILE:/tmp/krb5cc_1048_veRoBQ
string	LANG	en_US.UTF-8
string	LOADEDMODULES	modsappsdir/modsappsdir:ascp/3.5.6:sratoolkit/2.5.2:homer/default
string	LOGNAME	imk1
int	M	1048576
string	MAIL	/var/mail/imk1
int	mem	-1
int	minute	60
string	MODULE_VERSION	3.2.10
string	MODULE_VERSION_STACK	3.2.10
string	MODULEPATH	/usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$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/ucsc_tools/3.0.9:/software/weblogo/2.8.2:/software/homer/default/bin:/software/sratoolkit/2.5.2/bin/:/software/ascp/:/users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/srv/scratch/imk1/TFBindingPredictionProject/src/R-3.2.3/bin:/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/Najafabadi2015Data/hg38Mapping/ZNF136
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/Najafabadi2015Data/hg38Mapping/ZNF136
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 43899 22
string	SSH_CONNECTION	171.65.77.8 43899 171.65.76.63 22
string	SSH_TTY	/dev/pts/0
string	STY	29206.ZNF136.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	XDG_RUNTIME_DIR	/run/user/1048
string	XDG_SESSION_ID	1080
string	XFILESEARCHPATH	/usr/dt/app-defaults/%L/Dt

BigDataScript report: chipseq.bds

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