BigDataScript report: chipseq.bds

Script file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20170106_143729_024
Start time 2017-01-06 14:37:29
Run time 3 days 00:12:15.236
Tasks executed 13
Tasks failed 0
Tasks failed names 
 

		
  Arguments*  [-title, ZNF33A, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF33A/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/align/rep1/SRR1370903_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_143729_024/task.callpeak_spp.spp_rep1.line_57.id_10
chipseq.bds.20170106_143729_024/task.callpeak_macs2.macs2_rep1.line_71.id_11
chipseq.bds.20170106_143729_024/task.callpeak_spp.spp_rep1_pr1.line_57.id_12
chipseq.bds.20170106_143729_024/task.callpeak_spp.spp_rep1_pr2.line_57.id_13
chipseq.bds.20170106_143729_024/task.callpeak_macs2.macs2_rep1_pr1.line_71.id_14
chipseq.bds.20170106_143729_024/task.callpeak_macs2.macs2_rep1_pr2.line_71.id_15
chipseq.bds.20170106_143729_024/task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_16
chipseq.bds.20170106_143729_024/task.callpeak_idr.idr2_rep1_pr.line_73.id_17
chipseq.bds.20170106_143729_024/task.callpeak_idr.idr_final_qc.line_219.id_20
chipseq.bds.20170106_143729_024/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_21
chipseq.bds.20170106_143729_024/task.report.peak2hammock.line_412.id_22
chipseq.bds.20170106_143729_024/task.report.peak2hammock.line_412.id_23
chipseq.bds.20170106_143729_024/task.graphviz.report.line_97.id_24
 
 		 

	
  thread_42   thread_Root 	 
  
 		 

	
  thread_41   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   24270  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-06 14:37:36  
 
  End   2017-01-08 07:05:41  
 
  Elapsed   1 day 16:28:05  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/align/rep1/SRR1370903_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/ZNF33A/out/peak/spp/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/rep1/SRR1370903_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/ZNF33A/out/align/rep1/SRR1370903_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/ZNF33A/out/peak/spp/rep1 -speak=85 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/rep1/SRR1370903_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/ZNF33A/out/peak/spp/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 72

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/rep1/SRR1370903_1.nodup.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 74

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/rep1/SRR1370903_1.nodup.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf

# SYS command. line 77

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/rep1/SRR1370903_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/ZNF33A/out/peak/spp/rep1/SRR1370903_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/ZNF33A/out/peak/spp/rep1/SRR1370903_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/ZNF33A/out/peak/spp/rep1/SRR1370903_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--------------------
36220 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/align/rep1/SRR1370903_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 85 
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/ZNF33A/out/peak/spp/rep1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/rep1/SRR1370903_1.nodup.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/rep1/SRR1370903_1.nodup.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/rep1/SRR1370903_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/ZNF33A/out/align/rep1/SRR1370903_1.nodup.tagAlign.gz 
opened /tmp/24270.1.amd.q/Rtmpa7t5ot/SRR1370903_1.nodup.tagAlign8ed0418a6071
done. read 1904793 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/24270.1.amd.q/Rtmpa7t5ot/input15MReadsNSCLess1.05.50MSubsample.tagAlign8ed04627f5d7
done. read 50000000 fragments
Control data read length 68 
Calculating peak characteristics
Minimum cross-correlation value 0.02637889 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.0273808419968814 
Top 3 estimates for fragment length 85 
Window half size 330 
Phantom peak location 50 
Phantom peak Correlation 0.02793032 
Normalized Strand cross-correlation coefficient (NSC) 1.037983 
Relative Strand cross-correlation Coefficient (RSC) 0.6458258 
Phantom Peak Quality Tag 0 
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= 26.23752  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.03811336  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000597 
Detected 19680 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/ZNF33A/out/peak/spp/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	2323	2653	.	0	.	19.111552121673	-1	3.53160663193272	165

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	2323	2653	.	0	.	19.111552121673	-1	3.53160663193272	165


 
 		 

    
  
 
  Num   2  
 
  ID   task.callpeak_macs2.macs2_rep1.line_71.id_11  
 
  Name   macs2 rep1 
 
  Thread   thread_Root  
 
  PID   24271  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-06 14:37:37  
 
  End   2017-01-06 17:30:39  
 
  Elapsed   02:53:02  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/align/rep1/SRR1370903_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/ZNF33A/out/peak/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/signal/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/signal/macs2/rep1/SRR1370903_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/ZNF33A/out/align/rep1/SRR1370903_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/ZNF33A/out/peak/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 85 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/rep1/SRR1370903_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/ZNF33A/out/peak/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/rep1/SRR1370903_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/ZNF33A/out/align/rep1/SRR1370903_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/ZNF33A/out/peak/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 85 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/rep1/SRR1370903_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/ZNF33A/out/peak/macs2/rep1/SRR1370903_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/ZNF33A/out/peak/macs2/rep1/SRR1370903_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/ZNF33A/out/peak/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/rep1/SRR1370903_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/ZNF33A/out/peak/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/rep1/SRR1370903_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/ZNF33A/out/peak/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/rep1 -o "SRR1370903_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/ZNF33A/out/peak/macs2/rep1/SRR1370903_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/ZNF33A/out/peak/macs2/rep1/SRR1370903_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/ZNF33A/out/peak/macs2/rep1/SRR1370903_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/ZNF33A/out/peak/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/rep1/SRR1370903_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/ZNF33A/out/peak/macs2/rep1/SRR1370903_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/ZNF33A/out/signal/macs2/rep1/SRR1370903_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/ZNF33A/out/peak/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/rep1/SRR1370903_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/ZNF33A/out/align/rep1/SRR1370903_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/ZNF33A/out/peak/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/rep1 -o "SRR1370903_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/ZNF33A/out/peak/macs2/rep1/SRR1370903_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/ZNF33A/out/peak/macs2/rep1/SRR1370903_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/ZNF33A/out/peak/macs2/rep1/SRR1370903_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/ZNF33A/out/peak/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/rep1/SRR1370903_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/ZNF33A/out/peak/macs2/rep1/SRR1370903_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/ZNF33A/out/signal/macs2/rep1/SRR1370903_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/ZNF33A/out/peak/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/rep1/SRR1370903_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/ZNF33A/out/peak/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/rep1/SRR1370903_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--------------------
36223 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 14:38:00: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/align/rep1/SRR1370903_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/ZNF33A/out/peak/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 85 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/align/rep1/SRR1370903_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 14:38:00: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 14:38:00: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 14:38:07:  1000000 
INFO  @ Fri, 06 Jan 2017 14:38:13: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 14:38:20:  1000000 
INFO  @ Fri, 06 Jan 2017 14:38:26:  2000000 
INFO  @ Fri, 06 Jan 2017 14:38:34:  3000000 
INFO  @ Fri, 06 Jan 2017 14:38:42:  4000000 
INFO  @ Fri, 06 Jan 2017 14:38:50:  5000000 
INFO  @ Fri, 06 Jan 2017 14:38:57:  6000000 
INFO  @ Fri, 06 Jan 2017 14:39:03:  7000000 
INFO  @ Fri, 06 Jan 2017 14:39:10:  8000000 
INFO  @ Fri, 06 Jan 2017 14:39:16:  9000000 
INFO  @ Fri, 06 Jan 2017 14:39:23:  10000000 
INFO  @ Fri, 06 Jan 2017 14:39:31:  11000000 
INFO  @ Fri, 06 Jan 2017 14:39:38:  12000000 
INFO  @ Fri, 06 Jan 2017 14:39:45:  13000000 
INFO  @ Fri, 06 Jan 2017 14:39:52:  14000000 
INFO  @ Fri, 06 Jan 2017 14:39:58:  15000000 
INFO  @ Fri, 06 Jan 2017 14:40:05:  16000000 
INFO  @ Fri, 06 Jan 2017 14:40:11:  17000000 
INFO  @ Fri, 06 Jan 2017 14:40:18:  18000000 
INFO  @ Fri, 06 Jan 2017 14:40:25:  19000000 
INFO  @ Fri, 06 Jan 2017 14:40:32:  20000000 
INFO  @ Fri, 06 Jan 2017 14:40:39:  21000000 
INFO  @ Fri, 06 Jan 2017 14:40:45:  22000000 
INFO  @ Fri, 06 Jan 2017 14:40:52:  23000000 
INFO  @ Fri, 06 Jan 2017 14:40:59:  24000000 
INFO  @ Fri, 06 Jan 2017 14:41:06:  25000000 
INFO  @ Fri, 06 Jan 2017 14:41:14:  26000000 
INFO  @ Fri, 06 Jan 2017 14:41:21:  27000000 
INFO  @ Fri, 06 Jan 2017 14:41:27:  28000000 
INFO  @ Fri, 06 Jan 2017 14:41:34:  29000000 
INFO  @ Fri, 06 Jan 2017 14:41:41:  30000000 
INFO  @ Fri, 06 Jan 2017 14:41:48:  31000000 
INFO  @ Fri, 06 Jan 2017 14:41:54:  32000000 
INFO  @ Fri, 06 Jan 2017 14:42:02:  33000000 
INFO  @ Fri, 06 Jan 2017 14:42:09:  34000000 
INFO  @ Fri, 06 Jan 2017 14:42:16:  35000000 
INFO  @ Fri, 06 Jan 2017 14:42:24:  36000000 
INFO  @ Fri, 06 Jan 2017 14:42:31:  37000000 
INFO  @ Fri, 06 Jan 2017 14:42:39:  38000000 
INFO  @ Fri, 06 Jan 2017 14:42:46:  39000000 
INFO  @ Fri, 06 Jan 2017 14:42:54:  40000000 
INFO  @ Fri, 06 Jan 2017 14:43:02:  41000000 
INFO  @ Fri, 06 Jan 2017 14:43:10:  42000000 
INFO  @ Fri, 06 Jan 2017 14:43:17:  43000000 
INFO  @ Fri, 06 Jan 2017 14:43:25:  44000000 
INFO  @ Fri, 06 Jan 2017 14:43:33:  45000000 
INFO  @ Fri, 06 Jan 2017 14:43:41:  46000000 
INFO  @ Fri, 06 Jan 2017 14:43:49:  47000000 
INFO  @ Fri, 06 Jan 2017 14:43:56:  48000000 
INFO  @ Fri, 06 Jan 2017 14:44:05:  49000000 
INFO  @ Fri, 06 Jan 2017 14:44:13:  50000000 
INFO  @ Fri, 06 Jan 2017 14:44:17: #1 tag size is determined as 51 bps 
INFO  @ Fri, 06 Jan 2017 14:44:17: #1 tag size = 51 
INFO  @ Fri, 06 Jan 2017 14:44:17: #1  total tags in treatment: 1904793 
INFO  @ Fri, 06 Jan 2017 14:44:17: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 14:44:17: #1 finished! 
INFO  @ Fri, 06 Jan 2017 14:44:17: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 14:44:17: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 14:44:17: #2 Use 85 as fragment length 
INFO  @ Fri, 06 Jan 2017 14:44:17: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 14:44:17: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 14:44:17: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 14:53:06: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 14:53:06: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 14:53:06: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 14:53:06: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 14:53:06: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:12:03: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:12:43: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 15:13:18: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 15:13:44: Done! 
INFO  @ Fri, 06 Jan 2017 15:14:03: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/align/rep1/SRR1370903_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/ZNF33A/out/peak/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 85 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/align/rep1/SRR1370903_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 15:14:03: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:14:03: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:14:11:  1000000 
INFO  @ Fri, 06 Jan 2017 15:14:19: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:14:28:  1000000 
INFO  @ Fri, 06 Jan 2017 15:14:36:  2000000 
INFO  @ Fri, 06 Jan 2017 15:14:44:  3000000 
INFO  @ Fri, 06 Jan 2017 15:14:53:  4000000 
INFO  @ Fri, 06 Jan 2017 15:15:01:  5000000 
INFO  @ Fri, 06 Jan 2017 15:15:09:  6000000 
INFO  @ Fri, 06 Jan 2017 15:15:17:  7000000 
INFO  @ Fri, 06 Jan 2017 15:15:25:  8000000 
INFO  @ Fri, 06 Jan 2017 15:15:33:  9000000 
INFO  @ Fri, 06 Jan 2017 15:15:41:  10000000 
INFO  @ Fri, 06 Jan 2017 15:15:49:  11000000 
INFO  @ Fri, 06 Jan 2017 15:15:57:  12000000 
INFO  @ Fri, 06 Jan 2017 15:16:05:  13000000 
INFO  @ Fri, 06 Jan 2017 15:16:14:  14000000 
INFO  @ Fri, 06 Jan 2017 15:16:22:  15000000 
INFO  @ Fri, 06 Jan 2017 15:16:30:  16000000 
INFO  @ Fri, 06 Jan 2017 15:16:38:  17000000 
INFO  @ Fri, 06 Jan 2017 15:16:46:  18000000 
INFO  @ Fri, 06 Jan 2017 15:16:54:  19000000 
INFO  @ Fri, 06 Jan 2017 15:17:02:  20000000 
INFO  @ Fri, 06 Jan 2017 15:17:10:  21000000 
INFO  @ Fri, 06 Jan 2017 15:17:18:  22000000 
INFO  @ Fri, 06 Jan 2017 15:17:26:  23000000 
INFO  @ Fri, 06 Jan 2017 15:17:35:  24000000 
INFO  @ Fri, 06 Jan 2017 15:17:43:  25000000 
INFO  @ Fri, 06 Jan 2017 15:17:51:  26000000 
INFO  @ Fri, 06 Jan 2017 15:17:59:  27000000 
INFO  @ Fri, 06 Jan 2017 15:18:07:  28000000 
INFO  @ Fri, 06 Jan 2017 15:18:16:  29000000 
INFO  @ Fri, 06 Jan 2017 15:18:23:  30000000 
INFO  @ Fri, 06 Jan 2017 15:18:31:  31000000 
INFO  @ Fri, 06 Jan 2017 15:18:40:  32000000 
INFO  @ Fri, 06 Jan 2017 15:18:48:  33000000 
INFO  @ Fri, 06 Jan 2017 15:18:56:  34000000 
INFO  @ Fri, 06 Jan 2017 15:19:04:  35000000 
INFO  @ Fri, 06 Jan 2017 15:19:13:  36000000 
INFO  @ Fri, 06 Jan 2017 15:19:21:  37000000 
INFO  @ Fri, 06 Jan 2017 15:19:29:  38000000 
INFO  @ Fri, 06 Jan 2017 15:19:38:  39000000 
INFO  @ Fri, 06 Jan 2017 15:19:46:  40000000 
INFO  @ Fri, 06 Jan 2017 15:19:54:  41000000 
INFO  @ Fri, 06 Jan 2017 15:20:01:  42000000 
INFO  @ Fri, 06 Jan 2017 15:20:09:  43000000 
INFO  @ Fri, 06 Jan 2017 15:20:19:  44000000 
INFO  @ Fri, 06 Jan 2017 15:20:27:  45000000 
INFO  @ Fri, 06 Jan 2017 15:20:36:  46000000 
INFO  @ Fri, 06 Jan 2017 15:20:44:  47000000 
INFO  @ Fri, 06 Jan 2017 15:20:53:  48000000 
INFO  @ Fri, 06 Jan 2017 15:21:01:  49000000 
INFO  @ Fri, 06 Jan 2017 15:21:08:  50000000 
INFO  @ Fri, 06 Jan 2017 15:21:12: #1 tag size is determined as 51 bps 
INFO  @ Fri, 06 Jan 2017 15:21:12: #1 tag size = 51 
INFO  @ Fri, 06 Jan 2017 15:21:12: #1  total tags in treatment: 1904793 
INFO  @ Fri, 06 Jan 2017 15:21:12: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:21:12: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:21:12: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:21:12: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:21:12: #2 Use 85 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:21:12: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:21:12: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 15:21:12: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:30:00: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:54:06: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:54:07: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 15:54:08: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 15:54:09: Done! 
INFO  @ Fri, 06 Jan 2017 15:54:15: Read and build treatment bedGraph... 
INFO  @ Fri, 06 Jan 2017 15:54:32: Read and build control bedGraph... 
INFO  @ Fri, 06 Jan 2017 16:02:37: Build scoreTrackII... 
INFO  @ Fri, 06 Jan 2017 16:04:54: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Fri, 06 Jan 2017 16:24:01: Write bedGraph of scores... 
INFO  @ Fri, 06 Jan 2017 16:25:41: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_FE.bdg'! 
INFO  @ Fri, 06 Jan 2017 16:28:04: Read and build treatment bedGraph... 
INFO  @ Fri, 06 Jan 2017 16:28:21: Read and build control bedGraph... 
INFO  @ Fri, 06 Jan 2017 16:36:59: Build scoreTrackII... 
INFO  @ Fri, 06 Jan 2017 16:39:12: Values in your input bedGraph files will be multiplied by 1.904793 ... 
INFO  @ Fri, 06 Jan 2017 16:58:45: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Fri, 06 Jan 2017 17:00:33: Write bedGraph of scores... 
INFO  @ Fri, 06 Jan 2017 17:11:43: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_ppois.bdg'! 

 
 		 

    
  
 
  Num   3  
 
  ID   task.callpeak_spp.spp_rep1_pr1.line_57.id_12  
 
  Name   spp rep1-pr1 
 
  Thread   thread_Root  
 
  PID   24272  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-06 14:37:38  
 
  End   2017-01-09 14:44:25  
 
  Elapsed   3 days 00:06:46  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/align/pseudo_reps/rep1/pr1/SRR1370903_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/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.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/ZNF33A/out/align/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.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/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr1 -speak=85 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.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/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 72

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 74

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf

# SYS command. line 77

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz; fi

# SYS command. line 80

 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.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/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.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/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.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--------------------
36222 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/align/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.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 85 
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/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.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/ZNF33A/out/align/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign.gz 
opened /tmp/24272.1.amd.q/RtmpZD5nnw/SRR1370903_1.nodup.pr1.tagAlign8ee44e3ce027
done. read 952397 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/24272.1.amd.q/RtmpZD5nnw/input15MReadsNSCLess1.05.50MSubsample.tagAlign8ee418be8c4f
done. read 50000000 fragments
Control data read length 68 
Calculating peak characteristics
Minimum cross-correlation value 0.01343074 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.0139435637068306 
Top 3 estimates for fragment length 85 
Window half size 660 
Phantom peak location 50 
Phantom peak Correlation 0.01427503 
Normalized Strand cross-correlation coefficient (NSC) 1.038183 
Relative Strand cross-correlation Coefficient (RSC) 0.6074015 
Phantom Peak Quality Tag 0 
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= 52.46185  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.01906147  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000292 
Detected 10267 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/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	2194	2854	.	0	.	10.6417635794127	-1	3.16345955176999	330

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	2194	2854	.	0	.	10.6417635794127	-1	3.16345955176999	330


 
 		 

    
  
 
  Num   4  
 
  ID   task.callpeak_spp.spp_rep1_pr2.line_57.id_13  
 
  Name   spp rep1-pr2 
 
  Thread   thread_Root  
 
  PID   24273  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-06 14:37:39  
 
  End   2017-01-08 02:14:07  
 
  Elapsed   1 day 11:36:28  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/align/pseudo_reps/rep1/pr2/SRR1370903_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/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.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/ZNF33A/out/align/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.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/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr2 -speak=85 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.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/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 72

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 74

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf

# SYS command. line 77

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz; fi

# SYS command. line 80

 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.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/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.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/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.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--------------------
36221 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/align/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.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 85 
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/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr2 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.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/ZNF33A/out/align/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign.gz 
opened /tmp/24273.1.amd.q/RtmpgCskpk/SRR1370903_1.nodup.pr2.tagAlign8ec42f80183a
done. read 952396 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/24273.1.amd.q/RtmpgCskpk/input15MReadsNSCLess1.05.50MSubsample.tagAlign8ec4169f6b51
done. read 50000000 fragments
Control data read length 68 
Calculating peak characteristics
Minimum cross-correlation value 0.01347046 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.0139920602760023 
Top 3 estimates for fragment length 85 
Window half size 340 
Phantom peak location 55 
Phantom peak Correlation 0.01420438 
Normalized Strand cross-correlation coefficient (NSC) 1.038721 
Relative Strand cross-correlation Coefficient (RSC) 0.7107075 
Phantom Peak Quality Tag 0 
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= 52.45717  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.01906317  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.012478 
Detected 3658 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/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	1087	1427	.	0	.	7.60482781365181	-1	2.70156798505593	170

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	1087	1427	.	0	.	7.60482781365181	-1	2.70156798505593	170


 
 		 

    
  
 
  Num   5  
 
  ID   task.callpeak_macs2.macs2_rep1_pr1.line_71.id_14  
 
  Name   macs2 rep1-pr1 
 
  Thread   thread_Root  
 
  PID   24274  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-06 14:37:40  
 
  End   2017-01-06 16:00:34  
 
  Elapsed   01:22:54  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/align/pseudo_reps/rep1/pr1/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_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/ZNF33A/out/align/pseudo_reps/rep1/pr1/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 85 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_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/ZNF33A/out/align/pseudo_reps/rep1/pr1/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 85 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_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/ZNF33A/out/align/pseudo_reps/rep1/pr1/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_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--------------------
36219 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 14:38:00: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/align/pseudo_reps/rep1/pr1/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 85 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/align/pseudo_reps/rep1/pr1/SRR1370903_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 14:38:00: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 14:38:00: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 14:38:07: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 14:38:13:  1000000 
INFO  @ Fri, 06 Jan 2017 14:38:20:  2000000 
INFO  @ Fri, 06 Jan 2017 14:38:26:  3000000 
INFO  @ Fri, 06 Jan 2017 14:38:33:  4000000 
INFO  @ Fri, 06 Jan 2017 14:38:39:  5000000 
INFO  @ Fri, 06 Jan 2017 14:38:46:  6000000 
INFO  @ Fri, 06 Jan 2017 14:38:53:  7000000 
INFO  @ Fri, 06 Jan 2017 14:38:59:  8000000 
INFO  @ Fri, 06 Jan 2017 14:39:05:  9000000 
INFO  @ Fri, 06 Jan 2017 14:39:12:  10000000 
INFO  @ Fri, 06 Jan 2017 14:39:19:  11000000 
INFO  @ Fri, 06 Jan 2017 14:39:25:  12000000 
INFO  @ Fri, 06 Jan 2017 14:39:32:  13000000 
INFO  @ Fri, 06 Jan 2017 14:39:38:  14000000 
INFO  @ Fri, 06 Jan 2017 14:39:45:  15000000 
INFO  @ Fri, 06 Jan 2017 14:39:51:  16000000 
INFO  @ Fri, 06 Jan 2017 14:39:58:  17000000 
INFO  @ Fri, 06 Jan 2017 14:40:05:  18000000 
INFO  @ Fri, 06 Jan 2017 14:40:11:  19000000 
INFO  @ Fri, 06 Jan 2017 14:40:17:  20000000 
INFO  @ Fri, 06 Jan 2017 14:40:24:  21000000 
INFO  @ Fri, 06 Jan 2017 14:40:31:  22000000 
INFO  @ Fri, 06 Jan 2017 14:40:38:  23000000 
INFO  @ Fri, 06 Jan 2017 14:40:44:  24000000 
INFO  @ Fri, 06 Jan 2017 14:40:51:  25000000 
INFO  @ Fri, 06 Jan 2017 14:40:58:  26000000 
INFO  @ Fri, 06 Jan 2017 14:41:04:  27000000 
INFO  @ Fri, 06 Jan 2017 14:41:11:  28000000 
INFO  @ Fri, 06 Jan 2017 14:41:17:  29000000 
INFO  @ Fri, 06 Jan 2017 14:41:24:  30000000 
INFO  @ Fri, 06 Jan 2017 14:41:31:  31000000 
INFO  @ Fri, 06 Jan 2017 14:41:38:  32000000 
INFO  @ Fri, 06 Jan 2017 14:41:45:  33000000 
INFO  @ Fri, 06 Jan 2017 14:41:51:  34000000 
INFO  @ Fri, 06 Jan 2017 14:41:59:  35000000 
INFO  @ Fri, 06 Jan 2017 14:42:06:  36000000 
INFO  @ Fri, 06 Jan 2017 14:42:13:  37000000 
INFO  @ Fri, 06 Jan 2017 14:42:21:  38000000 
INFO  @ Fri, 06 Jan 2017 14:42:29:  39000000 
INFO  @ Fri, 06 Jan 2017 14:42:36:  40000000 
INFO  @ Fri, 06 Jan 2017 14:42:43:  41000000 
INFO  @ Fri, 06 Jan 2017 14:42:51:  42000000 
INFO  @ Fri, 06 Jan 2017 14:42:59:  43000000 
INFO  @ Fri, 06 Jan 2017 14:43:07:  44000000 
INFO  @ Fri, 06 Jan 2017 14:43:15:  45000000 
INFO  @ Fri, 06 Jan 2017 14:43:22:  46000000 
INFO  @ Fri, 06 Jan 2017 14:43:30:  47000000 
INFO  @ Fri, 06 Jan 2017 14:43:37:  48000000 
INFO  @ Fri, 06 Jan 2017 14:43:45:  49000000 
INFO  @ Fri, 06 Jan 2017 14:43:53:  50000000 
INFO  @ Fri, 06 Jan 2017 14:43:57: #1 tag size is determined as 51 bps 
INFO  @ Fri, 06 Jan 2017 14:43:57: #1 tag size = 51 
INFO  @ Fri, 06 Jan 2017 14:43:57: #1  total tags in treatment: 952397 
INFO  @ Fri, 06 Jan 2017 14:43:57: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 14:43:57: #1 finished! 
INFO  @ Fri, 06 Jan 2017 14:43:57: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 14:43:57: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 14:43:57: #2 Use 85 as fragment length 
INFO  @ Fri, 06 Jan 2017 14:43:57: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 14:43:57: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 14:43:57: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 14:52:26: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 14:52:26: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 14:52:26: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 14:52:26: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 14:52:26: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:10:12: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:10:42: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 15:11:03: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 15:11:19: Done! 
INFO  @ Fri, 06 Jan 2017 15:11:36: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/align/pseudo_reps/rep1/pr1/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 85 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/align/pseudo_reps/rep1/pr1/SRR1370903_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 15:11:36: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:11:36: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:11:44: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:11:52:  1000000 
INFO  @ Fri, 06 Jan 2017 15:12:01:  2000000 
INFO  @ Fri, 06 Jan 2017 15:12:09:  3000000 
INFO  @ Fri, 06 Jan 2017 15:12:17:  4000000 
INFO  @ Fri, 06 Jan 2017 15:12:25:  5000000 
INFO  @ Fri, 06 Jan 2017 15:12:33:  6000000 
INFO  @ Fri, 06 Jan 2017 15:12:41:  7000000 
INFO  @ Fri, 06 Jan 2017 15:12:49:  8000000 
INFO  @ Fri, 06 Jan 2017 15:12:57:  9000000 
INFO  @ Fri, 06 Jan 2017 15:13:05:  10000000 
INFO  @ Fri, 06 Jan 2017 15:13:13:  11000000 
INFO  @ Fri, 06 Jan 2017 15:13:21:  12000000 
INFO  @ Fri, 06 Jan 2017 15:13:29:  13000000 
INFO  @ Fri, 06 Jan 2017 15:13:37:  14000000 
INFO  @ Fri, 06 Jan 2017 15:13:45:  15000000 
INFO  @ Fri, 06 Jan 2017 15:13:54:  16000000 
INFO  @ Fri, 06 Jan 2017 15:14:02:  17000000 
INFO  @ Fri, 06 Jan 2017 15:14:10:  18000000 
INFO  @ Fri, 06 Jan 2017 15:14:17:  19000000 
INFO  @ Fri, 06 Jan 2017 15:14:26:  20000000 
INFO  @ Fri, 06 Jan 2017 15:14:34:  21000000 
INFO  @ Fri, 06 Jan 2017 15:14:42:  22000000 
INFO  @ Fri, 06 Jan 2017 15:14:49:  23000000 
INFO  @ Fri, 06 Jan 2017 15:14:58:  24000000 
INFO  @ Fri, 06 Jan 2017 15:15:06:  25000000 
INFO  @ Fri, 06 Jan 2017 15:15:14:  26000000 
INFO  @ Fri, 06 Jan 2017 15:15:22:  27000000 
INFO  @ Fri, 06 Jan 2017 15:15:30:  28000000 
INFO  @ Fri, 06 Jan 2017 15:15:38:  29000000 
INFO  @ Fri, 06 Jan 2017 15:15:47:  30000000 
INFO  @ Fri, 06 Jan 2017 15:15:55:  31000000 
INFO  @ Fri, 06 Jan 2017 15:16:03:  32000000 
INFO  @ Fri, 06 Jan 2017 15:16:11:  33000000 
INFO  @ Fri, 06 Jan 2017 15:16:19:  34000000 
INFO  @ Fri, 06 Jan 2017 15:16:27:  35000000 
INFO  @ Fri, 06 Jan 2017 15:16:35:  36000000 
INFO  @ Fri, 06 Jan 2017 15:16:43:  37000000 
INFO  @ Fri, 06 Jan 2017 15:16:51:  38000000 
INFO  @ Fri, 06 Jan 2017 15:16:58:  39000000 
INFO  @ Fri, 06 Jan 2017 15:17:06:  40000000 
INFO  @ Fri, 06 Jan 2017 15:17:14:  41000000 
INFO  @ Fri, 06 Jan 2017 15:17:22:  42000000 
INFO  @ Fri, 06 Jan 2017 15:17:30:  43000000 
INFO  @ Fri, 06 Jan 2017 15:17:38:  44000000 
INFO  @ Fri, 06 Jan 2017 15:17:46:  45000000 
INFO  @ Fri, 06 Jan 2017 15:17:54:  46000000 
INFO  @ Fri, 06 Jan 2017 15:18:02:  47000000 
INFO  @ Fri, 06 Jan 2017 15:18:09:  48000000 
INFO  @ Fri, 06 Jan 2017 15:18:17:  49000000 
INFO  @ Fri, 06 Jan 2017 15:18:25:  50000000 
INFO  @ Fri, 06 Jan 2017 15:18:29: #1 tag size is determined as 51 bps 
INFO  @ Fri, 06 Jan 2017 15:18:29: #1 tag size = 51 
INFO  @ Fri, 06 Jan 2017 15:18:29: #1  total tags in treatment: 952397 
INFO  @ Fri, 06 Jan 2017 15:18:29: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:18:29: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:18:29: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:18:29: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:18:29: #2 Use 85 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:18:29: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:18:29: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 15:18:29: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:26:57: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 16:00:31: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 16:00:31: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 16:00:31: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 16:00:31: Done! 

 
 		 

    
  
 
  Num   6  
 
  ID   task.callpeak_macs2.macs2_rep1_pr2.line_71.id_15  
 
  Name   macs2 rep1-pr2 
 
  Thread   thread_Root  
 
  PID   24346  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-06 16:00:36  
 
  End   2017-01-06 16:32:25  
 
  Elapsed   00:31:48  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/align/pseudo_reps/rep1/pr2/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_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/ZNF33A/out/align/pseudo_reps/rep1/pr2/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 85 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_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/ZNF33A/out/align/pseudo_reps/rep1/pr2/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 85 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_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/ZNF33A/out/align/pseudo_reps/rep1/pr2/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_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--------------------
11227 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 16:00:53: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/align/pseudo_reps/rep1/pr2/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 85 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/align/pseudo_reps/rep1/pr2/SRR1370903_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 16:00:53: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 16:00:53: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 16:00:55: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 16:00:58:  1000000 
INFO  @ Fri, 06 Jan 2017 16:01:00:  2000000 
INFO  @ Fri, 06 Jan 2017 16:01:02:  3000000 
INFO  @ Fri, 06 Jan 2017 16:01:04:  4000000 
INFO  @ Fri, 06 Jan 2017 16:01:06:  5000000 
INFO  @ Fri, 06 Jan 2017 16:01:07:  6000000 
INFO  @ Fri, 06 Jan 2017 16:01:09:  7000000 
INFO  @ Fri, 06 Jan 2017 16:01:10:  8000000 
INFO  @ Fri, 06 Jan 2017 16:01:12:  9000000 
INFO  @ Fri, 06 Jan 2017 16:01:14:  10000000 
INFO  @ Fri, 06 Jan 2017 16:01:16:  11000000 
INFO  @ Fri, 06 Jan 2017 16:01:18:  12000000 
INFO  @ Fri, 06 Jan 2017 16:01:19:  13000000 
INFO  @ Fri, 06 Jan 2017 16:01:21:  14000000 
INFO  @ Fri, 06 Jan 2017 16:01:22:  15000000 
INFO  @ Fri, 06 Jan 2017 16:01:24:  16000000 
INFO  @ Fri, 06 Jan 2017 16:01:26:  17000000 
INFO  @ Fri, 06 Jan 2017 16:01:27:  18000000 
INFO  @ Fri, 06 Jan 2017 16:01:30:  19000000 
INFO  @ Fri, 06 Jan 2017 16:01:32:  20000000 
INFO  @ Fri, 06 Jan 2017 16:01:35:  21000000 
INFO  @ Fri, 06 Jan 2017 16:01:38:  22000000 
INFO  @ Fri, 06 Jan 2017 16:01:39:  23000000 
INFO  @ Fri, 06 Jan 2017 16:01:41:  24000000 
INFO  @ Fri, 06 Jan 2017 16:01:43:  25000000 
INFO  @ Fri, 06 Jan 2017 16:01:44:  26000000 
INFO  @ Fri, 06 Jan 2017 16:01:46:  27000000 
INFO  @ Fri, 06 Jan 2017 16:01:47:  28000000 
INFO  @ Fri, 06 Jan 2017 16:01:49:  29000000 
INFO  @ Fri, 06 Jan 2017 16:01:50:  30000000 
INFO  @ Fri, 06 Jan 2017 16:01:52:  31000000 
INFO  @ Fri, 06 Jan 2017 16:01:54:  32000000 
INFO  @ Fri, 06 Jan 2017 16:01:55:  33000000 
INFO  @ Fri, 06 Jan 2017 16:01:57:  34000000 
INFO  @ Fri, 06 Jan 2017 16:01:58:  35000000 
INFO  @ Fri, 06 Jan 2017 16:02:00:  36000000 
INFO  @ Fri, 06 Jan 2017 16:02:02:  37000000 
INFO  @ Fri, 06 Jan 2017 16:02:03:  38000000 
INFO  @ Fri, 06 Jan 2017 16:02:05:  39000000 
INFO  @ Fri, 06 Jan 2017 16:02:07:  40000000 
INFO  @ Fri, 06 Jan 2017 16:02:08:  41000000 
INFO  @ Fri, 06 Jan 2017 16:02:10:  42000000 
INFO  @ Fri, 06 Jan 2017 16:02:11:  43000000 
INFO  @ Fri, 06 Jan 2017 16:02:13:  44000000 
INFO  @ Fri, 06 Jan 2017 16:02:15:  45000000 
INFO  @ Fri, 06 Jan 2017 16:02:16:  46000000 
INFO  @ Fri, 06 Jan 2017 16:02:18:  47000000 
INFO  @ Fri, 06 Jan 2017 16:02:19:  48000000 
INFO  @ Fri, 06 Jan 2017 16:02:21:  49000000 
INFO  @ Fri, 06 Jan 2017 16:02:23:  50000000 
INFO  @ Fri, 06 Jan 2017 16:02:24: #1 tag size is determined as 51 bps 
INFO  @ Fri, 06 Jan 2017 16:02:24: #1 tag size = 51 
INFO  @ Fri, 06 Jan 2017 16:02:24: #1  total tags in treatment: 952396 
INFO  @ Fri, 06 Jan 2017 16:02:24: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 16:02:24: #1 finished! 
INFO  @ Fri, 06 Jan 2017 16:02:24: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 16:02:24: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 16:02:24: #2 Use 85 as fragment length 
INFO  @ Fri, 06 Jan 2017 16:02:24: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 16:02:24: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 16:02:24: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 16:05:39: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 16:05:39: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 16:05:39: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 16:05:39: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 16:05:39: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 16:10:23: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 16:10:31: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 16:10:39: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 16:10:43: Done! 
INFO  @ Fri, 06 Jan 2017 16:10:51: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/align/pseudo_reps/rep1/pr2/SRR1370903_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/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 85 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/align/pseudo_reps/rep1/pr2/SRR1370903_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 16:10:51: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 16:10:51: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 16:10:53: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 16:10:55:  1000000 
INFO  @ Fri, 06 Jan 2017 16:10:57:  2000000 
INFO  @ Fri, 06 Jan 2017 16:10:59:  3000000 
INFO  @ Fri, 06 Jan 2017 16:11:01:  4000000 
INFO  @ Fri, 06 Jan 2017 16:11:03:  5000000 
INFO  @ Fri, 06 Jan 2017 16:11:05:  6000000 
INFO  @ Fri, 06 Jan 2017 16:11:06:  7000000 
INFO  @ Fri, 06 Jan 2017 16:11:08:  8000000 
INFO  @ Fri, 06 Jan 2017 16:11:10:  9000000 
INFO  @ Fri, 06 Jan 2017 16:11:11:  10000000 
INFO  @ Fri, 06 Jan 2017 16:11:13:  11000000 
INFO  @ Fri, 06 Jan 2017 16:11:15:  12000000 
INFO  @ Fri, 06 Jan 2017 16:11:16:  13000000 
INFO  @ Fri, 06 Jan 2017 16:11:18:  14000000 
INFO  @ Fri, 06 Jan 2017 16:11:20:  15000000 
INFO  @ Fri, 06 Jan 2017 16:11:22:  16000000 
INFO  @ Fri, 06 Jan 2017 16:11:24:  17000000 
INFO  @ Fri, 06 Jan 2017 16:11:26:  18000000 
INFO  @ Fri, 06 Jan 2017 16:11:27:  19000000 
INFO  @ Fri, 06 Jan 2017 16:11:29:  20000000 
INFO  @ Fri, 06 Jan 2017 16:11:31:  21000000 
INFO  @ Fri, 06 Jan 2017 16:11:32:  22000000 
INFO  @ Fri, 06 Jan 2017 16:11:34:  23000000 
INFO  @ Fri, 06 Jan 2017 16:11:35:  24000000 
INFO  @ Fri, 06 Jan 2017 16:11:37:  25000000 
INFO  @ Fri, 06 Jan 2017 16:11:39:  26000000 
INFO  @ Fri, 06 Jan 2017 16:11:40:  27000000 
INFO  @ Fri, 06 Jan 2017 16:11:42:  28000000 
INFO  @ Fri, 06 Jan 2017 16:11:44:  29000000 
INFO  @ Fri, 06 Jan 2017 16:11:45:  30000000 
INFO  @ Fri, 06 Jan 2017 16:11:47:  31000000 
INFO  @ Fri, 06 Jan 2017 16:11:48:  32000000 
INFO  @ Fri, 06 Jan 2017 16:11:50:  33000000 
INFO  @ Fri, 06 Jan 2017 16:11:52:  34000000 
INFO  @ Fri, 06 Jan 2017 16:11:53:  35000000 
INFO  @ Fri, 06 Jan 2017 16:11:55:  36000000 
INFO  @ Fri, 06 Jan 2017 16:11:57:  37000000 
INFO  @ Fri, 06 Jan 2017 16:11:59:  38000000 
INFO  @ Fri, 06 Jan 2017 16:12:00:  39000000 
INFO  @ Fri, 06 Jan 2017 16:12:02:  40000000 
INFO  @ Fri, 06 Jan 2017 16:12:03:  41000000 
INFO  @ Fri, 06 Jan 2017 16:12:05:  42000000 
INFO  @ Fri, 06 Jan 2017 16:12:07:  43000000 
INFO  @ Fri, 06 Jan 2017 16:12:09:  44000000 
INFO  @ Fri, 06 Jan 2017 16:12:10:  45000000 
INFO  @ Fri, 06 Jan 2017 16:12:12:  46000000 
INFO  @ Fri, 06 Jan 2017 16:12:14:  47000000 
INFO  @ Fri, 06 Jan 2017 16:12:15:  48000000 
INFO  @ Fri, 06 Jan 2017 16:12:17:  49000000 
INFO  @ Fri, 06 Jan 2017 16:12:19:  50000000 
INFO  @ Fri, 06 Jan 2017 16:12:21: #1 tag size is determined as 51 bps 
INFO  @ Fri, 06 Jan 2017 16:12:21: #1 tag size = 51 
INFO  @ Fri, 06 Jan 2017 16:12:21: #1  total tags in treatment: 952396 
INFO  @ Fri, 06 Jan 2017 16:12:21: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 16:12:21: #1 finished! 
INFO  @ Fri, 06 Jan 2017 16:12:21: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 16:12:21: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 16:12:21: #2 Use 85 as fragment length 
INFO  @ Fri, 06 Jan 2017 16:12:21: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 16:12:21: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 16:12:21: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 16:15:27: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 16:32:20: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 16:32:22: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 16:32:22: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 16:32:22: Done! 

 
 		 

    
  
 
  Num   7  
 
  ID   task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_16  
 
  Name   naive_overlap_thresh  
 
  Thread   thread_Root  
 
  PID   24877  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-09 14:44:26  
 
  End   2017-01-09 14:45:36  
 
  Elapsed   00:01:10  
 
  Timeout  01:00:00 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/overlap/SRR1370903_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/ZNF33A/out/peak/spp/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370903_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/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370903_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/ZNF33A/out/peak/spp/overlap/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/overlap/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/overlap/SRR1370903_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/ZNF33A/out/peak/spp/overlap/SRR1370903_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/ZNF33A/out/peak/spp/overlap/SRR1370903_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/ZNF33A/out/peak/spp/overlap/SRR1370903_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--------------------
22887 (process ID) old priority 0, new priority 10
Waiting for 59 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
chr19	39203694	39204354	.	0	.	9.78975314292798	-1	3.16345955176999	330

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
chr19	39203694	39204354	.	0	.	9.78975314292798	-1	3.16345955176999	330

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270467.1	1087	1427	.	0	.	7.60482781365181	-1	2.70156798505593	170

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270467.1	1087	1427	.	0	.	7.60482781365181	-1	2.70156798505593	170

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/overlap/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	1092	1422	.	0	.	14.1709190051033	-1	3.53160663193272	165

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/overlap/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	1092	1422	.	0	.	14.1709190051033	-1	3.53160663193272	165


 
 		 

    
  
 
  Num   8  
 
  ID   task.callpeak_idr.idr2_rep1_pr.line_73.id_17  
 
  Name   idr2 rep1-pr 
 
  Thread   thread_Root  
 
  PID   24878  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-09 14:45:38  
 
  End   2017-01-09 14:46:52  
 
  Elapsed   00:01:13  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/idr/pseudo_reps/rep1/ZNF33A_rep1-pr.IDR0.05.filt.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/idr/pseudo_reps/rep1/ZNF33A_rep1-pr.unthresholded-peaks.txt.png
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/idr/pseudo_reps/rep1/ZNF33A_rep1-pr.unthresholded-peaks.txt.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/idr/pseudo_reps/rep1/ZNF33A_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/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370903_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370903_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/idr/pseudo_reps/rep1/ZNF33A_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/ZNF33A/out/peak/idr/pseudo_reps/rep1/ZNF33A_rep1-pr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/idr/pseudo_reps/rep1/ZNF33A_rep1-pr.IDR0.05.13-col.bed.gz

# SYS command. line 87

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/idr/pseudo_reps/rep1/ZNF33A_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/ZNF33A/out/peak/idr/pseudo_reps/rep1/ZNF33A_rep1-pr.IDR0.05.narrowPeak.gz

# SYS command. line 88

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/idr/pseudo_reps/rep1/ZNF33A_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/ZNF33A/out/peak/idr/pseudo_reps/rep1/ZNF33A_rep1-pr.IDR0.05.12-col.bed.gz

# SYS command. line 90

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/idr/pseudo_reps/rep1/ZNF33A_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/ZNF33A/out/peak/idr/pseudo_reps/rep1/ZNF33A_rep1-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 91

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/idr/pseudo_reps/rep1/ZNF33A_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/ZNF33A/out/peak/idr/pseudo_reps/rep1/ZNF33A_rep1-pr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 92

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/idr/pseudo_reps/rep1/ZNF33A_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/ZNF33A/out/peak/idr/pseudo_reps/rep1/ZNF33A_rep1-pr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 94

 gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/idr/pseudo_reps/rep1/ZNF33A_rep1-pr.unthresholded-peaks.txt

# SYS command. line 95

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/idr/pseudo_reps/rep1/ZNF33A_rep1-pr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/idr/pseudo_reps/rep1/ZNF33A_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--------------------
22993 (process ID) old priority 0, new priority 10
Waiting for 53 seconds.

 
--------------------Stderr--------------------
Initial parameter values: [0.10 1.00 0.20 0.50]
Final parameter values: [0.00 0.24 0.34 0.94]
Number of reported peaks - 138/138 (100.0%)

Number of peaks passing IDR cutoff of 0.05 - 68/138 (49.3%)


 
 		 

    
  
 
  Num   9  
 
  ID   task.callpeak_idr.idr_final_qc.line_219.id_20  
 
  Name   idr final qc 
 
  Thread   thread_Root  
 
  PID   24881  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-09 14:46:54  
 
  End   2017-01-09 14:48:07  
 
  Elapsed   00:01:13  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/idr/pseudo_reps/rep1/ZNF33A_rep1-pr.IDR0.05.filt.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/qc/ZNF33A_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/ZNF33A/out/qc/ZNF33A_IDR_final.qc

# SYS command. line 224

 echo -e "0\t1	0	""0\tN/A\tN/A\tNaN\t1.0\t1" >> /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/qc/ZNF33A_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--------------------
23161 (process ID) old priority 0, new priority 10
Waiting for 60 seconds.

  
 		 

    
  
 
  Num   10  
 
  ID   task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_21  
 
  Name   blacklist_filter peak 1 
 
  Thread   thread_Root  
 
  PID   48062  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-09 14:48:09  
 
  End   2017-01-09 14:49:17  
 
  Elapsed   00:01:08  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/rep1/SRR1370903_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/ZNF33A/out/peak/spp/rep1/SRR1370903_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/ZNF33A/out/peak/spp/rep1/SRR1370903_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--------------------
48066 (process ID) old priority 0, new priority 10
Waiting for 60 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	2323	2653	.	0	.	19.111552121673	-1	3.53160663193272	165

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/rep1/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	2323	2653	.	0	.	19.111552121673	-1	3.53160663193272	165


 
 		 

    
  
 
  Num   11  
 
  ID   task.report.peak2hammock.line_412.id_22  
 
  Name   peak2hammock 
 
  Thread   thread_Root  
 
  PID   56473  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-09 14:49:18  
 
  End   2017-01-09 14:49:26  
 
  Elapsed   00:00:08  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/overlap/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/overlap/SRR1370903_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/ZNF33A/out/peak/spp/overlap/SRR1370903_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/ZNF33A/out/peak/spp/overlap/SRR1370903_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/ZNF33A/out/peak/spp/overlap/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/spp/overlap/SRR1370903_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/ZNF33A/out/peak/spp/overlap/SRR1370903_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp
 
 
   
--------------------Stdout--------------------
56478 (process ID) old priority 0, new priority 10

  
 		 

    
  
 
  Num   12  
 
  ID   task.report.peak2hammock.line_412.id_23  
 
  Name   peak2hammock 
 
  Thread   thread_Root  
 
  PID   720  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-09 14:49:27  
 
  End   2017-01-09 14:49:35  
 
  Elapsed   00:00:08  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/idr/pseudo_reps/rep1/ZNF33A_rep1-pr.IDR0.05.filt.12-col.bed.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/idr/pseudo_reps/rep1/ZNF33A_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/ZNF33A/out/peak/idr/pseudo_reps/rep1/ZNF33A_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/ZNF33A/out/peak/idr/pseudo_reps/rep1/ZNF33A_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/ZNF33A/out/peak/idr/pseudo_reps/rep1/ZNF33A_rep1-pr.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/idr/pseudo_reps/rep1/ZNF33A_rep1-pr.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/peak/idr/pseudo_reps/rep1/ZNF33A_rep1-pr.IDR0.05.filt.12-col.bed.tmp
 
 
   
--------------------Stdout--------------------
725 (process ID) old priority 0, new priority 10

  
 		 

    
  
 
  Num   13  
 
  ID   task.graphviz.report.line_97.id_24  
 
  Name   report 
 
  Thread   thread_Root  
 
  PID   1971  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-09 14:49:36  
 
  End   2017-01-09 14:49:44  
 
  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/ZNF33A/out/report/ZNF33A_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/report/ZNF33A_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/report/ZNF33A_workflow.svg" # to suppress dot font error (exit code=1)
 
 
   
--------------------Stdout--------------------
1977 (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, ZNF33A, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF33A/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF33A/out/align/rep1/SRR1370903_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/ZNF33A  

	
  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/ZNF33A  

	
  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  56885.ZNF33A.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