BigDataScript report: chipseq.bds

Script file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20170103_142501_057
Start time 2017-01-03 14:25:01
Run time 02:06:02.866
Tasks executed 5
Tasks failed 0
Tasks failed names 
 

		
  Arguments*  [-title, ZNF519, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF519/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/align/rep1/SRR1370893_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 

	

	* Values in global scope when program finished execution.





	
 Timeline 

	
	
	






	
 Task Graph 

	






	
 Parallel (threads) details 

	

    
  Thread ID      Parent           	 Tasks  

	
  thread_Root   None 	 
 chipseq.bds.20170103_142501_057/task.callpeak_macs2.macs2_rep1.line_71.id_10
chipseq.bds.20170103_142501_057/task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_11
chipseq.bds.20170103_142501_057/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_14
chipseq.bds.20170103_142501_057/task.report.peak2hammock.line_412.id_15
chipseq.bds.20170103_142501_057/task.graphviz.report.line_97.id_16
 
 		 

	
  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   22358  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-03 14:25:08  
 
  End   2017-01-03 16:18:41  
 
  Elapsed   01:53:33  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/align/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/signal/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/signal/macs2/rep1/SRR1370893_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/ZNF519/out/align/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 135 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/align/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 135 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1 -o "SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/signal/macs2/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/align/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1 -o "SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/signal/macs2/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_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--------------------
25601 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Tue, 03 Jan 2017 15:27:18: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/align/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 135 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/align/rep1/SRR1370893_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 15:27:18: #1 read tag files... 
INFO  @ Tue, 03 Jan 2017 15:27:18: #1 read treatment tags... 
INFO  @ Tue, 03 Jan 2017 15:27:20:  1000000 
INFO  @ Tue, 03 Jan 2017 15:27:22:  2000000 
INFO  @ Tue, 03 Jan 2017 15:27:24:  3000000 
INFO  @ Tue, 03 Jan 2017 15:27:25:  4000000 
INFO  @ Tue, 03 Jan 2017 15:27:27:  5000000 
INFO  @ Tue, 03 Jan 2017 15:27:29:  6000000 
INFO  @ Tue, 03 Jan 2017 15:27:30:  7000000 
INFO  @ Tue, 03 Jan 2017 15:27:32:  8000000 
INFO  @ Tue, 03 Jan 2017 15:27:33:  9000000 
INFO  @ Tue, 03 Jan 2017 15:27:35: #1.2 read input tags... 
INFO  @ Tue, 03 Jan 2017 15:27:37:  1000000 
INFO  @ Tue, 03 Jan 2017 15:27:38:  2000000 
INFO  @ Tue, 03 Jan 2017 15:27:40:  3000000 
INFO  @ Tue, 03 Jan 2017 15:27:42:  4000000 
INFO  @ Tue, 03 Jan 2017 15:27:43:  5000000 
INFO  @ Tue, 03 Jan 2017 15:27:45:  6000000 
INFO  @ Tue, 03 Jan 2017 15:27:47:  7000000 
INFO  @ Tue, 03 Jan 2017 15:27:48:  8000000 
INFO  @ Tue, 03 Jan 2017 15:27:50:  9000000 
INFO  @ Tue, 03 Jan 2017 15:27:51:  10000000 
INFO  @ Tue, 03 Jan 2017 15:27:53:  11000000 
INFO  @ Tue, 03 Jan 2017 15:27:55:  12000000 
INFO  @ Tue, 03 Jan 2017 15:27:56:  13000000 
INFO  @ Tue, 03 Jan 2017 15:27:58:  14000000 
INFO  @ Tue, 03 Jan 2017 15:27:59:  15000000 
INFO  @ Tue, 03 Jan 2017 15:28:01:  16000000 
INFO  @ Tue, 03 Jan 2017 15:28:03:  17000000 
INFO  @ Tue, 03 Jan 2017 15:28:04:  18000000 
INFO  @ Tue, 03 Jan 2017 15:28:06:  19000000 
INFO  @ Tue, 03 Jan 2017 15:28:08:  20000000 
INFO  @ Tue, 03 Jan 2017 15:28:09:  21000000 
INFO  @ Tue, 03 Jan 2017 15:28:11:  22000000 
INFO  @ Tue, 03 Jan 2017 15:28:13:  23000000 
INFO  @ Tue, 03 Jan 2017 15:28:14:  24000000 
INFO  @ Tue, 03 Jan 2017 15:28:16:  25000000 
INFO  @ Tue, 03 Jan 2017 15:28:18:  26000000 
INFO  @ Tue, 03 Jan 2017 15:28:19:  27000000 
INFO  @ Tue, 03 Jan 2017 15:28:21:  28000000 
INFO  @ Tue, 03 Jan 2017 15:28:23:  29000000 
INFO  @ Tue, 03 Jan 2017 15:28:25:  30000000 
INFO  @ Tue, 03 Jan 2017 15:28:26:  31000000 
INFO  @ Tue, 03 Jan 2017 15:28:28:  32000000 
INFO  @ Tue, 03 Jan 2017 15:28:30:  33000000 
INFO  @ Tue, 03 Jan 2017 15:28:32:  34000000 
INFO  @ Tue, 03 Jan 2017 15:28:33:  35000000 
INFO  @ Tue, 03 Jan 2017 15:28:35:  36000000 
INFO  @ Tue, 03 Jan 2017 15:28:36:  37000000 
INFO  @ Tue, 03 Jan 2017 15:28:38:  38000000 
INFO  @ Tue, 03 Jan 2017 15:28:40:  39000000 
INFO  @ Tue, 03 Jan 2017 15:28:41:  40000000 
INFO  @ Tue, 03 Jan 2017 15:28:43:  41000000 
INFO  @ Tue, 03 Jan 2017 15:28:45:  42000000 
INFO  @ Tue, 03 Jan 2017 15:28:46:  43000000 
INFO  @ Tue, 03 Jan 2017 15:28:48:  44000000 
INFO  @ Tue, 03 Jan 2017 15:28:50:  45000000 
INFO  @ Tue, 03 Jan 2017 15:28:51:  46000000 
INFO  @ Tue, 03 Jan 2017 15:28:53:  47000000 
INFO  @ Tue, 03 Jan 2017 15:28:55:  48000000 
INFO  @ Tue, 03 Jan 2017 15:28:56:  49000000 
INFO  @ Tue, 03 Jan 2017 15:28:58:  50000000 
INFO  @ Tue, 03 Jan 2017 15:29:00: #1 tag size is determined as 51 bps 
INFO  @ Tue, 03 Jan 2017 15:29:00: #1 tag size = 51 
INFO  @ Tue, 03 Jan 2017 15:29:00: #1  total tags in treatment: 9914366 
INFO  @ Tue, 03 Jan 2017 15:29:00: #1  total tags in control: 50000000 
INFO  @ Tue, 03 Jan 2017 15:29:00: #1 finished! 
INFO  @ Tue, 03 Jan 2017 15:29:00: #2 Build Peak Model... 
INFO  @ Tue, 03 Jan 2017 15:29:00: #2 Skipped... 
INFO  @ Tue, 03 Jan 2017 15:29:00: #2 Use 135 as fragment length 
INFO  @ Tue, 03 Jan 2017 15:29:00: #3 Call peaks... 
INFO  @ Tue, 03 Jan 2017 15:29:00: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Tue, 03 Jan 2017 15:29:00: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 03 Jan 2017 15:32:16: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 03 Jan 2017 15:32:16: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Tue, 03 Jan 2017 15:32:16: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Tue, 03 Jan 2017 15:32:16: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 03 Jan 2017 15:32:16: #3 Call peaks for each chromosome... 
INFO  @ Tue, 03 Jan 2017 15:37:21: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Tue, 03 Jan 2017 15:37:23: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Tue, 03 Jan 2017 15:37:24: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Tue, 03 Jan 2017 15:37:25: Done! 
INFO  @ Tue, 03 Jan 2017 15:37:28: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/align/rep1/SRR1370893_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/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 135 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/align/rep1/SRR1370893_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 15:37:28: #1 read tag files... 
INFO  @ Tue, 03 Jan 2017 15:37:28: #1 read treatment tags... 
INFO  @ Tue, 03 Jan 2017 15:37:30:  1000000 
INFO  @ Tue, 03 Jan 2017 15:37:31:  2000000 
INFO  @ Tue, 03 Jan 2017 15:37:33:  3000000 
INFO  @ Tue, 03 Jan 2017 15:37:34:  4000000 
INFO  @ Tue, 03 Jan 2017 15:37:36:  5000000 
INFO  @ Tue, 03 Jan 2017 15:37:37:  6000000 
INFO  @ Tue, 03 Jan 2017 15:37:39:  7000000 
INFO  @ Tue, 03 Jan 2017 15:37:40:  8000000 
INFO  @ Tue, 03 Jan 2017 15:37:42:  9000000 
INFO  @ Tue, 03 Jan 2017 15:37:43: #1.2 read input tags... 
INFO  @ Tue, 03 Jan 2017 15:37:58:  1000000 
INFO  @ Tue, 03 Jan 2017 15:37:59:  2000000 
INFO  @ Tue, 03 Jan 2017 15:38:01:  3000000 
INFO  @ Tue, 03 Jan 2017 15:38:02:  4000000 
INFO  @ Tue, 03 Jan 2017 15:38:04:  5000000 
INFO  @ Tue, 03 Jan 2017 15:38:05:  6000000 
INFO  @ Tue, 03 Jan 2017 15:38:07:  7000000 
INFO  @ Tue, 03 Jan 2017 15:38:08:  8000000 
INFO  @ Tue, 03 Jan 2017 15:38:10:  9000000 
INFO  @ Tue, 03 Jan 2017 15:38:11:  10000000 
INFO  @ Tue, 03 Jan 2017 15:38:13:  11000000 
INFO  @ Tue, 03 Jan 2017 15:38:14:  12000000 
INFO  @ Tue, 03 Jan 2017 15:38:16:  13000000 
INFO  @ Tue, 03 Jan 2017 15:38:17:  14000000 
INFO  @ Tue, 03 Jan 2017 15:38:19:  15000000 
INFO  @ Tue, 03 Jan 2017 15:38:20:  16000000 
INFO  @ Tue, 03 Jan 2017 15:38:22:  17000000 
INFO  @ Tue, 03 Jan 2017 15:38:23:  18000000 
INFO  @ Tue, 03 Jan 2017 15:38:25:  19000000 
INFO  @ Tue, 03 Jan 2017 15:38:26:  20000000 
INFO  @ Tue, 03 Jan 2017 15:38:28:  21000000 
INFO  @ Tue, 03 Jan 2017 15:38:29:  22000000 
INFO  @ Tue, 03 Jan 2017 15:38:31:  23000000 
INFO  @ Tue, 03 Jan 2017 15:38:32:  24000000 
INFO  @ Tue, 03 Jan 2017 15:38:34:  25000000 
INFO  @ Tue, 03 Jan 2017 15:38:36:  26000000 
INFO  @ Tue, 03 Jan 2017 15:38:37:  27000000 
INFO  @ Tue, 03 Jan 2017 15:38:39:  28000000 
INFO  @ Tue, 03 Jan 2017 15:38:40:  29000000 
INFO  @ Tue, 03 Jan 2017 15:38:42:  30000000 
INFO  @ Tue, 03 Jan 2017 15:38:43:  31000000 
INFO  @ Tue, 03 Jan 2017 15:38:45:  32000000 
INFO  @ Tue, 03 Jan 2017 15:38:46:  33000000 
INFO  @ Tue, 03 Jan 2017 15:38:48:  34000000 
INFO  @ Tue, 03 Jan 2017 15:38:49:  35000000 
INFO  @ Tue, 03 Jan 2017 15:38:51:  36000000 
INFO  @ Tue, 03 Jan 2017 15:38:52:  37000000 
INFO  @ Tue, 03 Jan 2017 15:38:54:  38000000 
INFO  @ Tue, 03 Jan 2017 15:38:55:  39000000 
INFO  @ Tue, 03 Jan 2017 15:38:56:  40000000 
INFO  @ Tue, 03 Jan 2017 15:38:58:  41000000 
INFO  @ Tue, 03 Jan 2017 15:39:00:  42000000 
INFO  @ Tue, 03 Jan 2017 15:39:01:  43000000 
INFO  @ Tue, 03 Jan 2017 15:39:03:  44000000 
INFO  @ Tue, 03 Jan 2017 15:39:04:  45000000 
INFO  @ Tue, 03 Jan 2017 15:39:06:  46000000 
INFO  @ Tue, 03 Jan 2017 15:39:07:  47000000 
INFO  @ Tue, 03 Jan 2017 15:39:09:  48000000 
INFO  @ Tue, 03 Jan 2017 15:39:11:  49000000 
INFO  @ Tue, 03 Jan 2017 15:39:12:  50000000 
INFO  @ Tue, 03 Jan 2017 15:39:14: #1 tag size is determined as 51 bps 
INFO  @ Tue, 03 Jan 2017 15:39:14: #1 tag size = 51 
INFO  @ Tue, 03 Jan 2017 15:39:14: #1  total tags in treatment: 9914366 
INFO  @ Tue, 03 Jan 2017 15:39:14: #1  total tags in control: 50000000 
INFO  @ Tue, 03 Jan 2017 15:39:14: #1 finished! 
INFO  @ Tue, 03 Jan 2017 15:39:14: #2 Build Peak Model... 
INFO  @ Tue, 03 Jan 2017 15:39:14: #2 Skipped... 
INFO  @ Tue, 03 Jan 2017 15:39:14: #2 Use 135 as fragment length 
INFO  @ Tue, 03 Jan 2017 15:39:14: #3 Call peaks... 
INFO  @ Tue, 03 Jan 2017 15:39:14: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Tue, 03 Jan 2017 15:39:14: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 03 Jan 2017 15:41:44: #3 Call peaks for each chromosome... 
INFO  @ Tue, 03 Jan 2017 15:44:23: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Tue, 03 Jan 2017 15:44:32: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Tue, 03 Jan 2017 15:44:40: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Tue, 03 Jan 2017 15:44:46: Done! 
INFO  @ Tue, 03 Jan 2017 15:45:03: Read and build treatment bedGraph... 
INFO  @ Tue, 03 Jan 2017 15:45:26: Read and build control bedGraph... 
INFO  @ Tue, 03 Jan 2017 15:47:23: Build scoreTrackII... 
INFO  @ Tue, 03 Jan 2017 15:47:59: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Tue, 03 Jan 2017 15:52:57: Write bedGraph of scores... 
INFO  @ Tue, 03 Jan 2017 15:55:12: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_FE.bdg'! 
INFO  @ Tue, 03 Jan 2017 15:59:25: Read and build treatment bedGraph... 
INFO  @ Tue, 03 Jan 2017 15:59:47: Read and build control bedGraph... 
INFO  @ Tue, 03 Jan 2017 16:01:44: Build scoreTrackII... 
INFO  @ Tue, 03 Jan 2017 16:02:20: Values in your input bedGraph files will be multiplied by 9.914366 ... 
INFO  @ Tue, 03 Jan 2017 16:07:34: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Tue, 03 Jan 2017 16:08:12: Write bedGraph of scores... 
INFO  @ Tue, 03 Jan 2017 16:11:06: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/macs2/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_ppois.bdg'! 

 
 		 

    
  
 
  Num   2  
 
  ID   task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_11  
 
  Name   naive_overlap_thresh  
 
  Thread   thread_Root  
 
  PID   22507  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-03 16:18:42  
 
  End   2017-01-03 16:29:29  
 
  Elapsed   00:10:47  
 
  Timeout  01:00:00 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/spp/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370893_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370893_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/spp/overlap/SRR1370893_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/ZNF519/out/peak/spp/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370893_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/ZNF519/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370893_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/ZNF519/out/peak/spp/overlap/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/spp/overlap/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/spp/overlap/SRR1370893_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/ZNF519/out/peak/spp/overlap/SRR1370893_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/ZNF519/out/peak/spp/overlap/SRR1370893_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/ZNF519/out/peak/spp/overlap/SRR1370893_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--------------------
14877 (process ID) old priority 0, new priority 10
Waiting for 45 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270466.1	920	1080	.	0	.	16.4878199906208	-1	3.54576055861237	80

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270466.1	920	1080	.	0	.	16.4878199906208	-1	3.54576055861237	80

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270467.1	3027	3187	.	0	.	11.9496706498659	-1	3.72582999032058	80

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270467.1	3027	3187	.	0	.	11.9496706498659	-1	3.72582999032058	80

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/spp/overlap/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
GL000216.2	652	812	.	0	.	6.91279889038472	-1	3.71259211082128	80

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/spp/overlap/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
GL000216.2	652	812	.	0	.	6.91279889038472	-1	3.71259211082128	80


 
 		 

    
  
 
  Num   3  
 
  ID   task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_14  
 
  Name   blacklist_filter peak 1 
 
  Thread   thread_Root  
 
  PID   45996  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-03 16:29:34  
 
  End   2017-01-03 16:30:42  
 
  Elapsed   00:01:08  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/spp/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/spp/rep1/SRR1370893_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/ZNF519/out/peak/spp/rep1/SRR1370893_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/ZNF519/out/peak/spp/rep1/SRR1370893_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--------------------
46004 (process ID) old priority 0, new priority 10
Waiting for 59 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/spp/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	2234	2394	.	0	.	26.0907154687901	-1	3.71259211082128	80

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/spp/rep1/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	2234	2394	.	0	.	26.0907154687901	-1	3.71259211082128	80


 
 		 

    
  
 
  Num   4  
 
  ID   task.report.peak2hammock.line_412.id_15  
 
  Name   peak2hammock 
 
  Thread   thread_Root  
 
  PID   50736  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-03 16:30:43  
 
  End   2017-01-03 16:30:53  
 
  Elapsed   00:00:10  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/spp/overlap/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/spp/overlap/SRR1370893_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/ZNF519/out/peak/spp/overlap/SRR1370893_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/ZNF519/out/peak/spp/overlap/SRR1370893_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/ZNF519/out/peak/spp/overlap/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/peak/spp/overlap/SRR1370893_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/ZNF519/out/peak/spp/overlap/SRR1370893_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp
 
 
   
--------------------Stdout--------------------
50744 (process ID) old priority 0, new priority 10

  
 		 

    
  
 
  Num   5  
 
  ID   task.graphviz.report.line_97.id_16  
 
  Name   report 
 
  Thread   thread_Root  
 
  PID   51635  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-03 16:30:54  
 
  End   2017-01-03 16:31:03  
 
  Elapsed   00:00:09  
 
  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/ZNF519/out/report/ZNF519_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/report/ZNF519_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/report/ZNF519_workflow.svg" # to suppress dot font error (exit code=1)
 
 
   
--------------------Stdout--------------------
51643 (process ID) old priority 0, new priority 10

  
 		 

	






	
 Global scope 

	Note: Global scope when program finished execution.
	

	
  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, ZNF519, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF519/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF519/out/align/rep1/SRR1370893_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/ZNF519  

	
  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/ZNF519  

	
  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  44261.ZNF519.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