BigDataScript report: chipseq.bds

Script file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20161106_211302_910
Start time 2016-11-06 21:13:02
Run time 00:15:45.578
Tasks executed 2
Tasks failed 0
Tasks failed names 
 

		
  Arguments*  [-title, ZF1, -nth, 5, -species, mm10, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out, -tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/align/rep1/ZF1_allReps.nodup.tagAlign.gz, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz, -gensz, mm, $] 

		
  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.20161106_211302_910/task.callpeak_macs2.macs2_rep1.line_67.id_10
chipseq.bds.20161106_211302_910/task.graphviz.report.line_97.id_13
 
 		 

	
  thread_42   thread_Root 	 
  
 		 

	
  thread_41   thread_Root 	 
  
 		 

	






	
 Task details 

	

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

    
  
 
  Num   1  
 
  ID   task.callpeak_macs2.macs2_rep1.line_67.id_10  
 
  Name   macs2 rep1 
 
  Thread   thread_Root  
 
  PID   4399  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-11-06 21:13:10  
 
  End   2016-11-06 21:28:40  
 
  Elapsed   00:15:30  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/align/rep1/ZF1_allReps.nodup.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/signal/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/signal/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bw
  
 
  Dependencies     
 
 		  
 
# SYS command. line 69

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

# SYS command. line 70

 export LC_COLLATE=C

# SYS command. line 75

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/align/rep1/ZF1_allReps.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --nomodel --shift 0 --extsize 115 --keep-dup all -B --SPMR

# SYS command. line 78

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.narrowPeak.gz

# SYS command. line 81

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_summits.bed

# SYS command. line 88

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/align/rep1/ZF1_allReps.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --broad --nomodel --shift 0 --extsize 115 --keep-dup all

# SYS command. line 91

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.broadPeak.gz

# SYS command. line 92

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gappedPeak.gz

# SYS command. line 95

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_summits.bed

# SYS command. line 100

 if [[ true == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.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 111

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1 -o "ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 114

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/mm10/mm10.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/mm10/mm10.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 115

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_FE.bdg

# SYS command. line 118

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 119

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/mm10/mm10.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/signal/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bw

# SYS command. line 120

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 126

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/align/rep1/ZF1_allReps.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 128

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.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 130

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1 -o "ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 133

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/mm10/mm10.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/mm10/mm10.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 134

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_ppois.bdg

# SYS command. line 137

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 138

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/mm10/mm10.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/signal/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bw

# SYS command. line 139

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 141

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 143

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
13570 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Sun, 06 Nov 2016 21:13:21: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/align/rep1/ZF1_allReps.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --nomodel --shift 0 --extsize 115 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/align/rep1/ZF1_allReps.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz']
# effective genome size = 1.87e+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  @ Sun, 06 Nov 2016 21:13:21: #1 read tag files... 
INFO  @ Sun, 06 Nov 2016 21:13:21: #1 read treatment tags... 
INFO  @ Sun, 06 Nov 2016 21:13:23:  1000000 
INFO  @ Sun, 06 Nov 2016 21:13:25:  2000000 
INFO  @ Sun, 06 Nov 2016 21:13:27:  3000000 
INFO  @ Sun, 06 Nov 2016 21:13:28:  4000000 
INFO  @ Sun, 06 Nov 2016 21:13:29:  5000000 
INFO  @ Sun, 06 Nov 2016 21:13:31:  6000000 
INFO  @ Sun, 06 Nov 2016 21:13:32:  7000000 
INFO  @ Sun, 06 Nov 2016 21:13:34:  8000000 
INFO  @ Sun, 06 Nov 2016 21:13:35:  9000000 
INFO  @ Sun, 06 Nov 2016 21:13:36:  10000000 
INFO  @ Sun, 06 Nov 2016 21:13:38:  11000000 
INFO  @ Sun, 06 Nov 2016 21:13:39:  12000000 
INFO  @ Sun, 06 Nov 2016 21:13:40:  13000000 
INFO  @ Sun, 06 Nov 2016 21:13:42:  14000000 
INFO  @ Sun, 06 Nov 2016 21:13:43:  15000000 
INFO  @ Sun, 06 Nov 2016 21:13:45:  16000000 
INFO  @ Sun, 06 Nov 2016 21:13:46:  17000000 
INFO  @ Sun, 06 Nov 2016 21:13:47:  18000000 
INFO  @ Sun, 06 Nov 2016 21:13:49:  19000000 
INFO  @ Sun, 06 Nov 2016 21:13:50:  20000000 
INFO  @ Sun, 06 Nov 2016 21:13:52: #1.2 read input tags... 
INFO  @ Sun, 06 Nov 2016 21:13:53:  1000000 
INFO  @ Sun, 06 Nov 2016 21:13:55:  2000000 
INFO  @ Sun, 06 Nov 2016 21:13:56:  3000000 
INFO  @ Sun, 06 Nov 2016 21:13:57: #1 tag size is determined as 47 bps 
INFO  @ Sun, 06 Nov 2016 21:13:57: #1 tag size = 47 
INFO  @ Sun, 06 Nov 2016 21:13:57: #1  total tags in treatment: 20883429 
INFO  @ Sun, 06 Nov 2016 21:13:57: #1  total tags in control: 3384182 
INFO  @ Sun, 06 Nov 2016 21:13:57: #1 finished! 
INFO  @ Sun, 06 Nov 2016 21:13:57: #2 Build Peak Model... 
INFO  @ Sun, 06 Nov 2016 21:13:57: #2 Skipped... 
INFO  @ Sun, 06 Nov 2016 21:13:57: #2 Use 115 as fragment length 
INFO  @ Sun, 06 Nov 2016 21:13:57: #3 Call peaks... 
INFO  @ Sun, 06 Nov 2016 21:13:57: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Sun, 06 Nov 2016 21:13:57: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 06 Nov 2016 21:14:27: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Sun, 06 Nov 2016 21:14:27: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Sun, 06 Nov 2016 21:14:27: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_control_lambda.bdg 
INFO  @ Sun, 06 Nov 2016 21:14:27: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Sun, 06 Nov 2016 21:14:27: #3 Call peaks for each chromosome... 
INFO  @ Sun, 06 Nov 2016 21:15:55: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 06 Nov 2016 21:15:55: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Sun, 06 Nov 2016 21:15:56: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_summits.bed 
INFO  @ Sun, 06 Nov 2016 21:15:56: Done! 
INFO  @ Sun, 06 Nov 2016 21:15:59: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/align/rep1/ZF1_allReps.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --broad --nomodel --shift 0 --extsize 115 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/align/rep1/ZF1_allReps.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz']
# effective genome size = 1.87e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Sun, 06 Nov 2016 21:15:59: #1 read tag files... 
INFO  @ Sun, 06 Nov 2016 21:15:59: #1 read treatment tags... 
INFO  @ Sun, 06 Nov 2016 21:16:01:  1000000 
INFO  @ Sun, 06 Nov 2016 21:16:03:  2000000 
INFO  @ Sun, 06 Nov 2016 21:16:05:  3000000 
INFO  @ Sun, 06 Nov 2016 21:16:07:  4000000 
INFO  @ Sun, 06 Nov 2016 21:16:08:  5000000 
INFO  @ Sun, 06 Nov 2016 21:16:09:  6000000 
INFO  @ Sun, 06 Nov 2016 21:16:11:  7000000 
INFO  @ Sun, 06 Nov 2016 21:16:13:  8000000 
INFO  @ Sun, 06 Nov 2016 21:16:14:  9000000 
INFO  @ Sun, 06 Nov 2016 21:16:15:  10000000 
INFO  @ Sun, 06 Nov 2016 21:16:17:  11000000 
INFO  @ Sun, 06 Nov 2016 21:16:18:  12000000 
INFO  @ Sun, 06 Nov 2016 21:16:19:  13000000 
INFO  @ Sun, 06 Nov 2016 21:16:21:  14000000 
INFO  @ Sun, 06 Nov 2016 21:16:22:  15000000 
INFO  @ Sun, 06 Nov 2016 21:16:24:  16000000 
INFO  @ Sun, 06 Nov 2016 21:16:25:  17000000 
INFO  @ Sun, 06 Nov 2016 21:16:26:  18000000 
INFO  @ Sun, 06 Nov 2016 21:16:28:  19000000 
INFO  @ Sun, 06 Nov 2016 21:16:29:  20000000 
INFO  @ Sun, 06 Nov 2016 21:16:30: #1.2 read input tags... 
INFO  @ Sun, 06 Nov 2016 21:16:32:  1000000 
INFO  @ Sun, 06 Nov 2016 21:16:33:  2000000 
INFO  @ Sun, 06 Nov 2016 21:16:35:  3000000 
INFO  @ Sun, 06 Nov 2016 21:16:35: #1 tag size is determined as 47 bps 
INFO  @ Sun, 06 Nov 2016 21:16:35: #1 tag size = 47 
INFO  @ Sun, 06 Nov 2016 21:16:35: #1  total tags in treatment: 20883429 
INFO  @ Sun, 06 Nov 2016 21:16:35: #1  total tags in control: 3384182 
INFO  @ Sun, 06 Nov 2016 21:16:35: #1 finished! 
INFO  @ Sun, 06 Nov 2016 21:16:35: #2 Build Peak Model... 
INFO  @ Sun, 06 Nov 2016 21:16:35: #2 Skipped... 
INFO  @ Sun, 06 Nov 2016 21:16:35: #2 Use 115 as fragment length 
INFO  @ Sun, 06 Nov 2016 21:16:35: #3 Call peaks... 
INFO  @ Sun, 06 Nov 2016 21:16:35: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Sun, 06 Nov 2016 21:16:35: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 06 Nov 2016 21:17:03: #3 Call peaks for each chromosome... 
INFO  @ Sun, 06 Nov 2016 21:17:29: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 06 Nov 2016 21:17:30: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.broadPeak 
INFO  @ Sun, 06 Nov 2016 21:17:30: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Sun, 06 Nov 2016 21:17:31: Done! 
INFO  @ Sun, 06 Nov 2016 21:17:35: Read and build treatment bedGraph... 
INFO  @ Sun, 06 Nov 2016 21:18:10: Read and build control bedGraph... 
INFO  @ Sun, 06 Nov 2016 21:18:20: Build scoreTrackII... 
INFO  @ Sun, 06 Nov 2016 21:18:33: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Sun, 06 Nov 2016 21:20:14: Write bedGraph of scores... 
INFO  @ Sun, 06 Nov 2016 21:21:24: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_FE.bdg'! 
INFO  @ Sun, 06 Nov 2016 21:24:19: Read and build treatment bedGraph... 
INFO  @ Sun, 06 Nov 2016 21:24:54: Read and build control bedGraph... 
INFO  @ Sun, 06 Nov 2016 21:25:04: Build scoreTrackII... 
INFO  @ Sun, 06 Nov 2016 21:25:20: Values in your input bedGraph files will be multiplied by 3.384182 ... 
INFO  @ Sun, 06 Nov 2016 21:27:04: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Sun, 06 Nov 2016 21:27:17: Write bedGraph of scores... 
INFO  @ Sun, 06 Nov 2016 21:27:38: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/peak/macs2/rep1/ZF1_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_ppois.bdg'! 

 
 		 

    
  
 
  Num   2  
 
  ID   task.graphviz.report.line_97.id_13  
 
  Name   report 
 
  Thread   thread_Root  
 
  PID   33233  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-11-06 21:28:44  
 
  End   2016-11-06 21:28:48  
 
  Elapsed   00:00:03  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files     
 
  Output files     
 
  Dependencies     
 
 		  
 
# SYS command. line 98

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

# SYS command. line 99

 dot -Tsvg /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/report/ZF1_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/report/ZF1_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/report/ZF1_workflow.svg" # to suppress dot font error (exit code=1)
 
 
   
--------------------Stdout--------------------
33237 (process ID) old priority 0, new priority 10

  
 		 

	






	
 Global scope 

	Note: Global scope when program finished execution.
	

	
  Type  Name  Value  

	
  string  _  /usr/bin/bds  

	
  bool  allowEmpty  false  

	
  string[]  args  [-title, ZF1, -nth, 5, -species, mm10, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out, -tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1/out/align/rep1/ZF1_allReps.nodup.tagAlign.gz, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz, -gensz, mm, $]  

	
  bool  canFail  false  

	
  int  cpus  -1  

	
  int  cpusLocal  56  

	
  int  day  86400  

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

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

	
  string  DISPLAY  localhost:12.0  

	
  real  E  2.718281828459045  

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

	
  int  G  1073741824  

	
  string  HOME  /users/imk1/  

	
  int  hour  3600  

	
  string  J2REDIR  /usr/lib/jvm/java-8-oracle/jre  

	
  string  J2SDKDIR  /usr/lib/jvm/java-8-oracle  

	
  string  JAVA_HOME  /usr/lib/jvm/java-8-oracle  

	
  int  K  1024  

	
  string  KERAS_DIR  /users/imk1/.local/lib/python2.7/site-packages/keras/  

	
  string  KRB5CCNAME  FILE:/tmp/krb5cc_1048_N5SeQf  

	
  string  LANG  en_US.UTF-8  

	
  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/persistent/imk1/TFBindingPredictionProject/src/rcade/:/srv/scratch/imk1/TFBindingPredictionProject/src/R-3.2.3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/users/imk1/edirect:/users/imk1/edirect  

	
  string  PERL5LIB  /users/imk1/perl5/lib/perl5  

	
  string  PERL_LOCAL_LIB_ROOT  /users/imk1/perl5  

	
  string  PERL_MB_OPT  --install_base \"/users/imk1/perl5\"  

	
  string  PERL_MM_OPT  INSTALL_BASE=/users/imk1/perl5  

	
  real  PI  3.141592653589793  

	
  string  ppwd  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1  

	
  string  programName  chipseq.bds  

	
  string  programPath  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/chipseq.bds  

	
  string  PWD  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF1  

	
  string  PYTHONPATH  /users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/  

	
  string  queue    

	
  int  retry  0  

	
  string  RULEFITBASE  /srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/  

	
  string  SHELL  /bin/bash  

	
  string  SHLVL  3  

	
  string  SSH_CLIENT  171.65.77.8 55144 22  

	
  string  SSH_CONNECTION  171.65.77.8 55144 171.65.76.63 22  

	
  string  SSH_TTY  /dev/pts/4  

	
  string  STY  30641.ZF1.BDS  

	
  string  system  sge  

	
  int  T  1099511627776  

	
  string  TERM  screen  

	
  string  TERMCAP  SC|screen|VT 100/ANSI X3.64 virtual terminal:\\\n\t:DO=\\E[%dB:LE=\\E[%dD:RI=\\E[%dC:UP=\\E[%dA:bs:bt=\\E[Z:\\\n\t:cd=\\E[J:ce=\\E[K:cl=\\E[H\\E[J:cm=\\E[%i%d;%dH:ct=\\E[3g:\\\n\t:do=^J:nd=\\E[C:pt:rc=\\E8:rs=\\Ec:sc=\\E7:st=\\EH:up=\\EM:\\\n\t:le=^H:bl=^G:cr=^M:it#8:ho=\\E[H:nw=\\EE:ta=^I:is=\\E)0:\\\n\t:li#24:co#80:am:xn:xv:LP:sr=\\EM:al=\\E[L:AL=\\E[%dL:\\\n\t:cs=\\E[%i%d;%dr:dl=\\E[M:DL=\\E[%dM:dc=\\E[P:DC=\\E[%dP:\\\n\t:im=\\E[4h:ei=\\E[4l:mi:IC=\\E[%d@:ks=\\E[?1h\\E=:\\\n\t:ke=\\E[?1l\\E>:vi=\\E[?25l:ve=\\E[34h\\E[?25h:vs=\\E[34l:\\\n\t:ti=\\E[?1049h:te=\\E[?1049l:Km=\\E[M:k0=\\E[10~:k1=\\EOP:\\\n\t:k2=\\EOQ:k3=\\EOR:k4=\\EOS:k5=\\E[15~:k6=\\E[17~:k7=\\E[18~:\\\n\t:k8=\\E[19~:k9=\\E[20~:k;=\\E[21~:F1=\\E[23~:F2=\\E[24~:\\\n\t:kh=\\E[1~:@1=\\E[1~:kH=\\E[4~:@7=\\E[4~:kN=\\E[6~:kP=\\E[5~:\\\n\t:kI=\\E[2~:kD=\\E[3~:ku=\\EOA:kd=\\EOB:kr=\\EOC:kl=\\EOD:  

	
  int  timeout  -1  

	
  string  USER  imk1  

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

	
  int  walltimeout  8640000  

	
  int  week  604800  

	
  string  WINDOW  0  

	
  string  XDG_RUNTIME_DIR  /run/user/1048  

	
  string  XDG_SESSION_ID  20  

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