BigDataScript report: chipseq.bds

Script file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20170413_132145_847
Start time 2017-04-13 13:21:45
Run time 02:58:37.807
Tasks executed 34
Tasks failed 0
Tasks failed names 
 

		
  Arguments*  [-title, ZBTB17_MACS2, -nth, 5, -species, hg38_ENCODE, -url_base, http://mitra.stanford.edu/kundaje/leepc12/imk_chipseq/ZBTB17_MACS2/out, -filt_bam1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.bam, -filt_bam2, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.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_132145_847/task.callpeak_macs2.macs2_n_s_pooled_rep.line_66.id_10
chipseq.bds.20170413_132145_847/task.callpeak_macs2.macs2_n_s_ppr1.line_66.id_11
chipseq.bds.20170413_132145_847/task.callpeak_macs2.macs2_n_s_ppr2.line_66.id_12
chipseq.bds.20170413_132145_847/task.callpeak_macs2.macs2_n_s_rep1.line_66.id_13
chipseq.bds.20170413_132145_847/task.callpeak_macs2.macs2_n_s_rep1_pr1.line_66.id_14
chipseq.bds.20170413_132145_847/task.callpeak_macs2.macs2_n_s_rep1_pr2.line_66.id_15
chipseq.bds.20170413_132145_847/task.callpeak_macs2.macs2_n_s_rep2.line_66.id_16
chipseq.bds.20170413_132145_847/task.callpeak_macs2.macs2_n_s_rep2_pr1.line_66.id_17
chipseq.bds.20170413_132145_847/task.callpeak_macs2.macs2_n_s_rep2_pr2.line_66.id_18
chipseq.bds.20170413_132145_847/task.callpeak_naive_overlap.naive_overlap.line_143.id_19
chipseq.bds.20170413_132145_847/task.callpeak_idr.idr2_rep1_rep2.line_74.id_20
chipseq.bds.20170413_132145_847/task.callpeak_idr.idr2_rep1_pr.line_74.id_21
chipseq.bds.20170413_132145_847/task.callpeak_idr.idr2_rep2_pr.line_74.id_22
chipseq.bds.20170413_132145_847/task.callpeak_idr.idr2_ppr.line_74.id_23
chipseq.bds.20170413_132145_847/task.sys.copy_file.line_131.id_32
chipseq.bds.20170413_132145_847/task.sys.copy_file.line_131.id_33
chipseq.bds.20170413_132145_847/task.sys.copy_file.line_131.id_34
chipseq.bds.20170413_132145_847/task.sys.copy_file.line_131.id_35
chipseq.bds.20170413_132145_847/task.callpeak_idr.idr_final_qc.line_283.id_36
chipseq.bds.20170413_132145_847/task.callpeak_idr.FRiP_rep1_pr.line_120.id_37
chipseq.bds.20170413_132145_847/task.callpeak_idr.FRiP_rep2_pr.line_120.id_38
chipseq.bds.20170413_132145_847/task.callpeak_idr.FRiP_ppr.line_120.id_39
chipseq.bds.20170413_132145_847/task.callpeak_idr.FRiP_rep1_rep2.line_120.id_40
chipseq.bds.20170413_132145_847/task.callpeak_blacklist_filter.blacklist_filter_peak_pooled.line_27.id_41
chipseq.bds.20170413_132145_847/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_42
chipseq.bds.20170413_132145_847/task.callpeak_blacklist_filter.blacklist_filter_peak_2.line_27.id_43
chipseq.bds.20170413_132145_847/task.report.peak2hammock.line_361.id_46
chipseq.bds.20170413_132145_847/task.report.peak2hammock.line_361.id_47
chipseq.bds.20170413_132145_847/task.report.peak2hammock.line_361.id_48
chipseq.bds.20170413_132145_847/task.report.peak2hammock.line_361.id_49
chipseq.bds.20170413_132145_847/task.report.peak2hammock.line_361.id_50
chipseq.bds.20170413_132145_847/task.graphviz.report.line_97.id_51
chipseq.bds.20170413_132145_847/task.report.pdf2png.line_328.id_52
chipseq.bds.20170413_132145_847/task.report.pdf2png.line_328.id_53
 
 		 

	
  thread_41   thread_Root 	 
  
 		 

	
  thread_42   thread_Root 	 
  
 		 

	
  thread_43   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   46807  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 13:21:58  
 
  End   2017-04-13 16:04:28  
 
  Elapsed   02:42:29  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/signal/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/signal/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/align/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 255 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep -o "ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/signal/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/align/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep -o "ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/signal/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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--------------------
14244 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 13:22:17: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 255 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_rep/ENCFF057NJA_ENCFF078YAS.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 13:22:17: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 13:22:17: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 13:22:20:  1000000 
INFO  @ Thu, 13 Apr 2017 13:22:22:  2000000 
INFO  @ Thu, 13 Apr 2017 13:22:24:  3000000 
INFO  @ Thu, 13 Apr 2017 13:22:26:  4000000 
INFO  @ Thu, 13 Apr 2017 13:22:28:  5000000 
INFO  @ Thu, 13 Apr 2017 13:22:30:  6000000 
INFO  @ Thu, 13 Apr 2017 13:22:32:  7000000 
INFO  @ Thu, 13 Apr 2017 13:22:34:  8000000 
INFO  @ Thu, 13 Apr 2017 13:22:36:  9000000 
INFO  @ Thu, 13 Apr 2017 13:22:38:  10000000 
INFO  @ Thu, 13 Apr 2017 13:22:40:  11000000 
INFO  @ Thu, 13 Apr 2017 13:22:42:  12000000 
INFO  @ Thu, 13 Apr 2017 13:22:44:  13000000 
INFO  @ Thu, 13 Apr 2017 13:22:46:  14000000 
INFO  @ Thu, 13 Apr 2017 13:22:48:  15000000 
INFO  @ Thu, 13 Apr 2017 13:22:50:  16000000 
INFO  @ Thu, 13 Apr 2017 13:22:52:  17000000 
INFO  @ Thu, 13 Apr 2017 13:22:54:  18000000 
INFO  @ Thu, 13 Apr 2017 13:22:57:  19000000 
INFO  @ Thu, 13 Apr 2017 13:22:59:  20000000 
INFO  @ Thu, 13 Apr 2017 13:23:01:  21000000 
INFO  @ Thu, 13 Apr 2017 13:23:03:  22000000 
INFO  @ Thu, 13 Apr 2017 13:23:05:  23000000 
INFO  @ Thu, 13 Apr 2017 13:23:07:  24000000 
INFO  @ Thu, 13 Apr 2017 13:23:09:  25000000 
INFO  @ Thu, 13 Apr 2017 13:23:11:  26000000 
INFO  @ Thu, 13 Apr 2017 13:23:13:  27000000 
INFO  @ Thu, 13 Apr 2017 13:23:15:  28000000 
INFO  @ Thu, 13 Apr 2017 13:23:17:  29000000 
INFO  @ Thu, 13 Apr 2017 13:23:20:  30000000 
INFO  @ Thu, 13 Apr 2017 13:23:22:  31000000 
INFO  @ Thu, 13 Apr 2017 13:23:24:  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 13:23:36:  38000000 
INFO  @ Thu, 13 Apr 2017 13:23:38:  39000000 
INFO  @ Thu, 13 Apr 2017 13:23:41:  40000000 
INFO  @ Thu, 13 Apr 2017 13:23:43:  41000000 
INFO  @ Thu, 13 Apr 2017 13:23:45:  42000000 
INFO  @ Thu, 13 Apr 2017 13:23:47:  43000000 
INFO  @ Thu, 13 Apr 2017 13:23:49:  44000000 
INFO  @ Thu, 13 Apr 2017 13:23:51:  45000000 
INFO  @ Thu, 13 Apr 2017 13:23:53:  46000000 
INFO  @ Thu, 13 Apr 2017 13:23:55:  47000000 
INFO  @ Thu, 13 Apr 2017 13:23:57:  48000000 
INFO  @ Thu, 13 Apr 2017 13:23:59:  49000000 
INFO  @ Thu, 13 Apr 2017 13:24:01:  50000000 
INFO  @ Thu, 13 Apr 2017 13:24:03:  51000000 
INFO  @ Thu, 13 Apr 2017 13:24:05:  52000000 
INFO  @ Thu, 13 Apr 2017 13:24:07:  53000000 
INFO  @ Thu, 13 Apr 2017 13:24:10:  54000000 
INFO  @ Thu, 13 Apr 2017 13:24:12:  55000000 
INFO  @ Thu, 13 Apr 2017 13:24:14:  56000000 
INFO  @ Thu, 13 Apr 2017 13:24:16:  57000000 
INFO  @ Thu, 13 Apr 2017 13:24:18:  58000000 
INFO  @ Thu, 13 Apr 2017 13:24:20:  59000000 
INFO  @ Thu, 13 Apr 2017 13:24:22:  60000000 
INFO  @ Thu, 13 Apr 2017 13:24:24:  61000000 
INFO  @ Thu, 13 Apr 2017 13:24:26:  62000000 
INFO  @ Thu, 13 Apr 2017 13:24:28:  63000000 
INFO  @ Thu, 13 Apr 2017 13:24:30:  64000000 
INFO  @ Thu, 13 Apr 2017 13:24:32:  65000000 
INFO  @ Thu, 13 Apr 2017 13:24:34:  66000000 
INFO  @ Thu, 13 Apr 2017 13:24:36:  67000000 
INFO  @ Thu, 13 Apr 2017 13:24:38:  68000000 
INFO  @ Thu, 13 Apr 2017 13:24:40:  69000000 
INFO  @ Thu, 13 Apr 2017 13:24:42:  70000000 
INFO  @ Thu, 13 Apr 2017 13:24:45:  71000000 
INFO  @ Thu, 13 Apr 2017 13:24:47:  72000000 
INFO  @ Thu, 13 Apr 2017 13:24:49:  73000000 
INFO  @ Thu, 13 Apr 2017 13:24:51:  74000000 
INFO  @ Thu, 13 Apr 2017 13:24:53:  75000000 
INFO  @ Thu, 13 Apr 2017 13:24:55:  76000000 
INFO  @ Thu, 13 Apr 2017 13:24:57:  77000000 
INFO  @ Thu, 13 Apr 2017 13:24:59:  78000000 
INFO  @ Thu, 13 Apr 2017 13:25:01:  79000000 
INFO  @ Thu, 13 Apr 2017 13:25:03:  80000000 
INFO  @ Thu, 13 Apr 2017 13:25:05:  81000000 
INFO  @ Thu, 13 Apr 2017 13:25:07:  82000000 
INFO  @ Thu, 13 Apr 2017 13:25:09:  83000000 
INFO  @ Thu, 13 Apr 2017 13:25:11:  84000000 
INFO  @ Thu, 13 Apr 2017 13:25:13:  85000000 
INFO  @ Thu, 13 Apr 2017 13:25:15:  86000000 
INFO  @ Thu, 13 Apr 2017 13:25:17:  87000000 
INFO  @ Thu, 13 Apr 2017 13:25:19:  88000000 
INFO  @ Thu, 13 Apr 2017 13:25:20:  89000000 
INFO  @ Thu, 13 Apr 2017 13:25:22:  90000000 
INFO  @ Thu, 13 Apr 2017 13:25:24:  91000000 
INFO  @ Thu, 13 Apr 2017 13:25:26:  92000000 
INFO  @ Thu, 13 Apr 2017 13:25:28:  93000000 
INFO  @ Thu, 13 Apr 2017 13:25:30:  94000000 
INFO  @ Thu, 13 Apr 2017 13:25:32:  95000000 
INFO  @ Thu, 13 Apr 2017 13:25:34:  96000000 
INFO  @ Thu, 13 Apr 2017 13:25:36:  97000000 
INFO  @ Thu, 13 Apr 2017 13:25:38:  98000000 
INFO  @ Thu, 13 Apr 2017 13:25:40:  99000000 
INFO  @ Thu, 13 Apr 2017 13:25:41:  100000000 
INFO  @ Thu, 13 Apr 2017 13:25:43:  101000000 
INFO  @ Thu, 13 Apr 2017 13:25:45:  102000000 
INFO  @ Thu, 13 Apr 2017 13:25:47:  103000000 
INFO  @ Thu, 13 Apr 2017 13:25:49:  104000000 
INFO  @ Thu, 13 Apr 2017 13:25:51:  105000000 
INFO  @ Thu, 13 Apr 2017 13:25:53:  106000000 
INFO  @ Thu, 13 Apr 2017 13:25:55:  107000000 
INFO  @ Thu, 13 Apr 2017 13:25:57:  108000000 
INFO  @ Thu, 13 Apr 2017 13:25:59:  109000000 
INFO  @ Thu, 13 Apr 2017 13:26:01:  110000000 
INFO  @ Thu, 13 Apr 2017 13:26:03:  111000000 
INFO  @ Thu, 13 Apr 2017 13:26:04:  112000000 
INFO  @ Thu, 13 Apr 2017 13:26:06:  113000000 
INFO  @ Thu, 13 Apr 2017 13:26:08:  114000000 
INFO  @ Thu, 13 Apr 2017 13:26:10:  115000000 
INFO  @ Thu, 13 Apr 2017 13:26:22: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 13:26:24:  1000000 
INFO  @ Thu, 13 Apr 2017 13:26:26:  2000000 
INFO  @ Thu, 13 Apr 2017 13:26:28:  3000000 
INFO  @ Thu, 13 Apr 2017 13:26:30:  4000000 
INFO  @ Thu, 13 Apr 2017 13:26:32:  5000000 
INFO  @ Thu, 13 Apr 2017 13:26:34:  6000000 
INFO  @ Thu, 13 Apr 2017 13:26:35:  7000000 
INFO  @ Thu, 13 Apr 2017 13:26:37:  8000000 
INFO  @ Thu, 13 Apr 2017 13:26:39:  9000000 
INFO  @ Thu, 13 Apr 2017 13:26:41:  10000000 
INFO  @ Thu, 13 Apr 2017 13:26:43:  11000000 
INFO  @ Thu, 13 Apr 2017 13:26:45:  12000000 
INFO  @ Thu, 13 Apr 2017 13:26:47:  13000000 
INFO  @ Thu, 13 Apr 2017 13:26:48:  14000000 
INFO  @ Thu, 13 Apr 2017 13:26:50:  15000000 
INFO  @ Thu, 13 Apr 2017 13:26:52:  16000000 
INFO  @ Thu, 13 Apr 2017 13:26:54:  17000000 
INFO  @ Thu, 13 Apr 2017 13:26:56:  18000000 
INFO  @ Thu, 13 Apr 2017 13:26:57:  19000000 
INFO  @ Thu, 13 Apr 2017 13:26:59:  20000000 
INFO  @ Thu, 13 Apr 2017 13:27:01:  21000000 
INFO  @ Thu, 13 Apr 2017 13:27:03:  22000000 
INFO  @ Thu, 13 Apr 2017 13:27:05:  23000000 
INFO  @ Thu, 13 Apr 2017 13:27:06:  24000000 
INFO  @ Thu, 13 Apr 2017 13:27:08:  25000000 
INFO  @ Thu, 13 Apr 2017 13:27:10:  26000000 
INFO  @ Thu, 13 Apr 2017 13:27:12:  27000000 
INFO  @ Thu, 13 Apr 2017 13:27:14:  28000000 
INFO  @ Thu, 13 Apr 2017 13:27:15:  29000000 
INFO  @ Thu, 13 Apr 2017 13:27:17:  30000000 
INFO  @ Thu, 13 Apr 2017 13:27:19:  31000000 
INFO  @ Thu, 13 Apr 2017 13:27:21:  32000000 
INFO  @ Thu, 13 Apr 2017 13:27:22:  33000000 
INFO  @ Thu, 13 Apr 2017 13:27:24:  34000000 
INFO  @ Thu, 13 Apr 2017 13:27:26:  35000000 
INFO  @ Thu, 13 Apr 2017 13:27:28:  36000000 
INFO  @ Thu, 13 Apr 2017 13:27:29:  37000000 
INFO  @ Thu, 13 Apr 2017 13:27:31:  38000000 
INFO  @ Thu, 13 Apr 2017 13:27:33:  39000000 
INFO  @ Thu, 13 Apr 2017 13:27:35:  40000000 
INFO  @ Thu, 13 Apr 2017 13:27:36:  41000000 
INFO  @ Thu, 13 Apr 2017 13:27:38:  42000000 
INFO  @ Thu, 13 Apr 2017 13:27:40:  43000000 
INFO  @ Thu, 13 Apr 2017 13:27:42:  44000000 
INFO  @ Thu, 13 Apr 2017 13:27:44:  45000000 
INFO  @ Thu, 13 Apr 2017 13:27:45:  46000000 
INFO  @ Thu, 13 Apr 2017 13:27:47:  47000000 
INFO  @ Thu, 13 Apr 2017 13:27:49:  48000000 
INFO  @ Thu, 13 Apr 2017 13:27:51:  49000000 
INFO  @ Thu, 13 Apr 2017 13:27:52:  50000000 
INFO  @ Thu, 13 Apr 2017 13:27:54:  51000000 
INFO  @ Thu, 13 Apr 2017 13:27:56:  52000000 
INFO  @ Thu, 13 Apr 2017 13:27:58:  53000000 
INFO  @ Thu, 13 Apr 2017 13:28:00:  54000000 
INFO  @ Thu, 13 Apr 2017 13:28:02:  55000000 
INFO  @ Thu, 13 Apr 2017 13:28:03:  56000000 
INFO  @ Thu, 13 Apr 2017 13:28:05:  57000000 
INFO  @ Thu, 13 Apr 2017 13:28:07:  58000000 
INFO  @ Thu, 13 Apr 2017 13:28:09:  59000000 
INFO  @ Thu, 13 Apr 2017 13:28:10:  60000000 
INFO  @ Thu, 13 Apr 2017 13:28:12:  61000000 
INFO  @ Thu, 13 Apr 2017 13:28:14:  62000000 
INFO  @ Thu, 13 Apr 2017 13:28:16:  63000000 
INFO  @ Thu, 13 Apr 2017 13:28:17:  64000000 
INFO  @ Thu, 13 Apr 2017 13:28:19:  65000000 
INFO  @ Thu, 13 Apr 2017 13:28:21:  66000000 
INFO  @ Thu, 13 Apr 2017 13:28:23:  67000000 
INFO  @ Thu, 13 Apr 2017 13:28:25:  68000000 
INFO  @ Thu, 13 Apr 2017 13:28:27:  69000000 
INFO  @ Thu, 13 Apr 2017 13:28:29:  70000000 
INFO  @ Thu, 13 Apr 2017 13:28:30:  71000000 
INFO  @ Thu, 13 Apr 2017 13:28:32:  72000000 
INFO  @ Thu, 13 Apr 2017 13:28:34:  73000000 
INFO  @ Thu, 13 Apr 2017 13:28:36:  74000000 
INFO  @ Thu, 13 Apr 2017 13:28:38:  75000000 
INFO  @ Thu, 13 Apr 2017 13:28:39:  76000000 
INFO  @ Thu, 13 Apr 2017 13:28:41:  77000000 
INFO  @ Thu, 13 Apr 2017 13:28:43:  78000000 
INFO  @ Thu, 13 Apr 2017 13:28:45:  79000000 
INFO  @ Thu, 13 Apr 2017 13:28:46:  80000000 
INFO  @ Thu, 13 Apr 2017 13:28:48:  81000000 
INFO  @ Thu, 13 Apr 2017 13:28:50:  82000000 
INFO  @ Thu, 13 Apr 2017 13:28:52:  83000000 
INFO  @ Thu, 13 Apr 2017 13:28:54:  84000000 
INFO  @ Thu, 13 Apr 2017 13:28:56:  85000000 
INFO  @ Thu, 13 Apr 2017 13:28:57:  86000000 
INFO  @ Thu, 13 Apr 2017 13:28:59:  87000000 
INFO  @ Thu, 13 Apr 2017 13:29:01:  88000000 
INFO  @ Thu, 13 Apr 2017 13:29:03:  89000000 
INFO  @ Thu, 13 Apr 2017 13:29:05:  90000000 
INFO  @ Thu, 13 Apr 2017 13:29:06:  91000000 
INFO  @ Thu, 13 Apr 2017 13:29:08:  92000000 
INFO  @ Thu, 13 Apr 2017 13:29:10:  93000000 
INFO  @ Thu, 13 Apr 2017 13:29:12:  94000000 
INFO  @ Thu, 13 Apr 2017 13:29:14:  95000000 
INFO  @ Thu, 13 Apr 2017 13:29:16:  96000000 
INFO  @ Thu, 13 Apr 2017 13:29:18:  97000000 
INFO  @ Thu, 13 Apr 2017 13:29:19:  98000000 
INFO  @ Thu, 13 Apr 2017 13:29:21:  99000000 
INFO  @ Thu, 13 Apr 2017 13:29:23: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 13:29:23: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 13:29:23: #1  total tags in treatment: 115595584 
INFO  @ Thu, 13 Apr 2017 13:29:23: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 13:29:23: #1 finished! 
INFO  @ Thu, 13 Apr 2017 13:29:23: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 13:29:23: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 13:29:23: #2 Use 255 as fragment length 
INFO  @ Thu, 13 Apr 2017 13:29:23: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 13:29:23: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 13:29:23: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 13:38:11: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 13:38:11: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 13:38:11: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 13:38:11: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 13:38:11: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 13:54:22: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 13:54:25: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 13:54:27: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 13:54:28: Done! 
INFO  @ Thu, 13 Apr 2017 13:54:33: Read and build treatment bedGraph... 
INFO  @ Thu, 13 Apr 2017 13:58:48: Read and build control bedGraph... 
INFO  @ Thu, 13 Apr 2017 14:02:10: Build scoreTrackII... 
INFO  @ Thu, 13 Apr 2017 14:05:08: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Thu, 13 Apr 2017 14:22:52: Write bedGraph of scores... 
INFO  @ Thu, 13 Apr 2017 14:34:53: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_FE.bdg'! 
INFO  @ Thu, 13 Apr 2017 15:01:57: Read and build treatment bedGraph... 
INFO  @ Thu, 13 Apr 2017 15:06:10: Read and build control bedGraph... 
INFO  @ Thu, 13 Apr 2017 15:09:30: Build scoreTrackII... 
INFO  @ Thu, 13 Apr 2017 15:12:00: Values in your input bedGraph files will be multiplied by 99.493262 ... 
INFO  @ Thu, 13 Apr 2017 15:28:05: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Thu, 13 Apr 2017 15:32:27: Write bedGraph of scores... 
INFO  @ Thu, 13 Apr 2017 15:42:15: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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   46808  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 13:21:58  
 
  End   2017-04-13 13:43:14  
 
  Elapsed   00:21:15  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 255 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1 -o "ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1 -o "ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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--------------------
28021 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 13:22:17: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 255 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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 13:22:17: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 13:22:17: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 13:22:19:  1000000 
INFO  @ Thu, 13 Apr 2017 13:22:20:  2000000 
INFO  @ Thu, 13 Apr 2017 13:22:22:  3000000 
INFO  @ Thu, 13 Apr 2017 13:22:24:  4000000 
INFO  @ Thu, 13 Apr 2017 13:22:25:  5000000 
INFO  @ Thu, 13 Apr 2017 13:22:27:  6000000 
INFO  @ Thu, 13 Apr 2017 13:22:28:  7000000 
INFO  @ Thu, 13 Apr 2017 13:22:30:  8000000 
INFO  @ Thu, 13 Apr 2017 13:22:32:  9000000 
INFO  @ Thu, 13 Apr 2017 13:22:33:  10000000 
INFO  @ Thu, 13 Apr 2017 13:22:35:  11000000 
INFO  @ Thu, 13 Apr 2017 13:22:36:  12000000 
INFO  @ Thu, 13 Apr 2017 13:22:38:  13000000 
INFO  @ Thu, 13 Apr 2017 13:22:39:  14000000 
INFO  @ Thu, 13 Apr 2017 13:22:41:  15000000 
INFO  @ Thu, 13 Apr 2017 13:22:43:  16000000 
INFO  @ Thu, 13 Apr 2017 13:22:44:  17000000 
INFO  @ Thu, 13 Apr 2017 13:22:46:  18000000 
INFO  @ Thu, 13 Apr 2017 13:22:48:  19000000 
INFO  @ Thu, 13 Apr 2017 13:22:49:  20000000 
INFO  @ Thu, 13 Apr 2017 13:22:51:  21000000 
INFO  @ Thu, 13 Apr 2017 13:22:53:  22000000 
INFO  @ Thu, 13 Apr 2017 13:22:54:  23000000 
INFO  @ Thu, 13 Apr 2017 13:22:56:  24000000 
INFO  @ Thu, 13 Apr 2017 13:22:58:  25000000 
INFO  @ Thu, 13 Apr 2017 13:23:00:  26000000 
INFO  @ Thu, 13 Apr 2017 13:23:01:  27000000 
INFO  @ Thu, 13 Apr 2017 13:23:03:  28000000 
INFO  @ Thu, 13 Apr 2017 13:23:05:  29000000 
INFO  @ Thu, 13 Apr 2017 13:23:06:  30000000 
INFO  @ Thu, 13 Apr 2017 13:23:08:  31000000 
INFO  @ Thu, 13 Apr 2017 13:23:09:  32000000 
INFO  @ Thu, 13 Apr 2017 13:23:11:  33000000 
INFO  @ Thu, 13 Apr 2017 13:23:12:  34000000 
INFO  @ Thu, 13 Apr 2017 13:23:14:  35000000 
INFO  @ Thu, 13 Apr 2017 13:23:16:  36000000 
INFO  @ Thu, 13 Apr 2017 13:23:17:  37000000 
INFO  @ Thu, 13 Apr 2017 13:23:19:  38000000 
INFO  @ Thu, 13 Apr 2017 13:23:21:  39000000 
INFO  @ Thu, 13 Apr 2017 13:23:22:  40000000 
INFO  @ Thu, 13 Apr 2017 13:23:24:  41000000 
INFO  @ Thu, 13 Apr 2017 13:23:25:  42000000 
INFO  @ Thu, 13 Apr 2017 13:23:27:  43000000 
INFO  @ Thu, 13 Apr 2017 13:23:29:  44000000 
INFO  @ Thu, 13 Apr 2017 13:23:30:  45000000 
INFO  @ Thu, 13 Apr 2017 13:23:32:  46000000 
INFO  @ Thu, 13 Apr 2017 13:23:33:  47000000 
INFO  @ Thu, 13 Apr 2017 13:23:35:  48000000 
INFO  @ Thu, 13 Apr 2017 13:23:37:  49000000 
INFO  @ Thu, 13 Apr 2017 13:23:38:  50000000 
INFO  @ Thu, 13 Apr 2017 13:23:40:  51000000 
INFO  @ Thu, 13 Apr 2017 13:23:41:  52000000 
INFO  @ Thu, 13 Apr 2017 13:23:43:  53000000 
INFO  @ Thu, 13 Apr 2017 13:23:45:  54000000 
INFO  @ Thu, 13 Apr 2017 13:23:46:  55000000 
INFO  @ Thu, 13 Apr 2017 13:23:48:  56000000 
INFO  @ Thu, 13 Apr 2017 13:23:49:  57000000 
INFO  @ Thu, 13 Apr 2017 13:23:55: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 13:23:56:  1000000 
INFO  @ Thu, 13 Apr 2017 13:23:57:  2000000 
INFO  @ Thu, 13 Apr 2017 13:23:59:  3000000 
INFO  @ Thu, 13 Apr 2017 13:24:00:  4000000 
INFO  @ Thu, 13 Apr 2017 13:24:02:  5000000 
INFO  @ Thu, 13 Apr 2017 13:24:03:  6000000 
INFO  @ Thu, 13 Apr 2017 13:24:05:  7000000 
INFO  @ Thu, 13 Apr 2017 13:24:06:  8000000 
INFO  @ Thu, 13 Apr 2017 13:24:08:  9000000 
INFO  @ Thu, 13 Apr 2017 13:24:09:  10000000 
INFO  @ Thu, 13 Apr 2017 13:24:10:  11000000 
INFO  @ Thu, 13 Apr 2017 13:24:12:  12000000 
INFO  @ Thu, 13 Apr 2017 13:24:13:  13000000 
INFO  @ Thu, 13 Apr 2017 13:24:15:  14000000 
INFO  @ Thu, 13 Apr 2017 13:24:16:  15000000 
INFO  @ Thu, 13 Apr 2017 13:24:18:  16000000 
INFO  @ Thu, 13 Apr 2017 13:24:19:  17000000 
INFO  @ Thu, 13 Apr 2017 13:24:20:  18000000 
INFO  @ Thu, 13 Apr 2017 13:24:22:  19000000 
INFO  @ Thu, 13 Apr 2017 13:24:23:  20000000 
INFO  @ Thu, 13 Apr 2017 13:24:25:  21000000 
INFO  @ Thu, 13 Apr 2017 13:24:26:  22000000 
INFO  @ Thu, 13 Apr 2017 13:24:28:  23000000 
INFO  @ Thu, 13 Apr 2017 13:24:29:  24000000 
INFO  @ Thu, 13 Apr 2017 13:24:31:  25000000 
INFO  @ Thu, 13 Apr 2017 13:24:32:  26000000 
INFO  @ Thu, 13 Apr 2017 13:24:34:  27000000 
INFO  @ Thu, 13 Apr 2017 13:24:35:  28000000 
INFO  @ Thu, 13 Apr 2017 13:24:37:  29000000 
INFO  @ Thu, 13 Apr 2017 13:24:38:  30000000 
INFO  @ Thu, 13 Apr 2017 13:24:39:  31000000 
INFO  @ Thu, 13 Apr 2017 13:24:41:  32000000 
INFO  @ Thu, 13 Apr 2017 13:24:43:  33000000 
INFO  @ Thu, 13 Apr 2017 13:24:44:  34000000 
INFO  @ Thu, 13 Apr 2017 13:24:46:  35000000 
INFO  @ Thu, 13 Apr 2017 13:24:47:  36000000 
INFO  @ Thu, 13 Apr 2017 13:24:48:  37000000 
INFO  @ Thu, 13 Apr 2017 13:24:50:  38000000 
INFO  @ Thu, 13 Apr 2017 13:24:51:  39000000 
INFO  @ Thu, 13 Apr 2017 13:24:53:  40000000 
INFO  @ Thu, 13 Apr 2017 13:24:54:  41000000 
INFO  @ Thu, 13 Apr 2017 13:24:55:  42000000 
INFO  @ Thu, 13 Apr 2017 13:24:57:  43000000 
INFO  @ Thu, 13 Apr 2017 13:24:58:  44000000 
INFO  @ Thu, 13 Apr 2017 13:25:00:  45000000 
INFO  @ Thu, 13 Apr 2017 13:25:01:  46000000 
INFO  @ Thu, 13 Apr 2017 13:25:02:  47000000 
INFO  @ Thu, 13 Apr 2017 13:25:04:  48000000 
INFO  @ Thu, 13 Apr 2017 13:25:05:  49000000 
INFO  @ Thu, 13 Apr 2017 13:25:07:  50000000 
INFO  @ Thu, 13 Apr 2017 13:25:08:  51000000 
INFO  @ Thu, 13 Apr 2017 13:25:10:  52000000 
INFO  @ Thu, 13 Apr 2017 13:25:11:  53000000 
INFO  @ Thu, 13 Apr 2017 13:25:12:  54000000 
INFO  @ Thu, 13 Apr 2017 13:25:14:  55000000 
INFO  @ Thu, 13 Apr 2017 13:25:15:  56000000 
INFO  @ Thu, 13 Apr 2017 13:25:17:  57000000 
INFO  @ Thu, 13 Apr 2017 13:25:18:  58000000 
INFO  @ Thu, 13 Apr 2017 13:25:20:  59000000 
INFO  @ Thu, 13 Apr 2017 13:25:21:  60000000 
INFO  @ Thu, 13 Apr 2017 13:25:23:  61000000 
INFO  @ Thu, 13 Apr 2017 13:25:24:  62000000 
INFO  @ Thu, 13 Apr 2017 13:25:26:  63000000 
INFO  @ Thu, 13 Apr 2017 13:25:27:  64000000 
INFO  @ Thu, 13 Apr 2017 13:25:29:  65000000 
INFO  @ Thu, 13 Apr 2017 13:25:30:  66000000 
INFO  @ Thu, 13 Apr 2017 13:25:32:  67000000 
INFO  @ Thu, 13 Apr 2017 13:25:33:  68000000 
INFO  @ Thu, 13 Apr 2017 13:25:35:  69000000 
INFO  @ Thu, 13 Apr 2017 13:25:36:  70000000 
INFO  @ Thu, 13 Apr 2017 13:25:38:  71000000 
INFO  @ Thu, 13 Apr 2017 13:25:39:  72000000 
INFO  @ Thu, 13 Apr 2017 13:25:41:  73000000 
INFO  @ Thu, 13 Apr 2017 13:25:42:  74000000 
INFO  @ Thu, 13 Apr 2017 13:25:43:  75000000 
INFO  @ Thu, 13 Apr 2017 13:25:45:  76000000 
INFO  @ Thu, 13 Apr 2017 13:25:46:  77000000 
INFO  @ Thu, 13 Apr 2017 13:25:47:  78000000 
INFO  @ Thu, 13 Apr 2017 13:25:49:  79000000 
INFO  @ Thu, 13 Apr 2017 13:25:50:  80000000 
INFO  @ Thu, 13 Apr 2017 13:25:52:  81000000 
INFO  @ Thu, 13 Apr 2017 13:25:53:  82000000 
INFO  @ Thu, 13 Apr 2017 13:25:54:  83000000 
INFO  @ Thu, 13 Apr 2017 13:25:56:  84000000 
INFO  @ Thu, 13 Apr 2017 13:25:57:  85000000 
INFO  @ Thu, 13 Apr 2017 13:25:59:  86000000 
INFO  @ Thu, 13 Apr 2017 13:26:00:  87000000 
INFO  @ Thu, 13 Apr 2017 13:26:01:  88000000 
INFO  @ Thu, 13 Apr 2017 13:26:03:  89000000 
INFO  @ Thu, 13 Apr 2017 13:26:05:  90000000 
INFO  @ Thu, 13 Apr 2017 13:26:06:  91000000 
INFO  @ Thu, 13 Apr 2017 13:26:07:  92000000 
INFO  @ Thu, 13 Apr 2017 13:26:09:  93000000 
INFO  @ Thu, 13 Apr 2017 13:26:11:  94000000 
INFO  @ Thu, 13 Apr 2017 13:26:12:  95000000 
INFO  @ Thu, 13 Apr 2017 13:26:13:  96000000 
INFO  @ Thu, 13 Apr 2017 13:26:15:  97000000 
INFO  @ Thu, 13 Apr 2017 13:26:16:  98000000 
INFO  @ Thu, 13 Apr 2017 13:26:17:  99000000 
INFO  @ Thu, 13 Apr 2017 13:26:19: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 13:26:19: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 13:26:19: #1  total tags in treatment: 57797794 
INFO  @ Thu, 13 Apr 2017 13:26:19: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 13:26:19: #1 finished! 
INFO  @ Thu, 13 Apr 2017 13:26:19: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 13:26:19: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 13:26:19: #2 Use 255 as fragment length 
INFO  @ Thu, 13 Apr 2017 13:26:19: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 13:26:19: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 13:26:19: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 13:32:16: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 13:32:16: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 13:32:16: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 13:32:16: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 13:32:16: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 13:43:07: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 13:43:08: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 13:43:09: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 13:43:10: Done! 

 
 		 

    
  
 
  Num   3  
 
  ID   task.callpeak_macs2.macs2_n_s_ppr2.line_66.id_12  
 
  Name   macs2 n/s ppr2 
 
  Thread   thread_Root  
 
  PID   46809  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 13:22:00  
 
  End   2017-04-13 13:44:06  
 
  Elapsed   00:22:05  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 255 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2 -o "ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2 -o "ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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--------------------
15530 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 13:22:21: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 255 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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 13:22:21: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 13:22:21: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 13:22:23:  1000000 
INFO  @ Thu, 13 Apr 2017 13:22:24:  2000000 
INFO  @ Thu, 13 Apr 2017 13:22:26:  3000000 
INFO  @ Thu, 13 Apr 2017 13:22:27:  4000000 
INFO  @ Thu, 13 Apr 2017 13:22:29:  5000000 
INFO  @ Thu, 13 Apr 2017 13:22:30:  6000000 
INFO  @ Thu, 13 Apr 2017 13:22:32:  7000000 
INFO  @ Thu, 13 Apr 2017 13:22:33:  8000000 
INFO  @ Thu, 13 Apr 2017 13:22:35:  9000000 
INFO  @ Thu, 13 Apr 2017 13:22:36:  10000000 
INFO  @ Thu, 13 Apr 2017 13:22:38:  11000000 
INFO  @ Thu, 13 Apr 2017 13:22:39:  12000000 
INFO  @ Thu, 13 Apr 2017 13:22:41:  13000000 
INFO  @ Thu, 13 Apr 2017 13:22:42:  14000000 
INFO  @ Thu, 13 Apr 2017 13:22:44:  15000000 
INFO  @ Thu, 13 Apr 2017 13:22:45:  16000000 
INFO  @ Thu, 13 Apr 2017 13:22:47:  17000000 
INFO  @ Thu, 13 Apr 2017 13:22:48:  18000000 
INFO  @ Thu, 13 Apr 2017 13:22:50:  19000000 
INFO  @ Thu, 13 Apr 2017 13:22:51:  20000000 
INFO  @ Thu, 13 Apr 2017 13:22:53:  21000000 
INFO  @ Thu, 13 Apr 2017 13:22:55:  22000000 
INFO  @ Thu, 13 Apr 2017 13:22:56:  23000000 
INFO  @ Thu, 13 Apr 2017 13:22:58:  24000000 
INFO  @ Thu, 13 Apr 2017 13:22:59:  25000000 
INFO  @ Thu, 13 Apr 2017 13:23:01:  26000000 
INFO  @ Thu, 13 Apr 2017 13:23:02:  27000000 
INFO  @ Thu, 13 Apr 2017 13:23:04:  28000000 
INFO  @ Thu, 13 Apr 2017 13:23:06:  29000000 
INFO  @ Thu, 13 Apr 2017 13:23:07:  30000000 
INFO  @ Thu, 13 Apr 2017 13:23:09:  31000000 
INFO  @ Thu, 13 Apr 2017 13:23:10:  32000000 
INFO  @ Thu, 13 Apr 2017 13:23:12:  33000000 
INFO  @ Thu, 13 Apr 2017 13:23:13:  34000000 
INFO  @ Thu, 13 Apr 2017 13:23:15:  35000000 
INFO  @ Thu, 13 Apr 2017 13:23:17:  36000000 
INFO  @ Thu, 13 Apr 2017 13:23:18:  37000000 
INFO  @ Thu, 13 Apr 2017 13:23:20:  38000000 
INFO  @ Thu, 13 Apr 2017 13:23:21:  39000000 
INFO  @ Thu, 13 Apr 2017 13:23:23:  40000000 
INFO  @ Thu, 13 Apr 2017 13:23:24:  41000000 
INFO  @ Thu, 13 Apr 2017 13:23:26:  42000000 
INFO  @ Thu, 13 Apr 2017 13:23:28:  43000000 
INFO  @ Thu, 13 Apr 2017 13:23:29:  44000000 
INFO  @ Thu, 13 Apr 2017 13:23:31:  45000000 
INFO  @ Thu, 13 Apr 2017 13:23:33:  46000000 
INFO  @ Thu, 13 Apr 2017 13:23:34:  47000000 
INFO  @ Thu, 13 Apr 2017 13:23:36:  48000000 
INFO  @ Thu, 13 Apr 2017 13:23:38:  49000000 
INFO  @ Thu, 13 Apr 2017 13:23:39:  50000000 
INFO  @ Thu, 13 Apr 2017 13:23:41:  51000000 
INFO  @ Thu, 13 Apr 2017 13:23:42:  52000000 
INFO  @ Thu, 13 Apr 2017 13:23:44:  53000000 
INFO  @ Thu, 13 Apr 2017 13:23:46:  54000000 
INFO  @ Thu, 13 Apr 2017 13:23:47:  55000000 
INFO  @ Thu, 13 Apr 2017 13:23:49:  56000000 
INFO  @ Thu, 13 Apr 2017 13:23:50:  57000000 
INFO  @ Thu, 13 Apr 2017 13:23:56: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 13:23:58:  1000000 
INFO  @ Thu, 13 Apr 2017 13:23:59:  2000000 
INFO  @ Thu, 13 Apr 2017 13:24:01:  3000000 
INFO  @ Thu, 13 Apr 2017 13:24:02:  4000000 
INFO  @ Thu, 13 Apr 2017 13:24:04:  5000000 
INFO  @ Thu, 13 Apr 2017 13:24:05:  6000000 
INFO  @ Thu, 13 Apr 2017 13:24:06:  7000000 
INFO  @ Thu, 13 Apr 2017 13:24:08:  8000000 
INFO  @ Thu, 13 Apr 2017 13:24:09:  9000000 
INFO  @ Thu, 13 Apr 2017 13:24:11:  10000000 
INFO  @ Thu, 13 Apr 2017 13:24:12:  11000000 
INFO  @ Thu, 13 Apr 2017 13:24:14:  12000000 
INFO  @ Thu, 13 Apr 2017 13:24:15:  13000000 
INFO  @ Thu, 13 Apr 2017 13:24:17:  14000000 
INFO  @ Thu, 13 Apr 2017 13:24:18:  15000000 
INFO  @ Thu, 13 Apr 2017 13:24:20:  16000000 
INFO  @ Thu, 13 Apr 2017 13:24:21:  17000000 
INFO  @ Thu, 13 Apr 2017 13:24:23:  18000000 
INFO  @ Thu, 13 Apr 2017 13:24:24:  19000000 
INFO  @ Thu, 13 Apr 2017 13:24:25:  20000000 
INFO  @ Thu, 13 Apr 2017 13:24:27:  21000000 
INFO  @ Thu, 13 Apr 2017 13:24:28:  22000000 
INFO  @ Thu, 13 Apr 2017 13:24:30:  23000000 
INFO  @ Thu, 13 Apr 2017 13:24:31:  24000000 
INFO  @ Thu, 13 Apr 2017 13:24:33:  25000000 
INFO  @ Thu, 13 Apr 2017 13:24:34:  26000000 
INFO  @ Thu, 13 Apr 2017 13:24:36:  27000000 
INFO  @ Thu, 13 Apr 2017 13:24:37:  28000000 
INFO  @ Thu, 13 Apr 2017 13:24:39:  29000000 
INFO  @ Thu, 13 Apr 2017 13:24:40:  30000000 
INFO  @ Thu, 13 Apr 2017 13:24:41:  31000000 
INFO  @ Thu, 13 Apr 2017 13:24:43:  32000000 
INFO  @ Thu, 13 Apr 2017 13:24:44:  33000000 
INFO  @ Thu, 13 Apr 2017 13:24:46:  34000000 
INFO  @ Thu, 13 Apr 2017 13:24:47:  35000000 
INFO  @ Thu, 13 Apr 2017 13:24:49:  36000000 
INFO  @ Thu, 13 Apr 2017 13:24:50:  37000000 
INFO  @ Thu, 13 Apr 2017 13:24:52:  38000000 
INFO  @ Thu, 13 Apr 2017 13:24:53:  39000000 
INFO  @ Thu, 13 Apr 2017 13:24:54:  40000000 
INFO  @ Thu, 13 Apr 2017 13:24:56:  41000000 
INFO  @ Thu, 13 Apr 2017 13:24:57:  42000000 
INFO  @ Thu, 13 Apr 2017 13:24:59:  43000000 
INFO  @ Thu, 13 Apr 2017 13:25:00:  44000000 
INFO  @ Thu, 13 Apr 2017 13:25:02:  45000000 
INFO  @ Thu, 13 Apr 2017 13:25:03:  46000000 
INFO  @ Thu, 13 Apr 2017 13:25:05:  47000000 
INFO  @ Thu, 13 Apr 2017 13:25:06:  48000000 
INFO  @ Thu, 13 Apr 2017 13:25:08:  49000000 
INFO  @ Thu, 13 Apr 2017 13:25:10:  50000000 
INFO  @ Thu, 13 Apr 2017 13:25:11:  51000000 
INFO  @ Thu, 13 Apr 2017 13:25:13:  52000000 
INFO  @ Thu, 13 Apr 2017 13:25:14:  53000000 
INFO  @ Thu, 13 Apr 2017 13:25:16:  54000000 
INFO  @ Thu, 13 Apr 2017 13:25:18:  55000000 
INFO  @ Thu, 13 Apr 2017 13:25:19:  56000000 
INFO  @ Thu, 13 Apr 2017 13:25:20:  57000000 
INFO  @ Thu, 13 Apr 2017 13:25:22:  58000000 
INFO  @ Thu, 13 Apr 2017 13:25:23:  59000000 
INFO  @ Thu, 13 Apr 2017 13:25:25:  60000000 
INFO  @ Thu, 13 Apr 2017 13:25:26:  61000000 
INFO  @ Thu, 13 Apr 2017 13:25:28:  62000000 
INFO  @ Thu, 13 Apr 2017 13:25:29:  63000000 
INFO  @ Thu, 13 Apr 2017 13:25:31:  64000000 
INFO  @ Thu, 13 Apr 2017 13:25:32:  65000000 
INFO  @ Thu, 13 Apr 2017 13:25:34:  66000000 
INFO  @ Thu, 13 Apr 2017 13:25:35:  67000000 
INFO  @ Thu, 13 Apr 2017 13:25:37:  68000000 
INFO  @ Thu, 13 Apr 2017 13:25:38:  69000000 
INFO  @ Thu, 13 Apr 2017 13:25:39:  70000000 
INFO  @ Thu, 13 Apr 2017 13:25:41:  71000000 
INFO  @ Thu, 13 Apr 2017 13:25:43:  72000000 
INFO  @ Thu, 13 Apr 2017 13:25:44:  73000000 
INFO  @ Thu, 13 Apr 2017 13:25:46:  74000000 
INFO  @ Thu, 13 Apr 2017 13:25:47:  75000000 
INFO  @ Thu, 13 Apr 2017 13:25:49:  76000000 
INFO  @ Thu, 13 Apr 2017 13:25:50:  77000000 
INFO  @ Thu, 13 Apr 2017 13:25:52:  78000000 
INFO  @ Thu, 13 Apr 2017 13:25:53:  79000000 
INFO  @ Thu, 13 Apr 2017 13:25:54:  80000000 
INFO  @ Thu, 13 Apr 2017 13:25:56:  81000000 
INFO  @ Thu, 13 Apr 2017 13:25:57:  82000000 
INFO  @ Thu, 13 Apr 2017 13:25:59:  83000000 
INFO  @ Thu, 13 Apr 2017 13:26:00:  84000000 
INFO  @ Thu, 13 Apr 2017 13:26:01:  85000000 
INFO  @ Thu, 13 Apr 2017 13:26:03:  86000000 
INFO  @ Thu, 13 Apr 2017 13:26:04:  87000000 
INFO  @ Thu, 13 Apr 2017 13:26:06:  88000000 
INFO  @ Thu, 13 Apr 2017 13:26:07:  89000000 
INFO  @ Thu, 13 Apr 2017 13:26:09:  90000000 
INFO  @ Thu, 13 Apr 2017 13:26:10:  91000000 
INFO  @ Thu, 13 Apr 2017 13:26:11:  92000000 
INFO  @ Thu, 13 Apr 2017 13:26:13:  93000000 
INFO  @ Thu, 13 Apr 2017 13:26:14:  94000000 
INFO  @ Thu, 13 Apr 2017 13:26:15:  95000000 
INFO  @ Thu, 13 Apr 2017 13:26:17:  96000000 
INFO  @ Thu, 13 Apr 2017 13:26:18:  97000000 
INFO  @ Thu, 13 Apr 2017 13:26:20:  98000000 
INFO  @ Thu, 13 Apr 2017 13:26:21:  99000000 
INFO  @ Thu, 13 Apr 2017 13:26:23: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 13:26:23: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 13:26:23: #1  total tags in treatment: 57797790 
INFO  @ Thu, 13 Apr 2017 13:26:23: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 13:26:23: #1 finished! 
INFO  @ Thu, 13 Apr 2017 13:26:23: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 13:26:23: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 13:26:23: #2 Use 255 as fragment length 
INFO  @ Thu, 13 Apr 2017 13:26:23: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 13:26:23: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 13:26:23: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 13:34:24: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 13:34:24: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 13:34:24: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 13:34:24: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 13:34:24: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 13:43:52: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 13:43:56: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 13:43:58: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 13:44:00: Done! 

 
 		 

    
  
 
  Num   4  
 
  ID   task.callpeak_macs2.macs2_n_s_rep1.line_66.id_13  
 
  Name   macs2 n/s rep1 
 
  Thread   thread_Root  
 
  PID   46810  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 13:22:01  
 
  End   2017-04-13 15:18:25  
 
  Elapsed   01:56:24  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/signal/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/signal/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 265 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1 -o "ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/signal/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1 -o "ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/signal/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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--------------------
14245 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 13:22:17: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 265 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.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 13:22:17: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 13:22:17: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 13:22:19:  1000000 
INFO  @ Thu, 13 Apr 2017 13:22:21:  2000000 
INFO  @ Thu, 13 Apr 2017 13:22:23:  3000000 
INFO  @ Thu, 13 Apr 2017 13:22:25:  4000000 
INFO  @ Thu, 13 Apr 2017 13:22:27:  5000000 
INFO  @ Thu, 13 Apr 2017 13:22:29:  6000000 
INFO  @ Thu, 13 Apr 2017 13:22:31:  7000000 
INFO  @ Thu, 13 Apr 2017 13:22:33:  8000000 
INFO  @ Thu, 13 Apr 2017 13:22:35:  9000000 
INFO  @ Thu, 13 Apr 2017 13:22:37:  10000000 
INFO  @ Thu, 13 Apr 2017 13:22:39:  11000000 
INFO  @ Thu, 13 Apr 2017 13:22:41:  12000000 
INFO  @ Thu, 13 Apr 2017 13:22:44:  13000000 
INFO  @ Thu, 13 Apr 2017 13:22:46:  14000000 
INFO  @ Thu, 13 Apr 2017 13:22:48:  15000000 
INFO  @ Thu, 13 Apr 2017 13:22:50:  16000000 
INFO  @ Thu, 13 Apr 2017 13:22:52:  17000000 
INFO  @ Thu, 13 Apr 2017 13:22:54:  18000000 
INFO  @ Thu, 13 Apr 2017 13:22:56:  19000000 
INFO  @ Thu, 13 Apr 2017 13:22:58:  20000000 
INFO  @ Thu, 13 Apr 2017 13:23:00:  21000000 
INFO  @ Thu, 13 Apr 2017 13:23:02:  22000000 
INFO  @ Thu, 13 Apr 2017 13:23:04:  23000000 
INFO  @ Thu, 13 Apr 2017 13:23:06:  24000000 
INFO  @ Thu, 13 Apr 2017 13:23:08:  25000000 
INFO  @ Thu, 13 Apr 2017 13:23:10:  26000000 
INFO  @ Thu, 13 Apr 2017 13:23:12:  27000000 
INFO  @ Thu, 13 Apr 2017 13:23:14:  28000000 
INFO  @ Thu, 13 Apr 2017 13:23:16:  29000000 
INFO  @ Thu, 13 Apr 2017 13:23:18:  30000000 
INFO  @ Thu, 13 Apr 2017 13:23:20:  31000000 
INFO  @ Thu, 13 Apr 2017 13:23:22:  32000000 
INFO  @ Thu, 13 Apr 2017 13:23:24:  33000000 
INFO  @ Thu, 13 Apr 2017 13:23:26:  34000000 
INFO  @ Thu, 13 Apr 2017 13:23:28:  35000000 
INFO  @ Thu, 13 Apr 2017 13:23:30:  36000000 
INFO  @ Thu, 13 Apr 2017 13:23:33:  37000000 
INFO  @ Thu, 13 Apr 2017 13:23:35:  38000000 
INFO  @ Thu, 13 Apr 2017 13:23:37:  39000000 
INFO  @ Thu, 13 Apr 2017 13:23:39:  40000000 
INFO  @ Thu, 13 Apr 2017 13:23:41:  41000000 
INFO  @ Thu, 13 Apr 2017 13:23:43:  42000000 
INFO  @ Thu, 13 Apr 2017 13:23:45:  43000000 
INFO  @ Thu, 13 Apr 2017 13:23:47:  44000000 
INFO  @ Thu, 13 Apr 2017 13:23:49:  45000000 
INFO  @ Thu, 13 Apr 2017 13:23:51:  46000000 
INFO  @ Thu, 13 Apr 2017 13:23:53:  47000000 
INFO  @ Thu, 13 Apr 2017 13:23:57: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 13:23:59:  1000000 
INFO  @ Thu, 13 Apr 2017 13:24:01:  2000000 
INFO  @ Thu, 13 Apr 2017 13:24:03:  3000000 
INFO  @ Thu, 13 Apr 2017 13:24:05:  4000000 
INFO  @ Thu, 13 Apr 2017 13:24:07:  5000000 
INFO  @ Thu, 13 Apr 2017 13:24:09:  6000000 
INFO  @ Thu, 13 Apr 2017 13:24:11:  7000000 
INFO  @ Thu, 13 Apr 2017 13:24:13:  8000000 
INFO  @ Thu, 13 Apr 2017 13:24:15:  9000000 
INFO  @ Thu, 13 Apr 2017 13:24:16:  10000000 
INFO  @ Thu, 13 Apr 2017 13:24:18:  11000000 
INFO  @ Thu, 13 Apr 2017 13:24:20:  12000000 
INFO  @ Thu, 13 Apr 2017 13:24:22:  13000000 
INFO  @ Thu, 13 Apr 2017 13:24:24:  14000000 
INFO  @ Thu, 13 Apr 2017 13:24:26:  15000000 
INFO  @ Thu, 13 Apr 2017 13:24:28:  16000000 
INFO  @ Thu, 13 Apr 2017 13:24:30:  17000000 
INFO  @ Thu, 13 Apr 2017 13:24:32:  18000000 
INFO  @ Thu, 13 Apr 2017 13:24:34:  19000000 
INFO  @ Thu, 13 Apr 2017 13:24:36:  20000000 
INFO  @ Thu, 13 Apr 2017 13:24:37:  21000000 
INFO  @ Thu, 13 Apr 2017 13:24:39:  22000000 
INFO  @ Thu, 13 Apr 2017 13:24:41:  23000000 
INFO  @ Thu, 13 Apr 2017 13:24:43:  24000000 
INFO  @ Thu, 13 Apr 2017 13:24:45:  25000000 
INFO  @ Thu, 13 Apr 2017 13:24:47:  26000000 
INFO  @ Thu, 13 Apr 2017 13:24:49:  27000000 
INFO  @ Thu, 13 Apr 2017 13:24:51:  28000000 
INFO  @ Thu, 13 Apr 2017 13:24:53:  29000000 
INFO  @ Thu, 13 Apr 2017 13:24:55:  30000000 
INFO  @ Thu, 13 Apr 2017 13:24:56:  31000000 
INFO  @ Thu, 13 Apr 2017 13:24:58:  32000000 
INFO  @ Thu, 13 Apr 2017 13:25:00:  33000000 
INFO  @ Thu, 13 Apr 2017 13:25:02:  34000000 
INFO  @ Thu, 13 Apr 2017 13:25:04:  35000000 
INFO  @ Thu, 13 Apr 2017 13:25:06:  36000000 
INFO  @ Thu, 13 Apr 2017 13:25:08:  37000000 
INFO  @ Thu, 13 Apr 2017 13:25:10:  38000000 
INFO  @ Thu, 13 Apr 2017 13:25:12:  39000000 
INFO  @ Thu, 13 Apr 2017 13:25:13:  40000000 
INFO  @ Thu, 13 Apr 2017 13:25:15:  41000000 
INFO  @ Thu, 13 Apr 2017 13:25:17:  42000000 
INFO  @ Thu, 13 Apr 2017 13:25:19:  43000000 
INFO  @ Thu, 13 Apr 2017 13:25:21:  44000000 
INFO  @ Thu, 13 Apr 2017 13:25:23:  45000000 
INFO  @ Thu, 13 Apr 2017 13:25:25:  46000000 
INFO  @ Thu, 13 Apr 2017 13:25:27:  47000000 
INFO  @ Thu, 13 Apr 2017 13:25:29:  48000000 
INFO  @ Thu, 13 Apr 2017 13:25:31:  49000000 
INFO  @ Thu, 13 Apr 2017 13:25:32:  50000000 
INFO  @ Thu, 13 Apr 2017 13:25:34:  51000000 
INFO  @ Thu, 13 Apr 2017 13:25:36:  52000000 
INFO  @ Thu, 13 Apr 2017 13:25:38:  53000000 
INFO  @ Thu, 13 Apr 2017 13:25:40:  54000000 
INFO  @ Thu, 13 Apr 2017 13:25:42:  55000000 
INFO  @ Thu, 13 Apr 2017 13:25:44:  56000000 
INFO  @ Thu, 13 Apr 2017 13:25:46:  57000000 
INFO  @ Thu, 13 Apr 2017 13:25:48:  58000000 
INFO  @ Thu, 13 Apr 2017 13:25:50:  59000000 
INFO  @ Thu, 13 Apr 2017 13:25:52:  60000000 
INFO  @ Thu, 13 Apr 2017 13:25:54:  61000000 
INFO  @ Thu, 13 Apr 2017 13:25:55:  62000000 
INFO  @ Thu, 13 Apr 2017 13:25:57:  63000000 
INFO  @ Thu, 13 Apr 2017 13:25:59:  64000000 
INFO  @ Thu, 13 Apr 2017 13:26:01:  65000000 
INFO  @ Thu, 13 Apr 2017 13:26:03:  66000000 
INFO  @ Thu, 13 Apr 2017 13:26:05:  67000000 
INFO  @ Thu, 13 Apr 2017 13:26:07:  68000000 
INFO  @ Thu, 13 Apr 2017 13:26:09:  69000000 
INFO  @ Thu, 13 Apr 2017 13:26:11:  70000000 
INFO  @ Thu, 13 Apr 2017 13:26:13:  71000000 
INFO  @ Thu, 13 Apr 2017 13:26:15:  72000000 
INFO  @ Thu, 13 Apr 2017 13:26:17:  73000000 
INFO  @ Thu, 13 Apr 2017 13:26:19:  74000000 
INFO  @ Thu, 13 Apr 2017 13:26:20:  75000000 
INFO  @ Thu, 13 Apr 2017 13:26:22:  76000000 
INFO  @ Thu, 13 Apr 2017 13:26:24:  77000000 
INFO  @ Thu, 13 Apr 2017 13:26:26:  78000000 
INFO  @ Thu, 13 Apr 2017 13:26:28:  79000000 
INFO  @ Thu, 13 Apr 2017 13:26:30:  80000000 
INFO  @ Thu, 13 Apr 2017 13:26:32:  81000000 
INFO  @ Thu, 13 Apr 2017 13:26:34:  82000000 
INFO  @ Thu, 13 Apr 2017 13:26:36:  83000000 
INFO  @ Thu, 13 Apr 2017 13:26:38:  84000000 
INFO  @ Thu, 13 Apr 2017 13:26:40:  85000000 
INFO  @ Thu, 13 Apr 2017 13:26:41:  86000000 
INFO  @ Thu, 13 Apr 2017 13:26:43:  87000000 
INFO  @ Thu, 13 Apr 2017 13:26:45:  88000000 
INFO  @ Thu, 13 Apr 2017 13:26:47:  89000000 
INFO  @ Thu, 13 Apr 2017 13:26:49:  90000000 
INFO  @ Thu, 13 Apr 2017 13:26:51:  91000000 
INFO  @ Thu, 13 Apr 2017 13:26:53:  92000000 
INFO  @ Thu, 13 Apr 2017 13:26:55:  93000000 
INFO  @ Thu, 13 Apr 2017 13:26:57:  94000000 
INFO  @ Thu, 13 Apr 2017 13:26:59:  95000000 
INFO  @ Thu, 13 Apr 2017 13:27:00:  96000000 
INFO  @ Thu, 13 Apr 2017 13:27:02:  97000000 
INFO  @ Thu, 13 Apr 2017 13:27:04:  98000000 
INFO  @ Thu, 13 Apr 2017 13:27:06:  99000000 
INFO  @ Thu, 13 Apr 2017 13:27:08: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 13:27:08: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 13:27:08: #1  total tags in treatment: 47187626 
INFO  @ Thu, 13 Apr 2017 13:27:08: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 13:27:08: #1 finished! 
INFO  @ Thu, 13 Apr 2017 13:27:08: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 13:27:08: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 13:27:08: #2 Use 265 as fragment length 
INFO  @ Thu, 13 Apr 2017 13:27:08: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 13:27:08: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 13:27:08: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 13:34:55: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 13:34:55: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 13:34:55: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 13:34:55: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 13:34:55: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 13:47:34: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 13:47:36: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 13:47:38: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 13:47:39: Done! 
INFO  @ Thu, 13 Apr 2017 13:47:43: Read and build treatment bedGraph... 
INFO  @ Thu, 13 Apr 2017 13:49:33: Read and build control bedGraph... 
INFO  @ Thu, 13 Apr 2017 13:52:53: Build scoreTrackII... 
INFO  @ Thu, 13 Apr 2017 13:54:38: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Thu, 13 Apr 2017 14:06:22: Write bedGraph of scores... 
INFO  @ Thu, 13 Apr 2017 14:14:18: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_FE.bdg'! 
INFO  @ Thu, 13 Apr 2017 14:33:50: Read and build treatment bedGraph... 
INFO  @ Thu, 13 Apr 2017 14:35:40: Read and build control bedGraph... 
INFO  @ Thu, 13 Apr 2017 14:39:02: Build scoreTrackII... 
INFO  @ Thu, 13 Apr 2017 14:40:48: Values in your input bedGraph files will be multiplied by 47.187626 ... 
INFO  @ Thu, 13 Apr 2017 14:52:36: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Thu, 13 Apr 2017 14:55:03: Write bedGraph of scores... 
INFO  @ Thu, 13 Apr 2017 15:01:32: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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   46811  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 13:22:02  
 
  End   2017-04-13 13:38:13  
 
  Elapsed   00:16:11  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 265 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1 -o "ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1 -o "ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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--------------------
28022 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 13:22:17: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 265 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF057NJA.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 13:22:17: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 13:22:17: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 13:22:19:  1000000 
INFO  @ Thu, 13 Apr 2017 13:22:20:  2000000 
INFO  @ Thu, 13 Apr 2017 13:22:22:  3000000 
INFO  @ Thu, 13 Apr 2017 13:22:23:  4000000 
INFO  @ Thu, 13 Apr 2017 13:22:25:  5000000 
INFO  @ Thu, 13 Apr 2017 13:22:26:  6000000 
INFO  @ Thu, 13 Apr 2017 13:22:28:  7000000 
INFO  @ Thu, 13 Apr 2017 13:22:29:  8000000 
INFO  @ Thu, 13 Apr 2017 13:22:31:  9000000 
INFO  @ Thu, 13 Apr 2017 13:22:32:  10000000 
INFO  @ Thu, 13 Apr 2017 13:22:34:  11000000 
INFO  @ Thu, 13 Apr 2017 13:22:36:  12000000 
INFO  @ Thu, 13 Apr 2017 13:22:37:  13000000 
INFO  @ Thu, 13 Apr 2017 13:22:39:  14000000 
INFO  @ Thu, 13 Apr 2017 13:22:40:  15000000 
INFO  @ Thu, 13 Apr 2017 13:22:42:  16000000 
INFO  @ Thu, 13 Apr 2017 13:22:43:  17000000 
INFO  @ Thu, 13 Apr 2017 13:22:45:  18000000 
INFO  @ Thu, 13 Apr 2017 13:22:46:  19000000 
INFO  @ Thu, 13 Apr 2017 13:22:48:  20000000 
INFO  @ Thu, 13 Apr 2017 13:22:50:  21000000 
INFO  @ Thu, 13 Apr 2017 13:22:51:  22000000 
INFO  @ Thu, 13 Apr 2017 13:22:53:  23000000 
INFO  @ Thu, 13 Apr 2017 13:22:55: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 13:22:56:  1000000 
INFO  @ Thu, 13 Apr 2017 13:22:58:  2000000 
INFO  @ Thu, 13 Apr 2017 13:22:59:  3000000 
INFO  @ Thu, 13 Apr 2017 13:23:00:  4000000 
INFO  @ Thu, 13 Apr 2017 13:23:02:  5000000 
INFO  @ Thu, 13 Apr 2017 13:23:03:  6000000 
INFO  @ Thu, 13 Apr 2017 13:23:04:  7000000 
INFO  @ Thu, 13 Apr 2017 13:23:06:  8000000 
INFO  @ Thu, 13 Apr 2017 13:23:07:  9000000 
INFO  @ Thu, 13 Apr 2017 13:23:09:  10000000 
INFO  @ Thu, 13 Apr 2017 13:23:10:  11000000 
INFO  @ Thu, 13 Apr 2017 13:23:11:  12000000 
INFO  @ Thu, 13 Apr 2017 13:23:13:  13000000 
INFO  @ Thu, 13 Apr 2017 13:23:14:  14000000 
INFO  @ Thu, 13 Apr 2017 13:23:15:  15000000 
INFO  @ Thu, 13 Apr 2017 13:23:17:  16000000 
INFO  @ Thu, 13 Apr 2017 13:23:18:  17000000 
INFO  @ Thu, 13 Apr 2017 13:23:20:  18000000 
INFO  @ Thu, 13 Apr 2017 13:23:21:  19000000 
INFO  @ Thu, 13 Apr 2017 13:23:22:  20000000 
INFO  @ Thu, 13 Apr 2017 13:23:24:  21000000 
INFO  @ Thu, 13 Apr 2017 13:23:25:  22000000 
INFO  @ Thu, 13 Apr 2017 13:23:27:  23000000 
INFO  @ Thu, 13 Apr 2017 13:23:28:  24000000 
INFO  @ Thu, 13 Apr 2017 13:23:29:  25000000 
INFO  @ Thu, 13 Apr 2017 13:23:31:  26000000 
INFO  @ Thu, 13 Apr 2017 13:23:32:  27000000 
INFO  @ Thu, 13 Apr 2017 13:23:34:  28000000 
INFO  @ Thu, 13 Apr 2017 13:23:35:  29000000 
INFO  @ Thu, 13 Apr 2017 13:23:36:  30000000 
INFO  @ Thu, 13 Apr 2017 13:23:38:  31000000 
INFO  @ Thu, 13 Apr 2017 13:23:39:  32000000 
INFO  @ Thu, 13 Apr 2017 13:23:40:  33000000 
INFO  @ Thu, 13 Apr 2017 13:23:42:  34000000 
INFO  @ Thu, 13 Apr 2017 13:23:43:  35000000 
INFO  @ Thu, 13 Apr 2017 13:23:45:  36000000 
INFO  @ Thu, 13 Apr 2017 13:23:46:  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 13:23:53:  42000000 
INFO  @ Thu, 13 Apr 2017 13:23:55:  43000000 
INFO  @ Thu, 13 Apr 2017 13:23:56:  44000000 
INFO  @ Thu, 13 Apr 2017 13:23:57:  45000000 
INFO  @ Thu, 13 Apr 2017 13:23:59:  46000000 
INFO  @ Thu, 13 Apr 2017 13:24:00:  47000000 
INFO  @ Thu, 13 Apr 2017 13:24:02:  48000000 
INFO  @ Thu, 13 Apr 2017 13:24:03:  49000000 
INFO  @ Thu, 13 Apr 2017 13:24:04:  50000000 
INFO  @ Thu, 13 Apr 2017 13:24:06:  51000000 
INFO  @ Thu, 13 Apr 2017 13:24:07:  52000000 
INFO  @ Thu, 13 Apr 2017 13:24:09:  53000000 
INFO  @ Thu, 13 Apr 2017 13:24:10:  54000000 
INFO  @ Thu, 13 Apr 2017 13:24:11:  55000000 
INFO  @ Thu, 13 Apr 2017 13:24:13:  56000000 
INFO  @ Thu, 13 Apr 2017 13:24:14:  57000000 
INFO  @ Thu, 13 Apr 2017 13:24:16:  58000000 
INFO  @ Thu, 13 Apr 2017 13:24:17:  59000000 
INFO  @ Thu, 13 Apr 2017 13:24:18:  60000000 
INFO  @ Thu, 13 Apr 2017 13:24:20:  61000000 
INFO  @ Thu, 13 Apr 2017 13:24:21:  62000000 
INFO  @ Thu, 13 Apr 2017 13:24:23:  63000000 
INFO  @ Thu, 13 Apr 2017 13:24:24:  64000000 
INFO  @ Thu, 13 Apr 2017 13:24:25:  65000000 
INFO  @ Thu, 13 Apr 2017 13:24:27:  66000000 
INFO  @ Thu, 13 Apr 2017 13:24:28:  67000000 
INFO  @ Thu, 13 Apr 2017 13:24:29:  68000000 
INFO  @ Thu, 13 Apr 2017 13:24:31:  69000000 
INFO  @ Thu, 13 Apr 2017 13:24:32:  70000000 
INFO  @ Thu, 13 Apr 2017 13:24:34:  71000000 
INFO  @ Thu, 13 Apr 2017 13:24:35:  72000000 
INFO  @ Thu, 13 Apr 2017 13:24:36:  73000000 
INFO  @ Thu, 13 Apr 2017 13:24:38:  74000000 
INFO  @ Thu, 13 Apr 2017 13:24:39:  75000000 
INFO  @ Thu, 13 Apr 2017 13:24:40:  76000000 
INFO  @ Thu, 13 Apr 2017 13:24:42:  77000000 
INFO  @ Thu, 13 Apr 2017 13:24:43:  78000000 
INFO  @ Thu, 13 Apr 2017 13:24:45:  79000000 
INFO  @ Thu, 13 Apr 2017 13:24:46:  80000000 
INFO  @ Thu, 13 Apr 2017 13:24:47:  81000000 
INFO  @ Thu, 13 Apr 2017 13:24:49:  82000000 
INFO  @ Thu, 13 Apr 2017 13:24:50:  83000000 
INFO  @ Thu, 13 Apr 2017 13:24:51:  84000000 
INFO  @ Thu, 13 Apr 2017 13:24:53:  85000000 
INFO  @ Thu, 13 Apr 2017 13:24:54:  86000000 
INFO  @ Thu, 13 Apr 2017 13:24:56:  87000000 
INFO  @ Thu, 13 Apr 2017 13:24:57:  88000000 
INFO  @ Thu, 13 Apr 2017 13:24:58:  89000000 
INFO  @ Thu, 13 Apr 2017 13:25:00:  90000000 
INFO  @ Thu, 13 Apr 2017 13:25:01:  91000000 
INFO  @ Thu, 13 Apr 2017 13:25:03:  92000000 
INFO  @ Thu, 13 Apr 2017 13:25:04:  93000000 
INFO  @ Thu, 13 Apr 2017 13:25:05:  94000000 
INFO  @ Thu, 13 Apr 2017 13:25:07:  95000000 
INFO  @ Thu, 13 Apr 2017 13:25:08:  96000000 
INFO  @ Thu, 13 Apr 2017 13:25:09:  97000000 
INFO  @ Thu, 13 Apr 2017 13:25:11:  98000000 
INFO  @ Thu, 13 Apr 2017 13:25:12:  99000000 
INFO  @ Thu, 13 Apr 2017 13:25:14: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 13:25:14: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 13:25:14: #1  total tags in treatment: 23593814 
INFO  @ Thu, 13 Apr 2017 13:25:14: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 13:25:14: #1 finished! 
INFO  @ Thu, 13 Apr 2017 13:25:14: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 13:25:14: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 13:25:14: #2 Use 265 as fragment length 
INFO  @ Thu, 13 Apr 2017 13:25:14: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 13:25:14: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 13:25:14: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 13:30:10: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 13:30:10: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 13:30:10: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 13:30:10: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 13:30:10: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 13:38:08: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 13:38:09: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 13:38:10: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 13:38:10: 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   46846  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 13:38:15  
 
  End   2017-04-13 14:00:54  
 
  Elapsed   00:22:38  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 265 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2 -o "ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2 -o "ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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--------------------
19668 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 13:38:32: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 265 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF057NJA.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 13:38:32: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 13:38:32: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 13:38:34:  1000000 
INFO  @ Thu, 13 Apr 2017 13:38:36:  2000000 
INFO  @ Thu, 13 Apr 2017 13:38:39:  3000000 
INFO  @ Thu, 13 Apr 2017 13:38:41:  4000000 
INFO  @ Thu, 13 Apr 2017 13:38:43:  5000000 
INFO  @ Thu, 13 Apr 2017 13:38:45:  6000000 
INFO  @ Thu, 13 Apr 2017 13:38:47:  7000000 
INFO  @ Thu, 13 Apr 2017 13:38:49:  8000000 
INFO  @ Thu, 13 Apr 2017 13:38:52:  9000000 
INFO  @ Thu, 13 Apr 2017 13:38:54:  10000000 
INFO  @ Thu, 13 Apr 2017 13:38:56:  11000000 
INFO  @ Thu, 13 Apr 2017 13:38:58:  12000000 
INFO  @ Thu, 13 Apr 2017 13:39:00:  13000000 
INFO  @ Thu, 13 Apr 2017 13:39:02:  14000000 
INFO  @ Thu, 13 Apr 2017 13:39:04:  15000000 
INFO  @ Thu, 13 Apr 2017 13:39:07:  16000000 
INFO  @ Thu, 13 Apr 2017 13:39:09:  17000000 
INFO  @ Thu, 13 Apr 2017 13:39:11:  18000000 
INFO  @ Thu, 13 Apr 2017 13:39:13:  19000000 
INFO  @ Thu, 13 Apr 2017 13:39:15:  20000000 
INFO  @ Thu, 13 Apr 2017 13:39:17:  21000000 
INFO  @ Thu, 13 Apr 2017 13:39:20:  22000000 
INFO  @ Thu, 13 Apr 2017 13:39:22:  23000000 
INFO  @ Thu, 13 Apr 2017 13:39:25: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 13:39:27:  1000000 
INFO  @ Thu, 13 Apr 2017 13:39:29:  2000000 
INFO  @ Thu, 13 Apr 2017 13:39:31:  3000000 
INFO  @ Thu, 13 Apr 2017 13:39:33:  4000000 
INFO  @ Thu, 13 Apr 2017 13:39:35:  5000000 
INFO  @ Thu, 13 Apr 2017 13:39:37:  6000000 
INFO  @ Thu, 13 Apr 2017 13:39:39:  7000000 
INFO  @ Thu, 13 Apr 2017 13:39:41:  8000000 
INFO  @ Thu, 13 Apr 2017 13:39:43:  9000000 
INFO  @ Thu, 13 Apr 2017 13:39:45:  10000000 
INFO  @ Thu, 13 Apr 2017 13:39:47:  11000000 
INFO  @ Thu, 13 Apr 2017 13:39:49:  12000000 
INFO  @ Thu, 13 Apr 2017 13:39:51:  13000000 
INFO  @ Thu, 13 Apr 2017 13:39:53:  14000000 
INFO  @ Thu, 13 Apr 2017 13:39:55:  15000000 
INFO  @ Thu, 13 Apr 2017 13:39:57:  16000000 
INFO  @ Thu, 13 Apr 2017 13:39:59:  17000000 
INFO  @ Thu, 13 Apr 2017 13:40:01:  18000000 
INFO  @ Thu, 13 Apr 2017 13:40:03:  19000000 
INFO  @ Thu, 13 Apr 2017 13:40:05:  20000000 
INFO  @ Thu, 13 Apr 2017 13:40:07:  21000000 
INFO  @ Thu, 13 Apr 2017 13:40:09:  22000000 
INFO  @ Thu, 13 Apr 2017 13:40:11:  23000000 
INFO  @ Thu, 13 Apr 2017 13:40:13:  24000000 
INFO  @ Thu, 13 Apr 2017 13:40:15:  25000000 
INFO  @ Thu, 13 Apr 2017 13:40:17:  26000000 
INFO  @ Thu, 13 Apr 2017 13:40:19:  27000000 
INFO  @ Thu, 13 Apr 2017 13:40:21:  28000000 
INFO  @ Thu, 13 Apr 2017 13:40:23:  29000000 
INFO  @ Thu, 13 Apr 2017 13:40:25:  30000000 
INFO  @ Thu, 13 Apr 2017 13:40:27:  31000000 
INFO  @ Thu, 13 Apr 2017 13:40:29:  32000000 
INFO  @ Thu, 13 Apr 2017 13:40:31:  33000000 
INFO  @ Thu, 13 Apr 2017 13:40:33:  34000000 
INFO  @ Thu, 13 Apr 2017 13:40:35:  35000000 
INFO  @ Thu, 13 Apr 2017 13:40:37:  36000000 
INFO  @ Thu, 13 Apr 2017 13:40:39:  37000000 
INFO  @ Thu, 13 Apr 2017 13:40:41:  38000000 
INFO  @ Thu, 13 Apr 2017 13:40:43:  39000000 
INFO  @ Thu, 13 Apr 2017 13:40:45:  40000000 
INFO  @ Thu, 13 Apr 2017 13:40:46:  41000000 
INFO  @ Thu, 13 Apr 2017 13:40:48:  42000000 
INFO  @ Thu, 13 Apr 2017 13:40:50:  43000000 
INFO  @ Thu, 13 Apr 2017 13:40:52:  44000000 
INFO  @ Thu, 13 Apr 2017 13:40:54:  45000000 
INFO  @ Thu, 13 Apr 2017 13:40:56:  46000000 
INFO  @ Thu, 13 Apr 2017 13:40:58:  47000000 
INFO  @ Thu, 13 Apr 2017 13:41:00:  48000000 
INFO  @ Thu, 13 Apr 2017 13:41:02:  49000000 
INFO  @ Thu, 13 Apr 2017 13:41:04:  50000000 
INFO  @ Thu, 13 Apr 2017 13:41:06:  51000000 
INFO  @ Thu, 13 Apr 2017 13:41:08:  52000000 
INFO  @ Thu, 13 Apr 2017 13:41:10:  53000000 
INFO  @ Thu, 13 Apr 2017 13:41:12:  54000000 
INFO  @ Thu, 13 Apr 2017 13:41:14:  55000000 
INFO  @ Thu, 13 Apr 2017 13:41:16:  56000000 
INFO  @ Thu, 13 Apr 2017 13:41:18:  57000000 
INFO  @ Thu, 13 Apr 2017 13:41:20:  58000000 
INFO  @ Thu, 13 Apr 2017 13:41:22:  59000000 
INFO  @ Thu, 13 Apr 2017 13:41:24:  60000000 
INFO  @ Thu, 13 Apr 2017 13:41:26:  61000000 
INFO  @ Thu, 13 Apr 2017 13:41:28:  62000000 
INFO  @ Thu, 13 Apr 2017 13:41:30:  63000000 
INFO  @ Thu, 13 Apr 2017 13:41:32:  64000000 
INFO  @ Thu, 13 Apr 2017 13:41:34:  65000000 
INFO  @ Thu, 13 Apr 2017 13:41:36:  66000000 
INFO  @ Thu, 13 Apr 2017 13:41:38:  67000000 
INFO  @ Thu, 13 Apr 2017 13:41:40:  68000000 
INFO  @ Thu, 13 Apr 2017 13:41:42:  69000000 
INFO  @ Thu, 13 Apr 2017 13:41:43:  70000000 
INFO  @ Thu, 13 Apr 2017 13:41:45:  71000000 
INFO  @ Thu, 13 Apr 2017 13:41:47:  72000000 
INFO  @ Thu, 13 Apr 2017 13:41:49:  73000000 
INFO  @ Thu, 13 Apr 2017 13:41:51:  74000000 
INFO  @ Thu, 13 Apr 2017 13:41:53:  75000000 
INFO  @ Thu, 13 Apr 2017 13:41:55:  76000000 
INFO  @ Thu, 13 Apr 2017 13:41:57:  77000000 
INFO  @ Thu, 13 Apr 2017 13:41:59:  78000000 
INFO  @ Thu, 13 Apr 2017 13:42:01:  79000000 
INFO  @ Thu, 13 Apr 2017 13:42:03:  80000000 
INFO  @ Thu, 13 Apr 2017 13:42:05:  81000000 
INFO  @ Thu, 13 Apr 2017 13:42:07:  82000000 
INFO  @ Thu, 13 Apr 2017 13:42:09:  83000000 
INFO  @ Thu, 13 Apr 2017 13:42:11:  84000000 
INFO  @ Thu, 13 Apr 2017 13:42:13:  85000000 
INFO  @ Thu, 13 Apr 2017 13:42:15:  86000000 
INFO  @ Thu, 13 Apr 2017 13:42:17:  87000000 
INFO  @ Thu, 13 Apr 2017 13:42:19:  88000000 
INFO  @ Thu, 13 Apr 2017 13:42:21:  89000000 
INFO  @ Thu, 13 Apr 2017 13:42:23:  90000000 
INFO  @ Thu, 13 Apr 2017 13:42:25:  91000000 
INFO  @ Thu, 13 Apr 2017 13:42:27:  92000000 
INFO  @ Thu, 13 Apr 2017 13:42:29:  93000000 
INFO  @ Thu, 13 Apr 2017 13:42:30:  94000000 
INFO  @ Thu, 13 Apr 2017 13:42:32:  95000000 
INFO  @ Thu, 13 Apr 2017 13:42:34:  96000000 
INFO  @ Thu, 13 Apr 2017 13:42:36:  97000000 
INFO  @ Thu, 13 Apr 2017 13:42:38:  98000000 
INFO  @ Thu, 13 Apr 2017 13:42:40:  99000000 
INFO  @ Thu, 13 Apr 2017 13:42:42: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 13:42:42: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 13:42:42: #1  total tags in treatment: 23593812 
INFO  @ Thu, 13 Apr 2017 13:42:42: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 13:42:42: #1 finished! 
INFO  @ Thu, 13 Apr 2017 13:42:42: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 13:42:42: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 13:42:42: #2 Use 265 as fragment length 
INFO  @ Thu, 13 Apr 2017 13:42:42: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 13:42:42: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 13:42:42: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 13:49:31: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 13:49:31: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 13:49:31: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 13:49:31: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 13:49:31: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 14:00:45: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 14:00:47: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 14:00:48: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 14:00:49: Done! 

 
 		 

    
  
 
  Num   7  
 
  ID   task.callpeak_macs2.macs2_n_s_rep2.line_66.id_16  
 
  Name   macs2 n/s rep2 
 
  Thread   thread_Root  
 
  PID   46848  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 13:43:16  
 
  End   2017-04-13 15:28:16  
 
  Elapsed   01:44:59  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/signal/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/signal/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 245 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2 -o "ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/signal/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2 -o "ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/signal/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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--------------------
25263 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 13:43:31: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 245 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.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 13:43:31: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 13:43:31: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 13:43:33:  1000000 
INFO  @ Thu, 13 Apr 2017 13:43:35:  2000000 
INFO  @ Thu, 13 Apr 2017 13:43:37:  3000000 
INFO  @ Thu, 13 Apr 2017 13:43:39:  4000000 
INFO  @ Thu, 13 Apr 2017 13:43:40:  5000000 
INFO  @ Thu, 13 Apr 2017 13:43:42:  6000000 
INFO  @ Thu, 13 Apr 2017 13:43:44:  7000000 
INFO  @ Thu, 13 Apr 2017 13:43:46:  8000000 
INFO  @ Thu, 13 Apr 2017 13:43:48:  9000000 
INFO  @ Thu, 13 Apr 2017 13:43:49:  10000000 
INFO  @ Thu, 13 Apr 2017 13:43:51:  11000000 
INFO  @ Thu, 13 Apr 2017 13:43:52:  12000000 
INFO  @ Thu, 13 Apr 2017 13:43:55:  13000000 
INFO  @ Thu, 13 Apr 2017 13:43:56:  14000000 
INFO  @ Thu, 13 Apr 2017 13:43:58:  15000000 
INFO  @ Thu, 13 Apr 2017 13:44:00:  16000000 
INFO  @ Thu, 13 Apr 2017 13:44:02:  17000000 
INFO  @ Thu, 13 Apr 2017 13:44:04:  18000000 
INFO  @ Thu, 13 Apr 2017 13:44:06:  19000000 
INFO  @ Thu, 13 Apr 2017 13:44:07:  20000000 
INFO  @ Thu, 13 Apr 2017 13:44:09:  21000000 
INFO  @ Thu, 13 Apr 2017 13:44:11:  22000000 
INFO  @ Thu, 13 Apr 2017 13:44:12:  23000000 
INFO  @ Thu, 13 Apr 2017 13:44:14:  24000000 
INFO  @ Thu, 13 Apr 2017 13:44:16:  25000000 
INFO  @ Thu, 13 Apr 2017 13:44:17:  26000000 
INFO  @ Thu, 13 Apr 2017 13:44:19:  27000000 
INFO  @ Thu, 13 Apr 2017 13:44:21:  28000000 
INFO  @ Thu, 13 Apr 2017 13:44:22:  29000000 
INFO  @ Thu, 13 Apr 2017 13:44:24:  30000000 
INFO  @ Thu, 13 Apr 2017 13:44:25:  31000000 
INFO  @ Thu, 13 Apr 2017 13:44:27:  32000000 
INFO  @ Thu, 13 Apr 2017 13:44:29:  33000000 
INFO  @ Thu, 13 Apr 2017 13:44:31:  34000000 
INFO  @ Thu, 13 Apr 2017 13:44:32:  35000000 
INFO  @ Thu, 13 Apr 2017 13:44:34:  36000000 
INFO  @ Thu, 13 Apr 2017 13:44:36:  37000000 
INFO  @ Thu, 13 Apr 2017 13:44:38:  38000000 
INFO  @ Thu, 13 Apr 2017 13:44:39:  39000000 
INFO  @ Thu, 13 Apr 2017 13:44:41:  40000000 
INFO  @ Thu, 13 Apr 2017 13:44:42:  41000000 
INFO  @ Thu, 13 Apr 2017 13:44:44:  42000000 
INFO  @ Thu, 13 Apr 2017 13:44:46:  43000000 
INFO  @ Thu, 13 Apr 2017 13:44:47:  44000000 
INFO  @ Thu, 13 Apr 2017 13:44:49:  45000000 
INFO  @ Thu, 13 Apr 2017 13:44:50:  46000000 
INFO  @ Thu, 13 Apr 2017 13:44:52:  47000000 
INFO  @ Thu, 13 Apr 2017 13:44:53:  48000000 
INFO  @ Thu, 13 Apr 2017 13:44:55:  49000000 
INFO  @ Thu, 13 Apr 2017 13:44:57:  50000000 
INFO  @ Thu, 13 Apr 2017 13:44:58:  51000000 
INFO  @ Thu, 13 Apr 2017 13:45:00:  52000000 
INFO  @ Thu, 13 Apr 2017 13:45:02:  53000000 
INFO  @ Thu, 13 Apr 2017 13:45:04:  54000000 
INFO  @ Thu, 13 Apr 2017 13:45:05:  55000000 
INFO  @ Thu, 13 Apr 2017 13:45:07:  56000000 
INFO  @ Thu, 13 Apr 2017 13:45:09:  57000000 
INFO  @ Thu, 13 Apr 2017 13:45:10:  58000000 
INFO  @ Thu, 13 Apr 2017 13:45:13:  59000000 
INFO  @ Thu, 13 Apr 2017 13:45:14:  60000000 
INFO  @ Thu, 13 Apr 2017 13:45:16:  61000000 
INFO  @ Thu, 13 Apr 2017 13:45:17:  62000000 
INFO  @ Thu, 13 Apr 2017 13:45:19:  63000000 
INFO  @ Thu, 13 Apr 2017 13:45:21:  64000000 
INFO  @ Thu, 13 Apr 2017 13:45:23:  65000000 
INFO  @ Thu, 13 Apr 2017 13:45:24:  66000000 
INFO  @ Thu, 13 Apr 2017 13:45:26:  67000000 
INFO  @ Thu, 13 Apr 2017 13:45:27:  68000000 
INFO  @ Thu, 13 Apr 2017 13:45:33: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 13:45:35:  1000000 
INFO  @ Thu, 13 Apr 2017 13:45:36:  2000000 
INFO  @ Thu, 13 Apr 2017 13:45:38:  3000000 
INFO  @ Thu, 13 Apr 2017 13:45:39:  4000000 
INFO  @ Thu, 13 Apr 2017 13:45:40:  5000000 
INFO  @ Thu, 13 Apr 2017 13:45:42:  6000000 
INFO  @ Thu, 13 Apr 2017 13:45:43:  7000000 
INFO  @ Thu, 13 Apr 2017 13:45:45:  8000000 
INFO  @ Thu, 13 Apr 2017 13:45:47:  9000000 
INFO  @ Thu, 13 Apr 2017 13:45:48:  10000000 
INFO  @ Thu, 13 Apr 2017 13:45:50:  11000000 
INFO  @ Thu, 13 Apr 2017 13:45:51:  12000000 
INFO  @ Thu, 13 Apr 2017 13:45:53:  13000000 
INFO  @ Thu, 13 Apr 2017 13:45:54:  14000000 
INFO  @ Thu, 13 Apr 2017 13:45:56:  15000000 
INFO  @ Thu, 13 Apr 2017 13:45:57:  16000000 
INFO  @ Thu, 13 Apr 2017 13:45:58:  17000000 
INFO  @ Thu, 13 Apr 2017 13:46:00:  18000000 
INFO  @ Thu, 13 Apr 2017 13:46:01:  19000000 
INFO  @ Thu, 13 Apr 2017 13:46:03:  20000000 
INFO  @ Thu, 13 Apr 2017 13:46:04:  21000000 
INFO  @ Thu, 13 Apr 2017 13:46:06:  22000000 
INFO  @ Thu, 13 Apr 2017 13:46:07:  23000000 
INFO  @ Thu, 13 Apr 2017 13:46:09:  24000000 
INFO  @ Thu, 13 Apr 2017 13:46:10:  25000000 
INFO  @ Thu, 13 Apr 2017 13:46:12:  26000000 
INFO  @ Thu, 13 Apr 2017 13:46:13:  27000000 
INFO  @ Thu, 13 Apr 2017 13:46:15:  28000000 
INFO  @ Thu, 13 Apr 2017 13:46:16:  29000000 
INFO  @ Thu, 13 Apr 2017 13:46:17:  30000000 
INFO  @ Thu, 13 Apr 2017 13:46:19:  31000000 
INFO  @ Thu, 13 Apr 2017 13:46:21:  32000000 
INFO  @ Thu, 13 Apr 2017 13:46:22:  33000000 
INFO  @ Thu, 13 Apr 2017 13:46:23:  34000000 
INFO  @ Thu, 13 Apr 2017 13:46:25:  35000000 
INFO  @ Thu, 13 Apr 2017 13:46:26:  36000000 
INFO  @ Thu, 13 Apr 2017 13:46:28:  37000000 
INFO  @ Thu, 13 Apr 2017 13:46:29:  38000000 
INFO  @ Thu, 13 Apr 2017 13:46:31:  39000000 
INFO  @ Thu, 13 Apr 2017 13:46:32:  40000000 
INFO  @ Thu, 13 Apr 2017 13:46:34:  41000000 
INFO  @ Thu, 13 Apr 2017 13:46:35:  42000000 
INFO  @ Thu, 13 Apr 2017 13:46:36:  43000000 
INFO  @ Thu, 13 Apr 2017 13:46:38:  44000000 
INFO  @ Thu, 13 Apr 2017 13:46:39:  45000000 
INFO  @ Thu, 13 Apr 2017 13:46:41:  46000000 
INFO  @ Thu, 13 Apr 2017 13:46:42:  47000000 
INFO  @ Thu, 13 Apr 2017 13:46:44:  48000000 
INFO  @ Thu, 13 Apr 2017 13:46:45:  49000000 
INFO  @ Thu, 13 Apr 2017 13:46:46:  50000000 
INFO  @ Thu, 13 Apr 2017 13:46:48:  51000000 
INFO  @ Thu, 13 Apr 2017 13:46:49:  52000000 
INFO  @ Thu, 13 Apr 2017 13:46:51:  53000000 
INFO  @ Thu, 13 Apr 2017 13:46:52:  54000000 
INFO  @ Thu, 13 Apr 2017 13:46:54:  55000000 
INFO  @ Thu, 13 Apr 2017 13:46:55:  56000000 
INFO  @ Thu, 13 Apr 2017 13:46:57:  57000000 
INFO  @ Thu, 13 Apr 2017 13:46:58:  58000000 
INFO  @ Thu, 13 Apr 2017 13:46:59:  59000000 
INFO  @ Thu, 13 Apr 2017 13:47:01:  60000000 
INFO  @ Thu, 13 Apr 2017 13:47:02:  61000000 
INFO  @ Thu, 13 Apr 2017 13:47:04:  62000000 
INFO  @ Thu, 13 Apr 2017 13:47:05:  63000000 
INFO  @ Thu, 13 Apr 2017 13:47:07:  64000000 
INFO  @ Thu, 13 Apr 2017 13:47:08:  65000000 
INFO  @ Thu, 13 Apr 2017 13:47:09:  66000000 
INFO  @ Thu, 13 Apr 2017 13:47:11:  67000000 
INFO  @ Thu, 13 Apr 2017 13:47:13:  68000000 
INFO  @ Thu, 13 Apr 2017 13:47:14:  69000000 
INFO  @ Thu, 13 Apr 2017 13:47:16:  70000000 
INFO  @ Thu, 13 Apr 2017 13:47:17:  71000000 
INFO  @ Thu, 13 Apr 2017 13:47:18:  72000000 
INFO  @ Thu, 13 Apr 2017 13:47:20:  73000000 
INFO  @ Thu, 13 Apr 2017 13:47:21:  74000000 
INFO  @ Thu, 13 Apr 2017 13:47:23:  75000000 
INFO  @ Thu, 13 Apr 2017 13:47:24:  76000000 
INFO  @ Thu, 13 Apr 2017 13:47:26:  77000000 
INFO  @ Thu, 13 Apr 2017 13:47:27:  78000000 
INFO  @ Thu, 13 Apr 2017 13:47:29:  79000000 
INFO  @ Thu, 13 Apr 2017 13:47:30:  80000000 
INFO  @ Thu, 13 Apr 2017 13:47:32:  81000000 
INFO  @ Thu, 13 Apr 2017 13:47:33:  82000000 
INFO  @ Thu, 13 Apr 2017 13:47:34:  83000000 
INFO  @ Thu, 13 Apr 2017 13:47:36:  84000000 
INFO  @ Thu, 13 Apr 2017 13:47:37:  85000000 
INFO  @ Thu, 13 Apr 2017 13:47:39:  86000000 
INFO  @ Thu, 13 Apr 2017 13:47:40:  87000000 
INFO  @ Thu, 13 Apr 2017 13:47:42:  88000000 
INFO  @ Thu, 13 Apr 2017 13:47:43:  89000000 
INFO  @ Thu, 13 Apr 2017 13:47:44:  90000000 
INFO  @ Thu, 13 Apr 2017 13:47:46:  91000000 
INFO  @ Thu, 13 Apr 2017 13:47:47:  92000000 
INFO  @ Thu, 13 Apr 2017 13:47:49:  93000000 
INFO  @ Thu, 13 Apr 2017 13:47:50:  94000000 
INFO  @ Thu, 13 Apr 2017 13:47:52:  95000000 
INFO  @ Thu, 13 Apr 2017 13:47:53:  96000000 
INFO  @ Thu, 13 Apr 2017 13:47:54:  97000000 
INFO  @ Thu, 13 Apr 2017 13:47:56:  98000000 
INFO  @ Thu, 13 Apr 2017 13:47:57:  99000000 
INFO  @ Thu, 13 Apr 2017 13:47:59: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 13:47:59: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 13:47:59: #1  total tags in treatment: 68407958 
INFO  @ Thu, 13 Apr 2017 13:47:59: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 13:47:59: #1 finished! 
INFO  @ Thu, 13 Apr 2017 13:47:59: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 13:47:59: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 13:47:59: #2 Use 245 as fragment length 
INFO  @ Thu, 13 Apr 2017 13:47:59: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 13:47:59: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 13:47:59: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 13:56:43: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 13:56:43: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 13:56:43: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 13:56:43: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 13:56:43: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 14:08:11: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 14:08:13: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 14:08:14: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 14:08:14: Done! 
INFO  @ Thu, 13 Apr 2017 14:08:18: Read and build treatment bedGraph... 
INFO  @ Thu, 13 Apr 2017 14:10:42: Read and build control bedGraph... 
INFO  @ Thu, 13 Apr 2017 14:13:39: Build scoreTrackII... 
INFO  @ Thu, 13 Apr 2017 14:15:39: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Thu, 13 Apr 2017 14:25:59: Write bedGraph of scores... 
INFO  @ Thu, 13 Apr 2017 14:34:01: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_FE.bdg'! 
INFO  @ Thu, 13 Apr 2017 14:50:24: Read and build treatment bedGraph... 
INFO  @ Thu, 13 Apr 2017 14:52:38: Read and build control bedGraph... 
INFO  @ Thu, 13 Apr 2017 14:55:12: Build scoreTrackII... 
INFO  @ Thu, 13 Apr 2017 14:56:24: Values in your input bedGraph files will be multiplied by 68.407958 ... 
INFO  @ Thu, 13 Apr 2017 15:06:12: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Thu, 13 Apr 2017 15:08:26: Write bedGraph of scores... 
INFO  @ Thu, 13 Apr 2017 15:14:12: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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   46849  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 13:44:08  
 
  End   2017-04-13 14:06:35  
 
  Elapsed   00:22:27  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 245 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1 -o "ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1 -o "ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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--------------------
29278 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 13:44:31: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 245 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF078YAS.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 13:44:31: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 13:44:31: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 13:44:34:  1000000 
INFO  @ Thu, 13 Apr 2017 13:44:36:  2000000 
INFO  @ Thu, 13 Apr 2017 13:44:37:  3000000 
INFO  @ Thu, 13 Apr 2017 13:44:39:  4000000 
INFO  @ Thu, 13 Apr 2017 13:44:41:  5000000 
INFO  @ Thu, 13 Apr 2017 13:44:42:  6000000 
INFO  @ Thu, 13 Apr 2017 13:44:44:  7000000 
INFO  @ Thu, 13 Apr 2017 13:44:45:  8000000 
INFO  @ Thu, 13 Apr 2017 13:44:47:  9000000 
INFO  @ Thu, 13 Apr 2017 13:44:49:  10000000 
INFO  @ Thu, 13 Apr 2017 13:44:50:  11000000 
INFO  @ Thu, 13 Apr 2017 13:44:52:  12000000 
INFO  @ Thu, 13 Apr 2017 13:44:53:  13000000 
INFO  @ Thu, 13 Apr 2017 13:44:55:  14000000 
INFO  @ Thu, 13 Apr 2017 13:44:57:  15000000 
INFO  @ Thu, 13 Apr 2017 13:44:59:  16000000 
INFO  @ Thu, 13 Apr 2017 13:45:00:  17000000 
INFO  @ Thu, 13 Apr 2017 13:45:02:  18000000 
INFO  @ Thu, 13 Apr 2017 13:45:03:  19000000 
INFO  @ Thu, 13 Apr 2017 13:45:05:  20000000 
INFO  @ Thu, 13 Apr 2017 13:45:07:  21000000 
INFO  @ Thu, 13 Apr 2017 13:45:09:  22000000 
INFO  @ Thu, 13 Apr 2017 13:45:10:  23000000 
INFO  @ Thu, 13 Apr 2017 13:45:12:  24000000 
INFO  @ Thu, 13 Apr 2017 13:45:14:  25000000 
INFO  @ Thu, 13 Apr 2017 13:45:15:  26000000 
INFO  @ Thu, 13 Apr 2017 13:45:17:  27000000 
INFO  @ Thu, 13 Apr 2017 13:45:18:  28000000 
INFO  @ Thu, 13 Apr 2017 13:45:20:  29000000 
INFO  @ Thu, 13 Apr 2017 13:45:21:  30000000 
INFO  @ Thu, 13 Apr 2017 13:45:24:  31000000 
INFO  @ Thu, 13 Apr 2017 13:45:25:  32000000 
INFO  @ Thu, 13 Apr 2017 13:45:27:  33000000 
INFO  @ Thu, 13 Apr 2017 13:45:29:  34000000 
INFO  @ Thu, 13 Apr 2017 13:45:31: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 13:45:33:  1000000 
INFO  @ Thu, 13 Apr 2017 13:45:35:  2000000 
INFO  @ Thu, 13 Apr 2017 13:45:36:  3000000 
INFO  @ Thu, 13 Apr 2017 13:45:37:  4000000 
INFO  @ Thu, 13 Apr 2017 13:45:39:  5000000 
INFO  @ Thu, 13 Apr 2017 13:45:40:  6000000 
INFO  @ Thu, 13 Apr 2017 13:45:42:  7000000 
INFO  @ Thu, 13 Apr 2017 13:45:43:  8000000 
INFO  @ Thu, 13 Apr 2017 13:45:45:  9000000 
INFO  @ Thu, 13 Apr 2017 13:45:46:  10000000 
INFO  @ Thu, 13 Apr 2017 13:45:47:  11000000 
INFO  @ Thu, 13 Apr 2017 13:45:49:  12000000 
INFO  @ Thu, 13 Apr 2017 13:45:50:  13000000 
INFO  @ Thu, 13 Apr 2017 13:45:52:  14000000 
INFO  @ Thu, 13 Apr 2017 13:45:53:  15000000 
INFO  @ Thu, 13 Apr 2017 13:45:55:  16000000 
INFO  @ Thu, 13 Apr 2017 13:45:56:  17000000 
INFO  @ Thu, 13 Apr 2017 13:45:58:  18000000 
INFO  @ Thu, 13 Apr 2017 13:45:59:  19000000 
INFO  @ Thu, 13 Apr 2017 13:46:01:  20000000 
INFO  @ Thu, 13 Apr 2017 13:46:02:  21000000 
INFO  @ Thu, 13 Apr 2017 13:46:04:  22000000 
INFO  @ Thu, 13 Apr 2017 13:46:05:  23000000 
INFO  @ Thu, 13 Apr 2017 13:46:07:  24000000 
INFO  @ Thu, 13 Apr 2017 13:46:08:  25000000 
INFO  @ Thu, 13 Apr 2017 13:46:10:  26000000 
INFO  @ Thu, 13 Apr 2017 13:46:11:  27000000 
INFO  @ Thu, 13 Apr 2017 13:46:13:  28000000 
INFO  @ Thu, 13 Apr 2017 13:46:14:  29000000 
INFO  @ Thu, 13 Apr 2017 13:46:16:  30000000 
INFO  @ Thu, 13 Apr 2017 13:46:17:  31000000 
INFO  @ Thu, 13 Apr 2017 13:46:18:  32000000 
INFO  @ Thu, 13 Apr 2017 13:46:20:  33000000 
INFO  @ Thu, 13 Apr 2017 13:46:21:  34000000 
INFO  @ Thu, 13 Apr 2017 13:46:23:  35000000 
INFO  @ Thu, 13 Apr 2017 13:46:24:  36000000 
INFO  @ Thu, 13 Apr 2017 13:46:26:  37000000 
INFO  @ Thu, 13 Apr 2017 13:46:27:  38000000 
INFO  @ Thu, 13 Apr 2017 13:46:28:  39000000 
INFO  @ Thu, 13 Apr 2017 13:46:30:  40000000 
INFO  @ Thu, 13 Apr 2017 13:46:31:  41000000 
INFO  @ Thu, 13 Apr 2017 13:46:33:  42000000 
INFO  @ Thu, 13 Apr 2017 13:46:34:  43000000 
INFO  @ Thu, 13 Apr 2017 13:46:36:  44000000 
INFO  @ Thu, 13 Apr 2017 13:46:37:  45000000 
INFO  @ Thu, 13 Apr 2017 13:46:39:  46000000 
INFO  @ Thu, 13 Apr 2017 13:46:40:  47000000 
INFO  @ Thu, 13 Apr 2017 13:46:41:  48000000 
INFO  @ Thu, 13 Apr 2017 13:46:43:  49000000 
INFO  @ Thu, 13 Apr 2017 13:46:44:  50000000 
INFO  @ Thu, 13 Apr 2017 13:46:46:  51000000 
INFO  @ Thu, 13 Apr 2017 13:46:47:  52000000 
INFO  @ Thu, 13 Apr 2017 13:46:49:  53000000 
INFO  @ Thu, 13 Apr 2017 13:46:50:  54000000 
INFO  @ Thu, 13 Apr 2017 13:46:52:  55000000 
INFO  @ Thu, 13 Apr 2017 13:46:53:  56000000 
INFO  @ Thu, 13 Apr 2017 13:46:55:  57000000 
INFO  @ Thu, 13 Apr 2017 13:46:56:  58000000 
INFO  @ Thu, 13 Apr 2017 13:46:58:  59000000 
INFO  @ Thu, 13 Apr 2017 13:46:59:  60000000 
INFO  @ Thu, 13 Apr 2017 13:47:01:  61000000 
INFO  @ Thu, 13 Apr 2017 13:47:02:  62000000 
INFO  @ Thu, 13 Apr 2017 13:47:04:  63000000 
INFO  @ Thu, 13 Apr 2017 13:47:05:  64000000 
INFO  @ Thu, 13 Apr 2017 13:47:06:  65000000 
INFO  @ Thu, 13 Apr 2017 13:47:08:  66000000 
INFO  @ Thu, 13 Apr 2017 13:47:09:  67000000 
INFO  @ Thu, 13 Apr 2017 13:47:11:  68000000 
INFO  @ Thu, 13 Apr 2017 13:47:12:  69000000 
INFO  @ Thu, 13 Apr 2017 13:47:13:  70000000 
INFO  @ Thu, 13 Apr 2017 13:47:15:  71000000 
INFO  @ Thu, 13 Apr 2017 13:47:17:  72000000 
INFO  @ Thu, 13 Apr 2017 13:47:18:  73000000 
INFO  @ Thu, 13 Apr 2017 13:47:19:  74000000 
INFO  @ Thu, 13 Apr 2017 13:47:21:  75000000 
INFO  @ Thu, 13 Apr 2017 13:47:22:  76000000 
INFO  @ Thu, 13 Apr 2017 13:47:24:  77000000 
INFO  @ Thu, 13 Apr 2017 13:47:25:  78000000 
INFO  @ Thu, 13 Apr 2017 13:47:27:  79000000 
INFO  @ Thu, 13 Apr 2017 13:47:28:  80000000 
INFO  @ Thu, 13 Apr 2017 13:47:29:  81000000 
INFO  @ Thu, 13 Apr 2017 13:47:31:  82000000 
INFO  @ Thu, 13 Apr 2017 13:47:32:  83000000 
INFO  @ Thu, 13 Apr 2017 13:47:34:  84000000 
INFO  @ Thu, 13 Apr 2017 13:47:35:  85000000 
INFO  @ Thu, 13 Apr 2017 13:47:36:  86000000 
INFO  @ Thu, 13 Apr 2017 13:47:38:  87000000 
INFO  @ Thu, 13 Apr 2017 13:47:39:  88000000 
INFO  @ Thu, 13 Apr 2017 13:47:41:  89000000 
INFO  @ Thu, 13 Apr 2017 13:47:42:  90000000 
INFO  @ Thu, 13 Apr 2017 13:47:43:  91000000 
INFO  @ Thu, 13 Apr 2017 13:47:45:  92000000 
INFO  @ Thu, 13 Apr 2017 13:47:46:  93000000 
INFO  @ Thu, 13 Apr 2017 13:47:48:  94000000 
INFO  @ Thu, 13 Apr 2017 13:47:49:  95000000 
INFO  @ Thu, 13 Apr 2017 13:47:50:  96000000 
INFO  @ Thu, 13 Apr 2017 13:47:52:  97000000 
INFO  @ Thu, 13 Apr 2017 13:47:53:  98000000 
INFO  @ Thu, 13 Apr 2017 13:47:54:  99000000 
INFO  @ Thu, 13 Apr 2017 13:47:56: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 13:47:56: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 13:47:56: #1  total tags in treatment: 34203980 
INFO  @ Thu, 13 Apr 2017 13:47:56: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 13:47:56: #1 finished! 
INFO  @ Thu, 13 Apr 2017 13:47:56: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 13:47:56: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 13:47:56: #2 Use 245 as fragment length 
INFO  @ Thu, 13 Apr 2017 13:47:56: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 13:47:56: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 13:47:56: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 13:56:35: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 13:56:35: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 13:56:35: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 13:56:35: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 13:56:35: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 14:06:30: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 14:06:31: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 14:06:32: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 14:06:32: 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   46865  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 14:00:56  
 
  End   2017-04-13 14:28:15  
 
  Elapsed   00:27:18  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 245 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2 -o "ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2 -o "ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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--------------------
27157 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 14:01:17: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 245 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF078YAS.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 14:01:17: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 14:01:17: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 14:01:19:  1000000 
INFO  @ Thu, 13 Apr 2017 14:01:21:  2000000 
INFO  @ Thu, 13 Apr 2017 14:01:23:  3000000 
INFO  @ Thu, 13 Apr 2017 14:01:26:  4000000 
INFO  @ Thu, 13 Apr 2017 14:01:28:  5000000 
INFO  @ Thu, 13 Apr 2017 14:01:30:  6000000 
INFO  @ Thu, 13 Apr 2017 14:01:32:  7000000 
INFO  @ Thu, 13 Apr 2017 14:01:34:  8000000 
INFO  @ Thu, 13 Apr 2017 14:01:36:  9000000 
INFO  @ Thu, 13 Apr 2017 14:01:38:  10000000 
INFO  @ Thu, 13 Apr 2017 14:01:40:  11000000 
INFO  @ Thu, 13 Apr 2017 14:01:42:  12000000 
INFO  @ Thu, 13 Apr 2017 14:01:45:  13000000 
INFO  @ Thu, 13 Apr 2017 14:01:47:  14000000 
INFO  @ Thu, 13 Apr 2017 14:01:49:  15000000 
INFO  @ Thu, 13 Apr 2017 14:01:51:  16000000 
INFO  @ Thu, 13 Apr 2017 14:01:53:  17000000 
INFO  @ Thu, 13 Apr 2017 14:01:55:  18000000 
INFO  @ Thu, 13 Apr 2017 14:01:57:  19000000 
INFO  @ Thu, 13 Apr 2017 14:02:00:  20000000 
INFO  @ Thu, 13 Apr 2017 14:02:02:  21000000 
INFO  @ Thu, 13 Apr 2017 14:02:04:  22000000 
INFO  @ Thu, 13 Apr 2017 14:02:06:  23000000 
INFO  @ Thu, 13 Apr 2017 14:02:08:  24000000 
INFO  @ Thu, 13 Apr 2017 14:02:10:  25000000 
INFO  @ Thu, 13 Apr 2017 14:02:13:  26000000 
INFO  @ Thu, 13 Apr 2017 14:02:15:  27000000 
INFO  @ Thu, 13 Apr 2017 14:02:17:  28000000 
INFO  @ Thu, 13 Apr 2017 14:02:19:  29000000 
INFO  @ Thu, 13 Apr 2017 14:02:21:  30000000 
INFO  @ Thu, 13 Apr 2017 14:02:23:  31000000 
INFO  @ Thu, 13 Apr 2017 14:02:25:  32000000 
INFO  @ Thu, 13 Apr 2017 14:02:27:  33000000 
INFO  @ Thu, 13 Apr 2017 14:02:29:  34000000 
INFO  @ Thu, 13 Apr 2017 14:02:33: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 14:02:35:  1000000 
INFO  @ Thu, 13 Apr 2017 14:02:37:  2000000 
INFO  @ Thu, 13 Apr 2017 14:02:39:  3000000 
INFO  @ Thu, 13 Apr 2017 14:02:41:  4000000 
INFO  @ Thu, 13 Apr 2017 14:02:43:  5000000 
INFO  @ Thu, 13 Apr 2017 14:02:45:  6000000 
INFO  @ Thu, 13 Apr 2017 14:02:46:  7000000 
INFO  @ Thu, 13 Apr 2017 14:02:48:  8000000 
INFO  @ Thu, 13 Apr 2017 14:02:50:  9000000 
INFO  @ Thu, 13 Apr 2017 14:02:52:  10000000 
INFO  @ Thu, 13 Apr 2017 14:02:54:  11000000 
INFO  @ Thu, 13 Apr 2017 14:02:55:  12000000 
INFO  @ Thu, 13 Apr 2017 14:02:57:  13000000 
INFO  @ Thu, 13 Apr 2017 14:02:59:  14000000 
INFO  @ Thu, 13 Apr 2017 14:03:01:  15000000 
INFO  @ Thu, 13 Apr 2017 14:03:03:  16000000 
INFO  @ Thu, 13 Apr 2017 14:03:05:  17000000 
INFO  @ Thu, 13 Apr 2017 14:03:07:  18000000 
INFO  @ Thu, 13 Apr 2017 14:03:09:  19000000 
INFO  @ Thu, 13 Apr 2017 14:03:11:  20000000 
INFO  @ Thu, 13 Apr 2017 14:03:12:  21000000 
INFO  @ Thu, 13 Apr 2017 14:03:14:  22000000 
INFO  @ Thu, 13 Apr 2017 14:03:16:  23000000 
INFO  @ Thu, 13 Apr 2017 14:03:18:  24000000 
INFO  @ Thu, 13 Apr 2017 14:03:20:  25000000 
INFO  @ Thu, 13 Apr 2017 14:03:22:  26000000 
INFO  @ Thu, 13 Apr 2017 14:03:23:  27000000 
INFO  @ Thu, 13 Apr 2017 14:03:25:  28000000 
INFO  @ Thu, 13 Apr 2017 14:03:27:  29000000 
INFO  @ Thu, 13 Apr 2017 14:03:29:  30000000 
INFO  @ Thu, 13 Apr 2017 14:03:31:  31000000 
INFO  @ Thu, 13 Apr 2017 14:03:33:  32000000 
INFO  @ Thu, 13 Apr 2017 14:03:35:  33000000 
INFO  @ Thu, 13 Apr 2017 14:03:37:  34000000 
INFO  @ Thu, 13 Apr 2017 14:03:39:  35000000 
INFO  @ Thu, 13 Apr 2017 14:03:40:  36000000 
INFO  @ Thu, 13 Apr 2017 14:03:42:  37000000 
INFO  @ Thu, 13 Apr 2017 14:03:44:  38000000 
INFO  @ Thu, 13 Apr 2017 14:03:46:  39000000 
INFO  @ Thu, 13 Apr 2017 14:03:48:  40000000 
INFO  @ Thu, 13 Apr 2017 14:03:49:  41000000 
INFO  @ Thu, 13 Apr 2017 14:03:51:  42000000 
INFO  @ Thu, 13 Apr 2017 14:03:53:  43000000 
INFO  @ Thu, 13 Apr 2017 14:03:55:  44000000 
INFO  @ Thu, 13 Apr 2017 14:03:57:  45000000 
INFO  @ Thu, 13 Apr 2017 14:03:59:  46000000 
INFO  @ Thu, 13 Apr 2017 14:04:00:  47000000 
INFO  @ Thu, 13 Apr 2017 14:04:02:  48000000 
INFO  @ Thu, 13 Apr 2017 14:04:04:  49000000 
INFO  @ Thu, 13 Apr 2017 14:04:06:  50000000 
INFO  @ Thu, 13 Apr 2017 14:04:08:  51000000 
INFO  @ Thu, 13 Apr 2017 14:04:10:  52000000 
INFO  @ Thu, 13 Apr 2017 14:04:11:  53000000 
INFO  @ Thu, 13 Apr 2017 14:04:13:  54000000 
INFO  @ Thu, 13 Apr 2017 14:04:15:  55000000 
INFO  @ Thu, 13 Apr 2017 14:04:17:  56000000 
INFO  @ Thu, 13 Apr 2017 14:04:19:  57000000 
INFO  @ Thu, 13 Apr 2017 14:04:20:  58000000 
INFO  @ Thu, 13 Apr 2017 14:04:22:  59000000 
INFO  @ Thu, 13 Apr 2017 14:04:24:  60000000 
INFO  @ Thu, 13 Apr 2017 14:04:26:  61000000 
INFO  @ Thu, 13 Apr 2017 14:04:28:  62000000 
INFO  @ Thu, 13 Apr 2017 14:04:30:  63000000 
INFO  @ Thu, 13 Apr 2017 14:04:31:  64000000 
INFO  @ Thu, 13 Apr 2017 14:04:33:  65000000 
INFO  @ Thu, 13 Apr 2017 14:04:35:  66000000 
INFO  @ Thu, 13 Apr 2017 14:04:37:  67000000 
INFO  @ Thu, 13 Apr 2017 14:04:39:  68000000 
INFO  @ Thu, 13 Apr 2017 14:04:41:  69000000 
INFO  @ Thu, 13 Apr 2017 14:04:42:  70000000 
INFO  @ Thu, 13 Apr 2017 14:04:44:  71000000 
INFO  @ Thu, 13 Apr 2017 14:04:46:  72000000 
INFO  @ Thu, 13 Apr 2017 14:04:48:  73000000 
INFO  @ Thu, 13 Apr 2017 14:04:50:  74000000 
INFO  @ Thu, 13 Apr 2017 14:04:52:  75000000 
INFO  @ Thu, 13 Apr 2017 14:04:53:  76000000 
INFO  @ Thu, 13 Apr 2017 14:04:55:  77000000 
INFO  @ Thu, 13 Apr 2017 14:04:57:  78000000 
INFO  @ Thu, 13 Apr 2017 14:04:59:  79000000 
INFO  @ Thu, 13 Apr 2017 14:05:01:  80000000 
INFO  @ Thu, 13 Apr 2017 14:05:03:  81000000 
INFO  @ Thu, 13 Apr 2017 14:05:04:  82000000 
INFO  @ Thu, 13 Apr 2017 14:05:06:  83000000 
INFO  @ Thu, 13 Apr 2017 14:05:08:  84000000 
INFO  @ Thu, 13 Apr 2017 14:05:10:  85000000 
INFO  @ Thu, 13 Apr 2017 14:05:12:  86000000 
INFO  @ Thu, 13 Apr 2017 14:05:13:  87000000 
INFO  @ Thu, 13 Apr 2017 14:05:15:  88000000 
INFO  @ Thu, 13 Apr 2017 14:05:17:  89000000 
INFO  @ Thu, 13 Apr 2017 14:05:19:  90000000 
INFO  @ Thu, 13 Apr 2017 14:05:21:  91000000 
INFO  @ Thu, 13 Apr 2017 14:05:23:  92000000 
INFO  @ Thu, 13 Apr 2017 14:05:25:  93000000 
INFO  @ Thu, 13 Apr 2017 14:05:26:  94000000 
INFO  @ Thu, 13 Apr 2017 14:05:28:  95000000 
INFO  @ Thu, 13 Apr 2017 14:05:30:  96000000 
INFO  @ Thu, 13 Apr 2017 14:05:32:  97000000 
INFO  @ Thu, 13 Apr 2017 14:05:34:  98000000 
INFO  @ Thu, 13 Apr 2017 14:05:35:  99000000 
INFO  @ Thu, 13 Apr 2017 14:05:37: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 14:05:37: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 14:05:37: #1  total tags in treatment: 34203978 
INFO  @ Thu, 13 Apr 2017 14:05:37: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 14:05:37: #1 finished! 
INFO  @ Thu, 13 Apr 2017 14:05:37: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 14:05:37: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 14:05:37: #2 Use 245 as fragment length 
INFO  @ Thu, 13 Apr 2017 14:05:37: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 14:05:37: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 13 Apr 2017 14:05:37: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 14:16:11: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 13 Apr 2017 14:16:11: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 13 Apr 2017 14:16:11: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_control_lambda.bdg 
INFO  @ Thu, 13 Apr 2017 14:16:11: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 13 Apr 2017 14:16:11: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 14:28:06: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 14:28:08: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 13 Apr 2017 14:28:10: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_summits.bed 
INFO  @ Thu, 13 Apr 2017 14:28:10: Done! 

 
 		 

    
  
 
  Num   10  
 
  ID   task.callpeak_naive_overlap.naive_overlap.line_143.id_19  
 
  Name   naive_overlap  
 
  Thread   thread_Root  
 
  PID   46917  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:04:29  
 
  End   2017-04-13 16:05:45  
 
  Elapsed   00:01:16  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInPsRep1AndPsRep2.narrowPeak.gz

# SYS command. line 154

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInReps.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInPsRep1AndPsRep2.narrowPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInReps.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.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--------------------
16052 (process ID) old priority 0, new priority 19
Waiting for 50 seconds.

  
 		 

    
  
 
  Num   11  
 
  ID   task.callpeak_idr.idr2_rep1_rep2.line_74.id_20  
 
  Name   idr2 rep1-rep2 
 
  Thread   thread_Root  
 
  PID   46918  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:05:47  
 
  End   2017-04-13 16:11:46  
 
  Elapsed   00:05:59  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB17_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB17_MACS2_rep1-rep2.unthresholded-peaks.txt.png
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB17_MACS2_rep1-rep2.IDR0.05.log.txt
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB17_MACS2_rep1-rep2.unthresholded-peaks.txt.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB17_MACS2_rep1-rep2.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB17_MACS2_rep1-rep2.IDR0.05.13-col.bed.gz

# SYS command. line 88

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB17_MACS2_rep1-rep2.IDR0.05.narrowPeak.gz

# SYS command. line 89

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB17_MACS2_rep1-rep2.IDR0.05.filt.13-col.bed.gz

# SYS command. line 92

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB17_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz

# SYS command. line 93

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB17_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz

# SYS command. line 95

 gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB17_MACS2_rep1-rep2.unthresholded-peaks.txt

# SYS command. line 96

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB17_MACS2_rep1-rep2.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB17_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--------------------
20784 (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   46919  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:05:48  
 
  End   2017-04-13 16:09:38  
 
  Elapsed   00:03:49  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB17_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB17_MACS2_rep1-pr.unthresholded-peaks.txt.png
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB17_MACS2_rep1-pr.IDR0.05.log.txt
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB17_MACS2_rep1-pr.unthresholded-peaks.txt.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB17_MACS2_rep1-pr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB17_MACS2_rep1-pr.IDR0.05.13-col.bed.gz

# SYS command. line 88

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB17_MACS2_rep1-pr.IDR0.05.narrowPeak.gz

# SYS command. line 89

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB17_MACS2_rep1-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 92

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB17_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 93

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB17_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 95

 gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB17_MACS2_rep1-pr.unthresholded-peaks.txt

# SYS command. line 96

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB17_MACS2_rep1-pr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB17_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--------------------
20781 (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   46920  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:05:49  
 
  End   2017-04-13 16:10:30  
 
  Elapsed   00:04:40  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB17_MACS2_rep2-pr.IDR0.05.filt.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB17_MACS2_rep2-pr.unthresholded-peaks.txt.png
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB17_MACS2_rep2-pr.IDR0.05.log.txt
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB17_MACS2_rep2-pr.unthresholded-peaks.txt.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB17_MACS2_rep2-pr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB17_MACS2_rep2-pr.IDR0.05.13-col.bed.gz

# SYS command. line 88

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB17_MACS2_rep2-pr.IDR0.05.narrowPeak.gz

# SYS command. line 89

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB17_MACS2_rep2-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 92

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB17_MACS2_rep2-pr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 93

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB17_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 95

 gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB17_MACS2_rep2-pr.unthresholded-peaks.txt

# SYS command. line 96

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB17_MACS2_rep2-pr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB17_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--------------------
20782 (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   46921  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:05:50  
 
  End   2017-04-13 16:12:07  
 
  Elapsed   00:06:16  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB17_MACS2_ppr.IDR0.05.filt.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB17_MACS2_ppr.unthresholded-peaks.txt.png
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB17_MACS2_ppr.IDR0.05.log.txt
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB17_MACS2_ppr.unthresholded-peaks.txt.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB17_MACS2_ppr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB17_MACS2_ppr.IDR0.05.13-col.bed.gz

# SYS command. line 88

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB17_MACS2_ppr.IDR0.05.narrowPeak.gz

# SYS command. line 89

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB17_MACS2_ppr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 92

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB17_MACS2_ppr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 93

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB17_MACS2_ppr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 95

 gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB17_MACS2_ppr.unthresholded-peaks.txt

# SYS command. line 96

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB17_MACS2_ppr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB17_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--------------------
20783 (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   43353  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:12:07  
 
  End   2017-04-13 16:12:08  
 
  Elapsed   00:00:00  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB17_MACS2_ppr.IDR0.05.filt.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/optimal_set/ZBTB17_MACS2_ppr.IDR0.05.filt.narrowPeak.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 133

 cp --remove-destination /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB17_MACS2_ppr.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/optimal_set/ZBTB17_MACS2_ppr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 134

 while [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/optimal_set/ZBTB17_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   43358  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:12:07  
 
  End   2017-04-13 16:12:08  
 
  Elapsed   00:00:00  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB17_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/conservative_set/ZBTB17_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 133

 cp --remove-destination /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB17_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/conservative_set/ZBTB17_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz

# SYS command. line 134

 while [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/conservative_set/ZBTB17_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   43370  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:12:08  
 
  End   2017-04-13 16:12:08  
 
  Elapsed   00:00:00  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB17_MACS2_ppr.IDR0.05.filt.12-col.bed.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/optimal_set/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB17_MACS2_ppr.IDR0.05.filt.12-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/optimal_set/ZBTB17_MACS2_ppr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 134

 while [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/optimal_set/ZBTB17_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   43378  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:12:08  
 
  End   2017-04-13 16:12:08  
 
  Elapsed   00:00:00  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB17_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/conservative_set/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB17_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/conservative_set/ZBTB17_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz

# SYS command. line 134

 while [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/conservative_set/ZBTB17_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   46922  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:12:10  
 
  End   2017-04-13 16:13:31  
 
  Elapsed   00:01:20  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB17_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB17_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB17_MACS2_rep2-pr.IDR0.05.filt.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB17_MACS2_ppr.IDR0.05.filt.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/qc/ZBTB17_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/ZBTB17_MACS2/out/qc/ZBTB17_MACS2_IDR_final.qc

# SYS command. line 288

 echo -e "47946\t27179	34332	""48894\t48894\t47946\tpooled_pseudo_rep\trep1-rep2\t1.019772243774246\t1.2631811324919975\tpass" >> /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/qc/ZBTB17_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--------------------
21509 (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   46923  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:12:11  
 
  End   2017-04-13 16:14:47  
 
  Elapsed   00:02:35  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB17_MACS2_rep1-pr.IDR0.05.filt.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB17_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/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.tagAlign.gz -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -s -l -133 -r 133 | \
			awk '{if ($2>=0 && $3>=0 && $2<=$3) print $0}' | \
			bedtools intersect -a stdin -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB17_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/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.tagAlign.gz | wc -l)

# SYS command. line 134

 awk 'BEGIN {print '${val1}'/'${val2}'}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB17_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--------------------
21508 (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   46924  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:12:12  
 
  End   2017-04-13 16:15:53  
 
  Elapsed   00:03:40  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB17_MACS2_rep2-pr.IDR0.05.filt.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB17_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/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.tagAlign.gz -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -s -l -123 -r 123 | \
			awk '{if ($2>=0 && $3>=0 && $2<=$3) print $0}' | \
			bedtools intersect -a stdin -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB17_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/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.tagAlign.gz | wc -l)

# SYS command. line 134

 awk 'BEGIN {print '${val1}'/'${val2}'}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB17_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--------------------
21503 (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   46925  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:12:14  
 
  End   2017-04-13 16:18:07  
 
  Elapsed   00:05:53  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB17_MACS2_ppr.IDR0.05.filt.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB17_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/ZBTB17_MACS2/out/align/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign.gz -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -s -l -128 -r 128 | \
			awk '{if ($2>=0 && $3>=0 && $2<=$3) print $0}' | \
			bedtools intersect -a stdin -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB17_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/ZBTB17_MACS2/out/align/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign.gz | wc -l)

# SYS command. line 134

 awk 'BEGIN {print '${val1}'/'${val2}'}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pooled_pseudo_reps/ZBTB17_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--------------------
21504 (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   46926  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:12:15  
 
  End   2017-04-13 16:17:41  
 
  Elapsed   00:05:26  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB17_MACS2_rep1-rep2.IDR0.05.filt.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB17_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/ZBTB17_MACS2/out/align/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign.gz -g /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/GRCh38_no_alt_analysis_set_GCA_000001405.15.chrom.sizes -s -l -128 -r 128 | \
			awk '{if ($2>=0 && $3>=0 && $2<=$3) print $0}' | \
			bedtools intersect -a stdin -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB17_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/ZBTB17_MACS2/out/align/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign.gz | wc -l)

# SYS command. line 134

 awk 'BEGIN {print '${val1}'/'${val2}'}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/true_reps/rep1-rep2/ZBTB17_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--------------------
43878 (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   6867  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:18:09  
 
  End   2017-04-13 16:19:18  
 
  Elapsed   00:01:08  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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--------------------
6871 (process ID) old priority 0, new priority 19
Waiting for 59 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   6955  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:18:11  
 
  End   2017-04-13 16:19:19  
 
  Elapsed   00:01:08  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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--------------------
6960 (process ID) old priority 0, new priority 19
Waiting for 59 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   6986  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:18:12  
 
  End   2017-04-13 16:19:20  
 
  Elapsed   00:01:08  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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--------------------
6991 (process ID) old priority 0, new priority 19
Waiting for 59 seconds.

  
 		 

    
  
 
  Num   27  
 
  ID   task.report.peak2hammock.line_361.id_46  
 
  Name   peak2hammock 
 
  Thread   thread_Root  
 
  PID   9819  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:19:21  
 
  End   2017-04-13 16:19:32  
 
  Elapsed   00:00:11  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp
 
 
   
--------------------Stdout--------------------
9823 (process ID) old priority 0, new priority 19

  
 		 

    
  
 
  Num   28  
 
  ID   task.report.peak2hammock.line_361.id_47  
 
  Name   peak2hammock 
 
  Thread   thread_Root  
 
  PID   10521  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:19:33  
 
  End   2017-04-13 16:19:42  
 
  Elapsed   00:00:09  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/optimal_set/ZBTB17_MACS2_ppr.IDR0.05.filt.12-col.bed.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/optimal_set/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/optimal_set/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/optimal_set/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/optimal_set/ZBTB17_MACS2_ppr.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/optimal_set/ZBTB17_MACS2_ppr.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 367

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/optimal_set/ZBTB17_MACS2_ppr.IDR0.05.filt.12-col.bed.tmp
 
 
   
--------------------Stdout--------------------
10525 (process ID) old priority 0, new priority 19

  
 		 

    
  
 
  Num   29  
 
  ID   task.report.peak2hammock.line_361.id_48  
 
  Name   peak2hammock 
 
  Thread   thread_Root  
 
  PID   11030  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:19:43  
 
  End   2017-04-13 16:19:53  
 
  Elapsed   00:00:09  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/conservative_set/ZBTB17_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/conservative_set/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/conservative_set/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/conservative_set/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/conservative_set/ZBTB17_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/conservative_set/ZBTB17_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 367

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/conservative_set/ZBTB17_MACS2_rep1-rep2.IDR0.05.filt.12-col.bed.tmp
 
 
   
--------------------Stdout--------------------
11034 (process ID) old priority 0, new priority 19

  
 		 

    
  
 
  Num   30  
 
  ID   task.report.peak2hammock.line_361.id_49  
 
  Name   peak2hammock 
 
  Thread   thread_Root  
 
  PID   11474  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:19:54  
 
  End   2017-04-13 16:20:03  
 
  Elapsed   00:00:09  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB17_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB17_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB17_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 367

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep1/ZBTB17_MACS2_rep1-pr.IDR0.05.filt.12-col.bed.tmp
 
 
   
--------------------Stdout--------------------
11478 (process ID) old priority 0, new priority 19

  
 		 

    
  
 
  Num   31  
 
  ID   task.report.peak2hammock.line_361.id_50  
 
  Name   peak2hammock 
 
  Thread   thread_Root  
 
  PID   11916  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:20:04  
 
  End   2017-04-13 16:20:13  
 
  Elapsed   00:00:09  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB17_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB17_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/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB17_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB17_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 367

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/idr/pseudo_reps/rep2/ZBTB17_MACS2_rep2-pr.IDR0.05.filt.12-col.bed.tmp
 
 
   
--------------------Stdout--------------------
11920 (process ID) old priority 0, new priority 19

  
 		 

    
  
 
  Num   32  
 
  ID   task.graphviz.report.line_97.id_51  
 
  Name   report 
 
  Thread   thread_Root  
 
  PID   12350  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:20:14  
 
  End   2017-04-13 16:20:23  
 
  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/ZBTB17_MACS2/out/report/ZBTB17_MACS2_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/report/ZBTB17_MACS2_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/report/ZBTB17_MACS2_workflow.svg" # to suppress dot font error (exit code=1)
 
 
   
--------------------Stdout--------------------
12354 (process ID) old priority 0, new priority 19

  
 		 

    
  
 
  Num   33  
 
  ID   task.report.pdf2png.line_328.id_52  
 
  Name   pdf2png 
 
  Thread   thread_Root  
 
  PID   12374  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:20:15  
 
  End   2017-04-13 16:20:23  
 
  Elapsed   00:00:08  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/qc/rep1/ENCFF057NJA.15M.cc.plot.pdf
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/qc/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/qc/rep1/ENCFF057NJA.15M.cc.plot.png \
			-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/qc/rep1/ENCFF057NJA.15M.cc.plot.pdf
 
 
   
--------------------Stdout--------------------
12380 (process ID) old priority 0, new priority 19

  
 		 

    
  
 
  Num   34  
 
  ID   task.report.pdf2png.line_328.id_53  
 
  Name   pdf2png 
 
  Thread   thread_Root  
 
  PID   12379  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 16:20:15  
 
  End   2017-04-13 16:20:23  
 
  Elapsed   00:00:08  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/qc/rep2/ENCFF078YAS.15M.cc.plot.pdf
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/qc/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/qc/rep2/ENCFF078YAS.15M.cc.plot.png \
			-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/qc/rep2/ENCFF078YAS.15M.cc.plot.pdf
 
 
   
--------------------Stdout--------------------
12388 (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, ZBTB17_MACS2, -nth, 5, -species, hg38_ENCODE, -url_base, http://mitra.stanford.edu/kundaje/leepc12/imk_chipseq/ZBTB17_MACS2/out, -filt_bam1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.bam, -filt_bam2, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.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/ZBTB17_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/ZBTB17_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  26642.ZBTB17_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