BigDataScript report: chipseq.bds

Script file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20170413_132201_300
Start time 2017-04-13 13:22:01
Run time 03:14:55.990
Tasks executed 34
Tasks failed 0
Tasks failed names 
 

		
  Arguments*  [-title, ZBTB26_MACS2, -nth, 5, -species, hg38_ENCODE, -url_base, http://mitra.stanford.edu/kundaje/leepc12/imk_chipseq/ZBTB26_MACS2/out, -filt_bam1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.bam, -filt_bam2, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.bam, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz, -pe, -macs2_for_idr, $] 

		
  System*  sge 

		
  Cpus*  -1 

		
  Exit value  0 

	

	* Values in global scope when program finished execution.





	
 Timeline 

	
	
	






	
 Task Graph 

	






	
 Parallel (threads) details 

	

    
  Thread ID      Parent           	 Tasks  

	
  thread_Root   None 	 
 chipseq.bds.20170413_132201_300/task.callpeak_macs2.macs2_n_s_pooled_rep.line_66.id_10
chipseq.bds.20170413_132201_300/task.callpeak_macs2.macs2_n_s_ppr1.line_66.id_11
chipseq.bds.20170413_132201_300/task.callpeak_macs2.macs2_n_s_ppr2.line_66.id_12
chipseq.bds.20170413_132201_300/task.callpeak_macs2.macs2_n_s_rep1.line_66.id_13
chipseq.bds.20170413_132201_300/task.callpeak_macs2.macs2_n_s_rep1_pr1.line_66.id_14
chipseq.bds.20170413_132201_300/task.callpeak_macs2.macs2_n_s_rep1_pr2.line_66.id_15
chipseq.bds.20170413_132201_300/task.callpeak_macs2.macs2_n_s_rep2.line_66.id_16
chipseq.bds.20170413_132201_300/task.callpeak_macs2.macs2_n_s_rep2_pr1.line_66.id_17
chipseq.bds.20170413_132201_300/task.callpeak_macs2.macs2_n_s_rep2_pr2.line_66.id_18
chipseq.bds.20170413_132201_300/task.callpeak_naive_overlap.naive_overlap.line_143.id_19
chipseq.bds.20170413_132201_300/task.callpeak_idr.idr2_rep1_rep2.line_74.id_20
chipseq.bds.20170413_132201_300/task.callpeak_idr.idr2_rep1_pr.line_74.id_21
chipseq.bds.20170413_132201_300/task.callpeak_idr.idr2_rep2_pr.line_74.id_22
chipseq.bds.20170413_132201_300/task.callpeak_idr.idr2_ppr.line_74.id_23
chipseq.bds.20170413_132201_300/task.sys.copy_file.line_131.id_32
chipseq.bds.20170413_132201_300/task.sys.copy_file.line_131.id_33
chipseq.bds.20170413_132201_300/task.sys.copy_file.line_131.id_34
chipseq.bds.20170413_132201_300/task.sys.copy_file.line_131.id_35
chipseq.bds.20170413_132201_300/task.callpeak_idr.idr_final_qc.line_283.id_36
chipseq.bds.20170413_132201_300/task.callpeak_idr.FRiP_rep1_pr.line_120.id_37
chipseq.bds.20170413_132201_300/task.callpeak_idr.FRiP_rep2_pr.line_120.id_38
chipseq.bds.20170413_132201_300/task.callpeak_idr.FRiP_ppr.line_120.id_39
chipseq.bds.20170413_132201_300/task.callpeak_idr.FRiP_rep1_rep2.line_120.id_40
chipseq.bds.20170413_132201_300/task.callpeak_blacklist_filter.blacklist_filter_peak_pooled.line_27.id_41
chipseq.bds.20170413_132201_300/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_42
chipseq.bds.20170413_132201_300/task.callpeak_blacklist_filter.blacklist_filter_peak_2.line_27.id_43
chipseq.bds.20170413_132201_300/task.report.peak2hammock.line_361.id_46
chipseq.bds.20170413_132201_300/task.report.peak2hammock.line_361.id_47
chipseq.bds.20170413_132201_300/task.report.peak2hammock.line_361.id_48
chipseq.bds.20170413_132201_300/task.report.peak2hammock.line_361.id_49
chipseq.bds.20170413_132201_300/task.report.peak2hammock.line_361.id_50
chipseq.bds.20170413_132201_300/task.graphviz.report.line_97.id_51
chipseq.bds.20170413_132201_300/task.report.pdf2png.line_328.id_52
chipseq.bds.20170413_132201_300/task.report.pdf2png.line_328.id_53
 
 		 

	
  thread_43   thread_Root 	 
  
 		 

	
  thread_41   thread_Root 	 
  
 		 

	
  thread_42   thread_Root 	 
  
 		 

	






	
 Task details 

	

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

    
  
 
  Num   1  
 
  ID   task.callpeak_macs2.macs2_n_s_pooled_rep.line_66.id_10  
 
  Name   macs2 n/s pooled_rep 
 
  Thread   thread_Root  
 
  PID   46812  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 13:22:14  
 
  End   2017-04-13 16:19:08  
 
  Elapsed   02:56:54  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/signal/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/signal/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw
  
 
  Dependencies     
 
 		  
 
# SYS command. line 68

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 69

 export LC_COLLATE=C

# SYS command. line 74

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 238 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 84

 if [[ true == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.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 94

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep -o "ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/signal/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.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 113

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep -o "ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/signal/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 126

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
15774 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 13:22:32: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 238 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.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  @ Thu, 13 Apr 2017 13:22:32: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 13:22:32: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 13:22:34:  1000000 
INFO  @ Thu, 13 Apr 2017 13:22:36:  2000000 
INFO  @ Thu, 13 Apr 2017 13:22:38:  3000000 
INFO  @ Thu, 13 Apr 2017 13:22:39:  4000000 
INFO  @ Thu, 13 Apr 2017 13:22:41:  5000000 
INFO  @ Thu, 13 Apr 2017 13:22:43:  6000000 
INFO  @ Thu, 13 Apr 2017 13:22:44:  7000000 
INFO  @ Thu, 13 Apr 2017 13:22:46:  8000000 
INFO  @ Thu, 13 Apr 2017 13:22:47:  9000000 
INFO  @ Thu, 13 Apr 2017 13:22:49:  10000000 
INFO  @ Thu, 13 Apr 2017 13:22:50:  11000000 
INFO  @ Thu, 13 Apr 2017 13:22:52:  12000000 
INFO  @ Thu, 13 Apr 2017 13:22:54:  13000000 
INFO  @ Thu, 13 Apr 2017 13:22:55:  14000000 
INFO  @ Thu, 13 Apr 2017 13:22:57:  15000000 
INFO  @ Thu, 13 Apr 2017 13:22:58:  16000000 
INFO  @ Thu, 13 Apr 2017 13:23:00:  17000000 
INFO  @ Thu, 13 Apr 2017 13:23:01:  18000000 
INFO  @ Thu, 13 Apr 2017 13:23:03:  19000000 
INFO  @ Thu, 13 Apr 2017 13:23:04:  20000000 
INFO  @ Thu, 13 Apr 2017 13:23:06:  21000000 
INFO  @ Thu, 13 Apr 2017 13:23:07:  22000000 
INFO  @ Thu, 13 Apr 2017 13:23:09:  23000000 
INFO  @ Thu, 13 Apr 2017 13:23:11:  24000000 
INFO  @ Thu, 13 Apr 2017 13:23:12:  25000000 
INFO  @ Thu, 13 Apr 2017 13:23:14:  26000000 
INFO  @ Thu, 13 Apr 2017 13:23:15:  27000000 
INFO  @ Thu, 13 Apr 2017 13:23:17:  28000000 
INFO  @ Thu, 13 Apr 2017 13:23:18:  29000000 
INFO  @ Thu, 13 Apr 2017 13:23:20:  30000000 
INFO  @ Thu, 13 Apr 2017 13:23:22:  31000000 
INFO  @ Thu, 13 Apr 2017 13:23:23:  32000000 
INFO  @ Thu, 13 Apr 2017 13:23:25:  33000000 
INFO  @ Thu, 13 Apr 2017 13:23:26:  34000000 
INFO  @ Thu, 13 Apr 2017 13:23:28:  35000000 
INFO  @ Thu, 13 Apr 2017 13:23:29:  36000000 
INFO  @ Thu, 13 Apr 2017 13:23:31:  37000000 
INFO  @ Thu, 13 Apr 2017 13:23:32:  38000000 
INFO  @ Thu, 13 Apr 2017 13:23:34:  39000000 
INFO  @ Thu, 13 Apr 2017 13:23:36:  40000000 
INFO  @ Thu, 13 Apr 2017 13:23:37:  41000000 
INFO  @ Thu, 13 Apr 2017 13:23:39:  42000000 
INFO  @ Thu, 13 Apr 2017 13:23:40:  43000000 
INFO  @ Thu, 13 Apr 2017 13:23:42:  44000000 
INFO  @ Thu, 13 Apr 2017 13:23:44:  45000000 
INFO  @ Thu, 13 Apr 2017 13:23:45:  46000000 
INFO  @ Thu, 13 Apr 2017 13:23:47:  47000000 
INFO  @ Thu, 13 Apr 2017 13:23:48:  48000000 
INFO  @ Thu, 13 Apr 2017 13:23:50:  49000000 
INFO  @ Thu, 13 Apr 2017 13:23:51:  50000000 
INFO  @ Thu, 13 Apr 2017 13:23:53:  51000000 
INFO  @ Thu, 13 Apr 2017 13:23:55:  52000000 
INFO  @ Thu, 13 Apr 2017 13:23:56:  53000000 
INFO  @ Thu, 13 Apr 2017 13:23:58:  54000000 
INFO  @ Thu, 13 Apr 2017 13:24:00:  55000000 
INFO  @ Thu, 13 Apr 2017 13:24:01:  56000000 
INFO  @ Thu, 13 Apr 2017 13:24:03:  57000000 
INFO  @ Thu, 13 Apr 2017 13:24:04:  58000000 
INFO  @ Thu, 13 Apr 2017 13:24:06:  59000000 
INFO  @ Thu, 13 Apr 2017 13:24:07:  60000000 
INFO  @ Thu, 13 Apr 2017 13:24:09:  61000000 
INFO  @ Thu, 13 Apr 2017 13:24:10:  62000000 
INFO  @ Thu, 13 Apr 2017 13:24:12:  63000000 
INFO  @ Thu, 13 Apr 2017 13:24:14:  64000000 
INFO  @ Thu, 13 Apr 2017 13:24:15:  65000000 
INFO  @ Thu, 13 Apr 2017 13:24:17:  66000000 
INFO  @ Thu, 13 Apr 2017 13:24:18:  67000000 
INFO  @ Thu, 13 Apr 2017 13:24:20:  68000000 
INFO  @ Thu, 13 Apr 2017 13:24:21:  69000000 
INFO  @ Thu, 13 Apr 2017 13:24:23:  70000000 
INFO  @ Thu, 13 Apr 2017 13:24:25:  71000000 
INFO  @ Thu, 13 Apr 2017 13:24:26:  72000000 
INFO  @ Thu, 13 Apr 2017 13:24:28:  73000000 
INFO  @ Thu, 13 Apr 2017 13:24:30:  74000000 
INFO  @ Thu, 13 Apr 2017 13:24:31:  75000000 
INFO  @ Thu, 13 Apr 2017 13:24:33:  76000000 
INFO  @ Thu, 13 Apr 2017 13:24:34:  77000000 
INFO  @ Thu, 13 Apr 2017 13:24:36:  78000000 
INFO  @ Thu, 13 Apr 2017 13:24:37:  79000000 
INFO  @ Thu, 13 Apr 2017 13:24:39:  80000000 
INFO  @ Thu, 13 Apr 2017 13:24:40:  81000000 
INFO  @ Thu, 13 Apr 2017 13:24:42:  82000000 
INFO  @ Thu, 13 Apr 2017 13:24:43:  83000000 
INFO  @ Thu, 13 Apr 2017 13:24:45:  84000000 
INFO  @ Thu, 13 Apr 2017 13:24:46:  85000000 
INFO  @ Thu, 13 Apr 2017 13:24:48:  86000000 
INFO  @ Thu, 13 Apr 2017 13:24:49:  87000000 
INFO  @ Thu, 13 Apr 2017 13:24:51:  88000000 
INFO  @ Thu, 13 Apr 2017 13:24:53:  89000000 
INFO  @ Thu, 13 Apr 2017 13:24:54:  90000000 
INFO  @ Thu, 13 Apr 2017 13:24:56:  91000000 
INFO  @ Thu, 13 Apr 2017 13:24:58:  92000000 
INFO  @ Thu, 13 Apr 2017 13:24:59:  93000000 
INFO  @ Thu, 13 Apr 2017 13:25:01:  94000000 
INFO  @ Thu, 13 Apr 2017 13:25:02:  95000000 
INFO  @ Thu, 13 Apr 2017 13:25:04:  96000000 
INFO  @ Thu, 13 Apr 2017 13:25:06:  97000000 
INFO  @ Thu, 13 Apr 2017 13:25:07:  98000000 
INFO  @ Thu, 13 Apr 2017 13:25:09:  99000000 
INFO  @ Thu, 13 Apr 2017 13:25:10:  100000000 
INFO  @ Thu, 13 Apr 2017 13:25:12:  101000000 
INFO  @ Thu, 13 Apr 2017 13:25:13:  102000000 
INFO  @ Thu, 13 Apr 2017 13:25:15:  103000000 
INFO  @ Thu, 13 Apr 2017 13:25:16:  104000000 
INFO  @ Thu, 13 Apr 2017 13:25:18:  105000000 
INFO  @ Thu, 13 Apr 2017 13:25:19:  106000000 
INFO  @ Thu, 13 Apr 2017 13:25:21:  107000000 
INFO  @ Thu, 13 Apr 2017 13:25:22:  108000000 
INFO  @ Thu, 13 Apr 2017 13:25:24:  109000000 
INFO  @ Thu, 13 Apr 2017 13:25:26:  110000000 
INFO  @ Thu, 13 Apr 2017 13:25:27:  111000000 
INFO  @ Thu, 13 Apr 2017 13:25:29:  112000000 
INFO  @ Thu, 13 Apr 2017 13:25:30:  113000000 
INFO  @ Thu, 13 Apr 2017 13:25:32:  114000000 
INFO  @ Thu, 13 Apr 2017 13:25:33:  115000000 
INFO  @ Thu, 13 Apr 2017 13:25:35:  116000000 
INFO  @ Thu, 13 Apr 2017 13:25:37:  117000000 
INFO  @ Thu, 13 Apr 2017 13:25:38:  118000000 
INFO  @ Thu, 13 Apr 2017 13:25:40:  119000000 
INFO  @ Thu, 13 Apr 2017 13:25:41:  120000000 
INFO  @ Thu, 13 Apr 2017 13:25:43:  121000000 
INFO  @ Thu, 13 Apr 2017 13:25:44:  122000000 
INFO  @ Thu, 13 Apr 2017 13:25:46:  123000000 
INFO  @ Thu, 13 Apr 2017 13:25:47:  124000000 
INFO  @ Thu, 13 Apr 2017 13:25:49:  125000000 
INFO  @ Thu, 13 Apr 2017 13:25:51:  126000000 
INFO  @ Thu, 13 Apr 2017 13:25:53:  127000000 
INFO  @ Thu, 13 Apr 2017 13:25:54:  128000000 
INFO  @ Thu, 13 Apr 2017 13:25:56:  129000000 
INFO  @ Thu, 13 Apr 2017 13:25:57:  130000000 
INFO  @ Thu, 13 Apr 2017 13:25:59:  131000000 
INFO  @ Thu, 13 Apr 2017 13:26:01:  132000000 
INFO  @ Thu, 13 Apr 2017 13:26:03:  133000000 
INFO  @ Thu, 13 Apr 2017 13:26:04:  134000000 
INFO  @ Thu, 13 Apr 2017 13:26:06:  135000000 
INFO  @ Thu, 13 Apr 2017 13:26:07:  136000000 
INFO  @ Thu, 13 Apr 2017 13:26:09:  137000000 
INFO  @ Thu, 13 Apr 2017 13:26:10:  138000000 
INFO  @ Thu, 13 Apr 2017 13:26:12:  139000000 
INFO  @ Thu, 13 Apr 2017 13:26:14:  140000000 
INFO  @ Thu, 13 Apr 2017 13:26:15:  141000000 
INFO  @ Thu, 13 Apr 2017 13:26:17:  142000000 
INFO  @ Thu, 13 Apr 2017 13:26:18:  143000000 
INFO  @ Thu, 13 Apr 2017 13:26:20:  144000000 
INFO  @ Thu, 13 Apr 2017 13:26:22:  145000000 
INFO  @ Thu, 13 Apr 2017 13:26:23:  146000000 
INFO  @ Thu, 13 Apr 2017 13:26:25:  147000000 
INFO  @ Thu, 13 Apr 2017 13:26:26:  148000000 
INFO  @ Thu, 13 Apr 2017 13:26:28:  149000000 
INFO  @ Thu, 13 Apr 2017 13:26:30:  150000000 
INFO  @ Thu, 13 Apr 2017 13:26:32:  151000000 
INFO  @ Thu, 13 Apr 2017 13:26:34:  152000000 
INFO  @ Thu, 13 Apr 2017 13:26:35:  153000000 
INFO  @ Thu, 13 Apr 2017 13:26:37:  154000000 
INFO  @ Thu, 13 Apr 2017 13:26:38:  155000000 
INFO  @ Thu, 13 Apr 2017 13:26:40:  156000000 
INFO  @ Thu, 13 Apr 2017 13:26:41:  157000000 
INFO  @ Thu, 13 Apr 2017 13:26:43:  158000000 
INFO  @ Thu, 13 Apr 2017 13:26:45:  159000000 
INFO  @ Thu, 13 Apr 2017 13:26:46:  160000000 
INFO  @ Thu, 13 Apr 2017 13:26:48:  161000000 
INFO  @ Thu, 13 Apr 2017 13:26:49:  162000000 
INFO  @ Thu, 13 Apr 2017 13:26:51:  163000000 
INFO  @ Thu, 13 Apr 2017 13:26:52:  164000000 
INFO  @ Thu, 13 Apr 2017 13:26:54:  165000000 
INFO  @ Thu, 13 Apr 2017 13:26:56:  166000000 
INFO  @ Thu, 13 Apr 2017 13:26:57:  167000000 
INFO  @ Thu, 13 Apr 2017 13:26:59:  168000000 
INFO  @ Thu, 13 Apr 2017 13:27:00:  169000000 
INFO  @ Thu, 13 Apr 2017 13:27:02:  170000000 
INFO  @ Thu, 13 Apr 2017 13:27:03:  171000000 
INFO  @ Thu, 13 Apr 2017 13:27:05:  172000000 
INFO  @ Thu, 13 Apr 2017 13:27:06:  173000000 
INFO  @ Thu, 13 Apr 2017 13:27:08:  174000000 
INFO  @ Thu, 13 Apr 2017 13:27:09:  175000000 
INFO  @ Thu, 13 Apr 2017 13:27:11:  176000000 
INFO  @ Thu, 13 Apr 2017 13:27:13:  177000000 
INFO  @ Thu, 13 Apr 2017 13:27:14:  178000000 
INFO  @ Thu, 13 Apr 2017 13:27:16:  179000000 
INFO  @ Thu, 13 Apr 2017 13:27:18:  180000000 
INFO  @ Thu, 13 Apr 2017 13:27:19:  181000000 
INFO  @ Thu, 13 Apr 2017 13:27:21:  182000000 
INFO  @ Thu, 13 Apr 2017 13:27:22:  183000000 
INFO  @ Thu, 13 Apr 2017 13:27:24:  184000000 
INFO  @ Thu, 13 Apr 2017 13:27:25:  185000000 
INFO  @ Thu, 13 Apr 2017 13:27:27:  186000000 
INFO  @ Thu, 13 Apr 2017 13:27:28:  187000000 
INFO  @ Thu, 13 Apr 2017 13:27:30:  188000000 
INFO  @ Thu, 13 Apr 2017 13:27:32:  189000000 
INFO  @ Thu, 13 Apr 2017 13:27:33:  190000000 
INFO  @ Thu, 13 Apr 2017 13:27:35:  191000000 
INFO  @ Thu, 13 Apr 2017 13:27:36:  192000000 
INFO  @ Thu, 13 Apr 2017 13:27:38:  193000000 
INFO  @ Thu, 13 Apr 2017 13:27:39:  194000000 
INFO  @ Thu, 13 Apr 2017 13:27:41:  195000000 
INFO  @ Thu, 13 Apr 2017 13:27:42:  196000000 
INFO  @ Thu, 13 Apr 2017 13:27:44:  197000000 
INFO  @ Thu, 13 Apr 2017 13:27:45:  198000000 
INFO  @ Thu, 13 Apr 2017 13:27:47:  199000000 
INFO  @ Thu, 13 Apr 2017 13:27:49:  200000000 
INFO  @ Thu, 13 Apr 2017 13:27:50:  201000000 
INFO  @ Thu, 13 Apr 2017 13:27:52:  202000000 
INFO  @ Thu, 13 Apr 2017 13:27:53:  203000000 
INFO  @ Thu, 13 Apr 2017 13:27:55:  204000000 
INFO  @ Thu, 13 Apr 2017 13:27:56:  205000000 
INFO  @ Thu, 13 Apr 2017 13:27:58:  206000000 
INFO  @ Thu, 13 Apr 2017 13:28:00:  207000000 
INFO  @ Thu, 13 Apr 2017 13:28:01:  208000000 
INFO  @ Thu, 13 Apr 2017 13:28:03:  209000000 
INFO  @ Thu, 13 Apr 2017 13:28:04:  210000000 
INFO  @ Thu, 13 Apr 2017 13:28:06:  211000000 
INFO  @ Thu, 13 Apr 2017 13:28:07:  212000000 
INFO  @ Thu, 13 Apr 2017 13:28:09:  213000000 
INFO  @ Thu, 13 Apr 2017 13:28:10:  214000000 
INFO  @ Thu, 13 Apr 2017 13:28:12:  215000000 
INFO  @ Thu, 13 Apr 2017 13:28:13:  216000000 
INFO  @ Thu, 13 Apr 2017 13:28:15:  217000000 
INFO  @ Thu, 13 Apr 2017 13:28:17:  218000000 
INFO  @ Thu, 13 Apr 2017 13:28:18:  219000000 
INFO  @ Thu, 13 Apr 2017 13:28:36: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 13:28:38:  1000000 
INFO  @ Thu, 13 Apr 2017 13:28:40:  2000000 
INFO  @ Thu, 13 Apr 2017 13:28:41:  3000000 
INFO  @ Thu, 13 Apr 2017 13:28:43:  4000000 
INFO  @ Thu, 13 Apr 2017 13:28:44:  5000000 
INFO  @ Thu, 13 Apr 2017 13:28:46:  6000000 
INFO  @ Thu, 13 Apr 2017 13:28:47:  7000000 
INFO  @ Thu, 13 Apr 2017 13:28:49:  8000000 
INFO  @ Thu, 13 Apr 2017 13:28:50:  9000000 
INFO  @ Thu, 13 Apr 2017 13:28:52:  10000000 
INFO  @ Thu, 13 Apr 2017 13:28:53:  11000000 
INFO  @ Thu, 13 Apr 2017 13:28:55:  12000000 
INFO  @ Thu, 13 Apr 2017 13:28:57:  13000000 
INFO  @ Thu, 13 Apr 2017 13:28:58:  14000000 
INFO  @ Thu, 13 Apr 2017 13:29:00:  15000000 
INFO  @ Thu, 13 Apr 2017 13:29:01:  16000000 
INFO  @ Thu, 13 Apr 2017 13:29:03:  17000000 
INFO  @ Thu, 13 Apr 2017 13:29:04:  18000000 
INFO  @ Thu, 13 Apr 2017 13:29:05:  19000000 
INFO  @ Thu, 13 Apr 2017 13:29:07:  20000000 
INFO  @ Thu, 13 Apr 2017 13:29:09:  21000000 
INFO  @ Thu, 13 Apr 2017 13:29:10:  22000000 
INFO  @ Thu, 13 Apr 2017 13:29:12:  23000000 
INFO  @ Thu, 13 Apr 2017 13:29:13:  24000000 
INFO  @ Thu, 13 Apr 2017 13:29:15:  25000000 
INFO  @ Thu, 13 Apr 2017 13:29:16:  26000000 
INFO  @ Thu, 13 Apr 2017 13:29:18:  27000000 
INFO  @ Thu, 13 Apr 2017 13:29:19:  28000000 
INFO  @ Thu, 13 Apr 2017 13:29:21:  29000000 
INFO  @ Thu, 13 Apr 2017 13:29:22:  30000000 
INFO  @ Thu, 13 Apr 2017 13:29:24:  31000000 
INFO  @ Thu, 13 Apr 2017 13:29:25:  32000000 
INFO  @ Thu, 13 Apr 2017 13:29:26:  33000000 
INFO  @ Thu, 13 Apr 2017 13:29:28:  34000000 
INFO  @ Thu, 13 Apr 2017 13:29:29:  35000000 
INFO  @ Thu, 13 Apr 2017 13:29:31:  36000000 
INFO  @ Thu, 13 Apr 2017 13:29:33:  37000000 
INFO  @ Thu, 13 Apr 2017 13:29:34:  38000000 
INFO  @ Thu, 13 Apr 2017 13:29:35:  39000000 
INFO  @ Thu, 13 Apr 2017 13:29:37:  40000000 
INFO  @ Thu, 13 Apr 2017 13:29:38:  41000000 
INFO  @ Thu, 13 Apr 2017 13:29:40:  42000000 
INFO  @ Thu, 13 Apr 2017 13:29:41:  43000000 
INFO  @ Thu, 13 Apr 2017 13:29:43:  44000000 
INFO  @ Thu, 13 Apr 2017 13:29:45:  45000000 
INFO  @ Thu, 13 Apr 2017 13:29:46:  46000000 
INFO  @ Thu, 13 Apr 2017 13:29:47:  47000000 
INFO  @ Thu, 13 Apr 2017 13:29:49:  48000000 
INFO  @ Thu, 13 Apr 2017 13:29:50:  49000000 
INFO  @ Thu, 13 Apr 2017 13:29:52:  50000000 
INFO  @ Thu, 13 Apr 2017 13:29:53:  51000000 
INFO  @ Thu, 13 Apr 2017 13:29:55:  52000000 
INFO  @ Thu, 13 Apr 2017 13:29:56:  53000000 
INFO  @ Thu, 13 Apr 2017 13:29:57:  54000000 
INFO  @ Thu, 13 Apr 2017 13:29:59:  55000000 
INFO  @ Thu, 13 Apr 2017 13:30:00:  56000000 
INFO  @ Thu, 13 Apr 2017 13:30:02:  57000000 
INFO  @ Thu, 13 Apr 2017 13:30:03:  58000000 
INFO  @ Thu, 13 Apr 2017 13:30:05:  59000000 
INFO  @ Thu, 13 Apr 2017 13:30:06:  60000000 
INFO  @ Thu, 13 Apr 2017 13:30:08:  61000000 
INFO  @ Thu, 13 Apr 2017 13:30:09:  62000000 
INFO  @ Thu, 13 Apr 2017 13:30:11:  63000000 
INFO  @ Thu, 13 Apr 2017 13:30:12:  64000000 
INFO  @ Thu, 13 Apr 2017 13:30:14:  65000000 
INFO  @ Thu, 13 Apr 2017 13:30:15:  66000000 
INFO  @ Thu, 13 Apr 2017 13:30:16:  67000000 
INFO  @ Thu, 13 Apr 2017 13:30:18:  68000000 
INFO  @ Thu, 13 Apr 2017 13:30:19:  69000000 
INFO  @ Thu, 13 Apr 2017 13:30:21:  70000000 
INFO  @ Thu, 13 Apr 2017 13:30:22:  71000000 
INFO  @ Thu, 13 Apr 2017 13:30:23:  72000000 
INFO  @ Thu, 13 Apr 2017 13:30:25:  73000000 
INFO  @ Thu, 13 Apr 2017 13:30:26:  74000000 
INFO  @ Thu, 13 Apr 2017 13:30:28:  75000000 
INFO  @ Thu, 13 Apr 2017 13:30:29:  76000000 
INFO  @ Thu, 13 Apr 2017 13:30:30:  77000000 
INFO  @ Thu, 13 Apr 2017 13:30:32:  78000000 
INFO  @ Thu, 13 Apr 2017 13:30:33:  79000000 
INFO  @ Thu, 13 Apr 2017 13:30:35:  80000000 
INFO  @ Thu, 13 Apr 2017 13:30:36:  81000000 
INFO  @ Thu, 13 Apr 2017 13:30:38:  82000000 
INFO  @ Thu, 13 Apr 2017 13:30:39:  83000000 
INFO  @ Thu, 13 Apr 2017 13:30:40:  84000000 
INFO  @ Thu, 13 Apr 2017 13:30:42:  85000000 
INFO  @ Thu, 13 Apr 2017 13:30:43:  86000000 
INFO  @ Thu, 13 Apr 2017 13:30:45:  87000000 
INFO  @ Thu, 13 Apr 2017 13:30:46:  88000000 
INFO  @ Thu, 13 Apr 2017 13:30:47:  89000000 
INFO  @ Thu, 13 Apr 2017 13:30:49:  90000000 
INFO  @ Thu, 13 Apr 2017 13:30:50:  91000000 
INFO  @ Thu, 13 Apr 2017 13:30:52:  92000000 
INFO  @ Thu, 13 Apr 2017 13:30:53:  93000000 
INFO  @ Thu, 13 Apr 2017 13:30:54:  94000000 
INFO  @ Thu, 13 Apr 2017 13:30:56:  95000000 
INFO  @ Thu, 13 Apr 2017 13:30:57:  96000000 
INFO  @ Thu, 13 Apr 2017 13:30:59:  97000000 
INFO  @ Thu, 13 Apr 2017 13:31:00:  98000000 
INFO  @ Thu, 13 Apr 2017 13:31:01:  99000000 
INFO  @ Thu, 13 Apr 2017 13:31:03: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 13:31:03: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 13:31:03: #1  total tags in treatment: 219735318 
INFO  @ Thu, 13 Apr 2017 13:31:03: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 13:31:03: #1 finished! 
INFO  @ Thu, 13 Apr 2017 13:31:03: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 13:31:03: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 13:31:03: #2 Use 238 as fragment length 
INFO  @ Thu, 13 Apr 2017 13:31:03: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 13:31:03: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 13:31:03: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 13:39:48: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 13:39:48: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 13:39:48: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 13:39:48: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 13:39:48: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 13:56:27: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 13:56:30: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 13:56:31: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 13:56:32: Done! 
INFO  @ Thu, 13 Apr 2017 13:56:43: Read and build treatment bedGraph... 
INFO  @ Thu, 13 Apr 2017 14:02:41: Read and build control bedGraph... 
INFO  @ Thu, 13 Apr 2017 14:05:26: Build scoreTrackII... 
INFO  @ Thu, 13 Apr 2017 14:07:59: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Thu, 13 Apr 2017 14:25:52: Write bedGraph of scores... 
INFO  @ Thu, 13 Apr 2017 14:39:25: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_FE.bdg'! 
INFO  @ Thu, 13 Apr 2017 15:17:59: Read and build treatment bedGraph... 
INFO  @ Thu, 13 Apr 2017 15:23:33: Read and build control bedGraph... 
INFO  @ Thu, 13 Apr 2017 15:26:08: Build scoreTrackII... 
INFO  @ Thu, 13 Apr 2017 15:28:17: Values in your input bedGraph files will be multiplied by 99.493262 ... 
INFO  @ Thu, 13 Apr 2017 15:45:37: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Thu, 13 Apr 2017 15:49:49: Write bedGraph of scores... 
INFO  @ Thu, 13 Apr 2017 15:57:23: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_ppois.bdg'! 

 
 		 

    
  
 
  Num   2  
 
  ID   task.callpeak_macs2.macs2_n_s_ppr1.line_66.id_11  
 
  Name   macs2 n/s ppr1 
 
  Thread   thread_Root  
 
  PID   46813  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 13:22:15  
 
  End   2017-04-13 13:54:11  
 
  Elapsed   00:31:55  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 68

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 69

 export LC_COLLATE=C

# SYS command. line 74

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 238 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 84

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.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 94

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1 -o "ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.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 113

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1 -o "ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 126

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
14531 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 13:22:32: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 238 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.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  @ Thu, 13 Apr 2017 13:22:32: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 13:22:32: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 13:22:34:  1000000 
INFO  @ Thu, 13 Apr 2017 13:22:36:  2000000 
INFO  @ Thu, 13 Apr 2017 13:22:38:  3000000 
INFO  @ Thu, 13 Apr 2017 13:22:40:  4000000 
INFO  @ Thu, 13 Apr 2017 13:22:42:  5000000 
INFO  @ Thu, 13 Apr 2017 13:22:44:  6000000 
INFO  @ Thu, 13 Apr 2017 13:22:46:  7000000 
INFO  @ Thu, 13 Apr 2017 13:22:48:  8000000 
INFO  @ Thu, 13 Apr 2017 13:22:50:  9000000 
INFO  @ Thu, 13 Apr 2017 13:22:52:  10000000 
INFO  @ Thu, 13 Apr 2017 13:22:54:  11000000 
INFO  @ Thu, 13 Apr 2017 13:22:56:  12000000 
INFO  @ Thu, 13 Apr 2017 13:22:58:  13000000 
INFO  @ Thu, 13 Apr 2017 13:23:00:  14000000 
INFO  @ Thu, 13 Apr 2017 13:23:02:  15000000 
INFO  @ Thu, 13 Apr 2017 13:23:04:  16000000 
INFO  @ Thu, 13 Apr 2017 13:23:06:  17000000 
INFO  @ Thu, 13 Apr 2017 13:23:08:  18000000 
INFO  @ Thu, 13 Apr 2017 13:23:10:  19000000 
INFO  @ Thu, 13 Apr 2017 13:23:12:  20000000 
INFO  @ Thu, 13 Apr 2017 13:23:15:  21000000 
INFO  @ Thu, 13 Apr 2017 13:23:17:  22000000 
INFO  @ Thu, 13 Apr 2017 13:23:19:  23000000 
INFO  @ Thu, 13 Apr 2017 13:23:21:  24000000 
INFO  @ Thu, 13 Apr 2017 13:23:23:  25000000 
INFO  @ Thu, 13 Apr 2017 13:23:25:  26000000 
INFO  @ Thu, 13 Apr 2017 13:23:27:  27000000 
INFO  @ Thu, 13 Apr 2017 13:23:29:  28000000 
INFO  @ Thu, 13 Apr 2017 13:23:31:  29000000 
INFO  @ Thu, 13 Apr 2017 13:23:34:  30000000 
INFO  @ Thu, 13 Apr 2017 13:23:36:  31000000 
INFO  @ Thu, 13 Apr 2017 13:23:38:  32000000 
INFO  @ Thu, 13 Apr 2017 13:23:40:  33000000 
INFO  @ Thu, 13 Apr 2017 13:23:42:  34000000 
INFO  @ Thu, 13 Apr 2017 13:23:44:  35000000 
INFO  @ Thu, 13 Apr 2017 13:23:46:  36000000 
INFO  @ Thu, 13 Apr 2017 13:23:48:  37000000 
INFO  @ Thu, 13 Apr 2017 13:23:50:  38000000 
INFO  @ Thu, 13 Apr 2017 13:23:53:  39000000 
INFO  @ Thu, 13 Apr 2017 13:23:55:  40000000 
INFO  @ Thu, 13 Apr 2017 13:23:57:  41000000 
INFO  @ Thu, 13 Apr 2017 13:23:59:  42000000 
INFO  @ Thu, 13 Apr 2017 13:24:01:  43000000 
INFO  @ Thu, 13 Apr 2017 13:24:03:  44000000 
INFO  @ Thu, 13 Apr 2017 13:24:05:  45000000 
INFO  @ Thu, 13 Apr 2017 13:24:07:  46000000 
INFO  @ Thu, 13 Apr 2017 13:24:09:  47000000 
INFO  @ Thu, 13 Apr 2017 13:24:11:  48000000 
INFO  @ Thu, 13 Apr 2017 13:24:13:  49000000 
INFO  @ Thu, 13 Apr 2017 13:24:16:  50000000 
INFO  @ Thu, 13 Apr 2017 13:24:18:  51000000 
INFO  @ Thu, 13 Apr 2017 13:24:20:  52000000 
INFO  @ Thu, 13 Apr 2017 13:24:22:  53000000 
INFO  @ Thu, 13 Apr 2017 13:24:24:  54000000 
INFO  @ Thu, 13 Apr 2017 13:24:26:  55000000 
INFO  @ Thu, 13 Apr 2017 13:24:28:  56000000 
INFO  @ Thu, 13 Apr 2017 13:24:30:  57000000 
INFO  @ Thu, 13 Apr 2017 13:24:32:  58000000 
INFO  @ Thu, 13 Apr 2017 13:24:34:  59000000 
INFO  @ Thu, 13 Apr 2017 13:24:36:  60000000 
INFO  @ Thu, 13 Apr 2017 13:24:38:  61000000 
INFO  @ Thu, 13 Apr 2017 13:24:40:  62000000 
INFO  @ Thu, 13 Apr 2017 13:24:43:  63000000 
INFO  @ Thu, 13 Apr 2017 13:24:45:  64000000 
INFO  @ Thu, 13 Apr 2017 13:24:47:  65000000 
INFO  @ Thu, 13 Apr 2017 13:24:49:  66000000 
INFO  @ Thu, 13 Apr 2017 13:24:51:  67000000 
INFO  @ Thu, 13 Apr 2017 13:24:52:  68000000 
INFO  @ Thu, 13 Apr 2017 13:24:54:  69000000 
INFO  @ Thu, 13 Apr 2017 13:24:56:  70000000 
INFO  @ Thu, 13 Apr 2017 13:24:58:  71000000 
INFO  @ Thu, 13 Apr 2017 13:25:00:  72000000 
INFO  @ Thu, 13 Apr 2017 13:25:02:  73000000 
INFO  @ Thu, 13 Apr 2017 13:25:04:  74000000 
INFO  @ Thu, 13 Apr 2017 13:25:06:  75000000 
INFO  @ Thu, 13 Apr 2017 13:25:08:  76000000 
INFO  @ Thu, 13 Apr 2017 13:25:10:  77000000 
INFO  @ Thu, 13 Apr 2017 13:25:12:  78000000 
INFO  @ Thu, 13 Apr 2017 13:25:14:  79000000 
INFO  @ Thu, 13 Apr 2017 13:25:16:  80000000 
INFO  @ Thu, 13 Apr 2017 13:25:18:  81000000 
INFO  @ Thu, 13 Apr 2017 13:25:20:  82000000 
INFO  @ Thu, 13 Apr 2017 13:25:22:  83000000 
INFO  @ Thu, 13 Apr 2017 13:25:24:  84000000 
INFO  @ Thu, 13 Apr 2017 13:25:26:  85000000 
INFO  @ Thu, 13 Apr 2017 13:25:28:  86000000 
INFO  @ Thu, 13 Apr 2017 13:25:30:  87000000 
INFO  @ Thu, 13 Apr 2017 13:25:32:  88000000 
INFO  @ Thu, 13 Apr 2017 13:25:34:  89000000 
INFO  @ Thu, 13 Apr 2017 13:25:36:  90000000 
INFO  @ Thu, 13 Apr 2017 13:25:38:  91000000 
INFO  @ Thu, 13 Apr 2017 13:25:40:  92000000 
INFO  @ Thu, 13 Apr 2017 13:25:42:  93000000 
INFO  @ Thu, 13 Apr 2017 13:25:44:  94000000 
INFO  @ Thu, 13 Apr 2017 13:25:46:  95000000 
INFO  @ Thu, 13 Apr 2017 13:25:48:  96000000 
INFO  @ Thu, 13 Apr 2017 13:25:50:  97000000 
INFO  @ Thu, 13 Apr 2017 13:25:52:  98000000 
INFO  @ Thu, 13 Apr 2017 13:25:54:  99000000 
INFO  @ Thu, 13 Apr 2017 13:25:56:  100000000 
INFO  @ Thu, 13 Apr 2017 13:25:58:  101000000 
INFO  @ Thu, 13 Apr 2017 13:26:00:  102000000 
INFO  @ Thu, 13 Apr 2017 13:26:02:  103000000 
INFO  @ Thu, 13 Apr 2017 13:26:04:  104000000 
INFO  @ Thu, 13 Apr 2017 13:26:06:  105000000 
INFO  @ Thu, 13 Apr 2017 13:26:08:  106000000 
INFO  @ Thu, 13 Apr 2017 13:26:10:  107000000 
INFO  @ Thu, 13 Apr 2017 13:26:12:  108000000 
INFO  @ Thu, 13 Apr 2017 13:26:14:  109000000 
INFO  @ Thu, 13 Apr 2017 13:26:25: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 13:26:27:  1000000 
INFO  @ Thu, 13 Apr 2017 13:26:29:  2000000 
INFO  @ Thu, 13 Apr 2017 13:26:31:  3000000 
INFO  @ Thu, 13 Apr 2017 13:26:33:  4000000 
INFO  @ Thu, 13 Apr 2017 13:26:34:  5000000 
INFO  @ Thu, 13 Apr 2017 13:26:36:  6000000 
INFO  @ Thu, 13 Apr 2017 13:26:38:  7000000 
INFO  @ Thu, 13 Apr 2017 13:26:40:  8000000 
INFO  @ Thu, 13 Apr 2017 13:26:42:  9000000 
INFO  @ Thu, 13 Apr 2017 13:26:44:  10000000 
INFO  @ Thu, 13 Apr 2017 13:26:45:  11000000 
INFO  @ Thu, 13 Apr 2017 13:26:47:  12000000 
INFO  @ Thu, 13 Apr 2017 13:26:49:  13000000 
INFO  @ Thu, 13 Apr 2017 13:26:51:  14000000 
INFO  @ Thu, 13 Apr 2017 13:26:53:  15000000 
INFO  @ Thu, 13 Apr 2017 13:26:55:  16000000 
INFO  @ Thu, 13 Apr 2017 13:26:57:  17000000 
INFO  @ Thu, 13 Apr 2017 13:26:58:  18000000 
INFO  @ Thu, 13 Apr 2017 13:27:00:  19000000 
INFO  @ Thu, 13 Apr 2017 13:27:02:  20000000 
INFO  @ Thu, 13 Apr 2017 13:27:04:  21000000 
INFO  @ Thu, 13 Apr 2017 13:27:06:  22000000 
INFO  @ Thu, 13 Apr 2017 13:27:07:  23000000 
INFO  @ Thu, 13 Apr 2017 13:27:09:  24000000 
INFO  @ Thu, 13 Apr 2017 13:27:11:  25000000 
INFO  @ Thu, 13 Apr 2017 13:27:13:  26000000 
INFO  @ Thu, 13 Apr 2017 13:27:15:  27000000 
INFO  @ Thu, 13 Apr 2017 13:27:17:  28000000 
INFO  @ Thu, 13 Apr 2017 13:27:18:  29000000 
INFO  @ Thu, 13 Apr 2017 13:27:20:  30000000 
INFO  @ Thu, 13 Apr 2017 13:27:22:  31000000 
INFO  @ Thu, 13 Apr 2017 13:27:24:  32000000 
INFO  @ Thu, 13 Apr 2017 13:27:26:  33000000 
INFO  @ Thu, 13 Apr 2017 13:27:28:  34000000 
INFO  @ Thu, 13 Apr 2017 13:27:29:  35000000 
INFO  @ Thu, 13 Apr 2017 13:27:31:  36000000 
INFO  @ Thu, 13 Apr 2017 13:27:33:  37000000 
INFO  @ Thu, 13 Apr 2017 13:27:35:  38000000 
INFO  @ Thu, 13 Apr 2017 13:27:37:  39000000 
INFO  @ Thu, 13 Apr 2017 13:27:39:  40000000 
INFO  @ Thu, 13 Apr 2017 13:27:40:  41000000 
INFO  @ Thu, 13 Apr 2017 13:27:42:  42000000 
INFO  @ Thu, 13 Apr 2017 13:27:44:  43000000 
INFO  @ Thu, 13 Apr 2017 13:27:46:  44000000 
INFO  @ Thu, 13 Apr 2017 13:27:48:  45000000 
INFO  @ Thu, 13 Apr 2017 13:27:50:  46000000 
INFO  @ Thu, 13 Apr 2017 13:27:51:  47000000 
INFO  @ Thu, 13 Apr 2017 13:27:53:  48000000 
INFO  @ Thu, 13 Apr 2017 13:27:55:  49000000 
INFO  @ Thu, 13 Apr 2017 13:27:57:  50000000 
INFO  @ Thu, 13 Apr 2017 13:27:59:  51000000 
INFO  @ Thu, 13 Apr 2017 13:28:01:  52000000 
INFO  @ Thu, 13 Apr 2017 13:28:02:  53000000 
INFO  @ Thu, 13 Apr 2017 13:28:04:  54000000 
INFO  @ Thu, 13 Apr 2017 13:28:06:  55000000 
INFO  @ Thu, 13 Apr 2017 13:28:08:  56000000 
INFO  @ Thu, 13 Apr 2017 13:28:10:  57000000 
INFO  @ Thu, 13 Apr 2017 13:28:12:  58000000 
INFO  @ Thu, 13 Apr 2017 13:28:13:  59000000 
INFO  @ Thu, 13 Apr 2017 13:28:15:  60000000 
INFO  @ Thu, 13 Apr 2017 13:28:17:  61000000 
INFO  @ Thu, 13 Apr 2017 13:28:19:  62000000 
INFO  @ Thu, 13 Apr 2017 13:28:21:  63000000 
INFO  @ Thu, 13 Apr 2017 13:28:23:  64000000 
INFO  @ Thu, 13 Apr 2017 13:28:24:  65000000 
INFO  @ Thu, 13 Apr 2017 13:28:26:  66000000 
INFO  @ Thu, 13 Apr 2017 13:28:28:  67000000 
INFO  @ Thu, 13 Apr 2017 13:28:30:  68000000 
INFO  @ Thu, 13 Apr 2017 13:28:32:  69000000 
INFO  @ Thu, 13 Apr 2017 13:28:34:  70000000 
INFO  @ Thu, 13 Apr 2017 13:28:35:  71000000 
INFO  @ Thu, 13 Apr 2017 13:28:37:  72000000 
INFO  @ Thu, 13 Apr 2017 13:28:39:  73000000 
INFO  @ Thu, 13 Apr 2017 13:28:41:  74000000 
INFO  @ Thu, 13 Apr 2017 13:28:43:  75000000 
INFO  @ Thu, 13 Apr 2017 13:28:44:  76000000 
INFO  @ Thu, 13 Apr 2017 13:28:46:  77000000 
INFO  @ Thu, 13 Apr 2017 13:28:48:  78000000 
INFO  @ Thu, 13 Apr 2017 13:28:50:  79000000 
INFO  @ Thu, 13 Apr 2017 13:28:52:  80000000 
INFO  @ Thu, 13 Apr 2017 13:28:53:  81000000 
INFO  @ Thu, 13 Apr 2017 13:28:55:  82000000 
INFO  @ Thu, 13 Apr 2017 13:28:57:  83000000 
INFO  @ Thu, 13 Apr 2017 13:28:59:  84000000 
INFO  @ Thu, 13 Apr 2017 13:29:01:  85000000 
INFO  @ Thu, 13 Apr 2017 13:29:03:  86000000 
INFO  @ Thu, 13 Apr 2017 13:29:04:  87000000 
INFO  @ Thu, 13 Apr 2017 13:29:06:  88000000 
INFO  @ Thu, 13 Apr 2017 13:29:08:  89000000 
INFO  @ Thu, 13 Apr 2017 13:29:10:  90000000 
INFO  @ Thu, 13 Apr 2017 13:29:12:  91000000 
INFO  @ Thu, 13 Apr 2017 13:29:13:  92000000 
INFO  @ Thu, 13 Apr 2017 13:29:15:  93000000 
INFO  @ Thu, 13 Apr 2017 13:29:17:  94000000 
INFO  @ Thu, 13 Apr 2017 13:29:19:  95000000 
INFO  @ Thu, 13 Apr 2017 13:29:21:  96000000 
INFO  @ Thu, 13 Apr 2017 13:29:23:  97000000 
INFO  @ Thu, 13 Apr 2017 13:29:24:  98000000 
INFO  @ Thu, 13 Apr 2017 13:29:26:  99000000 
INFO  @ Thu, 13 Apr 2017 13:29:28: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 13:29:28: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 13:29:28: #1  total tags in treatment: 109867660 
INFO  @ Thu, 13 Apr 2017 13:29:28: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 13:29:28: #1 finished! 
INFO  @ Thu, 13 Apr 2017 13:29:28: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 13:29:28: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 13:29:28: #2 Use 238 as fragment length 
INFO  @ Thu, 13 Apr 2017 13:29:28: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 13:29:28: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 13:29:28: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 13:37:55: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 13:37:55: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 13:37:55: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 13:37:55: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 13:37:55: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 13:54:05: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 13:54:06: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 13:54:06: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 13:54:06: Done! 

 
 		 

    
  
 
  Num   3  
 
  ID   task.callpeak_macs2.macs2_n_s_ppr2.line_66.id_12  
 
  Name   macs2 n/s ppr2 
 
  Thread   thread_Root  
 
  PID   46814  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 13:22:16  
 
  End   2017-04-13 13:48:39  
 
  Elapsed   00:26:23  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 68

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 69

 export LC_COLLATE=C

# SYS command. line 74

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 238 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 84

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.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 94

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2 -o "ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.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 113

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2 -o "ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 126

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
15775 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 13:22:33: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 238 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.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  @ Thu, 13 Apr 2017 13:22:33: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 13:22:33: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 13:22:35:  1000000 
INFO  @ Thu, 13 Apr 2017 13:22:36:  2000000 
INFO  @ Thu, 13 Apr 2017 13:22:38:  3000000 
INFO  @ Thu, 13 Apr 2017 13:22:39:  4000000 
INFO  @ Thu, 13 Apr 2017 13:22:41:  5000000 
INFO  @ Thu, 13 Apr 2017 13:22:43:  6000000 
INFO  @ Thu, 13 Apr 2017 13:22:44:  7000000 
INFO  @ Thu, 13 Apr 2017 13:22:46:  8000000 
INFO  @ Thu, 13 Apr 2017 13:22:47:  9000000 
INFO  @ Thu, 13 Apr 2017 13:22:49:  10000000 
INFO  @ Thu, 13 Apr 2017 13:22:51:  11000000 
INFO  @ Thu, 13 Apr 2017 13:22:52:  12000000 
INFO  @ Thu, 13 Apr 2017 13:22:54:  13000000 
INFO  @ Thu, 13 Apr 2017 13:22:55:  14000000 
INFO  @ Thu, 13 Apr 2017 13:22:57:  15000000 
INFO  @ Thu, 13 Apr 2017 13:22:58:  16000000 
INFO  @ Thu, 13 Apr 2017 13:23:00:  17000000 
INFO  @ Thu, 13 Apr 2017 13:23:01:  18000000 
INFO  @ Thu, 13 Apr 2017 13:23:03:  19000000 
INFO  @ Thu, 13 Apr 2017 13:23:05:  20000000 
INFO  @ Thu, 13 Apr 2017 13:23:06:  21000000 
INFO  @ Thu, 13 Apr 2017 13:23:08:  22000000 
INFO  @ Thu, 13 Apr 2017 13:23:09:  23000000 
INFO  @ Thu, 13 Apr 2017 13:23:11:  24000000 
INFO  @ Thu, 13 Apr 2017 13:23:12:  25000000 
INFO  @ Thu, 13 Apr 2017 13:23:14:  26000000 
INFO  @ Thu, 13 Apr 2017 13:23:15:  27000000 
INFO  @ Thu, 13 Apr 2017 13:23:17:  28000000 
INFO  @ Thu, 13 Apr 2017 13:23:18:  29000000 
INFO  @ Thu, 13 Apr 2017 13:23:20:  30000000 
INFO  @ Thu, 13 Apr 2017 13:23:21:  31000000 
INFO  @ Thu, 13 Apr 2017 13:23:23:  32000000 
INFO  @ Thu, 13 Apr 2017 13:23:25:  33000000 
INFO  @ Thu, 13 Apr 2017 13:23:26:  34000000 
INFO  @ Thu, 13 Apr 2017 13:23:28:  35000000 
INFO  @ Thu, 13 Apr 2017 13:23:29:  36000000 
INFO  @ Thu, 13 Apr 2017 13:23:31:  37000000 
INFO  @ Thu, 13 Apr 2017 13:23:32:  38000000 
INFO  @ Thu, 13 Apr 2017 13:23:34:  39000000 
INFO  @ Thu, 13 Apr 2017 13:23:36:  40000000 
INFO  @ Thu, 13 Apr 2017 13:23:37:  41000000 
INFO  @ Thu, 13 Apr 2017 13:23:39:  42000000 
INFO  @ Thu, 13 Apr 2017 13:23:40:  43000000 
INFO  @ Thu, 13 Apr 2017 13:23:42:  44000000 
INFO  @ Thu, 13 Apr 2017 13:23:44:  45000000 
INFO  @ Thu, 13 Apr 2017 13:23:45:  46000000 
INFO  @ Thu, 13 Apr 2017 13:23:47:  47000000 
INFO  @ Thu, 13 Apr 2017 13:23:48:  48000000 
INFO  @ Thu, 13 Apr 2017 13:23:50:  49000000 
INFO  @ Thu, 13 Apr 2017 13:23:52:  50000000 
INFO  @ Thu, 13 Apr 2017 13:23:54:  51000000 
INFO  @ Thu, 13 Apr 2017 13:23:55:  52000000 
INFO  @ Thu, 13 Apr 2017 13:23:57:  53000000 
INFO  @ Thu, 13 Apr 2017 13:23:58:  54000000 
INFO  @ Thu, 13 Apr 2017 13:24:00:  55000000 
INFO  @ Thu, 13 Apr 2017 13:24:02:  56000000 
INFO  @ Thu, 13 Apr 2017 13:24:03:  57000000 
INFO  @ Thu, 13 Apr 2017 13:24:05:  58000000 
INFO  @ Thu, 13 Apr 2017 13:24:06:  59000000 
INFO  @ Thu, 13 Apr 2017 13:24:08:  60000000 
INFO  @ Thu, 13 Apr 2017 13:24:10:  61000000 
INFO  @ Thu, 13 Apr 2017 13:24:11:  62000000 
INFO  @ Thu, 13 Apr 2017 13:24:13:  63000000 
INFO  @ Thu, 13 Apr 2017 13:24:14:  64000000 
INFO  @ Thu, 13 Apr 2017 13:24:16:  65000000 
INFO  @ Thu, 13 Apr 2017 13:24:18:  66000000 
INFO  @ Thu, 13 Apr 2017 13:24:20:  67000000 
INFO  @ Thu, 13 Apr 2017 13:24:21:  68000000 
INFO  @ Thu, 13 Apr 2017 13:24:23:  69000000 
INFO  @ Thu, 13 Apr 2017 13:24:25:  70000000 
INFO  @ Thu, 13 Apr 2017 13:24:26:  71000000 
INFO  @ Thu, 13 Apr 2017 13:24:28:  72000000 
INFO  @ Thu, 13 Apr 2017 13:24:29:  73000000 
INFO  @ Thu, 13 Apr 2017 13:24:31:  74000000 
INFO  @ Thu, 13 Apr 2017 13:24:32:  75000000 
INFO  @ Thu, 13 Apr 2017 13:24:34:  76000000 
INFO  @ Thu, 13 Apr 2017 13:24:36:  77000000 
INFO  @ Thu, 13 Apr 2017 13:24:37:  78000000 
INFO  @ Thu, 13 Apr 2017 13:24:39:  79000000 
INFO  @ Thu, 13 Apr 2017 13:24:40:  80000000 
INFO  @ Thu, 13 Apr 2017 13:24:42:  81000000 
INFO  @ Thu, 13 Apr 2017 13:24:43:  82000000 
INFO  @ Thu, 13 Apr 2017 13:24:45:  83000000 
INFO  @ Thu, 13 Apr 2017 13:24:47:  84000000 
INFO  @ Thu, 13 Apr 2017 13:24:48:  85000000 
INFO  @ Thu, 13 Apr 2017 13:24:50:  86000000 
INFO  @ Thu, 13 Apr 2017 13:24:51:  87000000 
INFO  @ Thu, 13 Apr 2017 13:24:53:  88000000 
INFO  @ Thu, 13 Apr 2017 13:24:54:  89000000 
INFO  @ Thu, 13 Apr 2017 13:24:56:  90000000 
INFO  @ Thu, 13 Apr 2017 13:24:57:  91000000 
INFO  @ Thu, 13 Apr 2017 13:24:59:  92000000 
INFO  @ Thu, 13 Apr 2017 13:25:00:  93000000 
INFO  @ Thu, 13 Apr 2017 13:25:02:  94000000 
INFO  @ Thu, 13 Apr 2017 13:25:03:  95000000 
INFO  @ Thu, 13 Apr 2017 13:25:05:  96000000 
INFO  @ Thu, 13 Apr 2017 13:25:07:  97000000 
INFO  @ Thu, 13 Apr 2017 13:25:08:  98000000 
INFO  @ Thu, 13 Apr 2017 13:25:10:  99000000 
INFO  @ Thu, 13 Apr 2017 13:25:11:  100000000 
INFO  @ Thu, 13 Apr 2017 13:25:13:  101000000 
INFO  @ Thu, 13 Apr 2017 13:25:14:  102000000 
INFO  @ Thu, 13 Apr 2017 13:25:16:  103000000 
INFO  @ Thu, 13 Apr 2017 13:25:17:  104000000 
INFO  @ Thu, 13 Apr 2017 13:25:19:  105000000 
INFO  @ Thu, 13 Apr 2017 13:25:21:  106000000 
INFO  @ Thu, 13 Apr 2017 13:25:22:  107000000 
INFO  @ Thu, 13 Apr 2017 13:25:24:  108000000 
INFO  @ Thu, 13 Apr 2017 13:25:25:  109000000 
INFO  @ Thu, 13 Apr 2017 13:25:35: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 13:25:37:  1000000 
INFO  @ Thu, 13 Apr 2017 13:25:38:  2000000 
INFO  @ Thu, 13 Apr 2017 13:25:39:  3000000 
INFO  @ Thu, 13 Apr 2017 13:25:41:  4000000 
INFO  @ Thu, 13 Apr 2017 13:25:43:  5000000 
INFO  @ Thu, 13 Apr 2017 13:25:44:  6000000 
INFO  @ Thu, 13 Apr 2017 13:25:45:  7000000 
INFO  @ Thu, 13 Apr 2017 13:25:47:  8000000 
INFO  @ Thu, 13 Apr 2017 13:25:48:  9000000 
INFO  @ Thu, 13 Apr 2017 13:25:50:  10000000 
INFO  @ Thu, 13 Apr 2017 13:25:52:  11000000 
INFO  @ Thu, 13 Apr 2017 13:25:53:  12000000 
INFO  @ Thu, 13 Apr 2017 13:25:55:  13000000 
INFO  @ Thu, 13 Apr 2017 13:25:56:  14000000 
INFO  @ Thu, 13 Apr 2017 13:25:58:  15000000 
INFO  @ Thu, 13 Apr 2017 13:25:59:  16000000 
INFO  @ Thu, 13 Apr 2017 13:26:01:  17000000 
INFO  @ Thu, 13 Apr 2017 13:26:02:  18000000 
INFO  @ Thu, 13 Apr 2017 13:26:04:  19000000 
INFO  @ Thu, 13 Apr 2017 13:26:05:  20000000 
INFO  @ Thu, 13 Apr 2017 13:26:07:  21000000 
INFO  @ Thu, 13 Apr 2017 13:26:08:  22000000 
INFO  @ Thu, 13 Apr 2017 13:26:10:  23000000 
INFO  @ Thu, 13 Apr 2017 13:26:11:  24000000 
INFO  @ Thu, 13 Apr 2017 13:26:13:  25000000 
INFO  @ Thu, 13 Apr 2017 13:26:14:  26000000 
INFO  @ Thu, 13 Apr 2017 13:26:15:  27000000 
INFO  @ Thu, 13 Apr 2017 13:26:17:  28000000 
INFO  @ Thu, 13 Apr 2017 13:26:18:  29000000 
INFO  @ Thu, 13 Apr 2017 13:26:20:  30000000 
INFO  @ Thu, 13 Apr 2017 13:26:21:  31000000 
INFO  @ Thu, 13 Apr 2017 13:26:23:  32000000 
INFO  @ Thu, 13 Apr 2017 13:26:24:  33000000 
INFO  @ Thu, 13 Apr 2017 13:26:25:  34000000 
INFO  @ Thu, 13 Apr 2017 13:26:27:  35000000 
INFO  @ Thu, 13 Apr 2017 13:26:28:  36000000 
INFO  @ Thu, 13 Apr 2017 13:26:30:  37000000 
INFO  @ Thu, 13 Apr 2017 13:26:31:  38000000 
INFO  @ Thu, 13 Apr 2017 13:26:33:  39000000 
INFO  @ Thu, 13 Apr 2017 13:26:34:  40000000 
INFO  @ Thu, 13 Apr 2017 13:26:36:  41000000 
INFO  @ Thu, 13 Apr 2017 13:26:37:  42000000 
INFO  @ Thu, 13 Apr 2017 13:26:39:  43000000 
INFO  @ Thu, 13 Apr 2017 13:26:40:  44000000 
INFO  @ Thu, 13 Apr 2017 13:26:41:  45000000 
INFO  @ Thu, 13 Apr 2017 13:26:43:  46000000 
INFO  @ Thu, 13 Apr 2017 13:26:44:  47000000 
INFO  @ Thu, 13 Apr 2017 13:26:46:  48000000 
INFO  @ Thu, 13 Apr 2017 13:26:47:  49000000 
INFO  @ Thu, 13 Apr 2017 13:26:49:  50000000 
INFO  @ Thu, 13 Apr 2017 13:26:50:  51000000 
INFO  @ Thu, 13 Apr 2017 13:26:52:  52000000 
INFO  @ Thu, 13 Apr 2017 13:26:53:  53000000 
INFO  @ Thu, 13 Apr 2017 13:26:55:  54000000 
INFO  @ Thu, 13 Apr 2017 13:26:56:  55000000 
INFO  @ Thu, 13 Apr 2017 13:26:58:  56000000 
INFO  @ Thu, 13 Apr 2017 13:26:59:  57000000 
INFO  @ Thu, 13 Apr 2017 13:27:01:  58000000 
INFO  @ Thu, 13 Apr 2017 13:27:02:  59000000 
INFO  @ Thu, 13 Apr 2017 13:27:04:  60000000 
INFO  @ Thu, 13 Apr 2017 13:27:05:  61000000 
INFO  @ Thu, 13 Apr 2017 13:27:07:  62000000 
INFO  @ Thu, 13 Apr 2017 13:27:09:  63000000 
INFO  @ Thu, 13 Apr 2017 13:27:10:  64000000 
INFO  @ Thu, 13 Apr 2017 13:27:11:  65000000 
INFO  @ Thu, 13 Apr 2017 13:27:13:  66000000 
INFO  @ Thu, 13 Apr 2017 13:27:14:  67000000 
INFO  @ Thu, 13 Apr 2017 13:27:16:  68000000 
INFO  @ Thu, 13 Apr 2017 13:27:17:  69000000 
INFO  @ Thu, 13 Apr 2017 13:27:19:  70000000 
INFO  @ Thu, 13 Apr 2017 13:27:20:  71000000 
INFO  @ Thu, 13 Apr 2017 13:27:22:  72000000 
INFO  @ Thu, 13 Apr 2017 13:27:24:  73000000 
INFO  @ Thu, 13 Apr 2017 13:27:25:  74000000 
INFO  @ Thu, 13 Apr 2017 13:27:27:  75000000 
INFO  @ Thu, 13 Apr 2017 13:27:28:  76000000 
INFO  @ Thu, 13 Apr 2017 13:27:30:  77000000 
INFO  @ Thu, 13 Apr 2017 13:27:31:  78000000 
INFO  @ Thu, 13 Apr 2017 13:27:33:  79000000 
INFO  @ Thu, 13 Apr 2017 13:27:34:  80000000 
INFO  @ Thu, 13 Apr 2017 13:27:36:  81000000 
INFO  @ Thu, 13 Apr 2017 13:27:37:  82000000 
INFO  @ Thu, 13 Apr 2017 13:27:39:  83000000 
INFO  @ Thu, 13 Apr 2017 13:27:40:  84000000 
INFO  @ Thu, 13 Apr 2017 13:27:42:  85000000 
INFO  @ Thu, 13 Apr 2017 13:27:43:  86000000 
INFO  @ Thu, 13 Apr 2017 13:27:44:  87000000 
INFO  @ Thu, 13 Apr 2017 13:27:46:  88000000 
INFO  @ Thu, 13 Apr 2017 13:27:47:  89000000 
INFO  @ Thu, 13 Apr 2017 13:27:49:  90000000 
INFO  @ Thu, 13 Apr 2017 13:27:51:  91000000 
INFO  @ Thu, 13 Apr 2017 13:27:52:  92000000 
INFO  @ Thu, 13 Apr 2017 13:27:53:  93000000 
INFO  @ Thu, 13 Apr 2017 13:27:55:  94000000 
INFO  @ Thu, 13 Apr 2017 13:27:56:  95000000 
INFO  @ Thu, 13 Apr 2017 13:27:58:  96000000 
INFO  @ Thu, 13 Apr 2017 13:27:59:  97000000 
INFO  @ Thu, 13 Apr 2017 13:28:01:  98000000 
INFO  @ Thu, 13 Apr 2017 13:28:02:  99000000 
INFO  @ Thu, 13 Apr 2017 13:28:03: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 13:28:03: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 13:28:03: #1  total tags in treatment: 109867658 
INFO  @ Thu, 13 Apr 2017 13:28:03: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 13:28:03: #1 finished! 
INFO  @ Thu, 13 Apr 2017 13:28:03: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 13:28:03: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 13:28:03: #2 Use 238 as fragment length 
INFO  @ Thu, 13 Apr 2017 13:28:03: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 13:28:03: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 13:28:03: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 13:36:25: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 13:36:25: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 13:36:25: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 13:36:25: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 13:36:25: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 13:48:29: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 13:48:33: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 13:48:35: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 13:48:35: Done! 

 
 		 

    
  
 
  Num   4  
 
  ID   task.callpeak_macs2.macs2_n_s_rep1.line_66.id_13  
 
  Name   macs2 n/s rep1 
 
  Thread   thread_Root  
 
  PID   46815  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 13:22:18  
 
  End   2017-04-13 15:35:25  
 
  Elapsed   02:13:07  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/signal/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/signal/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw
  
 
  Dependencies     
 
 		  
 
# SYS command. line 68

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 69

 export LC_COLLATE=C

# SYS command. line 74

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 235 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 84

 if [[ true == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.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 94

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1 -o "ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/signal/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.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 113

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1 -o "ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/signal/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 126

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
29025 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 13:22:31: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 235 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.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  @ Thu, 13 Apr 2017 13:22:31: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 13:22:31: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 13:22:33:  1000000 
INFO  @ Thu, 13 Apr 2017 13:22:34:  2000000 
INFO  @ Thu, 13 Apr 2017 13:22:36:  3000000 
INFO  @ Thu, 13 Apr 2017 13:22:38:  4000000 
INFO  @ Thu, 13 Apr 2017 13:22:39:  5000000 
INFO  @ Thu, 13 Apr 2017 13:22:41:  6000000 
INFO  @ Thu, 13 Apr 2017 13:22:42:  7000000 
INFO  @ Thu, 13 Apr 2017 13:22:44:  8000000 
INFO  @ Thu, 13 Apr 2017 13:22:46:  9000000 
INFO  @ Thu, 13 Apr 2017 13:22:48:  10000000 
INFO  @ Thu, 13 Apr 2017 13:22:49:  11000000 
INFO  @ Thu, 13 Apr 2017 13:22:51:  12000000 
INFO  @ Thu, 13 Apr 2017 13:22:52:  13000000 
INFO  @ Thu, 13 Apr 2017 13:22:54:  14000000 
INFO  @ Thu, 13 Apr 2017 13:22:56:  15000000 
INFO  @ Thu, 13 Apr 2017 13:22:57:  16000000 
INFO  @ Thu, 13 Apr 2017 13:22:59:  17000000 
INFO  @ Thu, 13 Apr 2017 13:23:01:  18000000 
INFO  @ Thu, 13 Apr 2017 13:23:02:  19000000 
INFO  @ Thu, 13 Apr 2017 13:23:04:  20000000 
INFO  @ Thu, 13 Apr 2017 13:23:05:  21000000 
INFO  @ Thu, 13 Apr 2017 13:23:07:  22000000 
INFO  @ Thu, 13 Apr 2017 13:23:09:  23000000 
INFO  @ Thu, 13 Apr 2017 13:23:10:  24000000 
INFO  @ Thu, 13 Apr 2017 13:23:12:  25000000 
INFO  @ Thu, 13 Apr 2017 13:23:14:  26000000 
INFO  @ Thu, 13 Apr 2017 13:23:16:  27000000 
INFO  @ Thu, 13 Apr 2017 13:23:18:  28000000 
INFO  @ Thu, 13 Apr 2017 13:23:20:  29000000 
INFO  @ Thu, 13 Apr 2017 13:23:22:  30000000 
INFO  @ Thu, 13 Apr 2017 13:23:23:  31000000 
INFO  @ Thu, 13 Apr 2017 13:23:25:  32000000 
INFO  @ Thu, 13 Apr 2017 13:23:26:  33000000 
INFO  @ Thu, 13 Apr 2017 13:23:28:  34000000 
INFO  @ Thu, 13 Apr 2017 13:23:30:  35000000 
INFO  @ Thu, 13 Apr 2017 13:23:32:  36000000 
INFO  @ Thu, 13 Apr 2017 13:23:34:  37000000 
INFO  @ Thu, 13 Apr 2017 13:23:35:  38000000 
INFO  @ Thu, 13 Apr 2017 13:23:37:  39000000 
INFO  @ Thu, 13 Apr 2017 13:23:38:  40000000 
INFO  @ Thu, 13 Apr 2017 13:23:40:  41000000 
INFO  @ Thu, 13 Apr 2017 13:23:42:  42000000 
INFO  @ Thu, 13 Apr 2017 13:23:44:  43000000 
INFO  @ Thu, 13 Apr 2017 13:23:46:  44000000 
INFO  @ Thu, 13 Apr 2017 13:23:47:  45000000 
INFO  @ Thu, 13 Apr 2017 13:23:49:  46000000 
INFO  @ Thu, 13 Apr 2017 13:23:50:  47000000 
INFO  @ Thu, 13 Apr 2017 13:23:52:  48000000 
INFO  @ Thu, 13 Apr 2017 13:23:54:  49000000 
INFO  @ Thu, 13 Apr 2017 13:23:55:  50000000 
INFO  @ Thu, 13 Apr 2017 13:23:57:  51000000 
INFO  @ Thu, 13 Apr 2017 13:23:59:  52000000 
INFO  @ Thu, 13 Apr 2017 13:24:01:  53000000 
INFO  @ Thu, 13 Apr 2017 13:24:03:  54000000 
INFO  @ Thu, 13 Apr 2017 13:24:04:  55000000 
INFO  @ Thu, 13 Apr 2017 13:24:06:  56000000 
INFO  @ Thu, 13 Apr 2017 13:24:08:  57000000 
INFO  @ Thu, 13 Apr 2017 13:24:09:  58000000 
INFO  @ Thu, 13 Apr 2017 13:24:11:  59000000 
INFO  @ Thu, 13 Apr 2017 13:24:12:  60000000 
INFO  @ Thu, 13 Apr 2017 13:24:14:  61000000 
INFO  @ Thu, 13 Apr 2017 13:24:16:  62000000 
INFO  @ Thu, 13 Apr 2017 13:24:18:  63000000 
INFO  @ Thu, 13 Apr 2017 13:24:20:  64000000 
INFO  @ Thu, 13 Apr 2017 13:24:22:  65000000 
INFO  @ Thu, 13 Apr 2017 13:24:24:  66000000 
INFO  @ Thu, 13 Apr 2017 13:24:26:  67000000 
INFO  @ Thu, 13 Apr 2017 13:24:27:  68000000 
INFO  @ Thu, 13 Apr 2017 13:24:29:  69000000 
INFO  @ Thu, 13 Apr 2017 13:24:31:  70000000 
INFO  @ Thu, 13 Apr 2017 13:24:33:  71000000 
INFO  @ Thu, 13 Apr 2017 13:24:34:  72000000 
INFO  @ Thu, 13 Apr 2017 13:24:36:  73000000 
INFO  @ Thu, 13 Apr 2017 13:24:38:  74000000 
INFO  @ Thu, 13 Apr 2017 13:24:40:  75000000 
INFO  @ Thu, 13 Apr 2017 13:24:41:  76000000 
INFO  @ Thu, 13 Apr 2017 13:24:43:  77000000 
INFO  @ Thu, 13 Apr 2017 13:24:44:  78000000 
INFO  @ Thu, 13 Apr 2017 13:24:46:  79000000 
INFO  @ Thu, 13 Apr 2017 13:24:48:  80000000 
INFO  @ Thu, 13 Apr 2017 13:24:49:  81000000 
INFO  @ Thu, 13 Apr 2017 13:24:51:  82000000 
INFO  @ Thu, 13 Apr 2017 13:24:53:  83000000 
INFO  @ Thu, 13 Apr 2017 13:24:55:  84000000 
INFO  @ Thu, 13 Apr 2017 13:24:56:  85000000 
INFO  @ Thu, 13 Apr 2017 13:24:58:  86000000 
INFO  @ Thu, 13 Apr 2017 13:25:00:  87000000 
INFO  @ Thu, 13 Apr 2017 13:25:02:  88000000 
INFO  @ Thu, 13 Apr 2017 13:25:04:  89000000 
INFO  @ Thu, 13 Apr 2017 13:25:05:  90000000 
INFO  @ Thu, 13 Apr 2017 13:25:07:  91000000 
INFO  @ Thu, 13 Apr 2017 13:25:09:  92000000 
INFO  @ Thu, 13 Apr 2017 13:25:11:  93000000 
INFO  @ Thu, 13 Apr 2017 13:25:13:  94000000 
INFO  @ Thu, 13 Apr 2017 13:25:14:  95000000 
INFO  @ Thu, 13 Apr 2017 13:25:16:  96000000 
INFO  @ Thu, 13 Apr 2017 13:25:17:  97000000 
INFO  @ Thu, 13 Apr 2017 13:25:19:  98000000 
INFO  @ Thu, 13 Apr 2017 13:25:21:  99000000 
INFO  @ Thu, 13 Apr 2017 13:25:23:  100000000 
INFO  @ Thu, 13 Apr 2017 13:25:24:  101000000 
INFO  @ Thu, 13 Apr 2017 13:25:26:  102000000 
INFO  @ Thu, 13 Apr 2017 13:25:27:  103000000 
INFO  @ Thu, 13 Apr 2017 13:25:29:  104000000 
INFO  @ Thu, 13 Apr 2017 13:25:31:  105000000 
INFO  @ Thu, 13 Apr 2017 13:25:32:  106000000 
INFO  @ Thu, 13 Apr 2017 13:25:34:  107000000 
INFO  @ Thu, 13 Apr 2017 13:25:36:  108000000 
INFO  @ Thu, 13 Apr 2017 13:25:37:  109000000 
INFO  @ Thu, 13 Apr 2017 13:25:39:  110000000 
INFO  @ Thu, 13 Apr 2017 13:25:40:  111000000 
INFO  @ Thu, 13 Apr 2017 13:25:42:  112000000 
INFO  @ Thu, 13 Apr 2017 13:25:44:  113000000 
INFO  @ Thu, 13 Apr 2017 13:25:45:  114000000 
INFO  @ Thu, 13 Apr 2017 13:25:47:  115000000 
INFO  @ Thu, 13 Apr 2017 13:25:49:  116000000 
INFO  @ Thu, 13 Apr 2017 13:25:50:  117000000 
INFO  @ Thu, 13 Apr 2017 13:25:52:  118000000 
INFO  @ Thu, 13 Apr 2017 13:25:54:  119000000 
INFO  @ Thu, 13 Apr 2017 13:25:55:  120000000 
INFO  @ Thu, 13 Apr 2017 13:25:57:  121000000 
INFO  @ Thu, 13 Apr 2017 13:25:58:  122000000 
INFO  @ Thu, 13 Apr 2017 13:26:00:  123000000 
INFO  @ Thu, 13 Apr 2017 13:26:02:  124000000 
INFO  @ Thu, 13 Apr 2017 13:26:03:  125000000 
INFO  @ Thu, 13 Apr 2017 13:26:05:  126000000 
INFO  @ Thu, 13 Apr 2017 13:26:07:  127000000 
INFO  @ Thu, 13 Apr 2017 13:26:17: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 13:26:19:  1000000 
INFO  @ Thu, 13 Apr 2017 13:26:21:  2000000 
INFO  @ Thu, 13 Apr 2017 13:26:22:  3000000 
INFO  @ Thu, 13 Apr 2017 13:26:23:  4000000 
INFO  @ Thu, 13 Apr 2017 13:26:25:  5000000 
INFO  @ Thu, 13 Apr 2017 13:26:26:  6000000 
INFO  @ Thu, 13 Apr 2017 13:26:28:  7000000 
INFO  @ Thu, 13 Apr 2017 13:26:30:  8000000 
INFO  @ Thu, 13 Apr 2017 13:26:32:  9000000 
INFO  @ Thu, 13 Apr 2017 13:26:33:  10000000 
INFO  @ Thu, 13 Apr 2017 13:26:34:  11000000 
INFO  @ Thu, 13 Apr 2017 13:26:36:  12000000 
INFO  @ Thu, 13 Apr 2017 13:26:37:  13000000 
INFO  @ Thu, 13 Apr 2017 13:26:39:  14000000 
INFO  @ Thu, 13 Apr 2017 13:26:40:  15000000 
INFO  @ Thu, 13 Apr 2017 13:26:42:  16000000 
INFO  @ Thu, 13 Apr 2017 13:26:43:  17000000 
INFO  @ Thu, 13 Apr 2017 13:26:45:  18000000 
INFO  @ Thu, 13 Apr 2017 13:26:46:  19000000 
INFO  @ Thu, 13 Apr 2017 13:26:47:  20000000 
INFO  @ Thu, 13 Apr 2017 13:26:49:  21000000 
INFO  @ Thu, 13 Apr 2017 13:26:50:  22000000 
INFO  @ Thu, 13 Apr 2017 13:26:52:  23000000 
INFO  @ Thu, 13 Apr 2017 13:26:53:  24000000 
INFO  @ Thu, 13 Apr 2017 13:26:54:  25000000 
INFO  @ Thu, 13 Apr 2017 13:26:56:  26000000 
INFO  @ Thu, 13 Apr 2017 13:26:57:  27000000 
INFO  @ Thu, 13 Apr 2017 13:26:59:  28000000 
INFO  @ Thu, 13 Apr 2017 13:27:00:  29000000 
INFO  @ Thu, 13 Apr 2017 13:27:02:  30000000 
INFO  @ Thu, 13 Apr 2017 13:27:03:  31000000 
INFO  @ Thu, 13 Apr 2017 13:27:05:  32000000 
INFO  @ Thu, 13 Apr 2017 13:27:07:  33000000 
INFO  @ Thu, 13 Apr 2017 13:27:08:  34000000 
INFO  @ Thu, 13 Apr 2017 13:27:09:  35000000 
INFO  @ Thu, 13 Apr 2017 13:27:11:  36000000 
INFO  @ Thu, 13 Apr 2017 13:27:12:  37000000 
INFO  @ Thu, 13 Apr 2017 13:27:14:  38000000 
INFO  @ Thu, 13 Apr 2017 13:27:15:  39000000 
INFO  @ Thu, 13 Apr 2017 13:27:17:  40000000 
INFO  @ Thu, 13 Apr 2017 13:27:18:  41000000 
INFO  @ Thu, 13 Apr 2017 13:27:20:  42000000 
INFO  @ Thu, 13 Apr 2017 13:27:21:  43000000 
INFO  @ Thu, 13 Apr 2017 13:27:23:  44000000 
INFO  @ Thu, 13 Apr 2017 13:27:24:  45000000 
INFO  @ Thu, 13 Apr 2017 13:27:26:  46000000 
INFO  @ Thu, 13 Apr 2017 13:27:27:  47000000 
INFO  @ Thu, 13 Apr 2017 13:27:29:  48000000 
INFO  @ Thu, 13 Apr 2017 13:27:30:  49000000 
INFO  @ Thu, 13 Apr 2017 13:27:31:  50000000 
INFO  @ Thu, 13 Apr 2017 13:27:33:  51000000 
INFO  @ Thu, 13 Apr 2017 13:27:34:  52000000 
INFO  @ Thu, 13 Apr 2017 13:27:36:  53000000 
INFO  @ Thu, 13 Apr 2017 13:27:37:  54000000 
INFO  @ Thu, 13 Apr 2017 13:27:38:  55000000 
INFO  @ Thu, 13 Apr 2017 13:27:40:  56000000 
INFO  @ Thu, 13 Apr 2017 13:27:41:  57000000 
INFO  @ Thu, 13 Apr 2017 13:27:43:  58000000 
INFO  @ Thu, 13 Apr 2017 13:27:44:  59000000 
INFO  @ Thu, 13 Apr 2017 13:27:46:  60000000 
INFO  @ Thu, 13 Apr 2017 13:27:47:  61000000 
INFO  @ Thu, 13 Apr 2017 13:27:49:  62000000 
INFO  @ Thu, 13 Apr 2017 13:27:51:  63000000 
INFO  @ Thu, 13 Apr 2017 13:27:53:  64000000 
INFO  @ Thu, 13 Apr 2017 13:27:54:  65000000 
INFO  @ Thu, 13 Apr 2017 13:27:55:  66000000 
INFO  @ Thu, 13 Apr 2017 13:27:57:  67000000 
INFO  @ Thu, 13 Apr 2017 13:27:58:  68000000 
INFO  @ Thu, 13 Apr 2017 13:28:00:  69000000 
INFO  @ Thu, 13 Apr 2017 13:28:01:  70000000 
INFO  @ Thu, 13 Apr 2017 13:28:03:  71000000 
INFO  @ Thu, 13 Apr 2017 13:28:04:  72000000 
INFO  @ Thu, 13 Apr 2017 13:28:06:  73000000 
INFO  @ Thu, 13 Apr 2017 13:28:07:  74000000 
INFO  @ Thu, 13 Apr 2017 13:28:09:  75000000 
INFO  @ Thu, 13 Apr 2017 13:28:10:  76000000 
INFO  @ Thu, 13 Apr 2017 13:28:11:  77000000 
INFO  @ Thu, 13 Apr 2017 13:28:13:  78000000 
INFO  @ Thu, 13 Apr 2017 13:28:14:  79000000 
INFO  @ Thu, 13 Apr 2017 13:28:16:  80000000 
INFO  @ Thu, 13 Apr 2017 13:28:18:  81000000 
INFO  @ Thu, 13 Apr 2017 13:28:20:  82000000 
INFO  @ Thu, 13 Apr 2017 13:28:21:  83000000 
INFO  @ Thu, 13 Apr 2017 13:28:23:  84000000 
INFO  @ Thu, 13 Apr 2017 13:28:24:  85000000 
INFO  @ Thu, 13 Apr 2017 13:28:26:  86000000 
INFO  @ Thu, 13 Apr 2017 13:28:27:  87000000 
INFO  @ Thu, 13 Apr 2017 13:28:29:  88000000 
INFO  @ Thu, 13 Apr 2017 13:28:31:  89000000 
INFO  @ Thu, 13 Apr 2017 13:28:33:  90000000 
INFO  @ Thu, 13 Apr 2017 13:28:34:  91000000 
INFO  @ Thu, 13 Apr 2017 13:28:36:  92000000 
INFO  @ Thu, 13 Apr 2017 13:28:37:  93000000 
INFO  @ Thu, 13 Apr 2017 13:28:39:  94000000 
INFO  @ Thu, 13 Apr 2017 13:28:40:  95000000 
INFO  @ Thu, 13 Apr 2017 13:28:42:  96000000 
INFO  @ Thu, 13 Apr 2017 13:28:44:  97000000 
INFO  @ Thu, 13 Apr 2017 13:28:45:  98000000 
INFO  @ Thu, 13 Apr 2017 13:28:46:  99000000 
INFO  @ Thu, 13 Apr 2017 13:28:48: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 13:28:48: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 13:28:48: #1  total tags in treatment: 127505544 
INFO  @ Thu, 13 Apr 2017 13:28:48: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 13:28:48: #1 finished! 
INFO  @ Thu, 13 Apr 2017 13:28:48: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 13:28:48: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 13:28:48: #2 Use 235 as fragment length 
INFO  @ Thu, 13 Apr 2017 13:28:48: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 13:28:48: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 13:28:48: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 13:36:22: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 13:36:22: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 13:36:22: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 13:36:22: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 13:36:22: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 13:50:39: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 13:50:39: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 13:50:39: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 13:50:39: Done! 
INFO  @ Thu, 13 Apr 2017 13:50:41: Read and build treatment bedGraph... 
INFO  @ Thu, 13 Apr 2017 13:54:09: Read and build control bedGraph... 
INFO  @ Thu, 13 Apr 2017 13:57:03: Build scoreTrackII... 
INFO  @ Thu, 13 Apr 2017 13:58:43: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Thu, 13 Apr 2017 14:11:32: Write bedGraph of scores... 
INFO  @ Thu, 13 Apr 2017 14:22:14: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_FE.bdg'! 
INFO  @ Thu, 13 Apr 2017 14:45:02: Read and build treatment bedGraph... 
INFO  @ Thu, 13 Apr 2017 14:48:47: Read and build control bedGraph... 
INFO  @ Thu, 13 Apr 2017 14:51:24: Build scoreTrackII... 
INFO  @ Thu, 13 Apr 2017 14:53:15: Values in your input bedGraph files will be multiplied by 99.493262 ... 
INFO  @ Thu, 13 Apr 2017 15:06:25: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Thu, 13 Apr 2017 15:09:50: Write bedGraph of scores... 
INFO  @ Thu, 13 Apr 2017 15:17:20: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_ppois.bdg'! 

 
 		 

    
  
 
  Num   5  
 
  ID   task.callpeak_macs2.macs2_n_s_rep1_pr1.line_66.id_14  
 
  Name   macs2 n/s rep1-pr1 
 
  Thread   thread_Root  
 
  PID   46816  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 13:22:19  
 
  End   2017-04-13 13:47:56  
 
  Elapsed   00:25:37  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 68

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 69

 export LC_COLLATE=C

# SYS command. line 74

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 235 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 84

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.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 94

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1 -o "ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.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 113

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1 -o "ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 126

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
14530 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 13:22:32: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 235 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.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  @ Thu, 13 Apr 2017 13:22:32: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 13:22:32: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 13:22:34:  1000000 
INFO  @ Thu, 13 Apr 2017 13:22:36:  2000000 
INFO  @ Thu, 13 Apr 2017 13:22:38:  3000000 
INFO  @ Thu, 13 Apr 2017 13:22:40:  4000000 
INFO  @ Thu, 13 Apr 2017 13:22:42:  5000000 
INFO  @ Thu, 13 Apr 2017 13:22:44:  6000000 
INFO  @ Thu, 13 Apr 2017 13:22:46:  7000000 
INFO  @ Thu, 13 Apr 2017 13:22:48:  8000000 
INFO  @ Thu, 13 Apr 2017 13:22:50:  9000000 
INFO  @ Thu, 13 Apr 2017 13:22:52:  10000000 
INFO  @ Thu, 13 Apr 2017 13:22:54:  11000000 
INFO  @ Thu, 13 Apr 2017 13:22:55:  12000000 
INFO  @ Thu, 13 Apr 2017 13:22:57:  13000000 
INFO  @ Thu, 13 Apr 2017 13:22:59:  14000000 
INFO  @ Thu, 13 Apr 2017 13:23:01:  15000000 
INFO  @ Thu, 13 Apr 2017 13:23:03:  16000000 
INFO  @ Thu, 13 Apr 2017 13:23:05:  17000000 
INFO  @ Thu, 13 Apr 2017 13:23:07:  18000000 
INFO  @ Thu, 13 Apr 2017 13:23:09:  19000000 
INFO  @ Thu, 13 Apr 2017 13:23:11:  20000000 
INFO  @ Thu, 13 Apr 2017 13:23:13:  21000000 
INFO  @ Thu, 13 Apr 2017 13:23:15:  22000000 
INFO  @ Thu, 13 Apr 2017 13:23:17:  23000000 
INFO  @ Thu, 13 Apr 2017 13:23:19:  24000000 
INFO  @ Thu, 13 Apr 2017 13:23:21:  25000000 
INFO  @ Thu, 13 Apr 2017 13:23:23:  26000000 
INFO  @ Thu, 13 Apr 2017 13:23:25:  27000000 
INFO  @ Thu, 13 Apr 2017 13:23:27:  28000000 
INFO  @ Thu, 13 Apr 2017 13:23:29:  29000000 
INFO  @ Thu, 13 Apr 2017 13:23:31:  30000000 
INFO  @ Thu, 13 Apr 2017 13:23:33:  31000000 
INFO  @ Thu, 13 Apr 2017 13:23:35:  32000000 
INFO  @ Thu, 13 Apr 2017 13:23:37:  33000000 
INFO  @ Thu, 13 Apr 2017 13:23:39:  34000000 
INFO  @ Thu, 13 Apr 2017 13:23:41:  35000000 
INFO  @ Thu, 13 Apr 2017 13:23:43:  36000000 
INFO  @ Thu, 13 Apr 2017 13:23:45:  37000000 
INFO  @ Thu, 13 Apr 2017 13:23:47:  38000000 
INFO  @ Thu, 13 Apr 2017 13:23:49:  39000000 
INFO  @ Thu, 13 Apr 2017 13:23:50:  40000000 
INFO  @ Thu, 13 Apr 2017 13:23:52:  41000000 
INFO  @ Thu, 13 Apr 2017 13:23:54:  42000000 
INFO  @ Thu, 13 Apr 2017 13:23:56:  43000000 
INFO  @ Thu, 13 Apr 2017 13:23:58:  44000000 
INFO  @ Thu, 13 Apr 2017 13:24:00:  45000000 
INFO  @ Thu, 13 Apr 2017 13:24:02:  46000000 
INFO  @ Thu, 13 Apr 2017 13:24:04:  47000000 
INFO  @ Thu, 13 Apr 2017 13:24:06:  48000000 
INFO  @ Thu, 13 Apr 2017 13:24:08:  49000000 
INFO  @ Thu, 13 Apr 2017 13:24:10:  50000000 
INFO  @ Thu, 13 Apr 2017 13:24:12:  51000000 
INFO  @ Thu, 13 Apr 2017 13:24:14:  52000000 
INFO  @ Thu, 13 Apr 2017 13:24:16:  53000000 
INFO  @ Thu, 13 Apr 2017 13:24:18:  54000000 
INFO  @ Thu, 13 Apr 2017 13:24:20:  55000000 
INFO  @ Thu, 13 Apr 2017 13:24:22:  56000000 
INFO  @ Thu, 13 Apr 2017 13:24:24:  57000000 
INFO  @ Thu, 13 Apr 2017 13:24:26:  58000000 
INFO  @ Thu, 13 Apr 2017 13:24:28:  59000000 
INFO  @ Thu, 13 Apr 2017 13:24:30:  60000000 
INFO  @ Thu, 13 Apr 2017 13:24:32:  61000000 
INFO  @ Thu, 13 Apr 2017 13:24:34:  62000000 
INFO  @ Thu, 13 Apr 2017 13:24:36:  63000000 
INFO  @ Thu, 13 Apr 2017 13:24:42: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 13:24:44:  1000000 
INFO  @ Thu, 13 Apr 2017 13:24:46:  2000000 
INFO  @ Thu, 13 Apr 2017 13:24:48:  3000000 
INFO  @ Thu, 13 Apr 2017 13:24:50:  4000000 
INFO  @ Thu, 13 Apr 2017 13:24:52:  5000000 
INFO  @ Thu, 13 Apr 2017 13:24:54:  6000000 
INFO  @ Thu, 13 Apr 2017 13:24:55:  7000000 
INFO  @ Thu, 13 Apr 2017 13:24:57:  8000000 
INFO  @ Thu, 13 Apr 2017 13:24:59:  9000000 
INFO  @ Thu, 13 Apr 2017 13:25:01:  10000000 
INFO  @ Thu, 13 Apr 2017 13:25:03:  11000000 
INFO  @ Thu, 13 Apr 2017 13:25:05:  12000000 
INFO  @ Thu, 13 Apr 2017 13:25:06:  13000000 
INFO  @ Thu, 13 Apr 2017 13:25:08:  14000000 
INFO  @ Thu, 13 Apr 2017 13:25:10:  15000000 
INFO  @ Thu, 13 Apr 2017 13:25:12:  16000000 
INFO  @ Thu, 13 Apr 2017 13:25:14:  17000000 
INFO  @ Thu, 13 Apr 2017 13:25:15:  18000000 
INFO  @ Thu, 13 Apr 2017 13:25:17:  19000000 
INFO  @ Thu, 13 Apr 2017 13:25:19:  20000000 
INFO  @ Thu, 13 Apr 2017 13:25:21:  21000000 
INFO  @ Thu, 13 Apr 2017 13:25:23:  22000000 
INFO  @ Thu, 13 Apr 2017 13:25:25:  23000000 
INFO  @ Thu, 13 Apr 2017 13:25:26:  24000000 
INFO  @ Thu, 13 Apr 2017 13:25:28:  25000000 
INFO  @ Thu, 13 Apr 2017 13:25:30:  26000000 
INFO  @ Thu, 13 Apr 2017 13:25:32:  27000000 
INFO  @ Thu, 13 Apr 2017 13:25:34:  28000000 
INFO  @ Thu, 13 Apr 2017 13:25:36:  29000000 
INFO  @ Thu, 13 Apr 2017 13:25:37:  30000000 
INFO  @ Thu, 13 Apr 2017 13:25:39:  31000000 
INFO  @ Thu, 13 Apr 2017 13:25:41:  32000000 
INFO  @ Thu, 13 Apr 2017 13:25:43:  33000000 
INFO  @ Thu, 13 Apr 2017 13:25:45:  34000000 
INFO  @ Thu, 13 Apr 2017 13:25:47:  35000000 
INFO  @ Thu, 13 Apr 2017 13:25:48:  36000000 
INFO  @ Thu, 13 Apr 2017 13:25:50:  37000000 
INFO  @ Thu, 13 Apr 2017 13:25:52:  38000000 
INFO  @ Thu, 13 Apr 2017 13:25:54:  39000000 
INFO  @ Thu, 13 Apr 2017 13:25:56:  40000000 
INFO  @ Thu, 13 Apr 2017 13:25:58:  41000000 
INFO  @ Thu, 13 Apr 2017 13:25:59:  42000000 
INFO  @ Thu, 13 Apr 2017 13:26:01:  43000000 
INFO  @ Thu, 13 Apr 2017 13:26:03:  44000000 
INFO  @ Thu, 13 Apr 2017 13:26:05:  45000000 
INFO  @ Thu, 13 Apr 2017 13:26:07:  46000000 
INFO  @ Thu, 13 Apr 2017 13:26:09:  47000000 
INFO  @ Thu, 13 Apr 2017 13:26:10:  48000000 
INFO  @ Thu, 13 Apr 2017 13:26:12:  49000000 
INFO  @ Thu, 13 Apr 2017 13:26:14:  50000000 
INFO  @ Thu, 13 Apr 2017 13:26:16:  51000000 
INFO  @ Thu, 13 Apr 2017 13:26:18:  52000000 
INFO  @ Thu, 13 Apr 2017 13:26:19:  53000000 
INFO  @ Thu, 13 Apr 2017 13:26:21:  54000000 
INFO  @ Thu, 13 Apr 2017 13:26:23:  55000000 
INFO  @ Thu, 13 Apr 2017 13:26:25:  56000000 
INFO  @ Thu, 13 Apr 2017 13:26:27:  57000000 
INFO  @ Thu, 13 Apr 2017 13:26:29:  58000000 
INFO  @ Thu, 13 Apr 2017 13:26:31:  59000000 
INFO  @ Thu, 13 Apr 2017 13:26:32:  60000000 
INFO  @ Thu, 13 Apr 2017 13:26:34:  61000000 
INFO  @ Thu, 13 Apr 2017 13:26:36:  62000000 
INFO  @ Thu, 13 Apr 2017 13:26:38:  63000000 
INFO  @ Thu, 13 Apr 2017 13:26:40:  64000000 
INFO  @ Thu, 13 Apr 2017 13:26:42:  65000000 
INFO  @ Thu, 13 Apr 2017 13:26:43:  66000000 
INFO  @ Thu, 13 Apr 2017 13:26:45:  67000000 
INFO  @ Thu, 13 Apr 2017 13:26:47:  68000000 
INFO  @ Thu, 13 Apr 2017 13:26:49:  69000000 
INFO  @ Thu, 13 Apr 2017 13:26:51:  70000000 
INFO  @ Thu, 13 Apr 2017 13:26:53:  71000000 
INFO  @ Thu, 13 Apr 2017 13:26:54:  72000000 
INFO  @ Thu, 13 Apr 2017 13:26:56:  73000000 
INFO  @ Thu, 13 Apr 2017 13:26:58:  74000000 
INFO  @ Thu, 13 Apr 2017 13:27:00:  75000000 
INFO  @ Thu, 13 Apr 2017 13:27:02:  76000000 
INFO  @ Thu, 13 Apr 2017 13:27:03:  77000000 
INFO  @ Thu, 13 Apr 2017 13:27:05:  78000000 
INFO  @ Thu, 13 Apr 2017 13:27:07:  79000000 
INFO  @ Thu, 13 Apr 2017 13:27:09:  80000000 
INFO  @ Thu, 13 Apr 2017 13:27:11:  81000000 
INFO  @ Thu, 13 Apr 2017 13:27:13:  82000000 
INFO  @ Thu, 13 Apr 2017 13:27:14:  83000000 
INFO  @ Thu, 13 Apr 2017 13:27:16:  84000000 
INFO  @ Thu, 13 Apr 2017 13:27:18:  85000000 
INFO  @ Thu, 13 Apr 2017 13:27:20:  86000000 
INFO  @ Thu, 13 Apr 2017 13:27:22:  87000000 
INFO  @ Thu, 13 Apr 2017 13:27:24:  88000000 
INFO  @ Thu, 13 Apr 2017 13:27:25:  89000000 
INFO  @ Thu, 13 Apr 2017 13:27:27:  90000000 
INFO  @ Thu, 13 Apr 2017 13:27:29:  91000000 
INFO  @ Thu, 13 Apr 2017 13:27:31:  92000000 
INFO  @ Thu, 13 Apr 2017 13:27:33:  93000000 
INFO  @ Thu, 13 Apr 2017 13:27:35:  94000000 
INFO  @ Thu, 13 Apr 2017 13:27:36:  95000000 
INFO  @ Thu, 13 Apr 2017 13:27:38:  96000000 
INFO  @ Thu, 13 Apr 2017 13:27:40:  97000000 
INFO  @ Thu, 13 Apr 2017 13:27:42:  98000000 
INFO  @ Thu, 13 Apr 2017 13:27:43:  99000000 
INFO  @ Thu, 13 Apr 2017 13:27:45: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 13:27:45: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 13:27:45: #1  total tags in treatment: 63752772 
INFO  @ Thu, 13 Apr 2017 13:27:45: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 13:27:45: #1 finished! 
INFO  @ Thu, 13 Apr 2017 13:27:45: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 13:27:45: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 13:27:45: #2 Use 235 as fragment length 
INFO  @ Thu, 13 Apr 2017 13:27:45: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 13:27:45: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 13:27:45: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 13:35:17: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 13:35:17: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 13:35:17: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 13:35:17: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 13:35:17: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 13:47:49: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 13:47:50: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 13:47:51: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 13:47:52: Done! 

 
 		 

    
  
 
  Num   6  
 
  ID   task.callpeak_macs2.macs2_n_s_rep1_pr2.line_66.id_15  
 
  Name   macs2 n/s rep1-pr2 
 
  Thread   thread_Root  
 
  PID   46858  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 13:47:59  
 
  End   2017-04-13 14:08:37  
 
  Elapsed   00:20:38  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 68

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 69

 export LC_COLLATE=C

# SYS command. line 74

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 235 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 84

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.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 94

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2 -o "ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.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 113

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2 -o "ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 126

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
30296 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 13:48:18: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 235 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.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  @ Thu, 13 Apr 2017 13:48:18: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 13:48:18: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 13:48:21:  1000000 
INFO  @ Thu, 13 Apr 2017 13:48:23:  2000000 
INFO  @ Thu, 13 Apr 2017 13:48:24:  3000000 
INFO  @ Thu, 13 Apr 2017 13:48:26:  4000000 
INFO  @ Thu, 13 Apr 2017 13:48:27:  5000000 
INFO  @ Thu, 13 Apr 2017 13:48:29:  6000000 
INFO  @ Thu, 13 Apr 2017 13:48:30:  7000000 
INFO  @ Thu, 13 Apr 2017 13:48:32:  8000000 
INFO  @ Thu, 13 Apr 2017 13:48:33:  9000000 
INFO  @ Thu, 13 Apr 2017 13:48:35:  10000000 
INFO  @ Thu, 13 Apr 2017 13:48:36:  11000000 
INFO  @ Thu, 13 Apr 2017 13:48:38:  12000000 
INFO  @ Thu, 13 Apr 2017 13:48:40:  13000000 
INFO  @ Thu, 13 Apr 2017 13:48:41:  14000000 
INFO  @ Thu, 13 Apr 2017 13:48:43:  15000000 
INFO  @ Thu, 13 Apr 2017 13:48:44:  16000000 
INFO  @ Thu, 13 Apr 2017 13:48:46:  17000000 
INFO  @ Thu, 13 Apr 2017 13:48:48:  18000000 
INFO  @ Thu, 13 Apr 2017 13:48:49:  19000000 
INFO  @ Thu, 13 Apr 2017 13:48:51:  20000000 
INFO  @ Thu, 13 Apr 2017 13:48:53:  21000000 
INFO  @ Thu, 13 Apr 2017 13:48:54:  22000000 
INFO  @ Thu, 13 Apr 2017 13:48:56:  23000000 
INFO  @ Thu, 13 Apr 2017 13:48:57:  24000000 
INFO  @ Thu, 13 Apr 2017 13:48:59:  25000000 
INFO  @ Thu, 13 Apr 2017 13:49:01:  26000000 
INFO  @ Thu, 13 Apr 2017 13:49:02:  27000000 
INFO  @ Thu, 13 Apr 2017 13:49:04:  28000000 
INFO  @ Thu, 13 Apr 2017 13:49:05:  29000000 
INFO  @ Thu, 13 Apr 2017 13:49:07:  30000000 
INFO  @ Thu, 13 Apr 2017 13:49:08:  31000000 
INFO  @ Thu, 13 Apr 2017 13:49:10:  32000000 
INFO  @ Thu, 13 Apr 2017 13:49:12:  33000000 
INFO  @ Thu, 13 Apr 2017 13:49:13:  34000000 
INFO  @ Thu, 13 Apr 2017 13:49:15:  35000000 
INFO  @ Thu, 13 Apr 2017 13:49:17:  36000000 
INFO  @ Thu, 13 Apr 2017 13:49:19:  37000000 
INFO  @ Thu, 13 Apr 2017 13:49:20:  38000000 
INFO  @ Thu, 13 Apr 2017 13:49:22:  39000000 
INFO  @ Thu, 13 Apr 2017 13:49:23:  40000000 
INFO  @ Thu, 13 Apr 2017 13:49:25:  41000000 
INFO  @ Thu, 13 Apr 2017 13:49:27:  42000000 
INFO  @ Thu, 13 Apr 2017 13:49:28:  43000000 
INFO  @ Thu, 13 Apr 2017 13:49:30:  44000000 
INFO  @ Thu, 13 Apr 2017 13:49:31:  45000000 
INFO  @ Thu, 13 Apr 2017 13:49:33:  46000000 
INFO  @ Thu, 13 Apr 2017 13:49:34:  47000000 
INFO  @ Thu, 13 Apr 2017 13:49:36:  48000000 
INFO  @ Thu, 13 Apr 2017 13:49:38:  49000000 
INFO  @ Thu, 13 Apr 2017 13:49:39:  50000000 
INFO  @ Thu, 13 Apr 2017 13:49:41:  51000000 
INFO  @ Thu, 13 Apr 2017 13:49:42:  52000000 
INFO  @ Thu, 13 Apr 2017 13:49:44:  53000000 
INFO  @ Thu, 13 Apr 2017 13:49:46:  54000000 
INFO  @ Thu, 13 Apr 2017 13:49:47:  55000000 
INFO  @ Thu, 13 Apr 2017 13:49:49:  56000000 
INFO  @ Thu, 13 Apr 2017 13:49:50:  57000000 
INFO  @ Thu, 13 Apr 2017 13:49:52:  58000000 
INFO  @ Thu, 13 Apr 2017 13:49:53:  59000000 
INFO  @ Thu, 13 Apr 2017 13:49:55:  60000000 
INFO  @ Thu, 13 Apr 2017 13:49:57:  61000000 
INFO  @ Thu, 13 Apr 2017 13:49:58:  62000000 
INFO  @ Thu, 13 Apr 2017 13:50:00:  63000000 
INFO  @ Thu, 13 Apr 2017 13:50:06: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 13:50:08:  1000000 
INFO  @ Thu, 13 Apr 2017 13:50:09:  2000000 
INFO  @ Thu, 13 Apr 2017 13:50:10:  3000000 
INFO  @ Thu, 13 Apr 2017 13:50:12:  4000000 
INFO  @ Thu, 13 Apr 2017 13:50:13:  5000000 
INFO  @ Thu, 13 Apr 2017 13:50:15:  6000000 
INFO  @ Thu, 13 Apr 2017 13:50:16:  7000000 
INFO  @ Thu, 13 Apr 2017 13:50:18:  8000000 
INFO  @ Thu, 13 Apr 2017 13:50:19:  9000000 
INFO  @ Thu, 13 Apr 2017 13:50:21:  10000000 
INFO  @ Thu, 13 Apr 2017 13:50:22:  11000000 
INFO  @ Thu, 13 Apr 2017 13:50:24:  12000000 
INFO  @ Thu, 13 Apr 2017 13:50:25:  13000000 
INFO  @ Thu, 13 Apr 2017 13:50:26:  14000000 
INFO  @ Thu, 13 Apr 2017 13:50:28:  15000000 
INFO  @ Thu, 13 Apr 2017 13:50:29:  16000000 
INFO  @ Thu, 13 Apr 2017 13:50:31:  17000000 
INFO  @ Thu, 13 Apr 2017 13:50:32:  18000000 
INFO  @ Thu, 13 Apr 2017 13:50:34:  19000000 
INFO  @ Thu, 13 Apr 2017 13:50:35:  20000000 
INFO  @ Thu, 13 Apr 2017 13:50:37:  21000000 
INFO  @ Thu, 13 Apr 2017 13:50:38:  22000000 
INFO  @ Thu, 13 Apr 2017 13:50:40:  23000000 
INFO  @ Thu, 13 Apr 2017 13:50:41:  24000000 
INFO  @ Thu, 13 Apr 2017 13:50:43:  25000000 
INFO  @ Thu, 13 Apr 2017 13:50:45:  26000000 
INFO  @ Thu, 13 Apr 2017 13:50:46:  27000000 
INFO  @ Thu, 13 Apr 2017 13:50:48:  28000000 
INFO  @ Thu, 13 Apr 2017 13:50:49:  29000000 
INFO  @ Thu, 13 Apr 2017 13:50:51:  30000000 
INFO  @ Thu, 13 Apr 2017 13:50:52:  31000000 
INFO  @ Thu, 13 Apr 2017 13:50:54:  32000000 
INFO  @ Thu, 13 Apr 2017 13:50:55:  33000000 
INFO  @ Thu, 13 Apr 2017 13:50:57:  34000000 
INFO  @ Thu, 13 Apr 2017 13:50:58:  35000000 
INFO  @ Thu, 13 Apr 2017 13:50:59:  36000000 
INFO  @ Thu, 13 Apr 2017 13:51:01:  37000000 
INFO  @ Thu, 13 Apr 2017 13:51:02:  38000000 
INFO  @ Thu, 13 Apr 2017 13:51:04:  39000000 
INFO  @ Thu, 13 Apr 2017 13:51:05:  40000000 
INFO  @ Thu, 13 Apr 2017 13:51:07:  41000000 
INFO  @ Thu, 13 Apr 2017 13:51:08:  42000000 
INFO  @ Thu, 13 Apr 2017 13:51:10:  43000000 
INFO  @ Thu, 13 Apr 2017 13:51:11:  44000000 
INFO  @ Thu, 13 Apr 2017 13:51:13:  45000000 
INFO  @ Thu, 13 Apr 2017 13:51:14:  46000000 
INFO  @ Thu, 13 Apr 2017 13:51:16:  47000000 
INFO  @ Thu, 13 Apr 2017 13:51:17:  48000000 
INFO  @ Thu, 13 Apr 2017 13:51:19:  49000000 
INFO  @ Thu, 13 Apr 2017 13:51:21:  50000000 
INFO  @ Thu, 13 Apr 2017 13:51:22:  51000000 
INFO  @ Thu, 13 Apr 2017 13:51:23:  52000000 
INFO  @ Thu, 13 Apr 2017 13:51:25:  53000000 
INFO  @ Thu, 13 Apr 2017 13:51:27:  54000000 
INFO  @ Thu, 13 Apr 2017 13:51:28:  55000000 
INFO  @ Thu, 13 Apr 2017 13:51:29:  56000000 
INFO  @ Thu, 13 Apr 2017 13:51:31:  57000000 
INFO  @ Thu, 13 Apr 2017 13:51:32:  58000000 
INFO  @ Thu, 13 Apr 2017 13:51:34:  59000000 
INFO  @ Thu, 13 Apr 2017 13:51:35:  60000000 
INFO  @ Thu, 13 Apr 2017 13:51:37:  61000000 
INFO  @ Thu, 13 Apr 2017 13:51:38:  62000000 
INFO  @ Thu, 13 Apr 2017 13:51:40:  63000000 
INFO  @ Thu, 13 Apr 2017 13:51:41:  64000000 
INFO  @ Thu, 13 Apr 2017 13:51:43:  65000000 
INFO  @ Thu, 13 Apr 2017 13:51:44:  66000000 
INFO  @ Thu, 13 Apr 2017 13:51:46:  67000000 
INFO  @ Thu, 13 Apr 2017 13:51:47:  68000000 
INFO  @ Thu, 13 Apr 2017 13:51:49:  69000000 
INFO  @ Thu, 13 Apr 2017 13:51:50:  70000000 
INFO  @ Thu, 13 Apr 2017 13:51:51:  71000000 
INFO  @ Thu, 13 Apr 2017 13:51:53:  72000000 
INFO  @ Thu, 13 Apr 2017 13:51:55:  73000000 
INFO  @ Thu, 13 Apr 2017 13:51:56:  74000000 
INFO  @ Thu, 13 Apr 2017 13:51:57:  75000000 
INFO  @ Thu, 13 Apr 2017 13:51:59:  76000000 
INFO  @ Thu, 13 Apr 2017 13:52:00:  77000000 
INFO  @ Thu, 13 Apr 2017 13:52:02:  78000000 
INFO  @ Thu, 13 Apr 2017 13:52:03:  79000000 
INFO  @ Thu, 13 Apr 2017 13:52:05:  80000000 
INFO  @ Thu, 13 Apr 2017 13:52:06:  81000000 
INFO  @ Thu, 13 Apr 2017 13:52:07:  82000000 
INFO  @ Thu, 13 Apr 2017 13:52:09:  83000000 
INFO  @ Thu, 13 Apr 2017 13:52:10:  84000000 
INFO  @ Thu, 13 Apr 2017 13:52:12:  85000000 
INFO  @ Thu, 13 Apr 2017 13:52:13:  86000000 
INFO  @ Thu, 13 Apr 2017 13:52:15:  87000000 
INFO  @ Thu, 13 Apr 2017 13:52:16:  88000000 
INFO  @ Thu, 13 Apr 2017 13:52:18:  89000000 
INFO  @ Thu, 13 Apr 2017 13:52:19:  90000000 
INFO  @ Thu, 13 Apr 2017 13:52:21:  91000000 
INFO  @ Thu, 13 Apr 2017 13:52:22:  92000000 
INFO  @ Thu, 13 Apr 2017 13:52:24:  93000000 
INFO  @ Thu, 13 Apr 2017 13:52:25:  94000000 
INFO  @ Thu, 13 Apr 2017 13:52:26:  95000000 
INFO  @ Thu, 13 Apr 2017 13:52:28:  96000000 
INFO  @ Thu, 13 Apr 2017 13:52:29:  97000000 
INFO  @ Thu, 13 Apr 2017 13:52:31:  98000000 
INFO  @ Thu, 13 Apr 2017 13:52:32:  99000000 
INFO  @ Thu, 13 Apr 2017 13:52:34: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 13:52:34: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 13:52:34: #1  total tags in treatment: 63752772 
INFO  @ Thu, 13 Apr 2017 13:52:34: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 13:52:34: #1 finished! 
INFO  @ Thu, 13 Apr 2017 13:52:34: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 13:52:34: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 13:52:34: #2 Use 235 as fragment length 
INFO  @ Thu, 13 Apr 2017 13:52:34: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 13:52:34: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 13:52:34: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 13:58:44: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 13:58:44: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 13:58:44: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 13:58:44: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 13:58:44: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 14:08:25: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 14:08:28: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 14:08:31: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 14:08:33: Done! 

 
 		 

    
  
 
  Num   7  
 
  ID   task.callpeak_macs2.macs2_n_s_rep2.line_66.id_16  
 
  Name   macs2 n/s rep2 
 
  Thread   thread_Root  
 
  PID   46859  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 13:48:43  
 
  End   2017-04-13 15:45:50  
 
  Elapsed   01:57:06  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/signal/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/signal/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw
  
 
  Dependencies     
 
 		  
 
# SYS command. line 68

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 69

 export LC_COLLATE=C

# SYS command. line 74

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 240 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 84

 if [[ true == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.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 94

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2 -o "ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/signal/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.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 113

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2 -o "ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/signal/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 126

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
39950 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 13:49:01: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.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/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.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  @ Thu, 13 Apr 2017 13:49:01: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 13:49:01: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 13:49:03:  1000000 
INFO  @ Thu, 13 Apr 2017 13:49:05:  2000000 
INFO  @ Thu, 13 Apr 2017 13:49:07:  3000000 
INFO  @ Thu, 13 Apr 2017 13:49:08:  4000000 
INFO  @ Thu, 13 Apr 2017 13:49:10:  5000000 
INFO  @ Thu, 13 Apr 2017 13:49:12:  6000000 
INFO  @ Thu, 13 Apr 2017 13:49:13:  7000000 
INFO  @ Thu, 13 Apr 2017 13:49:15:  8000000 
INFO  @ Thu, 13 Apr 2017 13:49:17:  9000000 
INFO  @ Thu, 13 Apr 2017 13:49:18:  10000000 
INFO  @ Thu, 13 Apr 2017 13:49:20:  11000000 
INFO  @ Thu, 13 Apr 2017 13:49:21:  12000000 
INFO  @ Thu, 13 Apr 2017 13:49:23:  13000000 
INFO  @ Thu, 13 Apr 2017 13:49:25:  14000000 
INFO  @ Thu, 13 Apr 2017 13:49:27:  15000000 
INFO  @ Thu, 13 Apr 2017 13:49:28:  16000000 
INFO  @ Thu, 13 Apr 2017 13:49:30:  17000000 
INFO  @ Thu, 13 Apr 2017 13:49:32:  18000000 
INFO  @ Thu, 13 Apr 2017 13:49:33:  19000000 
INFO  @ Thu, 13 Apr 2017 13:49:35:  20000000 
INFO  @ Thu, 13 Apr 2017 13:49:37:  21000000 
INFO  @ Thu, 13 Apr 2017 13:49:39:  22000000 
INFO  @ Thu, 13 Apr 2017 13:49:41:  23000000 
INFO  @ Thu, 13 Apr 2017 13:49:42:  24000000 
INFO  @ Thu, 13 Apr 2017 13:49:45:  25000000 
INFO  @ Thu, 13 Apr 2017 13:49:46:  26000000 
INFO  @ Thu, 13 Apr 2017 13:49:48:  27000000 
INFO  @ Thu, 13 Apr 2017 13:49:49:  28000000 
INFO  @ Thu, 13 Apr 2017 13:49:51:  29000000 
INFO  @ Thu, 13 Apr 2017 13:49:52:  30000000 
INFO  @ Thu, 13 Apr 2017 13:49:54:  31000000 
INFO  @ Thu, 13 Apr 2017 13:49:56:  32000000 
INFO  @ Thu, 13 Apr 2017 13:49:57:  33000000 
INFO  @ Thu, 13 Apr 2017 13:49:59:  34000000 
INFO  @ Thu, 13 Apr 2017 13:50:01:  35000000 
INFO  @ Thu, 13 Apr 2017 13:50:02:  36000000 
INFO  @ Thu, 13 Apr 2017 13:50:04:  37000000 
INFO  @ Thu, 13 Apr 2017 13:50:06:  38000000 
INFO  @ Thu, 13 Apr 2017 13:50:07:  39000000 
INFO  @ Thu, 13 Apr 2017 13:50:09:  40000000 
INFO  @ Thu, 13 Apr 2017 13:50:10:  41000000 
INFO  @ Thu, 13 Apr 2017 13:50:12:  42000000 
INFO  @ Thu, 13 Apr 2017 13:50:14:  43000000 
INFO  @ Thu, 13 Apr 2017 13:50:15:  44000000 
INFO  @ Thu, 13 Apr 2017 13:50:17:  45000000 
INFO  @ Thu, 13 Apr 2017 13:50:19:  46000000 
INFO  @ Thu, 13 Apr 2017 13:50:21:  47000000 
INFO  @ Thu, 13 Apr 2017 13:50:23:  48000000 
INFO  @ Thu, 13 Apr 2017 13:50:24:  49000000 
INFO  @ Thu, 13 Apr 2017 13:50:26:  50000000 
INFO  @ Thu, 13 Apr 2017 13:50:27:  51000000 
INFO  @ Thu, 13 Apr 2017 13:50:29:  52000000 
INFO  @ Thu, 13 Apr 2017 13:50:30:  53000000 
INFO  @ Thu, 13 Apr 2017 13:50:32:  54000000 
INFO  @ Thu, 13 Apr 2017 13:50:33:  55000000 
INFO  @ Thu, 13 Apr 2017 13:50:35:  56000000 
INFO  @ Thu, 13 Apr 2017 13:50:37:  57000000 
INFO  @ Thu, 13 Apr 2017 13:50:38:  58000000 
INFO  @ Thu, 13 Apr 2017 13:50:40:  59000000 
INFO  @ Thu, 13 Apr 2017 13:50:41:  60000000 
INFO  @ Thu, 13 Apr 2017 13:50:43:  61000000 
INFO  @ Thu, 13 Apr 2017 13:50:44:  62000000 
INFO  @ Thu, 13 Apr 2017 13:50:46:  63000000 
INFO  @ Thu, 13 Apr 2017 13:50:48:  64000000 
INFO  @ Thu, 13 Apr 2017 13:50:49:  65000000 
INFO  @ Thu, 13 Apr 2017 13:50:51:  66000000 
INFO  @ Thu, 13 Apr 2017 13:50:53:  67000000 
INFO  @ Thu, 13 Apr 2017 13:50:55:  68000000 
INFO  @ Thu, 13 Apr 2017 13:50:56:  69000000 
INFO  @ Thu, 13 Apr 2017 13:50:58:  70000000 
INFO  @ Thu, 13 Apr 2017 13:51:00:  71000000 
INFO  @ Thu, 13 Apr 2017 13:51:01:  72000000 
INFO  @ Thu, 13 Apr 2017 13:51:03:  73000000 
INFO  @ Thu, 13 Apr 2017 13:51:05:  74000000 
INFO  @ Thu, 13 Apr 2017 13:51:06:  75000000 
INFO  @ Thu, 13 Apr 2017 13:51:08:  76000000 
INFO  @ Thu, 13 Apr 2017 13:51:09:  77000000 
INFO  @ Thu, 13 Apr 2017 13:51:11:  78000000 
INFO  @ Thu, 13 Apr 2017 13:51:13:  79000000 
INFO  @ Thu, 13 Apr 2017 13:51:14:  80000000 
INFO  @ Thu, 13 Apr 2017 13:51:16:  81000000 
INFO  @ Thu, 13 Apr 2017 13:51:18:  82000000 
INFO  @ Thu, 13 Apr 2017 13:51:19:  83000000 
INFO  @ Thu, 13 Apr 2017 13:51:21:  84000000 
INFO  @ Thu, 13 Apr 2017 13:51:22:  85000000 
INFO  @ Thu, 13 Apr 2017 13:51:24:  86000000 
INFO  @ Thu, 13 Apr 2017 13:51:26:  87000000 
INFO  @ Thu, 13 Apr 2017 13:51:27:  88000000 
INFO  @ Thu, 13 Apr 2017 13:51:29:  89000000 
INFO  @ Thu, 13 Apr 2017 13:51:31:  90000000 
INFO  @ Thu, 13 Apr 2017 13:51:32:  91000000 
INFO  @ Thu, 13 Apr 2017 13:51:34:  92000000 
INFO  @ Thu, 13 Apr 2017 13:51:41: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 13:51:42:  1000000 
INFO  @ Thu, 13 Apr 2017 13:51:44:  2000000 
INFO  @ Thu, 13 Apr 2017 13:51:45:  3000000 
INFO  @ Thu, 13 Apr 2017 13:51:47:  4000000 
INFO  @ Thu, 13 Apr 2017 13:51:48:  5000000 
INFO  @ Thu, 13 Apr 2017 13:51:49:  6000000 
INFO  @ Thu, 13 Apr 2017 13:51:51:  7000000 
INFO  @ Thu, 13 Apr 2017 13:51:52:  8000000 
INFO  @ Thu, 13 Apr 2017 13:51:54:  9000000 
INFO  @ Thu, 13 Apr 2017 13:51:55:  10000000 
INFO  @ Thu, 13 Apr 2017 13:51:57:  11000000 
INFO  @ Thu, 13 Apr 2017 13:51:58:  12000000 
INFO  @ Thu, 13 Apr 2017 13:52:00:  13000000 
INFO  @ Thu, 13 Apr 2017 13:52:01:  14000000 
INFO  @ Thu, 13 Apr 2017 13:52:03:  15000000 
INFO  @ Thu, 13 Apr 2017 13:52:04:  16000000 
INFO  @ Thu, 13 Apr 2017 13:52:06:  17000000 
INFO  @ Thu, 13 Apr 2017 13:52:07:  18000000 
INFO  @ Thu, 13 Apr 2017 13:52:08:  19000000 
INFO  @ Thu, 13 Apr 2017 13:52:10:  20000000 
INFO  @ Thu, 13 Apr 2017 13:52:11:  21000000 
INFO  @ Thu, 13 Apr 2017 13:52:13:  22000000 
INFO  @ Thu, 13 Apr 2017 13:52:14:  23000000 
INFO  @ Thu, 13 Apr 2017 13:52:16:  24000000 
INFO  @ Thu, 13 Apr 2017 13:52:17:  25000000 
INFO  @ Thu, 13 Apr 2017 13:52:19:  26000000 
INFO  @ Thu, 13 Apr 2017 13:52:20:  27000000 
INFO  @ Thu, 13 Apr 2017 13:52:21:  28000000 
INFO  @ Thu, 13 Apr 2017 13:52:23:  29000000 
INFO  @ Thu, 13 Apr 2017 13:52:24:  30000000 
INFO  @ Thu, 13 Apr 2017 13:52:26:  31000000 
INFO  @ Thu, 13 Apr 2017 13:52:27:  32000000 
INFO  @ Thu, 13 Apr 2017 13:52:29:  33000000 
INFO  @ Thu, 13 Apr 2017 13:52:30:  34000000 
INFO  @ Thu, 13 Apr 2017 13:52:31:  35000000 
INFO  @ Thu, 13 Apr 2017 13:52:33:  36000000 
INFO  @ Thu, 13 Apr 2017 13:52:34:  37000000 
INFO  @ Thu, 13 Apr 2017 13:52:36:  38000000 
INFO  @ Thu, 13 Apr 2017 13:52:37:  39000000 
INFO  @ Thu, 13 Apr 2017 13:52:39:  40000000 
INFO  @ Thu, 13 Apr 2017 13:52:40:  41000000 
INFO  @ Thu, 13 Apr 2017 13:52:42:  42000000 
INFO  @ Thu, 13 Apr 2017 13:52:43:  43000000 
INFO  @ Thu, 13 Apr 2017 13:52:44:  44000000 
INFO  @ Thu, 13 Apr 2017 13:52:46:  45000000 
INFO  @ Thu, 13 Apr 2017 13:52:47:  46000000 
INFO  @ Thu, 13 Apr 2017 13:52:49:  47000000 
INFO  @ Thu, 13 Apr 2017 13:52:50:  48000000 
INFO  @ Thu, 13 Apr 2017 13:52:51:  49000000 
INFO  @ Thu, 13 Apr 2017 13:52:53:  50000000 
INFO  @ Thu, 13 Apr 2017 13:52:54:  51000000 
INFO  @ Thu, 13 Apr 2017 13:52:56:  52000000 
INFO  @ Thu, 13 Apr 2017 13:52:57:  53000000 
INFO  @ Thu, 13 Apr 2017 13:52:59:  54000000 
INFO  @ Thu, 13 Apr 2017 13:53:00:  55000000 
INFO  @ Thu, 13 Apr 2017 13:53:02:  56000000 
INFO  @ Thu, 13 Apr 2017 13:53:03:  57000000 
INFO  @ Thu, 13 Apr 2017 13:53:05:  58000000 
INFO  @ Thu, 13 Apr 2017 13:53:06:  59000000 
INFO  @ Thu, 13 Apr 2017 13:53:08:  60000000 
INFO  @ Thu, 13 Apr 2017 13:53:09:  61000000 
INFO  @ Thu, 13 Apr 2017 13:53:11:  62000000 
INFO  @ Thu, 13 Apr 2017 13:53:12:  63000000 
INFO  @ Thu, 13 Apr 2017 13:53:13:  64000000 
INFO  @ Thu, 13 Apr 2017 13:53:15:  65000000 
INFO  @ Thu, 13 Apr 2017 13:53:16:  66000000 
INFO  @ Thu, 13 Apr 2017 13:53:18:  67000000 
INFO  @ Thu, 13 Apr 2017 13:53:19:  68000000 
INFO  @ Thu, 13 Apr 2017 13:53:21:  69000000 
INFO  @ Thu, 13 Apr 2017 13:53:22:  70000000 
INFO  @ Thu, 13 Apr 2017 13:53:23:  71000000 
INFO  @ Thu, 13 Apr 2017 13:53:25:  72000000 
INFO  @ Thu, 13 Apr 2017 13:53:26:  73000000 
INFO  @ Thu, 13 Apr 2017 13:53:28:  74000000 
INFO  @ Thu, 13 Apr 2017 13:53:29:  75000000 
INFO  @ Thu, 13 Apr 2017 13:53:31:  76000000 
INFO  @ Thu, 13 Apr 2017 13:53:32:  77000000 
INFO  @ Thu, 13 Apr 2017 13:53:33:  78000000 
INFO  @ Thu, 13 Apr 2017 13:53:35:  79000000 
INFO  @ Thu, 13 Apr 2017 13:53:36:  80000000 
INFO  @ Thu, 13 Apr 2017 13:53:38:  81000000 
INFO  @ Thu, 13 Apr 2017 13:53:39:  82000000 
INFO  @ Thu, 13 Apr 2017 13:53:41:  83000000 
INFO  @ Thu, 13 Apr 2017 13:53:42:  84000000 
INFO  @ Thu, 13 Apr 2017 13:53:44:  85000000 
INFO  @ Thu, 13 Apr 2017 13:53:45:  86000000 
INFO  @ Thu, 13 Apr 2017 13:53:46:  87000000 
INFO  @ Thu, 13 Apr 2017 13:53:48:  88000000 
INFO  @ Thu, 13 Apr 2017 13:53:49:  89000000 
INFO  @ Thu, 13 Apr 2017 13:53:51:  90000000 
INFO  @ Thu, 13 Apr 2017 13:53:52:  91000000 
INFO  @ Thu, 13 Apr 2017 13:53:54:  92000000 
INFO  @ Thu, 13 Apr 2017 13:53:55:  93000000 
INFO  @ Thu, 13 Apr 2017 13:53:57:  94000000 
INFO  @ Thu, 13 Apr 2017 13:53:58:  95000000 
INFO  @ Thu, 13 Apr 2017 13:54:00:  96000000 
INFO  @ Thu, 13 Apr 2017 13:54:01:  97000000 
INFO  @ Thu, 13 Apr 2017 13:54:03:  98000000 
INFO  @ Thu, 13 Apr 2017 13:54:04:  99000000 
INFO  @ Thu, 13 Apr 2017 13:54:06: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 13:54:06: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 13:54:06: #1  total tags in treatment: 92229774 
INFO  @ Thu, 13 Apr 2017 13:54:06: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 13:54:06: #1 finished! 
INFO  @ Thu, 13 Apr 2017 13:54:06: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 13:54:06: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 13:54:06: #2 Use 240 as fragment length 
INFO  @ Thu, 13 Apr 2017 13:54:06: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 13:54:06: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 13:54:06: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 14:03:25: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 14:03:25: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 14:03:25: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 14:03:25: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 14:03:25: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 14:16:36: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 14:16:37: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 14:16:37: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 14:16:37: Done! 
INFO  @ Thu, 13 Apr 2017 14:16:39: Read and build treatment bedGraph... 
INFO  @ Thu, 13 Apr 2017 14:19:31: Read and build control bedGraph... 
INFO  @ Thu, 13 Apr 2017 14:22:22: Build scoreTrackII... 
INFO  @ Thu, 13 Apr 2017 14:24:21: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Thu, 13 Apr 2017 14:36:08: Write bedGraph of scores... 
INFO  @ Thu, 13 Apr 2017 14:45:18: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_FE.bdg'! 
INFO  @ Thu, 13 Apr 2017 15:03:55: Read and build treatment bedGraph... 
INFO  @ Thu, 13 Apr 2017 15:06:52: Read and build control bedGraph... 
INFO  @ Thu, 13 Apr 2017 15:09:45: Build scoreTrackII... 
INFO  @ Thu, 13 Apr 2017 15:11:07: Values in your input bedGraph files will be multiplied by 92.229774 ... 
INFO  @ Thu, 13 Apr 2017 15:22:15: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Thu, 13 Apr 2017 15:24:52: Write bedGraph of scores... 
INFO  @ Thu, 13 Apr 2017 15:31:05: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_ppois.bdg'! 

 
 		 

    
  
 
  Num   8  
 
  ID   task.callpeak_macs2.macs2_n_s_rep2_pr1.line_66.id_17  
 
  Name   macs2 n/s rep2-pr1 
 
  Thread   thread_Root  
 
  PID   46860  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 13:54:13  
 
  End   2017-04-13 14:19:02  
 
  Elapsed   00:24:48  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 68

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 69

 export LC_COLLATE=C

# SYS command. line 74

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 240 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 84

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.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 94

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1 -o "ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.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 113

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1 -o "ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 126

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
33810 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 13:54:33: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.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/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.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  @ Thu, 13 Apr 2017 13:54:33: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 13:54:33: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 13:54:36:  1000000 
INFO  @ Thu, 13 Apr 2017 13:54:38:  2000000 
INFO  @ Thu, 13 Apr 2017 13:54:39:  3000000 
INFO  @ Thu, 13 Apr 2017 13:54:41:  4000000 
INFO  @ Thu, 13 Apr 2017 13:54:43:  5000000 
INFO  @ Thu, 13 Apr 2017 13:54:44:  6000000 
INFO  @ Thu, 13 Apr 2017 13:54:46:  7000000 
INFO  @ Thu, 13 Apr 2017 13:54:47:  8000000 
INFO  @ Thu, 13 Apr 2017 13:54:49:  9000000 
INFO  @ Thu, 13 Apr 2017 13:54:51:  10000000 
INFO  @ Thu, 13 Apr 2017 13:54:52:  11000000 
INFO  @ Thu, 13 Apr 2017 13:54:54:  12000000 
INFO  @ Thu, 13 Apr 2017 13:54:55:  13000000 
INFO  @ Thu, 13 Apr 2017 13:54:57:  14000000 
INFO  @ Thu, 13 Apr 2017 13:54:59:  15000000 
INFO  @ Thu, 13 Apr 2017 13:55:00:  16000000 
INFO  @ Thu, 13 Apr 2017 13:55:02:  17000000 
INFO  @ Thu, 13 Apr 2017 13:55:03:  18000000 
INFO  @ Thu, 13 Apr 2017 13:55:05:  19000000 
INFO  @ Thu, 13 Apr 2017 13:55:06:  20000000 
INFO  @ Thu, 13 Apr 2017 13:55:08:  21000000 
INFO  @ Thu, 13 Apr 2017 13:55:10:  22000000 
INFO  @ Thu, 13 Apr 2017 13:55:11:  23000000 
INFO  @ Thu, 13 Apr 2017 13:55:13:  24000000 
INFO  @ Thu, 13 Apr 2017 13:55:14:  25000000 
INFO  @ Thu, 13 Apr 2017 13:55:16:  26000000 
INFO  @ Thu, 13 Apr 2017 13:55:18:  27000000 
INFO  @ Thu, 13 Apr 2017 13:55:19:  28000000 
INFO  @ Thu, 13 Apr 2017 13:55:21:  29000000 
INFO  @ Thu, 13 Apr 2017 13:55:22:  30000000 
INFO  @ Thu, 13 Apr 2017 13:55:24:  31000000 
INFO  @ Thu, 13 Apr 2017 13:55:26:  32000000 
INFO  @ Thu, 13 Apr 2017 13:55:27:  33000000 
INFO  @ Thu, 13 Apr 2017 13:55:29:  34000000 
INFO  @ Thu, 13 Apr 2017 13:55:30:  35000000 
INFO  @ Thu, 13 Apr 2017 13:55:32:  36000000 
INFO  @ Thu, 13 Apr 2017 13:55:34:  37000000 
INFO  @ Thu, 13 Apr 2017 13:55:35:  38000000 
INFO  @ Thu, 13 Apr 2017 13:55:37:  39000000 
INFO  @ Thu, 13 Apr 2017 13:55:38:  40000000 
INFO  @ Thu, 13 Apr 2017 13:55:40:  41000000 
INFO  @ Thu, 13 Apr 2017 13:55:42:  42000000 
INFO  @ Thu, 13 Apr 2017 13:55:43:  43000000 
INFO  @ Thu, 13 Apr 2017 13:55:45:  44000000 
INFO  @ Thu, 13 Apr 2017 13:55:47:  45000000 
INFO  @ Thu, 13 Apr 2017 13:55:48:  46000000 
INFO  @ Thu, 13 Apr 2017 13:55:51: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 13:55:53:  1000000 
INFO  @ Thu, 13 Apr 2017 13:55:54:  2000000 
INFO  @ Thu, 13 Apr 2017 13:55:56:  3000000 
INFO  @ Thu, 13 Apr 2017 13:55:57:  4000000 
INFO  @ Thu, 13 Apr 2017 13:55:59:  5000000 
INFO  @ Thu, 13 Apr 2017 13:56:00:  6000000 
INFO  @ Thu, 13 Apr 2017 13:56:02:  7000000 
INFO  @ Thu, 13 Apr 2017 13:56:03:  8000000 
INFO  @ Thu, 13 Apr 2017 13:56:05:  9000000 
INFO  @ Thu, 13 Apr 2017 13:56:06:  10000000 
INFO  @ Thu, 13 Apr 2017 13:56:08:  11000000 
INFO  @ Thu, 13 Apr 2017 13:56:09:  12000000 
INFO  @ Thu, 13 Apr 2017 13:56:11:  13000000 
INFO  @ Thu, 13 Apr 2017 13:56:12:  14000000 
INFO  @ Thu, 13 Apr 2017 13:56:14:  15000000 
INFO  @ Thu, 13 Apr 2017 13:56:15:  16000000 
INFO  @ Thu, 13 Apr 2017 13:56:17:  17000000 
INFO  @ Thu, 13 Apr 2017 13:56:18:  18000000 
INFO  @ Thu, 13 Apr 2017 13:56:20:  19000000 
INFO  @ Thu, 13 Apr 2017 13:56:21:  20000000 
INFO  @ Thu, 13 Apr 2017 13:56:23:  21000000 
INFO  @ Thu, 13 Apr 2017 13:56:24:  22000000 
INFO  @ Thu, 13 Apr 2017 13:56:25:  23000000 
INFO  @ Thu, 13 Apr 2017 13:56:27:  24000000 
INFO  @ Thu, 13 Apr 2017 13:56:28:  25000000 
INFO  @ Thu, 13 Apr 2017 13:56:30:  26000000 
INFO  @ Thu, 13 Apr 2017 13:56:31:  27000000 
INFO  @ Thu, 13 Apr 2017 13:56:33:  28000000 
INFO  @ Thu, 13 Apr 2017 13:56:34:  29000000 
INFO  @ Thu, 13 Apr 2017 13:56:36:  30000000 
INFO  @ Thu, 13 Apr 2017 13:56:37:  31000000 
INFO  @ Thu, 13 Apr 2017 13:56:39:  32000000 
INFO  @ Thu, 13 Apr 2017 13:56:40:  33000000 
INFO  @ Thu, 13 Apr 2017 13:56:42:  34000000 
INFO  @ Thu, 13 Apr 2017 13:56:43:  35000000 
INFO  @ Thu, 13 Apr 2017 13:56:44:  36000000 
INFO  @ Thu, 13 Apr 2017 13:56:46:  37000000 
INFO  @ Thu, 13 Apr 2017 13:56:47:  38000000 
INFO  @ Thu, 13 Apr 2017 13:56:49:  39000000 
INFO  @ Thu, 13 Apr 2017 13:56:50:  40000000 
INFO  @ Thu, 13 Apr 2017 13:56:52:  41000000 
INFO  @ Thu, 13 Apr 2017 13:56:53:  42000000 
INFO  @ Thu, 13 Apr 2017 13:56:55:  43000000 
INFO  @ Thu, 13 Apr 2017 13:56:56:  44000000 
INFO  @ Thu, 13 Apr 2017 13:56:58:  45000000 
INFO  @ Thu, 13 Apr 2017 13:56:59:  46000000 
INFO  @ Thu, 13 Apr 2017 13:57:01:  47000000 
INFO  @ Thu, 13 Apr 2017 13:57:02:  48000000 
INFO  @ Thu, 13 Apr 2017 13:57:04:  49000000 
INFO  @ Thu, 13 Apr 2017 13:57:05:  50000000 
INFO  @ Thu, 13 Apr 2017 13:57:06:  51000000 
INFO  @ Thu, 13 Apr 2017 13:57:08:  52000000 
INFO  @ Thu, 13 Apr 2017 13:57:09:  53000000 
INFO  @ Thu, 13 Apr 2017 13:57:11:  54000000 
INFO  @ Thu, 13 Apr 2017 13:57:12:  55000000 
INFO  @ Thu, 13 Apr 2017 13:57:14:  56000000 
INFO  @ Thu, 13 Apr 2017 13:57:15:  57000000 
INFO  @ Thu, 13 Apr 2017 13:57:17:  58000000 
INFO  @ Thu, 13 Apr 2017 13:57:18:  59000000 
INFO  @ Thu, 13 Apr 2017 13:57:20:  60000000 
INFO  @ Thu, 13 Apr 2017 13:57:21:  61000000 
INFO  @ Thu, 13 Apr 2017 13:57:23:  62000000 
INFO  @ Thu, 13 Apr 2017 13:57:24:  63000000 
INFO  @ Thu, 13 Apr 2017 13:57:25:  64000000 
INFO  @ Thu, 13 Apr 2017 13:57:27:  65000000 
INFO  @ Thu, 13 Apr 2017 13:57:28:  66000000 
INFO  @ Thu, 13 Apr 2017 13:57:30:  67000000 
INFO  @ Thu, 13 Apr 2017 13:57:31:  68000000 
INFO  @ Thu, 13 Apr 2017 13:57:33:  69000000 
INFO  @ Thu, 13 Apr 2017 13:57:34:  70000000 
INFO  @ Thu, 13 Apr 2017 13:57:36:  71000000 
INFO  @ Thu, 13 Apr 2017 13:57:37:  72000000 
INFO  @ Thu, 13 Apr 2017 13:57:39:  73000000 
INFO  @ Thu, 13 Apr 2017 13:57:40:  74000000 
INFO  @ Thu, 13 Apr 2017 13:57:42:  75000000 
INFO  @ Thu, 13 Apr 2017 13:57:43:  76000000 
INFO  @ Thu, 13 Apr 2017 13:57:45:  77000000 
INFO  @ Thu, 13 Apr 2017 13:57:46:  78000000 
INFO  @ Thu, 13 Apr 2017 13:57:48:  79000000 
INFO  @ Thu, 13 Apr 2017 13:57:49:  80000000 
INFO  @ Thu, 13 Apr 2017 13:57:51:  81000000 
INFO  @ Thu, 13 Apr 2017 13:57:52:  82000000 
INFO  @ Thu, 13 Apr 2017 13:57:54:  83000000 
INFO  @ Thu, 13 Apr 2017 13:57:55:  84000000 
INFO  @ Thu, 13 Apr 2017 13:57:57:  85000000 
INFO  @ Thu, 13 Apr 2017 13:57:58:  86000000 
INFO  @ Thu, 13 Apr 2017 13:58:00:  87000000 
INFO  @ Thu, 13 Apr 2017 13:58:01:  88000000 
INFO  @ Thu, 13 Apr 2017 13:58:03:  89000000 
INFO  @ Thu, 13 Apr 2017 13:58:04:  90000000 
INFO  @ Thu, 13 Apr 2017 13:58:06:  91000000 
INFO  @ Thu, 13 Apr 2017 13:58:07:  92000000 
INFO  @ Thu, 13 Apr 2017 13:58:09:  93000000 
INFO  @ Thu, 13 Apr 2017 13:58:10:  94000000 
INFO  @ Thu, 13 Apr 2017 13:58:12:  95000000 
INFO  @ Thu, 13 Apr 2017 13:58:13:  96000000 
INFO  @ Thu, 13 Apr 2017 13:58:14:  97000000 
INFO  @ Thu, 13 Apr 2017 13:58:16:  98000000 
INFO  @ Thu, 13 Apr 2017 13:58:17:  99000000 
INFO  @ Thu, 13 Apr 2017 13:58:19: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 13:58:19: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 13:58:19: #1  total tags in treatment: 46114888 
INFO  @ Thu, 13 Apr 2017 13:58:19: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 13:58:19: #1 finished! 
INFO  @ Thu, 13 Apr 2017 13:58:19: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 13:58:19: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 13:58:19: #2 Use 240 as fragment length 
INFO  @ Thu, 13 Apr 2017 13:58:19: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 13:58:19: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 13:58:19: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 14:07:46: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 14:07:46: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 14:07:46: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 14:07:46: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 14:07:46: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 14:18:40: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 14:18:43: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 14:18:44: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 14:18:47: Done! 

 
 		 

    
  
 
  Num   9  
 
  ID   task.callpeak_macs2.macs2_n_s_rep2_pr2.line_66.id_18  
 
  Name   macs2 n/s rep2-pr2 
 
  Thread   thread_Root  
 
  PID   46868  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 14:08:40  
 
  End   2017-04-13 14:34:25  
 
  Elapsed   00:25:45  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 68

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 69

 export LC_COLLATE=C

# SYS command. line 74

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 240 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 84

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.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 94

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2 -o "ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.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 113

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2 -o "ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 126

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
29211 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 14:09:02: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.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/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.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  @ Thu, 13 Apr 2017 14:09:02: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 14:09:02: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 14:09:04:  1000000 
INFO  @ Thu, 13 Apr 2017 14:09:06:  2000000 
INFO  @ Thu, 13 Apr 2017 14:09:09:  3000000 
INFO  @ Thu, 13 Apr 2017 14:09:11:  4000000 
INFO  @ Thu, 13 Apr 2017 14:09:13:  5000000 
INFO  @ Thu, 13 Apr 2017 14:09:15:  6000000 
INFO  @ Thu, 13 Apr 2017 14:09:17:  7000000 
INFO  @ Thu, 13 Apr 2017 14:09:19:  8000000 
INFO  @ Thu, 13 Apr 2017 14:09:22:  9000000 
INFO  @ Thu, 13 Apr 2017 14:09:24:  10000000 
INFO  @ Thu, 13 Apr 2017 14:09:26:  11000000 
INFO  @ Thu, 13 Apr 2017 14:09:28:  12000000 
INFO  @ Thu, 13 Apr 2017 14:09:30:  13000000 
INFO  @ Thu, 13 Apr 2017 14:09:32:  14000000 
INFO  @ Thu, 13 Apr 2017 14:09:34:  15000000 
INFO  @ Thu, 13 Apr 2017 14:09:37:  16000000 
INFO  @ Thu, 13 Apr 2017 14:09:39:  17000000 
INFO  @ Thu, 13 Apr 2017 14:09:41:  18000000 
INFO  @ Thu, 13 Apr 2017 14:09:43:  19000000 
INFO  @ Thu, 13 Apr 2017 14:09:45:  20000000 
INFO  @ Thu, 13 Apr 2017 14:09:47:  21000000 
INFO  @ Thu, 13 Apr 2017 14:09:50:  22000000 
INFO  @ Thu, 13 Apr 2017 14:09:52:  23000000 
INFO  @ Thu, 13 Apr 2017 14:09:54:  24000000 
INFO  @ Thu, 13 Apr 2017 14:09:56:  25000000 
INFO  @ Thu, 13 Apr 2017 14:09:58:  26000000 
INFO  @ Thu, 13 Apr 2017 14:10:00:  27000000 
INFO  @ Thu, 13 Apr 2017 14:10:02:  28000000 
INFO  @ Thu, 13 Apr 2017 14:10:05:  29000000 
INFO  @ Thu, 13 Apr 2017 14:10:07:  30000000 
INFO  @ Thu, 13 Apr 2017 14:10:09:  31000000 
INFO  @ Thu, 13 Apr 2017 14:10:11:  32000000 
INFO  @ Thu, 13 Apr 2017 14:10:13:  33000000 
INFO  @ Thu, 13 Apr 2017 14:10:15:  34000000 
INFO  @ Thu, 13 Apr 2017 14:10:17:  35000000 
INFO  @ Thu, 13 Apr 2017 14:10:19:  36000000 
INFO  @ Thu, 13 Apr 2017 14:10:22:  37000000 
INFO  @ Thu, 13 Apr 2017 14:10:24:  38000000 
INFO  @ Thu, 13 Apr 2017 14:10:26:  39000000 
INFO  @ Thu, 13 Apr 2017 14:10:28:  40000000 
INFO  @ Thu, 13 Apr 2017 14:10:30:  41000000 
INFO  @ Thu, 13 Apr 2017 14:10:32:  42000000 
INFO  @ Thu, 13 Apr 2017 14:10:34:  43000000 
INFO  @ Thu, 13 Apr 2017 14:10:37:  44000000 
INFO  @ Thu, 13 Apr 2017 14:10:39:  45000000 
INFO  @ Thu, 13 Apr 2017 14:10:41:  46000000 
INFO  @ Thu, 13 Apr 2017 14:10:45: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 14:10:47:  1000000 
INFO  @ Thu, 13 Apr 2017 14:10:49:  2000000 
INFO  @ Thu, 13 Apr 2017 14:10:52:  3000000 
INFO  @ Thu, 13 Apr 2017 14:10:53:  4000000 
INFO  @ Thu, 13 Apr 2017 14:10:56:  5000000 
INFO  @ Thu, 13 Apr 2017 14:10:58:  6000000 
INFO  @ Thu, 13 Apr 2017 14:11:00:  7000000 
INFO  @ Thu, 13 Apr 2017 14:11:02:  8000000 
INFO  @ Thu, 13 Apr 2017 14:11:04:  9000000 
INFO  @ Thu, 13 Apr 2017 14:11:06:  10000000 
INFO  @ Thu, 13 Apr 2017 14:11:08:  11000000 
INFO  @ Thu, 13 Apr 2017 14:11:10:  12000000 
INFO  @ Thu, 13 Apr 2017 14:11:12:  13000000 
INFO  @ Thu, 13 Apr 2017 14:11:14:  14000000 
INFO  @ Thu, 13 Apr 2017 14:11:16:  15000000 
INFO  @ Thu, 13 Apr 2017 14:11:18:  16000000 
INFO  @ Thu, 13 Apr 2017 14:11:20:  17000000 
INFO  @ Thu, 13 Apr 2017 14:11:22:  18000000 
INFO  @ Thu, 13 Apr 2017 14:11:24:  19000000 
INFO  @ Thu, 13 Apr 2017 14:11:26:  20000000 
INFO  @ Thu, 13 Apr 2017 14:11:28:  21000000 
INFO  @ Thu, 13 Apr 2017 14:11:30:  22000000 
INFO  @ Thu, 13 Apr 2017 14:11:32:  23000000 
INFO  @ Thu, 13 Apr 2017 14:11:34:  24000000 
INFO  @ Thu, 13 Apr 2017 14:11:36:  25000000 
INFO  @ Thu, 13 Apr 2017 14:11:38:  26000000 
INFO  @ Thu, 13 Apr 2017 14:11:40:  27000000 
INFO  @ Thu, 13 Apr 2017 14:11:42:  28000000 
INFO  @ Thu, 13 Apr 2017 14:11:44:  29000000 
INFO  @ Thu, 13 Apr 2017 14:11:46:  30000000 
INFO  @ Thu, 13 Apr 2017 14:11:48:  31000000 
INFO  @ Thu, 13 Apr 2017 14:11:50:  32000000 
INFO  @ Thu, 13 Apr 2017 14:11:52:  33000000 
INFO  @ Thu, 13 Apr 2017 14:11:54:  34000000 
INFO  @ Thu, 13 Apr 2017 14:11:56:  35000000 
INFO  @ Thu, 13 Apr 2017 14:11:58:  36000000 
INFO  @ Thu, 13 Apr 2017 14:12:00:  37000000 
INFO  @ Thu, 13 Apr 2017 14:12:02:  38000000 
INFO  @ Thu, 13 Apr 2017 14:12:04:  39000000 
INFO  @ Thu, 13 Apr 2017 14:12:06:  40000000 
INFO  @ Thu, 13 Apr 2017 14:12:08:  41000000 
INFO  @ Thu, 13 Apr 2017 14:12:10:  42000000 
INFO  @ Thu, 13 Apr 2017 14:12:12:  43000000 
INFO  @ Thu, 13 Apr 2017 14:12:14:  44000000 
INFO  @ Thu, 13 Apr 2017 14:12:16:  45000000 
INFO  @ Thu, 13 Apr 2017 14:12:18:  46000000 
INFO  @ Thu, 13 Apr 2017 14:12:20:  47000000 
INFO  @ Thu, 13 Apr 2017 14:12:22:  48000000 
INFO  @ Thu, 13 Apr 2017 14:12:24:  49000000 
INFO  @ Thu, 13 Apr 2017 14:12:26:  50000000 
INFO  @ Thu, 13 Apr 2017 14:12:28:  51000000 
INFO  @ Thu, 13 Apr 2017 14:12:30:  52000000 
INFO  @ Thu, 13 Apr 2017 14:12:32:  53000000 
INFO  @ Thu, 13 Apr 2017 14:12:34:  54000000 
INFO  @ Thu, 13 Apr 2017 14:12:36:  55000000 
INFO  @ Thu, 13 Apr 2017 14:12:38:  56000000 
INFO  @ Thu, 13 Apr 2017 14:12:40:  57000000 
INFO  @ Thu, 13 Apr 2017 14:12:42:  58000000 
INFO  @ Thu, 13 Apr 2017 14:12:44:  59000000 
INFO  @ Thu, 13 Apr 2017 14:12:47:  60000000 
INFO  @ Thu, 13 Apr 2017 14:12:49:  61000000 
INFO  @ Thu, 13 Apr 2017 14:12:50:  62000000 
INFO  @ Thu, 13 Apr 2017 14:12:52:  63000000 
INFO  @ Thu, 13 Apr 2017 14:12:55:  64000000 
INFO  @ Thu, 13 Apr 2017 14:12:57:  65000000 
INFO  @ Thu, 13 Apr 2017 14:12:59:  66000000 
INFO  @ Thu, 13 Apr 2017 14:13:01:  67000000 
INFO  @ Thu, 13 Apr 2017 14:13:03:  68000000 
INFO  @ Thu, 13 Apr 2017 14:13:05:  69000000 
INFO  @ Thu, 13 Apr 2017 14:13:07:  70000000 
INFO  @ Thu, 13 Apr 2017 14:13:09:  71000000 
INFO  @ Thu, 13 Apr 2017 14:13:11:  72000000 
INFO  @ Thu, 13 Apr 2017 14:13:13:  73000000 
INFO  @ Thu, 13 Apr 2017 14:13:15:  74000000 
INFO  @ Thu, 13 Apr 2017 14:13:17:  75000000 
INFO  @ Thu, 13 Apr 2017 14:13:19:  76000000 
INFO  @ Thu, 13 Apr 2017 14:13:21:  77000000 
INFO  @ Thu, 13 Apr 2017 14:13:23:  78000000 
INFO  @ Thu, 13 Apr 2017 14:13:25:  79000000 
INFO  @ Thu, 13 Apr 2017 14:13:27:  80000000 
INFO  @ Thu, 13 Apr 2017 14:13:29:  81000000 
INFO  @ Thu, 13 Apr 2017 14:13:31:  82000000 
INFO  @ Thu, 13 Apr 2017 14:13:33:  83000000 
INFO  @ Thu, 13 Apr 2017 14:13:35:  84000000 
INFO  @ Thu, 13 Apr 2017 14:13:37:  85000000 
INFO  @ Thu, 13 Apr 2017 14:13:39:  86000000 
INFO  @ Thu, 13 Apr 2017 14:13:41:  87000000 
INFO  @ Thu, 13 Apr 2017 14:13:43:  88000000 
INFO  @ Thu, 13 Apr 2017 14:13:45:  89000000 
INFO  @ Thu, 13 Apr 2017 14:13:47:  90000000 
INFO  @ Thu, 13 Apr 2017 14:13:49:  91000000 
INFO  @ Thu, 13 Apr 2017 14:13:51:  92000000 
INFO  @ Thu, 13 Apr 2017 14:13:53:  93000000 
INFO  @ Thu, 13 Apr 2017 14:13:55:  94000000 
INFO  @ Thu, 13 Apr 2017 14:13:57:  95000000 
INFO  @ Thu, 13 Apr 2017 14:13:59:  96000000 
INFO  @ Thu, 13 Apr 2017 14:14:01:  97000000 
INFO  @ Thu, 13 Apr 2017 14:14:03:  98000000 
INFO  @ Thu, 13 Apr 2017 14:14:05:  99000000 
INFO  @ Thu, 13 Apr 2017 14:14:07: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 14:14:07: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 14:14:07: #1  total tags in treatment: 46114886 
INFO  @ Thu, 13 Apr 2017 14:14:07: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 14:14:07: #1 finished! 
INFO  @ Thu, 13 Apr 2017 14:14:07: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 14:14:07: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 14:14:07: #2 Use 240 as fragment length 
INFO  @ Thu, 13 Apr 2017 14:14:07: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 14:14:07: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 14:14:07: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 14:21:33: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 14:21:33: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 14:21:33: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 14:21:33: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 14:21:33: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 14:34:20: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 14:34:20: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 14:34:21: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 14:34:21: Done! 

 
 		 

    
  
 
  Num   10  
 
  ID   task.callpeak_naive_overlap.naive_overlap.line_143.id_19  
 
  Name   naive_overlap  
 
  Thread   thread_Root  
 
  PID   46927  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:19:10  
 
  End   2017-04-13 16:20:30  
 
  Elapsed   00:01:19  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 145

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 148

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz) | awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$13-$12; if (($21/s1 >= 0.5) || ($21/s2 >= 0.5)) {print $0}}' | cut -f 1-10 | sort | uniq | intersectBed  -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz) | awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$13-$12; if (($21/s1 >= 0.5) || ($21/s2 >= 0.5)) {print $0}}' | cut -f 1-10 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInReps.narrowPeak.gz

# SYS command. line 151

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz) | awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$13-$12; if (($21/s1 >= 0.5) || ($21/s2 >= 0.5)) {print $0}}' | cut -f 1-10 | sort | uniq | intersectBed  -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz) |    awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$13-$12; if (($21/s1 >= 0.5) || ($21/s2 >= 0.5)) {print $0}}' | cut -f 1-10 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInPsRep1AndPsRep2.narrowPeak.gz

# SYS command. line 154

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInReps.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInPsRep1AndPsRep2.narrowPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.narrowPeak.gz

# SYS command. line 156

 bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.narrowPeak.gz) -b <(zcat -f /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/hg38.blacklist.bed.gz)  | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz

# SYS command. line 158

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInReps.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.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--------------------
9842 (process ID) old priority 0, new priority 19
Waiting for 58 seconds.

  
 		 

    
  
 
  Num   11  
 
  ID   task.callpeak_idr.idr2_rep1_rep2.line_74.id_20  
 
  Name   idr2 rep1-rep2 
 
  Thread   thread_Root  
 
  PID   46928  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:20:32  
 
  End   2017-04-13 16:22:07  
 
  Elapsed   00:01:35  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.unthresholded-peaks.txt.png
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.log.txt
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.unthresholded-peaks.txt.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 76

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq_py3 | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq_py3; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 78

 idr --samples /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.unthresholded-peaks.txt --rank signal.value --soft-idr-threshold 0.05 \
			--plot --use-best-multisummit-IDR --log-output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.log.txt

# SYS command. line 82

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

# SYS command. line 85

 awk 'BEGIN{OFS="\t"} $12>='"${idr_thresh_transformed}"' {if ($2<0) $2=0; print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,"0"}' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.13-col.bed.gz

# SYS command. line 88

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.narrowPeak.gz

# SYS command. line 89

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.12-col.bed.gz

# SYS command. line 91

 bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.13-col.bed.gz) -b <(zcat -f /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/hg38.blacklist.bed.gz) | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.13-col.bed.gz

# SYS command. line 92

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz

# SYS command. line 93

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz

# SYS command. line 95

 gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.unthresholded-peaks.txt

# SYS command. line 96

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.13-col.bed.gz

# SYS command. line 98

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
13431 (process ID) old priority 0, new priority 19

  
 		 

    
  
 
  Num   12  
 
  ID   task.callpeak_idr.idr2_rep1_pr.line_74.id_21  
 
  Name   idr2 rep1-pr 
 
  Thread   thread_Root  
 
  PID   46929  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:20:33  
 
  End   2017-04-13 16:21:52  
 
  Elapsed   00:01:19  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.unthresholded-peaks.txt.png
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.log.txt
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.unthresholded-peaks.txt.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 76

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq_py3 | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq_py3; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 78

 idr --samples /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.unthresholded-peaks.txt --rank signal.value --soft-idr-threshold 0.05 \
			--plot --use-best-multisummit-IDR --log-output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.log.txt

# SYS command. line 82

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

# SYS command. line 85

 awk 'BEGIN{OFS="\t"} $12>='"${idr_thresh_transformed}"' {if ($2<0) $2=0; print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,"0"}' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.13-col.bed.gz

# SYS command. line 88

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.narrowPeak.gz

# SYS command. line 89

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.12-col.bed.gz

# SYS command. line 91

 bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.13-col.bed.gz) -b <(zcat -f /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/hg38.blacklist.bed.gz) | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 92

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 93

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 95

 gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.unthresholded-peaks.txt

# SYS command. line 96

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 98

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
13429 (process ID) old priority 0, new priority 19

  
 		 

    
  
 
  Num   13  
 
  ID   task.callpeak_idr.idr2_rep2_pr.line_74.id_22  
 
  Name   idr2 rep2-pr 
 
  Thread   thread_Root  
 
  PID   46930  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:20:33  
 
  End   2017-04-13 16:23:39  
 
  Elapsed   00:03:05  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.unthresholded-peaks.txt.png
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.log.txt
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.unthresholded-peaks.txt.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 76

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq_py3 | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq_py3; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 78

 idr --samples /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.unthresholded-peaks.txt --rank signal.value --soft-idr-threshold 0.05 \
			--plot --use-best-multisummit-IDR --log-output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.log.txt

# SYS command. line 82

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

# SYS command. line 85

 awk 'BEGIN{OFS="\t"} $12>='"${idr_thresh_transformed}"' {if ($2<0) $2=0; print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,"0"}' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.13-col.bed.gz

# SYS command. line 88

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.narrowPeak.gz

# SYS command. line 89

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.12-col.bed.gz

# SYS command. line 91

 bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.13-col.bed.gz) -b <(zcat -f /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/hg38.blacklist.bed.gz) | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 92

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 93

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 95

 gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.unthresholded-peaks.txt

# SYS command. line 96

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 98

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
23943 (process ID) old priority 0, new priority 19

  
 		 

    
  
 
  Num   14  
 
  ID   task.callpeak_idr.idr2_ppr.line_74.id_23  
 
  Name   idr2 ppr 
 
  Thread   thread_Root  
 
  PID   46931  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:20:34  
 
  End   2017-04-13 16:23:01  
 
  Elapsed   00:02:26  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.filt.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.unthresholded-peaks.txt.png
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.log.txt
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.unthresholded-peaks.txt.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.filt.12-col.bed.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 76

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq_py3 | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq_py3; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 78

 idr --samples /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.unthresholded-peaks.txt --rank signal.value --soft-idr-threshold 0.05 \
			--plot --use-best-multisummit-IDR --log-output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.log.txt

# SYS command. line 82

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

# SYS command. line 85

 awk 'BEGIN{OFS="\t"} $12>='"${idr_thresh_transformed}"' {if ($2<0) $2=0; print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,"0"}' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.13-col.bed.gz

# SYS command. line 88

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.narrowPeak.gz

# SYS command. line 89

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.12-col.bed.gz

# SYS command. line 91

 bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.13-col.bed.gz) -b <(zcat -f /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/hg38.blacklist.bed.gz) | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 92

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 93

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 95

 gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.unthresholded-peaks.txt

# SYS command. line 96

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 98

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
13430 (process ID) old priority 0, new priority 19

  
 		 

    
  
 
  Num   15  
 
  ID   task.sys.copy_file.line_131.id_32  
 
  Name   copy file 
 
  Thread   thread_Root  
 
  PID   23963  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:23:39  
 
  End   2017-04-13 16:23:39  
 
  Elapsed   00:00:00  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.filt.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/optimal_set/ZBTB26_MACS2_ppr.IDR0.05.filt.narrowPeak.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 133

 cp --remove-destination /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/optimal_set/ZBTB26_MACS2_ppr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 134

 while [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/optimal_set/ZBTB26_MACS2_ppr.IDR0.05.filt.narrowPeak.gz ]; do echo FOUND DELAYED WRITE, WAITING...; sleep 0.1; done
 
 
     
 		 

    
  
 
  Num   16  
 
  ID   task.sys.copy_file.line_131.id_33  
 
  Name   copy file 
 
  Thread   thread_Root  
 
  PID   23966  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:23:39  
 
  End   2017-04-13 16:23:39  
 
  Elapsed   00:00:00  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/conservative_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 133

 cp --remove-destination /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/conservative_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz

# SYS command. line 134

 while [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/conservative_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz ]; do echo FOUND DELAYED WRITE, WAITING...; sleep 0.1; done
 
 
     
 		 

    
  
 
  Num   17  
 
  ID   task.sys.copy_file.line_131.id_34  
 
  Name   copy file 
 
  Thread   thread_Root  
 
  PID   23982  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:23:39  
 
  End   2017-04-13 16:23:39  
 
  Elapsed   00:00:00  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.filt.12-col.bed.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/optimal_set/ZBTB26_MACS2_ppr.IDR0.05.filt.12-col.bed.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 133

 cp --remove-destination /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.filt.12-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/optimal_set/ZBTB26_MACS2_ppr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 134

 while [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/optimal_set/ZBTB26_MACS2_ppr.IDR0.05.filt.12-col.bed.gz ]; do echo FOUND DELAYED WRITE, WAITING...; sleep 0.1; done
 
 
     
 		 

    
  
 
  Num   18  
 
  ID   task.sys.copy_file.line_131.id_35  
 
  Name   copy file 
 
  Thread   thread_Root  
 
  PID   23995  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:23:39  
 
  End   2017-04-13 16:23:39  
 
  Elapsed   00:00:00  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/conservative_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 133

 cp --remove-destination /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/conservative_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz

# SYS command. line 134

 while [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/conservative_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz ]; do echo FOUND DELAYED WRITE, WAITING...; sleep 0.1; done
 
 
     
 		 

    
  
 
  Num   19  
 
  ID   task.callpeak_idr.idr_final_qc.line_283.id_36  
 
  Name   idr final qc 
 
  Thread   thread_Root  
 
  PID   46932  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:23:41  
 
  End   2017-04-13 16:25:00  
 
  Elapsed   00:01:18  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.filt.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/ZBTB26_MACS2_IDR_final.qc
  
 
  Dependencies     
 
 		  
 
# SYS command. line 285

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 287

 echo -e "Nt\tN1	N2	""Np\tN_opt\tN_consv\topt_set\tconsv_set\trescue_ratio\tself_consistency_ratio\treproducibility_test" > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/ZBTB26_MACS2_IDR_final.qc

# SYS command. line 288

 echo -e "14736\t13262	12807	""14999\t14999\t14736\tpooled_pseudo_rep\trep1-rep2\t1.0178474484256244\t1.0355274459280082\tpass" >> /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/ZBTB26_MACS2_IDR_final.qc

# SYS command. line 290

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
24425 (process ID) old priority 0, new priority 19
Waiting for 60 seconds.

  
 		 

    
  
 
  Num   20  
 
  ID   task.callpeak_idr.FRiP_rep1_pr.line_120.id_37  
 
  Name   FRiP rep1-pr 
 
  Thread   thread_Root  
 
  PID   46933  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:23:42  
 
  End   2017-04-13 16:28:59  
 
  Elapsed   00:05:16  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.FRiP.qc
  
 
  Dependencies     
 
 		  
 
# SYS command. line 121

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 123

 val1=$(bedtools slop -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.tagAlign.gz -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -s -l -118 -r 118 | \
			awk '{if ($2>=0 && $3>=0 && $2<=$3) print $0}' | \
			bedtools intersect -a stdin -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz -wa -u | wc -l)

# SYS command. line 133

 val2=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.tagAlign.gz | wc -l)

# SYS command. line 134

 awk 'BEGIN {print '${val1}'/'${val2}'}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.FRiP.qc

# SYS command. line 135

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
24424 (process ID) old priority 0, new priority 19

  
 		 

    
  
 
  Num   21  
 
  ID   task.callpeak_idr.FRiP_rep2_pr.line_120.id_38  
 
  Name   FRiP rep2-pr 
 
  Thread   thread_Root  
 
  PID   46934  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:23:43  
 
  End   2017-04-13 16:28:29  
 
  Elapsed   00:04:45  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.narrowPeak.FRiP.qc
  
 
  Dependencies     
 
 		  
 
# SYS command. line 121

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 123

 val1=$(bedtools slop -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.tagAlign.gz -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -s -l -120 -r 120 | \
			awk '{if ($2>=0 && $3>=0 && $2<=$3) print $0}' | \
			bedtools intersect -a stdin -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.narrowPeak.gz -wa -u | wc -l)

# SYS command. line 133

 val2=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.tagAlign.gz | wc -l)

# SYS command. line 134

 awk 'BEGIN {print '${val1}'/'${val2}'}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.narrowPeak.FRiP.qc

# SYS command. line 135

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
25070 (process ID) old priority 0, new priority 19

  
 		 

    
  
 
  Num   22  
 
  ID   task.callpeak_idr.FRiP_ppr.line_120.id_39  
 
  Name   FRiP ppr 
 
  Thread   thread_Root  
 
  PID   46935  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:23:44  
 
  End   2017-04-13 16:33:08  
 
  Elapsed   00:09:23  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.filt.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.filt.narrowPeak.FRiP.qc
  
 
  Dependencies     
 
 		  
 
# SYS command. line 121

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 123

 val1=$(bedtools slop -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign.gz -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -s -l -119 -r 119 | \
			awk '{if ($2>=0 && $3>=0 && $2<=$3) print $0}' | \
			bedtools intersect -a stdin -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.filt.narrowPeak.gz -wa -u | wc -l)

# SYS command. line 133

 val2=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign.gz | wc -l)

# SYS command. line 134

 awk 'BEGIN {print '${val1}'/'${val2}'}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB26_MACS2_ppr.IDR0.05.filt.narrowPeak.FRiP.qc

# SYS command. line 135

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
24423 (process ID) old priority 0, new priority 19

  
 		 

    
  
 
  Num   23  
 
  ID   task.callpeak_idr.FRiP_rep1_rep2.line_120.id_40  
 
  Name   FRiP rep1-rep2 
 
  Thread   thread_Root  
 
  PID   46936  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:23:46  
 
  End   2017-04-13 16:34:45  
 
  Elapsed   00:10:59  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.FRiP.qc
  
 
  Dependencies     
 
 		  
 
# SYS command. line 121

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 123

 val1=$(bedtools slop -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign.gz -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -s -l -119 -r 119 | \
			awk '{if ($2>=0 && $3>=0 && $2<=$3) print $0}' | \
			bedtools intersect -a stdin -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz -wa -u | wc -l)

# SYS command. line 133

 val2=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign.gz | wc -l)

# SYS command. line 134

 awk 'BEGIN {print '${val1}'/'${val2}'}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.FRiP.qc

# SYS command. line 135

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
25071 (process ID) old priority 0, new priority 19

  
 		 

    
  
 
  Num   24  
 
  ID   task.callpeak_blacklist_filter.blacklist_filter_peak_pooled.line_27.id_41  
 
  Name   blacklist_filter peak_pooled 
 
  Thread   thread_Root  
 
  PID   5666  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:34:48  
 
  End   2017-04-13 16:35:56  
 
  Elapsed   00:01:08  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.filt.narrowPeak.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 29

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 31

 bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/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/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.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--------------------
5670 (process ID) old priority 0, new priority 19
Waiting for 60 seconds.

  
 		 

    
  
 
  Num   25  
 
  ID   task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_42  
 
  Name   blacklist_filter peak 1 
 
  Thread   thread_Root  
 
  PID   5685  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:34:49  
 
  End   2017-04-13 16:35:57  
 
  Elapsed   00:01:08  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.filt.narrowPeak.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 29

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 31

 bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/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/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.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--------------------
5690 (process ID) old priority 0, new priority 19
Waiting for 60 seconds.

  
 		 

    
  
 
  Num   26  
 
  ID   task.callpeak_blacklist_filter.blacklist_filter_peak_2.line_27.id_43  
 
  Name   blacklist_filter peak 2 
 
  Thread   thread_Root  
 
  PID   5702  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:34:49  
 
  End   2017-04-13 16:35:58  
 
  Elapsed   00:01:08  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.filt.narrowPeak.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 29

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 31

 bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/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/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.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--------------------
5707 (process ID) old priority 0, new priority 19
Waiting for 60 seconds.

  
 		 

    
  
 
  Num   27  
 
  ID   task.report.peak2hammock.line_361.id_46  
 
  Name   peak2hammock 
 
  Thread   thread_Root  
 
  PID   8767  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:35:59  
 
  End   2017-04-13 16:36:08  
 
  Elapsed   00:00:09  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.narrowPeak.hammock.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 363

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 364

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp

# SYS command. line 366

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.narrowPeak.hammock

# SYS command. line 367

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp
 
 
   
--------------------Stdout--------------------
8771 (process ID) old priority 0, new priority 19

  
 		 

    
  
 
  Num   28  
 
  ID   task.report.peak2hammock.line_361.id_47  
 
  Name   peak2hammock 
 
  Thread   thread_Root  
 
  PID   9300  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:36:09  
 
  End   2017-04-13 16:36:18  
 
  Elapsed   00:00:09  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/optimal_set/ZBTB26_MACS2_ppr.IDR0.05.filt.12-col.bed.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/optimal_set/ZBTB26_MACS2_ppr.IDR0.05.filt.12-col.bed.hammock.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 363

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 364

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/optimal_set/ZBTB26_MACS2_ppr.IDR0.05.filt.12-col.bed.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/optimal_set/ZBTB26_MACS2_ppr.IDR0.05.filt.12-col.bed.tmp

# SYS command. line 366

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/optimal_set/ZBTB26_MACS2_ppr.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/optimal_set/ZBTB26_MACS2_ppr.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 367

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/optimal_set/ZBTB26_MACS2_ppr.IDR0.05.filt.12-col.bed.tmp
 
 
   
--------------------Stdout--------------------
9304 (process ID) old priority 0, new priority 19

  
 		 

    
  
 
  Num   29  
 
  ID   task.report.peak2hammock.line_361.id_48  
 
  Name   peak2hammock 
 
  Thread   thread_Root  
 
  PID   9733  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:36:19  
 
  End   2017-04-13 16:36:28  
 
  Elapsed   00:00:09  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/conservative_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/conservative_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.hammock.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 363

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 364

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/conservative_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/conservative_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.tmp

# SYS command. line 366

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/conservative_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/conservative_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 367

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/conservative_set/ZBTB26_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.tmp
 
 
   
--------------------Stdout--------------------
9737 (process ID) old priority 0, new priority 19

  
 		 

    
  
 
  Num   30  
 
  ID   task.report.peak2hammock.line_361.id_49  
 
  Name   peak2hammock 
 
  Thread   thread_Root  
 
  PID   10416  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:36:29  
 
  End   2017-04-13 16:36:37  
 
  Elapsed   00:00:08  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.hammock.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 363

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 364

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.tmp

# SYS command. line 366

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 367

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB26_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.tmp
 
 
   
--------------------Stdout--------------------
10420 (process ID) old priority 0, new priority 19

  
 		 

    
  
 
  Num   31  
 
  ID   task.report.peak2hammock.line_361.id_50  
 
  Name   peak2hammock 
 
  Thread   thread_Root  
 
  PID   11133  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:36:38  
 
  End   2017-04-13 16:36:47  
 
  Elapsed   00:00:08  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.hammock.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 363

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 364

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.tmp

# SYS command. line 366

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 367

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB26_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.tmp
 
 
   
--------------------Stdout--------------------
11137 (process ID) old priority 0, new priority 19

  
 		 

    
  
 
  Num   32  
 
  ID   task.graphviz.report.line_97.id_51  
 
  Name   report 
 
  Thread   thread_Root  
 
  PID   11794  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:36:48  
 
  End   2017-04-13 16:36:56  
 
  Elapsed   00:00:08  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files     
 
  Output files     
 
  Dependencies     
 
 		  
 
# SYS command. line 98

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 99

 dot -Tsvg /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/report/ZBTB26_MACS2_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/report/ZBTB26_MACS2_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/report/ZBTB26_MACS2_workflow.svg" # to suppress dot font error (exit code=1)
 
 
   
--------------------Stdout--------------------
11798 (process ID) old priority 0, new priority 19

  
 		 

    
  
 
  Num   33  
 
  ID   task.report.pdf2png.line_328.id_52  
 
  Name   pdf2png 
 
  Thread   thread_Root  
 
  PID   11861  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:36:48  
 
  End   2017-04-13 16:36:57  
 
  Elapsed   00:00:08  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep1/ENCFF066ZSK.15M.cc.plot.pdf
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep1/ENCFF066ZSK.15M.cc.plot.png
  
 
  Dependencies     
 
 		  
 
# SYS command. line 329

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 330

 gs -dFirstPage=1 -dLastPage=1 -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -r110x110 \
			-dUseCropBox -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -sDEVICE=png16m \
			-sOutputFile=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep1/ENCFF066ZSK.15M.cc.plot.png \
			-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep1/ENCFF066ZSK.15M.cc.plot.pdf
 
 
   
--------------------Stdout--------------------
11867 (process ID) old priority 0, new priority 19

  
 		 

    
  
 
  Num   34  
 
  ID   task.report.pdf2png.line_328.id_53  
 
  Name   pdf2png 
 
  Thread   thread_Root  
 
  PID   11866  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:36:48  
 
  End   2017-04-13 16:36:57  
 
  Elapsed   00:00:08  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep2/ENCFF241VRG.15M.cc.plot.pdf
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep2/ENCFF241VRG.15M.cc.plot.png
  
 
  Dependencies     
 
 		  
 
# SYS command. line 329

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 330

 gs -dFirstPage=1 -dLastPage=1 -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -r110x110 \
			-dUseCropBox -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -sDEVICE=png16m \
			-sOutputFile=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep2/ENCFF241VRG.15M.cc.plot.png \
			-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/qc/rep2/ENCFF241VRG.15M.cc.plot.pdf
 
 
   
--------------------Stdout--------------------
11876 (process ID) old priority 0, new priority 19

  
 		 

	






	
 Global scope 

	Note: Global scope when program finished execution.
	

	
  Type  Name  Value  

	
  string  _  /usr/bin/bds  

	
  bool  allowEmpty  false  

	
  string[]  args  [-title, ZBTB26_MACS2, -nth, 5, -species, hg38_ENCODE, -url_base, http://mitra.stanford.edu/kundaje/leepc12/imk_chipseq/ZBTB26_MACS2/out, -filt_bam1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.bam, -filt_bam2, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.bam, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz, -pe, -macs2_for_idr, $]  

	
  bool  canFail  false  

	
  string  CPATH  /users/imk1/anaconda2/pkgs/gsl-1.16-1/include  

	
  int  cpus  -1  

	
  int  cpusLocal  56  

	
  int  day  86400  

	
  string  DEEPLIFT_DIR  /srv/scratch/imk1/TFBindingPredictionProject/src/deeplift/deeplift  

	
  string  DERBY_HOME  /usr/lib/jvm/java-8-oracle/db  

	
  string  DISPLAY  localhost:12.0  

	
  real  E  2.718281828459045  

	
  string  ENHANCER_SCRIPTS_DIR  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/  

	
  string  EVENT_NOEPOLL  1  

	
  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_CCx82k  

	
  string  LANG  en_US.UTF-8  

	
  string  LIBRARY_PATH  /users/imk1/anaconda2/pkgs/gsl-1.16-1/lib  

	
  string  LOADEDMODULES    

	
  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  MODULESHOME  /software/env_module/3.2.10  

	
  string  NLSPATH  /usr/dt/lib/nls/msg/%L/%N.cat  

	
  string  node    

	
  int  P  1125899906842624  

	
  string  PATH  /users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/rcade/:/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:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/av_scripts//exec:/users/imk1/edirect:/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  

	
  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/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2  

	
  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/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2  

	
  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  4  

	
  string  SSH_CLIENT  171.65.77.8 57066 22  

	
  string  SSH_CONNECTION  171.65.77.8 57067 171.65.76.63 22  

	
  string  SSH_TTY  /dev/pts/4  

	
  string  STY  27524.ZBTB26_MACS2.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  TMUX  /tmp/tmux-1048/default,43619,2  

	
  string  TMUX_PANE  %2  

	
  string  USER  imk1  

	
  string  UTIL_SCRIPTS_DIR  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/av_scripts/  

	
  int  walltimeout  8640000  

	
  int  week  604800  

	
  string  WINDOW  0  

	
  string  XDG_RUNTIME_DIR  /run/user/1048  

	
  string  XDG_SESSION_ID  67062  

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