Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20170103_142503_097
Start time	2017-01-03 14:25:03
Run time	03:09:12.940
Tasks executed	7
Tasks failed	0
Tasks failed names
Arguments*	[-title, ZNF528, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF528/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/align/rep1/SRR1370882_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_142503_097/task.callpeak_macs2.macs2_rep1.line_71.id_10 chipseq.bds.20170103_142503_097/task.callpeak_macs2.macs2_rep1_pr1.line_71.id_11 chipseq.bds.20170103_142503_097/task.callpeak_macs2.macs2_rep1_pr2.line_71.id_12 chipseq.bds.20170103_142503_097/task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_13 chipseq.bds.20170103_142503_097/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_16 chipseq.bds.20170103_142503_097/task.report.peak2hammock.line_412.id_17 chipseq.bds.20170103_142503_097/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	22359

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

Start	2017-01-03 14:25:09
End	2017-01-03 16:35:23
Elapsed	02:10:14
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/align/rep1/SRR1370882_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/ZNF528/out/peak/macs2/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/signal/macs2/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/signal/macs2/rep1/SRR1370882_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/ZNF528/out/align/rep1/SRR1370882_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/ZNF528/out/peak/macs2/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 180 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/rep1/SRR1370882_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/ZNF528/out/peak/macs2/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/rep1/SRR1370882_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/ZNF528/out/align/rep1/SRR1370882_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/ZNF528/out/peak/macs2/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 180 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/rep1/SRR1370882_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/ZNF528/out/peak/macs2/rep1/SRR1370882_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/ZNF528/out/peak/macs2/rep1/SRR1370882_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/ZNF528/out/peak/macs2/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/rep1/SRR1370882_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/ZNF528/out/peak/macs2/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/rep1/SRR1370882_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/ZNF528/out/peak/macs2/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/rep1 -o "SRR1370882_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/ZNF528/out/peak/macs2/rep1/SRR1370882_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/ZNF528/out/peak/macs2/rep1/SRR1370882_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/ZNF528/out/peak/macs2/rep1/SRR1370882_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/ZNF528/out/peak/macs2/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/rep1/SRR1370882_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/ZNF528/out/peak/macs2/rep1/SRR1370882_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/ZNF528/out/signal/macs2/rep1/SRR1370882_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/ZNF528/out/peak/macs2/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/rep1/SRR1370882_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/ZNF528/out/align/rep1/SRR1370882_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/ZNF528/out/peak/macs2/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/rep1 -o "SRR1370882_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/ZNF528/out/peak/macs2/rep1/SRR1370882_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/ZNF528/out/peak/macs2/rep1/SRR1370882_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/ZNF528/out/peak/macs2/rep1/SRR1370882_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/ZNF528/out/peak/macs2/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/rep1/SRR1370882_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/ZNF528/out/peak/macs2/rep1/SRR1370882_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/ZNF528/out/signal/macs2/rep1/SRR1370882_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/ZNF528/out/peak/macs2/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/rep1/SRR1370882_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/ZNF528/out/peak/macs2/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/rep1/SRR1370882_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--------------------
25721 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Tue, 03 Jan 2017 15:27:47: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/align/rep1/SRR1370882_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/ZNF528/out/peak/macs2/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 180 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/align/rep1/SRR1370882_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 15:27:47: #1 read tag files... 
INFO  @ Tue, 03 Jan 2017 15:27:47: #1 read treatment tags... 
INFO  @ Tue, 03 Jan 2017 15:27:48:  1000000 
INFO  @ Tue, 03 Jan 2017 15:27:50:  2000000 
INFO  @ Tue, 03 Jan 2017 15:27:51:  3000000 
INFO  @ Tue, 03 Jan 2017 15:27:53:  4000000 
INFO  @ Tue, 03 Jan 2017 15:27:54:  5000000 
INFO  @ Tue, 03 Jan 2017 15:27:56:  6000000 
INFO  @ Tue, 03 Jan 2017 15:27:57:  7000000 
INFO  @ Tue, 03 Jan 2017 15:28:01:  8000000 
INFO  @ Tue, 03 Jan 2017 15:28:02:  9000000 
INFO  @ Tue, 03 Jan 2017 15:28:04:  10000000 
INFO  @ Tue, 03 Jan 2017 15:28:06:  11000000 
INFO  @ Tue, 03 Jan 2017 15:28:07:  12000000 
INFO  @ Tue, 03 Jan 2017 15:28:09:  13000000 
INFO  @ Tue, 03 Jan 2017 15:28:11:  14000000 
INFO  @ Tue, 03 Jan 2017 15:28:12:  15000000 
INFO  @ Tue, 03 Jan 2017 15:28:14:  16000000 
INFO  @ Tue, 03 Jan 2017 15:28:15:  17000000 
INFO  @ Tue, 03 Jan 2017 15:28:17:  18000000 
INFO  @ Tue, 03 Jan 2017 15:28:19:  19000000 
INFO  @ Tue, 03 Jan 2017 15:28:20:  20000000 
INFO  @ Tue, 03 Jan 2017 15:28:22:  21000000 
INFO  @ Tue, 03 Jan 2017 15:28:23:  22000000 
INFO  @ Tue, 03 Jan 2017 15:28:25:  23000000 
INFO  @ Tue, 03 Jan 2017 15:28:26:  24000000 
INFO  @ Tue, 03 Jan 2017 15:28:28:  25000000 
INFO  @ Tue, 03 Jan 2017 15:28:29:  26000000 
INFO  @ Tue, 03 Jan 2017 15:28:31:  27000000 
INFO  @ Tue, 03 Jan 2017 15:28:33:  28000000 
INFO  @ Tue, 03 Jan 2017 15:28:34:  29000000 
INFO  @ Tue, 03 Jan 2017 15:28:36:  30000000 
INFO  @ Tue, 03 Jan 2017 15:28:37:  31000000 
INFO  @ Tue, 03 Jan 2017 15:28:43: #1.2 read input tags... 
INFO  @ Tue, 03 Jan 2017 15:28:46:  1000000 
INFO  @ Tue, 03 Jan 2017 15:28:47:  2000000 
INFO  @ Tue, 03 Jan 2017 15:28:49:  3000000 
INFO  @ Tue, 03 Jan 2017 15:28:50:  4000000 
INFO  @ Tue, 03 Jan 2017 15:28:52:  5000000 
INFO  @ Tue, 03 Jan 2017 15:28:53:  6000000 
INFO  @ Tue, 03 Jan 2017 15:28:55:  7000000 
INFO  @ Tue, 03 Jan 2017 15:28:56:  8000000 
INFO  @ Tue, 03 Jan 2017 15:28:58:  9000000 
INFO  @ Tue, 03 Jan 2017 15:28:59:  10000000 
INFO  @ Tue, 03 Jan 2017 15:29:01:  11000000 
INFO  @ Tue, 03 Jan 2017 15:29:02:  12000000 
INFO  @ Tue, 03 Jan 2017 15:29:04:  13000000 
INFO  @ Tue, 03 Jan 2017 15:29:05:  14000000 
INFO  @ Tue, 03 Jan 2017 15:29:07:  15000000 
INFO  @ Tue, 03 Jan 2017 15:29:08:  16000000 
INFO  @ Tue, 03 Jan 2017 15:29:09:  17000000 
INFO  @ Tue, 03 Jan 2017 15:29:11:  18000000 
INFO  @ Tue, 03 Jan 2017 15:29:12:  19000000 
INFO  @ Tue, 03 Jan 2017 15:29:14:  20000000 
INFO  @ Tue, 03 Jan 2017 15:29:15:  21000000 
INFO  @ Tue, 03 Jan 2017 15:29:17:  22000000 
INFO  @ Tue, 03 Jan 2017 15:29:19:  23000000 
INFO  @ Tue, 03 Jan 2017 15:29:20:  24000000 
INFO  @ Tue, 03 Jan 2017 15:29:22:  25000000 
INFO  @ Tue, 03 Jan 2017 15:29:23:  26000000 
INFO  @ Tue, 03 Jan 2017 15:29:25:  27000000 
INFO  @ Tue, 03 Jan 2017 15:29:26:  28000000 
INFO  @ Tue, 03 Jan 2017 15:29:28:  29000000 
INFO  @ Tue, 03 Jan 2017 15:29:29:  30000000 
INFO  @ Tue, 03 Jan 2017 15:29:31:  31000000 
INFO  @ Tue, 03 Jan 2017 15:29:32:  32000000 
INFO  @ Tue, 03 Jan 2017 15:29:34:  33000000 
INFO  @ Tue, 03 Jan 2017 15:29:36:  34000000 
INFO  @ Tue, 03 Jan 2017 15:29:37:  35000000 
INFO  @ Tue, 03 Jan 2017 15:29:39:  36000000 
INFO  @ Tue, 03 Jan 2017 15:29:40:  37000000 
INFO  @ Tue, 03 Jan 2017 15:29:42:  38000000 
INFO  @ Tue, 03 Jan 2017 15:29:43:  39000000 
INFO  @ Tue, 03 Jan 2017 15:29:45:  40000000 
INFO  @ Tue, 03 Jan 2017 15:29:46:  41000000 
INFO  @ Tue, 03 Jan 2017 15:29:48:  42000000 
INFO  @ Tue, 03 Jan 2017 15:29:49:  43000000 
INFO  @ Tue, 03 Jan 2017 15:29:51:  44000000 
INFO  @ Tue, 03 Jan 2017 15:29:52:  45000000 
INFO  @ Tue, 03 Jan 2017 15:29:53:  46000000 
INFO  @ Tue, 03 Jan 2017 15:29:55:  47000000 
INFO  @ Tue, 03 Jan 2017 15:29:57:  48000000 
INFO  @ Tue, 03 Jan 2017 15:29:58:  49000000 
INFO  @ Tue, 03 Jan 2017 15:30:00:  50000000 
INFO  @ Tue, 03 Jan 2017 15:30:02: #1 tag size is determined as 103 bps 
INFO  @ Tue, 03 Jan 2017 15:30:02: #1 tag size = 103 
INFO  @ Tue, 03 Jan 2017 15:30:02: #1  total tags in treatment: 31255109 
INFO  @ Tue, 03 Jan 2017 15:30:02: #1  total tags in control: 50000000 
INFO  @ Tue, 03 Jan 2017 15:30:02: #1 finished! 
INFO  @ Tue, 03 Jan 2017 15:30:02: #2 Build Peak Model... 
INFO  @ Tue, 03 Jan 2017 15:30:02: #2 Skipped... 
INFO  @ Tue, 03 Jan 2017 15:30:02: #2 Use 180 as fragment length 
INFO  @ Tue, 03 Jan 2017 15:30:02: #3 Call peaks... 
INFO  @ Tue, 03 Jan 2017 15:30:02: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Tue, 03 Jan 2017 15:30:02: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 03 Jan 2017 15:32:55: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 03 Jan 2017 15:32:55: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Tue, 03 Jan 2017 15:32:55: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Tue, 03 Jan 2017 15:32:55: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 03 Jan 2017 15:32:55: #3 Call peaks for each chromosome... 
INFO  @ Tue, 03 Jan 2017 15:38:57: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Tue, 03 Jan 2017 15:38:59: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Tue, 03 Jan 2017 15:39:02: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Tue, 03 Jan 2017 15:39:03: Done! 
INFO  @ Tue, 03 Jan 2017 15:39:07: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/align/rep1/SRR1370882_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/ZNF528/out/peak/macs2/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 180 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/align/rep1/SRR1370882_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 15:39:07: #1 read tag files... 
INFO  @ Tue, 03 Jan 2017 15:39:07: #1 read treatment tags... 
INFO  @ Tue, 03 Jan 2017 15:39:09:  1000000 
INFO  @ Tue, 03 Jan 2017 15:39:11:  2000000 
INFO  @ Tue, 03 Jan 2017 15:39:12:  3000000 
INFO  @ Tue, 03 Jan 2017 15:39:14:  4000000 
INFO  @ Tue, 03 Jan 2017 15:39:15:  5000000 
INFO  @ Tue, 03 Jan 2017 15:39:17:  6000000 
INFO  @ Tue, 03 Jan 2017 15:39:18:  7000000 
INFO  @ Tue, 03 Jan 2017 15:39:20:  8000000 
INFO  @ Tue, 03 Jan 2017 15:39:21:  9000000 
INFO  @ Tue, 03 Jan 2017 15:39:23:  10000000 
INFO  @ Tue, 03 Jan 2017 15:39:24:  11000000 
INFO  @ Tue, 03 Jan 2017 15:39:26:  12000000 
INFO  @ Tue, 03 Jan 2017 15:39:27:  13000000 
INFO  @ Tue, 03 Jan 2017 15:39:29:  14000000 
INFO  @ Tue, 03 Jan 2017 15:39:31:  15000000 
INFO  @ Tue, 03 Jan 2017 15:39:32:  16000000 
INFO  @ Tue, 03 Jan 2017 15:39:34:  17000000 
INFO  @ Tue, 03 Jan 2017 15:39:35:  18000000 
INFO  @ Tue, 03 Jan 2017 15:39:37:  19000000 
INFO  @ Tue, 03 Jan 2017 15:39:38:  20000000 
INFO  @ Tue, 03 Jan 2017 15:39:40:  21000000 
INFO  @ Tue, 03 Jan 2017 15:39:41:  22000000 
INFO  @ Tue, 03 Jan 2017 15:39:43:  23000000 
INFO  @ Tue, 03 Jan 2017 15:39:44:  24000000 
INFO  @ Tue, 03 Jan 2017 15:39:46:  25000000 
INFO  @ Tue, 03 Jan 2017 15:39:47:  26000000 
INFO  @ Tue, 03 Jan 2017 15:39:49:  27000000 
INFO  @ Tue, 03 Jan 2017 15:39:50:  28000000 
INFO  @ Tue, 03 Jan 2017 15:39:52:  29000000 
INFO  @ Tue, 03 Jan 2017 15:39:53:  30000000 
INFO  @ Tue, 03 Jan 2017 15:39:55:  31000000 
INFO  @ Tue, 03 Jan 2017 15:39:56: #1.2 read input tags... 
INFO  @ Tue, 03 Jan 2017 15:39:58:  1000000 
INFO  @ Tue, 03 Jan 2017 15:39:59:  2000000 
INFO  @ Tue, 03 Jan 2017 15:40:01:  3000000 
INFO  @ Tue, 03 Jan 2017 15:40:03:  4000000 
INFO  @ Tue, 03 Jan 2017 15:40:04:  5000000 
INFO  @ Tue, 03 Jan 2017 15:40:06:  6000000 
INFO  @ Tue, 03 Jan 2017 15:40:07:  7000000 
INFO  @ Tue, 03 Jan 2017 15:40:09:  8000000 
INFO  @ Tue, 03 Jan 2017 15:40:10:  9000000 
INFO  @ Tue, 03 Jan 2017 15:40:12:  10000000 
INFO  @ Tue, 03 Jan 2017 15:40:13:  11000000 
INFO  @ Tue, 03 Jan 2017 15:40:15:  12000000 
INFO  @ Tue, 03 Jan 2017 15:40:17:  13000000 
INFO  @ Tue, 03 Jan 2017 15:40:18:  14000000 
INFO  @ Tue, 03 Jan 2017 15:40:20:  15000000 
INFO  @ Tue, 03 Jan 2017 15:40:21:  16000000 
INFO  @ Tue, 03 Jan 2017 15:40:23:  17000000 
INFO  @ Tue, 03 Jan 2017 15:40:24:  18000000 
INFO  @ Tue, 03 Jan 2017 15:40:26:  19000000 
INFO  @ Tue, 03 Jan 2017 15:40:28:  20000000 
INFO  @ Tue, 03 Jan 2017 15:40:29:  21000000 
INFO  @ Tue, 03 Jan 2017 15:40:31:  22000000 
INFO  @ Tue, 03 Jan 2017 15:40:32:  23000000 
INFO  @ Tue, 03 Jan 2017 15:40:34:  24000000 
INFO  @ Tue, 03 Jan 2017 15:40:35:  25000000 
INFO  @ Tue, 03 Jan 2017 15:40:37:  26000000 
INFO  @ Tue, 03 Jan 2017 15:40:38:  27000000 
INFO  @ Tue, 03 Jan 2017 15:40:40:  28000000 
INFO  @ Tue, 03 Jan 2017 15:40:41:  29000000 
INFO  @ Tue, 03 Jan 2017 15:40:43:  30000000 
INFO  @ Tue, 03 Jan 2017 15:40:44:  31000000 
INFO  @ Tue, 03 Jan 2017 15:40:46:  32000000 
INFO  @ Tue, 03 Jan 2017 15:40:47:  33000000 
INFO  @ Tue, 03 Jan 2017 15:40:49:  34000000 
INFO  @ Tue, 03 Jan 2017 15:40:50:  35000000 
INFO  @ Tue, 03 Jan 2017 15:40:52:  36000000 
INFO  @ Tue, 03 Jan 2017 15:40:54:  37000000 
INFO  @ Tue, 03 Jan 2017 15:40:55:  38000000 
INFO  @ Tue, 03 Jan 2017 15:40:57:  39000000 
INFO  @ Tue, 03 Jan 2017 15:40:58:  40000000 
INFO  @ Tue, 03 Jan 2017 15:41:00:  41000000 
INFO  @ Tue, 03 Jan 2017 15:41:01:  42000000 
INFO  @ Tue, 03 Jan 2017 15:41:03:  43000000 
INFO  @ Tue, 03 Jan 2017 15:41:04:  44000000 
INFO  @ Tue, 03 Jan 2017 15:41:06:  45000000 
INFO  @ Tue, 03 Jan 2017 15:41:07:  46000000 
INFO  @ Tue, 03 Jan 2017 15:41:09:  47000000 
INFO  @ Tue, 03 Jan 2017 15:41:10:  48000000 
INFO  @ Tue, 03 Jan 2017 15:41:12:  49000000 
INFO  @ Tue, 03 Jan 2017 15:41:13:  50000000 
INFO  @ Tue, 03 Jan 2017 15:41:15: #1 tag size is determined as 103 bps 
INFO  @ Tue, 03 Jan 2017 15:41:15: #1 tag size = 103 
INFO  @ Tue, 03 Jan 2017 15:41:15: #1  total tags in treatment: 31255109 
INFO  @ Tue, 03 Jan 2017 15:41:15: #1  total tags in control: 50000000 
INFO  @ Tue, 03 Jan 2017 15:41:15: #1 finished! 
INFO  @ Tue, 03 Jan 2017 15:41:15: #2 Build Peak Model... 
INFO  @ Tue, 03 Jan 2017 15:41:15: #2 Skipped... 
INFO  @ Tue, 03 Jan 2017 15:41:15: #2 Use 180 as fragment length 
INFO  @ Tue, 03 Jan 2017 15:41:15: #3 Call peaks... 
INFO  @ Tue, 03 Jan 2017 15:41:15: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Tue, 03 Jan 2017 15:41:15: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 03 Jan 2017 15:44:33: #3 Call peaks for each chromosome... 
INFO  @ Tue, 03 Jan 2017 15:47:13: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Tue, 03 Jan 2017 15:47:20: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Tue, 03 Jan 2017 15:47:24: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Tue, 03 Jan 2017 15:47:27: Done! 
INFO  @ Tue, 03 Jan 2017 15:47:40: Read and build treatment bedGraph... 
INFO  @ Tue, 03 Jan 2017 15:48:44: Read and build control bedGraph... 
INFO  @ Tue, 03 Jan 2017 15:50:31: Build scoreTrackII... 
INFO  @ Tue, 03 Jan 2017 15:51:31: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Tue, 03 Jan 2017 15:57:39: Write bedGraph of scores... 
INFO  @ Tue, 03 Jan 2017 16:01:49: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_FE.bdg'! 
INFO  @ Tue, 03 Jan 2017 16:11:34: Read and build treatment bedGraph... 
INFO  @ Tue, 03 Jan 2017 16:12:40: Read and build control bedGraph... 
INFO  @ Tue, 03 Jan 2017 16:14:26: Build scoreTrackII... 
INFO  @ Tue, 03 Jan 2017 16:15:24: Values in your input bedGraph files will be multiplied by 31.255109 ... 
INFO  @ Tue, 03 Jan 2017 16:22:04: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Tue, 03 Jan 2017 16:22:49: Write bedGraph of scores... 
INFO  @ Tue, 03 Jan 2017 16:26:21: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/rep1/SRR1370882_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	22360

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

Start	2017-01-03 14:25:12
End	2017-01-03 15:46:09
Elapsed	01:20:57
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/align/pseudo_reps/rep1/pr1/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_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/ZNF528/out/align/pseudo_reps/rep1/pr1/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 180 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_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/ZNF528/out/align/pseudo_reps/rep1/pr1/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 180 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_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/ZNF528/out/align/pseudo_reps/rep1/pr1/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_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--------------------
25720 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Tue, 03 Jan 2017 15:27:47: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/align/pseudo_reps/rep1/pr1/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 180 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/align/pseudo_reps/rep1/pr1/SRR1370882_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 15:27:47: #1 read tag files... 
INFO  @ Tue, 03 Jan 2017 15:27:47: #1 read treatment tags... 
INFO  @ Tue, 03 Jan 2017 15:27:48:  1000000 
INFO  @ Tue, 03 Jan 2017 15:27:50:  2000000 
INFO  @ Tue, 03 Jan 2017 15:27:52:  3000000 
INFO  @ Tue, 03 Jan 2017 15:27:53:  4000000 
INFO  @ Tue, 03 Jan 2017 15:27:55:  5000000 
INFO  @ Tue, 03 Jan 2017 15:27:57:  6000000 
INFO  @ Tue, 03 Jan 2017 15:28:01:  7000000 
INFO  @ Tue, 03 Jan 2017 15:28:03:  8000000 
INFO  @ Tue, 03 Jan 2017 15:28:04:  9000000 
INFO  @ Tue, 03 Jan 2017 15:28:06:  10000000 
INFO  @ Tue, 03 Jan 2017 15:28:08:  11000000 
INFO  @ Tue, 03 Jan 2017 15:28:09:  12000000 
INFO  @ Tue, 03 Jan 2017 15:28:11:  13000000 
INFO  @ Tue, 03 Jan 2017 15:28:13:  14000000 
INFO  @ Tue, 03 Jan 2017 15:28:14:  15000000 
INFO  @ Tue, 03 Jan 2017 15:28:17: #1.2 read input tags... 
INFO  @ Tue, 03 Jan 2017 15:28:18:  1000000 
INFO  @ Tue, 03 Jan 2017 15:28:20:  2000000 
INFO  @ Tue, 03 Jan 2017 15:28:21:  3000000 
INFO  @ Tue, 03 Jan 2017 15:28:23:  4000000 
INFO  @ Tue, 03 Jan 2017 15:28:25:  5000000 
INFO  @ Tue, 03 Jan 2017 15:28:26:  6000000 
INFO  @ Tue, 03 Jan 2017 15:28:28:  7000000 
INFO  @ Tue, 03 Jan 2017 15:28:29:  8000000 
INFO  @ Tue, 03 Jan 2017 15:28:31:  9000000 
INFO  @ Tue, 03 Jan 2017 15:28:32:  10000000 
INFO  @ Tue, 03 Jan 2017 15:28:34:  11000000 
INFO  @ Tue, 03 Jan 2017 15:28:36:  12000000 
INFO  @ Tue, 03 Jan 2017 15:28:37:  13000000 
INFO  @ Tue, 03 Jan 2017 15:28:39:  14000000 
INFO  @ Tue, 03 Jan 2017 15:28:40:  15000000 
INFO  @ Tue, 03 Jan 2017 15:28:42:  16000000 
INFO  @ Tue, 03 Jan 2017 15:28:43:  17000000 
INFO  @ Tue, 03 Jan 2017 15:28:45:  18000000 
INFO  @ Tue, 03 Jan 2017 15:28:47:  19000000 
INFO  @ Tue, 03 Jan 2017 15:28:48:  20000000 
INFO  @ Tue, 03 Jan 2017 15:28:50:  21000000 
INFO  @ Tue, 03 Jan 2017 15:28:52:  22000000 
INFO  @ Tue, 03 Jan 2017 15:28:53:  23000000 
INFO  @ Tue, 03 Jan 2017 15:28:55:  24000000 
INFO  @ Tue, 03 Jan 2017 15:28:57:  25000000 
INFO  @ Tue, 03 Jan 2017 15:28:58:  26000000 
INFO  @ Tue, 03 Jan 2017 15:29:00:  27000000 
INFO  @ Tue, 03 Jan 2017 15:29:01:  28000000 
INFO  @ Tue, 03 Jan 2017 15:29:03:  29000000 
INFO  @ Tue, 03 Jan 2017 15:29:04:  30000000 
INFO  @ Tue, 03 Jan 2017 15:29:06:  31000000 
INFO  @ Tue, 03 Jan 2017 15:29:07:  32000000 
INFO  @ Tue, 03 Jan 2017 15:29:09:  33000000 
INFO  @ Tue, 03 Jan 2017 15:29:10:  34000000 
INFO  @ Tue, 03 Jan 2017 15:29:12:  35000000 
INFO  @ Tue, 03 Jan 2017 15:29:14:  36000000 
INFO  @ Tue, 03 Jan 2017 15:29:15:  37000000 
INFO  @ Tue, 03 Jan 2017 15:29:17:  38000000 
INFO  @ Tue, 03 Jan 2017 15:29:18:  39000000 
INFO  @ Tue, 03 Jan 2017 15:29:20:  40000000 
INFO  @ Tue, 03 Jan 2017 15:29:21:  41000000 
INFO  @ Tue, 03 Jan 2017 15:29:23:  42000000 
INFO  @ Tue, 03 Jan 2017 15:29:24:  43000000 
INFO  @ Tue, 03 Jan 2017 15:29:26:  44000000 
INFO  @ Tue, 03 Jan 2017 15:29:27:  45000000 
INFO  @ Tue, 03 Jan 2017 15:29:29:  46000000 
INFO  @ Tue, 03 Jan 2017 15:29:30:  47000000 
INFO  @ Tue, 03 Jan 2017 15:29:32:  48000000 
INFO  @ Tue, 03 Jan 2017 15:29:33:  49000000 
INFO  @ Tue, 03 Jan 2017 15:29:35:  50000000 
INFO  @ Tue, 03 Jan 2017 15:29:37: #1 tag size is determined as 108 bps 
INFO  @ Tue, 03 Jan 2017 15:29:37: #1 tag size = 108 
INFO  @ Tue, 03 Jan 2017 15:29:37: #1  total tags in treatment: 15627555 
INFO  @ Tue, 03 Jan 2017 15:29:37: #1  total tags in control: 50000000 
INFO  @ Tue, 03 Jan 2017 15:29:37: #1 finished! 
INFO  @ Tue, 03 Jan 2017 15:29:37: #2 Build Peak Model... 
INFO  @ Tue, 03 Jan 2017 15:29:37: #2 Skipped... 
INFO  @ Tue, 03 Jan 2017 15:29:37: #2 Use 180 as fragment length 
INFO  @ Tue, 03 Jan 2017 15:29:37: #3 Call peaks... 
INFO  @ Tue, 03 Jan 2017 15:29:37: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Tue, 03 Jan 2017 15:29:37: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 03 Jan 2017 15:33:10: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 03 Jan 2017 15:33:10: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Tue, 03 Jan 2017 15:33:10: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Tue, 03 Jan 2017 15:33:10: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 03 Jan 2017 15:33:10: #3 Call peaks for each chromosome... 
INFO  @ Tue, 03 Jan 2017 15:38:25: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Tue, 03 Jan 2017 15:38:31: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Tue, 03 Jan 2017 15:38:35: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Tue, 03 Jan 2017 15:38:40: Done! 
INFO  @ Tue, 03 Jan 2017 15:38:43: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/align/pseudo_reps/rep1/pr1/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 180 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/align/pseudo_reps/rep1/pr1/SRR1370882_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 15:38:43: #1 read tag files... 
INFO  @ Tue, 03 Jan 2017 15:38:43: #1 read treatment tags... 
INFO  @ Tue, 03 Jan 2017 15:38:46:  1000000 
INFO  @ Tue, 03 Jan 2017 15:38:47:  2000000 
INFO  @ Tue, 03 Jan 2017 15:38:49:  3000000 
INFO  @ Tue, 03 Jan 2017 15:38:50:  4000000 
INFO  @ Tue, 03 Jan 2017 15:38:52:  5000000 
INFO  @ Tue, 03 Jan 2017 15:38:54:  6000000 
INFO  @ Tue, 03 Jan 2017 15:38:55:  7000000 
INFO  @ Tue, 03 Jan 2017 15:38:58:  8000000 
INFO  @ Tue, 03 Jan 2017 15:38:59:  9000000 
INFO  @ Tue, 03 Jan 2017 15:39:01:  10000000 
INFO  @ Tue, 03 Jan 2017 15:39:03:  11000000 
INFO  @ Tue, 03 Jan 2017 15:39:04:  12000000 
INFO  @ Tue, 03 Jan 2017 15:39:06:  13000000 
INFO  @ Tue, 03 Jan 2017 15:39:08:  14000000 
INFO  @ Tue, 03 Jan 2017 15:39:10:  15000000 
INFO  @ Tue, 03 Jan 2017 15:39:12: #1.2 read input tags... 
INFO  @ Tue, 03 Jan 2017 15:39:14:  1000000 
INFO  @ Tue, 03 Jan 2017 15:39:16:  2000000 
INFO  @ Tue, 03 Jan 2017 15:39:17:  3000000 
INFO  @ Tue, 03 Jan 2017 15:39:19:  4000000 
INFO  @ Tue, 03 Jan 2017 15:39:20:  5000000 
INFO  @ Tue, 03 Jan 2017 15:39:22:  6000000 
INFO  @ Tue, 03 Jan 2017 15:39:23:  7000000 
INFO  @ Tue, 03 Jan 2017 15:39:25:  8000000 
INFO  @ Tue, 03 Jan 2017 15:39:26:  9000000 
INFO  @ Tue, 03 Jan 2017 15:39:28:  10000000 
INFO  @ Tue, 03 Jan 2017 15:39:29:  11000000 
INFO  @ Tue, 03 Jan 2017 15:39:31:  12000000 
INFO  @ Tue, 03 Jan 2017 15:39:33:  13000000 
INFO  @ Tue, 03 Jan 2017 15:39:34:  14000000 
INFO  @ Tue, 03 Jan 2017 15:39:36:  15000000 
INFO  @ Tue, 03 Jan 2017 15:39:37:  16000000 
INFO  @ Tue, 03 Jan 2017 15:39:39:  17000000 
INFO  @ Tue, 03 Jan 2017 15:39:40:  18000000 
INFO  @ Tue, 03 Jan 2017 15:39:42:  19000000 
INFO  @ Tue, 03 Jan 2017 15:39:43:  20000000 
INFO  @ Tue, 03 Jan 2017 15:39:45:  21000000 
INFO  @ Tue, 03 Jan 2017 15:39:46:  22000000 
INFO  @ Tue, 03 Jan 2017 15:39:48:  23000000 
INFO  @ Tue, 03 Jan 2017 15:39:49:  24000000 
INFO  @ Tue, 03 Jan 2017 15:39:51:  25000000 
INFO  @ Tue, 03 Jan 2017 15:39:52:  26000000 
INFO  @ Tue, 03 Jan 2017 15:39:54:  27000000 
INFO  @ Tue, 03 Jan 2017 15:39:55:  28000000 
INFO  @ Tue, 03 Jan 2017 15:39:57:  29000000 
INFO  @ Tue, 03 Jan 2017 15:39:58:  30000000 
INFO  @ Tue, 03 Jan 2017 15:40:00:  31000000 
INFO  @ Tue, 03 Jan 2017 15:40:01:  32000000 
INFO  @ Tue, 03 Jan 2017 15:40:03:  33000000 
INFO  @ Tue, 03 Jan 2017 15:40:04:  34000000 
INFO  @ Tue, 03 Jan 2017 15:40:06:  35000000 
INFO  @ Tue, 03 Jan 2017 15:40:07:  36000000 
INFO  @ Tue, 03 Jan 2017 15:40:09:  37000000 
INFO  @ Tue, 03 Jan 2017 15:40:10:  38000000 
INFO  @ Tue, 03 Jan 2017 15:40:12:  39000000 
INFO  @ Tue, 03 Jan 2017 15:40:14:  40000000 
INFO  @ Tue, 03 Jan 2017 15:40:15:  41000000 
INFO  @ Tue, 03 Jan 2017 15:40:17:  42000000 
INFO  @ Tue, 03 Jan 2017 15:40:18:  43000000 
INFO  @ Tue, 03 Jan 2017 15:40:20:  44000000 
INFO  @ Tue, 03 Jan 2017 15:40:21:  45000000 
INFO  @ Tue, 03 Jan 2017 15:40:23:  46000000 
INFO  @ Tue, 03 Jan 2017 15:40:24:  47000000 
INFO  @ Tue, 03 Jan 2017 15:40:26:  48000000 
INFO  @ Tue, 03 Jan 2017 15:40:27:  49000000 
INFO  @ Tue, 03 Jan 2017 15:40:29:  50000000 
INFO  @ Tue, 03 Jan 2017 15:40:30: #1 tag size is determined as 108 bps 
INFO  @ Tue, 03 Jan 2017 15:40:30: #1 tag size = 108 
INFO  @ Tue, 03 Jan 2017 15:40:30: #1  total tags in treatment: 15627555 
INFO  @ Tue, 03 Jan 2017 15:40:30: #1  total tags in control: 50000000 
INFO  @ Tue, 03 Jan 2017 15:40:30: #1 finished! 
INFO  @ Tue, 03 Jan 2017 15:40:30: #2 Build Peak Model... 
INFO  @ Tue, 03 Jan 2017 15:40:30: #2 Skipped... 
INFO  @ Tue, 03 Jan 2017 15:40:30: #2 Use 180 as fragment length 
INFO  @ Tue, 03 Jan 2017 15:40:30: #3 Call peaks... 
INFO  @ Tue, 03 Jan 2017 15:40:30: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Tue, 03 Jan 2017 15:40:30: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 03 Jan 2017 15:43:05: #3 Call peaks for each chromosome... 
INFO  @ Tue, 03 Jan 2017 15:45:36: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Tue, 03 Jan 2017 15:45:44: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Tue, 03 Jan 2017 15:45:49: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Tue, 03 Jan 2017 15:45:54: Done!

Num	3
ID	task.callpeak_macs2.macs2_rep1_pr2.line_71.id_12
Name	macs2 rep1-pr2
Thread	thread_Root
PID	22361

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

Start	2017-01-03 14:25:13
End	2017-01-03 15:46:08
Elapsed	01:20:55
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/align/pseudo_reps/rep1/pr2/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_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/ZNF528/out/align/pseudo_reps/rep1/pr2/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 180 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_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/ZNF528/out/align/pseudo_reps/rep1/pr2/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 180 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_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/ZNF528/out/align/pseudo_reps/rep1/pr2/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_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--------------------
32279 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Tue, 03 Jan 2017 15:28:04: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/align/pseudo_reps/rep1/pr2/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 180 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/align/pseudo_reps/rep1/pr2/SRR1370882_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 15:28:04: #1 read tag files... 
INFO  @ Tue, 03 Jan 2017 15:28:04: #1 read treatment tags... 
INFO  @ Tue, 03 Jan 2017 15:28:07:  1000000 
INFO  @ Tue, 03 Jan 2017 15:28:08:  2000000 
INFO  @ Tue, 03 Jan 2017 15:28:10:  3000000 
INFO  @ Tue, 03 Jan 2017 15:28:12:  4000000 
INFO  @ Tue, 03 Jan 2017 15:28:13:  5000000 
INFO  @ Tue, 03 Jan 2017 15:28:15:  6000000 
INFO  @ Tue, 03 Jan 2017 15:28:17:  7000000 
INFO  @ Tue, 03 Jan 2017 15:28:18:  8000000 
INFO  @ Tue, 03 Jan 2017 15:28:20:  9000000 
INFO  @ Tue, 03 Jan 2017 15:28:21:  10000000 
INFO  @ Tue, 03 Jan 2017 15:28:23:  11000000 
INFO  @ Tue, 03 Jan 2017 15:28:25:  12000000 
INFO  @ Tue, 03 Jan 2017 15:28:26:  13000000 
INFO  @ Tue, 03 Jan 2017 15:28:28:  14000000 
INFO  @ Tue, 03 Jan 2017 15:28:29:  15000000 
INFO  @ Tue, 03 Jan 2017 15:28:32: #1.2 read input tags... 
INFO  @ Tue, 03 Jan 2017 15:28:33:  1000000 
INFO  @ Tue, 03 Jan 2017 15:28:35:  2000000 
INFO  @ Tue, 03 Jan 2017 15:28:37:  3000000 
INFO  @ Tue, 03 Jan 2017 15:28:38:  4000000 
INFO  @ Tue, 03 Jan 2017 15:28:40:  5000000 
INFO  @ Tue, 03 Jan 2017 15:28:41:  6000000 
INFO  @ Tue, 03 Jan 2017 15:28:43:  7000000 
INFO  @ Tue, 03 Jan 2017 15:28:44:  8000000 
INFO  @ Tue, 03 Jan 2017 15:28:46:  9000000 
INFO  @ Tue, 03 Jan 2017 15:28:47:  10000000 
INFO  @ Tue, 03 Jan 2017 15:28:49:  11000000 
INFO  @ Tue, 03 Jan 2017 15:28:50:  12000000 
INFO  @ Tue, 03 Jan 2017 15:28:52:  13000000 
INFO  @ Tue, 03 Jan 2017 15:28:53:  14000000 
INFO  @ Tue, 03 Jan 2017 15:28:55:  15000000 
INFO  @ Tue, 03 Jan 2017 15:28:56:  16000000 
INFO  @ Tue, 03 Jan 2017 15:28:58:  17000000 
INFO  @ Tue, 03 Jan 2017 15:28:59:  18000000 
INFO  @ Tue, 03 Jan 2017 15:29:01:  19000000 
INFO  @ Tue, 03 Jan 2017 15:29:02:  20000000 
INFO  @ Tue, 03 Jan 2017 15:29:04:  21000000 
INFO  @ Tue, 03 Jan 2017 15:29:05:  22000000 
INFO  @ Tue, 03 Jan 2017 15:29:07:  23000000 
INFO  @ Tue, 03 Jan 2017 15:29:08:  24000000 
INFO  @ Tue, 03 Jan 2017 15:29:10:  25000000 
INFO  @ Tue, 03 Jan 2017 15:29:11:  26000000 
INFO  @ Tue, 03 Jan 2017 15:29:13:  27000000 
INFO  @ Tue, 03 Jan 2017 15:29:14:  28000000 
INFO  @ Tue, 03 Jan 2017 15:29:16:  29000000 
INFO  @ Tue, 03 Jan 2017 15:29:17:  30000000 
INFO  @ Tue, 03 Jan 2017 15:29:19:  31000000 
INFO  @ Tue, 03 Jan 2017 15:29:21:  32000000 
INFO  @ Tue, 03 Jan 2017 15:29:22:  33000000 
INFO  @ Tue, 03 Jan 2017 15:29:24:  34000000 
INFO  @ Tue, 03 Jan 2017 15:29:25:  35000000 
INFO  @ Tue, 03 Jan 2017 15:29:27:  36000000 
INFO  @ Tue, 03 Jan 2017 15:29:28:  37000000 
INFO  @ Tue, 03 Jan 2017 15:29:30:  38000000 
INFO  @ Tue, 03 Jan 2017 15:29:31:  39000000 
INFO  @ Tue, 03 Jan 2017 15:29:33:  40000000 
INFO  @ Tue, 03 Jan 2017 15:29:34:  41000000 
INFO  @ Tue, 03 Jan 2017 15:29:36:  42000000 
INFO  @ Tue, 03 Jan 2017 15:29:37:  43000000 
INFO  @ Tue, 03 Jan 2017 15:29:39:  44000000 
INFO  @ Tue, 03 Jan 2017 15:29:40:  45000000 
INFO  @ Tue, 03 Jan 2017 15:29:42:  46000000 
INFO  @ Tue, 03 Jan 2017 15:29:43:  47000000 
INFO  @ Tue, 03 Jan 2017 15:29:45:  48000000 
INFO  @ Tue, 03 Jan 2017 15:29:46:  49000000 
INFO  @ Tue, 03 Jan 2017 15:29:48:  50000000 
INFO  @ Tue, 03 Jan 2017 15:29:50: #1 tag size is determined as 109 bps 
INFO  @ Tue, 03 Jan 2017 15:29:50: #1 tag size = 109 
INFO  @ Tue, 03 Jan 2017 15:29:50: #1  total tags in treatment: 15627554 
INFO  @ Tue, 03 Jan 2017 15:29:50: #1  total tags in control: 50000000 
INFO  @ Tue, 03 Jan 2017 15:29:50: #1 finished! 
INFO  @ Tue, 03 Jan 2017 15:29:50: #2 Build Peak Model... 
INFO  @ Tue, 03 Jan 2017 15:29:50: #2 Skipped... 
INFO  @ Tue, 03 Jan 2017 15:29:50: #2 Use 180 as fragment length 
INFO  @ Tue, 03 Jan 2017 15:29:50: #3 Call peaks... 
INFO  @ Tue, 03 Jan 2017 15:29:50: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Tue, 03 Jan 2017 15:29:50: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 03 Jan 2017 15:32:40: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 03 Jan 2017 15:32:40: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Tue, 03 Jan 2017 15:32:40: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Tue, 03 Jan 2017 15:32:40: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 03 Jan 2017 15:32:40: #3 Call peaks for each chromosome... 
INFO  @ Tue, 03 Jan 2017 15:37:29: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Tue, 03 Jan 2017 15:37:30: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Tue, 03 Jan 2017 15:37:31: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Tue, 03 Jan 2017 15:37:32: Done! 
INFO  @ Tue, 03 Jan 2017 15:38:02: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/align/pseudo_reps/rep1/pr2/SRR1370882_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/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 180 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/align/pseudo_reps/rep1/pr2/SRR1370882_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 15:38:02: #1 read tag files... 
INFO  @ Tue, 03 Jan 2017 15:38:02: #1 read treatment tags... 
INFO  @ Tue, 03 Jan 2017 15:38:05:  1000000 
INFO  @ Tue, 03 Jan 2017 15:38:07:  2000000 
INFO  @ Tue, 03 Jan 2017 15:38:08:  3000000 
INFO  @ Tue, 03 Jan 2017 15:38:10:  4000000 
INFO  @ Tue, 03 Jan 2017 15:38:12:  5000000 
INFO  @ Tue, 03 Jan 2017 15:38:13:  6000000 
INFO  @ Tue, 03 Jan 2017 15:38:15:  7000000 
INFO  @ Tue, 03 Jan 2017 15:38:16:  8000000 
INFO  @ Tue, 03 Jan 2017 15:38:18:  9000000 
INFO  @ Tue, 03 Jan 2017 15:38:20:  10000000 
INFO  @ Tue, 03 Jan 2017 15:38:21:  11000000 
INFO  @ Tue, 03 Jan 2017 15:38:23:  12000000 
INFO  @ Tue, 03 Jan 2017 15:38:25:  13000000 
INFO  @ Tue, 03 Jan 2017 15:38:26:  14000000 
INFO  @ Tue, 03 Jan 2017 15:38:28:  15000000 
INFO  @ Tue, 03 Jan 2017 15:38:30: #1.2 read input tags... 
INFO  @ Tue, 03 Jan 2017 15:38:33:  1000000 
INFO  @ Tue, 03 Jan 2017 15:38:34:  2000000 
INFO  @ Tue, 03 Jan 2017 15:38:36:  3000000 
INFO  @ Tue, 03 Jan 2017 15:38:37:  4000000 
INFO  @ Tue, 03 Jan 2017 15:38:39:  5000000 
INFO  @ Tue, 03 Jan 2017 15:38:41:  6000000 
INFO  @ Tue, 03 Jan 2017 15:38:42:  7000000 
INFO  @ Tue, 03 Jan 2017 15:38:44:  8000000 
INFO  @ Tue, 03 Jan 2017 15:38:45:  9000000 
INFO  @ Tue, 03 Jan 2017 15:38:47:  10000000 
INFO  @ Tue, 03 Jan 2017 15:38:48:  11000000 
INFO  @ Tue, 03 Jan 2017 15:38:50:  12000000 
INFO  @ Tue, 03 Jan 2017 15:38:51:  13000000 
INFO  @ Tue, 03 Jan 2017 15:38:53:  14000000 
INFO  @ Tue, 03 Jan 2017 15:38:55:  15000000 
INFO  @ Tue, 03 Jan 2017 15:38:56:  16000000 
INFO  @ Tue, 03 Jan 2017 15:38:58:  17000000 
INFO  @ Tue, 03 Jan 2017 15:39:00:  18000000 
INFO  @ Tue, 03 Jan 2017 15:39:01:  19000000 
INFO  @ Tue, 03 Jan 2017 15:39:03:  20000000 
INFO  @ Tue, 03 Jan 2017 15:39:04:  21000000 
INFO  @ Tue, 03 Jan 2017 15:39:06:  22000000 
INFO  @ Tue, 03 Jan 2017 15:39:07:  23000000 
INFO  @ Tue, 03 Jan 2017 15:39:09:  24000000 
INFO  @ Tue, 03 Jan 2017 15:39:11:  25000000 
INFO  @ Tue, 03 Jan 2017 15:39:12:  26000000 
INFO  @ Tue, 03 Jan 2017 15:39:14:  27000000 
INFO  @ Tue, 03 Jan 2017 15:39:15:  28000000 
INFO  @ Tue, 03 Jan 2017 15:39:17:  29000000 
INFO  @ Tue, 03 Jan 2017 15:39:19:  30000000 
INFO  @ Tue, 03 Jan 2017 15:39:20:  31000000 
INFO  @ Tue, 03 Jan 2017 15:39:22:  32000000 
INFO  @ Tue, 03 Jan 2017 15:39:23:  33000000 
INFO  @ Tue, 03 Jan 2017 15:39:25:  34000000 
INFO  @ Tue, 03 Jan 2017 15:39:27:  35000000 
INFO  @ Tue, 03 Jan 2017 15:39:29:  36000000 
INFO  @ Tue, 03 Jan 2017 15:39:30:  37000000 
INFO  @ Tue, 03 Jan 2017 15:39:32:  38000000 
INFO  @ Tue, 03 Jan 2017 15:39:34:  39000000 
INFO  @ Tue, 03 Jan 2017 15:39:35:  40000000 
INFO  @ Tue, 03 Jan 2017 15:39:37:  41000000 
INFO  @ Tue, 03 Jan 2017 15:39:39:  42000000 
INFO  @ Tue, 03 Jan 2017 15:39:40:  43000000 
INFO  @ Tue, 03 Jan 2017 15:39:42:  44000000 
INFO  @ Tue, 03 Jan 2017 15:39:43:  45000000 
INFO  @ Tue, 03 Jan 2017 15:39:45:  46000000 
INFO  @ Tue, 03 Jan 2017 15:39:46:  47000000 
INFO  @ Tue, 03 Jan 2017 15:39:48:  48000000 
INFO  @ Tue, 03 Jan 2017 15:39:49:  49000000 
INFO  @ Tue, 03 Jan 2017 15:39:51:  50000000 
INFO  @ Tue, 03 Jan 2017 15:39:53: #1 tag size is determined as 109 bps 
INFO  @ Tue, 03 Jan 2017 15:39:53: #1 tag size = 109 
INFO  @ Tue, 03 Jan 2017 15:39:53: #1  total tags in treatment: 15627554 
INFO  @ Tue, 03 Jan 2017 15:39:53: #1  total tags in control: 50000000 
INFO  @ Tue, 03 Jan 2017 15:39:53: #1 finished! 
INFO  @ Tue, 03 Jan 2017 15:39:53: #2 Build Peak Model... 
INFO  @ Tue, 03 Jan 2017 15:39:53: #2 Skipped... 
INFO  @ Tue, 03 Jan 2017 15:39:53: #2 Use 180 as fragment length 
INFO  @ Tue, 03 Jan 2017 15:39:53: #3 Call peaks... 
INFO  @ Tue, 03 Jan 2017 15:39:53: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Tue, 03 Jan 2017 15:39:53: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 03 Jan 2017 15:42:51: #3 Call peaks for each chromosome... 
INFO  @ Tue, 03 Jan 2017 15:45:40: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Tue, 03 Jan 2017 15:45:44: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Tue, 03 Jan 2017 15:45:49: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370882_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Tue, 03 Jan 2017 15:45:54: Done!

Num	4
ID	task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_13
Name	naive_overlap_thresh
Thread	thread_Root
PID	22584

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

Start	2017-01-03 16:35:25
End	2017-01-03 17:32:14
Elapsed	00:56:48
Timeout	01:00:00
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/spp/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370882_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/spp/overlap/SRR1370882_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/ZNF528/out/peak/spp/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370882_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/ZNF528/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370882_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/ZNF528/out/peak/spp/overlap/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/spp/overlap/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/spp/overlap/SRR1370882_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/ZNF528/out/peak/spp/overlap/SRR1370882_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/ZNF528/out/peak/spp/overlap/SRR1370882_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/ZNF528/out/peak/spp/overlap/SRR1370882_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--------------------
2089 (process ID) old priority 0, new priority 10
Waiting for 52 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270466.1	205	605	.	0	.	28.4383352522618	-1	3.04519254043131	200

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270466.1	205	605	.	0	.	28.4383352522618	-1	3.04519254043131	200

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270467.1	3008	3408	.	0	.	42.6466852076936	-1	3.61584488287469	200

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270467.1	3008	3408	.	0	.	42.6466852076936	-1	3.61584488287469	200

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/spp/overlap/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
GL000208.1	35292	35692	.	0	.	13.979431675779	-1	2.63818333972147	200

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/spp/overlap/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
GL000208.1	35292	35692	.	0	.	13.979431675779	-1	2.63818333972147	200

Num	5
ID	task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_16
Name	blacklist_filter peak 1
Thread	thread_Root
PID	50104

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

Start	2017-01-03 17:32:18
End	2017-01-03 17:33:33
Elapsed	00:01:15
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/spp/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/spp/rep1/SRR1370882_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/ZNF528/out/peak/spp/rep1/SRR1370882_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/ZNF528/out/peak/spp/rep1/SRR1370882_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--------------------
50109 (process ID) old priority 0, new priority 10
Waiting for 59 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/spp/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	3008	3408	.	0	.	70.0792442174442	-1	3.7059491949103	200

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/spp/rep1/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	3008	3408	.	0	.	70.0792442174442	-1	3.7059491949103	200

Num	6
ID	task.report.peak2hammock.line_412.id_17
Name	peak2hammock
Thread	thread_Root
PID	54984

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

Start	2017-01-03 17:33:34
End	2017-01-03 17:33:54
Elapsed	00:00:20
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/spp/overlap/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/spp/overlap/SRR1370882_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/ZNF528/out/peak/spp/overlap/SRR1370882_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/ZNF528/out/peak/spp/overlap/SRR1370882_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/ZNF528/out/peak/spp/overlap/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/peak/spp/overlap/SRR1370882_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/ZNF528/out/peak/spp/overlap/SRR1370882_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp

   
--------------------Stdout--------------------
54988 (process ID) old priority 0, new priority 10

Num	7
ID	task.graphviz.report.line_97.id_18
Name	report
Thread	thread_Root
PID	56523

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

Start	2017-01-03 17:33:55
End	2017-01-03 17:34:15
Elapsed	00:00:20
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/ZNF528/out/report/ZNF528_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/report/ZNF528_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/report/ZNF528_workflow.svg" # to suppress dot font error (exit code=1)

   
--------------------Stdout--------------------
56527 (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, ZNF528, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF528/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF528/out/align/rep1/SRR1370882_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/ZNF528
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/ZNF528
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	44439.ZNF528.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