Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20170103_142412_861
Start time	2017-01-03 14:24:12
Run time	19:51:41.837
Tasks executed	10
Tasks failed	0
Tasks failed names
Arguments*	[-title, YY1, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/YY1/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/align/rep1/SRR1370875_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.20170103_142412_861/task.callpeak_macs2.macs2_rep1.line_71.id_10 chipseq.bds.20170103_142412_861/task.callpeak_macs2.macs2_rep1_pr1.line_71.id_11 chipseq.bds.20170103_142412_861/task.callpeak_macs2.macs2_rep1_pr2.line_71.id_12 chipseq.bds.20170103_142412_861/task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_13 chipseq.bds.20170103_142412_861/task.callpeak_idr.idr2_rep1_pr.line_73.id_14 chipseq.bds.20170103_142412_861/task.callpeak_idr.idr_final_qc.line_219.id_17 chipseq.bds.20170103_142412_861/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_18 chipseq.bds.20170103_142412_861/task.report.peak2hammock.line_412.id_19 chipseq.bds.20170103_142412_861/task.report.peak2hammock.line_412.id_20 chipseq.bds.20170103_142412_861/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	22343

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

Start	2017-01-03 14:24:19
End	2017-01-03 21:44:37
Elapsed	07:20:17
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/align/rep1/SRR1370875_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/YY1/out/peak/macs2/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/signal/macs2/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/signal/macs2/rep1/SRR1370875_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/YY1/out/align/rep1/SRR1370875_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/YY1/out/peak/macs2/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/rep1/SRR1370875_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/YY1/out/peak/macs2/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/rep1/SRR1370875_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/YY1/out/align/rep1/SRR1370875_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/YY1/out/peak/macs2/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/rep1/SRR1370875_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/YY1/out/peak/macs2/rep1/SRR1370875_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/YY1/out/peak/macs2/rep1/SRR1370875_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/YY1/out/peak/macs2/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/rep1/SRR1370875_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/YY1/out/peak/macs2/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/rep1/SRR1370875_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/YY1/out/peak/macs2/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/rep1 -o "SRR1370875_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/YY1/out/peak/macs2/rep1/SRR1370875_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/YY1/out/peak/macs2/rep1/SRR1370875_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/YY1/out/peak/macs2/rep1/SRR1370875_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/YY1/out/peak/macs2/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/rep1/SRR1370875_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/YY1/out/peak/macs2/rep1/SRR1370875_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/YY1/out/signal/macs2/rep1/SRR1370875_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/YY1/out/peak/macs2/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/rep1/SRR1370875_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/YY1/out/align/rep1/SRR1370875_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/YY1/out/peak/macs2/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/rep1 -o "SRR1370875_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/YY1/out/peak/macs2/rep1/SRR1370875_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/YY1/out/peak/macs2/rep1/SRR1370875_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/YY1/out/peak/macs2/rep1/SRR1370875_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/YY1/out/peak/macs2/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/rep1/SRR1370875_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/YY1/out/peak/macs2/rep1/SRR1370875_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/YY1/out/signal/macs2/rep1/SRR1370875_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/YY1/out/peak/macs2/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/rep1/SRR1370875_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/YY1/out/peak/macs2/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/rep1/SRR1370875_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--------------------
23644 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Tue, 03 Jan 2017 14:31:27: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/align/rep1/SRR1370875_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/YY1/out/peak/macs2/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/align/rep1/SRR1370875_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  @ Tue, 03 Jan 2017 14:31:27: #1 read tag files... 
INFO  @ Tue, 03 Jan 2017 14:31:27: #1 read treatment tags... 
INFO  @ Tue, 03 Jan 2017 14:31:35:  1000000 
INFO  @ Tue, 03 Jan 2017 14:31:42:  2000000 
INFO  @ Tue, 03 Jan 2017 14:31:50:  3000000 
INFO  @ Tue, 03 Jan 2017 14:31:58:  4000000 
INFO  @ Tue, 03 Jan 2017 14:32:06:  5000000 
INFO  @ Tue, 03 Jan 2017 14:32:14:  6000000 
INFO  @ Tue, 03 Jan 2017 14:32:22:  7000000 
INFO  @ Tue, 03 Jan 2017 14:32:30:  8000000 
INFO  @ Tue, 03 Jan 2017 14:32:37:  9000000 
INFO  @ Tue, 03 Jan 2017 14:32:43:  10000000 
INFO  @ Tue, 03 Jan 2017 14:32:49:  11000000 
INFO  @ Tue, 03 Jan 2017 14:32:56:  12000000 
INFO  @ Tue, 03 Jan 2017 14:33:02:  13000000 
INFO  @ Tue, 03 Jan 2017 14:33:08:  14000000 
INFO  @ Tue, 03 Jan 2017 14:33:14:  15000000 
INFO  @ Tue, 03 Jan 2017 14:33:17: #1.2 read input tags... 
INFO  @ Tue, 03 Jan 2017 14:33:23:  1000000 
INFO  @ Tue, 03 Jan 2017 14:33:29:  2000000 
INFO  @ Tue, 03 Jan 2017 14:33:35:  3000000 
INFO  @ Tue, 03 Jan 2017 14:33:41:  4000000 
INFO  @ Tue, 03 Jan 2017 14:33:47:  5000000 
INFO  @ Tue, 03 Jan 2017 14:33:53:  6000000 
INFO  @ Tue, 03 Jan 2017 14:33:59:  7000000 
INFO  @ Tue, 03 Jan 2017 14:34:05:  8000000 
INFO  @ Tue, 03 Jan 2017 14:34:11:  9000000 
INFO  @ Tue, 03 Jan 2017 14:34:17:  10000000 
INFO  @ Tue, 03 Jan 2017 14:34:23:  11000000 
INFO  @ Tue, 03 Jan 2017 14:34:29:  12000000 
INFO  @ Tue, 03 Jan 2017 14:34:35:  13000000 
INFO  @ Tue, 03 Jan 2017 14:34:41:  14000000 
INFO  @ Tue, 03 Jan 2017 14:34:47:  15000000 
INFO  @ Tue, 03 Jan 2017 14:34:53:  16000000 
INFO  @ Tue, 03 Jan 2017 14:34:59:  17000000 
INFO  @ Tue, 03 Jan 2017 14:35:05:  18000000 
INFO  @ Tue, 03 Jan 2017 14:35:12:  19000000 
INFO  @ Tue, 03 Jan 2017 14:35:18:  20000000 
INFO  @ Tue, 03 Jan 2017 14:35:24:  21000000 
INFO  @ Tue, 03 Jan 2017 14:35:30:  22000000 
INFO  @ Tue, 03 Jan 2017 14:35:36:  23000000 
INFO  @ Tue, 03 Jan 2017 14:35:42:  24000000 
INFO  @ Tue, 03 Jan 2017 14:35:48:  25000000 
INFO  @ Tue, 03 Jan 2017 14:35:54:  26000000 
INFO  @ Tue, 03 Jan 2017 14:36:00:  27000000 
INFO  @ Tue, 03 Jan 2017 14:36:06:  28000000 
INFO  @ Tue, 03 Jan 2017 14:36:12:  29000000 
INFO  @ Tue, 03 Jan 2017 14:36:19:  30000000 
INFO  @ Tue, 03 Jan 2017 14:36:25:  31000000 
INFO  @ Tue, 03 Jan 2017 14:36:31:  32000000 
INFO  @ Tue, 03 Jan 2017 14:36:37:  33000000 
INFO  @ Tue, 03 Jan 2017 14:36:43:  34000000 
INFO  @ Tue, 03 Jan 2017 14:36:49:  35000000 
INFO  @ Tue, 03 Jan 2017 14:36:56:  36000000 
INFO  @ Tue, 03 Jan 2017 14:37:02:  37000000 
INFO  @ Tue, 03 Jan 2017 14:37:08:  38000000 
INFO  @ Tue, 03 Jan 2017 14:37:14:  39000000 
INFO  @ Tue, 03 Jan 2017 14:37:20:  40000000 
INFO  @ Tue, 03 Jan 2017 14:37:26:  41000000 
INFO  @ Tue, 03 Jan 2017 14:37:32:  42000000 
INFO  @ Tue, 03 Jan 2017 14:37:38:  43000000 
INFO  @ Tue, 03 Jan 2017 14:37:44:  44000000 
INFO  @ Tue, 03 Jan 2017 14:37:50:  45000000 
INFO  @ Tue, 03 Jan 2017 14:37:56:  46000000 
INFO  @ Tue, 03 Jan 2017 14:38:02:  47000000 
INFO  @ Tue, 03 Jan 2017 14:38:08:  48000000 
INFO  @ Tue, 03 Jan 2017 14:38:14:  49000000 
INFO  @ Tue, 03 Jan 2017 14:38:20:  50000000 
INFO  @ Tue, 03 Jan 2017 14:38:24: #1 tag size is determined as 69 bps 
INFO  @ Tue, 03 Jan 2017 14:38:24: #1 tag size = 69 
INFO  @ Tue, 03 Jan 2017 14:38:24: #1  total tags in treatment: 15415343 
INFO  @ Tue, 03 Jan 2017 14:38:24: #1  total tags in control: 50000000 
INFO  @ Tue, 03 Jan 2017 14:38:24: #1 finished! 
INFO  @ Tue, 03 Jan 2017 14:38:24: #2 Build Peak Model... 
INFO  @ Tue, 03 Jan 2017 14:38:24: #2 Skipped... 
INFO  @ Tue, 03 Jan 2017 14:38:24: #2 Use 145 as fragment length 
INFO  @ Tue, 03 Jan 2017 14:38:24: #3 Call peaks... 
INFO  @ Tue, 03 Jan 2017 14:38:24: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Tue, 03 Jan 2017 14:38:24: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 03 Jan 2017 15:09:33: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 03 Jan 2017 15:09:33: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Tue, 03 Jan 2017 15:09:33: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Tue, 03 Jan 2017 15:09:33: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 03 Jan 2017 15:09:33: #3 Call peaks for each chromosome... 
INFO  @ Tue, 03 Jan 2017 16:26:06: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Tue, 03 Jan 2017 16:26:11: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Tue, 03 Jan 2017 16:26:14: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Tue, 03 Jan 2017 16:26:17: Done! 
INFO  @ Tue, 03 Jan 2017 16:26:24: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/align/rep1/SRR1370875_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/YY1/out/peak/macs2/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/align/rep1/SRR1370875_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  @ Tue, 03 Jan 2017 16:26:24: #1 read tag files... 
INFO  @ Tue, 03 Jan 2017 16:26:24: #1 read treatment tags... 
INFO  @ Tue, 03 Jan 2017 16:26:33:  1000000 
INFO  @ Tue, 03 Jan 2017 16:26:40:  2000000 
INFO  @ Tue, 03 Jan 2017 16:26:48:  3000000 
INFO  @ Tue, 03 Jan 2017 16:26:56:  4000000 
INFO  @ Tue, 03 Jan 2017 16:27:04:  5000000 
INFO  @ Tue, 03 Jan 2017 16:27:12:  6000000 
INFO  @ Tue, 03 Jan 2017 16:27:20:  7000000 
INFO  @ Tue, 03 Jan 2017 16:27:28:  8000000 
INFO  @ Tue, 03 Jan 2017 16:27:36:  9000000 
INFO  @ Tue, 03 Jan 2017 16:27:44:  10000000 
INFO  @ Tue, 03 Jan 2017 16:27:52:  11000000 
INFO  @ Tue, 03 Jan 2017 16:28:00:  12000000 
INFO  @ Tue, 03 Jan 2017 16:28:08:  13000000 
INFO  @ Tue, 03 Jan 2017 16:28:15:  14000000 
INFO  @ Tue, 03 Jan 2017 16:28:23:  15000000 
INFO  @ Tue, 03 Jan 2017 16:28:27: #1.2 read input tags... 
INFO  @ Tue, 03 Jan 2017 16:28:35:  1000000 
INFO  @ Tue, 03 Jan 2017 16:28:43:  2000000 
INFO  @ Tue, 03 Jan 2017 16:28:52:  3000000 
INFO  @ Tue, 03 Jan 2017 16:29:00:  4000000 
INFO  @ Tue, 03 Jan 2017 16:29:08:  5000000 
INFO  @ Tue, 03 Jan 2017 16:29:16:  6000000 
INFO  @ Tue, 03 Jan 2017 16:29:24:  7000000 
INFO  @ Tue, 03 Jan 2017 16:29:32:  8000000 
INFO  @ Tue, 03 Jan 2017 16:29:40:  9000000 
INFO  @ Tue, 03 Jan 2017 16:29:48:  10000000 
INFO  @ Tue, 03 Jan 2017 16:29:56:  11000000 
INFO  @ Tue, 03 Jan 2017 16:30:04:  12000000 
INFO  @ Tue, 03 Jan 2017 16:30:12:  13000000 
INFO  @ Tue, 03 Jan 2017 16:30:20:  14000000 
INFO  @ Tue, 03 Jan 2017 16:30:29:  15000000 
INFO  @ Tue, 03 Jan 2017 16:30:37:  16000000 
INFO  @ Tue, 03 Jan 2017 16:30:45:  17000000 
INFO  @ Tue, 03 Jan 2017 16:30:53:  18000000 
INFO  @ Tue, 03 Jan 2017 16:31:02:  19000000 
INFO  @ Tue, 03 Jan 2017 16:31:10:  20000000 
INFO  @ Tue, 03 Jan 2017 16:31:18:  21000000 
INFO  @ Tue, 03 Jan 2017 16:31:26:  22000000 
INFO  @ Tue, 03 Jan 2017 16:31:35:  23000000 
INFO  @ Tue, 03 Jan 2017 16:31:43:  24000000 
INFO  @ Tue, 03 Jan 2017 16:31:51:  25000000 
INFO  @ Tue, 03 Jan 2017 16:31:59:  26000000 
INFO  @ Tue, 03 Jan 2017 16:32:07:  27000000 
INFO  @ Tue, 03 Jan 2017 16:32:15:  28000000 
INFO  @ Tue, 03 Jan 2017 16:32:23:  29000000 
INFO  @ Tue, 03 Jan 2017 16:32:31:  30000000 
INFO  @ Tue, 03 Jan 2017 16:32:39:  31000000 
INFO  @ Tue, 03 Jan 2017 16:32:47:  32000000 
INFO  @ Tue, 03 Jan 2017 16:32:55:  33000000 
INFO  @ Tue, 03 Jan 2017 16:33:04:  34000000 
INFO  @ Tue, 03 Jan 2017 16:33:12:  35000000 
INFO  @ Tue, 03 Jan 2017 16:33:20:  36000000 
INFO  @ Tue, 03 Jan 2017 16:33:28:  37000000 
INFO  @ Tue, 03 Jan 2017 16:33:37:  38000000 
INFO  @ Tue, 03 Jan 2017 16:33:45:  39000000 
INFO  @ Tue, 03 Jan 2017 16:33:53:  40000000 
INFO  @ Tue, 03 Jan 2017 16:34:01:  41000000 
INFO  @ Tue, 03 Jan 2017 16:34:10:  42000000 
INFO  @ Tue, 03 Jan 2017 16:34:18:  43000000 
INFO  @ Tue, 03 Jan 2017 16:34:25:  44000000 
INFO  @ Tue, 03 Jan 2017 16:34:33:  45000000 
INFO  @ Tue, 03 Jan 2017 16:34:40:  46000000 
INFO  @ Tue, 03 Jan 2017 16:34:47:  47000000 
INFO  @ Tue, 03 Jan 2017 16:34:53:  48000000 
INFO  @ Tue, 03 Jan 2017 16:35:00:  49000000 
INFO  @ Tue, 03 Jan 2017 16:35:06:  50000000 
INFO  @ Tue, 03 Jan 2017 16:35:09: #1 tag size is determined as 69 bps 
INFO  @ Tue, 03 Jan 2017 16:35:09: #1 tag size = 69 
INFO  @ Tue, 03 Jan 2017 16:35:09: #1  total tags in treatment: 15415343 
INFO  @ Tue, 03 Jan 2017 16:35:09: #1  total tags in control: 50000000 
INFO  @ Tue, 03 Jan 2017 16:35:09: #1 finished! 
INFO  @ Tue, 03 Jan 2017 16:35:09: #2 Build Peak Model... 
INFO  @ Tue, 03 Jan 2017 16:35:09: #2 Skipped... 
INFO  @ Tue, 03 Jan 2017 16:35:09: #2 Use 145 as fragment length 
INFO  @ Tue, 03 Jan 2017 16:35:09: #3 Call peaks... 
INFO  @ Tue, 03 Jan 2017 16:35:09: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Tue, 03 Jan 2017 16:35:09: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 03 Jan 2017 17:05:37: #3 Call peaks for each chromosome... 
INFO  @ Tue, 03 Jan 2017 17:17:04: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Tue, 03 Jan 2017 17:19:04: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Tue, 03 Jan 2017 17:20:19: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Tue, 03 Jan 2017 17:22:01: Done! 
INFO  @ Tue, 03 Jan 2017 17:24:34: Read and build treatment bedGraph... 
INFO  @ Tue, 03 Jan 2017 17:29:34: Read and build control bedGraph... 
INFO  @ Tue, 03 Jan 2017 17:42:18: Build scoreTrackII... 
INFO  @ Tue, 03 Jan 2017 17:45:38: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Tue, 03 Jan 2017 18:12:49: Write bedGraph of scores... 
INFO  @ Tue, 03 Jan 2017 18:26:45: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_FE.bdg'! 
INFO  @ Tue, 03 Jan 2017 19:36:27: Read and build treatment bedGraph... 
INFO  @ Tue, 03 Jan 2017 19:38:39: Read and build control bedGraph... 
INFO  @ Tue, 03 Jan 2017 19:49:34: Build scoreTrackII... 
INFO  @ Tue, 03 Jan 2017 19:57:08: Values in your input bedGraph files will be multiplied by 15.415343 ... 
INFO  @ Tue, 03 Jan 2017 20:15:49: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Tue, 03 Jan 2017 20:17:38: Write bedGraph of scores... 
INFO  @ Tue, 03 Jan 2017 20:38:23: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/rep1/SRR1370875_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	22344

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

Start	2017-01-03 14:24:21
End	2017-01-03 17:20:52
Elapsed	02:56:31
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/align/pseudo_reps/rep1/pr1/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_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/YY1/out/align/pseudo_reps/rep1/pr1/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_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/YY1/out/align/pseudo_reps/rep1/pr1/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_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/YY1/out/align/pseudo_reps/rep1/pr1/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_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--------------------
23645 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Tue, 03 Jan 2017 14:31:27: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/align/pseudo_reps/rep1/pr1/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/align/pseudo_reps/rep1/pr1/SRR1370875_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  @ Tue, 03 Jan 2017 14:31:27: #1 read tag files... 
INFO  @ Tue, 03 Jan 2017 14:31:27: #1 read treatment tags... 
INFO  @ Tue, 03 Jan 2017 14:31:35:  1000000 
INFO  @ Tue, 03 Jan 2017 14:31:43:  2000000 
INFO  @ Tue, 03 Jan 2017 14:31:51:  3000000 
INFO  @ Tue, 03 Jan 2017 14:31:59:  4000000 
INFO  @ Tue, 03 Jan 2017 14:32:07:  5000000 
INFO  @ Tue, 03 Jan 2017 14:32:15:  6000000 
INFO  @ Tue, 03 Jan 2017 14:32:22:  7000000 
INFO  @ Tue, 03 Jan 2017 14:32:29: #1.2 read input tags... 
INFO  @ Tue, 03 Jan 2017 14:32:36:  1000000 
INFO  @ Tue, 03 Jan 2017 14:32:42:  2000000 
INFO  @ Tue, 03 Jan 2017 14:32:49:  3000000 
INFO  @ Tue, 03 Jan 2017 14:32:55:  4000000 
INFO  @ Tue, 03 Jan 2017 14:33:01:  5000000 
INFO  @ Tue, 03 Jan 2017 14:33:07:  6000000 
INFO  @ Tue, 03 Jan 2017 14:33:13:  7000000 
INFO  @ Tue, 03 Jan 2017 14:33:20:  8000000 
INFO  @ Tue, 03 Jan 2017 14:33:26:  9000000 
INFO  @ Tue, 03 Jan 2017 14:33:32:  10000000 
INFO  @ Tue, 03 Jan 2017 14:33:38:  11000000 
INFO  @ Tue, 03 Jan 2017 14:33:44:  12000000 
INFO  @ Tue, 03 Jan 2017 14:33:50:  13000000 
INFO  @ Tue, 03 Jan 2017 14:33:56:  14000000 
INFO  @ Tue, 03 Jan 2017 14:34:02:  15000000 
INFO  @ Tue, 03 Jan 2017 14:34:08:  16000000 
INFO  @ Tue, 03 Jan 2017 14:34:14:  17000000 
INFO  @ Tue, 03 Jan 2017 14:34:20:  18000000 
INFO  @ Tue, 03 Jan 2017 14:34:27:  19000000 
INFO  @ Tue, 03 Jan 2017 14:34:33:  20000000 
INFO  @ Tue, 03 Jan 2017 14:34:39:  21000000 
INFO  @ Tue, 03 Jan 2017 14:34:45:  22000000 
INFO  @ Tue, 03 Jan 2017 14:34:51:  23000000 
INFO  @ Tue, 03 Jan 2017 14:34:57:  24000000 
INFO  @ Tue, 03 Jan 2017 14:35:03:  25000000 
INFO  @ Tue, 03 Jan 2017 14:35:09:  26000000 
INFO  @ Tue, 03 Jan 2017 14:35:15:  27000000 
INFO  @ Tue, 03 Jan 2017 14:35:21:  28000000 
INFO  @ Tue, 03 Jan 2017 14:35:28:  29000000 
INFO  @ Tue, 03 Jan 2017 14:35:34:  30000000 
INFO  @ Tue, 03 Jan 2017 14:35:40:  31000000 
INFO  @ Tue, 03 Jan 2017 14:35:46:  32000000 
INFO  @ Tue, 03 Jan 2017 14:35:53:  33000000 
INFO  @ Tue, 03 Jan 2017 14:35:59:  34000000 
INFO  @ Tue, 03 Jan 2017 14:36:05:  35000000 
INFO  @ Tue, 03 Jan 2017 14:36:11:  36000000 
INFO  @ Tue, 03 Jan 2017 14:36:18:  37000000 
INFO  @ Tue, 03 Jan 2017 14:36:24:  38000000 
INFO  @ Tue, 03 Jan 2017 14:36:30:  39000000 
INFO  @ Tue, 03 Jan 2017 14:36:36:  40000000 
INFO  @ Tue, 03 Jan 2017 14:36:42:  41000000 
INFO  @ Tue, 03 Jan 2017 14:36:48:  42000000 
INFO  @ Tue, 03 Jan 2017 14:36:55:  43000000 
INFO  @ Tue, 03 Jan 2017 14:37:01:  44000000 
INFO  @ Tue, 03 Jan 2017 14:37:07:  45000000 
INFO  @ Tue, 03 Jan 2017 14:37:13:  46000000 
INFO  @ Tue, 03 Jan 2017 14:37:19:  47000000 
INFO  @ Tue, 03 Jan 2017 14:37:26:  48000000 
INFO  @ Tue, 03 Jan 2017 14:37:32:  49000000 
INFO  @ Tue, 03 Jan 2017 14:37:38:  50000000 
INFO  @ Tue, 03 Jan 2017 14:37:41: #1 tag size is determined as 68 bps 
INFO  @ Tue, 03 Jan 2017 14:37:41: #1 tag size = 68 
INFO  @ Tue, 03 Jan 2017 14:37:41: #1  total tags in treatment: 7707672 
INFO  @ Tue, 03 Jan 2017 14:37:41: #1  total tags in control: 50000000 
INFO  @ Tue, 03 Jan 2017 14:37:41: #1 finished! 
INFO  @ Tue, 03 Jan 2017 14:37:41: #2 Build Peak Model... 
INFO  @ Tue, 03 Jan 2017 14:37:41: #2 Skipped... 
INFO  @ Tue, 03 Jan 2017 14:37:41: #2 Use 145 as fragment length 
INFO  @ Tue, 03 Jan 2017 14:37:41: #3 Call peaks... 
INFO  @ Tue, 03 Jan 2017 14:37:41: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Tue, 03 Jan 2017 14:37:41: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 03 Jan 2017 15:09:20: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 03 Jan 2017 15:09:20: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Tue, 03 Jan 2017 15:09:20: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Tue, 03 Jan 2017 15:09:20: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 03 Jan 2017 15:09:20: #3 Call peaks for each chromosome... 
INFO  @ Tue, 03 Jan 2017 16:24:22: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Tue, 03 Jan 2017 16:24:33: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Tue, 03 Jan 2017 16:24:38: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Tue, 03 Jan 2017 16:24:42: Done! 
INFO  @ Tue, 03 Jan 2017 16:24:57: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/align/pseudo_reps/rep1/pr1/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/align/pseudo_reps/rep1/pr1/SRR1370875_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  @ Tue, 03 Jan 2017 16:24:57: #1 read tag files... 
INFO  @ Tue, 03 Jan 2017 16:24:57: #1 read treatment tags... 
INFO  @ Tue, 03 Jan 2017 16:25:10:  1000000 
INFO  @ Tue, 03 Jan 2017 16:25:18:  2000000 
INFO  @ Tue, 03 Jan 2017 16:25:26:  3000000 
INFO  @ Tue, 03 Jan 2017 16:25:34:  4000000 
INFO  @ Tue, 03 Jan 2017 16:25:41:  5000000 
INFO  @ Tue, 03 Jan 2017 16:25:49:  6000000 
INFO  @ Tue, 03 Jan 2017 16:25:58:  7000000 
INFO  @ Tue, 03 Jan 2017 16:26:06: #1.2 read input tags... 
INFO  @ Tue, 03 Jan 2017 16:26:14:  1000000 
INFO  @ Tue, 03 Jan 2017 16:26:22:  2000000 
INFO  @ Tue, 03 Jan 2017 16:26:30:  3000000 
INFO  @ Tue, 03 Jan 2017 16:26:37:  4000000 
INFO  @ Tue, 03 Jan 2017 16:26:45:  5000000 
INFO  @ Tue, 03 Jan 2017 16:26:53:  6000000 
INFO  @ Tue, 03 Jan 2017 16:27:01:  7000000 
INFO  @ Tue, 03 Jan 2017 16:27:09:  8000000 
INFO  @ Tue, 03 Jan 2017 16:27:16:  9000000 
INFO  @ Tue, 03 Jan 2017 16:27:24:  10000000 
INFO  @ Tue, 03 Jan 2017 16:27:32:  11000000 
INFO  @ Tue, 03 Jan 2017 16:27:40:  12000000 
INFO  @ Tue, 03 Jan 2017 16:27:48:  13000000 
INFO  @ Tue, 03 Jan 2017 16:27:56:  14000000 
INFO  @ Tue, 03 Jan 2017 16:28:04:  15000000 
INFO  @ Tue, 03 Jan 2017 16:28:12:  16000000 
INFO  @ Tue, 03 Jan 2017 16:28:20:  17000000 
INFO  @ Tue, 03 Jan 2017 16:28:28:  18000000 
INFO  @ Tue, 03 Jan 2017 16:28:36:  19000000 
INFO  @ Tue, 03 Jan 2017 16:28:44:  20000000 
INFO  @ Tue, 03 Jan 2017 16:28:53:  21000000 
INFO  @ Tue, 03 Jan 2017 16:29:01:  22000000 
INFO  @ Tue, 03 Jan 2017 16:29:09:  23000000 
INFO  @ Tue, 03 Jan 2017 16:29:17:  24000000 
INFO  @ Tue, 03 Jan 2017 16:29:25:  25000000 
INFO  @ Tue, 03 Jan 2017 16:29:33:  26000000 
INFO  @ Tue, 03 Jan 2017 16:29:41:  27000000 
INFO  @ Tue, 03 Jan 2017 16:29:50:  28000000 
INFO  @ Tue, 03 Jan 2017 16:29:58:  29000000 
INFO  @ Tue, 03 Jan 2017 16:30:06:  30000000 
INFO  @ Tue, 03 Jan 2017 16:30:14:  31000000 
INFO  @ Tue, 03 Jan 2017 16:30:22:  32000000 
INFO  @ Tue, 03 Jan 2017 16:30:30:  33000000 
INFO  @ Tue, 03 Jan 2017 16:30:39:  34000000 
INFO  @ Tue, 03 Jan 2017 16:30:47:  35000000 
INFO  @ Tue, 03 Jan 2017 16:30:55:  36000000 
INFO  @ Tue, 03 Jan 2017 16:31:03:  37000000 
INFO  @ Tue, 03 Jan 2017 16:31:11:  38000000 
INFO  @ Tue, 03 Jan 2017 16:31:19:  39000000 
INFO  @ Tue, 03 Jan 2017 16:31:27:  40000000 
INFO  @ Tue, 03 Jan 2017 16:31:35:  41000000 
INFO  @ Tue, 03 Jan 2017 16:31:43:  42000000 
INFO  @ Tue, 03 Jan 2017 16:31:52:  43000000 
INFO  @ Tue, 03 Jan 2017 16:32:00:  44000000 
INFO  @ Tue, 03 Jan 2017 16:32:08:  45000000 
INFO  @ Tue, 03 Jan 2017 16:32:16:  46000000 
INFO  @ Tue, 03 Jan 2017 16:32:24:  47000000 
INFO  @ Tue, 03 Jan 2017 16:32:32:  48000000 
INFO  @ Tue, 03 Jan 2017 16:32:41:  49000000 
INFO  @ Tue, 03 Jan 2017 16:32:49:  50000000 
INFO  @ Tue, 03 Jan 2017 16:32:53: #1 tag size is determined as 68 bps 
INFO  @ Tue, 03 Jan 2017 16:32:53: #1 tag size = 68 
INFO  @ Tue, 03 Jan 2017 16:32:53: #1  total tags in treatment: 7707672 
INFO  @ Tue, 03 Jan 2017 16:32:53: #1  total tags in control: 50000000 
INFO  @ Tue, 03 Jan 2017 16:32:53: #1 finished! 
INFO  @ Tue, 03 Jan 2017 16:32:53: #2 Build Peak Model... 
INFO  @ Tue, 03 Jan 2017 16:32:53: #2 Skipped... 
INFO  @ Tue, 03 Jan 2017 16:32:53: #2 Use 145 as fragment length 
INFO  @ Tue, 03 Jan 2017 16:32:53: #3 Call peaks... 
INFO  @ Tue, 03 Jan 2017 16:32:53: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Tue, 03 Jan 2017 16:32:53: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 03 Jan 2017 16:59:16: #3 Call peaks for each chromosome... 
INFO  @ Tue, 03 Jan 2017 17:15:44: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Tue, 03 Jan 2017 17:16:19: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Tue, 03 Jan 2017 17:16:46: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370875_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Tue, 03 Jan 2017 17:17:18: Done!

Num	3
ID	task.callpeak_macs2.macs2_rep1_pr2.line_71.id_12
Name	macs2 rep1-pr2
Thread	thread_Root
PID	22345

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

Start	2017-01-03 14:24:22
End	2017-01-03 15:36:15
Elapsed	01:11:53
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/align/pseudo_reps/rep1/pr2/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_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/YY1/out/align/pseudo_reps/rep1/pr2/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_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/YY1/out/align/pseudo_reps/rep1/pr2/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_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/YY1/out/align/pseudo_reps/rep1/pr2/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_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--------------------
30596 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Tue, 03 Jan 2017 15:19:40: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/align/pseudo_reps/rep1/pr2/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/align/pseudo_reps/rep1/pr2/SRR1370875_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  @ Tue, 03 Jan 2017 15:19:40: #1 read tag files... 
INFO  @ Tue, 03 Jan 2017 15:19:40: #1 read treatment tags... 
INFO  @ Tue, 03 Jan 2017 15:19:44:  1000000 
INFO  @ Tue, 03 Jan 2017 15:19:45:  2000000 
INFO  @ Tue, 03 Jan 2017 15:19:47:  3000000 
INFO  @ Tue, 03 Jan 2017 15:19:48:  4000000 
INFO  @ Tue, 03 Jan 2017 15:19:50:  5000000 
INFO  @ Tue, 03 Jan 2017 15:19:52:  6000000 
INFO  @ Tue, 03 Jan 2017 15:19:53:  7000000 
INFO  @ Tue, 03 Jan 2017 15:19:55: #1.2 read input tags... 
INFO  @ Tue, 03 Jan 2017 15:19:57:  1000000 
INFO  @ Tue, 03 Jan 2017 15:19:59:  2000000 
INFO  @ Tue, 03 Jan 2017 15:20:00:  3000000 
INFO  @ Tue, 03 Jan 2017 15:20:02:  4000000 
INFO  @ Tue, 03 Jan 2017 15:20:03:  5000000 
INFO  @ Tue, 03 Jan 2017 15:20:05:  6000000 
INFO  @ Tue, 03 Jan 2017 15:20:06:  7000000 
INFO  @ Tue, 03 Jan 2017 15:20:08:  8000000 
INFO  @ Tue, 03 Jan 2017 15:20:10:  9000000 
INFO  @ Tue, 03 Jan 2017 15:20:11:  10000000 
INFO  @ Tue, 03 Jan 2017 15:20:14:  11000000 
INFO  @ Tue, 03 Jan 2017 15:20:16:  12000000 
INFO  @ Tue, 03 Jan 2017 15:20:18:  13000000 
INFO  @ Tue, 03 Jan 2017 15:20:20:  14000000 
INFO  @ Tue, 03 Jan 2017 15:20:22:  15000000 
INFO  @ Tue, 03 Jan 2017 15:20:24:  16000000 
INFO  @ Tue, 03 Jan 2017 15:20:25:  17000000 
INFO  @ Tue, 03 Jan 2017 15:20:27:  18000000 
INFO  @ Tue, 03 Jan 2017 15:20:29:  19000000 
INFO  @ Tue, 03 Jan 2017 15:20:31:  20000000 
INFO  @ Tue, 03 Jan 2017 15:20:34:  21000000 
INFO  @ Tue, 03 Jan 2017 15:20:35:  22000000 
INFO  @ Tue, 03 Jan 2017 15:20:37:  23000000 
INFO  @ Tue, 03 Jan 2017 15:20:39:  24000000 
INFO  @ Tue, 03 Jan 2017 15:20:40:  25000000 
INFO  @ Tue, 03 Jan 2017 15:20:42:  26000000 
INFO  @ Tue, 03 Jan 2017 15:20:44:  27000000 
INFO  @ Tue, 03 Jan 2017 15:20:45:  28000000 
INFO  @ Tue, 03 Jan 2017 15:20:47:  29000000 
INFO  @ Tue, 03 Jan 2017 15:20:48:  30000000 
INFO  @ Tue, 03 Jan 2017 15:20:50:  31000000 
INFO  @ Tue, 03 Jan 2017 15:20:51:  32000000 
INFO  @ Tue, 03 Jan 2017 15:20:53:  33000000 
INFO  @ Tue, 03 Jan 2017 15:20:54:  34000000 
INFO  @ Tue, 03 Jan 2017 15:20:56:  35000000 
INFO  @ Tue, 03 Jan 2017 15:20:57:  36000000 
INFO  @ Tue, 03 Jan 2017 15:20:59:  37000000 
INFO  @ Tue, 03 Jan 2017 15:21:00:  38000000 
INFO  @ Tue, 03 Jan 2017 15:21:02:  39000000 
INFO  @ Tue, 03 Jan 2017 15:21:03:  40000000 
INFO  @ Tue, 03 Jan 2017 15:21:05:  41000000 
INFO  @ Tue, 03 Jan 2017 15:21:06:  42000000 
INFO  @ Tue, 03 Jan 2017 15:21:08:  43000000 
INFO  @ Tue, 03 Jan 2017 15:21:09:  44000000 
INFO  @ Tue, 03 Jan 2017 15:21:11:  45000000 
INFO  @ Tue, 03 Jan 2017 15:21:12:  46000000 
INFO  @ Tue, 03 Jan 2017 15:21:14:  47000000 
INFO  @ Tue, 03 Jan 2017 15:21:15:  48000000 
INFO  @ Tue, 03 Jan 2017 15:21:17:  49000000 
INFO  @ Tue, 03 Jan 2017 15:21:18:  50000000 
INFO  @ Tue, 03 Jan 2017 15:21:20: #1 tag size is determined as 69 bps 
INFO  @ Tue, 03 Jan 2017 15:21:20: #1 tag size = 69 
INFO  @ Tue, 03 Jan 2017 15:21:20: #1  total tags in treatment: 7707671 
INFO  @ Tue, 03 Jan 2017 15:21:20: #1  total tags in control: 50000000 
INFO  @ Tue, 03 Jan 2017 15:21:20: #1 finished! 
INFO  @ Tue, 03 Jan 2017 15:21:20: #2 Build Peak Model... 
INFO  @ Tue, 03 Jan 2017 15:21:20: #2 Skipped... 
INFO  @ Tue, 03 Jan 2017 15:21:20: #2 Use 145 as fragment length 
INFO  @ Tue, 03 Jan 2017 15:21:20: #3 Call peaks... 
INFO  @ Tue, 03 Jan 2017 15:21:20: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Tue, 03 Jan 2017 15:21:20: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 03 Jan 2017 15:24:06: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 03 Jan 2017 15:24:06: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Tue, 03 Jan 2017 15:24:06: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Tue, 03 Jan 2017 15:24:06: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 03 Jan 2017 15:24:06: #3 Call peaks for each chromosome... 
INFO  @ Tue, 03 Jan 2017 15:28:47: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Tue, 03 Jan 2017 15:28:49: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Tue, 03 Jan 2017 15:28:50: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Tue, 03 Jan 2017 15:28:51: Done! 
INFO  @ Tue, 03 Jan 2017 15:28:56: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/align/pseudo_reps/rep1/pr2/SRR1370875_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/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/align/pseudo_reps/rep1/pr2/SRR1370875_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  @ Tue, 03 Jan 2017 15:28:56: #1 read tag files... 
INFO  @ Tue, 03 Jan 2017 15:28:56: #1 read treatment tags... 
INFO  @ Tue, 03 Jan 2017 15:28:58:  1000000 
INFO  @ Tue, 03 Jan 2017 15:28:59:  2000000 
INFO  @ Tue, 03 Jan 2017 15:29:01:  3000000 
INFO  @ Tue, 03 Jan 2017 15:29:02:  4000000 
INFO  @ Tue, 03 Jan 2017 15:29:04:  5000000 
INFO  @ Tue, 03 Jan 2017 15:29:06:  6000000 
INFO  @ Tue, 03 Jan 2017 15:29:07:  7000000 
INFO  @ Tue, 03 Jan 2017 15:29:09: #1.2 read input tags... 
INFO  @ Tue, 03 Jan 2017 15:29:11:  1000000 
INFO  @ Tue, 03 Jan 2017 15:29:12:  2000000 
INFO  @ Tue, 03 Jan 2017 15:29:14:  3000000 
INFO  @ Tue, 03 Jan 2017 15:29:15:  4000000 
INFO  @ Tue, 03 Jan 2017 15:29:17:  5000000 
INFO  @ Tue, 03 Jan 2017 15:29:18:  6000000 
INFO  @ Tue, 03 Jan 2017 15:29:20:  7000000 
INFO  @ Tue, 03 Jan 2017 15:29:21:  8000000 
INFO  @ Tue, 03 Jan 2017 15:29:23:  9000000 
INFO  @ Tue, 03 Jan 2017 15:29:24:  10000000 
INFO  @ Tue, 03 Jan 2017 15:29:26:  11000000 
INFO  @ Tue, 03 Jan 2017 15:29:27:  12000000 
INFO  @ Tue, 03 Jan 2017 15:29:29:  13000000 
INFO  @ Tue, 03 Jan 2017 15:29:30:  14000000 
INFO  @ Tue, 03 Jan 2017 15:29:32:  15000000 
INFO  @ Tue, 03 Jan 2017 15:29:33:  16000000 
INFO  @ Tue, 03 Jan 2017 15:29:35:  17000000 
INFO  @ Tue, 03 Jan 2017 15:29:36:  18000000 
INFO  @ Tue, 03 Jan 2017 15:29:38:  19000000 
INFO  @ Tue, 03 Jan 2017 15:29:39:  20000000 
INFO  @ Tue, 03 Jan 2017 15:29:41:  21000000 
INFO  @ Tue, 03 Jan 2017 15:29:42:  22000000 
INFO  @ Tue, 03 Jan 2017 15:29:44:  23000000 
INFO  @ Tue, 03 Jan 2017 15:29:45:  24000000 
INFO  @ Tue, 03 Jan 2017 15:29:47:  25000000 
INFO  @ Tue, 03 Jan 2017 15:29:48:  26000000 
INFO  @ Tue, 03 Jan 2017 15:29:50:  27000000 
INFO  @ Tue, 03 Jan 2017 15:29:51:  28000000 
INFO  @ Tue, 03 Jan 2017 15:29:53:  29000000 
INFO  @ Tue, 03 Jan 2017 15:29:54:  30000000 
INFO  @ Tue, 03 Jan 2017 15:29:56:  31000000 
INFO  @ Tue, 03 Jan 2017 15:29:57:  32000000 
INFO  @ Tue, 03 Jan 2017 15:29:59:  33000000 
INFO  @ Tue, 03 Jan 2017 15:30:00:  34000000 
INFO  @ Tue, 03 Jan 2017 15:30:01:  35000000 
INFO  @ Tue, 03 Jan 2017 15:30:03:  36000000 
INFO  @ Tue, 03 Jan 2017 15:30:04:  37000000 
INFO  @ Tue, 03 Jan 2017 15:30:06:  38000000 
INFO  @ Tue, 03 Jan 2017 15:30:07:  39000000 
INFO  @ Tue, 03 Jan 2017 15:30:09:  40000000 
INFO  @ Tue, 03 Jan 2017 15:30:10:  41000000 
INFO  @ Tue, 03 Jan 2017 15:30:12:  42000000 
INFO  @ Tue, 03 Jan 2017 15:30:13:  43000000 
INFO  @ Tue, 03 Jan 2017 15:30:15:  44000000 
INFO  @ Tue, 03 Jan 2017 15:30:16:  45000000 
INFO  @ Tue, 03 Jan 2017 15:30:18:  46000000 
INFO  @ Tue, 03 Jan 2017 15:30:19:  47000000 
INFO  @ Tue, 03 Jan 2017 15:30:21:  48000000 
INFO  @ Tue, 03 Jan 2017 15:30:22:  49000000 
INFO  @ Tue, 03 Jan 2017 15:30:24:  50000000 
INFO  @ Tue, 03 Jan 2017 15:30:25: #1 tag size is determined as 69 bps 
INFO  @ Tue, 03 Jan 2017 15:30:25: #1 tag size = 69 
INFO  @ Tue, 03 Jan 2017 15:30:25: #1  total tags in treatment: 7707671 
INFO  @ Tue, 03 Jan 2017 15:30:25: #1  total tags in control: 50000000 
INFO  @ Tue, 03 Jan 2017 15:30:25: #1 finished! 
INFO  @ Tue, 03 Jan 2017 15:30:25: #2 Build Peak Model... 
INFO  @ Tue, 03 Jan 2017 15:30:25: #2 Skipped... 
INFO  @ Tue, 03 Jan 2017 15:30:25: #2 Use 145 as fragment length 
INFO  @ Tue, 03 Jan 2017 15:30:25: #3 Call peaks... 
INFO  @ Tue, 03 Jan 2017 15:30:25: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Tue, 03 Jan 2017 15:30:25: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 03 Jan 2017 15:33:03: #3 Call peaks for each chromosome... 
INFO  @ Tue, 03 Jan 2017 15:35:40: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Tue, 03 Jan 2017 15:35:47: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Tue, 03 Jan 2017 15:35:52: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370875_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Tue, 03 Jan 2017 15:35:58: Done!

Num	4
ID	task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_13
Name	naive_overlap_thresh
Thread	thread_Root
PID	22891

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

Start	2017-01-03 21:44:39
End	2017-01-03 22:33:22
Elapsed	00:48:43
Timeout	01:00:00
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/spp/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370875_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370875_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/spp/overlap/SRR1370875_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/YY1/out/peak/spp/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370875_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/YY1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370875_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/YY1/out/peak/spp/overlap/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/spp/overlap/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/spp/overlap/SRR1370875_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/YY1/out/peak/spp/overlap/SRR1370875_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/YY1/out/peak/spp/overlap/SRR1370875_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/YY1/out/peak/spp/overlap/SRR1370875_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--------------------
18048 (process ID) old priority 0, new priority 10
Waiting for 49 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL383563.3	161041	161377	.	0	.	18.9639844747327	-1	3.82769228867445	168

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL383563.3	161041	161377	.	0	.	18.9639844747327	-1	3.82769228867445	168

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270733.1	167977	168307	.	0	.	15.7381637757084	-1	4.08193029697918	165

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270733.1	167977	168307	.	0	.	15.7381637757084	-1	4.08193029697918	165

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/spp/overlap/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
GL000009.2	124666	124996	.	0	.	19.7256742908108	-1	4.32819605994855	165

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/spp/overlap/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
GL000009.2	124666	124996	.	0	.	19.7256742908108	-1	4.32819605994855	165

Num	5
ID	task.callpeak_idr.idr2_rep1_pr.line_73.id_14
Name	idr2 rep1-pr
Thread	thread_Root
PID	22994

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

Start	2017-01-03 22:33:23
End	2017-01-03 23:06:52
Elapsed	00:33:29
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370875_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370875_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/spp/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/idr/pseudo_reps/rep1/YY1_rep1-pr.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/idr/pseudo_reps/rep1/YY1_rep1-pr.unthresholded-peaks.txt.png /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/idr/pseudo_reps/rep1/YY1_rep1-pr.unthresholded-peaks.txt.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/idr/pseudo_reps/rep1/YY1_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/YY1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370875_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370875_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/spp/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/idr/pseudo_reps/rep1/YY1_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/YY1/out/peak/idr/pseudo_reps/rep1/YY1_rep1-pr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/idr/pseudo_reps/rep1/YY1_rep1-pr.IDR0.05.13-col.bed.gz

# SYS command. line 87

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/idr/pseudo_reps/rep1/YY1_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/YY1/out/peak/idr/pseudo_reps/rep1/YY1_rep1-pr.IDR0.05.narrowPeak.gz

# SYS command. line 88

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/idr/pseudo_reps/rep1/YY1_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/YY1/out/peak/idr/pseudo_reps/rep1/YY1_rep1-pr.IDR0.05.12-col.bed.gz

# SYS command. line 90

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/idr/pseudo_reps/rep1/YY1_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/YY1/out/peak/idr/pseudo_reps/rep1/YY1_rep1-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 91

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/idr/pseudo_reps/rep1/YY1_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/YY1/out/peak/idr/pseudo_reps/rep1/YY1_rep1-pr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 92

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/idr/pseudo_reps/rep1/YY1_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/YY1/out/peak/idr/pseudo_reps/rep1/YY1_rep1-pr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 94

 gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/idr/pseudo_reps/rep1/YY1_rep1-pr.unthresholded-peaks.txt

# SYS command. line 95

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/idr/pseudo_reps/rep1/YY1_rep1-pr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/idr/pseudo_reps/rep1/YY1_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--------------------
36547 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Initial parameter values: [0.10 1.00 0.20 0.50]
Final parameter values: [1.20 1.24 0.83 0.36]
Number of reported peaks - 65354/65354 (100.0%)

Number of peaks passing IDR cutoff of 0.05 - 9475/65354 (14.5%)

Num	6
ID	task.callpeak_idr.idr_final_qc.line_219.id_17
Name	idr final qc
Thread	thread_Root
PID	23554

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

Start	2017-01-03 23:06:54
End	2017-01-04 10:14:16
Elapsed	11:07:22
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/idr/pseudo_reps/rep1/YY1_rep1-pr.IDR0.05.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/qc/YY1_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/YY1/out/qc/YY1_IDR_final.qc

# SYS command. line 224

 echo -e "0\t304	0	""0\tN/A\tN/A\tNaN\t1.0\t1" >> /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/qc/YY1_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--------------------
12843 (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	44011

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

Start	2017-01-04 10:14:18
End	2017-01-04 10:15:26
Elapsed	00:01:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/spp/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/spp/rep1/SRR1370875_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/YY1/out/peak/spp/rep1/SRR1370875_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/YY1/out/peak/spp/rep1/SRR1370875_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--------------------
44015 (process ID) old priority 0, new priority 10
Waiting for 59 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/spp/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
GL383563.3	161044	161374	.	0	.	30.9862017893373	-1	4.32819605994855	165

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/spp/rep1/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
GL383563.3	161044	161374	.	0	.	30.9862017893373	-1	4.32819605994855	165

Num	8
ID	task.report.peak2hammock.line_412.id_19
Name	peak2hammock
Thread	thread_Root
PID	55499

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

Start	2017-01-04 10:15:27
End	2017-01-04 10:15:35
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/spp/overlap/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/spp/overlap/SRR1370875_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/YY1/out/peak/spp/overlap/SRR1370875_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/YY1/out/peak/spp/overlap/SRR1370875_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/YY1/out/peak/spp/overlap/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/spp/overlap/SRR1370875_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/YY1/out/peak/spp/overlap/SRR1370875_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp

   
--------------------Stdout--------------------
55505 (process ID) old priority 0, new priority 10

Num	9
ID	task.report.peak2hammock.line_412.id_20
Name	peak2hammock
Thread	thread_Root
PID	57095

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

Start	2017-01-04 10:15:36
End	2017-01-04 10:15:45
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/idr/pseudo_reps/rep1/YY1_rep1-pr.IDR0.05.filt.12-col.bed.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/idr/pseudo_reps/rep1/YY1_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/YY1/out/peak/idr/pseudo_reps/rep1/YY1_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/YY1/out/peak/idr/pseudo_reps/rep1/YY1_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/YY1/out/peak/idr/pseudo_reps/rep1/YY1_rep1-pr.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/idr/pseudo_reps/rep1/YY1_rep1-pr.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/peak/idr/pseudo_reps/rep1/YY1_rep1-pr.IDR0.05.filt.12-col.bed.tmp

   
--------------------Stdout--------------------
57099 (process ID) old priority 0, new priority 10

Num	10
ID	task.graphviz.report.line_97.id_21
Name	report
Thread	thread_Root
PID	1257

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

Start	2017-01-04 10:15:46
End	2017-01-04 10:15:54
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/YY1/out/report/YY1_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/report/YY1_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/report/YY1_workflow.svg" # to suppress dot font error (exit code=1)

   
--------------------Stdout--------------------
1261 (process ID) old priority 0, new priority 10

Type	Name	Value
string	_	/usr/bin/bds
string	_LMFILES_	/software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/samtools/1.2:/software/modulefiles/ucsc_tools/3.0.9
bool	allowEmpty	false
string[]	args	[-title, YY1, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/YY1/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/YY1/out/align/rep1/SRR1370875_1.bam, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz, -final_stage, idr, $]
string	C_INCLUDE_PATH	/software/samtools/samtools-1.2/include/htslib
bool	canFail	false
int	cpus	-1
int	cpusLocal	56
int	day	86400
string	DEEPLIFT_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift
string	DERBY_HOME	/usr/lib/jvm/java-8-oracle/db
string	DISPLAY	localhost:12.0
real	E	2.718281828459045
string	ENHANCER_SCRIPTS_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/
int	G	1073741824
string	HOME	/users/imk1/
int	hour	3600
string	J2REDIR	/usr/lib/jvm/java-8-oracle/jre
string	J2SDKDIR	/usr/lib/jvm/java-8-oracle
string	JAVA_HOME	/usr/lib/jvm/java-8-oracle
int	K	1024
string	KERAS_DIR	/users/imk1/.local/lib/python2.7/site-packages/keras/
string	KRB5CCNAME	FILE:/tmp/krb5cc_1048_cTVn8v
string	LANG	en_US.UTF-8
string	LOADEDMODULES	modsappsdir/modsappsdir:samtools/1.2:ucsc_tools/3.0.9
string	LOGNAME	imk1
int	M	1048576
string	MAIL	/var/mail/imk1
string	MANPATH	/software/samtools/samtools-1.2/share/man:/usr/share/man
int	mem	-1
int	minute	60
string	MODULE_VERSION	3.2.10
string	MODULE_VERSION_STACK	3.2.10
string	MODULEPATH	/usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$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	/users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/rcade/:/software/samtools/samtools-1.2/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:/software/ucsc_tools/3.0.9:/software/ucsc_tools/3.0.9/blat
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/YY1
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/YY1
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	SAMTOOLS_HOME	/software/samtools/samtools-1.2/bin
string	SCREEN_Name	CTCF_2015
string	SHELL	/bin/bash
string	SHLVL	3
string	SSH_CLIENT	171.65.77.8 32898 22
string	SSH_CONNECTION	171.65.77.8 32898 171.65.76.63 22
string	SSH_TTY	/dev/pts/4
string	STY	40273.YY1.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	9035
string	XFILESEARCHPATH	/usr/dt/app-defaults/%L/Dt

BigDataScript report: chipseq.bds

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