BigDataScript report: chipseq.bds

Script file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20170106_144623_369
Start time 2017-01-06 14:46:23
Run time 20:33:37.225
Tasks executed 11
Tasks failed 0
Tasks failed names 
 

		
  Arguments*  [-title, ZNF675, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF675/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/align/rep1/SRR1370874_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.20170106_144623_369/task.callpeak_macs2.macs2_rep1.line_71.id_10
chipseq.bds.20170106_144623_369/task.callpeak_spp.spp_rep1_pr2.line_57.id_11
chipseq.bds.20170106_144623_369/task.callpeak_macs2.macs2_rep1_pr1.line_71.id_12
chipseq.bds.20170106_144623_369/task.callpeak_macs2.macs2_rep1_pr2.line_71.id_13
chipseq.bds.20170106_144623_369/task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_14
chipseq.bds.20170106_144623_369/task.callpeak_idr.idr2_rep1_pr.line_73.id_15
chipseq.bds.20170106_144623_369/task.callpeak_idr.idr_final_qc.line_219.id_18
chipseq.bds.20170106_144623_369/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_19
chipseq.bds.20170106_144623_369/task.report.peak2hammock.line_412.id_20
chipseq.bds.20170106_144623_369/task.report.peak2hammock.line_412.id_21
chipseq.bds.20170106_144623_369/task.graphviz.report.line_97.id_22
 
 		 

	
  thread_41   thread_Root 	 
  
 		 

	
  thread_42   thread_Root 	 
  
 		 

	






	
 Task details 

	

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

    
  
 
  Num   1  
 
  ID   task.callpeak_macs2.macs2_rep1.line_71.id_10  
 
  Name   macs2 rep1 
 
  Thread   thread_Root  
 
  PID   24309  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-06 14:46:30  
 
  End   2017-01-06 15:47:30  
 
  Elapsed   01:01:00  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/align/rep1/SRR1370874_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/ZNF675/out/peak/macs2/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/signal/macs2/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/signal/macs2/rep1/SRR1370874_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/ZNF675/out/align/rep1/SRR1370874_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/ZNF675/out/peak/macs2/rep1/SRR1370874_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/ZNF675/out/peak/macs2/rep1/SRR1370874_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/ZNF675/out/peak/macs2/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/rep1/SRR1370874_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/ZNF675/out/align/rep1/SRR1370874_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/ZNF675/out/peak/macs2/rep1/SRR1370874_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/ZNF675/out/peak/macs2/rep1/SRR1370874_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/ZNF675/out/peak/macs2/rep1/SRR1370874_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/ZNF675/out/peak/macs2/rep1/SRR1370874_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/ZNF675/out/peak/macs2/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/rep1/SRR1370874_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/ZNF675/out/peak/macs2/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/rep1/SRR1370874_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/ZNF675/out/peak/macs2/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/rep1 -o "SRR1370874_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/ZNF675/out/peak/macs2/rep1/SRR1370874_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/ZNF675/out/peak/macs2/rep1/SRR1370874_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/ZNF675/out/peak/macs2/rep1/SRR1370874_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/ZNF675/out/peak/macs2/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/rep1/SRR1370874_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/ZNF675/out/peak/macs2/rep1/SRR1370874_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/ZNF675/out/signal/macs2/rep1/SRR1370874_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/ZNF675/out/peak/macs2/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/rep1/SRR1370874_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/ZNF675/out/align/rep1/SRR1370874_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/ZNF675/out/peak/macs2/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/rep1 -o "SRR1370874_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/ZNF675/out/peak/macs2/rep1/SRR1370874_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/ZNF675/out/peak/macs2/rep1/SRR1370874_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/ZNF675/out/peak/macs2/rep1/SRR1370874_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/ZNF675/out/peak/macs2/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/rep1/SRR1370874_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/ZNF675/out/peak/macs2/rep1/SRR1370874_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/ZNF675/out/signal/macs2/rep1/SRR1370874_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/ZNF675/out/peak/macs2/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/rep1/SRR1370874_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/ZNF675/out/peak/macs2/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/rep1/SRR1370874_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--------------------
30902 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 14:49:09: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/align/rep1/SRR1370874_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/ZNF675/out/peak/macs2/rep1/SRR1370874_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/ZNF675/out/peak/macs2/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/align/rep1/SRR1370874_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  @ Fri, 06 Jan 2017 14:49:09: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 14:49:09: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 14:49:10:  1000000 
INFO  @ Fri, 06 Jan 2017 14:49:12:  2000000 
INFO  @ Fri, 06 Jan 2017 14:49:13:  3000000 
INFO  @ Fri, 06 Jan 2017 14:49:15:  4000000 
INFO  @ Fri, 06 Jan 2017 14:49:16:  5000000 
INFO  @ Fri, 06 Jan 2017 14:49:18:  6000000 
INFO  @ Fri, 06 Jan 2017 14:49:19:  7000000 
INFO  @ Fri, 06 Jan 2017 14:49:21:  8000000 
INFO  @ Fri, 06 Jan 2017 14:49:22:  9000000 
INFO  @ Fri, 06 Jan 2017 14:49:24:  10000000 
INFO  @ Fri, 06 Jan 2017 14:49:25:  11000000 
INFO  @ Fri, 06 Jan 2017 14:49:27:  12000000 
INFO  @ Fri, 06 Jan 2017 14:49:28:  13000000 
INFO  @ Fri, 06 Jan 2017 14:49:29: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 14:49:31:  1000000 
INFO  @ Fri, 06 Jan 2017 14:49:32:  2000000 
INFO  @ Fri, 06 Jan 2017 14:49:34:  3000000 
INFO  @ Fri, 06 Jan 2017 14:49:35:  4000000 
INFO  @ Fri, 06 Jan 2017 14:49:37:  5000000 
INFO  @ Fri, 06 Jan 2017 14:49:38:  6000000 
INFO  @ Fri, 06 Jan 2017 14:49:40:  7000000 
INFO  @ Fri, 06 Jan 2017 14:49:41:  8000000 
INFO  @ Fri, 06 Jan 2017 14:49:43:  9000000 
INFO  @ Fri, 06 Jan 2017 14:49:44:  10000000 
INFO  @ Fri, 06 Jan 2017 14:49:46:  11000000 
INFO  @ Fri, 06 Jan 2017 14:49:47:  12000000 
INFO  @ Fri, 06 Jan 2017 14:49:49:  13000000 
INFO  @ Fri, 06 Jan 2017 14:49:50:  14000000 
INFO  @ Fri, 06 Jan 2017 14:49:52:  15000000 
INFO  @ Fri, 06 Jan 2017 14:49:53:  16000000 
INFO  @ Fri, 06 Jan 2017 14:49:55:  17000000 
INFO  @ Fri, 06 Jan 2017 14:49:56:  18000000 
INFO  @ Fri, 06 Jan 2017 14:49:58:  19000000 
INFO  @ Fri, 06 Jan 2017 14:49:59:  20000000 
INFO  @ Fri, 06 Jan 2017 14:50:01:  21000000 
INFO  @ Fri, 06 Jan 2017 14:50:02:  22000000 
INFO  @ Fri, 06 Jan 2017 14:50:04:  23000000 
INFO  @ Fri, 06 Jan 2017 14:50:05:  24000000 
INFO  @ Fri, 06 Jan 2017 14:50:07:  25000000 
INFO  @ Fri, 06 Jan 2017 14:50:09:  26000000 
INFO  @ Fri, 06 Jan 2017 14:50:10:  27000000 
INFO  @ Fri, 06 Jan 2017 14:50:12:  28000000 
INFO  @ Fri, 06 Jan 2017 14:50:13:  29000000 
INFO  @ Fri, 06 Jan 2017 14:50:15:  30000000 
INFO  @ Fri, 06 Jan 2017 14:50:16:  31000000 
INFO  @ Fri, 06 Jan 2017 14:50:18:  32000000 
INFO  @ Fri, 06 Jan 2017 14:50:20:  33000000 
INFO  @ Fri, 06 Jan 2017 14:50:21:  34000000 
INFO  @ Fri, 06 Jan 2017 14:50:23:  35000000 
INFO  @ Fri, 06 Jan 2017 14:50:25:  36000000 
INFO  @ Fri, 06 Jan 2017 14:50:26:  37000000 
INFO  @ Fri, 06 Jan 2017 14:50:28:  38000000 
INFO  @ Fri, 06 Jan 2017 14:50:29:  39000000 
INFO  @ Fri, 06 Jan 2017 14:50:31:  40000000 
INFO  @ Fri, 06 Jan 2017 14:50:32:  41000000 
INFO  @ Fri, 06 Jan 2017 14:50:34:  42000000 
INFO  @ Fri, 06 Jan 2017 14:50:35:  43000000 
INFO  @ Fri, 06 Jan 2017 14:50:37:  44000000 
INFO  @ Fri, 06 Jan 2017 14:50:39:  45000000 
INFO  @ Fri, 06 Jan 2017 14:50:40:  46000000 
INFO  @ Fri, 06 Jan 2017 14:50:41:  47000000 
INFO  @ Fri, 06 Jan 2017 14:50:43:  48000000 
INFO  @ Fri, 06 Jan 2017 14:50:44:  49000000 
INFO  @ Fri, 06 Jan 2017 14:50:46:  50000000 
INFO  @ Fri, 06 Jan 2017 14:50:48: #1 tag size is determined as 66 bps 
INFO  @ Fri, 06 Jan 2017 14:50:48: #1 tag size = 66 
INFO  @ Fri, 06 Jan 2017 14:50:48: #1  total tags in treatment: 13227107 
INFO  @ Fri, 06 Jan 2017 14:50:48: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 14:50:48: #1 finished! 
INFO  @ Fri, 06 Jan 2017 14:50:48: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 14:50:48: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 14:50:48: #2 Use 145 as fragment length 
INFO  @ Fri, 06 Jan 2017 14:50:48: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 14:50:48: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 14:50:48: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 14:53:53: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 14:53:53: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 14:53:53: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 14:53:53: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 14:53:53: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 14:59:05: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 14:59:06: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 14:59:06: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 14:59:07: Done! 
INFO  @ Fri, 06 Jan 2017 14:59:10: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/align/rep1/SRR1370874_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/ZNF675/out/peak/macs2/rep1/SRR1370874_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/ZNF675/out/peak/macs2/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/align/rep1/SRR1370874_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  @ Fri, 06 Jan 2017 14:59:10: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 14:59:10: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 14:59:11:  1000000 
INFO  @ Fri, 06 Jan 2017 14:59:13:  2000000 
INFO  @ Fri, 06 Jan 2017 14:59:14:  3000000 
INFO  @ Fri, 06 Jan 2017 14:59:16:  4000000 
INFO  @ Fri, 06 Jan 2017 14:59:17:  5000000 
INFO  @ Fri, 06 Jan 2017 14:59:19:  6000000 
INFO  @ Fri, 06 Jan 2017 14:59:20:  7000000 
INFO  @ Fri, 06 Jan 2017 14:59:22:  8000000 
INFO  @ Fri, 06 Jan 2017 14:59:23:  9000000 
INFO  @ Fri, 06 Jan 2017 14:59:25:  10000000 
INFO  @ Fri, 06 Jan 2017 14:59:26:  11000000 
INFO  @ Fri, 06 Jan 2017 14:59:28:  12000000 
INFO  @ Fri, 06 Jan 2017 14:59:30:  13000000 
INFO  @ Fri, 06 Jan 2017 14:59:30: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 14:59:32:  1000000 
INFO  @ Fri, 06 Jan 2017 14:59:33:  2000000 
INFO  @ Fri, 06 Jan 2017 14:59:35:  3000000 
INFO  @ Fri, 06 Jan 2017 14:59:36:  4000000 
INFO  @ Fri, 06 Jan 2017 14:59:38:  5000000 
INFO  @ Fri, 06 Jan 2017 14:59:39:  6000000 
INFO  @ Fri, 06 Jan 2017 14:59:41:  7000000 
INFO  @ Fri, 06 Jan 2017 14:59:42:  8000000 
INFO  @ Fri, 06 Jan 2017 14:59:44:  9000000 
INFO  @ Fri, 06 Jan 2017 14:59:45:  10000000 
INFO  @ Fri, 06 Jan 2017 14:59:47:  11000000 
INFO  @ Fri, 06 Jan 2017 14:59:49:  12000000 
INFO  @ Fri, 06 Jan 2017 14:59:50:  13000000 
INFO  @ Fri, 06 Jan 2017 14:59:52:  14000000 
INFO  @ Fri, 06 Jan 2017 14:59:53:  15000000 
INFO  @ Fri, 06 Jan 2017 14:59:55:  16000000 
INFO  @ Fri, 06 Jan 2017 14:59:56:  17000000 
INFO  @ Fri, 06 Jan 2017 14:59:58:  18000000 
INFO  @ Fri, 06 Jan 2017 14:59:59:  19000000 
INFO  @ Fri, 06 Jan 2017 15:00:01:  20000000 
INFO  @ Fri, 06 Jan 2017 15:00:02:  21000000 
INFO  @ Fri, 06 Jan 2017 15:00:04:  22000000 
INFO  @ Fri, 06 Jan 2017 15:00:05:  23000000 
INFO  @ Fri, 06 Jan 2017 15:00:07:  24000000 
INFO  @ Fri, 06 Jan 2017 15:00:08:  25000000 
INFO  @ Fri, 06 Jan 2017 15:00:10:  26000000 
INFO  @ Fri, 06 Jan 2017 15:00:11:  27000000 
INFO  @ Fri, 06 Jan 2017 15:00:13:  28000000 
INFO  @ Fri, 06 Jan 2017 15:00:15:  29000000 
INFO  @ Fri, 06 Jan 2017 15:00:18:  30000000 
INFO  @ Fri, 06 Jan 2017 15:00:19:  31000000 
INFO  @ Fri, 06 Jan 2017 15:00:21:  32000000 
INFO  @ Fri, 06 Jan 2017 15:00:22:  33000000 
INFO  @ Fri, 06 Jan 2017 15:00:24:  34000000 
INFO  @ Fri, 06 Jan 2017 15:00:25:  35000000 
INFO  @ Fri, 06 Jan 2017 15:00:27:  36000000 
INFO  @ Fri, 06 Jan 2017 15:00:28:  37000000 
INFO  @ Fri, 06 Jan 2017 15:00:30:  38000000 
INFO  @ Fri, 06 Jan 2017 15:00:31:  39000000 
INFO  @ Fri, 06 Jan 2017 15:00:33:  40000000 
INFO  @ Fri, 06 Jan 2017 15:00:34:  41000000 
INFO  @ Fri, 06 Jan 2017 15:00:36:  42000000 
INFO  @ Fri, 06 Jan 2017 15:00:37:  43000000 
INFO  @ Fri, 06 Jan 2017 15:00:39:  44000000 
INFO  @ Fri, 06 Jan 2017 15:00:40:  45000000 
INFO  @ Fri, 06 Jan 2017 15:00:42:  46000000 
INFO  @ Fri, 06 Jan 2017 15:00:43:  47000000 
INFO  @ Fri, 06 Jan 2017 15:00:45:  48000000 
INFO  @ Fri, 06 Jan 2017 15:00:46:  49000000 
INFO  @ Fri, 06 Jan 2017 15:00:48:  50000000 
INFO  @ Fri, 06 Jan 2017 15:00:50: #1 tag size is determined as 66 bps 
INFO  @ Fri, 06 Jan 2017 15:00:50: #1 tag size = 66 
INFO  @ Fri, 06 Jan 2017 15:00:50: #1  total tags in treatment: 13227107 
INFO  @ Fri, 06 Jan 2017 15:00:50: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:00:50: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:00:50: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:00:50: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:00:50: #2 Use 145 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:00:50: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:00:50: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 15:00:50: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:03:52: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:07:24: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:07:32: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 15:07:37: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 15:07:42: Done! 
INFO  @ Fri, 06 Jan 2017 15:07:58: Read and build treatment bedGraph... 
INFO  @ Fri, 06 Jan 2017 15:08:27: Read and build control bedGraph... 
INFO  @ Fri, 06 Jan 2017 15:10:24: Build scoreTrackII... 
INFO  @ Fri, 06 Jan 2017 15:11:13: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Fri, 06 Jan 2017 15:18:51: Write bedGraph of scores... 
INFO  @ Fri, 06 Jan 2017 15:21:35: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_FE.bdg'! 
INFO  @ Fri, 06 Jan 2017 15:27:37: Read and build treatment bedGraph... 
INFO  @ Fri, 06 Jan 2017 15:28:05: Read and build control bedGraph... 
INFO  @ Fri, 06 Jan 2017 15:29:56: Build scoreTrackII... 
INFO  @ Fri, 06 Jan 2017 15:30:44: Values in your input bedGraph files will be multiplied by 13.227107 ... 
INFO  @ Fri, 06 Jan 2017 15:35:52: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Fri, 06 Jan 2017 15:36:32: Write bedGraph of scores... 
INFO  @ Fri, 06 Jan 2017 15:39:32: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_ppois.bdg'! 

 
 		 

    
  
 
  Num   2  
 
  ID   task.callpeak_spp.spp_rep1_pr2.line_57.id_11  
 
  Name   spp rep1-pr2 
 
  Thread   thread_Root  
 
  PID   24310  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-06 14:46:32  
 
  End   2017-01-07 11:13:49  
 
  Elapsed   20:27:17  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/align/pseudo_reps/rep1/pr2/SRR1370874_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/ZNF675/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf
  
 
  Dependencies     
 
 		  
 
# SYS command. line 59

 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 62

 if [ $(which run_spp_nodups.R 2> /dev/null | wc -l || echo) == "1" ]; then RUN_SPP=$(which run_spp_nodups.R); \
		    else RUN_SPP=$(which run_spp.R); \
		    fi

# SYS command. line 66

 Rscript ${RUN_SPP} -c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/align/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz \
			-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/pseudo_reps/rep1/pr2 -speak=145 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz | awk 'BEGIN{OFS="\t"}{ if ($2<0) $2=0; print $1,int($2),int($3),$4,$5,$6,$7,$8,$9,$10;}' | gzip -f -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 72

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 74

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf

# SYS command. line 77

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz; fi

# SYS command. line 80

 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi

# SYS command. line 82

 if [[ true == "true" ]]; then \
			bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.filt.regionPeak.gz; \
		fi

# SYS command. line 86

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
5866 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/align/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 145 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: 3e+05 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/pseudo_reps/rep1/pr2 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore 
Overwrite files?: TRUE

Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/align/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign.gz 
opened /tmp/24310.1.q/Rtmpw9KDtT/SRR1370874_1.nodup.pr2.tagAlign172d23391958
done. read 6613553 fragments
ChIP data read length 69 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
opened /tmp/24310.1.q/Rtmpw9KDtT/input15MReadsNSCLess1.05.50MSubsample.tagAlign172d186f5dd6
done. read 50000000 fragments
Control data read length 68 
Calculating peak characteristics
Minimum cross-correlation value 0.08372574 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.113444985520241 
Top 3 estimates for fragment length 145 
Window half size 285 
Phantom peak location 75 
Phantom peak Correlation 0.1055005 
Normalized Strand cross-correlation coefficient (NSC) 1.354959 
Relative Strand cross-correlation Coefficient (RSC) 1.364847 
Phantom Peak Quality Tag 1 
null device 
          1 
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 7.821272  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.1278564  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000211 
Detected 139044 peaks 

 
--------------------Stderr--------------------
Loading required package: caTools
There were 50 or more warnings (use warnings() to see the first 50)
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KN196487.1	2440	2724	.	0	.	20.7870724760909	-1	3.80895329915591	142

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KN196487.1	2440	2724	.	0	.	20.7870724760909	-1	3.80895329915591	142


 
 		 

    
  
 
  Num   3  
 
  ID   task.callpeak_macs2.macs2_rep1_pr1.line_71.id_12  
 
  Name   macs2 rep1-pr1 
 
  Thread   thread_Root  
 
  PID   24311  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-06 14:46:33  
 
  End   2017-01-06 15:09:52  
 
  Elapsed   00:23:19  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/align/pseudo_reps/rep1/pr1/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_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/ZNF675/out/align/pseudo_reps/rep1/pr1/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_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/ZNF675/out/align/pseudo_reps/rep1/pr1/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_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/ZNF675/out/align/pseudo_reps/rep1/pr1/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_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--------------------
31092 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 14:50:53: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/align/pseudo_reps/rep1/pr1/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/align/pseudo_reps/rep1/pr1/SRR1370874_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  @ Fri, 06 Jan 2017 14:50:53: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 14:50:53: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 14:50:55:  1000000 
INFO  @ Fri, 06 Jan 2017 14:50:57:  2000000 
INFO  @ Fri, 06 Jan 2017 14:50:58:  3000000 
INFO  @ Fri, 06 Jan 2017 14:51:00:  4000000 
INFO  @ Fri, 06 Jan 2017 14:51:01:  5000000 
INFO  @ Fri, 06 Jan 2017 14:51:03:  6000000 
INFO  @ Fri, 06 Jan 2017 14:51:04: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 14:51:06:  1000000 
INFO  @ Fri, 06 Jan 2017 14:51:07:  2000000 
INFO  @ Fri, 06 Jan 2017 14:51:09:  3000000 
INFO  @ Fri, 06 Jan 2017 14:51:11:  4000000 
INFO  @ Fri, 06 Jan 2017 14:51:12:  5000000 
INFO  @ Fri, 06 Jan 2017 14:51:14:  6000000 
INFO  @ Fri, 06 Jan 2017 14:51:15:  7000000 
INFO  @ Fri, 06 Jan 2017 14:51:17:  8000000 
INFO  @ Fri, 06 Jan 2017 14:51:18:  9000000 
INFO  @ Fri, 06 Jan 2017 14:51:20:  10000000 
INFO  @ Fri, 06 Jan 2017 14:51:21:  11000000 
INFO  @ Fri, 06 Jan 2017 14:51:23:  12000000 
INFO  @ Fri, 06 Jan 2017 14:51:24:  13000000 
INFO  @ Fri, 06 Jan 2017 14:51:26:  14000000 
INFO  @ Fri, 06 Jan 2017 14:51:27:  15000000 
INFO  @ Fri, 06 Jan 2017 14:51:29:  16000000 
INFO  @ Fri, 06 Jan 2017 14:51:31:  17000000 
INFO  @ Fri, 06 Jan 2017 14:51:32:  18000000 
INFO  @ Fri, 06 Jan 2017 14:51:34:  19000000 
INFO  @ Fri, 06 Jan 2017 14:51:35:  20000000 
INFO  @ Fri, 06 Jan 2017 14:51:37:  21000000 
INFO  @ Fri, 06 Jan 2017 14:51:38:  22000000 
INFO  @ Fri, 06 Jan 2017 14:51:40:  23000000 
INFO  @ Fri, 06 Jan 2017 14:51:41:  24000000 
INFO  @ Fri, 06 Jan 2017 14:51:43:  25000000 
INFO  @ Fri, 06 Jan 2017 14:51:44:  26000000 
INFO  @ Fri, 06 Jan 2017 14:51:46:  27000000 
INFO  @ Fri, 06 Jan 2017 14:51:47:  28000000 
INFO  @ Fri, 06 Jan 2017 14:51:49:  29000000 
INFO  @ Fri, 06 Jan 2017 14:51:50:  30000000 
INFO  @ Fri, 06 Jan 2017 14:51:52:  31000000 
INFO  @ Fri, 06 Jan 2017 14:51:54:  32000000 
INFO  @ Fri, 06 Jan 2017 14:51:55:  33000000 
INFO  @ Fri, 06 Jan 2017 14:51:57:  34000000 
INFO  @ Fri, 06 Jan 2017 14:51:59:  35000000 
INFO  @ Fri, 06 Jan 2017 14:52:00:  36000000 
INFO  @ Fri, 06 Jan 2017 14:52:02:  37000000 
INFO  @ Fri, 06 Jan 2017 14:52:03:  38000000 
INFO  @ Fri, 06 Jan 2017 14:52:05:  39000000 
INFO  @ Fri, 06 Jan 2017 14:52:06:  40000000 
INFO  @ Fri, 06 Jan 2017 14:52:08:  41000000 
INFO  @ Fri, 06 Jan 2017 14:52:09:  42000000 
INFO  @ Fri, 06 Jan 2017 14:52:11:  43000000 
INFO  @ Fri, 06 Jan 2017 14:52:12:  44000000 
INFO  @ Fri, 06 Jan 2017 14:52:14:  45000000 
INFO  @ Fri, 06 Jan 2017 14:52:15:  46000000 
INFO  @ Fri, 06 Jan 2017 14:52:17:  47000000 
INFO  @ Fri, 06 Jan 2017 14:52:18:  48000000 
INFO  @ Fri, 06 Jan 2017 14:52:20:  49000000 
INFO  @ Fri, 06 Jan 2017 14:52:21:  50000000 
INFO  @ Fri, 06 Jan 2017 14:52:23: #1 tag size is determined as 67 bps 
INFO  @ Fri, 06 Jan 2017 14:52:23: #1 tag size = 67 
INFO  @ Fri, 06 Jan 2017 14:52:23: #1  total tags in treatment: 6613554 
INFO  @ Fri, 06 Jan 2017 14:52:23: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 14:52:23: #1 finished! 
INFO  @ Fri, 06 Jan 2017 14:52:23: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 14:52:23: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 14:52:23: #2 Use 145 as fragment length 
INFO  @ Fri, 06 Jan 2017 14:52:23: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 14:52:23: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 14:52:23: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 14:55:23: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 14:55:23: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 14:55:23: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 14:55:23: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 14:55:23: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:00:20: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:00:22: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 15:00:23: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 15:00:23: Done! 
INFO  @ Fri, 06 Jan 2017 15:00:26: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/align/pseudo_reps/rep1/pr1/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/align/pseudo_reps/rep1/pr1/SRR1370874_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  @ Fri, 06 Jan 2017 15:00:26: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:00:26: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:00:28:  1000000 
INFO  @ Fri, 06 Jan 2017 15:00:30:  2000000 
INFO  @ Fri, 06 Jan 2017 15:00:32:  3000000 
INFO  @ Fri, 06 Jan 2017 15:00:33:  4000000 
INFO  @ Fri, 06 Jan 2017 15:00:35:  5000000 
INFO  @ Fri, 06 Jan 2017 15:00:36:  6000000 
INFO  @ Fri, 06 Jan 2017 15:00:38: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:00:39:  1000000 
INFO  @ Fri, 06 Jan 2017 15:00:41:  2000000 
INFO  @ Fri, 06 Jan 2017 15:00:42:  3000000 
INFO  @ Fri, 06 Jan 2017 15:00:44:  4000000 
INFO  @ Fri, 06 Jan 2017 15:00:45:  5000000 
INFO  @ Fri, 06 Jan 2017 15:00:47:  6000000 
INFO  @ Fri, 06 Jan 2017 15:00:48:  7000000 
INFO  @ Fri, 06 Jan 2017 15:00:50:  8000000 
INFO  @ Fri, 06 Jan 2017 15:00:51:  9000000 
INFO  @ Fri, 06 Jan 2017 15:00:53:  10000000 
INFO  @ Fri, 06 Jan 2017 15:00:55:  11000000 
INFO  @ Fri, 06 Jan 2017 15:00:56:  12000000 
INFO  @ Fri, 06 Jan 2017 15:00:58:  13000000 
INFO  @ Fri, 06 Jan 2017 15:00:59:  14000000 
INFO  @ Fri, 06 Jan 2017 15:01:01:  15000000 
INFO  @ Fri, 06 Jan 2017 15:01:02:  16000000 
INFO  @ Fri, 06 Jan 2017 15:01:04:  17000000 
INFO  @ Fri, 06 Jan 2017 15:01:05:  18000000 
INFO  @ Fri, 06 Jan 2017 15:01:07:  19000000 
INFO  @ Fri, 06 Jan 2017 15:01:08:  20000000 
INFO  @ Fri, 06 Jan 2017 15:01:10:  21000000 
INFO  @ Fri, 06 Jan 2017 15:01:11:  22000000 
INFO  @ Fri, 06 Jan 2017 15:01:13:  23000000 
INFO  @ Fri, 06 Jan 2017 15:01:15:  24000000 
INFO  @ Fri, 06 Jan 2017 15:01:16:  25000000 
INFO  @ Fri, 06 Jan 2017 15:01:18:  26000000 
INFO  @ Fri, 06 Jan 2017 15:01:19:  27000000 
INFO  @ Fri, 06 Jan 2017 15:01:21:  28000000 
INFO  @ Fri, 06 Jan 2017 15:01:22:  29000000 
INFO  @ Fri, 06 Jan 2017 15:01:24:  30000000 
INFO  @ Fri, 06 Jan 2017 15:01:25:  31000000 
INFO  @ Fri, 06 Jan 2017 15:01:27:  32000000 
INFO  @ Fri, 06 Jan 2017 15:01:28:  33000000 
INFO  @ Fri, 06 Jan 2017 15:01:30:  34000000 
INFO  @ Fri, 06 Jan 2017 15:01:31:  35000000 
INFO  @ Fri, 06 Jan 2017 15:01:33:  36000000 
INFO  @ Fri, 06 Jan 2017 15:01:34:  37000000 
INFO  @ Fri, 06 Jan 2017 15:01:36:  38000000 
INFO  @ Fri, 06 Jan 2017 15:01:38:  39000000 
INFO  @ Fri, 06 Jan 2017 15:01:39:  40000000 
INFO  @ Fri, 06 Jan 2017 15:01:41:  41000000 
INFO  @ Fri, 06 Jan 2017 15:01:42:  42000000 
INFO  @ Fri, 06 Jan 2017 15:01:44:  43000000 
INFO  @ Fri, 06 Jan 2017 15:01:45:  44000000 
INFO  @ Fri, 06 Jan 2017 15:01:47:  45000000 
INFO  @ Fri, 06 Jan 2017 15:01:48:  46000000 
INFO  @ Fri, 06 Jan 2017 15:01:50:  47000000 
INFO  @ Fri, 06 Jan 2017 15:01:51:  48000000 
INFO  @ Fri, 06 Jan 2017 15:01:53:  49000000 
INFO  @ Fri, 06 Jan 2017 15:01:54:  50000000 
INFO  @ Fri, 06 Jan 2017 15:01:56: #1 tag size is determined as 67 bps 
INFO  @ Fri, 06 Jan 2017 15:01:56: #1 tag size = 67 
INFO  @ Fri, 06 Jan 2017 15:01:56: #1  total tags in treatment: 6613554 
INFO  @ Fri, 06 Jan 2017 15:01:56: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:01:56: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:01:56: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:01:56: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:01:56: #2 Use 145 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:01:56: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:01:56: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 15:01:56: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:05:01: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:09:08: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:09:17: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 15:09:22: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370874_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 15:09:30: Done! 

 
 		 

    
  
 
  Num   4  
 
  ID   task.callpeak_macs2.macs2_rep1_pr2.line_71.id_13  
 
  Name   macs2 rep1-pr2 
 
  Thread   thread_Root  
 
  PID   24312  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-06 14:46:34  
 
  End   2017-01-06 15:28:41  
 
  Elapsed   00:42:07  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/align/pseudo_reps/rep1/pr2/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_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/ZNF675/out/align/pseudo_reps/rep1/pr2/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_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/ZNF675/out/align/pseudo_reps/rep1/pr2/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_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/ZNF675/out/align/pseudo_reps/rep1/pr2/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_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--------------------
6797 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 15:09:41: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/align/pseudo_reps/rep1/pr2/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/align/pseudo_reps/rep1/pr2/SRR1370874_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  @ Fri, 06 Jan 2017 15:09:41: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:09:41: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:09:43:  1000000 
INFO  @ Fri, 06 Jan 2017 15:09:45:  2000000 
INFO  @ Fri, 06 Jan 2017 15:09:47:  3000000 
INFO  @ Fri, 06 Jan 2017 15:09:48:  4000000 
INFO  @ Fri, 06 Jan 2017 15:09:50:  5000000 
INFO  @ Fri, 06 Jan 2017 15:09:51:  6000000 
INFO  @ Fri, 06 Jan 2017 15:09:53: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:09:54:  1000000 
INFO  @ Fri, 06 Jan 2017 15:09:56:  2000000 
INFO  @ Fri, 06 Jan 2017 15:09:58:  3000000 
INFO  @ Fri, 06 Jan 2017 15:09:59:  4000000 
INFO  @ Fri, 06 Jan 2017 15:10:01:  5000000 
INFO  @ Fri, 06 Jan 2017 15:10:02:  6000000 
INFO  @ Fri, 06 Jan 2017 15:10:04:  7000000 
INFO  @ Fri, 06 Jan 2017 15:10:05:  8000000 
INFO  @ Fri, 06 Jan 2017 15:10:07:  9000000 
INFO  @ Fri, 06 Jan 2017 15:10:08:  10000000 
INFO  @ Fri, 06 Jan 2017 15:10:10:  11000000 
INFO  @ Fri, 06 Jan 2017 15:10:11:  12000000 
INFO  @ Fri, 06 Jan 2017 15:10:13:  13000000 
INFO  @ Fri, 06 Jan 2017 15:10:14:  14000000 
INFO  @ Fri, 06 Jan 2017 15:10:16:  15000000 
INFO  @ Fri, 06 Jan 2017 15:10:18:  16000000 
INFO  @ Fri, 06 Jan 2017 15:10:19:  17000000 
INFO  @ Fri, 06 Jan 2017 15:10:22:  18000000 
INFO  @ Fri, 06 Jan 2017 15:10:23:  19000000 
INFO  @ Fri, 06 Jan 2017 15:10:25:  20000000 
INFO  @ Fri, 06 Jan 2017 15:10:27:  21000000 
INFO  @ Fri, 06 Jan 2017 15:10:28:  22000000 
INFO  @ Fri, 06 Jan 2017 15:10:30:  23000000 
INFO  @ Fri, 06 Jan 2017 15:10:31:  24000000 
INFO  @ Fri, 06 Jan 2017 15:10:33:  25000000 
INFO  @ Fri, 06 Jan 2017 15:10:34:  26000000 
INFO  @ Fri, 06 Jan 2017 15:10:36:  27000000 
INFO  @ Fri, 06 Jan 2017 15:10:37:  28000000 
INFO  @ Fri, 06 Jan 2017 15:10:39:  29000000 
INFO  @ Fri, 06 Jan 2017 15:10:40:  30000000 
INFO  @ Fri, 06 Jan 2017 15:10:42:  31000000 
INFO  @ Fri, 06 Jan 2017 15:10:43:  32000000 
INFO  @ Fri, 06 Jan 2017 15:10:45:  33000000 
INFO  @ Fri, 06 Jan 2017 15:10:46:  34000000 
INFO  @ Fri, 06 Jan 2017 15:10:48:  35000000 
INFO  @ Fri, 06 Jan 2017 15:10:49:  36000000 
INFO  @ Fri, 06 Jan 2017 15:10:51:  37000000 
INFO  @ Fri, 06 Jan 2017 15:10:53:  38000000 
INFO  @ Fri, 06 Jan 2017 15:10:54:  39000000 
INFO  @ Fri, 06 Jan 2017 15:10:56:  40000000 
INFO  @ Fri, 06 Jan 2017 15:10:57:  41000000 
INFO  @ Fri, 06 Jan 2017 15:10:59:  42000000 
INFO  @ Fri, 06 Jan 2017 15:11:00:  43000000 
INFO  @ Fri, 06 Jan 2017 15:11:02:  44000000 
INFO  @ Fri, 06 Jan 2017 15:11:03:  45000000 
INFO  @ Fri, 06 Jan 2017 15:11:05:  46000000 
INFO  @ Fri, 06 Jan 2017 15:11:06:  47000000 
INFO  @ Fri, 06 Jan 2017 15:11:08:  48000000 
INFO  @ Fri, 06 Jan 2017 15:11:10:  49000000 
INFO  @ Fri, 06 Jan 2017 15:11:11:  50000000 
INFO  @ Fri, 06 Jan 2017 15:11:13: #1 tag size is determined as 69 bps 
INFO  @ Fri, 06 Jan 2017 15:11:13: #1 tag size = 69 
INFO  @ Fri, 06 Jan 2017 15:11:13: #1  total tags in treatment: 6613553 
INFO  @ Fri, 06 Jan 2017 15:11:13: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:11:13: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:11:13: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:11:13: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:11:13: #2 Use 145 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:11:13: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:11:13: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 15:11:13: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:14:23: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 15:14:23: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 15:14:23: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 15:14:23: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 15:14:23: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:19:07: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:19:08: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 15:19:09: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 15:19:10: Done! 
INFO  @ Fri, 06 Jan 2017 15:19:13: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/align/pseudo_reps/rep1/pr2/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_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/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/align/pseudo_reps/rep1/pr2/SRR1370874_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  @ Fri, 06 Jan 2017 15:19:13: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:19:13: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:19:15:  1000000 
INFO  @ Fri, 06 Jan 2017 15:19:17:  2000000 
INFO  @ Fri, 06 Jan 2017 15:19:19:  3000000 
INFO  @ Fri, 06 Jan 2017 15:19:21:  4000000 
INFO  @ Fri, 06 Jan 2017 15:19:23:  5000000 
INFO  @ Fri, 06 Jan 2017 15:19:25:  6000000 
INFO  @ Fri, 06 Jan 2017 15:19:26: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:19:28:  1000000 
INFO  @ Fri, 06 Jan 2017 15:19:30:  2000000 
INFO  @ Fri, 06 Jan 2017 15:19:32:  3000000 
INFO  @ Fri, 06 Jan 2017 15:19:33:  4000000 
INFO  @ Fri, 06 Jan 2017 15:19:35:  5000000 
INFO  @ Fri, 06 Jan 2017 15:19:37:  6000000 
INFO  @ Fri, 06 Jan 2017 15:19:39:  7000000 
INFO  @ Fri, 06 Jan 2017 15:19:41:  8000000 
INFO  @ Fri, 06 Jan 2017 15:19:42:  9000000 
INFO  @ Fri, 06 Jan 2017 15:19:44:  10000000 
INFO  @ Fri, 06 Jan 2017 15:19:46:  11000000 
INFO  @ Fri, 06 Jan 2017 15:19:47:  12000000 
INFO  @ Fri, 06 Jan 2017 15:19:49:  13000000 
INFO  @ Fri, 06 Jan 2017 15:19:51:  14000000 
INFO  @ Fri, 06 Jan 2017 15:19:53:  15000000 
INFO  @ Fri, 06 Jan 2017 15:19:54:  16000000 
INFO  @ Fri, 06 Jan 2017 15:19:56:  17000000 
INFO  @ Fri, 06 Jan 2017 15:19:58:  18000000 
INFO  @ Fri, 06 Jan 2017 15:20:00:  19000000 
INFO  @ Fri, 06 Jan 2017 15:20:02:  20000000 
INFO  @ Fri, 06 Jan 2017 15:20:03:  21000000 
INFO  @ Fri, 06 Jan 2017 15:20:05:  22000000 
INFO  @ Fri, 06 Jan 2017 15:20:07:  23000000 
INFO  @ Fri, 06 Jan 2017 15:20:09:  24000000 
INFO  @ Fri, 06 Jan 2017 15:20:10:  25000000 
INFO  @ Fri, 06 Jan 2017 15:20:12:  26000000 
INFO  @ Fri, 06 Jan 2017 15:20:14:  27000000 
INFO  @ Fri, 06 Jan 2017 15:20:15:  28000000 
INFO  @ Fri, 06 Jan 2017 15:20:17:  29000000 
INFO  @ Fri, 06 Jan 2017 15:20:18:  30000000 
INFO  @ Fri, 06 Jan 2017 15:20:20:  31000000 
INFO  @ Fri, 06 Jan 2017 15:20:22:  32000000 
INFO  @ Fri, 06 Jan 2017 15:20:23:  33000000 
INFO  @ Fri, 06 Jan 2017 15:20:25:  34000000 
INFO  @ Fri, 06 Jan 2017 15:20:27:  35000000 
INFO  @ Fri, 06 Jan 2017 15:20:29:  36000000 
INFO  @ Fri, 06 Jan 2017 15:20:30:  37000000 
INFO  @ Fri, 06 Jan 2017 15:20:32:  38000000 
INFO  @ Fri, 06 Jan 2017 15:20:34:  39000000 
INFO  @ Fri, 06 Jan 2017 15:20:35:  40000000 
INFO  @ Fri, 06 Jan 2017 15:20:37:  41000000 
INFO  @ Fri, 06 Jan 2017 15:20:39:  42000000 
INFO  @ Fri, 06 Jan 2017 15:20:41:  43000000 
INFO  @ Fri, 06 Jan 2017 15:20:42:  44000000 
INFO  @ Fri, 06 Jan 2017 15:20:44:  45000000 
INFO  @ Fri, 06 Jan 2017 15:20:46:  46000000 
INFO  @ Fri, 06 Jan 2017 15:20:47:  47000000 
INFO  @ Fri, 06 Jan 2017 15:20:49:  48000000 
INFO  @ Fri, 06 Jan 2017 15:20:51:  49000000 
INFO  @ Fri, 06 Jan 2017 15:20:52:  50000000 
INFO  @ Fri, 06 Jan 2017 15:20:54: #1 tag size is determined as 69 bps 
INFO  @ Fri, 06 Jan 2017 15:20:54: #1 tag size = 69 
INFO  @ Fri, 06 Jan 2017 15:20:54: #1  total tags in treatment: 6613553 
INFO  @ Fri, 06 Jan 2017 15:20:54: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:20:54: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:20:54: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:20:54: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:20:54: #2 Use 145 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:20:54: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:20:54: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 15:20:54: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:24:27: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:28:02: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:28:11: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 15:28:16: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 15:28:21: Done! 

 
 		 

    
  
 
  Num   5  
 
  ID   task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_14  
 
  Name   naive_overlap_thresh  
 
  Thread   thread_Root  
 
  PID   24380  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-07 11:13:51  
 
  End   2017-01-07 11:15:08  
 
  Elapsed   00:01:17  
 
  Timeout  01:00:00 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370874_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/overlap/SRR1370874_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/ZNF675/out/peak/spp/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370874_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/ZNF675/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370874_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/ZNF675/out/peak/spp/overlap/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/overlap/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/overlap/SRR1370874_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/ZNF675/out/peak/spp/overlap/SRR1370874_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/ZNF675/out/peak/spp/overlap/SRR1370874_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/ZNF675/out/peak/spp/overlap/SRR1370874_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--------------------
30282 (process ID) old priority 0, new priority 10
Waiting for 58 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270467.1	2151	2435	.	0	.	31.3309203335945	-1	4.09701423117803	142

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270467.1	2151	2435	.	0	.	31.3309203335945	-1	4.09701423117803	142

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KN196487.1	2440	2724	.	0	.	20.7870724760909	-1	3.80895329915591	142

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KN196487.1	2440	2724	.	0	.	20.7870724760909	-1	3.80895329915591	142

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/overlap/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
GL000009.2	64084	64368	.	0	.	13.860048651566	-1	4.17269048175585	142

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/overlap/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
GL000009.2	64084	64368	.	0	.	13.860048651566	-1	4.17269048175585	142


 
 		 

    
  
 
  Num   6  
 
  ID   task.callpeak_idr.idr2_rep1_pr.line_73.id_15  
 
  Name   idr2 rep1-pr 
 
  Thread   thread_Root  
 
  PID   24381  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-07 11:15:10  
 
  End   2017-01-07 11:17:00  
 
  Elapsed   00:01:50  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370874_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/idr/pseudo_reps/rep1/ZNF675_rep1-pr.IDR0.05.filt.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/idr/pseudo_reps/rep1/ZNF675_rep1-pr.unthresholded-peaks.txt.png
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/idr/pseudo_reps/rep1/ZNF675_rep1-pr.unthresholded-peaks.txt.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/idr/pseudo_reps/rep1/ZNF675_rep1-pr.IDR0.05.filt.12-col.bed.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 75

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq_py3 | wc -l) != "0" ]]; then source activate aquas_chipseq_py3; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 77

 idr --samples /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370874_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/idr/pseudo_reps/rep1/ZNF675_rep1-pr.unthresholded-peaks.txt --rank signal.value --soft-idr-threshold 0.05 \
			--plot --use-best-multisummit-IDR

# SYS command. line 81

 idr_thresh_transformed=$(awk -v p=0.05 'BEGIN{print -log(p)/log(10)}')

# SYS command. line 84

 awk 'BEGIN{OFS="\t"} $12>='"${idr_thresh_transformed}"' {if ($2<0) $2=0; print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,"0"}' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/idr/pseudo_reps/rep1/ZNF675_rep1-pr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/idr/pseudo_reps/rep1/ZNF675_rep1-pr.IDR0.05.13-col.bed.gz

# SYS command. line 87

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/idr/pseudo_reps/rep1/ZNF675_rep1-pr.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/idr/pseudo_reps/rep1/ZNF675_rep1-pr.IDR0.05.narrowPeak.gz

# SYS command. line 88

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/idr/pseudo_reps/rep1/ZNF675_rep1-pr.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/idr/pseudo_reps/rep1/ZNF675_rep1-pr.IDR0.05.12-col.bed.gz

# SYS command. line 90

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/idr/pseudo_reps/rep1/ZNF675_rep1-pr.IDR0.05.13-col.bed.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz | grep -P 'chr[dXY]+[ 	]' | awk 'BEGIN{OFS="	"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/idr/pseudo_reps/rep1/ZNF675_rep1-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 91

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/idr/pseudo_reps/rep1/ZNF675_rep1-pr.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="	"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/idr/pseudo_reps/rep1/ZNF675_rep1-pr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 92

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/idr/pseudo_reps/rep1/ZNF675_rep1-pr.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="	"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/idr/pseudo_reps/rep1/ZNF675_rep1-pr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 94

 gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/idr/pseudo_reps/rep1/ZNF675_rep1-pr.unthresholded-peaks.txt

# SYS command. line 95

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/idr/pseudo_reps/rep1/ZNF675_rep1-pr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/idr/pseudo_reps/rep1/ZNF675_rep1-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 97

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
30391 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Initial parameter values: [0.10 1.00 0.20 0.50]
Final parameter values: [3.05 1.08 0.94 0.38]
Number of reported peaks - 13554/13554 (100.0%)

Number of peaks passing IDR cutoff of 0.05 - 5280/13554 (39.0%)


 
 		 

    
  
 
  Num   7  
 
  ID   task.callpeak_idr.idr_final_qc.line_219.id_18  
 
  Name   idr final qc 
 
  Thread   thread_Root  
 
  PID   24382  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-07 11:17:01  
 
  End   2017-01-07 11:18:22  
 
  Elapsed   00:01:21  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/idr/pseudo_reps/rep1/ZNF675_rep1-pr.IDR0.05.filt.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/qc/ZNF675_IDR_final.qc
  
 
  Dependencies     
 
 		  
 
# SYS command. line 221

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

# SYS command. line 223

 echo -e "Nt\tN1	N2	""Np\tconservative_set\toptimal_set\trescue_ratio\tself_consistency_ratio\treproducibility" > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/qc/ZNF675_IDR_final.qc

# SYS command. line 224

 echo -e "0\t332	0	""0\tN/A\tN/A\tNaN\t1.0\t1" >> /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/qc/ZNF675_IDR_final.qc

# SYS command. line 226

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
30548 (process ID) old priority 0, new priority 10
Waiting for 59 seconds.

  
 		 

    
  
 
  Num   8  
 
  ID   task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_19  
 
  Name   blacklist_filter peak 1 
 
  Thread   thread_Root  
 
  PID   56134  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-07 11:18:24  
 
  End   2017-01-07 11:19:32  
 
  Elapsed   00:01:08  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/rep1/SRR1370874_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/ZNF675/out/peak/spp/rep1/SRR1370874_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/ZNF675/out/peak/spp/rep1/SRR1370874_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--------------------
56138 (process ID) old priority 0, new priority 10
Waiting for 59 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KN196487.1	2553	2837	.	0	.	45.6363032386754	-1	4.17269048175585	142

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/rep1/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KN196487.1	2553	2837	.	0	.	45.6363032386754	-1	4.17269048175585	142


 
 		 

    
  
 
  Num   9  
 
  ID   task.report.peak2hammock.line_412.id_20  
 
  Name   peak2hammock 
 
  Thread   thread_Root  
 
  PID   3184  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-07 11:19:33  
 
  End   2017-01-07 11:19:41  
 
  Elapsed   00:00:08  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/overlap/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/overlap/SRR1370874_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/ZNF675/out/peak/spp/overlap/SRR1370874_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/ZNF675/out/peak/spp/overlap/SRR1370874_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/ZNF675/out/peak/spp/overlap/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/spp/overlap/SRR1370874_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/ZNF675/out/peak/spp/overlap/SRR1370874_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp
 
 
   
--------------------Stdout--------------------
3188 (process ID) old priority 0, new priority 10

  
 		 

    
  
 
  Num   10  
 
  ID   task.report.peak2hammock.line_412.id_21  
 
  Name   peak2hammock 
 
  Thread   thread_Root  
 
  PID   3753  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-07 11:19:42  
 
  End   2017-01-07 11:19:51  
 
  Elapsed   00:00:08  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/idr/pseudo_reps/rep1/ZNF675_rep1-pr.IDR0.05.filt.12-col.bed.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/idr/pseudo_reps/rep1/ZNF675_rep1-pr.IDR0.05.filt.12-col.bed.hammock.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 414

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

# SYS command. line 415

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/idr/pseudo_reps/rep1/ZNF675_rep1-pr.IDR0.05.filt.12-col.bed.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/idr/pseudo_reps/rep1/ZNF675_rep1-pr.IDR0.05.filt.12-col.bed.tmp

# SYS command. line 417

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/idr/pseudo_reps/rep1/ZNF675_rep1-pr.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/idr/pseudo_reps/rep1/ZNF675_rep1-pr.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/peak/idr/pseudo_reps/rep1/ZNF675_rep1-pr.IDR0.05.filt.12-col.bed.tmp
 
 
   
--------------------Stdout--------------------
3757 (process ID) old priority 0, new priority 10

  
 		 

    
  
 
  Num   11  
 
  ID   task.graphviz.report.line_97.id_22  
 
  Name   report 
 
  Thread   thread_Root  
 
  PID   4385  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-07 11:19:52  
 
  End   2017-01-07 11:20:00  
 
  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/ZNF675/out/report/ZNF675_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/report/ZNF675_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/report/ZNF675_workflow.svg" # to suppress dot font error (exit code=1)
 
 
   
--------------------Stdout--------------------
4390 (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/ascp/3.5.6:/software/modulefiles/sratoolkit/2.5.2:/software/modulefiles/homer/default  

	
  bool  allowEmpty  false  

	
  string[]  args  [-title, ZNF675, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF675/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF675/out/align/rep1/SRR1370874_1.bam, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz, -final_stage, idr, $]  

	
  string  ASCPKEY  /software/ascp/etc/asperaweb_id_dsa.openssh  

	
  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:10.0  

	
  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_veRoBQ  

	
  string  LANG  en_US.UTF-8  

	
  string  LOADEDMODULES  modsappsdir/modsappsdir:ascp/3.5.6:sratoolkit/2.5.2:homer/default  

	
  string  LOGNAME  imk1  

	
  int  M  1048576  

	
  string  MAIL  /var/mail/imk1  

	
  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  /software/ucsc_tools/3.0.9:/software/weblogo/2.8.2:/software/homer/default/bin:/software/sratoolkit/2.5.2/bin/:/software/ascp/:/users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/srv/scratch/imk1/TFBindingPredictionProject/src/R-3.2.3/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  

	
  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/ZNF675  

	
  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/ZNF675  

	
  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  SHELL  /bin/bash  

	
  string  SHLVL  3  

	
  string  SSH_CLIENT  171.65.77.8 43899 22  

	
  string  SSH_CONNECTION  171.65.77.8 43899 171.65.76.63 22  

	
  string  SSH_TTY  /dev/pts/0  

	
  string  STY  30400.ZNF675.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  1080  

	
  string  XFILESEARCHPATH  /usr/dt/app-defaults/%L/Dt