BigDataScript report: chipseq.bds

Script file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20170125_175151_499
Start time 2017-01-25 17:51:51
Run time 00:32:43.172
Tasks executed 14
Tasks failed 0
Tasks failed names 
 

		
  Arguments*  [-species, hg38, -tag1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/rep1/ENCFF001FJZ.nodup.tagAlign.gz, -tag2, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/rep2/ENCFF001FJY.nodup.tagAlign.gz, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz, -final_stage, idr, -chrsz, /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes, -no_pseudo_rep, -histone, -out_dir, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3, $] 

		
  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.20170125_175151_499/task.callpeak_macs2.macs2_pooled_rep.line_71.id_10
chipseq.bds.20170125_175151_499/task.callpeak_macs2.macs2_ppr1.line_71.id_11
chipseq.bds.20170125_175151_499/task.callpeak_macs2.macs2_ppr2.line_71.id_12
chipseq.bds.20170125_175151_499/task.callpeak_macs2.macs2_rep1.line_71.id_13
chipseq.bds.20170125_175151_499/task.callpeak_macs2.macs2_rep2.line_71.id_14
chipseq.bds.20170125_175151_499/task.callpeak_naive_overlap.naive_overlap_thresh.line_143.id_15
chipseq.bds.20170125_175151_499/task.callpeak_naive_overlap.naive_overlap_thresh.line_143.id_16
chipseq.bds.20170125_175151_499/task.callpeak_naive_overlap.naive_overlap_thresh.line_143.id_17
chipseq.bds.20170125_175151_499/task.callpeak_blacklist_filter.blacklist_filter_peak_pooled.line_27.id_18
chipseq.bds.20170125_175151_499/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_19
chipseq.bds.20170125_175151_499/task.callpeak_blacklist_filter.blacklist_filter_peak_2.line_27.id_20
chipseq.bds.20170125_175151_499/task.report.peak2hammock.line_412.id_21
chipseq.bds.20170125_175151_499/task.report.peak2hammock.line_412.id_22
chipseq.bds.20170125_175151_499/task.graphviz.report.line_97.id_23
 
 		 

	
  thread_42   thread_Root 	 
  
 		 

	
  thread_41   thread_Root 	 
  
 		 

	
  thread_43   thread_Root 	 
  
 		 

	






	
 Task details 

	

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

    
  
 
  Num   1  
 
  ID   task.callpeak_macs2.macs2_pooled_rep.line_71.id_10  
 
  Name   macs2 pooled_rep 
 
  Thread   thread_Root  
 
  PID   35576  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-25 17:52:06  
 
  End   2017-01-25 18:21:36  
 
  Elapsed   00:29:30  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/signal/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/signal/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.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/EncodeOtherHek293Data/H3K4me3/align/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 123 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 123 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 110

 if [[ true == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.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/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep -o "ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -g /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/signal/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.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/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep -o "ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 143

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -g /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/signal/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.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--------------------
14330 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Wed, 25 Jan 2017 17:52:24: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 123 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.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  @ Wed, 25 Jan 2017 17:52:24: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 17:52:24: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 17:52:25:  1000000 
INFO  @ Wed, 25 Jan 2017 17:52:27:  2000000 
INFO  @ Wed, 25 Jan 2017 17:52:28:  3000000 
INFO  @ Wed, 25 Jan 2017 17:52:30:  4000000 
INFO  @ Wed, 25 Jan 2017 17:52:31:  5000000 
INFO  @ Wed, 25 Jan 2017 17:52:32:  6000000 
INFO  @ Wed, 25 Jan 2017 17:52:34:  7000000 
INFO  @ Wed, 25 Jan 2017 17:52:35:  8000000 
INFO  @ Wed, 25 Jan 2017 17:52:37:  9000000 
INFO  @ Wed, 25 Jan 2017 17:52:38:  10000000 
INFO  @ Wed, 25 Jan 2017 17:52:39:  11000000 
INFO  @ Wed, 25 Jan 2017 17:52:41:  12000000 
INFO  @ Wed, 25 Jan 2017 17:52:42:  13000000 
INFO  @ Wed, 25 Jan 2017 17:52:44:  14000000 
INFO  @ Wed, 25 Jan 2017 17:52:45:  15000000 
INFO  @ Wed, 25 Jan 2017 17:52:47:  16000000 
INFO  @ Wed, 25 Jan 2017 17:52:48:  17000000 
INFO  @ Wed, 25 Jan 2017 17:52:50:  18000000 
INFO  @ Wed, 25 Jan 2017 17:52:51:  19000000 
INFO  @ Wed, 25 Jan 2017 17:52:53:  20000000 
INFO  @ Wed, 25 Jan 2017 17:52:54:  21000000 
INFO  @ Wed, 25 Jan 2017 17:52:56:  22000000 
INFO  @ Wed, 25 Jan 2017 17:52:57:  23000000 
INFO  @ Wed, 25 Jan 2017 17:52:59:  24000000 
INFO  @ Wed, 25 Jan 2017 17:53:01:  25000000 
INFO  @ Wed, 25 Jan 2017 17:53:02:  26000000 
INFO  @ Wed, 25 Jan 2017 17:53:03:  27000000 
INFO  @ Wed, 25 Jan 2017 17:53:05:  28000000 
INFO  @ Wed, 25 Jan 2017 17:53:06:  29000000 
INFO  @ Wed, 25 Jan 2017 17:53:08:  30000000 
INFO  @ Wed, 25 Jan 2017 17:53:09:  31000000 
INFO  @ Wed, 25 Jan 2017 17:53:11:  32000000 
INFO  @ Wed, 25 Jan 2017 17:53:12:  33000000 
INFO  @ Wed, 25 Jan 2017 17:53:14:  34000000 
INFO  @ Wed, 25 Jan 2017 17:53:16: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 17:53:18:  1000000 
INFO  @ Wed, 25 Jan 2017 17:53:19:  2000000 
INFO  @ Wed, 25 Jan 2017 17:53:21:  3000000 
INFO  @ Wed, 25 Jan 2017 17:53:22:  4000000 
INFO  @ Wed, 25 Jan 2017 17:53:24:  5000000 
INFO  @ Wed, 25 Jan 2017 17:53:25:  6000000 
INFO  @ Wed, 25 Jan 2017 17:53:27:  7000000 
INFO  @ Wed, 25 Jan 2017 17:53:28:  8000000 
INFO  @ Wed, 25 Jan 2017 17:53:30:  9000000 
INFO  @ Wed, 25 Jan 2017 17:53:31:  10000000 
INFO  @ Wed, 25 Jan 2017 17:53:33:  11000000 
INFO  @ Wed, 25 Jan 2017 17:53:34: #1 tag size is determined as 36 bps 
INFO  @ Wed, 25 Jan 2017 17:53:34: #1 tag size = 36 
INFO  @ Wed, 25 Jan 2017 17:53:34: #1  total tags in treatment: 34983396 
INFO  @ Wed, 25 Jan 2017 17:53:34: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 17:53:34: #1 finished! 
INFO  @ Wed, 25 Jan 2017 17:53:34: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 17:53:34: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 17:53:34: #2 Use 123 as fragment length 
INFO  @ Wed, 25 Jan 2017 17:53:34: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 17:53:34: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Wed, 25 Jan 2017 17:53:34: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 17:54:39: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Wed, 25 Jan 2017 17:54:39: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Wed, 25 Jan 2017 17:54:39: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg 
INFO  @ Wed, 25 Jan 2017 17:54:39: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Wed, 25 Jan 2017 17:54:39: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 17:57:25: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 17:57:25: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Wed, 25 Jan 2017 17:57:26: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed 
INFO  @ Wed, 25 Jan 2017 17:57:26: Done! 
INFO  @ Wed, 25 Jan 2017 17:57:29: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 123 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.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  @ Wed, 25 Jan 2017 17:57:29: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 17:57:29: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 17:57:31:  1000000 
INFO  @ Wed, 25 Jan 2017 17:57:32:  2000000 
INFO  @ Wed, 25 Jan 2017 17:57:34:  3000000 
INFO  @ Wed, 25 Jan 2017 17:57:35:  4000000 
INFO  @ Wed, 25 Jan 2017 17:57:37:  5000000 
INFO  @ Wed, 25 Jan 2017 17:57:38:  6000000 
INFO  @ Wed, 25 Jan 2017 17:57:40:  7000000 
INFO  @ Wed, 25 Jan 2017 17:57:41:  8000000 
INFO  @ Wed, 25 Jan 2017 17:57:42:  9000000 
INFO  @ Wed, 25 Jan 2017 17:57:44:  10000000 
INFO  @ Wed, 25 Jan 2017 17:57:45:  11000000 
INFO  @ Wed, 25 Jan 2017 17:57:47:  12000000 
INFO  @ Wed, 25 Jan 2017 17:57:48:  13000000 
INFO  @ Wed, 25 Jan 2017 17:57:50:  14000000 
INFO  @ Wed, 25 Jan 2017 17:57:51:  15000000 
INFO  @ Wed, 25 Jan 2017 17:57:52:  16000000 
INFO  @ Wed, 25 Jan 2017 17:57:54:  17000000 
INFO  @ Wed, 25 Jan 2017 17:57:55:  18000000 
INFO  @ Wed, 25 Jan 2017 17:57:57:  19000000 
INFO  @ Wed, 25 Jan 2017 17:57:58:  20000000 
INFO  @ Wed, 25 Jan 2017 17:58:00:  21000000 
INFO  @ Wed, 25 Jan 2017 17:58:01:  22000000 
INFO  @ Wed, 25 Jan 2017 17:58:03:  23000000 
INFO  @ Wed, 25 Jan 2017 17:58:04:  24000000 
INFO  @ Wed, 25 Jan 2017 17:58:05:  25000000 
INFO  @ Wed, 25 Jan 2017 17:58:07:  26000000 
INFO  @ Wed, 25 Jan 2017 17:58:08:  27000000 
INFO  @ Wed, 25 Jan 2017 17:58:10:  28000000 
INFO  @ Wed, 25 Jan 2017 17:58:11:  29000000 
INFO  @ Wed, 25 Jan 2017 17:58:13:  30000000 
INFO  @ Wed, 25 Jan 2017 17:58:14:  31000000 
INFO  @ Wed, 25 Jan 2017 17:58:16:  32000000 
INFO  @ Wed, 25 Jan 2017 17:58:17:  33000000 
INFO  @ Wed, 25 Jan 2017 17:58:19:  34000000 
INFO  @ Wed, 25 Jan 2017 17:58:21: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 17:58:23:  1000000 
INFO  @ Wed, 25 Jan 2017 17:58:24:  2000000 
INFO  @ Wed, 25 Jan 2017 17:58:26:  3000000 
INFO  @ Wed, 25 Jan 2017 17:58:27:  4000000 
INFO  @ Wed, 25 Jan 2017 17:58:28:  5000000 
INFO  @ Wed, 25 Jan 2017 17:58:30:  6000000 
INFO  @ Wed, 25 Jan 2017 17:58:31:  7000000 
INFO  @ Wed, 25 Jan 2017 17:58:33:  8000000 
INFO  @ Wed, 25 Jan 2017 17:58:34:  9000000 
INFO  @ Wed, 25 Jan 2017 17:58:36:  10000000 
INFO  @ Wed, 25 Jan 2017 17:58:38:  11000000 
INFO  @ Wed, 25 Jan 2017 17:58:39: #1 tag size is determined as 36 bps 
INFO  @ Wed, 25 Jan 2017 17:58:39: #1 tag size = 36 
INFO  @ Wed, 25 Jan 2017 17:58:39: #1  total tags in treatment: 34983396 
INFO  @ Wed, 25 Jan 2017 17:58:39: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 17:58:39: #1 finished! 
INFO  @ Wed, 25 Jan 2017 17:58:39: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 17:58:39: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 17:58:39: #2 Use 123 as fragment length 
INFO  @ Wed, 25 Jan 2017 17:58:39: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 17:58:39: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Wed, 25 Jan 2017 17:58:39: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 17:59:46: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 18:01:00: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 18:01:01: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak 
INFO  @ Wed, 25 Jan 2017 18:01:02: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Wed, 25 Jan 2017 18:01:03: Done! 
INFO  @ Wed, 25 Jan 2017 18:01:07: Read and build treatment bedGraph... 
INFO  @ Wed, 25 Jan 2017 18:01:53: Read and build control bedGraph... 
INFO  @ Wed, 25 Jan 2017 18:02:29: Build scoreTrackII... 
INFO  @ Wed, 25 Jan 2017 18:03:00: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Wed, 25 Jan 2017 18:05:48: Write bedGraph of scores... 
INFO  @ Wed, 25 Jan 2017 18:07:39: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_FE.bdg'! 
INFO  @ Wed, 25 Jan 2017 18:12:11: Read and build treatment bedGraph... 
INFO  @ Wed, 25 Jan 2017 18:12:59: Read and build control bedGraph... 
INFO  @ Wed, 25 Jan 2017 18:13:37: Build scoreTrackII... 
INFO  @ Wed, 25 Jan 2017 18:14:10: Values in your input bedGraph files will be multiplied by 11.467883 ... 
INFO  @ Wed, 25 Jan 2017 18:17:06: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Wed, 25 Jan 2017 18:17:28: Write bedGraph of scores... 
INFO  @ Wed, 25 Jan 2017 18:18:30: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_ppois.bdg'! 

 
 		 

    
  
 
  Num   2  
 
  ID   task.callpeak_macs2.macs2_ppr1.line_71.id_11  
 
  Name   macs2 ppr1 
 
  Thread   thread_Root  
 
  PID   35577  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-25 17:52:07  
 
  End   2017-01-25 17:58:59  
 
  Elapsed   00:06:51  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.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/EncodeOtherHek293Data/H3K4me3/align/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 123 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 123 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 110

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.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/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1 -o "ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -g /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.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/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1 -o "ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 143

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -g /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.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--------------------
48015 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Wed, 25 Jan 2017 17:52:23: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 123 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.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  @ Wed, 25 Jan 2017 17:52:23: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 17:52:23: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 17:52:25:  1000000 
INFO  @ Wed, 25 Jan 2017 17:52:27:  2000000 
INFO  @ Wed, 25 Jan 2017 17:52:29:  3000000 
INFO  @ Wed, 25 Jan 2017 17:52:30:  4000000 
INFO  @ Wed, 25 Jan 2017 17:52:32:  5000000 
INFO  @ Wed, 25 Jan 2017 17:52:34:  6000000 
INFO  @ Wed, 25 Jan 2017 17:52:35:  7000000 
INFO  @ Wed, 25 Jan 2017 17:52:37:  8000000 
INFO  @ Wed, 25 Jan 2017 17:52:39:  9000000 
INFO  @ Wed, 25 Jan 2017 17:52:40:  10000000 
INFO  @ Wed, 25 Jan 2017 17:52:42:  11000000 
INFO  @ Wed, 25 Jan 2017 17:52:43:  12000000 
INFO  @ Wed, 25 Jan 2017 17:52:45:  13000000 
INFO  @ Wed, 25 Jan 2017 17:52:47:  14000000 
INFO  @ Wed, 25 Jan 2017 17:52:48:  15000000 
INFO  @ Wed, 25 Jan 2017 17:52:50:  16000000 
INFO  @ Wed, 25 Jan 2017 17:52:51:  17000000 
INFO  @ Wed, 25 Jan 2017 17:52:53: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 17:52:55:  1000000 
INFO  @ Wed, 25 Jan 2017 17:52:57:  2000000 
INFO  @ Wed, 25 Jan 2017 17:52:58:  3000000 
INFO  @ Wed, 25 Jan 2017 17:53:00:  4000000 
INFO  @ Wed, 25 Jan 2017 17:53:01:  5000000 
INFO  @ Wed, 25 Jan 2017 17:53:03:  6000000 
INFO  @ Wed, 25 Jan 2017 17:53:04:  7000000 
INFO  @ Wed, 25 Jan 2017 17:53:06:  8000000 
INFO  @ Wed, 25 Jan 2017 17:53:07:  9000000 
INFO  @ Wed, 25 Jan 2017 17:53:09:  10000000 
INFO  @ Wed, 25 Jan 2017 17:53:10:  11000000 
INFO  @ Wed, 25 Jan 2017 17:53:11: #1 tag size is determined as 36 bps 
INFO  @ Wed, 25 Jan 2017 17:53:11: #1 tag size = 36 
INFO  @ Wed, 25 Jan 2017 17:53:11: #1  total tags in treatment: 17491698 
INFO  @ Wed, 25 Jan 2017 17:53:11: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 17:53:11: #1 finished! 
INFO  @ Wed, 25 Jan 2017 17:53:11: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 17:53:11: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 17:53:11: #2 Use 123 as fragment length 
INFO  @ Wed, 25 Jan 2017 17:53:11: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 17:53:11: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Wed, 25 Jan 2017 17:53:11: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 17:54:04: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Wed, 25 Jan 2017 17:54:04: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Wed, 25 Jan 2017 17:54:04: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg 
INFO  @ Wed, 25 Jan 2017 17:54:04: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Wed, 25 Jan 2017 17:54:04: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 17:56:08: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 17:56:09: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Wed, 25 Jan 2017 17:56:11: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed 
INFO  @ Wed, 25 Jan 2017 17:56:13: Done! 
INFO  @ Wed, 25 Jan 2017 17:56:16: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 123 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.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  @ Wed, 25 Jan 2017 17:56:16: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 17:56:16: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 17:56:18:  1000000 
INFO  @ Wed, 25 Jan 2017 17:56:19:  2000000 
INFO  @ Wed, 25 Jan 2017 17:56:21:  3000000 
INFO  @ Wed, 25 Jan 2017 17:56:22:  4000000 
INFO  @ Wed, 25 Jan 2017 17:56:24:  5000000 
INFO  @ Wed, 25 Jan 2017 17:56:26:  6000000 
INFO  @ Wed, 25 Jan 2017 17:56:27:  7000000 
INFO  @ Wed, 25 Jan 2017 17:56:29:  8000000 
INFO  @ Wed, 25 Jan 2017 17:56:30:  9000000 
INFO  @ Wed, 25 Jan 2017 17:56:32:  10000000 
INFO  @ Wed, 25 Jan 2017 17:56:33:  11000000 
INFO  @ Wed, 25 Jan 2017 17:56:35:  12000000 
INFO  @ Wed, 25 Jan 2017 17:56:37:  13000000 
INFO  @ Wed, 25 Jan 2017 17:56:38:  14000000 
INFO  @ Wed, 25 Jan 2017 17:56:40:  15000000 
INFO  @ Wed, 25 Jan 2017 17:56:41:  16000000 
INFO  @ Wed, 25 Jan 2017 17:56:43:  17000000 
INFO  @ Wed, 25 Jan 2017 17:56:45: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 17:56:46:  1000000 
INFO  @ Wed, 25 Jan 2017 17:56:48:  2000000 
INFO  @ Wed, 25 Jan 2017 17:56:49:  3000000 
INFO  @ Wed, 25 Jan 2017 17:56:51:  4000000 
INFO  @ Wed, 25 Jan 2017 17:56:52:  5000000 
INFO  @ Wed, 25 Jan 2017 17:56:54:  6000000 
INFO  @ Wed, 25 Jan 2017 17:56:55:  7000000 
INFO  @ Wed, 25 Jan 2017 17:56:57:  8000000 
INFO  @ Wed, 25 Jan 2017 17:56:58:  9000000 
INFO  @ Wed, 25 Jan 2017 17:57:00:  10000000 
INFO  @ Wed, 25 Jan 2017 17:57:01:  11000000 
INFO  @ Wed, 25 Jan 2017 17:57:02: #1 tag size is determined as 36 bps 
INFO  @ Wed, 25 Jan 2017 17:57:02: #1 tag size = 36 
INFO  @ Wed, 25 Jan 2017 17:57:02: #1  total tags in treatment: 17491698 
INFO  @ Wed, 25 Jan 2017 17:57:02: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 17:57:02: #1 finished! 
INFO  @ Wed, 25 Jan 2017 17:57:02: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 17:57:02: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 17:57:02: #2 Use 123 as fragment length 
INFO  @ Wed, 25 Jan 2017 17:57:02: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 17:57:02: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Wed, 25 Jan 2017 17:57:02: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 17:57:53: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 17:58:49: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 17:58:50: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak 
INFO  @ Wed, 25 Jan 2017 17:58:51: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Wed, 25 Jan 2017 17:58:51: Done! 

 
 		 

    
  
 
  Num   3  
 
  ID   task.callpeak_macs2.macs2_ppr2.line_71.id_12  
 
  Name   macs2 ppr2 
 
  Thread   thread_Root  
 
  PID   35578  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-25 17:52:08  
 
  End   2017-01-25 17:58:59  
 
  Elapsed   00:06:51  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.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/EncodeOtherHek293Data/H3K4me3/align/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 123 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 123 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 110

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.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/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2 -o "ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -g /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.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/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2 -o "ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 143

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -g /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.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--------------------
48016 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Wed, 25 Jan 2017 17:52:23: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 123 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.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  @ Wed, 25 Jan 2017 17:52:23: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 17:52:23: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 17:52:25:  1000000 
INFO  @ Wed, 25 Jan 2017 17:52:27:  2000000 
INFO  @ Wed, 25 Jan 2017 17:52:28:  3000000 
INFO  @ Wed, 25 Jan 2017 17:52:30:  4000000 
INFO  @ Wed, 25 Jan 2017 17:52:32:  5000000 
INFO  @ Wed, 25 Jan 2017 17:52:33:  6000000 
INFO  @ Wed, 25 Jan 2017 17:52:35:  7000000 
INFO  @ Wed, 25 Jan 2017 17:52:36:  8000000 
INFO  @ Wed, 25 Jan 2017 17:52:38:  9000000 
INFO  @ Wed, 25 Jan 2017 17:52:40:  10000000 
INFO  @ Wed, 25 Jan 2017 17:52:41:  11000000 
INFO  @ Wed, 25 Jan 2017 17:52:43:  12000000 
INFO  @ Wed, 25 Jan 2017 17:52:44:  13000000 
INFO  @ Wed, 25 Jan 2017 17:52:46:  14000000 
INFO  @ Wed, 25 Jan 2017 17:52:48:  15000000 
INFO  @ Wed, 25 Jan 2017 17:52:49:  16000000 
INFO  @ Wed, 25 Jan 2017 17:52:51:  17000000 
INFO  @ Wed, 25 Jan 2017 17:52:53: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 17:52:54:  1000000 
INFO  @ Wed, 25 Jan 2017 17:52:56:  2000000 
INFO  @ Wed, 25 Jan 2017 17:52:57:  3000000 
INFO  @ Wed, 25 Jan 2017 17:52:59:  4000000 
INFO  @ Wed, 25 Jan 2017 17:53:00:  5000000 
INFO  @ Wed, 25 Jan 2017 17:53:02:  6000000 
INFO  @ Wed, 25 Jan 2017 17:53:03:  7000000 
INFO  @ Wed, 25 Jan 2017 17:53:05:  8000000 
INFO  @ Wed, 25 Jan 2017 17:53:06:  9000000 
INFO  @ Wed, 25 Jan 2017 17:53:08:  10000000 
INFO  @ Wed, 25 Jan 2017 17:53:09:  11000000 
INFO  @ Wed, 25 Jan 2017 17:53:10: #1 tag size is determined as 36 bps 
INFO  @ Wed, 25 Jan 2017 17:53:10: #1 tag size = 36 
INFO  @ Wed, 25 Jan 2017 17:53:10: #1  total tags in treatment: 17491698 
INFO  @ Wed, 25 Jan 2017 17:53:10: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 17:53:10: #1 finished! 
INFO  @ Wed, 25 Jan 2017 17:53:10: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 17:53:10: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 17:53:10: #2 Use 123 as fragment length 
INFO  @ Wed, 25 Jan 2017 17:53:10: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 17:53:10: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Wed, 25 Jan 2017 17:53:10: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 17:54:02: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Wed, 25 Jan 2017 17:54:02: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Wed, 25 Jan 2017 17:54:02: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg 
INFO  @ Wed, 25 Jan 2017 17:54:02: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Wed, 25 Jan 2017 17:54:02: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 17:56:13: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 17:56:14: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Wed, 25 Jan 2017 17:56:14: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed 
INFO  @ Wed, 25 Jan 2017 17:56:14: Done! 
INFO  @ Wed, 25 Jan 2017 17:56:17: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 123 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.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  @ Wed, 25 Jan 2017 17:56:17: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 17:56:17: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 17:56:19:  1000000 
INFO  @ Wed, 25 Jan 2017 17:56:20:  2000000 
INFO  @ Wed, 25 Jan 2017 17:56:22:  3000000 
INFO  @ Wed, 25 Jan 2017 17:56:23:  4000000 
INFO  @ Wed, 25 Jan 2017 17:56:25:  5000000 
INFO  @ Wed, 25 Jan 2017 17:56:27:  6000000 
INFO  @ Wed, 25 Jan 2017 17:56:28:  7000000 
INFO  @ Wed, 25 Jan 2017 17:56:30:  8000000 
INFO  @ Wed, 25 Jan 2017 17:56:31:  9000000 
INFO  @ Wed, 25 Jan 2017 17:56:33:  10000000 
INFO  @ Wed, 25 Jan 2017 17:56:34:  11000000 
INFO  @ Wed, 25 Jan 2017 17:56:36:  12000000 
INFO  @ Wed, 25 Jan 2017 17:56:38:  13000000 
INFO  @ Wed, 25 Jan 2017 17:56:39:  14000000 
INFO  @ Wed, 25 Jan 2017 17:56:41:  15000000 
INFO  @ Wed, 25 Jan 2017 17:56:42:  16000000 
INFO  @ Wed, 25 Jan 2017 17:56:44:  17000000 
INFO  @ Wed, 25 Jan 2017 17:56:46: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 17:56:47:  1000000 
INFO  @ Wed, 25 Jan 2017 17:56:49:  2000000 
INFO  @ Wed, 25 Jan 2017 17:56:50:  3000000 
INFO  @ Wed, 25 Jan 2017 17:56:52:  4000000 
INFO  @ Wed, 25 Jan 2017 17:56:53:  5000000 
INFO  @ Wed, 25 Jan 2017 17:56:55:  6000000 
INFO  @ Wed, 25 Jan 2017 17:56:56:  7000000 
INFO  @ Wed, 25 Jan 2017 17:56:58:  8000000 
INFO  @ Wed, 25 Jan 2017 17:56:59:  9000000 
INFO  @ Wed, 25 Jan 2017 17:57:01:  10000000 
INFO  @ Wed, 25 Jan 2017 17:57:02:  11000000 
INFO  @ Wed, 25 Jan 2017 17:57:03: #1 tag size is determined as 36 bps 
INFO  @ Wed, 25 Jan 2017 17:57:03: #1 tag size = 36 
INFO  @ Wed, 25 Jan 2017 17:57:03: #1  total tags in treatment: 17491698 
INFO  @ Wed, 25 Jan 2017 17:57:03: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 17:57:03: #1 finished! 
INFO  @ Wed, 25 Jan 2017 17:57:03: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 17:57:03: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 17:57:03: #2 Use 123 as fragment length 
INFO  @ Wed, 25 Jan 2017 17:57:03: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 17:57:03: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Wed, 25 Jan 2017 17:57:03: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 17:57:55: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 17:58:50: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 17:58:51: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak 
INFO  @ Wed, 25 Jan 2017 17:58:52: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Wed, 25 Jan 2017 17:58:53: Done! 

 
 		 

    
  
 
  Num   4  
 
  ID   task.callpeak_macs2.macs2_rep1.line_71.id_13  
 
  Name   macs2 rep1 
 
  Thread   thread_Root  
 
  PID   35579  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-25 17:52:09  
 
  End   2017-01-25 18:15:36  
 
  Elapsed   00:23:27  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/rep1/ENCFF001FJZ.nodup.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/signal/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/signal/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.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/EncodeOtherHek293Data/H3K4me3/align/rep1/ENCFF001FJZ.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 125 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/rep1/ENCFF001FJZ.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 125 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 110

 if [[ true == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.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/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1 -o "ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -g /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/signal/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/rep1/ENCFF001FJZ.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.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/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1 -o "ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 143

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -g /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/signal/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.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--------------------
48017 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Wed, 25 Jan 2017 17:52:23: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/rep1/ENCFF001FJZ.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 125 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/rep1/ENCFF001FJZ.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.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  @ Wed, 25 Jan 2017 17:52:23: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 17:52:23: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 17:52:25:  1000000 
INFO  @ Wed, 25 Jan 2017 17:52:27:  2000000 
INFO  @ Wed, 25 Jan 2017 17:52:28:  3000000 
INFO  @ Wed, 25 Jan 2017 17:52:30:  4000000 
INFO  @ Wed, 25 Jan 2017 17:52:31:  5000000 
INFO  @ Wed, 25 Jan 2017 17:52:33:  6000000 
INFO  @ Wed, 25 Jan 2017 17:52:34:  7000000 
INFO  @ Wed, 25 Jan 2017 17:52:36:  8000000 
INFO  @ Wed, 25 Jan 2017 17:52:37:  9000000 
INFO  @ Wed, 25 Jan 2017 17:52:39:  10000000 
INFO  @ Wed, 25 Jan 2017 17:52:41:  11000000 
INFO  @ Wed, 25 Jan 2017 17:52:42:  12000000 
INFO  @ Wed, 25 Jan 2017 17:52:44:  13000000 
INFO  @ Wed, 25 Jan 2017 17:52:45:  14000000 
INFO  @ Wed, 25 Jan 2017 17:52:47:  15000000 
INFO  @ Wed, 25 Jan 2017 17:52:48:  16000000 
INFO  @ Wed, 25 Jan 2017 17:52:50:  17000000 
INFO  @ Wed, 25 Jan 2017 17:52:51:  18000000 
INFO  @ Wed, 25 Jan 2017 17:52:53:  19000000 
INFO  @ Wed, 25 Jan 2017 17:52:55:  20000000 
INFO  @ Wed, 25 Jan 2017 17:52:55: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 17:52:57:  1000000 
INFO  @ Wed, 25 Jan 2017 17:52:59:  2000000 
INFO  @ Wed, 25 Jan 2017 17:53:01:  3000000 
INFO  @ Wed, 25 Jan 2017 17:53:02:  4000000 
INFO  @ Wed, 25 Jan 2017 17:53:04:  5000000 
INFO  @ Wed, 25 Jan 2017 17:53:05:  6000000 
INFO  @ Wed, 25 Jan 2017 17:53:07:  7000000 
INFO  @ Wed, 25 Jan 2017 17:53:08:  8000000 
INFO  @ Wed, 25 Jan 2017 17:53:10:  9000000 
INFO  @ Wed, 25 Jan 2017 17:53:11:  10000000 
INFO  @ Wed, 25 Jan 2017 17:53:13:  11000000 
INFO  @ Wed, 25 Jan 2017 17:53:14: #1 tag size is determined as 36 bps 
INFO  @ Wed, 25 Jan 2017 17:53:14: #1 tag size = 36 
INFO  @ Wed, 25 Jan 2017 17:53:14: #1  total tags in treatment: 20280850 
INFO  @ Wed, 25 Jan 2017 17:53:14: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 17:53:14: #1 finished! 
INFO  @ Wed, 25 Jan 2017 17:53:14: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 17:53:14: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 17:53:14: #2 Use 125 as fragment length 
INFO  @ Wed, 25 Jan 2017 17:53:14: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 17:53:14: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Wed, 25 Jan 2017 17:53:14: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 17:54:10: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Wed, 25 Jan 2017 17:54:10: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Wed, 25 Jan 2017 17:54:10: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg 
INFO  @ Wed, 25 Jan 2017 17:54:10: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Wed, 25 Jan 2017 17:54:10: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 17:56:22: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 17:56:23: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Wed, 25 Jan 2017 17:56:23: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed 
INFO  @ Wed, 25 Jan 2017 17:56:23: Done! 
INFO  @ Wed, 25 Jan 2017 17:56:26: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/rep1/ENCFF001FJZ.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 125 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/rep1/ENCFF001FJZ.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.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  @ Wed, 25 Jan 2017 17:56:26: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 17:56:26: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 17:56:27:  1000000 
INFO  @ Wed, 25 Jan 2017 17:56:29:  2000000 
INFO  @ Wed, 25 Jan 2017 17:56:31:  3000000 
INFO  @ Wed, 25 Jan 2017 17:56:33:  4000000 
INFO  @ Wed, 25 Jan 2017 17:56:35:  5000000 
INFO  @ Wed, 25 Jan 2017 17:56:37:  6000000 
INFO  @ Wed, 25 Jan 2017 17:56:39:  7000000 
INFO  @ Wed, 25 Jan 2017 17:56:40:  8000000 
INFO  @ Wed, 25 Jan 2017 17:56:42:  9000000 
INFO  @ Wed, 25 Jan 2017 17:56:44:  10000000 
INFO  @ Wed, 25 Jan 2017 17:56:45:  11000000 
INFO  @ Wed, 25 Jan 2017 17:56:47:  12000000 
INFO  @ Wed, 25 Jan 2017 17:56:49:  13000000 
INFO  @ Wed, 25 Jan 2017 17:56:51:  14000000 
INFO  @ Wed, 25 Jan 2017 17:56:53:  15000000 
INFO  @ Wed, 25 Jan 2017 17:56:55:  16000000 
INFO  @ Wed, 25 Jan 2017 17:56:57:  17000000 
INFO  @ Wed, 25 Jan 2017 17:56:58:  18000000 
INFO  @ Wed, 25 Jan 2017 17:57:00:  19000000 
INFO  @ Wed, 25 Jan 2017 17:57:01:  20000000 
INFO  @ Wed, 25 Jan 2017 17:57:02: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 17:57:04:  1000000 
INFO  @ Wed, 25 Jan 2017 17:57:06:  2000000 
INFO  @ Wed, 25 Jan 2017 17:57:08:  3000000 
INFO  @ Wed, 25 Jan 2017 17:57:10:  4000000 
INFO  @ Wed, 25 Jan 2017 17:57:11:  5000000 
INFO  @ Wed, 25 Jan 2017 17:57:13:  6000000 
INFO  @ Wed, 25 Jan 2017 17:57:15:  7000000 
INFO  @ Wed, 25 Jan 2017 17:57:17:  8000000 
INFO  @ Wed, 25 Jan 2017 17:57:18:  9000000 
INFO  @ Wed, 25 Jan 2017 17:57:20:  10000000 
INFO  @ Wed, 25 Jan 2017 17:57:21:  11000000 
INFO  @ Wed, 25 Jan 2017 17:57:22: #1 tag size is determined as 36 bps 
INFO  @ Wed, 25 Jan 2017 17:57:22: #1 tag size = 36 
INFO  @ Wed, 25 Jan 2017 17:57:22: #1  total tags in treatment: 20280850 
INFO  @ Wed, 25 Jan 2017 17:57:22: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 17:57:22: #1 finished! 
INFO  @ Wed, 25 Jan 2017 17:57:22: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 17:57:22: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 17:57:22: #2 Use 125 as fragment length 
INFO  @ Wed, 25 Jan 2017 17:57:22: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 17:57:22: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Wed, 25 Jan 2017 17:57:22: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 17:58:20: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 17:59:24: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 17:59:25: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak 
INFO  @ Wed, 25 Jan 2017 17:59:26: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Wed, 25 Jan 2017 17:59:26: Done! 
INFO  @ Wed, 25 Jan 2017 17:59:32: Read and build treatment bedGraph... 
INFO  @ Wed, 25 Jan 2017 18:00:01: Read and build control bedGraph... 
INFO  @ Wed, 25 Jan 2017 18:00:34: Build scoreTrackII... 
INFO  @ Wed, 25 Jan 2017 18:00:57: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Wed, 25 Jan 2017 18:03:19: Write bedGraph of scores... 
INFO  @ Wed, 25 Jan 2017 18:04:32: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_FE.bdg'! 
INFO  @ Wed, 25 Jan 2017 18:07:24: Read and build treatment bedGraph... 
INFO  @ Wed, 25 Jan 2017 18:07:52: Read and build control bedGraph... 
INFO  @ Wed, 25 Jan 2017 18:08:26: Build scoreTrackII... 
INFO  @ Wed, 25 Jan 2017 18:08:45: Values in your input bedGraph files will be multiplied by 11.467883 ... 
INFO  @ Wed, 25 Jan 2017 18:11:10: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Wed, 25 Jan 2017 18:11:27: Write bedGraph of scores... 
INFO  @ Wed, 25 Jan 2017 18:12:34: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_ppois.bdg'! 

 
 		 

    
  
 
  Num   5  
 
  ID   task.callpeak_macs2.macs2_rep2.line_71.id_14  
 
  Name   macs2 rep2 
 
  Thread   thread_Root  
 
  PID   35593  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-25 17:59:02  
 
  End   2017-01-25 18:20:48  
 
  Elapsed   00:21:45  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/rep2/ENCFF001FJY.nodup.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/signal/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/signal/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.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/EncodeOtherHek293Data/H3K4me3/align/rep2/ENCFF001FJY.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 120 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/rep2/ENCFF001FJY.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 120 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 110

 if [[ true == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.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/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2 -o "ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -g /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/signal/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/rep2/ENCFF001FJY.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.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/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2 -o "ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 143

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -g /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/signal/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.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--------------------
15532 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Wed, 25 Jan 2017 17:59:25: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/rep2/ENCFF001FJY.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 120 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/rep2/ENCFF001FJY.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.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  @ Wed, 25 Jan 2017 17:59:25: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 17:59:25: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 17:59:27:  1000000 
INFO  @ Wed, 25 Jan 2017 17:59:28:  2000000 
INFO  @ Wed, 25 Jan 2017 17:59:30:  3000000 
INFO  @ Wed, 25 Jan 2017 17:59:31:  4000000 
INFO  @ Wed, 25 Jan 2017 17:59:33:  5000000 
INFO  @ Wed, 25 Jan 2017 17:59:34:  6000000 
INFO  @ Wed, 25 Jan 2017 17:59:36:  7000000 
INFO  @ Wed, 25 Jan 2017 17:59:37:  8000000 
INFO  @ Wed, 25 Jan 2017 17:59:39:  9000000 
INFO  @ Wed, 25 Jan 2017 17:59:41:  10000000 
INFO  @ Wed, 25 Jan 2017 17:59:43:  11000000 
INFO  @ Wed, 25 Jan 2017 17:59:44:  12000000 
INFO  @ Wed, 25 Jan 2017 17:59:46:  13000000 
INFO  @ Wed, 25 Jan 2017 17:59:47:  14000000 
INFO  @ Wed, 25 Jan 2017 17:59:48: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 17:59:50:  1000000 
INFO  @ Wed, 25 Jan 2017 17:59:52:  2000000 
INFO  @ Wed, 25 Jan 2017 17:59:53:  3000000 
INFO  @ Wed, 25 Jan 2017 17:59:55:  4000000 
INFO  @ Wed, 25 Jan 2017 17:59:56:  5000000 
INFO  @ Wed, 25 Jan 2017 17:59:58:  6000000 
INFO  @ Wed, 25 Jan 2017 17:59:59:  7000000 
INFO  @ Wed, 25 Jan 2017 18:00:01:  8000000 
INFO  @ Wed, 25 Jan 2017 18:00:02:  9000000 
INFO  @ Wed, 25 Jan 2017 18:00:04:  10000000 
INFO  @ Wed, 25 Jan 2017 18:00:06:  11000000 
INFO  @ Wed, 25 Jan 2017 18:00:06: #1 tag size is determined as 35 bps 
INFO  @ Wed, 25 Jan 2017 18:00:06: #1 tag size = 35 
INFO  @ Wed, 25 Jan 2017 18:00:06: #1  total tags in treatment: 14702546 
INFO  @ Wed, 25 Jan 2017 18:00:06: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 18:00:06: #1 finished! 
INFO  @ Wed, 25 Jan 2017 18:00:06: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 18:00:06: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 18:00:06: #2 Use 120 as fragment length 
INFO  @ Wed, 25 Jan 2017 18:00:06: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 18:00:06: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Wed, 25 Jan 2017 18:00:06: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 18:01:02: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Wed, 25 Jan 2017 18:01:02: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Wed, 25 Jan 2017 18:01:02: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg 
INFO  @ Wed, 25 Jan 2017 18:01:02: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Wed, 25 Jan 2017 18:01:02: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 18:03:05: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 18:03:06: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Wed, 25 Jan 2017 18:03:06: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed 
INFO  @ Wed, 25 Jan 2017 18:03:06: Done! 
INFO  @ Wed, 25 Jan 2017 18:03:10: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/rep2/ENCFF001FJY.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 120 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/rep2/ENCFF001FJY.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.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  @ Wed, 25 Jan 2017 18:03:10: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 18:03:10: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 18:03:11:  1000000 
INFO  @ Wed, 25 Jan 2017 18:03:13:  2000000 
INFO  @ Wed, 25 Jan 2017 18:03:14:  3000000 
INFO  @ Wed, 25 Jan 2017 18:03:16:  4000000 
INFO  @ Wed, 25 Jan 2017 18:03:17:  5000000 
INFO  @ Wed, 25 Jan 2017 18:03:19:  6000000 
INFO  @ Wed, 25 Jan 2017 18:03:20:  7000000 
INFO  @ Wed, 25 Jan 2017 18:03:22:  8000000 
INFO  @ Wed, 25 Jan 2017 18:03:23:  9000000 
INFO  @ Wed, 25 Jan 2017 18:03:25:  10000000 
INFO  @ Wed, 25 Jan 2017 18:03:26:  11000000 
INFO  @ Wed, 25 Jan 2017 18:03:27:  12000000 
INFO  @ Wed, 25 Jan 2017 18:03:29:  13000000 
INFO  @ Wed, 25 Jan 2017 18:03:30:  14000000 
INFO  @ Wed, 25 Jan 2017 18:03:31: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 18:03:33:  1000000 
INFO  @ Wed, 25 Jan 2017 18:03:35:  2000000 
INFO  @ Wed, 25 Jan 2017 18:03:36:  3000000 
INFO  @ Wed, 25 Jan 2017 18:03:38:  4000000 
INFO  @ Wed, 25 Jan 2017 18:03:39:  5000000 
INFO  @ Wed, 25 Jan 2017 18:03:41:  6000000 
INFO  @ Wed, 25 Jan 2017 18:03:42:  7000000 
INFO  @ Wed, 25 Jan 2017 18:03:43:  8000000 
INFO  @ Wed, 25 Jan 2017 18:03:45:  9000000 
INFO  @ Wed, 25 Jan 2017 18:03:46:  10000000 
INFO  @ Wed, 25 Jan 2017 18:03:48:  11000000 
INFO  @ Wed, 25 Jan 2017 18:03:48: #1 tag size is determined as 35 bps 
INFO  @ Wed, 25 Jan 2017 18:03:48: #1 tag size = 35 
INFO  @ Wed, 25 Jan 2017 18:03:48: #1  total tags in treatment: 14702546 
INFO  @ Wed, 25 Jan 2017 18:03:48: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 18:03:48: #1 finished! 
INFO  @ Wed, 25 Jan 2017 18:03:48: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 18:03:48: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 18:03:48: #2 Use 120 as fragment length 
INFO  @ Wed, 25 Jan 2017 18:03:48: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 18:03:48: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Wed, 25 Jan 2017 18:03:48: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 18:04:38: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 18:05:34: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 18:05:36: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak 
INFO  @ Wed, 25 Jan 2017 18:05:36: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Wed, 25 Jan 2017 18:05:38: Done! 
INFO  @ Wed, 25 Jan 2017 18:05:45: Read and build treatment bedGraph... 
INFO  @ Wed, 25 Jan 2017 18:06:07: Read and build control bedGraph... 
INFO  @ Wed, 25 Jan 2017 18:06:43: Build scoreTrackII... 
INFO  @ Wed, 25 Jan 2017 18:07:05: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Wed, 25 Jan 2017 18:09:10: Write bedGraph of scores... 
INFO  @ Wed, 25 Jan 2017 18:10:06: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_FE.bdg'! 
INFO  @ Wed, 25 Jan 2017 18:12:38: Read and build treatment bedGraph... 
INFO  @ Wed, 25 Jan 2017 18:13:02: Read and build control bedGraph... 
INFO  @ Wed, 25 Jan 2017 18:13:39: Build scoreTrackII... 
INFO  @ Wed, 25 Jan 2017 18:14:00: Values in your input bedGraph files will be multiplied by 11.467883 ... 
INFO  @ Wed, 25 Jan 2017 18:16:10: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Wed, 25 Jan 2017 18:16:26: Write bedGraph of scores... 
INFO  @ Wed, 25 Jan 2017 18:17:32: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_ppois.bdg'! 

 
 		 

    
  
 
  Num   6  
 
  ID   task.callpeak_naive_overlap.naive_overlap_thresh.line_143.id_15  
 
  Name   naive_overlap_thresh  
 
  Thread   thread_Root  
 
  PID   35600  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-25 18:21:38  
 
  End   2017-01-25 18:22:52  
 
  Elapsed   00:01:14  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 145

 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 148

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz) | awk 'BEGIN{FS="	";OFS="	"} {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/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz) | awk 'BEGIN{FS="	";OFS="	"} {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/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.narrowPeak.gz

# SYS command. line 151

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz) | awk 'BEGIN{FS="	";OFS="	"} {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/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz) |    awk 'BEGIN{FS="	";OFS="	"} {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/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.narrowPeak.gz

# SYS command. line 154

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.narrowPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.narrowPeak.gz

# SYS command. line 156

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.narrowPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz  | grep -P 'chr[0-9XY]+(?!_)' | awk 'BEGIN{OFS="	"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz

# SYS command. line 158

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.narrowPeak.gz

# SYS command. line 160

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
5823 (process ID) old priority 0, new priority 10
Waiting for 57 seconds.

  
 		 

    
  
 
  Num   7  
 
  ID   task.callpeak_naive_overlap.naive_overlap_thresh.line_143.id_16  
 
  Name   naive_overlap_thresh  
 
  Thread   thread_Root  
 
  PID   35601  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-25 18:21:39  
 
  End   2017-01-25 18:22:53  
 
  Elapsed   00:01:14  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 145

 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 148

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz) | awk 'BEGIN{FS="	";OFS="	"} {s1=$3-$2; s2=$18-$17; if (($31/s1 >= 0.5) || ($31/s2 >= 0.5)) {print $0}}' | cut -f 1-15 | sort | uniq | intersectBed  -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz) | awk 'BEGIN{FS="	";OFS="	"} {s1=$3-$2; s2=$18-$17; if (($31/s1 >= 0.5) || ($31/s2 >= 0.5)) {print $0}}' | cut -f 1-15 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.gappedPeak.gz

# SYS command. line 151

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz) | awk 'BEGIN{FS="	";OFS="	"} {s1=$3-$2; s2=$18-$17; if (($31/s1 >= 0.5) || ($31/s2 >= 0.5)) {print $0}}' | cut -f 1-15 | sort | uniq | intersectBed  -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz) |    awk 'BEGIN{FS="	";OFS="	"} {s1=$3-$2; s2=$18-$17; if (($31/s1 >= 0.5) || ($31/s2 >= 0.5)) {print $0}}' | cut -f 1-15 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.gappedPeak.gz

# SYS command. line 154

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.gappedPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.gappedPeak.gz

# SYS command. line 156

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.gappedPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz  | grep -P 'chr[0-9XY]+(?!_)' | awk 'BEGIN{OFS="	"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz

# SYS command. line 158

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.gappedPeak.gz

# SYS command. line 160

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
5822 (process ID) old priority 0, new priority 10
Waiting for 56 seconds.

  
 		 

    
  
 
  Num   8  
 
  ID   task.callpeak_naive_overlap.naive_overlap_thresh.line_143.id_17  
 
  Name   naive_overlap_thresh  
 
  Thread   thread_Root  
 
  PID   35602  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-25 18:21:40  
 
  End   2017-01-25 18:22:53  
 
  Elapsed   00:01:12  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.broadPeak.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 145

 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 148

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz) | awk 'BEGIN{FS="	";OFS="	"} {s1=$3-$2; s2=$12-$11; if (($19/s1 >= 0.5) || ($19/s2 >= 0.5)) {print $0}}' | cut -f 1-9 | sort | uniq | intersectBed  -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz) | awk 'BEGIN{FS="	";OFS="	"} {s1=$3-$2; s2=$12-$11; if (($19/s1 >= 0.5) || ($19/s2 >= 0.5)) {print $0}}' | cut -f 1-9 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.broadPeak.gz

# SYS command. line 151

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF001FJZ.nodup.pr1_ENCFF001FJY.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz) | awk 'BEGIN{FS="	";OFS="	"} {s1=$3-$2; s2=$12-$11; if (($19/s1 >= 0.5) || ($19/s2 >= 0.5)) {print $0}}' | cut -f 1-9 | sort | uniq | intersectBed  -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF001FJZ.nodup.pr2_ENCFF001FJY.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz) |    awk 'BEGIN{FS="	";OFS="	"} {s1=$3-$2; s2=$12-$11; if (($19/s1 >= 0.5) || ($19/s2 >= 0.5)) {print $0}}' | cut -f 1-9 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.broadPeak.gz

# SYS command. line 154

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.broadPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.broadPeak.gz

# SYS command. line 156

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.broadPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz  | grep -P 'chr[0-9XY]+(?!_)' | awk 'BEGIN{OFS="	"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.broadPeak.gz

# SYS command. line 158

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.broadPeak.gz

# SYS command. line 160

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
5824 (process ID) old priority 0, new priority 10
Waiting for 57 seconds.

  
 		 

    
  
 
  Num   9  
 
  ID   task.callpeak_blacklist_filter.blacklist_filter_peak_pooled.line_27.id_18  
 
  Name   blacklist_filter peak_pooled 
 
  Thread   thread_Root  
 
  PID   39407  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-25 18:22:55  
 
  End   2017-01-25 18:24:03  
 
  Elapsed   00:01:07  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.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/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.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/EncodeOtherHek293Data/H3K4me3/peak/macs2/pooled_rep/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.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--------------------
39412 (process ID) old priority 0, new priority 10
Waiting for 59 seconds.

  
 		 

    
  
 
  Num   10  
 
  ID   task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_19  
 
  Name   blacklist_filter peak 1 
 
  Thread   thread_Root  
 
  PID   39543  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-25 18:22:57  
 
  End   2017-01-25 18:24:04  
 
  Elapsed   00:01:07  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.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/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.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/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep1/ENCFF001FJZ.nodup.tagAlign_x_ENCFF001HNC.nodup.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--------------------
39548 (process ID) old priority 0, new priority 10
Waiting for 59 seconds.

  
 		 

    
  
 
  Num   11  
 
  ID   task.callpeak_blacklist_filter.blacklist_filter_peak_2.line_27.id_20  
 
  Name   blacklist_filter peak 2 
 
  Thread   thread_Root  
 
  PID   39597  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-25 18:22:57  
 
  End   2017-01-25 18:24:05  
 
  Elapsed   00:01:08  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.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/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.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/EncodeOtherHek293Data/H3K4me3/peak/macs2/rep2/ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.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--------------------
39602 (process ID) old priority 0, new priority 10
Waiting for 60 seconds.

  
 		 

    
  
 
  Num   12  
 
  ID   task.report.peak2hammock.line_412.id_21  
 
  Name   peak2hammock 
 
  Thread   thread_Root  
 
  PID   43463  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-25 18:24:06  
 
  End   2017-01-25 18:24:15  
 
  Elapsed   00:00:09  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.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/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp

# SYS command. line 417

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp
 
 
   
--------------------Stdout--------------------
43468 (process ID) old priority 0, new priority 10

  
 		 

    
  
 
  Num   13  
 
  ID   task.report.peak2hammock.line_412.id_22  
 
  Name   peak2hammock 
 
  Thread   thread_Root  
 
  PID   44118  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-25 18:24:16  
 
  End   2017-01-25 18:24:25  
 
  Elapsed   00:00:09  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.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/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp

# SYS command. line 417

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/gappedpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/peak/macs2/overlap/ENCFF001FJZ.nodup_ENCFF001FJY.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp
 
 
   
--------------------Stdout--------------------
44122 (process ID) old priority 0, new priority 10

  
 		 

    
  
 
  Num   14  
 
  ID   task.graphviz.report.line_97.id_23  
 
  Name   report 
 
  Thread   thread_Root  
 
  PID   44663  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-25 18:24:26  
 
  End   2017-01-25 18:24:34  
 
  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/EncodeOtherHek293Data/H3K4me3/report/H3K4me3_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/report/H3K4me3_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/report/H3K4me3_workflow.svg" # to suppress dot font error (exit code=1)
 
 
   
--------------------Stdout--------------------
44668 (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/homer/default:/software/modulefiles/Matlab/MCR2010b:/software/modulefiles/align2rawsignal/2.0:/software/modulefiles/Matlab/R2014b  

	
  bool  allowEmpty  false  

	
  string[]  args  [-species, hg38, -tag1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/rep1/ENCFF001FJZ.nodup.tagAlign.gz, -tag2, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/rep2/ENCFF001FJY.nodup.tagAlign.gz, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz, -final_stage, idr, -chrsz, /mnt/data/annotations/by_organism/human/hg20.GRCh38/hg38.chrom.sizes, -no_pseudo_rep, -histone, -out_dir, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K4me3, $]  

	
  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:13.0  

	
  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_wplrRU  

	
  string  LANG  en_US.UTF-8  

	
  string  LOADEDMODULES  modsappsdir/modsappsdir:homer/default:Matlab/MCR2010b:align2rawsignal/2.0:Matlab/R2014b  

	
  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/Matlab/R2014b/bin:/software/align2rawsignal/2.0/bin:/software/ucsc_tools/3.0.9:/software/weblogo/2.8.2:/software/homer/default/bin:/users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/rcade/:/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/EncodeOtherHek293Data/H3K4me3  

	
  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/EncodeOtherHek293Data/H3K4me3  

	
  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 42954 22  

	
  string  SSH_CONNECTION  171.65.77.8 42954 171.65.76.63 22  

	
  string  SSH_TTY  /dev/pts/152  

	
  string  STY  52593.H3K4me3.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  XAPPLRESDIR  /software/Matlab/MCR2010b/v714/X11/app-defaults  

	
  string  XDG_RUNTIME_DIR  /run/user/1048  

	
  string  XDG_SESSION_ID  22185  

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