BigDataScript report: chipseq.bds

Script file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20170106_143138_961
Start time 2017-01-06 14:31:38
Run time 15:34:07.746
Tasks executed 11
Tasks failed 0
Tasks failed names 
 

		
  Arguments*  [-title, ZNF200, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF200/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/align/rep1/SRR1370891_1.bam, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz, -final_stage, 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.20170106_143138_961/task.callpeak_spp.spp_rep1.line_57.id_10
chipseq.bds.20170106_143138_961/task.callpeak_macs2.macs2_rep1.line_71.id_11
chipseq.bds.20170106_143138_961/task.callpeak_macs2.macs2_rep1_pr1.line_71.id_12
chipseq.bds.20170106_143138_961/task.callpeak_macs2.macs2_rep1_pr2.line_71.id_13
chipseq.bds.20170106_143138_961/task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_14
chipseq.bds.20170106_143138_961/task.callpeak_idr.idr2_rep1_pr.line_73.id_15
chipseq.bds.20170106_143138_961/task.callpeak_idr.idr_final_qc.line_219.id_18
chipseq.bds.20170106_143138_961/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_19
chipseq.bds.20170106_143138_961/task.report.peak2hammock.line_412.id_20
chipseq.bds.20170106_143138_961/task.report.peak2hammock.line_412.id_21
chipseq.bds.20170106_143138_961/task.graphviz.report.line_97.id_22
 
 		 

	
  thread_41   thread_Root 	 
  
 		 

	
  thread_42   thread_Root 	 
  
 		 

	






	
 Task details 

	

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

    
  
 
  Num   1  
 
  ID   task.callpeak_spp.spp_rep1.line_57.id_10  
 
  Name   spp rep1 
 
  Thread   thread_Root  
 
  PID   24247  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-06 14:31:46  
 
  End   2017-01-07 06:00:20  
 
  Elapsed   15:28:34  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/align/rep1/SRR1370891_1.nodup.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf
  
 
  Dependencies     
 
 		  
 
# SYS command. line 59

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

# SYS command. line 62

 if [ $(which run_spp_nodups.R 2> /dev/null | wc -l || echo) == "1" ]; then RUN_SPP=$(which run_spp_nodups.R); \
		    else RUN_SPP=$(which run_spp.R); \
		    fi

# SYS command. line 66

 Rscript ${RUN_SPP} -c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/align/rep1/SRR1370891_1.nodup.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz \
			-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/rep1 -speak=150 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/rep1/SRR1370891_1.nodup.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz | awk 'BEGIN{OFS="\t"}{ if ($2<0) $2=0; print $1,int($2),int($3),$4,$5,$6,$7,$8,$9,$10;}' | gzip -f -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 72

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/rep1/SRR1370891_1.nodup.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 74

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/rep1/SRR1370891_1.nodup.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf

# SYS command. line 77

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz; fi

# SYS command. line 80

 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi

# SYS command. line 82

 if [[ true == "true" ]]; then \
			bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.filt.regionPeak.gz; \
		fi

# SYS command. line 86

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
29666 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/align/rep1/SRR1370891_1.nodup.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 150 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: 3e+05 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/rep1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/rep1/SRR1370891_1.nodup.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/rep1/SRR1370891_1.nodup.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore 
Overwrite files?: TRUE

Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/align/rep1/SRR1370891_1.nodup.tagAlign.gz 
opened /tmp/24247.1.q/Rtmp7ygjqF/SRR1370891_1.nodup.tagAlign74db7e1e732
done. read 14881524 fragments
ChIP data read length 51 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
opened /tmp/24247.1.q/Rtmp7ygjqF/input15MReadsNSCLess1.05.50MSubsample.tagAlign74db4e6c977b
done. read 50000000 fragments
Control data read length 68 
Calculating peak characteristics
Minimum cross-correlation value 0.1737303 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.1781813690566 
Top 3 estimates for fragment length 150 
Window half size 195 
Phantom peak location 50 
Phantom peak Correlation 0.1759375 
Normalized Strand cross-correlation coefficient (NSC) 1.02562 
Relative Strand cross-correlation Coefficient (RSC) 2.016592 
Phantom Peak Quality Tag 2 
null device 
          1 
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 3.35615  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.2979604  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.00005 
Detected 415016 peaks 

 
--------------------Stderr--------------------
Loading required package: caTools
There were 50 or more warnings (use warnings() to see the first 50)
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	2218	2414	.	0	.	17.0917587359986	-1	2.4902326336086	98

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	2218	2414	.	0	.	17.0917587359986	-1	2.4902326336086	98


 
 		 

    
  
 
  Num   2  
 
  ID   task.callpeak_macs2.macs2_rep1.line_71.id_11  
 
  Name   macs2 rep1 
 
  Thread   thread_Root  
 
  PID   24248  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-06 14:31:47  
 
  End   2017-01-06 15:28:02  
 
  Elapsed   00:56:15  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/align/rep1/SRR1370891_1.nodup.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/signal/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/signal/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw
  
 
  Dependencies     
 
 		  
 
# SYS command. line 73

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

# SYS command. line 74

 export LC_COLLATE=C

# SYS command. line 79

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/align/rep1/SRR1370891_1.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/align/rep1/SRR1370891_1.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 110

 if [[ true == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 121

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1 -o "SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/signal/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/align/rep1/SRR1370891_1.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

# SYS command. line 140

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1 -o "SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 143

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/signal/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg

# SYS command. line 153

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
29668 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 14:32:09: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/align/rep1/SRR1370891_1.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/align/rep1/SRR1370891_1.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.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  @ Fri, 06 Jan 2017 14:32:09: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 14:32:09: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 14:32:11:  1000000 
INFO  @ Fri, 06 Jan 2017 14:32:13:  2000000 
INFO  @ Fri, 06 Jan 2017 14:32:15:  3000000 
INFO  @ Fri, 06 Jan 2017 14:32:16:  4000000 
INFO  @ Fri, 06 Jan 2017 14:32:18:  5000000 
INFO  @ Fri, 06 Jan 2017 14:32:20:  6000000 
INFO  @ Fri, 06 Jan 2017 14:32:22:  7000000 
INFO  @ Fri, 06 Jan 2017 14:32:23:  8000000 
INFO  @ Fri, 06 Jan 2017 14:32:25:  9000000 
INFO  @ Fri, 06 Jan 2017 14:32:27:  10000000 
INFO  @ Fri, 06 Jan 2017 14:32:29:  11000000 
INFO  @ Fri, 06 Jan 2017 14:32:30:  12000000 
INFO  @ Fri, 06 Jan 2017 14:32:32:  13000000 
INFO  @ Fri, 06 Jan 2017 14:32:34:  14000000 
INFO  @ Fri, 06 Jan 2017 14:32:35: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 14:32:37:  1000000 
INFO  @ Fri, 06 Jan 2017 14:32:39:  2000000 
INFO  @ Fri, 06 Jan 2017 14:32:41:  3000000 
INFO  @ Fri, 06 Jan 2017 14:32:42:  4000000 
INFO  @ Fri, 06 Jan 2017 14:32:44:  5000000 
INFO  @ Fri, 06 Jan 2017 14:32:46:  6000000 
INFO  @ Fri, 06 Jan 2017 14:32:48:  7000000 
INFO  @ Fri, 06 Jan 2017 14:32:49:  8000000 
INFO  @ Fri, 06 Jan 2017 14:32:51:  9000000 
INFO  @ Fri, 06 Jan 2017 14:32:53:  10000000 
INFO  @ Fri, 06 Jan 2017 14:32:55:  11000000 
INFO  @ Fri, 06 Jan 2017 14:32:56:  12000000 
INFO  @ Fri, 06 Jan 2017 14:32:58:  13000000 
INFO  @ Fri, 06 Jan 2017 14:33:00:  14000000 
INFO  @ Fri, 06 Jan 2017 14:33:02:  15000000 
INFO  @ Fri, 06 Jan 2017 14:33:04:  16000000 
INFO  @ Fri, 06 Jan 2017 14:33:05:  17000000 
INFO  @ Fri, 06 Jan 2017 14:33:07:  18000000 
INFO  @ Fri, 06 Jan 2017 14:33:09:  19000000 
INFO  @ Fri, 06 Jan 2017 14:33:10:  20000000 
INFO  @ Fri, 06 Jan 2017 14:33:12:  21000000 
INFO  @ Fri, 06 Jan 2017 14:33:14:  22000000 
INFO  @ Fri, 06 Jan 2017 14:33:16:  23000000 
INFO  @ Fri, 06 Jan 2017 14:33:18:  24000000 
INFO  @ Fri, 06 Jan 2017 14:33:19:  25000000 
INFO  @ Fri, 06 Jan 2017 14:33:21:  26000000 
INFO  @ Fri, 06 Jan 2017 14:33:23:  27000000 
INFO  @ Fri, 06 Jan 2017 14:33:24:  28000000 
INFO  @ Fri, 06 Jan 2017 14:33:26:  29000000 
INFO  @ Fri, 06 Jan 2017 14:33:28:  30000000 
INFO  @ Fri, 06 Jan 2017 14:33:30:  31000000 
INFO  @ Fri, 06 Jan 2017 14:33:31:  32000000 
INFO  @ Fri, 06 Jan 2017 14:33:33:  33000000 
INFO  @ Fri, 06 Jan 2017 14:33:35:  34000000 
INFO  @ Fri, 06 Jan 2017 14:33:37:  35000000 
INFO  @ Fri, 06 Jan 2017 14:33:38:  36000000 
INFO  @ Fri, 06 Jan 2017 14:33:40:  37000000 
INFO  @ Fri, 06 Jan 2017 14:33:42:  38000000 
INFO  @ Fri, 06 Jan 2017 14:33:44:  39000000 
INFO  @ Fri, 06 Jan 2017 14:33:45:  40000000 
INFO  @ Fri, 06 Jan 2017 14:33:47:  41000000 
INFO  @ Fri, 06 Jan 2017 14:33:49:  42000000 
INFO  @ Fri, 06 Jan 2017 14:33:51:  43000000 
INFO  @ Fri, 06 Jan 2017 14:33:52:  44000000 
INFO  @ Fri, 06 Jan 2017 14:33:54:  45000000 
INFO  @ Fri, 06 Jan 2017 14:33:56:  46000000 
INFO  @ Fri, 06 Jan 2017 14:33:58:  47000000 
INFO  @ Fri, 06 Jan 2017 14:33:59:  48000000 
INFO  @ Fri, 06 Jan 2017 14:34:01:  49000000 
INFO  @ Fri, 06 Jan 2017 14:34:04:  50000000 
INFO  @ Fri, 06 Jan 2017 14:34:06: #1 tag size is determined as 47 bps 
INFO  @ Fri, 06 Jan 2017 14:34:06: #1 tag size = 47 
INFO  @ Fri, 06 Jan 2017 14:34:06: #1  total tags in treatment: 14881524 
INFO  @ Fri, 06 Jan 2017 14:34:06: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 14:34:06: #1 finished! 
INFO  @ Fri, 06 Jan 2017 14:34:06: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 14:34:06: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 14:34:06: #2 Use 150 as fragment length 
INFO  @ Fri, 06 Jan 2017 14:34:06: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 14:34:06: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 14:34:06: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 14:37:28: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 14:37:28: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 14:37:28: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 14:37:28: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 14:37:28: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 14:43:07: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 14:43:07: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 14:43:07: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 14:43:08: Done! 
INFO  @ Fri, 06 Jan 2017 14:43:10: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/align/rep1/SRR1370891_1.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/align/rep1/SRR1370891_1.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Fri, 06 Jan 2017 14:43:10: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 14:43:10: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 14:43:12:  1000000 
INFO  @ Fri, 06 Jan 2017 14:43:14:  2000000 
INFO  @ Fri, 06 Jan 2017 14:43:16:  3000000 
INFO  @ Fri, 06 Jan 2017 14:43:18:  4000000 
INFO  @ Fri, 06 Jan 2017 14:43:19:  5000000 
INFO  @ Fri, 06 Jan 2017 14:43:21:  6000000 
INFO  @ Fri, 06 Jan 2017 14:43:23:  7000000 
INFO  @ Fri, 06 Jan 2017 14:43:25:  8000000 
INFO  @ Fri, 06 Jan 2017 14:43:27:  9000000 
INFO  @ Fri, 06 Jan 2017 14:43:29:  10000000 
INFO  @ Fri, 06 Jan 2017 14:43:30:  11000000 
INFO  @ Fri, 06 Jan 2017 14:43:32:  12000000 
INFO  @ Fri, 06 Jan 2017 14:43:34:  13000000 
INFO  @ Fri, 06 Jan 2017 14:43:36:  14000000 
INFO  @ Fri, 06 Jan 2017 14:43:38: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 14:43:40:  1000000 
INFO  @ Fri, 06 Jan 2017 14:43:42:  2000000 
INFO  @ Fri, 06 Jan 2017 14:43:44:  3000000 
INFO  @ Fri, 06 Jan 2017 14:43:45:  4000000 
INFO  @ Fri, 06 Jan 2017 14:43:47:  5000000 
INFO  @ Fri, 06 Jan 2017 14:43:49:  6000000 
INFO  @ Fri, 06 Jan 2017 14:43:51:  7000000 
INFO  @ Fri, 06 Jan 2017 14:43:53:  8000000 
INFO  @ Fri, 06 Jan 2017 14:43:55:  9000000 
INFO  @ Fri, 06 Jan 2017 14:43:56:  10000000 
INFO  @ Fri, 06 Jan 2017 14:43:58:  11000000 
INFO  @ Fri, 06 Jan 2017 14:44:00:  12000000 
INFO  @ Fri, 06 Jan 2017 14:44:02:  13000000 
INFO  @ Fri, 06 Jan 2017 14:44:04:  14000000 
INFO  @ Fri, 06 Jan 2017 14:44:06:  15000000 
INFO  @ Fri, 06 Jan 2017 14:44:08:  16000000 
INFO  @ Fri, 06 Jan 2017 14:44:10:  17000000 
INFO  @ Fri, 06 Jan 2017 14:44:11:  18000000 
INFO  @ Fri, 06 Jan 2017 14:44:13:  19000000 
INFO  @ Fri, 06 Jan 2017 14:44:15:  20000000 
INFO  @ Fri, 06 Jan 2017 14:44:17:  21000000 
INFO  @ Fri, 06 Jan 2017 14:44:19:  22000000 
INFO  @ Fri, 06 Jan 2017 14:44:21:  23000000 
INFO  @ Fri, 06 Jan 2017 14:44:23:  24000000 
INFO  @ Fri, 06 Jan 2017 14:44:24:  25000000 
INFO  @ Fri, 06 Jan 2017 14:44:26:  26000000 
INFO  @ Fri, 06 Jan 2017 14:44:28:  27000000 
INFO  @ Fri, 06 Jan 2017 14:44:30:  28000000 
INFO  @ Fri, 06 Jan 2017 14:44:32:  29000000 
INFO  @ Fri, 06 Jan 2017 14:44:34:  30000000 
INFO  @ Fri, 06 Jan 2017 14:44:35:  31000000 
INFO  @ Fri, 06 Jan 2017 14:44:37:  32000000 
INFO  @ Fri, 06 Jan 2017 14:44:39:  33000000 
INFO  @ Fri, 06 Jan 2017 14:44:41:  34000000 
INFO  @ Fri, 06 Jan 2017 14:44:43:  35000000 
INFO  @ Fri, 06 Jan 2017 14:44:45:  36000000 
INFO  @ Fri, 06 Jan 2017 14:44:48:  37000000 
INFO  @ Fri, 06 Jan 2017 14:44:50:  38000000 
INFO  @ Fri, 06 Jan 2017 14:44:51:  39000000 
INFO  @ Fri, 06 Jan 2017 14:44:53:  40000000 
INFO  @ Fri, 06 Jan 2017 14:44:55:  41000000 
INFO  @ Fri, 06 Jan 2017 14:44:57:  42000000 
INFO  @ Fri, 06 Jan 2017 14:44:59:  43000000 
INFO  @ Fri, 06 Jan 2017 14:45:01:  44000000 
INFO  @ Fri, 06 Jan 2017 14:45:02:  45000000 
INFO  @ Fri, 06 Jan 2017 14:45:04:  46000000 
INFO  @ Fri, 06 Jan 2017 14:45:06:  47000000 
INFO  @ Fri, 06 Jan 2017 14:45:08:  48000000 
INFO  @ Fri, 06 Jan 2017 14:45:10:  49000000 
INFO  @ Fri, 06 Jan 2017 14:45:11:  50000000 
INFO  @ Fri, 06 Jan 2017 14:45:13: #1 tag size is determined as 47 bps 
INFO  @ Fri, 06 Jan 2017 14:45:13: #1 tag size = 47 
INFO  @ Fri, 06 Jan 2017 14:45:13: #1  total tags in treatment: 14881524 
INFO  @ Fri, 06 Jan 2017 14:45:13: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 14:45:13: #1 finished! 
INFO  @ Fri, 06 Jan 2017 14:45:13: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 14:45:13: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 14:45:13: #2 Use 150 as fragment length 
INFO  @ Fri, 06 Jan 2017 14:45:13: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 14:45:13: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 14:45:13: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 14:47:49: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 14:50:04: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 14:50:11: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 14:50:15: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 14:50:19: Done! 
INFO  @ Fri, 06 Jan 2017 14:50:35: Read and build treatment bedGraph... 
INFO  @ Fri, 06 Jan 2017 14:51:05: Read and build control bedGraph... 
INFO  @ Fri, 06 Jan 2017 14:52:55: Build scoreTrackII... 
INFO  @ Fri, 06 Jan 2017 14:53:44: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Fri, 06 Jan 2017 14:58:54: Write bedGraph of scores... 
INFO  @ Fri, 06 Jan 2017 15:01:49: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_FE.bdg'! 
INFO  @ Fri, 06 Jan 2017 15:07:56: Read and build treatment bedGraph... 
INFO  @ Fri, 06 Jan 2017 15:08:29: Read and build control bedGraph... 
INFO  @ Fri, 06 Jan 2017 15:10:25: Build scoreTrackII... 
INFO  @ Fri, 06 Jan 2017 15:11:07: Values in your input bedGraph files will be multiplied by 14.881524 ... 
INFO  @ Fri, 06 Jan 2017 15:16:19: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Fri, 06 Jan 2017 15:16:55: Write bedGraph of scores... 
INFO  @ Fri, 06 Jan 2017 15:19:56: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_ppois.bdg'! 

 
 		 

    
  
 
  Num   3  
 
  ID   task.callpeak_macs2.macs2_rep1_pr1.line_71.id_12  
 
  Name   macs2 rep1-pr1 
 
  Thread   thread_Root  
 
  PID   24249  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-06 14:31:50  
 
  End   2017-01-06 14:48:16  
 
  Elapsed   00:16:25  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/align/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 73

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

# SYS command. line 74

 export LC_COLLATE=C

# SYS command. line 79

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/align/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/align/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 110

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 121

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/align/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

# SYS command. line 140

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 143

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg

# SYS command. line 153

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
29665 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 14:32:08: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/align/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/align/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.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  @ Fri, 06 Jan 2017 14:32:08: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 14:32:08: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 14:32:10:  1000000 
INFO  @ Fri, 06 Jan 2017 14:32:12:  2000000 
INFO  @ Fri, 06 Jan 2017 14:32:13:  3000000 
INFO  @ Fri, 06 Jan 2017 14:32:15:  4000000 
INFO  @ Fri, 06 Jan 2017 14:32:17:  5000000 
INFO  @ Fri, 06 Jan 2017 14:32:18:  6000000 
INFO  @ Fri, 06 Jan 2017 14:32:20:  7000000 
INFO  @ Fri, 06 Jan 2017 14:32:21: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 14:32:23:  1000000 
INFO  @ Fri, 06 Jan 2017 14:32:24:  2000000 
INFO  @ Fri, 06 Jan 2017 14:32:26:  3000000 
INFO  @ Fri, 06 Jan 2017 14:32:28:  4000000 
INFO  @ Fri, 06 Jan 2017 14:32:29:  5000000 
INFO  @ Fri, 06 Jan 2017 14:32:31:  6000000 
INFO  @ Fri, 06 Jan 2017 14:32:32:  7000000 
INFO  @ Fri, 06 Jan 2017 14:32:34:  8000000 
INFO  @ Fri, 06 Jan 2017 14:32:35:  9000000 
INFO  @ Fri, 06 Jan 2017 14:32:37:  10000000 
INFO  @ Fri, 06 Jan 2017 14:32:39:  11000000 
INFO  @ Fri, 06 Jan 2017 14:32:40:  12000000 
INFO  @ Fri, 06 Jan 2017 14:32:42:  13000000 
INFO  @ Fri, 06 Jan 2017 14:32:43:  14000000 
INFO  @ Fri, 06 Jan 2017 14:32:45:  15000000 
INFO  @ Fri, 06 Jan 2017 14:32:46:  16000000 
INFO  @ Fri, 06 Jan 2017 14:32:48:  17000000 
INFO  @ Fri, 06 Jan 2017 14:32:50:  18000000 
INFO  @ Fri, 06 Jan 2017 14:32:51:  19000000 
INFO  @ Fri, 06 Jan 2017 14:32:53:  20000000 
INFO  @ Fri, 06 Jan 2017 14:32:54:  21000000 
INFO  @ Fri, 06 Jan 2017 14:32:56:  22000000 
INFO  @ Fri, 06 Jan 2017 14:32:57:  23000000 
INFO  @ Fri, 06 Jan 2017 14:32:59:  24000000 
INFO  @ Fri, 06 Jan 2017 14:33:01:  25000000 
INFO  @ Fri, 06 Jan 2017 14:33:02:  26000000 
INFO  @ Fri, 06 Jan 2017 14:33:04:  27000000 
INFO  @ Fri, 06 Jan 2017 14:33:05:  28000000 
INFO  @ Fri, 06 Jan 2017 14:33:07:  29000000 
INFO  @ Fri, 06 Jan 2017 14:33:08:  30000000 
INFO  @ Fri, 06 Jan 2017 14:33:10:  31000000 
INFO  @ Fri, 06 Jan 2017 14:33:12:  32000000 
INFO  @ Fri, 06 Jan 2017 14:33:13:  33000000 
INFO  @ Fri, 06 Jan 2017 14:33:15:  34000000 
INFO  @ Fri, 06 Jan 2017 14:33:16:  35000000 
INFO  @ Fri, 06 Jan 2017 14:33:18:  36000000 
INFO  @ Fri, 06 Jan 2017 14:33:19:  37000000 
INFO  @ Fri, 06 Jan 2017 14:33:21:  38000000 
INFO  @ Fri, 06 Jan 2017 14:33:22:  39000000 
INFO  @ Fri, 06 Jan 2017 14:33:24:  40000000 
INFO  @ Fri, 06 Jan 2017 14:33:26:  41000000 
INFO  @ Fri, 06 Jan 2017 14:33:27:  42000000 
INFO  @ Fri, 06 Jan 2017 14:33:29:  43000000 
INFO  @ Fri, 06 Jan 2017 14:33:30:  44000000 
INFO  @ Fri, 06 Jan 2017 14:33:32:  45000000 
INFO  @ Fri, 06 Jan 2017 14:33:33:  46000000 
INFO  @ Fri, 06 Jan 2017 14:33:35:  47000000 
INFO  @ Fri, 06 Jan 2017 14:33:37:  48000000 
INFO  @ Fri, 06 Jan 2017 14:33:38:  49000000 
INFO  @ Fri, 06 Jan 2017 14:33:40:  50000000 
INFO  @ Fri, 06 Jan 2017 14:33:41: #1 tag size is determined as 51 bps 
INFO  @ Fri, 06 Jan 2017 14:33:41: #1 tag size = 51 
INFO  @ Fri, 06 Jan 2017 14:33:41: #1  total tags in treatment: 7440762 
INFO  @ Fri, 06 Jan 2017 14:33:41: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 14:33:41: #1 finished! 
INFO  @ Fri, 06 Jan 2017 14:33:41: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 14:33:41: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 14:33:41: #2 Use 150 as fragment length 
INFO  @ Fri, 06 Jan 2017 14:33:41: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 14:33:41: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 14:33:41: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 14:36:08: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 14:36:08: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 14:36:08: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 14:36:08: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 14:36:08: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 14:40:39: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 14:40:40: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 14:40:40: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 14:40:41: Done! 
INFO  @ Fri, 06 Jan 2017 14:40:44: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/align/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/align/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Fri, 06 Jan 2017 14:40:44: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 14:40:44: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 14:40:46:  1000000 
INFO  @ Fri, 06 Jan 2017 14:40:48:  2000000 
INFO  @ Fri, 06 Jan 2017 14:40:49:  3000000 
INFO  @ Fri, 06 Jan 2017 14:40:51:  4000000 
INFO  @ Fri, 06 Jan 2017 14:40:53:  5000000 
INFO  @ Fri, 06 Jan 2017 14:40:54:  6000000 
INFO  @ Fri, 06 Jan 2017 14:40:56:  7000000 
INFO  @ Fri, 06 Jan 2017 14:40:57: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 14:40:59:  1000000 
INFO  @ Fri, 06 Jan 2017 14:41:00:  2000000 
INFO  @ Fri, 06 Jan 2017 14:41:02:  3000000 
INFO  @ Fri, 06 Jan 2017 14:41:04:  4000000 
INFO  @ Fri, 06 Jan 2017 14:41:05:  5000000 
INFO  @ Fri, 06 Jan 2017 14:41:07:  6000000 
INFO  @ Fri, 06 Jan 2017 14:41:08:  7000000 
INFO  @ Fri, 06 Jan 2017 14:41:10:  8000000 
INFO  @ Fri, 06 Jan 2017 14:41:11:  9000000 
INFO  @ Fri, 06 Jan 2017 14:41:13:  10000000 
INFO  @ Fri, 06 Jan 2017 14:41:14:  11000000 
INFO  @ Fri, 06 Jan 2017 14:41:16:  12000000 
INFO  @ Fri, 06 Jan 2017 14:41:18:  13000000 
INFO  @ Fri, 06 Jan 2017 14:41:19:  14000000 
INFO  @ Fri, 06 Jan 2017 14:41:21:  15000000 
INFO  @ Fri, 06 Jan 2017 14:41:22:  16000000 
INFO  @ Fri, 06 Jan 2017 14:41:24:  17000000 
INFO  @ Fri, 06 Jan 2017 14:41:25:  18000000 
INFO  @ Fri, 06 Jan 2017 14:41:27:  19000000 
INFO  @ Fri, 06 Jan 2017 14:41:29:  20000000 
INFO  @ Fri, 06 Jan 2017 14:41:30:  21000000 
INFO  @ Fri, 06 Jan 2017 14:41:32:  22000000 
INFO  @ Fri, 06 Jan 2017 14:41:33:  23000000 
INFO  @ Fri, 06 Jan 2017 14:41:35:  24000000 
INFO  @ Fri, 06 Jan 2017 14:41:36:  25000000 
INFO  @ Fri, 06 Jan 2017 14:41:38:  26000000 
INFO  @ Fri, 06 Jan 2017 14:41:39:  27000000 
INFO  @ Fri, 06 Jan 2017 14:41:41:  28000000 
INFO  @ Fri, 06 Jan 2017 14:41:42:  29000000 
INFO  @ Fri, 06 Jan 2017 14:41:44:  30000000 
INFO  @ Fri, 06 Jan 2017 14:41:45:  31000000 
INFO  @ Fri, 06 Jan 2017 14:41:47:  32000000 
INFO  @ Fri, 06 Jan 2017 14:41:48:  33000000 
INFO  @ Fri, 06 Jan 2017 14:41:50:  34000000 
INFO  @ Fri, 06 Jan 2017 14:41:51:  35000000 
INFO  @ Fri, 06 Jan 2017 14:41:53:  36000000 
INFO  @ Fri, 06 Jan 2017 14:41:55:  37000000 
INFO  @ Fri, 06 Jan 2017 14:41:56:  38000000 
INFO  @ Fri, 06 Jan 2017 14:41:58:  39000000 
INFO  @ Fri, 06 Jan 2017 14:41:59:  40000000 
INFO  @ Fri, 06 Jan 2017 14:42:01:  41000000 
INFO  @ Fri, 06 Jan 2017 14:42:02:  42000000 
INFO  @ Fri, 06 Jan 2017 14:42:04:  43000000 
INFO  @ Fri, 06 Jan 2017 14:42:05:  44000000 
INFO  @ Fri, 06 Jan 2017 14:42:07:  45000000 
INFO  @ Fri, 06 Jan 2017 14:42:08:  46000000 
INFO  @ Fri, 06 Jan 2017 14:42:10:  47000000 
INFO  @ Fri, 06 Jan 2017 14:42:11:  48000000 
INFO  @ Fri, 06 Jan 2017 14:42:13:  49000000 
INFO  @ Fri, 06 Jan 2017 14:42:15:  50000000 
INFO  @ Fri, 06 Jan 2017 14:42:16: #1 tag size is determined as 51 bps 
INFO  @ Fri, 06 Jan 2017 14:42:16: #1 tag size = 51 
INFO  @ Fri, 06 Jan 2017 14:42:16: #1  total tags in treatment: 7440762 
INFO  @ Fri, 06 Jan 2017 14:42:16: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 14:42:16: #1 finished! 
INFO  @ Fri, 06 Jan 2017 14:42:16: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 14:42:16: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 14:42:16: #2 Use 150 as fragment length 
INFO  @ Fri, 06 Jan 2017 14:42:16: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 14:42:16: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 14:42:16: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 14:44:50: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 14:47:41: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 14:47:47: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 14:47:52: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 14:47:57: Done! 

 
 		 

    
  
 
  Num   4  
 
  ID   task.callpeak_macs2.macs2_rep1_pr2.line_71.id_13  
 
  Name   macs2 rep1-pr2 
 
  Thread   thread_Root  
 
  PID   24250  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-06 14:31:51  
 
  End   2017-01-06 14:50:35  
 
  Elapsed   00:18:43  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/align/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 73

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

# SYS command. line 74

 export LC_COLLATE=C

# SYS command. line 79

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/align/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/align/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 110

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 121

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/align/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

# SYS command. line 140

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 143

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg

# SYS command. line 153

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
29667 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 14:32:09: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/align/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/align/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.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  @ Fri, 06 Jan 2017 14:32:09: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 14:32:09: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 14:32:11:  1000000 
INFO  @ Fri, 06 Jan 2017 14:32:13:  2000000 
INFO  @ Fri, 06 Jan 2017 14:32:14:  3000000 
INFO  @ Fri, 06 Jan 2017 14:32:16:  4000000 
INFO  @ Fri, 06 Jan 2017 14:32:18:  5000000 
INFO  @ Fri, 06 Jan 2017 14:32:20:  6000000 
INFO  @ Fri, 06 Jan 2017 14:32:21:  7000000 
INFO  @ Fri, 06 Jan 2017 14:32:23: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 14:32:24:  1000000 
INFO  @ Fri, 06 Jan 2017 14:32:26:  2000000 
INFO  @ Fri, 06 Jan 2017 14:32:28:  3000000 
INFO  @ Fri, 06 Jan 2017 14:32:29:  4000000 
INFO  @ Fri, 06 Jan 2017 14:32:31:  5000000 
INFO  @ Fri, 06 Jan 2017 14:32:32:  6000000 
INFO  @ Fri, 06 Jan 2017 14:32:34:  7000000 
INFO  @ Fri, 06 Jan 2017 14:32:36:  8000000 
INFO  @ Fri, 06 Jan 2017 14:32:37:  9000000 
INFO  @ Fri, 06 Jan 2017 14:32:39:  10000000 
INFO  @ Fri, 06 Jan 2017 14:32:40:  11000000 
INFO  @ Fri, 06 Jan 2017 14:32:42:  12000000 
INFO  @ Fri, 06 Jan 2017 14:32:44:  13000000 
INFO  @ Fri, 06 Jan 2017 14:32:46:  14000000 
INFO  @ Fri, 06 Jan 2017 14:32:47:  15000000 
INFO  @ Fri, 06 Jan 2017 14:32:49:  16000000 
INFO  @ Fri, 06 Jan 2017 14:32:51:  17000000 
INFO  @ Fri, 06 Jan 2017 14:32:52:  18000000 
INFO  @ Fri, 06 Jan 2017 14:32:54:  19000000 
INFO  @ Fri, 06 Jan 2017 14:32:56:  20000000 
INFO  @ Fri, 06 Jan 2017 14:32:57:  21000000 
INFO  @ Fri, 06 Jan 2017 14:32:59:  22000000 
INFO  @ Fri, 06 Jan 2017 14:33:01:  23000000 
INFO  @ Fri, 06 Jan 2017 14:33:02:  24000000 
INFO  @ Fri, 06 Jan 2017 14:33:04:  25000000 
INFO  @ Fri, 06 Jan 2017 14:33:05:  26000000 
INFO  @ Fri, 06 Jan 2017 14:33:07:  27000000 
INFO  @ Fri, 06 Jan 2017 14:33:09:  28000000 
INFO  @ Fri, 06 Jan 2017 14:33:10:  29000000 
INFO  @ Fri, 06 Jan 2017 14:33:12:  30000000 
INFO  @ Fri, 06 Jan 2017 14:33:14:  31000000 
INFO  @ Fri, 06 Jan 2017 14:33:15:  32000000 
INFO  @ Fri, 06 Jan 2017 14:33:17:  33000000 
INFO  @ Fri, 06 Jan 2017 14:33:19:  34000000 
INFO  @ Fri, 06 Jan 2017 14:33:20:  35000000 
INFO  @ Fri, 06 Jan 2017 14:33:22:  36000000 
INFO  @ Fri, 06 Jan 2017 14:33:24:  37000000 
INFO  @ Fri, 06 Jan 2017 14:33:25:  38000000 
INFO  @ Fri, 06 Jan 2017 14:33:27:  39000000 
INFO  @ Fri, 06 Jan 2017 14:33:28:  40000000 
INFO  @ Fri, 06 Jan 2017 14:33:30:  41000000 
INFO  @ Fri, 06 Jan 2017 14:33:32:  42000000 
INFO  @ Fri, 06 Jan 2017 14:33:33:  43000000 
INFO  @ Fri, 06 Jan 2017 14:33:35:  44000000 
INFO  @ Fri, 06 Jan 2017 14:33:37:  45000000 
INFO  @ Fri, 06 Jan 2017 14:33:38:  46000000 
INFO  @ Fri, 06 Jan 2017 14:33:40:  47000000 
INFO  @ Fri, 06 Jan 2017 14:33:42:  48000000 
INFO  @ Fri, 06 Jan 2017 14:33:43:  49000000 
INFO  @ Fri, 06 Jan 2017 14:33:45:  50000000 
INFO  @ Fri, 06 Jan 2017 14:33:47: #1 tag size is determined as 51 bps 
INFO  @ Fri, 06 Jan 2017 14:33:47: #1 tag size = 51 
INFO  @ Fri, 06 Jan 2017 14:33:47: #1  total tags in treatment: 7440762 
INFO  @ Fri, 06 Jan 2017 14:33:47: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 14:33:47: #1 finished! 
INFO  @ Fri, 06 Jan 2017 14:33:47: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 14:33:47: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 14:33:47: #2 Use 150 as fragment length 
INFO  @ Fri, 06 Jan 2017 14:33:47: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 14:33:47: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 14:33:47: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 14:37:14: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 14:37:14: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 14:37:14: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 14:37:14: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 14:37:14: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 14:42:27: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 14:42:29: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 14:42:29: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 14:42:30: Done! 
INFO  @ Fri, 06 Jan 2017 14:42:33: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/align/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/align/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Fri, 06 Jan 2017 14:42:33: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 14:42:33: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 14:42:35:  1000000 
INFO  @ Fri, 06 Jan 2017 14:42:36:  2000000 
INFO  @ Fri, 06 Jan 2017 14:42:38:  3000000 
INFO  @ Fri, 06 Jan 2017 14:42:39:  4000000 
INFO  @ Fri, 06 Jan 2017 14:42:41:  5000000 
INFO  @ Fri, 06 Jan 2017 14:42:43:  6000000 
INFO  @ Fri, 06 Jan 2017 14:42:44:  7000000 
INFO  @ Fri, 06 Jan 2017 14:42:46: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 14:42:47:  1000000 
INFO  @ Fri, 06 Jan 2017 14:42:49:  2000000 
INFO  @ Fri, 06 Jan 2017 14:42:50:  3000000 
INFO  @ Fri, 06 Jan 2017 14:42:52:  4000000 
INFO  @ Fri, 06 Jan 2017 14:42:53:  5000000 
INFO  @ Fri, 06 Jan 2017 14:42:55:  6000000 
INFO  @ Fri, 06 Jan 2017 14:42:56:  7000000 
INFO  @ Fri, 06 Jan 2017 14:42:58:  8000000 
INFO  @ Fri, 06 Jan 2017 14:43:00:  9000000 
INFO  @ Fri, 06 Jan 2017 14:43:01:  10000000 
INFO  @ Fri, 06 Jan 2017 14:43:03:  11000000 
INFO  @ Fri, 06 Jan 2017 14:43:04:  12000000 
INFO  @ Fri, 06 Jan 2017 14:43:06:  13000000 
INFO  @ Fri, 06 Jan 2017 14:43:07:  14000000 
INFO  @ Fri, 06 Jan 2017 14:43:09:  15000000 
INFO  @ Fri, 06 Jan 2017 14:43:11:  16000000 
INFO  @ Fri, 06 Jan 2017 14:43:12:  17000000 
INFO  @ Fri, 06 Jan 2017 14:43:14:  18000000 
INFO  @ Fri, 06 Jan 2017 14:43:15:  19000000 
INFO  @ Fri, 06 Jan 2017 14:43:17:  20000000 
INFO  @ Fri, 06 Jan 2017 14:43:18:  21000000 
INFO  @ Fri, 06 Jan 2017 14:43:20:  22000000 
INFO  @ Fri, 06 Jan 2017 14:43:21:  23000000 
INFO  @ Fri, 06 Jan 2017 14:43:23:  24000000 
INFO  @ Fri, 06 Jan 2017 14:43:24:  25000000 
INFO  @ Fri, 06 Jan 2017 14:43:26:  26000000 
INFO  @ Fri, 06 Jan 2017 14:43:27:  27000000 
INFO  @ Fri, 06 Jan 2017 14:43:29:  28000000 
INFO  @ Fri, 06 Jan 2017 14:43:30:  29000000 
INFO  @ Fri, 06 Jan 2017 14:43:32:  30000000 
INFO  @ Fri, 06 Jan 2017 14:43:34:  31000000 
INFO  @ Fri, 06 Jan 2017 14:43:36:  32000000 
INFO  @ Fri, 06 Jan 2017 14:43:37:  33000000 
INFO  @ Fri, 06 Jan 2017 14:43:39:  34000000 
INFO  @ Fri, 06 Jan 2017 14:43:41:  35000000 
INFO  @ Fri, 06 Jan 2017 14:43:42:  36000000 
INFO  @ Fri, 06 Jan 2017 14:43:44:  37000000 
INFO  @ Fri, 06 Jan 2017 14:43:45:  38000000 
INFO  @ Fri, 06 Jan 2017 14:43:47:  39000000 
INFO  @ Fri, 06 Jan 2017 14:43:48:  40000000 
INFO  @ Fri, 06 Jan 2017 14:43:50:  41000000 
INFO  @ Fri, 06 Jan 2017 14:43:52:  42000000 
INFO  @ Fri, 06 Jan 2017 14:43:53:  43000000 
INFO  @ Fri, 06 Jan 2017 14:43:55:  44000000 
INFO  @ Fri, 06 Jan 2017 14:43:56:  45000000 
INFO  @ Fri, 06 Jan 2017 14:43:58:  46000000 
INFO  @ Fri, 06 Jan 2017 14:43:59:  47000000 
INFO  @ Fri, 06 Jan 2017 14:44:01:  48000000 
INFO  @ Fri, 06 Jan 2017 14:44:03:  49000000 
INFO  @ Fri, 06 Jan 2017 14:44:04:  50000000 
INFO  @ Fri, 06 Jan 2017 14:44:06: #1 tag size is determined as 51 bps 
INFO  @ Fri, 06 Jan 2017 14:44:06: #1 tag size = 51 
INFO  @ Fri, 06 Jan 2017 14:44:06: #1  total tags in treatment: 7440762 
INFO  @ Fri, 06 Jan 2017 14:44:06: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 14:44:06: #1 finished! 
INFO  @ Fri, 06 Jan 2017 14:44:06: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 14:44:06: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 14:44:06: #2 Use 150 as fragment length 
INFO  @ Fri, 06 Jan 2017 14:44:06: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 14:44:06: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 14:44:06: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 14:46:41: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 14:50:00: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 14:50:07: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 14:50:13: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 14:50:18: Done! 

 
 		 

    
  
 
  Num   5  
 
  ID   task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_14  
 
  Name   naive_overlap_thresh  
 
  Thread   thread_Root  
 
  PID   24371  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-07 06:00:22  
 
  End   2017-01-07 06:01:38  
 
  Elapsed   00:01:15  
 
  Timeout  01:00:00 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/overlap/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 61

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

# SYS command. line 64

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.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/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.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/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/overlap/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/overlap/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/overlap/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz

# SYS command. line 72

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/overlap/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz  | grep -P 'chr[dXY]+[ 	]' | awk 'BEGIN{OFS="	"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/overlap/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/overlap/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz

# SYS command. line 76

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
25543 (process ID) old priority 0, new priority 10
Waiting for 58 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270467.1	2158	2354	.	0	.	20.6373889132584	-1	3.04306426516181	98

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270467.1	2158	2354	.	0	.	20.6373889132584	-1	3.04306426516181	98

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270467.1	2837	3037	.	0	.	10.5141813073654	-1	3.72969922631617	100

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270467.1	2837	3037	.	0	.	10.5141813073654	-1	3.72969922631617	100

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/overlap/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
GL000216.2	289	485	.	0	.	3.82892494827815	-1	1.99853861902773	98

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/overlap/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
GL000216.2	289	485	.	0	.	3.82892494827815	-1	1.99853861902773	98


 
 		 

    
  
 
  Num   6  
 
  ID   task.callpeak_idr.idr2_rep1_pr.line_73.id_15  
 
  Name   idr2 rep1-pr 
 
  Thread   thread_Root  
 
  PID   24372  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-07 06:01:39  
 
  End   2017-01-07 06:02:53  
 
  Elapsed   00:01:14  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/idr/pseudo_reps/rep1/ZNF200_rep1-pr.IDR0.05.filt.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/idr/pseudo_reps/rep1/ZNF200_rep1-pr.unthresholded-peaks.txt.png
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/idr/pseudo_reps/rep1/ZNF200_rep1-pr.unthresholded-peaks.txt.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/idr/pseudo_reps/rep1/ZNF200_rep1-pr.IDR0.05.filt.12-col.bed.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 75

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq_py3 | wc -l) != "0" ]]; then source activate aquas_chipseq_py3; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 77

 idr --samples /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370891_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370891_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/idr/pseudo_reps/rep1/ZNF200_rep1-pr.unthresholded-peaks.txt --rank signal.value --soft-idr-threshold 0.05 \
			--plot --use-best-multisummit-IDR

# SYS command. line 81

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

# SYS command. line 84

 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/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/idr/pseudo_reps/rep1/ZNF200_rep1-pr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/idr/pseudo_reps/rep1/ZNF200_rep1-pr.IDR0.05.13-col.bed.gz

# SYS command. line 87

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/idr/pseudo_reps/rep1/ZNF200_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/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/idr/pseudo_reps/rep1/ZNF200_rep1-pr.IDR0.05.narrowPeak.gz

# SYS command. line 88

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/idr/pseudo_reps/rep1/ZNF200_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/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/idr/pseudo_reps/rep1/ZNF200_rep1-pr.IDR0.05.12-col.bed.gz

# SYS command. line 90

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/idr/pseudo_reps/rep1/ZNF200_rep1-pr.IDR0.05.13-col.bed.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz | grep -P 'chr[dXY]+[ 	]' | awk 'BEGIN{OFS="	"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/idr/pseudo_reps/rep1/ZNF200_rep1-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 91

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/idr/pseudo_reps/rep1/ZNF200_rep1-pr.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="	"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/idr/pseudo_reps/rep1/ZNF200_rep1-pr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 92

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/idr/pseudo_reps/rep1/ZNF200_rep1-pr.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="	"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/idr/pseudo_reps/rep1/ZNF200_rep1-pr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 94

 gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/idr/pseudo_reps/rep1/ZNF200_rep1-pr.unthresholded-peaks.txt

# SYS command. line 95

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/idr/pseudo_reps/rep1/ZNF200_rep1-pr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/idr/pseudo_reps/rep1/ZNF200_rep1-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 97

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
25647 (process ID) old priority 0, new priority 10
Waiting for 23 seconds.

 
--------------------Stderr--------------------
Initial parameter values: [0.10 1.00 0.20 0.50]
Final parameter values: [2.20 1.00 0.76 0.11]
Number of reported peaks - 5477/5477 (100.0%)

Number of peaks passing IDR cutoff of 0.05 - 419/5477 (7.7%)


 
 		 

    
  
 
  Num   7  
 
  ID   task.callpeak_idr.idr_final_qc.line_219.id_18  
 
  Name   idr final qc 
 
  Thread   thread_Root  
 
  PID   24373  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-07 06:02:55  
 
  End   2017-01-07 06:04:06  
 
  Elapsed   00:01:11  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/idr/pseudo_reps/rep1/ZNF200_rep1-pr.IDR0.05.filt.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/qc/ZNF200_IDR_final.qc
  
 
  Dependencies     
 
 		  
 
# SYS command. line 221

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

# SYS command. line 223

 echo -e "Nt\tN1	N2	""Np\tconservative_set\toptimal_set\trescue_ratio\tself_consistency_ratio\treproducibility" > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/qc/ZNF200_IDR_final.qc

# SYS command. line 224

 echo -e "0\t8	0	""0\tN/A\tN/A\tNaN\t1.0\t1" >> /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/qc/ZNF200_IDR_final.qc

# SYS command. line 226

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
25811 (process ID) old priority 0, new priority 10
Waiting for 59 seconds.

  
 		 

    
  
 
  Num   8  
 
  ID   task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_19  
 
  Name   blacklist_filter peak 1 
 
  Thread   thread_Root  
 
  PID   30940  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-07 06:04:08  
 
  End   2017-01-07 06:05:18  
 
  Elapsed   00:01:09  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.filt.narrowPeak.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 29

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

# SYS command. line 31

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz \
			| awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' \
			| grep -P 'chr[\dXY]+[ \t]' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.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--------------------
30944 (process ID) old priority 0, new priority 10
Waiting for 60 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	2218	2414	.	0	.	17.0917587359986	-1	2.4902326336086	98

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/rep1/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	2218	2414	.	0	.	17.0917587359986	-1	2.4902326336086	98


 
 		 

    
  
 
  Num   9  
 
  ID   task.report.peak2hammock.line_412.id_20  
 
  Name   peak2hammock 
 
  Thread   thread_Root  
 
  PID   35077  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-07 06:05:19  
 
  End   2017-01-07 06:05:27  
 
  Elapsed   00:00:08  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/overlap/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/overlap/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.hammock.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 414

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

# SYS command. line 415

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/overlap/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/overlap/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp

# SYS command. line 417

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/overlap/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/overlap/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/spp/overlap/SRR1370891_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp
 
 
   
--------------------Stdout--------------------
35081 (process ID) old priority 0, new priority 10

  
 		 

    
  
 
  Num   10  
 
  ID   task.report.peak2hammock.line_412.id_21  
 
  Name   peak2hammock 
 
  Thread   thread_Root  
 
  PID   35708  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-07 06:05:28  
 
  End   2017-01-07 06:05:37  
 
  Elapsed   00:00:08  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/idr/pseudo_reps/rep1/ZNF200_rep1-pr.IDR0.05.filt.12-col.bed.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/idr/pseudo_reps/rep1/ZNF200_rep1-pr.IDR0.05.filt.12-col.bed.hammock.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 414

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

# SYS command. line 415

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/idr/pseudo_reps/rep1/ZNF200_rep1-pr.IDR0.05.filt.12-col.bed.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/idr/pseudo_reps/rep1/ZNF200_rep1-pr.IDR0.05.filt.12-col.bed.tmp

# SYS command. line 417

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/idr/pseudo_reps/rep1/ZNF200_rep1-pr.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/idr/pseudo_reps/rep1/ZNF200_rep1-pr.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/peak/idr/pseudo_reps/rep1/ZNF200_rep1-pr.IDR0.05.filt.12-col.bed.tmp
 
 
   
--------------------Stdout--------------------
35712 (process ID) old priority 0, new priority 10

  
 		 

    
  
 
  Num   11  
 
  ID   task.graphviz.report.line_97.id_22  
 
  Name   report 
 
  Thread   thread_Root  
 
  PID   36305  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-07 06:05:38  
 
  End   2017-01-07 06:05:46  
 
  Elapsed   00:00:08  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files     
 
  Output files     
 
  Dependencies     
 
 		  
 
# SYS command. line 98

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

# SYS command. line 99

 dot -Tsvg /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/report/ZNF200_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/report/ZNF200_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/report/ZNF200_workflow.svg" # to suppress dot font error (exit code=1)
 
 
   
--------------------Stdout--------------------
36309 (process ID) old priority 0, new priority 10

  
 		 

	






	
 Global scope 

	Note: Global scope when program finished execution.
	

	
  Type  Name  Value  

	
  string  _  /usr/bin/bds  

	
  string  _LMFILES_  /software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/ascp/3.5.6:/software/modulefiles/sratoolkit/2.5.2:/software/modulefiles/homer/default  

	
  bool  allowEmpty  false  

	
  string[]  args  [-title, ZNF200, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF200/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF200/out/align/rep1/SRR1370891_1.bam, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz, -final_stage, idr, $]  

	
  string  ASCPKEY  /software/ascp/etc/asperaweb_id_dsa.openssh  

	
  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:10.0  

	
  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_veRoBQ  

	
  string  LANG  en_US.UTF-8  

	
  string  LOADEDMODULES  modsappsdir/modsappsdir:ascp/3.5.6:sratoolkit/2.5.2:homer/default  

	
  string  LOGNAME  imk1  

	
  int  M  1048576  

	
  string  MAIL  /var/mail/imk1  

	
  int  mem  -1  

	
  int  minute  60  

	
  string  MODULE_VERSION  3.2.10  

	
  string  MODULE_VERSION_STACK  3.2.10  

	
  string  MODULEPATH  /usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles  

	
  string  MODULESAPPSDIR  /software  

	
  string  MODULESHOME  /software/env_module/3.2.10  

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

	
  string  node    

	
  int  P  1125899906842624  

	
  string  PATH  /software/ucsc_tools/3.0.9:/software/weblogo/2.8.2:/software/homer/default/bin:/software/sratoolkit/2.5.2/bin/:/software/ascp/:/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/Najafabadi2015Data/hg38Mapping/ZNF200  

	
  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/Najafabadi2015Data/hg38Mapping/ZNF200  

	
  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 43899 22  

	
  string  SSH_CONNECTION  171.65.77.8 43899 171.65.76.63 22  

	
  string  SSH_TTY  /dev/pts/0  

	
  string  STY  37455.ZNF200.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  1080  

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