Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20170103_142524_672
Start time	2017-01-03 14:25:24
Run time	06:20:14.063
Tasks executed	7
Tasks failed	0
Tasks failed names
Arguments*	[-title, ZSCAN22, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZSCAN22/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/align/rep1/SRR1370878_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_142524_672/task.callpeak_macs2.macs2_rep1.line_71.id_10 chipseq.bds.20170103_142524_672/task.callpeak_macs2.macs2_rep1_pr1.line_71.id_11 chipseq.bds.20170103_142524_672/task.callpeak_macs2.macs2_rep1_pr2.line_71.id_12 chipseq.bds.20170103_142524_672/task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_13 chipseq.bds.20170103_142524_672/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_16 chipseq.bds.20170103_142524_672/task.report.peak2hammock.line_412.id_17 chipseq.bds.20170103_142524_672/task.graphviz.report.line_97.id_18
thread_41	thread_Root
thread_42	thread_Root

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.callpeak_macs2.macs2_rep1.line_71.id_10
Name	macs2 rep1
Thread	thread_Root
PID	22371

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

Start	2017-01-03 14:25:31
End	2017-01-03 16:40:13
Elapsed	02:14:42
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/align/rep1/SRR1370878_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/ZSCAN22/out/peak/macs2/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/signal/macs2/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/signal/macs2/rep1/SRR1370878_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/ZSCAN22/out/align/rep1/SRR1370878_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/ZSCAN22/out/peak/macs2/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 160 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/rep1/SRR1370878_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/ZSCAN22/out/peak/macs2/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/rep1/SRR1370878_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/ZSCAN22/out/align/rep1/SRR1370878_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/ZSCAN22/out/peak/macs2/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 160 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/rep1/SRR1370878_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/ZSCAN22/out/peak/macs2/rep1/SRR1370878_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/ZSCAN22/out/peak/macs2/rep1/SRR1370878_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/ZSCAN22/out/peak/macs2/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/rep1/SRR1370878_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/ZSCAN22/out/peak/macs2/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/rep1/SRR1370878_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/ZSCAN22/out/peak/macs2/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/rep1 -o "SRR1370878_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/ZSCAN22/out/peak/macs2/rep1/SRR1370878_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/ZSCAN22/out/peak/macs2/rep1/SRR1370878_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/ZSCAN22/out/peak/macs2/rep1/SRR1370878_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/ZSCAN22/out/peak/macs2/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/rep1/SRR1370878_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/ZSCAN22/out/peak/macs2/rep1/SRR1370878_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/ZSCAN22/out/signal/macs2/rep1/SRR1370878_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/ZSCAN22/out/peak/macs2/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/rep1/SRR1370878_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/ZSCAN22/out/align/rep1/SRR1370878_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/ZSCAN22/out/peak/macs2/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/rep1 -o "SRR1370878_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/ZSCAN22/out/peak/macs2/rep1/SRR1370878_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/ZSCAN22/out/peak/macs2/rep1/SRR1370878_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/ZSCAN22/out/peak/macs2/rep1/SRR1370878_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/ZSCAN22/out/peak/macs2/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/rep1/SRR1370878_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/ZSCAN22/out/peak/macs2/rep1/SRR1370878_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/ZSCAN22/out/signal/macs2/rep1/SRR1370878_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/ZSCAN22/out/peak/macs2/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/rep1/SRR1370878_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/ZSCAN22/out/peak/macs2/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/rep1/SRR1370878_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--------------------
26753 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Tue, 03 Jan 2017 15:34:01: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/align/rep1/SRR1370878_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/ZSCAN22/out/peak/macs2/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 160 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/align/rep1/SRR1370878_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 15:34:01: #1 read tag files... 
INFO  @ Tue, 03 Jan 2017 15:34:01: #1 read treatment tags... 
INFO  @ Tue, 03 Jan 2017 15:34:03:  1000000 
INFO  @ Tue, 03 Jan 2017 15:34:04:  2000000 
INFO  @ Tue, 03 Jan 2017 15:34:06:  3000000 
INFO  @ Tue, 03 Jan 2017 15:34:08:  4000000 
INFO  @ Tue, 03 Jan 2017 15:34:09:  5000000 
INFO  @ Tue, 03 Jan 2017 15:34:11:  6000000 
INFO  @ Tue, 03 Jan 2017 15:34:12:  7000000 
INFO  @ Tue, 03 Jan 2017 15:34:14:  8000000 
INFO  @ Tue, 03 Jan 2017 15:34:15:  9000000 
INFO  @ Tue, 03 Jan 2017 15:34:17:  10000000 
INFO  @ Tue, 03 Jan 2017 15:34:19:  11000000 
INFO  @ Tue, 03 Jan 2017 15:34:20:  12000000 
INFO  @ Tue, 03 Jan 2017 15:34:22:  13000000 
INFO  @ Tue, 03 Jan 2017 15:34:24:  14000000 
INFO  @ Tue, 03 Jan 2017 15:34:25:  15000000 
INFO  @ Tue, 03 Jan 2017 15:34:27:  16000000 
INFO  @ Tue, 03 Jan 2017 15:34:29:  17000000 
INFO  @ Tue, 03 Jan 2017 15:34:30:  18000000 
INFO  @ Tue, 03 Jan 2017 15:34:32:  19000000 
INFO  @ Tue, 03 Jan 2017 15:34:34:  20000000 
INFO  @ Tue, 03 Jan 2017 15:34:35:  21000000 
INFO  @ Tue, 03 Jan 2017 15:34:37:  22000000 
INFO  @ Tue, 03 Jan 2017 15:34:38:  23000000 
INFO  @ Tue, 03 Jan 2017 15:34:40:  24000000 
INFO  @ Tue, 03 Jan 2017 15:34:41:  25000000 
INFO  @ Tue, 03 Jan 2017 15:34:43:  26000000 
INFO  @ Tue, 03 Jan 2017 15:34:44: #1.2 read input tags... 
INFO  @ Tue, 03 Jan 2017 15:34:46:  1000000 
INFO  @ Tue, 03 Jan 2017 15:34:48:  2000000 
INFO  @ Tue, 03 Jan 2017 15:34:49:  3000000 
INFO  @ Tue, 03 Jan 2017 15:34:51:  4000000 
INFO  @ Tue, 03 Jan 2017 15:34:52:  5000000 
INFO  @ Tue, 03 Jan 2017 15:34:54:  6000000 
INFO  @ Tue, 03 Jan 2017 15:34:55:  7000000 
INFO  @ Tue, 03 Jan 2017 15:34:57:  8000000 
INFO  @ Tue, 03 Jan 2017 15:34:58:  9000000 
INFO  @ Tue, 03 Jan 2017 15:35:00:  10000000 
INFO  @ Tue, 03 Jan 2017 15:35:01:  11000000 
INFO  @ Tue, 03 Jan 2017 15:35:03:  12000000 
INFO  @ Tue, 03 Jan 2017 15:35:04:  13000000 
INFO  @ Tue, 03 Jan 2017 15:35:06:  14000000 
INFO  @ Tue, 03 Jan 2017 15:35:07:  15000000 
INFO  @ Tue, 03 Jan 2017 15:35:09:  16000000 
INFO  @ Tue, 03 Jan 2017 15:35:10:  17000000 
INFO  @ Tue, 03 Jan 2017 15:35:12:  18000000 
INFO  @ Tue, 03 Jan 2017 15:35:13:  19000000 
INFO  @ Tue, 03 Jan 2017 15:35:15:  20000000 
INFO  @ Tue, 03 Jan 2017 15:35:16:  21000000 
INFO  @ Tue, 03 Jan 2017 15:35:18:  22000000 
INFO  @ Tue, 03 Jan 2017 15:35:19:  23000000 
INFO  @ Tue, 03 Jan 2017 15:35:21:  24000000 
INFO  @ Tue, 03 Jan 2017 15:35:22:  25000000 
INFO  @ Tue, 03 Jan 2017 15:35:24:  26000000 
INFO  @ Tue, 03 Jan 2017 15:35:25:  27000000 
INFO  @ Tue, 03 Jan 2017 15:35:27:  28000000 
INFO  @ Tue, 03 Jan 2017 15:35:28:  29000000 
INFO  @ Tue, 03 Jan 2017 15:35:30:  30000000 
INFO  @ Tue, 03 Jan 2017 15:35:31:  31000000 
INFO  @ Tue, 03 Jan 2017 15:35:33:  32000000 
INFO  @ Tue, 03 Jan 2017 15:35:34:  33000000 
INFO  @ Tue, 03 Jan 2017 15:35:36:  34000000 
INFO  @ Tue, 03 Jan 2017 15:35:37:  35000000 
INFO  @ Tue, 03 Jan 2017 15:35:39:  36000000 
INFO  @ Tue, 03 Jan 2017 15:35:40:  37000000 
INFO  @ Tue, 03 Jan 2017 15:35:42:  38000000 
INFO  @ Tue, 03 Jan 2017 15:35:43:  39000000 
INFO  @ Tue, 03 Jan 2017 15:35:45:  40000000 
INFO  @ Tue, 03 Jan 2017 15:35:46:  41000000 
INFO  @ Tue, 03 Jan 2017 15:35:48:  42000000 
INFO  @ Tue, 03 Jan 2017 15:35:49:  43000000 
INFO  @ Tue, 03 Jan 2017 15:35:51:  44000000 
INFO  @ Tue, 03 Jan 2017 15:35:52:  45000000 
INFO  @ Tue, 03 Jan 2017 15:35:54:  46000000 
INFO  @ Tue, 03 Jan 2017 15:35:55:  47000000 
INFO  @ Tue, 03 Jan 2017 15:35:57:  48000000 
INFO  @ Tue, 03 Jan 2017 15:35:58:  49000000 
INFO  @ Tue, 03 Jan 2017 15:36:00:  50000000 
INFO  @ Tue, 03 Jan 2017 15:36:02: #1 tag size is determined as 96 bps 
INFO  @ Tue, 03 Jan 2017 15:36:02: #1 tag size = 96 
INFO  @ Tue, 03 Jan 2017 15:36:02: #1  total tags in treatment: 26861431 
INFO  @ Tue, 03 Jan 2017 15:36:02: #1  total tags in control: 50000000 
INFO  @ Tue, 03 Jan 2017 15:36:02: #1 finished! 
INFO  @ Tue, 03 Jan 2017 15:36:02: #2 Build Peak Model... 
INFO  @ Tue, 03 Jan 2017 15:36:02: #2 Skipped... 
INFO  @ Tue, 03 Jan 2017 15:36:02: #2 Use 160 as fragment length 
INFO  @ Tue, 03 Jan 2017 15:36:02: #3 Call peaks... 
INFO  @ Tue, 03 Jan 2017 15:36:02: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Tue, 03 Jan 2017 15:36:02: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 03 Jan 2017 15:38:48: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 03 Jan 2017 15:38:48: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Tue, 03 Jan 2017 15:38:48: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Tue, 03 Jan 2017 15:38:48: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 03 Jan 2017 15:38:48: #3 Call peaks for each chromosome... 
INFO  @ Tue, 03 Jan 2017 15:44:49: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Tue, 03 Jan 2017 15:44:51: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Tue, 03 Jan 2017 15:44:52: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Tue, 03 Jan 2017 15:44:53: Done! 
INFO  @ Tue, 03 Jan 2017 15:44:56: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/align/rep1/SRR1370878_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/ZSCAN22/out/peak/macs2/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 160 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/align/rep1/SRR1370878_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 15:44:56: #1 read tag files... 
INFO  @ Tue, 03 Jan 2017 15:44:56: #1 read treatment tags... 
INFO  @ Tue, 03 Jan 2017 15:44:58:  1000000 
INFO  @ Tue, 03 Jan 2017 15:44:59:  2000000 
INFO  @ Tue, 03 Jan 2017 15:45:01:  3000000 
INFO  @ Tue, 03 Jan 2017 15:45:02:  4000000 
INFO  @ Tue, 03 Jan 2017 15:45:04:  5000000 
INFO  @ Tue, 03 Jan 2017 15:45:05:  6000000 
INFO  @ Tue, 03 Jan 2017 15:45:07:  7000000 
INFO  @ Tue, 03 Jan 2017 15:45:08:  8000000 
INFO  @ Tue, 03 Jan 2017 15:45:10:  9000000 
INFO  @ Tue, 03 Jan 2017 15:45:11:  10000000 
INFO  @ Tue, 03 Jan 2017 15:45:13:  11000000 
INFO  @ Tue, 03 Jan 2017 15:45:14:  12000000 
INFO  @ Tue, 03 Jan 2017 15:45:15:  13000000 
INFO  @ Tue, 03 Jan 2017 15:45:17:  14000000 
INFO  @ Tue, 03 Jan 2017 15:45:18:  15000000 
INFO  @ Tue, 03 Jan 2017 15:45:20:  16000000 
INFO  @ Tue, 03 Jan 2017 15:45:21:  17000000 
INFO  @ Tue, 03 Jan 2017 15:45:23:  18000000 
INFO  @ Tue, 03 Jan 2017 15:45:24:  19000000 
INFO  @ Tue, 03 Jan 2017 15:45:26:  20000000 
INFO  @ Tue, 03 Jan 2017 15:45:27:  21000000 
INFO  @ Tue, 03 Jan 2017 15:45:29:  22000000 
INFO  @ Tue, 03 Jan 2017 15:45:30:  23000000 
INFO  @ Tue, 03 Jan 2017 15:45:32:  24000000 
INFO  @ Tue, 03 Jan 2017 15:45:33:  25000000 
INFO  @ Tue, 03 Jan 2017 15:45:35:  26000000 
INFO  @ Tue, 03 Jan 2017 15:45:36: #1.2 read input tags... 
INFO  @ Tue, 03 Jan 2017 15:45:38:  1000000 
INFO  @ Tue, 03 Jan 2017 15:45:39:  2000000 
INFO  @ Tue, 03 Jan 2017 15:45:41:  3000000 
INFO  @ Tue, 03 Jan 2017 15:45:42:  4000000 
INFO  @ Tue, 03 Jan 2017 15:45:44:  5000000 
INFO  @ Tue, 03 Jan 2017 15:45:45:  6000000 
INFO  @ Tue, 03 Jan 2017 15:45:47:  7000000 
INFO  @ Tue, 03 Jan 2017 15:45:48:  8000000 
INFO  @ Tue, 03 Jan 2017 15:45:50:  9000000 
INFO  @ Tue, 03 Jan 2017 15:45:51:  10000000 
INFO  @ Tue, 03 Jan 2017 15:45:53:  11000000 
INFO  @ Tue, 03 Jan 2017 15:45:54:  12000000 
INFO  @ Tue, 03 Jan 2017 15:45:56:  13000000 
INFO  @ Tue, 03 Jan 2017 15:45:57:  14000000 
INFO  @ Tue, 03 Jan 2017 15:45:59:  15000000 
INFO  @ Tue, 03 Jan 2017 15:46:00:  16000000 
INFO  @ Tue, 03 Jan 2017 15:46:02:  17000000 
INFO  @ Tue, 03 Jan 2017 15:46:03:  18000000 
INFO  @ Tue, 03 Jan 2017 15:46:05:  19000000 
INFO  @ Tue, 03 Jan 2017 15:46:06:  20000000 
INFO  @ Tue, 03 Jan 2017 15:46:08:  21000000 
INFO  @ Tue, 03 Jan 2017 15:46:09:  22000000 
INFO  @ Tue, 03 Jan 2017 15:46:11:  23000000 
INFO  @ Tue, 03 Jan 2017 15:46:12:  24000000 
INFO  @ Tue, 03 Jan 2017 15:46:14:  25000000 
INFO  @ Tue, 03 Jan 2017 15:46:15:  26000000 
INFO  @ Tue, 03 Jan 2017 15:46:17:  27000000 
INFO  @ Tue, 03 Jan 2017 15:46:19:  28000000 
INFO  @ Tue, 03 Jan 2017 15:46:20:  29000000 
INFO  @ Tue, 03 Jan 2017 15:46:22:  30000000 
INFO  @ Tue, 03 Jan 2017 15:46:24:  31000000 
INFO  @ Tue, 03 Jan 2017 15:46:25:  32000000 
INFO  @ Tue, 03 Jan 2017 15:46:26:  33000000 
INFO  @ Tue, 03 Jan 2017 15:46:28:  34000000 
INFO  @ Tue, 03 Jan 2017 15:46:29:  35000000 
INFO  @ Tue, 03 Jan 2017 15:46:31:  36000000 
INFO  @ Tue, 03 Jan 2017 15:46:32:  37000000 
INFO  @ Tue, 03 Jan 2017 15:46:34:  38000000 
INFO  @ Tue, 03 Jan 2017 15:46:35:  39000000 
INFO  @ Tue, 03 Jan 2017 15:46:37:  40000000 
INFO  @ Tue, 03 Jan 2017 15:46:38:  41000000 
INFO  @ Tue, 03 Jan 2017 15:46:40:  42000000 
INFO  @ Tue, 03 Jan 2017 15:46:41:  43000000 
INFO  @ Tue, 03 Jan 2017 15:46:43:  44000000 
INFO  @ Tue, 03 Jan 2017 15:46:44:  45000000 
INFO  @ Tue, 03 Jan 2017 15:46:46:  46000000 
INFO  @ Tue, 03 Jan 2017 15:46:47:  47000000 
INFO  @ Tue, 03 Jan 2017 15:46:49:  48000000 
INFO  @ Tue, 03 Jan 2017 15:46:50:  49000000 
INFO  @ Tue, 03 Jan 2017 15:46:52:  50000000 
INFO  @ Tue, 03 Jan 2017 15:46:53: #1 tag size is determined as 96 bps 
INFO  @ Tue, 03 Jan 2017 15:46:53: #1 tag size = 96 
INFO  @ Tue, 03 Jan 2017 15:46:53: #1  total tags in treatment: 26861431 
INFO  @ Tue, 03 Jan 2017 15:46:53: #1  total tags in control: 50000000 
INFO  @ Tue, 03 Jan 2017 15:46:53: #1 finished! 
INFO  @ Tue, 03 Jan 2017 15:46:53: #2 Build Peak Model... 
INFO  @ Tue, 03 Jan 2017 15:46:53: #2 Skipped... 
INFO  @ Tue, 03 Jan 2017 15:46:53: #2 Use 160 as fragment length 
INFO  @ Tue, 03 Jan 2017 15:46:53: #3 Call peaks... 
INFO  @ Tue, 03 Jan 2017 15:46:53: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Tue, 03 Jan 2017 15:46:53: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 03 Jan 2017 15:49:38: #3 Call peaks for each chromosome... 
INFO  @ Tue, 03 Jan 2017 15:52:19: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Tue, 03 Jan 2017 15:52:25: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Tue, 03 Jan 2017 15:52:30: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Tue, 03 Jan 2017 15:52:35: Done! 
INFO  @ Tue, 03 Jan 2017 15:53:14: Read and build treatment bedGraph... 
INFO  @ Tue, 03 Jan 2017 15:54:15: Read and build control bedGraph... 
INFO  @ Tue, 03 Jan 2017 15:56:16: Build scoreTrackII... 
INFO  @ Tue, 03 Jan 2017 15:57:09: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Tue, 03 Jan 2017 16:03:16: Write bedGraph of scores... 
INFO  @ Tue, 03 Jan 2017 16:07:19: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_FE.bdg'! 
INFO  @ Tue, 03 Jan 2017 16:15:41: Read and build treatment bedGraph... 
INFO  @ Tue, 03 Jan 2017 16:16:38: Read and build control bedGraph... 
INFO  @ Tue, 03 Jan 2017 16:18:37: Build scoreTrackII... 
INFO  @ Tue, 03 Jan 2017 16:19:35: Values in your input bedGraph files will be multiplied by 26.861431 ... 
INFO  @ Tue, 03 Jan 2017 16:25:51: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Tue, 03 Jan 2017 16:26:42: Write bedGraph of scores... 
INFO  @ Tue, 03 Jan 2017 16:30:30: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/rep1/SRR1370878_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	22372

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

Start	2017-01-03 14:25:33
End	2017-01-03 15:52:09
Elapsed	01:26:35
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/align/pseudo_reps/rep1/pr1/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_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/ZSCAN22/out/align/pseudo_reps/rep1/pr1/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 160 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_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/ZSCAN22/out/align/pseudo_reps/rep1/pr1/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 160 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_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/ZSCAN22/out/align/pseudo_reps/rep1/pr1/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_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--------------------
26861 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Tue, 03 Jan 2017 15:34:32: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/align/pseudo_reps/rep1/pr1/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 160 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/align/pseudo_reps/rep1/pr1/SRR1370878_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 15:34:32: #1 read tag files... 
INFO  @ Tue, 03 Jan 2017 15:34:32: #1 read treatment tags... 
INFO  @ Tue, 03 Jan 2017 15:34:34:  1000000 
INFO  @ Tue, 03 Jan 2017 15:34:36:  2000000 
INFO  @ Tue, 03 Jan 2017 15:34:38:  3000000 
INFO  @ Tue, 03 Jan 2017 15:34:40:  4000000 
INFO  @ Tue, 03 Jan 2017 15:34:41:  5000000 
INFO  @ Tue, 03 Jan 2017 15:34:43:  6000000 
INFO  @ Tue, 03 Jan 2017 15:34:44:  7000000 
INFO  @ Tue, 03 Jan 2017 15:34:46:  8000000 
INFO  @ Tue, 03 Jan 2017 15:34:48:  9000000 
INFO  @ Tue, 03 Jan 2017 15:34:49:  10000000 
INFO  @ Tue, 03 Jan 2017 15:34:51:  11000000 
INFO  @ Tue, 03 Jan 2017 15:34:53:  12000000 
INFO  @ Tue, 03 Jan 2017 15:34:54:  13000000 
INFO  @ Tue, 03 Jan 2017 15:34:56: #1.2 read input tags... 
INFO  @ Tue, 03 Jan 2017 15:34:58:  1000000 
INFO  @ Tue, 03 Jan 2017 15:34:59:  2000000 
INFO  @ Tue, 03 Jan 2017 15:35:01:  3000000 
INFO  @ Tue, 03 Jan 2017 15:35:02:  4000000 
INFO  @ Tue, 03 Jan 2017 15:35:04:  5000000 
INFO  @ Tue, 03 Jan 2017 15:35:05:  6000000 
INFO  @ Tue, 03 Jan 2017 15:35:07:  7000000 
INFO  @ Tue, 03 Jan 2017 15:35:08:  8000000 
INFO  @ Tue, 03 Jan 2017 15:35:10:  9000000 
INFO  @ Tue, 03 Jan 2017 15:35:11:  10000000 
INFO  @ Tue, 03 Jan 2017 15:35:13:  11000000 
INFO  @ Tue, 03 Jan 2017 15:35:14:  12000000 
INFO  @ Tue, 03 Jan 2017 15:35:16:  13000000 
INFO  @ Tue, 03 Jan 2017 15:35:17:  14000000 
INFO  @ Tue, 03 Jan 2017 15:35:19:  15000000 
INFO  @ Tue, 03 Jan 2017 15:35:20:  16000000 
INFO  @ Tue, 03 Jan 2017 15:35:23:  17000000 
INFO  @ Tue, 03 Jan 2017 15:35:28:  18000000 
INFO  @ Tue, 03 Jan 2017 15:35:33:  19000000 
INFO  @ Tue, 03 Jan 2017 15:35:35:  20000000 
INFO  @ Tue, 03 Jan 2017 15:35:36:  21000000 
INFO  @ Tue, 03 Jan 2017 15:35:38:  22000000 
INFO  @ Tue, 03 Jan 2017 15:35:39:  23000000 
INFO  @ Tue, 03 Jan 2017 15:35:41:  24000000 
INFO  @ Tue, 03 Jan 2017 15:35:42:  25000000 
INFO  @ Tue, 03 Jan 2017 15:35:44:  26000000 
INFO  @ Tue, 03 Jan 2017 15:35:45:  27000000 
INFO  @ Tue, 03 Jan 2017 15:35:47:  28000000 
INFO  @ Tue, 03 Jan 2017 15:35:49:  29000000 
INFO  @ Tue, 03 Jan 2017 15:35:50:  30000000 
INFO  @ Tue, 03 Jan 2017 15:35:52:  31000000 
INFO  @ Tue, 03 Jan 2017 15:35:53:  32000000 
INFO  @ Tue, 03 Jan 2017 15:35:55:  33000000 
INFO  @ Tue, 03 Jan 2017 15:35:56:  34000000 
INFO  @ Tue, 03 Jan 2017 15:35:58:  35000000 
INFO  @ Tue, 03 Jan 2017 15:35:59:  36000000 
INFO  @ Tue, 03 Jan 2017 15:36:01:  37000000 
INFO  @ Tue, 03 Jan 2017 15:36:02:  38000000 
INFO  @ Tue, 03 Jan 2017 15:36:04:  39000000 
INFO  @ Tue, 03 Jan 2017 15:36:05:  40000000 
INFO  @ Tue, 03 Jan 2017 15:36:07:  41000000 
INFO  @ Tue, 03 Jan 2017 15:36:08:  42000000 
INFO  @ Tue, 03 Jan 2017 15:36:10:  43000000 
INFO  @ Tue, 03 Jan 2017 15:36:11:  44000000 
INFO  @ Tue, 03 Jan 2017 15:36:13:  45000000 
INFO  @ Tue, 03 Jan 2017 15:36:15:  46000000 
INFO  @ Tue, 03 Jan 2017 15:36:16:  47000000 
INFO  @ Tue, 03 Jan 2017 15:36:18:  48000000 
INFO  @ Tue, 03 Jan 2017 15:36:19:  49000000 
INFO  @ Tue, 03 Jan 2017 15:36:21:  50000000 
INFO  @ Tue, 03 Jan 2017 15:36:22: #1 tag size is determined as 109 bps 
INFO  @ Tue, 03 Jan 2017 15:36:22: #1 tag size = 109 
INFO  @ Tue, 03 Jan 2017 15:36:22: #1  total tags in treatment: 13430716 
INFO  @ Tue, 03 Jan 2017 15:36:22: #1  total tags in control: 50000000 
INFO  @ Tue, 03 Jan 2017 15:36:22: #1 finished! 
INFO  @ Tue, 03 Jan 2017 15:36:22: #2 Build Peak Model... 
INFO  @ Tue, 03 Jan 2017 15:36:22: #2 Skipped... 
INFO  @ Tue, 03 Jan 2017 15:36:22: #2 Use 160 as fragment length 
INFO  @ Tue, 03 Jan 2017 15:36:22: #3 Call peaks... 
INFO  @ Tue, 03 Jan 2017 15:36:22: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Tue, 03 Jan 2017 15:36:22: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 03 Jan 2017 15:39:03: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 03 Jan 2017 15:39:03: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Tue, 03 Jan 2017 15:39:03: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Tue, 03 Jan 2017 15:39:03: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 03 Jan 2017 15:39:03: #3 Call peaks for each chromosome... 
INFO  @ Tue, 03 Jan 2017 15:44:23: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Tue, 03 Jan 2017 15:44:26: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Tue, 03 Jan 2017 15:44:27: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Tue, 03 Jan 2017 15:44:28: Done! 
INFO  @ Tue, 03 Jan 2017 15:44:32: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/align/pseudo_reps/rep1/pr1/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 160 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/align/pseudo_reps/rep1/pr1/SRR1370878_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 15:44:32: #1 read tag files... 
INFO  @ Tue, 03 Jan 2017 15:44:32: #1 read treatment tags... 
INFO  @ Tue, 03 Jan 2017 15:44:34:  1000000 
INFO  @ Tue, 03 Jan 2017 15:44:36:  2000000 
INFO  @ Tue, 03 Jan 2017 15:44:37:  3000000 
INFO  @ Tue, 03 Jan 2017 15:44:39:  4000000 
INFO  @ Tue, 03 Jan 2017 15:44:41:  5000000 
INFO  @ Tue, 03 Jan 2017 15:44:42:  6000000 
INFO  @ Tue, 03 Jan 2017 15:44:44:  7000000 
INFO  @ Tue, 03 Jan 2017 15:44:46:  8000000 
INFO  @ Tue, 03 Jan 2017 15:44:47:  9000000 
INFO  @ Tue, 03 Jan 2017 15:44:49:  10000000 
INFO  @ Tue, 03 Jan 2017 15:44:50:  11000000 
INFO  @ Tue, 03 Jan 2017 15:44:52:  12000000 
INFO  @ Tue, 03 Jan 2017 15:44:54:  13000000 
INFO  @ Tue, 03 Jan 2017 15:44:55: #1.2 read input tags... 
INFO  @ Tue, 03 Jan 2017 15:44:57:  1000000 
INFO  @ Tue, 03 Jan 2017 15:44:58:  2000000 
INFO  @ Tue, 03 Jan 2017 15:45:00:  3000000 
INFO  @ Tue, 03 Jan 2017 15:45:02:  4000000 
INFO  @ Tue, 03 Jan 2017 15:45:03:  5000000 
INFO  @ Tue, 03 Jan 2017 15:45:05:  6000000 
INFO  @ Tue, 03 Jan 2017 15:45:06:  7000000 
INFO  @ Tue, 03 Jan 2017 15:45:08:  8000000 
INFO  @ Tue, 03 Jan 2017 15:45:09:  9000000 
INFO  @ Tue, 03 Jan 2017 15:45:11:  10000000 
INFO  @ Tue, 03 Jan 2017 15:45:12:  11000000 
INFO  @ Tue, 03 Jan 2017 15:45:14:  12000000 
INFO  @ Tue, 03 Jan 2017 15:45:15:  13000000 
INFO  @ Tue, 03 Jan 2017 15:45:17:  14000000 
INFO  @ Tue, 03 Jan 2017 15:45:18:  15000000 
INFO  @ Tue, 03 Jan 2017 15:45:20:  16000000 
INFO  @ Tue, 03 Jan 2017 15:45:22:  17000000 
INFO  @ Tue, 03 Jan 2017 15:45:26:  18000000 
INFO  @ Tue, 03 Jan 2017 15:45:31:  19000000 
INFO  @ Tue, 03 Jan 2017 15:45:33:  20000000 
INFO  @ Tue, 03 Jan 2017 15:45:34:  21000000 
INFO  @ Tue, 03 Jan 2017 15:45:36:  22000000 
INFO  @ Tue, 03 Jan 2017 15:45:38:  23000000 
INFO  @ Tue, 03 Jan 2017 15:45:39:  24000000 
INFO  @ Tue, 03 Jan 2017 15:45:41:  25000000 
INFO  @ Tue, 03 Jan 2017 15:45:43:  26000000 
INFO  @ Tue, 03 Jan 2017 15:45:44:  27000000 
INFO  @ Tue, 03 Jan 2017 15:45:46:  28000000 
INFO  @ Tue, 03 Jan 2017 15:45:47:  29000000 
INFO  @ Tue, 03 Jan 2017 15:45:49:  30000000 
INFO  @ Tue, 03 Jan 2017 15:45:50:  31000000 
INFO  @ Tue, 03 Jan 2017 15:45:52:  32000000 
INFO  @ Tue, 03 Jan 2017 15:45:53:  33000000 
INFO  @ Tue, 03 Jan 2017 15:45:55:  34000000 
INFO  @ Tue, 03 Jan 2017 15:45:56:  35000000 
INFO  @ Tue, 03 Jan 2017 15:45:58:  36000000 
INFO  @ Tue, 03 Jan 2017 15:45:59:  37000000 
INFO  @ Tue, 03 Jan 2017 15:46:01:  38000000 
INFO  @ Tue, 03 Jan 2017 15:46:02:  39000000 
INFO  @ Tue, 03 Jan 2017 15:46:04:  40000000 
INFO  @ Tue, 03 Jan 2017 15:46:06:  41000000 
INFO  @ Tue, 03 Jan 2017 15:46:07:  42000000 
INFO  @ Tue, 03 Jan 2017 15:46:09:  43000000 
INFO  @ Tue, 03 Jan 2017 15:46:10:  44000000 
INFO  @ Tue, 03 Jan 2017 15:46:12:  45000000 
INFO  @ Tue, 03 Jan 2017 15:46:13:  46000000 
INFO  @ Tue, 03 Jan 2017 15:46:15:  47000000 
INFO  @ Tue, 03 Jan 2017 15:46:16:  48000000 
INFO  @ Tue, 03 Jan 2017 15:46:18:  49000000 
INFO  @ Tue, 03 Jan 2017 15:46:20:  50000000 
INFO  @ Tue, 03 Jan 2017 15:46:22: #1 tag size is determined as 109 bps 
INFO  @ Tue, 03 Jan 2017 15:46:22: #1 tag size = 109 
INFO  @ Tue, 03 Jan 2017 15:46:22: #1  total tags in treatment: 13430716 
INFO  @ Tue, 03 Jan 2017 15:46:22: #1  total tags in control: 50000000 
INFO  @ Tue, 03 Jan 2017 15:46:22: #1 finished! 
INFO  @ Tue, 03 Jan 2017 15:46:22: #2 Build Peak Model... 
INFO  @ Tue, 03 Jan 2017 15:46:22: #2 Skipped... 
INFO  @ Tue, 03 Jan 2017 15:46:22: #2 Use 160 as fragment length 
INFO  @ Tue, 03 Jan 2017 15:46:22: #3 Call peaks... 
INFO  @ Tue, 03 Jan 2017 15:46:22: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Tue, 03 Jan 2017 15:46:22: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 03 Jan 2017 15:48:54: #3 Call peaks for each chromosome... 
INFO  @ Tue, 03 Jan 2017 15:51:32: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Tue, 03 Jan 2017 15:51:39: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Tue, 03 Jan 2017 15:51:44: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370878_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Tue, 03 Jan 2017 15:51:50: Done!

Num	3
ID	task.callpeak_macs2.macs2_rep1_pr2.line_71.id_12
Name	macs2 rep1-pr2
Thread	thread_Root
PID	22373

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

Start	2017-01-03 14:25:33
End	2017-01-03 15:53:58
Elapsed	01:28:25
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/align/pseudo_reps/rep1/pr2/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_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/ZSCAN22/out/align/pseudo_reps/rep1/pr2/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 160 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_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/ZSCAN22/out/align/pseudo_reps/rep1/pr2/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 160 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_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/ZSCAN22/out/align/pseudo_reps/rep1/pr2/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_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--------------------
33496 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Tue, 03 Jan 2017 15:36:32: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/align/pseudo_reps/rep1/pr2/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 160 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/align/pseudo_reps/rep1/pr2/SRR1370878_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 15:36:32: #1 read tag files... 
INFO  @ Tue, 03 Jan 2017 15:36:32: #1 read treatment tags... 
INFO  @ Tue, 03 Jan 2017 15:36:39:  1000000 
INFO  @ Tue, 03 Jan 2017 15:36:41:  2000000 
INFO  @ Tue, 03 Jan 2017 15:36:42:  3000000 
INFO  @ Tue, 03 Jan 2017 15:36:44:  4000000 
INFO  @ Tue, 03 Jan 2017 15:36:46:  5000000 
INFO  @ Tue, 03 Jan 2017 15:36:47:  6000000 
INFO  @ Tue, 03 Jan 2017 15:36:49:  7000000 
INFO  @ Tue, 03 Jan 2017 15:36:51:  8000000 
INFO  @ Tue, 03 Jan 2017 15:36:52:  9000000 
INFO  @ Tue, 03 Jan 2017 15:36:54:  10000000 
INFO  @ Tue, 03 Jan 2017 15:36:56:  11000000 
INFO  @ Tue, 03 Jan 2017 15:36:58:  12000000 
INFO  @ Tue, 03 Jan 2017 15:37:00:  13000000 
INFO  @ Tue, 03 Jan 2017 15:37:01: #1.2 read input tags... 
INFO  @ Tue, 03 Jan 2017 15:37:03:  1000000 
INFO  @ Tue, 03 Jan 2017 15:37:04:  2000000 
INFO  @ Tue, 03 Jan 2017 15:37:06:  3000000 
INFO  @ Tue, 03 Jan 2017 15:37:08:  4000000 
INFO  @ Tue, 03 Jan 2017 15:37:09:  5000000 
INFO  @ Tue, 03 Jan 2017 15:37:11:  6000000 
INFO  @ Tue, 03 Jan 2017 15:37:12:  7000000 
INFO  @ Tue, 03 Jan 2017 15:37:14:  8000000 
INFO  @ Tue, 03 Jan 2017 15:37:16:  9000000 
INFO  @ Tue, 03 Jan 2017 15:37:17:  10000000 
INFO  @ Tue, 03 Jan 2017 15:37:19:  11000000 
INFO  @ Tue, 03 Jan 2017 15:37:21:  12000000 
INFO  @ Tue, 03 Jan 2017 15:37:22:  13000000 
INFO  @ Tue, 03 Jan 2017 15:37:24:  14000000 
INFO  @ Tue, 03 Jan 2017 15:37:25:  15000000 
INFO  @ Tue, 03 Jan 2017 15:37:27:  16000000 
INFO  @ Tue, 03 Jan 2017 15:37:29:  17000000 
INFO  @ Tue, 03 Jan 2017 15:37:30:  18000000 
INFO  @ Tue, 03 Jan 2017 15:37:32:  19000000 
INFO  @ Tue, 03 Jan 2017 15:37:33:  20000000 
INFO  @ Tue, 03 Jan 2017 15:37:35:  21000000 
INFO  @ Tue, 03 Jan 2017 15:37:36:  22000000 
INFO  @ Tue, 03 Jan 2017 15:37:38:  23000000 
INFO  @ Tue, 03 Jan 2017 15:37:39:  24000000 
INFO  @ Tue, 03 Jan 2017 15:37:41:  25000000 
INFO  @ Tue, 03 Jan 2017 15:37:42:  26000000 
INFO  @ Tue, 03 Jan 2017 15:37:44:  27000000 
INFO  @ Tue, 03 Jan 2017 15:37:45:  28000000 
INFO  @ Tue, 03 Jan 2017 15:37:47:  29000000 
INFO  @ Tue, 03 Jan 2017 15:37:48:  30000000 
INFO  @ Tue, 03 Jan 2017 15:37:50:  31000000 
INFO  @ Tue, 03 Jan 2017 15:37:51:  32000000 
INFO  @ Tue, 03 Jan 2017 15:37:53:  33000000 
INFO  @ Tue, 03 Jan 2017 15:37:54:  34000000 
INFO  @ Tue, 03 Jan 2017 15:37:56:  35000000 
INFO  @ Tue, 03 Jan 2017 15:37:57:  36000000 
INFO  @ Tue, 03 Jan 2017 15:37:59:  37000000 
INFO  @ Tue, 03 Jan 2017 15:38:01:  38000000 
INFO  @ Tue, 03 Jan 2017 15:38:02:  39000000 
INFO  @ Tue, 03 Jan 2017 15:38:04:  40000000 
INFO  @ Tue, 03 Jan 2017 15:38:05:  41000000 
INFO  @ Tue, 03 Jan 2017 15:38:07:  42000000 
INFO  @ Tue, 03 Jan 2017 15:38:09:  43000000 
INFO  @ Tue, 03 Jan 2017 15:38:10:  44000000 
INFO  @ Tue, 03 Jan 2017 15:38:12:  45000000 
INFO  @ Tue, 03 Jan 2017 15:38:13:  46000000 
INFO  @ Tue, 03 Jan 2017 15:38:15:  47000000 
INFO  @ Tue, 03 Jan 2017 15:38:16:  48000000 
INFO  @ Tue, 03 Jan 2017 15:38:18:  49000000 
INFO  @ Tue, 03 Jan 2017 15:38:20:  50000000 
INFO  @ Tue, 03 Jan 2017 15:38:21: #1 tag size is determined as 109 bps 
INFO  @ Tue, 03 Jan 2017 15:38:21: #1 tag size = 109 
INFO  @ Tue, 03 Jan 2017 15:38:21: #1  total tags in treatment: 13430715 
INFO  @ Tue, 03 Jan 2017 15:38:21: #1  total tags in control: 50000000 
INFO  @ Tue, 03 Jan 2017 15:38:21: #1 finished! 
INFO  @ Tue, 03 Jan 2017 15:38:21: #2 Build Peak Model... 
INFO  @ Tue, 03 Jan 2017 15:38:21: #2 Skipped... 
INFO  @ Tue, 03 Jan 2017 15:38:21: #2 Use 160 as fragment length 
INFO  @ Tue, 03 Jan 2017 15:38:21: #3 Call peaks... 
INFO  @ Tue, 03 Jan 2017 15:38:21: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Tue, 03 Jan 2017 15:38:21: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 03 Jan 2017 15:41:07: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 03 Jan 2017 15:41:07: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Tue, 03 Jan 2017 15:41:07: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Tue, 03 Jan 2017 15:41:07: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 03 Jan 2017 15:41:07: #3 Call peaks for each chromosome... 
INFO  @ Tue, 03 Jan 2017 15:46:13: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Tue, 03 Jan 2017 15:46:14: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Tue, 03 Jan 2017 15:46:17: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Tue, 03 Jan 2017 15:46:18: Done! 
INFO  @ Tue, 03 Jan 2017 15:46:21: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/align/pseudo_reps/rep1/pr2/SRR1370878_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/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 160 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/align/pseudo_reps/rep1/pr2/SRR1370878_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 15:46:21: #1 read tag files... 
INFO  @ Tue, 03 Jan 2017 15:46:21: #1 read treatment tags... 
INFO  @ Tue, 03 Jan 2017 15:46:23:  1000000 
INFO  @ Tue, 03 Jan 2017 15:46:25:  2000000 
INFO  @ Tue, 03 Jan 2017 15:46:26:  3000000 
INFO  @ Tue, 03 Jan 2017 15:46:28:  4000000 
INFO  @ Tue, 03 Jan 2017 15:46:30:  5000000 
INFO  @ Tue, 03 Jan 2017 15:46:31:  6000000 
INFO  @ Tue, 03 Jan 2017 15:46:33:  7000000 
INFO  @ Tue, 03 Jan 2017 15:46:35:  8000000 
INFO  @ Tue, 03 Jan 2017 15:46:36:  9000000 
INFO  @ Tue, 03 Jan 2017 15:46:38:  10000000 
INFO  @ Tue, 03 Jan 2017 15:46:40:  11000000 
INFO  @ Tue, 03 Jan 2017 15:46:41:  12000000 
INFO  @ Tue, 03 Jan 2017 15:46:43:  13000000 
INFO  @ Tue, 03 Jan 2017 15:46:45: #1.2 read input tags... 
INFO  @ Tue, 03 Jan 2017 15:46:46:  1000000 
INFO  @ Tue, 03 Jan 2017 15:46:48:  2000000 
INFO  @ Tue, 03 Jan 2017 15:46:50:  3000000 
INFO  @ Tue, 03 Jan 2017 15:46:51:  4000000 
INFO  @ Tue, 03 Jan 2017 15:46:53:  5000000 
INFO  @ Tue, 03 Jan 2017 15:46:55:  6000000 
INFO  @ Tue, 03 Jan 2017 15:46:56:  7000000 
INFO  @ Tue, 03 Jan 2017 15:46:58:  8000000 
INFO  @ Tue, 03 Jan 2017 15:46:59:  9000000 
INFO  @ Tue, 03 Jan 2017 15:47:01:  10000000 
INFO  @ Tue, 03 Jan 2017 15:47:03:  11000000 
INFO  @ Tue, 03 Jan 2017 15:47:04:  12000000 
INFO  @ Tue, 03 Jan 2017 15:47:06:  13000000 
INFO  @ Tue, 03 Jan 2017 15:47:08:  14000000 
INFO  @ Tue, 03 Jan 2017 15:47:09:  15000000 
INFO  @ Tue, 03 Jan 2017 15:47:11:  16000000 
INFO  @ Tue, 03 Jan 2017 15:47:13:  17000000 
INFO  @ Tue, 03 Jan 2017 15:47:14:  18000000 
INFO  @ Tue, 03 Jan 2017 15:47:16:  19000000 
INFO  @ Tue, 03 Jan 2017 15:47:17:  20000000 
INFO  @ Tue, 03 Jan 2017 15:47:19:  21000000 
INFO  @ Tue, 03 Jan 2017 15:47:20:  22000000 
INFO  @ Tue, 03 Jan 2017 15:47:22:  23000000 
INFO  @ Tue, 03 Jan 2017 15:47:24:  24000000 
INFO  @ Tue, 03 Jan 2017 15:47:26:  25000000 
INFO  @ Tue, 03 Jan 2017 15:47:28:  26000000 
INFO  @ Tue, 03 Jan 2017 15:47:29:  27000000 
INFO  @ Tue, 03 Jan 2017 15:47:31:  28000000 
INFO  @ Tue, 03 Jan 2017 15:47:33:  29000000 
INFO  @ Tue, 03 Jan 2017 15:47:34:  30000000 
INFO  @ Tue, 03 Jan 2017 15:47:36:  31000000 
INFO  @ Tue, 03 Jan 2017 15:47:38:  32000000 
INFO  @ Tue, 03 Jan 2017 15:47:39:  33000000 
INFO  @ Tue, 03 Jan 2017 15:47:41:  34000000 
INFO  @ Tue, 03 Jan 2017 15:47:42:  35000000 
INFO  @ Tue, 03 Jan 2017 15:47:44:  36000000 
INFO  @ Tue, 03 Jan 2017 15:47:46:  37000000 
INFO  @ Tue, 03 Jan 2017 15:47:47:  38000000 
INFO  @ Tue, 03 Jan 2017 15:47:49:  39000000 
INFO  @ Tue, 03 Jan 2017 15:47:50:  40000000 
INFO  @ Tue, 03 Jan 2017 15:47:52:  41000000 
INFO  @ Tue, 03 Jan 2017 15:47:54:  42000000 
INFO  @ Tue, 03 Jan 2017 15:47:55:  43000000 
INFO  @ Tue, 03 Jan 2017 15:47:57:  44000000 
INFO  @ Tue, 03 Jan 2017 15:47:58:  45000000 
INFO  @ Tue, 03 Jan 2017 15:48:00:  46000000 
INFO  @ Tue, 03 Jan 2017 15:48:02:  47000000 
INFO  @ Tue, 03 Jan 2017 15:48:03:  48000000 
INFO  @ Tue, 03 Jan 2017 15:48:05:  49000000 
INFO  @ Tue, 03 Jan 2017 15:48:06:  50000000 
INFO  @ Tue, 03 Jan 2017 15:48:08: #1 tag size is determined as 109 bps 
INFO  @ Tue, 03 Jan 2017 15:48:08: #1 tag size = 109 
INFO  @ Tue, 03 Jan 2017 15:48:08: #1  total tags in treatment: 13430715 
INFO  @ Tue, 03 Jan 2017 15:48:08: #1  total tags in control: 50000000 
INFO  @ Tue, 03 Jan 2017 15:48:08: #1 finished! 
INFO  @ Tue, 03 Jan 2017 15:48:08: #2 Build Peak Model... 
INFO  @ Tue, 03 Jan 2017 15:48:08: #2 Skipped... 
INFO  @ Tue, 03 Jan 2017 15:48:08: #2 Use 160 as fragment length 
INFO  @ Tue, 03 Jan 2017 15:48:08: #3 Call peaks... 
INFO  @ Tue, 03 Jan 2017 15:48:08: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Tue, 03 Jan 2017 15:48:08: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 03 Jan 2017 15:50:50: #3 Call peaks for each chromosome... 
INFO  @ Tue, 03 Jan 2017 15:53:24: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Tue, 03 Jan 2017 15:53:31: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Tue, 03 Jan 2017 15:53:36: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370878_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Tue, 03 Jan 2017 15:53:41: Done!

Num	4
ID	task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_13
Name	naive_overlap_thresh
Thread	thread_Root
PID	22599

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

Start	2017-01-03 16:40:14
End	2017-01-03 20:44:00
Elapsed	04:03:45
Timeout	01:00:00
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/spp/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370878_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370878_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/spp/overlap/SRR1370878_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/ZSCAN22/out/peak/spp/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370878_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/ZSCAN22/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370878_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/ZSCAN22/out/peak/spp/overlap/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/spp/overlap/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/spp/overlap/SRR1370878_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/ZSCAN22/out/peak/spp/overlap/SRR1370878_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/ZSCAN22/out/peak/spp/overlap/SRR1370878_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/ZSCAN22/out/peak/spp/overlap/SRR1370878_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--------------------
40174 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL000219.1	100131	100292	.	0	.	54.0182213698306	-1	4.06149017662482	84

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL000219.1	100131	100292	.	0	.	54.0182213698306	-1	4.06149017662482	84

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL000219.1	100128	100273	.	0	.	43.3881805712111	-1	4.04285104255079	67

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL000219.1	100128	100273	.	0	.	43.3881805712111	-1	4.04285104255079	67

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/spp/overlap/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
GL000195.1	137374	137758	.	0	.	8.29459390316418	-1	1.4197367368394	192

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/spp/overlap/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
GL000195.1	137374	137758	.	0	.	8.29459390316418	-1	1.4197367368394	192

Num	5
ID	task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_16
Name	blacklist_filter peak 1
Thread	thread_Root
PID	35910

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

Start	2017-01-03 20:44:03
End	2017-01-03 20:45:13
Elapsed	00:01:10
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/spp/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/spp/rep1/SRR1370878_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/ZSCAN22/out/peak/spp/rep1/SRR1370878_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/ZSCAN22/out/peak/spp/rep1/SRR1370878_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--------------------
35914 (process ID) old priority 0, new priority 10
Waiting for 59 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/spp/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
GL000219.1	100094	100321	.	0	.	94.9048162818697	-1	4.01940710801888	93

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/spp/rep1/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
GL000219.1	100094	100321	.	0	.	94.9048162818697	-1	4.01940710801888	93

Num	6
ID	task.report.peak2hammock.line_412.id_17
Name	peak2hammock
Thread	thread_Root
PID	40886

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

Start	2017-01-03 20:45:14
End	2017-01-03 20:45:27
Elapsed	00:00:12
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/spp/overlap/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/spp/overlap/SRR1370878_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/ZSCAN22/out/peak/spp/overlap/SRR1370878_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/ZSCAN22/out/peak/spp/overlap/SRR1370878_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/ZSCAN22/out/peak/spp/overlap/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/peak/spp/overlap/SRR1370878_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/ZSCAN22/out/peak/spp/overlap/SRR1370878_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp

   
--------------------Stdout--------------------
40890 (process ID) old priority 0, new priority 10

Num	7
ID	task.graphviz.report.line_97.id_18
Name	report
Thread	thread_Root
PID	41760

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

Start	2017-01-03 20:45:28
End	2017-01-03 20:45:38
Elapsed	00:00:10
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/ZSCAN22/out/report/ZSCAN22_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/report/ZSCAN22_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/report/ZSCAN22_workflow.svg" # to suppress dot font error (exit code=1)

   
--------------------Stdout--------------------
41764 (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, ZSCAN22, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZSCAN22/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN22/out/align/rep1/SRR1370878_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/ZSCAN22
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/ZSCAN22
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	46318.ZSCAN22.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

Timeline

Task Graph

Parallel (threads) details

Task details

Global scope