BigDataScript report: chipseq.bds

Script file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20170125_175032_067
Start time 2017-01-25 17:50:32
Run time 00:31:40.916
Tasks executed 14
Tasks failed 0
Tasks failed names 
 

		
  Arguments*  [-species, hg38, -tag1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/rep1/ENCFF002ABA.nodup.tagAlign.gz, -tag2, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/rep2/H3K27acRep2.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/H3K27ac, $] 

		
  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_175032_067/task.callpeak_macs2.macs2_pooled_rep.line_71.id_10
chipseq.bds.20170125_175032_067/task.callpeak_macs2.macs2_ppr1.line_71.id_11
chipseq.bds.20170125_175032_067/task.callpeak_macs2.macs2_ppr2.line_71.id_12
chipseq.bds.20170125_175032_067/task.callpeak_macs2.macs2_rep1.line_71.id_13
chipseq.bds.20170125_175032_067/task.callpeak_macs2.macs2_rep2.line_71.id_14
chipseq.bds.20170125_175032_067/task.callpeak_naive_overlap.naive_overlap_thresh.line_143.id_15
chipseq.bds.20170125_175032_067/task.callpeak_naive_overlap.naive_overlap_thresh.line_143.id_16
chipseq.bds.20170125_175032_067/task.callpeak_naive_overlap.naive_overlap_thresh.line_143.id_17
chipseq.bds.20170125_175032_067/task.callpeak_blacklist_filter.blacklist_filter_peak_pooled.line_27.id_18
chipseq.bds.20170125_175032_067/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_19
chipseq.bds.20170125_175032_067/task.callpeak_blacklist_filter.blacklist_filter_peak_2.line_27.id_20
chipseq.bds.20170125_175032_067/task.report.peak2hammock.line_412.id_21
chipseq.bds.20170125_175032_067/task.report.peak2hammock.line_412.id_22
chipseq.bds.20170125_175032_067/task.graphviz.report.line_97.id_23
 
 		 

	
  thread_41   thread_Root 	 
  
 		 

	
  thread_43   thread_Root 	 
  
 		 

	
  thread_42   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   35572  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-25 17:50:41  
 
  End   2017-01-25 18:18:08  
 
  Elapsed   00:27:26  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/signal/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/signal/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/align/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 203 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 203 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep -o "ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/signal/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep -o "ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/signal/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.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--------------------
14129 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Wed, 25 Jan 2017 17:51:00: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 203 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.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 17:51:00: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 17:51:00: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 17:51:01:  1000000 
INFO  @ Wed, 25 Jan 2017 17:51:03:  2000000 
INFO  @ Wed, 25 Jan 2017 17:51:04:  3000000 
INFO  @ Wed, 25 Jan 2017 17:51:06:  4000000 
INFO  @ Wed, 25 Jan 2017 17:51:07:  5000000 
INFO  @ Wed, 25 Jan 2017 17:51:09:  6000000 
INFO  @ Wed, 25 Jan 2017 17:51:10:  7000000 
INFO  @ Wed, 25 Jan 2017 17:51:12:  8000000 
INFO  @ Wed, 25 Jan 2017 17:51:13:  9000000 
INFO  @ Wed, 25 Jan 2017 17:51:15:  10000000 
INFO  @ Wed, 25 Jan 2017 17:51:16:  11000000 
INFO  @ Wed, 25 Jan 2017 17:51:18:  12000000 
INFO  @ Wed, 25 Jan 2017 17:51:19:  13000000 
INFO  @ Wed, 25 Jan 2017 17:51:21:  14000000 
INFO  @ Wed, 25 Jan 2017 17:51:22:  15000000 
INFO  @ Wed, 25 Jan 2017 17:51:23:  16000000 
INFO  @ Wed, 25 Jan 2017 17:51:25:  17000000 
INFO  @ Wed, 25 Jan 2017 17:51:26: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 17:51:28:  1000000 
INFO  @ Wed, 25 Jan 2017 17:51:29:  2000000 
INFO  @ Wed, 25 Jan 2017 17:51:31:  3000000 
INFO  @ Wed, 25 Jan 2017 17:51:32:  4000000 
INFO  @ Wed, 25 Jan 2017 17:51:33:  5000000 
INFO  @ Wed, 25 Jan 2017 17:51:35:  6000000 
INFO  @ Wed, 25 Jan 2017 17:51:36:  7000000 
INFO  @ Wed, 25 Jan 2017 17:51:38:  8000000 
INFO  @ Wed, 25 Jan 2017 17:51:39:  9000000 
INFO  @ Wed, 25 Jan 2017 17:51:41:  10000000 
INFO  @ Wed, 25 Jan 2017 17:51:42:  11000000 
INFO  @ Wed, 25 Jan 2017 17:51:43: #1 tag size is determined as 36 bps 
INFO  @ Wed, 25 Jan 2017 17:51:43: #1 tag size = 36 
INFO  @ Wed, 25 Jan 2017 17:51:43: #1  total tags in treatment: 17320808 
INFO  @ Wed, 25 Jan 2017 17:51:43: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 17:51:43: #1 finished! 
INFO  @ Wed, 25 Jan 2017 17:51:43: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 17:51:43: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 17:51:43: #2 Use 203 as fragment length 
INFO  @ Wed, 25 Jan 2017 17:51:43: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 17:51:43: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Wed, 25 Jan 2017 17:51:43: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 17:52:39: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Wed, 25 Jan 2017 17:52:39: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Wed, 25 Jan 2017 17:52:39: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg 
INFO  @ Wed, 25 Jan 2017 17:52:39: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Wed, 25 Jan 2017 17:52:39: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 17:55:02: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 17:55:03: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Wed, 25 Jan 2017 17:55:06: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed 
INFO  @ Wed, 25 Jan 2017 17:55:07: Done! 
INFO  @ Wed, 25 Jan 2017 17:55:11: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 203 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.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 17:55:11: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 17:55:11: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 17:55:13:  1000000 
INFO  @ Wed, 25 Jan 2017 17:55:14:  2000000 
INFO  @ Wed, 25 Jan 2017 17:55:16:  3000000 
INFO  @ Wed, 25 Jan 2017 17:55:18:  4000000 
INFO  @ Wed, 25 Jan 2017 17:55:19:  5000000 
INFO  @ Wed, 25 Jan 2017 17:55:21:  6000000 
INFO  @ Wed, 25 Jan 2017 17:55:23:  7000000 
INFO  @ Wed, 25 Jan 2017 17:55:24:  8000000 
INFO  @ Wed, 25 Jan 2017 17:55:26:  9000000 
INFO  @ Wed, 25 Jan 2017 17:55:28:  10000000 
INFO  @ Wed, 25 Jan 2017 17:55:30:  11000000 
INFO  @ Wed, 25 Jan 2017 17:55:31:  12000000 
INFO  @ Wed, 25 Jan 2017 17:55:33:  13000000 
INFO  @ Wed, 25 Jan 2017 17:55:34:  14000000 
INFO  @ Wed, 25 Jan 2017 17:55:36:  15000000 
INFO  @ Wed, 25 Jan 2017 17:55:38:  16000000 
INFO  @ Wed, 25 Jan 2017 17:55:39:  17000000 
INFO  @ Wed, 25 Jan 2017 17:55:40: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 17:55:42:  1000000 
INFO  @ Wed, 25 Jan 2017 17:55:44:  2000000 
INFO  @ Wed, 25 Jan 2017 17:55:45:  3000000 
INFO  @ Wed, 25 Jan 2017 17:55:47:  4000000 
INFO  @ Wed, 25 Jan 2017 17:55:49:  5000000 
INFO  @ Wed, 25 Jan 2017 17:55:50:  6000000 
INFO  @ Wed, 25 Jan 2017 17:55:52:  7000000 
INFO  @ Wed, 25 Jan 2017 17:55:54:  8000000 
INFO  @ Wed, 25 Jan 2017 17:55:55:  9000000 
INFO  @ Wed, 25 Jan 2017 17:55:57:  10000000 
INFO  @ Wed, 25 Jan 2017 17:55:59:  11000000 
INFO  @ Wed, 25 Jan 2017 17:56:00: #1 tag size is determined as 36 bps 
INFO  @ Wed, 25 Jan 2017 17:56:00: #1 tag size = 36 
INFO  @ Wed, 25 Jan 2017 17:56:00: #1  total tags in treatment: 17320808 
INFO  @ Wed, 25 Jan 2017 17:56:00: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 17:56:00: #1 finished! 
INFO  @ Wed, 25 Jan 2017 17:56:00: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 17:56:00: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 17:56:00: #2 Use 203 as fragment length 
INFO  @ Wed, 25 Jan 2017 17:56:00: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 17:56:00: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Wed, 25 Jan 2017 17:56:00: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 17:56:59: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 17:58:03: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 17:58:06: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak 
INFO  @ Wed, 25 Jan 2017 17:58:07: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Wed, 25 Jan 2017 17:58:08: Done! 
INFO  @ Wed, 25 Jan 2017 17:58:13: Read and build treatment bedGraph... 
INFO  @ Wed, 25 Jan 2017 17:58:51: Read and build control bedGraph... 
INFO  @ Wed, 25 Jan 2017 17:59:28: Build scoreTrackII... 
INFO  @ Wed, 25 Jan 2017 17:59:57: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Wed, 25 Jan 2017 18:02:33: Write bedGraph of scores... 
INFO  @ Wed, 25 Jan 2017 18:04:16: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_FE.bdg'! 
INFO  @ Wed, 25 Jan 2017 18:08:35: Read and build treatment bedGraph... 
INFO  @ Wed, 25 Jan 2017 18:09:13: Read and build control bedGraph... 
INFO  @ Wed, 25 Jan 2017 18:09:49: Build scoreTrackII... 
INFO  @ Wed, 25 Jan 2017 18:10:15: Values in your input bedGraph files will be multiplied by 11.467883 ... 
INFO  @ Wed, 25 Jan 2017 18:12:53: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Wed, 25 Jan 2017 18:13:14: Write bedGraph of scores... 
INFO  @ Wed, 25 Jan 2017 18:14:29: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.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   35573  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-25 17:50:42  
 
  End   2017-01-25 17:57:03  
 
  Elapsed   00:06:20  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.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/H3K27ac/align/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 203 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 203 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1 -o "ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1 -o "ENCFF002ABA.nodup.pr1_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.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--------------------
47505 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Wed, 25 Jan 2017 17:50:59: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 203 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.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 17:50:59: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 17:50:59: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 17:51:00:  1000000 
INFO  @ Wed, 25 Jan 2017 17:51:02:  2000000 
INFO  @ Wed, 25 Jan 2017 17:51:04:  3000000 
INFO  @ Wed, 25 Jan 2017 17:51:05:  4000000 
INFO  @ Wed, 25 Jan 2017 17:51:07:  5000000 
INFO  @ Wed, 25 Jan 2017 17:51:08:  6000000 
INFO  @ Wed, 25 Jan 2017 17:51:10:  7000000 
INFO  @ Wed, 25 Jan 2017 17:51:12:  8000000 
INFO  @ Wed, 25 Jan 2017 17:51:13: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 17:51:15:  1000000 
INFO  @ Wed, 25 Jan 2017 17:51:17:  2000000 
INFO  @ Wed, 25 Jan 2017 17:51:19:  3000000 
INFO  @ Wed, 25 Jan 2017 17:51:20:  4000000 
INFO  @ Wed, 25 Jan 2017 17:51:22:  5000000 
INFO  @ Wed, 25 Jan 2017 17:51:23:  6000000 
INFO  @ Wed, 25 Jan 2017 17:51:25:  7000000 
INFO  @ Wed, 25 Jan 2017 17:51:27:  8000000 
INFO  @ Wed, 25 Jan 2017 17:51:28:  9000000 
INFO  @ Wed, 25 Jan 2017 17:51:30:  10000000 
INFO  @ Wed, 25 Jan 2017 17:51:31:  11000000 
INFO  @ Wed, 25 Jan 2017 17:51:32: #1 tag size is determined as 36 bps 
INFO  @ Wed, 25 Jan 2017 17:51:32: #1 tag size = 36 
INFO  @ Wed, 25 Jan 2017 17:51:32: #1  total tags in treatment: 8660404 
INFO  @ Wed, 25 Jan 2017 17:51:32: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 17:51:32: #1 finished! 
INFO  @ Wed, 25 Jan 2017 17:51:32: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 17:51:32: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 17:51:32: #2 Use 203 as fragment length 
INFO  @ Wed, 25 Jan 2017 17:51:32: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 17:51:32: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Wed, 25 Jan 2017 17:51:32: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 17:52:24: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Wed, 25 Jan 2017 17:52:24: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Wed, 25 Jan 2017 17:52:24: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg 
INFO  @ Wed, 25 Jan 2017 17:52:24: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Wed, 25 Jan 2017 17:52:24: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 17:54:15: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 17:54:16: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Wed, 25 Jan 2017 17:54:18: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed 
INFO  @ Wed, 25 Jan 2017 17:54:19: Done! 
INFO  @ Wed, 25 Jan 2017 17:54:21: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 203 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.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 17:54:21: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 17:54:21: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 17:54:23:  1000000 
INFO  @ Wed, 25 Jan 2017 17:54:25:  2000000 
INFO  @ Wed, 25 Jan 2017 17:54:26:  3000000 
INFO  @ Wed, 25 Jan 2017 17:54:28:  4000000 
INFO  @ Wed, 25 Jan 2017 17:54:30:  5000000 
INFO  @ Wed, 25 Jan 2017 17:54:32:  6000000 
INFO  @ Wed, 25 Jan 2017 17:54:33:  7000000 
INFO  @ Wed, 25 Jan 2017 17:54:35:  8000000 
INFO  @ Wed, 25 Jan 2017 17:54:37: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 17:54:38:  1000000 
INFO  @ Wed, 25 Jan 2017 17:54:40:  2000000 
INFO  @ Wed, 25 Jan 2017 17:54:41:  3000000 
INFO  @ Wed, 25 Jan 2017 17:54:43:  4000000 
INFO  @ Wed, 25 Jan 2017 17:54:45:  5000000 
INFO  @ Wed, 25 Jan 2017 17:54:46:  6000000 
INFO  @ Wed, 25 Jan 2017 17:54:48:  7000000 
INFO  @ Wed, 25 Jan 2017 17:54:49:  8000000 
INFO  @ Wed, 25 Jan 2017 17:54:51:  9000000 
INFO  @ Wed, 25 Jan 2017 17:54:53:  10000000 
INFO  @ Wed, 25 Jan 2017 17:54:54:  11000000 
INFO  @ Wed, 25 Jan 2017 17:54:55: #1 tag size is determined as 36 bps 
INFO  @ Wed, 25 Jan 2017 17:54:55: #1 tag size = 36 
INFO  @ Wed, 25 Jan 2017 17:54:55: #1  total tags in treatment: 8660404 
INFO  @ Wed, 25 Jan 2017 17:54:55: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 17:54:55: #1 finished! 
INFO  @ Wed, 25 Jan 2017 17:54:55: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 17:54:55: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 17:54:55: #2 Use 203 as fragment length 
INFO  @ Wed, 25 Jan 2017 17:54:55: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 17:54:55: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Wed, 25 Jan 2017 17:54:55: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 17:55:54: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 17:56:40: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 17:56:44: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak 
INFO  @ Wed, 25 Jan 2017 17:56:49: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Wed, 25 Jan 2017 17:56:53: Done! 

 
 		 

    
  
 
  Num   3  
 
  ID   task.callpeak_macs2.macs2_ppr2.line_71.id_12  
 
  Name   macs2 ppr2 
 
  Thread   thread_Root  
 
  PID   35574  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-25 17:50:44  
 
  End   2017-01-25 17:56:52  
 
  Elapsed   00:06:07  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.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/H3K27ac/align/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 203 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 203 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2 -o "ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2 -o "ENCFF002ABA.nodup.pr2_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.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--------------------
14228 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Wed, 25 Jan 2017 17:51:12: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 203 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.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 17:51:12: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 17:51:12: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 17:51:13:  1000000 
INFO  @ Wed, 25 Jan 2017 17:51:15:  2000000 
INFO  @ Wed, 25 Jan 2017 17:51:17:  3000000 
INFO  @ Wed, 25 Jan 2017 17:51:18:  4000000 
INFO  @ Wed, 25 Jan 2017 17:51:20:  5000000 
INFO  @ Wed, 25 Jan 2017 17:51:21:  6000000 
INFO  @ Wed, 25 Jan 2017 17:51:22:  7000000 
INFO  @ Wed, 25 Jan 2017 17:51:24:  8000000 
INFO  @ Wed, 25 Jan 2017 17:51:25: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 17:51:27:  1000000 
INFO  @ Wed, 25 Jan 2017 17:51:28:  2000000 
INFO  @ Wed, 25 Jan 2017 17:51:30:  3000000 
INFO  @ Wed, 25 Jan 2017 17:51:31:  4000000 
INFO  @ Wed, 25 Jan 2017 17:51:33:  5000000 
INFO  @ Wed, 25 Jan 2017 17:51:34:  6000000 
INFO  @ Wed, 25 Jan 2017 17:51:35:  7000000 
INFO  @ Wed, 25 Jan 2017 17:51:36:  8000000 
INFO  @ Wed, 25 Jan 2017 17:51:38:  9000000 
INFO  @ Wed, 25 Jan 2017 17:51:39:  10000000 
INFO  @ Wed, 25 Jan 2017 17:51:40:  11000000 
INFO  @ Wed, 25 Jan 2017 17:51:41: #1 tag size is determined as 36 bps 
INFO  @ Wed, 25 Jan 2017 17:51:41: #1 tag size = 36 
INFO  @ Wed, 25 Jan 2017 17:51:41: #1  total tags in treatment: 8660404 
INFO  @ Wed, 25 Jan 2017 17:51:41: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 17:51:41: #1 finished! 
INFO  @ Wed, 25 Jan 2017 17:51:41: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 17:51:41: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 17:51:41: #2 Use 203 as fragment length 
INFO  @ Wed, 25 Jan 2017 17:51:41: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 17:51:41: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Wed, 25 Jan 2017 17:51:41: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 17:52:26: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Wed, 25 Jan 2017 17:52:26: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Wed, 25 Jan 2017 17:52:26: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg 
INFO  @ Wed, 25 Jan 2017 17:52:26: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Wed, 25 Jan 2017 17:52:26: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 17:54:11: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 17:54:12: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Wed, 25 Jan 2017 17:54:12: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed 
INFO  @ Wed, 25 Jan 2017 17:54:13: Done! 
INFO  @ Wed, 25 Jan 2017 17:54:18: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 203 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.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 17:54:18: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 17:54:18: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 17:54:20:  1000000 
INFO  @ Wed, 25 Jan 2017 17:54:22:  2000000 
INFO  @ Wed, 25 Jan 2017 17:54:23:  3000000 
INFO  @ Wed, 25 Jan 2017 17:54:25:  4000000 
INFO  @ Wed, 25 Jan 2017 17:54:27:  5000000 
INFO  @ Wed, 25 Jan 2017 17:54:28:  6000000 
INFO  @ Wed, 25 Jan 2017 17:54:30:  7000000 
INFO  @ Wed, 25 Jan 2017 17:54:32:  8000000 
INFO  @ Wed, 25 Jan 2017 17:54:33: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 17:54:35:  1000000 
INFO  @ Wed, 25 Jan 2017 17:54:37:  2000000 
INFO  @ Wed, 25 Jan 2017 17:54:38:  3000000 
INFO  @ Wed, 25 Jan 2017 17:54:40:  4000000 
INFO  @ Wed, 25 Jan 2017 17:54:41:  5000000 
INFO  @ Wed, 25 Jan 2017 17:54:43:  6000000 
INFO  @ Wed, 25 Jan 2017 17:54:44:  7000000 
INFO  @ Wed, 25 Jan 2017 17:54:46:  8000000 
INFO  @ Wed, 25 Jan 2017 17:54:47:  9000000 
INFO  @ Wed, 25 Jan 2017 17:54:49:  10000000 
INFO  @ Wed, 25 Jan 2017 17:54:50:  11000000 
INFO  @ Wed, 25 Jan 2017 17:54:51: #1 tag size is determined as 36 bps 
INFO  @ Wed, 25 Jan 2017 17:54:51: #1 tag size = 36 
INFO  @ Wed, 25 Jan 2017 17:54:51: #1  total tags in treatment: 8660404 
INFO  @ Wed, 25 Jan 2017 17:54:51: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 17:54:51: #1 finished! 
INFO  @ Wed, 25 Jan 2017 17:54:51: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 17:54:51: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 17:54:51: #2 Use 203 as fragment length 
INFO  @ Wed, 25 Jan 2017 17:54:51: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 17:54:51: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Wed, 25 Jan 2017 17:54:51: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 17:55:39: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 17:56:31: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 17:56:35: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak 
INFO  @ Wed, 25 Jan 2017 17:56:37: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Wed, 25 Jan 2017 17:56:40: Done! 

 
 		 

    
  
 
  Num   4  
 
  ID   task.callpeak_macs2.macs2_rep1.line_71.id_13  
 
  Name   macs2 rep1 
 
  Thread   thread_Root  
 
  PID   35575  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-25 17:50:45  
 
  End   2017-01-25 18:06:16  
 
  Elapsed   00:15:30  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/rep1/ENCFF002ABA.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/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/signal/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/signal/macs2/rep1/ENCFF002ABA.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/H3K27ac/align/rep1/ENCFF002ABA.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/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 240 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.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/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/rep1/ENCFF002ABA.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/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 240 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.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/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.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/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.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/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.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/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1 -o "ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.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/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.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/H3K27ac/signal/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/rep1/ENCFF002ABA.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/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1 -o "ENCFF002ABA.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/H3K27ac/peak/macs2/rep1/ENCFF002ABA.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/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.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/H3K27ac/signal/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.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--------------------
47639 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Wed, 25 Jan 2017 17:51:09: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/rep1/ENCFF002ABA.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/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 240 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/rep1/ENCFF002ABA.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 17:51:09: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 17:51:09: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 17:51:11:  1000000 
INFO  @ Wed, 25 Jan 2017 17:51:12:  2000000 
INFO  @ Wed, 25 Jan 2017 17:51:14:  3000000 
INFO  @ Wed, 25 Jan 2017 17:51:16:  4000000 
INFO  @ Wed, 25 Jan 2017 17:51:17: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 17:51:19:  1000000 
INFO  @ Wed, 25 Jan 2017 17:51:20:  2000000 
INFO  @ Wed, 25 Jan 2017 17:51:22:  3000000 
INFO  @ Wed, 25 Jan 2017 17:51:23:  4000000 
INFO  @ Wed, 25 Jan 2017 17:51:25:  5000000 
INFO  @ Wed, 25 Jan 2017 17:51:27:  6000000 
INFO  @ Wed, 25 Jan 2017 17:51:28:  7000000 
INFO  @ Wed, 25 Jan 2017 17:51:30:  8000000 
INFO  @ Wed, 25 Jan 2017 17:51:31:  9000000 
INFO  @ Wed, 25 Jan 2017 17:51:33:  10000000 
INFO  @ Wed, 25 Jan 2017 17:51:35:  11000000 
INFO  @ Wed, 25 Jan 2017 17:51:36: #1 tag size is determined as 36 bps 
INFO  @ Wed, 25 Jan 2017 17:51:36: #1 tag size = 36 
INFO  @ Wed, 25 Jan 2017 17:51:36: #1  total tags in treatment: 4885600 
INFO  @ Wed, 25 Jan 2017 17:51:36: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 17:51:36: #1 finished! 
INFO  @ Wed, 25 Jan 2017 17:51:36: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 17:51:36: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 17:51:36: #2 Use 240 as fragment length 
INFO  @ Wed, 25 Jan 2017 17:51:36: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 17:51:36: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Wed, 25 Jan 2017 17:51:36: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 17:52:22: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Wed, 25 Jan 2017 17:52:22: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Wed, 25 Jan 2017 17:52:22: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg 
INFO  @ Wed, 25 Jan 2017 17:52:22: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Wed, 25 Jan 2017 17:52:22: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 17:53:49: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 17:53:52: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Wed, 25 Jan 2017 17:53:52: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed 
INFO  @ Wed, 25 Jan 2017 17:53:53: Done! 
INFO  @ Wed, 25 Jan 2017 17:53:56: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/rep1/ENCFF002ABA.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/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 240 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/rep1/ENCFF002ABA.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 17:53:56: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 17:53:56: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 17:53:58:  1000000 
INFO  @ Wed, 25 Jan 2017 17:53:59:  2000000 
INFO  @ Wed, 25 Jan 2017 17:54:01:  3000000 
INFO  @ Wed, 25 Jan 2017 17:54:02:  4000000 
INFO  @ Wed, 25 Jan 2017 17:54:03: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 17:54:05:  1000000 
INFO  @ Wed, 25 Jan 2017 17:54:07:  2000000 
INFO  @ Wed, 25 Jan 2017 17:54:08:  3000000 
INFO  @ Wed, 25 Jan 2017 17:54:10:  4000000 
INFO  @ Wed, 25 Jan 2017 17:54:11:  5000000 
INFO  @ Wed, 25 Jan 2017 17:54:13:  6000000 
INFO  @ Wed, 25 Jan 2017 17:54:14:  7000000 
INFO  @ Wed, 25 Jan 2017 17:54:16:  8000000 
INFO  @ Wed, 25 Jan 2017 17:54:17:  9000000 
INFO  @ Wed, 25 Jan 2017 17:54:19:  10000000 
INFO  @ Wed, 25 Jan 2017 17:54:20:  11000000 
INFO  @ Wed, 25 Jan 2017 17:54:21: #1 tag size is determined as 36 bps 
INFO  @ Wed, 25 Jan 2017 17:54:21: #1 tag size = 36 
INFO  @ Wed, 25 Jan 2017 17:54:21: #1  total tags in treatment: 4885600 
INFO  @ Wed, 25 Jan 2017 17:54:21: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 17:54:21: #1 finished! 
INFO  @ Wed, 25 Jan 2017 17:54:21: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 17:54:21: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 17:54:21: #2 Use 240 as fragment length 
INFO  @ Wed, 25 Jan 2017 17:54:21: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 17:54:21: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Wed, 25 Jan 2017 17:54:21: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 17:55:02: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 17:55:51: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 17:55:54: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak 
INFO  @ Wed, 25 Jan 2017 17:55:58: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Wed, 25 Jan 2017 17:56:02: Done! 
INFO  @ Wed, 25 Jan 2017 17:56:15: Read and build treatment bedGraph... 
INFO  @ Wed, 25 Jan 2017 17:56:25: Read and build control bedGraph... 
INFO  @ Wed, 25 Jan 2017 17:56:53: Build scoreTrackII... 
INFO  @ Wed, 25 Jan 2017 17:57:04: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Wed, 25 Jan 2017 17:58:38: Write bedGraph of scores... 
INFO  @ Wed, 25 Jan 2017 17:59:12: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_FE.bdg'! 
INFO  @ Wed, 25 Jan 2017 18:00:33: Read and build treatment bedGraph... 
INFO  @ Wed, 25 Jan 2017 18:00:43: Read and build control bedGraph... 
INFO  @ Wed, 25 Jan 2017 18:01:11: Build scoreTrackII... 
INFO  @ Wed, 25 Jan 2017 18:01:26: Values in your input bedGraph files will be multiplied by 4.885600 ... 
INFO  @ Wed, 25 Jan 2017 18:02:53: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Wed, 25 Jan 2017 18:03:04: Write bedGraph of scores... 
INFO  @ Wed, 25 Jan 2017 18:03:55: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.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   35592  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-25 17:56:55  
 
  End   2017-01-25 18:19:04  
 
  Elapsed   00:22:09  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/rep2/H3K27acRep2.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/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/signal/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/signal/macs2/rep2/H3K27acRep2.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/H3K27ac/align/rep2/H3K27acRep2.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/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 165 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.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/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/rep2/H3K27acRep2.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/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 165 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.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/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.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/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.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/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.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/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2 -o "H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.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/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.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/H3K27ac/signal/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/rep2/H3K27acRep2.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/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2 -o "H3K27acRep2.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/H3K27ac/peak/macs2/rep2/H3K27acRep2.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/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.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/H3K27ac/signal/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.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--------------------
800 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Wed, 25 Jan 2017 17:57:11: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/rep2/H3K27acRep2.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/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 165 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/rep2/H3K27acRep2.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 17:57:11: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 17:57:11: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 17:57:12:  1000000 
INFO  @ Wed, 25 Jan 2017 17:57:14:  2000000 
INFO  @ Wed, 25 Jan 2017 17:57:15:  3000000 
INFO  @ Wed, 25 Jan 2017 17:57:17:  4000000 
INFO  @ Wed, 25 Jan 2017 17:57:18:  5000000 
INFO  @ Wed, 25 Jan 2017 17:57:20:  6000000 
INFO  @ Wed, 25 Jan 2017 17:57:21:  7000000 
INFO  @ Wed, 25 Jan 2017 17:57:23:  8000000 
INFO  @ Wed, 25 Jan 2017 17:57:24:  9000000 
INFO  @ Wed, 25 Jan 2017 17:57:26:  10000000 
INFO  @ Wed, 25 Jan 2017 17:57:27:  11000000 
INFO  @ Wed, 25 Jan 2017 17:57:29:  12000000 
INFO  @ Wed, 25 Jan 2017 17:57:30: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 17:57:32:  1000000 
INFO  @ Wed, 25 Jan 2017 17:57:33:  2000000 
INFO  @ Wed, 25 Jan 2017 17:57:35:  3000000 
INFO  @ Wed, 25 Jan 2017 17:57:36:  4000000 
INFO  @ Wed, 25 Jan 2017 17:57:38:  5000000 
INFO  @ Wed, 25 Jan 2017 17:57:39:  6000000 
INFO  @ Wed, 25 Jan 2017 17:57:41:  7000000 
INFO  @ Wed, 25 Jan 2017 17:57:42:  8000000 
INFO  @ Wed, 25 Jan 2017 17:57:44:  9000000 
INFO  @ Wed, 25 Jan 2017 17:57:45:  10000000 
INFO  @ Wed, 25 Jan 2017 17:57:47:  11000000 
INFO  @ Wed, 25 Jan 2017 17:57:48: #1 tag size is determined as 35 bps 
INFO  @ Wed, 25 Jan 2017 17:57:48: #1 tag size = 35 
INFO  @ Wed, 25 Jan 2017 17:57:48: #1  total tags in treatment: 12435208 
INFO  @ Wed, 25 Jan 2017 17:57:48: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 17:57:48: #1 finished! 
INFO  @ Wed, 25 Jan 2017 17:57:48: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 17:57:48: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 17:57:48: #2 Use 165 as fragment length 
INFO  @ Wed, 25 Jan 2017 17:57:48: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 17:57:48: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Wed, 25 Jan 2017 17:57:48: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 17:58:39: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Wed, 25 Jan 2017 17:58:39: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Wed, 25 Jan 2017 17:58:39: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg 
INFO  @ Wed, 25 Jan 2017 17:58:39: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Wed, 25 Jan 2017 17:58:39: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 18:00:41: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 18:00:42: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Wed, 25 Jan 2017 18:00:43: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed 
INFO  @ Wed, 25 Jan 2017 18:00:43: Done! 
INFO  @ Wed, 25 Jan 2017 18:00:46: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/rep2/H3K27acRep2.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/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 165 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/rep2/H3K27acRep2.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 18:00:46: #1 read tag files... 
INFO  @ Wed, 25 Jan 2017 18:00:46: #1 read treatment tags... 
INFO  @ Wed, 25 Jan 2017 18:00:48:  1000000 
INFO  @ Wed, 25 Jan 2017 18:00:49:  2000000 
INFO  @ Wed, 25 Jan 2017 18:00:51:  3000000 
INFO  @ Wed, 25 Jan 2017 18:00:52:  4000000 
INFO  @ Wed, 25 Jan 2017 18:00:54:  5000000 
INFO  @ Wed, 25 Jan 2017 18:00:56:  6000000 
INFO  @ Wed, 25 Jan 2017 18:00:57:  7000000 
INFO  @ Wed, 25 Jan 2017 18:00:59:  8000000 
INFO  @ Wed, 25 Jan 2017 18:01:00:  9000000 
INFO  @ Wed, 25 Jan 2017 18:01:02:  10000000 
INFO  @ Wed, 25 Jan 2017 18:01:03:  11000000 
INFO  @ Wed, 25 Jan 2017 18:01:05:  12000000 
INFO  @ Wed, 25 Jan 2017 18:01:06: #1.2 read input tags... 
INFO  @ Wed, 25 Jan 2017 18:01:08:  1000000 
INFO  @ Wed, 25 Jan 2017 18:01:09:  2000000 
INFO  @ Wed, 25 Jan 2017 18:01:11:  3000000 
INFO  @ Wed, 25 Jan 2017 18:01:12:  4000000 
INFO  @ Wed, 25 Jan 2017 18:01:14:  5000000 
INFO  @ Wed, 25 Jan 2017 18:01:15:  6000000 
INFO  @ Wed, 25 Jan 2017 18:01:17:  7000000 
INFO  @ Wed, 25 Jan 2017 18:01:18:  8000000 
INFO  @ Wed, 25 Jan 2017 18:01:20:  9000000 
INFO  @ Wed, 25 Jan 2017 18:01:22:  10000000 
INFO  @ Wed, 25 Jan 2017 18:01:23:  11000000 
INFO  @ Wed, 25 Jan 2017 18:01:24: #1 tag size is determined as 35 bps 
INFO  @ Wed, 25 Jan 2017 18:01:24: #1 tag size = 35 
INFO  @ Wed, 25 Jan 2017 18:01:24: #1  total tags in treatment: 12435208 
INFO  @ Wed, 25 Jan 2017 18:01:24: #1  total tags in control: 11467883 
INFO  @ Wed, 25 Jan 2017 18:01:24: #1 finished! 
INFO  @ Wed, 25 Jan 2017 18:01:24: #2 Build Peak Model... 
INFO  @ Wed, 25 Jan 2017 18:01:24: #2 Skipped... 
INFO  @ Wed, 25 Jan 2017 18:01:24: #2 Use 165 as fragment length 
INFO  @ Wed, 25 Jan 2017 18:01:24: #3 Call peaks... 
INFO  @ Wed, 25 Jan 2017 18:01:24: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Wed, 25 Jan 2017 18:01:24: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 25 Jan 2017 18:02:16: #3 Call peaks for each chromosome... 
INFO  @ Wed, 25 Jan 2017 18:02:54: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Wed, 25 Jan 2017 18:02:56: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak 
INFO  @ Wed, 25 Jan 2017 18:02:59: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Wed, 25 Jan 2017 18:03:02: Done! 
INFO  @ Wed, 25 Jan 2017 18:03:09: Read and build treatment bedGraph... 
INFO  @ Wed, 25 Jan 2017 18:03:37: Read and build control bedGraph... 
INFO  @ Wed, 25 Jan 2017 18:04:10: Build scoreTrackII... 
INFO  @ Wed, 25 Jan 2017 18:04:29: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Wed, 25 Jan 2017 18:06:43: Write bedGraph of scores... 
INFO  @ Wed, 25 Jan 2017 18:08:00: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_FE.bdg'! 
INFO  @ Wed, 25 Jan 2017 18:10:53: Read and build treatment bedGraph... 
INFO  @ Wed, 25 Jan 2017 18:11:19: Read and build control bedGraph... 
INFO  @ Wed, 25 Jan 2017 18:11:52: Build scoreTrackII... 
INFO  @ Wed, 25 Jan 2017 18:12:11: Values in your input bedGraph files will be multiplied by 11.467883 ... 
INFO  @ Wed, 25 Jan 2017 18:14:33: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Wed, 25 Jan 2017 18:14:49: Write bedGraph of scores... 
INFO  @ Wed, 25 Jan 2017 18:15:59: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.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   35597  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-25 18:19:06  
 
  End   2017-01-25 18:20:24  
 
  Elapsed   00:01:18  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.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/H3K27ac/peak/macs2/rep2/H3K27acRep2.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/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.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/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.narrowPeak.gz

# SYS command. line 154

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.narrowPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz

# SYS command. line 158

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.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--------------------
16526 (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   35598  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-25 18:19:06  
 
  End   2017-01-25 18:20:24  
 
  Elapsed   00:01:17  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.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/H3K27ac/peak/macs2/rep2/H3K27acRep2.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/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.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/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.gappedPeak.gz

# SYS command. line 154

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.gappedPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz

# SYS command. line 158

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.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--------------------
5317 (process ID) old priority 0, new priority 10
Waiting for 43 seconds.

  
 		 

    
  
 
  Num   8  
 
  ID   task.callpeak_naive_overlap.naive_overlap_thresh.line_143.id_17  
 
  Name   naive_overlap_thresh  
 
  Thread   thread_Root  
 
  PID   35599  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-25 18:19:08  
 
  End   2017-01-25 18:20:23  
 
  Elapsed   00:01:15  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.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/H3K27ac/peak/macs2/rep2/H3K27acRep2.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/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_H3K27acRep2.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/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.broadPeak.gz

# SYS command. line 154

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInPsRep1AndPsRep2.broadPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.broadPeak.gz

# SYS command. line 158

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInReps.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.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--------------------
5316 (process ID) old priority 0, new priority 10
Waiting for 45 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   30567  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-25 18:20:27  
 
  End   2017-01-25 18:21:39  
 
  Elapsed   00:01:12  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/peak/macs2/pooled_rep/ENCFF002ABA.nodup_H3K27acRep2.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--------------------
30571 (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   30651  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-25 18:20:28  
 
  End   2017-01-25 18:21:39  
 
  Elapsed   00:01:11  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep1/ENCFF002ABA.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/H3K27ac/peak/macs2/rep1/ENCFF002ABA.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/H3K27ac/peak/macs2/rep1/ENCFF002ABA.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--------------------
30656 (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   30716  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-25 18:20:28  
 
  End   2017-01-25 18:21:40  
 
  Elapsed   00:01:11  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/rep2/H3K27acRep2.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/H3K27ac/peak/macs2/rep2/H3K27acRep2.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/H3K27ac/peak/macs2/rep2/H3K27acRep2.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--------------------
30721 (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   35091  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-25 18:21:41  
 
  End   2017-01-25 18:21:50  
 
  Elapsed   00:00:09  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp
 
 
   
--------------------Stdout--------------------
35096 (process ID) old priority 0, new priority 10

  
 		 

    
  
 
  Num   13  
 
  ID   task.report.peak2hammock.line_412.id_22  
 
  Name   peak2hammock 
 
  Thread   thread_Root  
 
  PID   35729  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-25 18:21:51  
 
  End   2017-01-25 18:22:02  
 
  Elapsed   00:00:10  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.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/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/peak/macs2/overlap/ENCFF002ABA.nodup_H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp
 
 
   
--------------------Stdout--------------------
35733 (process ID) old priority 0, new priority 10

  
 		 

    
  
 
  Num   14  
 
  ID   task.graphviz.report.line_97.id_23  
 
  Name   report 
 
  Thread   thread_Root  
 
  PID   36472  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-25 18:22:03  
 
  End   2017-01-25 18:22:12  
 
  Elapsed   00:00:09  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files     
 
  Output files     
 
  Dependencies     
 
 		  
 
# SYS command. line 98

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

# SYS command. line 99

 dot -Tsvg /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/report/H3K27ac_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/report/H3K27ac_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/report/H3K27ac_workflow.svg" # to suppress dot font error (exit code=1)
 
 
   
--------------------Stdout--------------------
36476 (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/H3K27ac/align/rep1/ENCFF002ABA.nodup.tagAlign.gz, -tag2, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/H3K27ac/align/rep2/H3K27acRep2.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/H3K27ac, $]  

	
  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/H3K27ac  

	
  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/H3K27ac  

	
  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  48092.H3K27ac.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