BigDataScript report: chipseq.bds

Script file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20170103_142452_522
Start time 2017-01-03 14:24:52
Run time 01:58:40.786
Tasks executed 7
Tasks failed 0
Tasks failed names 
 

		
  Arguments*  [-title, ZNF41, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF41/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/align/rep1/SRR1370887_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_142452_522/task.callpeak_macs2.macs2_rep1.line_71.id_10
chipseq.bds.20170103_142452_522/task.callpeak_macs2.macs2_rep1_pr1.line_71.id_11
chipseq.bds.20170103_142452_522/task.callpeak_macs2.macs2_rep1_pr2.line_71.id_12
chipseq.bds.20170103_142452_522/task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_13
chipseq.bds.20170103_142452_522/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_16
chipseq.bds.20170103_142452_522/task.report.peak2hammock.line_412.id_17
chipseq.bds.20170103_142452_522/task.graphviz.report.line_97.id_18
 
 		 

	
  thread_42   thread_Root 	 
  
 		 

	
  thread_41   thread_Root 	 
  
 		 

	






	
 Task details 

	

    
  Task              Execution              Time   Dependencies       Task program, Errors, StdOut / StdErr  

    
  
 
  Num   1  
 
  ID   task.callpeak_macs2.macs2_rep1.line_71.id_10  
 
  Name   macs2 rep1 
 
  Thread   thread_Root  
 
  PID   22355  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-03 14:24:59  
 
  End   2017-01-03 16:15:27  
 
  Elapsed   01:50:27  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/align/rep1/SRR1370887_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/ZNF41/out/peak/macs2/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/signal/macs2/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/signal/macs2/rep1/SRR1370887_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/ZNF41/out/align/rep1/SRR1370887_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/ZNF41/out/peak/macs2/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/rep1/SRR1370887_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/ZNF41/out/peak/macs2/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/rep1/SRR1370887_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/ZNF41/out/align/rep1/SRR1370887_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/ZNF41/out/peak/macs2/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/rep1/SRR1370887_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/ZNF41/out/peak/macs2/rep1/SRR1370887_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/ZNF41/out/peak/macs2/rep1/SRR1370887_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/ZNF41/out/peak/macs2/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/rep1/SRR1370887_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/ZNF41/out/peak/macs2/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/rep1/SRR1370887_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/ZNF41/out/peak/macs2/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/rep1 -o "SRR1370887_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/ZNF41/out/peak/macs2/rep1/SRR1370887_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/ZNF41/out/peak/macs2/rep1/SRR1370887_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/ZNF41/out/peak/macs2/rep1/SRR1370887_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/ZNF41/out/peak/macs2/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/rep1/SRR1370887_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/ZNF41/out/peak/macs2/rep1/SRR1370887_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/ZNF41/out/signal/macs2/rep1/SRR1370887_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/ZNF41/out/peak/macs2/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/rep1/SRR1370887_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/ZNF41/out/align/rep1/SRR1370887_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/ZNF41/out/peak/macs2/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/rep1 -o "SRR1370887_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/ZNF41/out/peak/macs2/rep1/SRR1370887_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/ZNF41/out/peak/macs2/rep1/SRR1370887_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/ZNF41/out/peak/macs2/rep1/SRR1370887_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/ZNF41/out/peak/macs2/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/rep1/SRR1370887_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/ZNF41/out/peak/macs2/rep1/SRR1370887_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/ZNF41/out/signal/macs2/rep1/SRR1370887_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/ZNF41/out/peak/macs2/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/rep1/SRR1370887_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/ZNF41/out/peak/macs2/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/rep1/SRR1370887_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--------------------
31826 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Tue, 03 Jan 2017 15:25:01: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/align/rep1/SRR1370887_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/ZNF41/out/peak/macs2/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/align/rep1/SRR1370887_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 15:25:01: #1 read tag files... 
INFO  @ Tue, 03 Jan 2017 15:25:01: #1 read treatment tags... 
INFO  @ Tue, 03 Jan 2017 15:25:04:  1000000 
INFO  @ Tue, 03 Jan 2017 15:25:05:  2000000 
INFO  @ Tue, 03 Jan 2017 15:25:06:  3000000 
INFO  @ Tue, 03 Jan 2017 15:25:08:  4000000 
INFO  @ Tue, 03 Jan 2017 15:25:09:  5000000 
INFO  @ Tue, 03 Jan 2017 15:25:11:  6000000 
INFO  @ Tue, 03 Jan 2017 15:25:12:  7000000 
INFO  @ Tue, 03 Jan 2017 15:25:14:  8000000 
INFO  @ Tue, 03 Jan 2017 15:25:15:  9000000 
INFO  @ Tue, 03 Jan 2017 15:25:16: #1.2 read input tags... 
INFO  @ Tue, 03 Jan 2017 15:25:18:  1000000 
INFO  @ Tue, 03 Jan 2017 15:25:20:  2000000 
INFO  @ Tue, 03 Jan 2017 15:25:21:  3000000 
INFO  @ Tue, 03 Jan 2017 15:25:23:  4000000 
INFO  @ Tue, 03 Jan 2017 15:25:25:  5000000 
INFO  @ Tue, 03 Jan 2017 15:25:26:  6000000 
INFO  @ Tue, 03 Jan 2017 15:25:28:  7000000 
INFO  @ Tue, 03 Jan 2017 15:25:29:  8000000 
INFO  @ Tue, 03 Jan 2017 15:25:31:  9000000 
INFO  @ Tue, 03 Jan 2017 15:25:32:  10000000 
INFO  @ Tue, 03 Jan 2017 15:25:34:  11000000 
INFO  @ Tue, 03 Jan 2017 15:25:35:  12000000 
INFO  @ Tue, 03 Jan 2017 15:25:37:  13000000 
INFO  @ Tue, 03 Jan 2017 15:25:39:  14000000 
INFO  @ Tue, 03 Jan 2017 15:25:40:  15000000 
INFO  @ Tue, 03 Jan 2017 15:25:42:  16000000 
INFO  @ Tue, 03 Jan 2017 15:25:44:  17000000 
INFO  @ Tue, 03 Jan 2017 15:25:45:  18000000 
INFO  @ Tue, 03 Jan 2017 15:25:47:  19000000 
INFO  @ Tue, 03 Jan 2017 15:25:49:  20000000 
INFO  @ Tue, 03 Jan 2017 15:25:50:  21000000 
INFO  @ Tue, 03 Jan 2017 15:25:52:  22000000 
INFO  @ Tue, 03 Jan 2017 15:25:53:  23000000 
INFO  @ Tue, 03 Jan 2017 15:25:55:  24000000 
INFO  @ Tue, 03 Jan 2017 15:25:56:  25000000 
INFO  @ Tue, 03 Jan 2017 15:25:58:  26000000 
INFO  @ Tue, 03 Jan 2017 15:25:59:  27000000 
INFO  @ Tue, 03 Jan 2017 15:26:01:  28000000 
INFO  @ Tue, 03 Jan 2017 15:26:02:  29000000 
INFO  @ Tue, 03 Jan 2017 15:26:04:  30000000 
INFO  @ Tue, 03 Jan 2017 15:26:05:  31000000 
INFO  @ Tue, 03 Jan 2017 15:26:07:  32000000 
INFO  @ Tue, 03 Jan 2017 15:26:08:  33000000 
INFO  @ Tue, 03 Jan 2017 15:26:10:  34000000 
INFO  @ Tue, 03 Jan 2017 15:26:11:  35000000 
INFO  @ Tue, 03 Jan 2017 15:26:13:  36000000 
INFO  @ Tue, 03 Jan 2017 15:26:14:  37000000 
INFO  @ Tue, 03 Jan 2017 15:26:16:  38000000 
INFO  @ Tue, 03 Jan 2017 15:26:17:  39000000 
INFO  @ Tue, 03 Jan 2017 15:26:19:  40000000 
INFO  @ Tue, 03 Jan 2017 15:26:20:  41000000 
INFO  @ Tue, 03 Jan 2017 15:26:22:  42000000 
INFO  @ Tue, 03 Jan 2017 15:26:23:  43000000 
INFO  @ Tue, 03 Jan 2017 15:26:25:  44000000 
INFO  @ Tue, 03 Jan 2017 15:26:26:  45000000 
INFO  @ Tue, 03 Jan 2017 15:26:28:  46000000 
INFO  @ Tue, 03 Jan 2017 15:26:29:  47000000 
INFO  @ Tue, 03 Jan 2017 15:26:31:  48000000 
INFO  @ Tue, 03 Jan 2017 15:26:32:  49000000 
INFO  @ Tue, 03 Jan 2017 15:26:34:  50000000 
INFO  @ Tue, 03 Jan 2017 15:26:36: #1 tag size is determined as 68 bps 
INFO  @ Tue, 03 Jan 2017 15:26:36: #1 tag size = 68 
INFO  @ Tue, 03 Jan 2017 15:26:36: #1  total tags in treatment: 9544736 
INFO  @ Tue, 03 Jan 2017 15:26:36: #1  total tags in control: 50000000 
INFO  @ Tue, 03 Jan 2017 15:26:36: #1 finished! 
INFO  @ Tue, 03 Jan 2017 15:26:36: #2 Build Peak Model... 
INFO  @ Tue, 03 Jan 2017 15:26:36: #2 Skipped... 
INFO  @ Tue, 03 Jan 2017 15:26:36: #2 Use 145 as fragment length 
INFO  @ Tue, 03 Jan 2017 15:26:36: #3 Call peaks... 
INFO  @ Tue, 03 Jan 2017 15:26:36: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Tue, 03 Jan 2017 15:26:36: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 03 Jan 2017 15:29:14: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 03 Jan 2017 15:29:14: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Tue, 03 Jan 2017 15:29:14: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Tue, 03 Jan 2017 15:29:14: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 03 Jan 2017 15:29:14: #3 Call peaks for each chromosome... 
INFO  @ Tue, 03 Jan 2017 15:33:49: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Tue, 03 Jan 2017 15:33:49: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Tue, 03 Jan 2017 15:33:50: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Tue, 03 Jan 2017 15:33:50: Done! 
INFO  @ Tue, 03 Jan 2017 15:33:53: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/align/rep1/SRR1370887_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/ZNF41/out/peak/macs2/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/align/rep1/SRR1370887_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 15:33:53: #1 read tag files... 
INFO  @ Tue, 03 Jan 2017 15:33:53: #1 read treatment tags... 
INFO  @ Tue, 03 Jan 2017 15:33:55:  1000000 
INFO  @ Tue, 03 Jan 2017 15:33:56:  2000000 
INFO  @ Tue, 03 Jan 2017 15:33:58:  3000000 
INFO  @ Tue, 03 Jan 2017 15:33:59:  4000000 
INFO  @ Tue, 03 Jan 2017 15:34:01:  5000000 
INFO  @ Tue, 03 Jan 2017 15:34:02:  6000000 
INFO  @ Tue, 03 Jan 2017 15:34:04:  7000000 
INFO  @ Tue, 03 Jan 2017 15:34:06:  8000000 
INFO  @ Tue, 03 Jan 2017 15:34:07:  9000000 
INFO  @ Tue, 03 Jan 2017 15:34:08: #1.2 read input tags... 
INFO  @ Tue, 03 Jan 2017 15:34:10:  1000000 
INFO  @ Tue, 03 Jan 2017 15:34:11:  2000000 
INFO  @ Tue, 03 Jan 2017 15:34:13:  3000000 
INFO  @ Tue, 03 Jan 2017 15:34:14:  4000000 
INFO  @ Tue, 03 Jan 2017 15:34:16:  5000000 
INFO  @ Tue, 03 Jan 2017 15:34:17:  6000000 
INFO  @ Tue, 03 Jan 2017 15:34:19:  7000000 
INFO  @ Tue, 03 Jan 2017 15:34:20:  8000000 
INFO  @ Tue, 03 Jan 2017 15:34:22:  9000000 
INFO  @ Tue, 03 Jan 2017 15:34:23:  10000000 
INFO  @ Tue, 03 Jan 2017 15:34:25:  11000000 
INFO  @ Tue, 03 Jan 2017 15:34:27:  12000000 
INFO  @ Tue, 03 Jan 2017 15:34:28:  13000000 
INFO  @ Tue, 03 Jan 2017 15:34:30:  14000000 
INFO  @ Tue, 03 Jan 2017 15:34:31:  15000000 
INFO  @ Tue, 03 Jan 2017 15:34:33:  16000000 
INFO  @ Tue, 03 Jan 2017 15:34:34:  17000000 
INFO  @ Tue, 03 Jan 2017 15:34:36:  18000000 
INFO  @ Tue, 03 Jan 2017 15:34:37:  19000000 
INFO  @ Tue, 03 Jan 2017 15:34:39:  20000000 
INFO  @ Tue, 03 Jan 2017 15:34:40:  21000000 
INFO  @ Tue, 03 Jan 2017 15:34:42:  22000000 
INFO  @ Tue, 03 Jan 2017 15:34:43:  23000000 
INFO  @ Tue, 03 Jan 2017 15:34:45:  24000000 
INFO  @ Tue, 03 Jan 2017 15:34:46:  25000000 
INFO  @ Tue, 03 Jan 2017 15:34:48:  26000000 
INFO  @ Tue, 03 Jan 2017 15:34:49:  27000000 
INFO  @ Tue, 03 Jan 2017 15:34:51:  28000000 
INFO  @ Tue, 03 Jan 2017 15:34:52:  29000000 
INFO  @ Tue, 03 Jan 2017 15:34:53:  30000000 
INFO  @ Tue, 03 Jan 2017 15:34:55:  31000000 
INFO  @ Tue, 03 Jan 2017 15:34:57:  32000000 
INFO  @ Tue, 03 Jan 2017 15:34:58:  33000000 
INFO  @ Tue, 03 Jan 2017 15:35:00:  34000000 
INFO  @ Tue, 03 Jan 2017 15:35:01:  35000000 
INFO  @ Tue, 03 Jan 2017 15:35:02:  36000000 
INFO  @ Tue, 03 Jan 2017 15:35:04:  37000000 
INFO  @ Tue, 03 Jan 2017 15:35:05:  38000000 
INFO  @ Tue, 03 Jan 2017 15:35:07:  39000000 
INFO  @ Tue, 03 Jan 2017 15:35:08:  40000000 
INFO  @ Tue, 03 Jan 2017 15:35:10:  41000000 
INFO  @ Tue, 03 Jan 2017 15:35:11:  42000000 
INFO  @ Tue, 03 Jan 2017 15:35:13:  43000000 
INFO  @ Tue, 03 Jan 2017 15:35:14:  44000000 
INFO  @ Tue, 03 Jan 2017 15:35:16:  45000000 
INFO  @ Tue, 03 Jan 2017 15:35:17:  46000000 
INFO  @ Tue, 03 Jan 2017 15:35:19:  47000000 
INFO  @ Tue, 03 Jan 2017 15:35:20:  48000000 
INFO  @ Tue, 03 Jan 2017 15:35:22:  49000000 
INFO  @ Tue, 03 Jan 2017 15:35:23:  50000000 
INFO  @ Tue, 03 Jan 2017 15:35:25: #1 tag size is determined as 68 bps 
INFO  @ Tue, 03 Jan 2017 15:35:25: #1 tag size = 68 
INFO  @ Tue, 03 Jan 2017 15:35:25: #1  total tags in treatment: 9544736 
INFO  @ Tue, 03 Jan 2017 15:35:25: #1  total tags in control: 50000000 
INFO  @ Tue, 03 Jan 2017 15:35:25: #1 finished! 
INFO  @ Tue, 03 Jan 2017 15:35:25: #2 Build Peak Model... 
INFO  @ Tue, 03 Jan 2017 15:35:25: #2 Skipped... 
INFO  @ Tue, 03 Jan 2017 15:35:25: #2 Use 145 as fragment length 
INFO  @ Tue, 03 Jan 2017 15:35:25: #3 Call peaks... 
INFO  @ Tue, 03 Jan 2017 15:35:25: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Tue, 03 Jan 2017 15:35:25: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 03 Jan 2017 15:38:03: #3 Call peaks for each chromosome... 
INFO  @ Tue, 03 Jan 2017 15:40:28: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Tue, 03 Jan 2017 15:40:35: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Tue, 03 Jan 2017 15:40:40: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Tue, 03 Jan 2017 15:40:45: Done! 
INFO  @ Tue, 03 Jan 2017 15:41:01: Read and build treatment bedGraph... 
INFO  @ Tue, 03 Jan 2017 15:41:21: Read and build control bedGraph... 
INFO  @ Tue, 03 Jan 2017 15:43:08: Build scoreTrackII... 
INFO  @ Tue, 03 Jan 2017 15:43:51: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Tue, 03 Jan 2017 15:48:38: Write bedGraph of scores... 
INFO  @ Tue, 03 Jan 2017 15:50:42: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_FE.bdg'! 
INFO  @ Tue, 03 Jan 2017 15:55:49: Read and build treatment bedGraph... 
INFO  @ Tue, 03 Jan 2017 15:56:09: Read and build control bedGraph... 
INFO  @ Tue, 03 Jan 2017 15:57:57: Build scoreTrackII... 
INFO  @ Tue, 03 Jan 2017 15:58:36: Values in your input bedGraph files will be multiplied by 9.544736 ... 
INFO  @ Tue, 03 Jan 2017 16:03:28: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Tue, 03 Jan 2017 16:04:04: Write bedGraph of scores... 
INFO  @ Tue, 03 Jan 2017 16:07:01: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/rep1/SRR1370887_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   22356  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-03 14:25:02  
 
  End   2017-01-03 15:41:46  
 
  Elapsed   01:16:43  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/align/pseudo_reps/rep1/pr1/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_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/ZNF41/out/align/pseudo_reps/rep1/pr1/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_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/ZNF41/out/align/pseudo_reps/rep1/pr1/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_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/ZNF41/out/align/pseudo_reps/rep1/pr1/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_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--------------------
32003 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Tue, 03 Jan 2017 15:25:50: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/align/pseudo_reps/rep1/pr1/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/align/pseudo_reps/rep1/pr1/SRR1370887_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 15:25:50: #1 read tag files... 
INFO  @ Tue, 03 Jan 2017 15:25:50: #1 read treatment tags... 
INFO  @ Tue, 03 Jan 2017 15:25:52:  1000000 
INFO  @ Tue, 03 Jan 2017 15:25:54:  2000000 
INFO  @ Tue, 03 Jan 2017 15:25:55:  3000000 
INFO  @ Tue, 03 Jan 2017 15:25:57:  4000000 
INFO  @ Tue, 03 Jan 2017 15:25:59: #1.2 read input tags... 
INFO  @ Tue, 03 Jan 2017 15:26:00:  1000000 
INFO  @ Tue, 03 Jan 2017 15:26:02:  2000000 
INFO  @ Tue, 03 Jan 2017 15:26:03:  3000000 
INFO  @ Tue, 03 Jan 2017 15:26:05:  4000000 
INFO  @ Tue, 03 Jan 2017 15:26:06:  5000000 
INFO  @ Tue, 03 Jan 2017 15:26:08:  6000000 
INFO  @ Tue, 03 Jan 2017 15:26:09:  7000000 
INFO  @ Tue, 03 Jan 2017 15:26:11:  8000000 
INFO  @ Tue, 03 Jan 2017 15:26:12:  9000000 
INFO  @ Tue, 03 Jan 2017 15:26:14:  10000000 
INFO  @ Tue, 03 Jan 2017 15:26:15:  11000000 
INFO  @ Tue, 03 Jan 2017 15:26:17:  12000000 
INFO  @ Tue, 03 Jan 2017 15:26:18:  13000000 
INFO  @ Tue, 03 Jan 2017 15:26:20:  14000000 
INFO  @ Tue, 03 Jan 2017 15:26:21:  15000000 
INFO  @ Tue, 03 Jan 2017 15:26:23:  16000000 
INFO  @ Tue, 03 Jan 2017 15:26:24:  17000000 
INFO  @ Tue, 03 Jan 2017 15:26:26:  18000000 
INFO  @ Tue, 03 Jan 2017 15:26:28:  19000000 
INFO  @ Tue, 03 Jan 2017 15:26:29:  20000000 
INFO  @ Tue, 03 Jan 2017 15:26:31:  21000000 
INFO  @ Tue, 03 Jan 2017 15:26:32:  22000000 
INFO  @ Tue, 03 Jan 2017 15:26:34:  23000000 
INFO  @ Tue, 03 Jan 2017 15:26:35:  24000000 
INFO  @ Tue, 03 Jan 2017 15:26:37:  25000000 
INFO  @ Tue, 03 Jan 2017 15:26:39:  26000000 
INFO  @ Tue, 03 Jan 2017 15:26:40:  27000000 
INFO  @ Tue, 03 Jan 2017 15:26:42:  28000000 
INFO  @ Tue, 03 Jan 2017 15:26:43:  29000000 
INFO  @ Tue, 03 Jan 2017 15:26:45:  30000000 
INFO  @ Tue, 03 Jan 2017 15:26:46:  31000000 
INFO  @ Tue, 03 Jan 2017 15:26:48:  32000000 
INFO  @ Tue, 03 Jan 2017 15:26:49:  33000000 
INFO  @ Tue, 03 Jan 2017 15:26:51:  34000000 
INFO  @ Tue, 03 Jan 2017 15:26:53:  35000000 
INFO  @ Tue, 03 Jan 2017 15:26:54:  36000000 
INFO  @ Tue, 03 Jan 2017 15:26:56:  37000000 
INFO  @ Tue, 03 Jan 2017 15:26:57:  38000000 
INFO  @ Tue, 03 Jan 2017 15:26:59:  39000000 
INFO  @ Tue, 03 Jan 2017 15:27:00:  40000000 
INFO  @ Tue, 03 Jan 2017 15:27:02:  41000000 
INFO  @ Tue, 03 Jan 2017 15:27:03:  42000000 
INFO  @ Tue, 03 Jan 2017 15:27:05:  43000000 
INFO  @ Tue, 03 Jan 2017 15:27:07:  44000000 
INFO  @ Tue, 03 Jan 2017 15:27:08:  45000000 
INFO  @ Tue, 03 Jan 2017 15:27:10:  46000000 
INFO  @ Tue, 03 Jan 2017 15:27:11:  47000000 
INFO  @ Tue, 03 Jan 2017 15:27:13:  48000000 
INFO  @ Tue, 03 Jan 2017 15:27:15:  49000000 
INFO  @ Tue, 03 Jan 2017 15:27:16:  50000000 
INFO  @ Tue, 03 Jan 2017 15:27:18: #1 tag size is determined as 68 bps 
INFO  @ Tue, 03 Jan 2017 15:27:18: #1 tag size = 68 
INFO  @ Tue, 03 Jan 2017 15:27:18: #1  total tags in treatment: 4772368 
INFO  @ Tue, 03 Jan 2017 15:27:18: #1  total tags in control: 50000000 
INFO  @ Tue, 03 Jan 2017 15:27:18: #1 finished! 
INFO  @ Tue, 03 Jan 2017 15:27:18: #2 Build Peak Model... 
INFO  @ Tue, 03 Jan 2017 15:27:18: #2 Skipped... 
INFO  @ Tue, 03 Jan 2017 15:27:18: #2 Use 145 as fragment length 
INFO  @ Tue, 03 Jan 2017 15:27:18: #3 Call peaks... 
INFO  @ Tue, 03 Jan 2017 15:27:18: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Tue, 03 Jan 2017 15:27:18: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 03 Jan 2017 15:29:48: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 03 Jan 2017 15:29:48: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Tue, 03 Jan 2017 15:29:48: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Tue, 03 Jan 2017 15:29:48: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 03 Jan 2017 15:29:48: #3 Call peaks for each chromosome... 
INFO  @ Tue, 03 Jan 2017 15:34:07: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Tue, 03 Jan 2017 15:34:08: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Tue, 03 Jan 2017 15:34:10: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Tue, 03 Jan 2017 15:34:12: Done! 
INFO  @ Tue, 03 Jan 2017 15:34:15: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/align/pseudo_reps/rep1/pr1/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/align/pseudo_reps/rep1/pr1/SRR1370887_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 15:34:15: #1 read tag files... 
INFO  @ Tue, 03 Jan 2017 15:34:15: #1 read treatment tags... 
INFO  @ Tue, 03 Jan 2017 15:34:18:  1000000 
INFO  @ Tue, 03 Jan 2017 15:34:19:  2000000 
INFO  @ Tue, 03 Jan 2017 15:34:21:  3000000 
INFO  @ Tue, 03 Jan 2017 15:34:22:  4000000 
INFO  @ Tue, 03 Jan 2017 15:34:24: #1.2 read input tags... 
INFO  @ Tue, 03 Jan 2017 15:34:26:  1000000 
INFO  @ Tue, 03 Jan 2017 15:34:27:  2000000 
INFO  @ Tue, 03 Jan 2017 15:34:29:  3000000 
INFO  @ Tue, 03 Jan 2017 15:34:31:  4000000 
INFO  @ Tue, 03 Jan 2017 15:34:32:  5000000 
INFO  @ Tue, 03 Jan 2017 15:34:34:  6000000 
INFO  @ Tue, 03 Jan 2017 15:34:35:  7000000 
INFO  @ Tue, 03 Jan 2017 15:34:37:  8000000 
INFO  @ Tue, 03 Jan 2017 15:34:38:  9000000 
INFO  @ Tue, 03 Jan 2017 15:34:40:  10000000 
INFO  @ Tue, 03 Jan 2017 15:34:42:  11000000 
INFO  @ Tue, 03 Jan 2017 15:34:43:  12000000 
INFO  @ Tue, 03 Jan 2017 15:34:45:  13000000 
INFO  @ Tue, 03 Jan 2017 15:34:46:  14000000 
INFO  @ Tue, 03 Jan 2017 15:34:48:  15000000 
INFO  @ Tue, 03 Jan 2017 15:34:49:  16000000 
INFO  @ Tue, 03 Jan 2017 15:34:51:  17000000 
INFO  @ Tue, 03 Jan 2017 15:34:53:  18000000 
INFO  @ Tue, 03 Jan 2017 15:34:54:  19000000 
INFO  @ Tue, 03 Jan 2017 15:34:56:  20000000 
INFO  @ Tue, 03 Jan 2017 15:34:57:  21000000 
INFO  @ Tue, 03 Jan 2017 15:34:59:  22000000 
INFO  @ Tue, 03 Jan 2017 15:35:00:  23000000 
INFO  @ Tue, 03 Jan 2017 15:35:02:  24000000 
INFO  @ Tue, 03 Jan 2017 15:35:04:  25000000 
INFO  @ Tue, 03 Jan 2017 15:35:05:  26000000 
INFO  @ Tue, 03 Jan 2017 15:35:07:  27000000 
INFO  @ Tue, 03 Jan 2017 15:35:08:  28000000 
INFO  @ Tue, 03 Jan 2017 15:35:10:  29000000 
INFO  @ Tue, 03 Jan 2017 15:35:11:  30000000 
INFO  @ Tue, 03 Jan 2017 15:35:13:  31000000 
INFO  @ Tue, 03 Jan 2017 15:35:15:  32000000 
INFO  @ Tue, 03 Jan 2017 15:35:16:  33000000 
INFO  @ Tue, 03 Jan 2017 15:35:18:  34000000 
INFO  @ Tue, 03 Jan 2017 15:35:19:  35000000 
INFO  @ Tue, 03 Jan 2017 15:35:21:  36000000 
INFO  @ Tue, 03 Jan 2017 15:35:22:  37000000 
INFO  @ Tue, 03 Jan 2017 15:35:24:  38000000 
INFO  @ Tue, 03 Jan 2017 15:35:26:  39000000 
INFO  @ Tue, 03 Jan 2017 15:35:27:  40000000 
INFO  @ Tue, 03 Jan 2017 15:35:29:  41000000 
INFO  @ Tue, 03 Jan 2017 15:35:31:  42000000 
INFO  @ Tue, 03 Jan 2017 15:35:32:  43000000 
INFO  @ Tue, 03 Jan 2017 15:35:34:  44000000 
INFO  @ Tue, 03 Jan 2017 15:35:35:  45000000 
INFO  @ Tue, 03 Jan 2017 15:35:37:  46000000 
INFO  @ Tue, 03 Jan 2017 15:35:38:  47000000 
INFO  @ Tue, 03 Jan 2017 15:35:40:  48000000 
INFO  @ Tue, 03 Jan 2017 15:35:41:  49000000 
INFO  @ Tue, 03 Jan 2017 15:35:43:  50000000 
INFO  @ Tue, 03 Jan 2017 15:35:45: #1 tag size is determined as 68 bps 
INFO  @ Tue, 03 Jan 2017 15:35:45: #1 tag size = 68 
INFO  @ Tue, 03 Jan 2017 15:35:45: #1  total tags in treatment: 4772368 
INFO  @ Tue, 03 Jan 2017 15:35:45: #1  total tags in control: 50000000 
INFO  @ Tue, 03 Jan 2017 15:35:45: #1 finished! 
INFO  @ Tue, 03 Jan 2017 15:35:45: #2 Build Peak Model... 
INFO  @ Tue, 03 Jan 2017 15:35:45: #2 Skipped... 
INFO  @ Tue, 03 Jan 2017 15:35:45: #2 Use 145 as fragment length 
INFO  @ Tue, 03 Jan 2017 15:35:45: #3 Call peaks... 
INFO  @ Tue, 03 Jan 2017 15:35:45: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Tue, 03 Jan 2017 15:35:45: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 03 Jan 2017 15:38:17: #3 Call peaks for each chromosome... 
INFO  @ Tue, 03 Jan 2017 15:41:01: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Tue, 03 Jan 2017 15:41:11: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Tue, 03 Jan 2017 15:41:18: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370887_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Tue, 03 Jan 2017 15:41:26: Done! 

 
 		 

    
  
 
  Num   3  
 
  ID   task.callpeak_macs2.macs2_rep1_pr2.line_71.id_12  
 
  Name   macs2 rep1-pr2 
 
  Thread   thread_Root  
 
  PID   22357  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-03 14:25:04  
 
  End   2017-01-03 15:43:09  
 
  Elapsed   01:18:05  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/align/pseudo_reps/rep1/pr2/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_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/ZNF41/out/align/pseudo_reps/rep1/pr2/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_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/ZNF41/out/align/pseudo_reps/rep1/pr2/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_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/ZNF41/out/align/pseudo_reps/rep1/pr2/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_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--------------------
32137 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Tue, 03 Jan 2017 15:27:04: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/align/pseudo_reps/rep1/pr2/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/align/pseudo_reps/rep1/pr2/SRR1370887_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 15:27:04: #1 read tag files... 
INFO  @ Tue, 03 Jan 2017 15:27:04: #1 read treatment tags... 
INFO  @ Tue, 03 Jan 2017 15:27:08:  1000000 
INFO  @ Tue, 03 Jan 2017 15:27:09:  2000000 
INFO  @ Tue, 03 Jan 2017 15:27:11:  3000000 
INFO  @ Tue, 03 Jan 2017 15:27:13:  4000000 
INFO  @ Tue, 03 Jan 2017 15:27:14: #1.2 read input tags... 
INFO  @ Tue, 03 Jan 2017 15:27:16:  1000000 
INFO  @ Tue, 03 Jan 2017 15:27:17:  2000000 
INFO  @ Tue, 03 Jan 2017 15:27:19:  3000000 
INFO  @ Tue, 03 Jan 2017 15:27:20:  4000000 
INFO  @ Tue, 03 Jan 2017 15:27:22:  5000000 
INFO  @ Tue, 03 Jan 2017 15:27:24:  6000000 
INFO  @ Tue, 03 Jan 2017 15:27:25:  7000000 
INFO  @ Tue, 03 Jan 2017 15:27:27:  8000000 
INFO  @ Tue, 03 Jan 2017 15:27:28:  9000000 
INFO  @ Tue, 03 Jan 2017 15:27:30:  10000000 
INFO  @ Tue, 03 Jan 2017 15:27:31:  11000000 
INFO  @ Tue, 03 Jan 2017 15:27:33:  12000000 
INFO  @ Tue, 03 Jan 2017 15:27:34:  13000000 
INFO  @ Tue, 03 Jan 2017 15:27:36:  14000000 
INFO  @ Tue, 03 Jan 2017 15:27:37:  15000000 
INFO  @ Tue, 03 Jan 2017 15:27:39:  16000000 
INFO  @ Tue, 03 Jan 2017 15:27:40:  17000000 
INFO  @ Tue, 03 Jan 2017 15:27:42:  18000000 
INFO  @ Tue, 03 Jan 2017 15:27:43:  19000000 
INFO  @ Tue, 03 Jan 2017 15:27:45:  20000000 
INFO  @ Tue, 03 Jan 2017 15:27:46:  21000000 
INFO  @ Tue, 03 Jan 2017 15:27:48:  22000000 
INFO  @ Tue, 03 Jan 2017 15:27:49:  23000000 
INFO  @ Tue, 03 Jan 2017 15:27:51:  24000000 
INFO  @ Tue, 03 Jan 2017 15:27:52:  25000000 
INFO  @ Tue, 03 Jan 2017 15:27:54:  26000000 
INFO  @ Tue, 03 Jan 2017 15:27:55:  27000000 
INFO  @ Tue, 03 Jan 2017 15:27:57:  28000000 
INFO  @ Tue, 03 Jan 2017 15:27:58:  29000000 
INFO  @ Tue, 03 Jan 2017 15:28:00:  30000000 
INFO  @ Tue, 03 Jan 2017 15:28:01:  31000000 
INFO  @ Tue, 03 Jan 2017 15:28:03:  32000000 
INFO  @ Tue, 03 Jan 2017 15:28:05:  33000000 
INFO  @ Tue, 03 Jan 2017 15:28:06:  34000000 
INFO  @ Tue, 03 Jan 2017 15:28:08:  35000000 
INFO  @ Tue, 03 Jan 2017 15:28:10:  36000000 
INFO  @ Tue, 03 Jan 2017 15:28:11:  37000000 
INFO  @ Tue, 03 Jan 2017 15:28:13:  38000000 
INFO  @ Tue, 03 Jan 2017 15:28:15:  39000000 
INFO  @ Tue, 03 Jan 2017 15:28:16:  40000000 
INFO  @ Tue, 03 Jan 2017 15:28:18:  41000000 
INFO  @ Tue, 03 Jan 2017 15:28:19:  42000000 
INFO  @ Tue, 03 Jan 2017 15:28:21:  43000000 
INFO  @ Tue, 03 Jan 2017 15:28:22:  44000000 
INFO  @ Tue, 03 Jan 2017 15:28:24:  45000000 
INFO  @ Tue, 03 Jan 2017 15:28:25:  46000000 
INFO  @ Tue, 03 Jan 2017 15:28:27:  47000000 
INFO  @ Tue, 03 Jan 2017 15:28:28:  48000000 
INFO  @ Tue, 03 Jan 2017 15:28:30:  49000000 
INFO  @ Tue, 03 Jan 2017 15:28:32:  50000000 
INFO  @ Tue, 03 Jan 2017 15:28:34: #1 tag size is determined as 69 bps 
INFO  @ Tue, 03 Jan 2017 15:28:34: #1 tag size = 69 
INFO  @ Tue, 03 Jan 2017 15:28:34: #1  total tags in treatment: 4772368 
INFO  @ Tue, 03 Jan 2017 15:28:34: #1  total tags in control: 50000000 
INFO  @ Tue, 03 Jan 2017 15:28:34: #1 finished! 
INFO  @ Tue, 03 Jan 2017 15:28:34: #2 Build Peak Model... 
INFO  @ Tue, 03 Jan 2017 15:28:34: #2 Skipped... 
INFO  @ Tue, 03 Jan 2017 15:28:34: #2 Use 145 as fragment length 
INFO  @ Tue, 03 Jan 2017 15:28:34: #3 Call peaks... 
INFO  @ Tue, 03 Jan 2017 15:28:34: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Tue, 03 Jan 2017 15:28:34: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 03 Jan 2017 15:31:08: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 03 Jan 2017 15:31:08: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Tue, 03 Jan 2017 15:31:08: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Tue, 03 Jan 2017 15:31:08: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 03 Jan 2017 15:31:08: #3 Call peaks for each chromosome... 
INFO  @ Tue, 03 Jan 2017 15:35:22: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Tue, 03 Jan 2017 15:35:24: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Tue, 03 Jan 2017 15:35:25: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Tue, 03 Jan 2017 15:35:26: Done! 
INFO  @ Tue, 03 Jan 2017 15:35:29: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/align/pseudo_reps/rep1/pr2/SRR1370887_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/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/align/pseudo_reps/rep1/pr2/SRR1370887_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 15:35:29: #1 read tag files... 
INFO  @ Tue, 03 Jan 2017 15:35:29: #1 read treatment tags... 
INFO  @ Tue, 03 Jan 2017 15:35:31:  1000000 
INFO  @ Tue, 03 Jan 2017 15:35:32:  2000000 
INFO  @ Tue, 03 Jan 2017 15:35:34:  3000000 
INFO  @ Tue, 03 Jan 2017 15:35:36:  4000000 
INFO  @ Tue, 03 Jan 2017 15:35:37: #1.2 read input tags... 
INFO  @ Tue, 03 Jan 2017 15:35:39:  1000000 
INFO  @ Tue, 03 Jan 2017 15:35:40:  2000000 
INFO  @ Tue, 03 Jan 2017 15:35:42:  3000000 
INFO  @ Tue, 03 Jan 2017 15:35:44:  4000000 
INFO  @ Tue, 03 Jan 2017 15:35:45:  5000000 
INFO  @ Tue, 03 Jan 2017 15:35:47:  6000000 
INFO  @ Tue, 03 Jan 2017 15:35:48:  7000000 
INFO  @ Tue, 03 Jan 2017 15:35:50:  8000000 
INFO  @ Tue, 03 Jan 2017 15:35:51:  9000000 
INFO  @ Tue, 03 Jan 2017 15:35:53:  10000000 
INFO  @ Tue, 03 Jan 2017 15:35:54:  11000000 
INFO  @ Tue, 03 Jan 2017 15:35:56:  12000000 
INFO  @ Tue, 03 Jan 2017 15:35:58:  13000000 
INFO  @ Tue, 03 Jan 2017 15:35:59:  14000000 
INFO  @ Tue, 03 Jan 2017 15:36:01:  15000000 
INFO  @ Tue, 03 Jan 2017 15:36:02:  16000000 
INFO  @ Tue, 03 Jan 2017 15:36:04:  17000000 
INFO  @ Tue, 03 Jan 2017 15:36:06:  18000000 
INFO  @ Tue, 03 Jan 2017 15:36:07:  19000000 
INFO  @ Tue, 03 Jan 2017 15:36:09:  20000000 
INFO  @ Tue, 03 Jan 2017 15:36:11:  21000000 
INFO  @ Tue, 03 Jan 2017 15:36:12:  22000000 
INFO  @ Tue, 03 Jan 2017 15:36:14:  23000000 
INFO  @ Tue, 03 Jan 2017 15:36:15:  24000000 
INFO  @ Tue, 03 Jan 2017 15:36:17:  25000000 
INFO  @ Tue, 03 Jan 2017 15:36:19:  26000000 
INFO  @ Tue, 03 Jan 2017 15:36:20:  27000000 
INFO  @ Tue, 03 Jan 2017 15:36:22:  28000000 
INFO  @ Tue, 03 Jan 2017 15:36:23:  29000000 
INFO  @ Tue, 03 Jan 2017 15:36:25:  30000000 
INFO  @ Tue, 03 Jan 2017 15:36:26:  31000000 
INFO  @ Tue, 03 Jan 2017 15:36:28:  32000000 
INFO  @ Tue, 03 Jan 2017 15:36:30:  33000000 
INFO  @ Tue, 03 Jan 2017 15:36:31:  34000000 
INFO  @ Tue, 03 Jan 2017 15:36:33:  35000000 
INFO  @ Tue, 03 Jan 2017 15:36:34:  36000000 
INFO  @ Tue, 03 Jan 2017 15:36:36:  37000000 
INFO  @ Tue, 03 Jan 2017 15:36:37:  38000000 
INFO  @ Tue, 03 Jan 2017 15:36:39:  39000000 
INFO  @ Tue, 03 Jan 2017 15:36:41:  40000000 
INFO  @ Tue, 03 Jan 2017 15:36:42:  41000000 
INFO  @ Tue, 03 Jan 2017 15:36:44:  42000000 
INFO  @ Tue, 03 Jan 2017 15:36:45:  43000000 
INFO  @ Tue, 03 Jan 2017 15:36:47:  44000000 
INFO  @ Tue, 03 Jan 2017 15:36:48:  45000000 
INFO  @ Tue, 03 Jan 2017 15:36:50:  46000000 
INFO  @ Tue, 03 Jan 2017 15:36:52:  47000000 
INFO  @ Tue, 03 Jan 2017 15:36:53:  48000000 
INFO  @ Tue, 03 Jan 2017 15:36:55:  49000000 
INFO  @ Tue, 03 Jan 2017 15:36:56:  50000000 
INFO  @ Tue, 03 Jan 2017 15:36:58: #1 tag size is determined as 69 bps 
INFO  @ Tue, 03 Jan 2017 15:36:58: #1 tag size = 69 
INFO  @ Tue, 03 Jan 2017 15:36:58: #1  total tags in treatment: 4772368 
INFO  @ Tue, 03 Jan 2017 15:36:58: #1  total tags in control: 50000000 
INFO  @ Tue, 03 Jan 2017 15:36:58: #1 finished! 
INFO  @ Tue, 03 Jan 2017 15:36:58: #2 Build Peak Model... 
INFO  @ Tue, 03 Jan 2017 15:36:58: #2 Skipped... 
INFO  @ Tue, 03 Jan 2017 15:36:58: #2 Use 145 as fragment length 
INFO  @ Tue, 03 Jan 2017 15:36:58: #3 Call peaks... 
INFO  @ Tue, 03 Jan 2017 15:36:58: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Tue, 03 Jan 2017 15:36:58: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 03 Jan 2017 15:39:28: #3 Call peaks for each chromosome... 
INFO  @ Tue, 03 Jan 2017 15:42:22: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Tue, 03 Jan 2017 15:42:33: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Tue, 03 Jan 2017 15:42:40: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370887_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Tue, 03 Jan 2017 15:42:47: Done! 

 
 		 

    
  
 
  Num   4  
 
  ID   task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_13  
 
  Name   naive_overlap_thresh  
 
  Thread   thread_Root  
 
  PID   22498  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-03 16:15:29  
 
  End   2017-01-03 16:22:00  
 
  Elapsed   00:06:31  
 
  Timeout  01:00:00 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/spp/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370887_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370887_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/spp/overlap/SRR1370887_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/ZNF41/out/peak/spp/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370887_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/ZNF41/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370887_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/ZNF41/out/peak/spp/overlap/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/spp/overlap/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/spp/overlap/SRR1370887_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/ZNF41/out/peak/spp/overlap/SRR1370887_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/ZNF41/out/peak/spp/overlap/SRR1370887_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/ZNF41/out/peak/spp/overlap/SRR1370887_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--------------------
14062 (process ID) old priority 0, new priority 10
Waiting for 51 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270467.1	2177	2377	.	0	.	15.8402546944263	-1	3.20141860680356	100

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270467.1	2177	2377	.	0	.	15.8402546944263	-1	3.20141860680356	100

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KN196487.1	2559	2759	.	0	.	16.7335251631645	-1	3.10496867038323	100

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KN196487.1	2559	2759	.	0	.	16.7335251631645	-1	3.10496867038323	100

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/spp/overlap/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
GL000208.1	46819	47019	.	0	.	6.59799092388305	-1	3.29495095446524	100

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/spp/overlap/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
GL000208.1	46819	47019	.	0	.	6.59799092388305	-1	3.29495095446524	100


 
 		 

    
  
 
  Num   5  
 
  ID   task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_16  
 
  Name   blacklist_filter peak 1 
 
  Thread   thread_Root  
 
  PID   5997  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-03 16:22:05  
 
  End   2017-01-03 16:23:14  
 
  Elapsed   00:01:09  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/spp/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/spp/rep1/SRR1370887_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/ZNF41/out/peak/spp/rep1/SRR1370887_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/ZNF41/out/peak/spp/rep1/SRR1370887_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--------------------
6001 (process ID) old priority 0, new priority 10
Waiting for 60 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/spp/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KN196487.1	2548	2748	.	0	.	28.0038490591021	-1	3.29495095446524	100

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/spp/rep1/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KN196487.1	2548	2748	.	0	.	28.0038490591021	-1	3.29495095446524	100


 
 		 

    
  
 
  Num   6  
 
  ID   task.report.peak2hammock.line_412.id_17  
 
  Name   peak2hammock 
 
  Thread   thread_Root  
 
  PID   10822  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-03 16:23:15  
 
  End   2017-01-03 16:23:23  
 
  Elapsed   00:00:08  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/spp/overlap/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/spp/overlap/SRR1370887_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/ZNF41/out/peak/spp/overlap/SRR1370887_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/ZNF41/out/peak/spp/overlap/SRR1370887_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/ZNF41/out/peak/spp/overlap/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/peak/spp/overlap/SRR1370887_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/ZNF41/out/peak/spp/overlap/SRR1370887_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp
 
 
   
--------------------Stdout--------------------
10828 (process ID) old priority 0, new priority 10

  
 		 

    
  
 
  Num   7  
 
  ID   task.graphviz.report.line_97.id_18  
 
  Name   report 
 
  Thread   thread_Root  
 
  PID   11478  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-03 16:23:24  
 
  End   2017-01-03 16:23:33  
 
  Elapsed   00:00:08  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files     
 
  Output files     
 
  Dependencies     
 
 		  
 
# SYS command. line 98

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

# SYS command. line 99

 dot -Tsvg /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/report/ZNF41_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/report/ZNF41_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/report/ZNF41_workflow.svg" # to suppress dot font error (exit code=1)
 
 
   
--------------------Stdout--------------------
11482 (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, ZNF41, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF41/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF41/out/align/rep1/SRR1370887_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/ZNF41  

	
  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/ZNF41  

	
  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  43634.ZNF41.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