BigDataScript report: chipseq.bds

Script file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20161213_081401_319
Start time 2016-12-13 08:14:01
Run time 3 days 08:16:29.475
Tasks executed 9
Tasks failed 0
Tasks failed names 
 

		
  Arguments*  [-title, MZF1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/MZF1/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/rep1/SRR1370902_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.20161213_081401_319/task.callpeak_spp.spp_rep1.line_54.id_10
chipseq.bds.20161213_081401_319/task.callpeak_spp.spp_rep1_pr1.line_54.id_11
chipseq.bds.20161213_081401_319/task.callpeak_spp.spp_rep1_pr2.line_54.id_12
chipseq.bds.20161213_081401_319/task.callpeak_naive_overlap.naive_overlap_thresh.line_47.id_13
chipseq.bds.20161213_081401_319/task.callpeak_idr.idr2_rep1_pr.line_70.id_14
chipseq.bds.20161213_081401_319/task.callpeak_idr.idr_final_qc.line_205.id_17
chipseq.bds.20161213_081401_319/task.report.peak2hammock.line_357.id_18
chipseq.bds.20161213_081401_319/task.report.peak2hammock.line_357.id_19
chipseq.bds.20161213_081401_319/task.graphviz.report.line_97.id_20
 
 		 

	
  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_54.id_10  
 
  Name   spp rep1 
 
  Thread   thread_Root  
 
  PID   18055  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-12-13 08:14:07  
 
  End   2016-12-13 23:30:02  
 
  Elapsed   15:15:55  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/rep1/SRR1370902_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/MZF1/out/peak/spp/rep1/SRR1370902_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/rep1/SRR1370902_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/rep1/SRR1370902_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf
  
 
  Dependencies     
 
 		  
 
# SYS command. line 56

 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 59

 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 63

 Rscript ${RUN_SPP} -c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/rep1/SRR1370902_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/MZF1/out/peak/spp/rep1 -speak=145 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/rep1/SRR1370902_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore

# SYS command. line 67

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/rep1/SRR1370902_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/MZF1/out/peak/spp/rep1/SRR1370902_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 69

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/rep1/SRR1370902_1.nodup.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 71

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/rep1/SRR1370902_1.nodup.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/rep1/SRR1370902_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf

# SYS command. line 74

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/rep1/SRR1370902_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/rep1/SRR1370902_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz; fi

# SYS command. line 77

 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/rep1/SRR1370902_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi

# SYS command. line 79

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
18104 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/rep1/SRR1370902_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 145 
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/MZF1/out/peak/spp/rep1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/rep1/SRR1370902_1.nodup.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/rep1/SRR1370902_1.nodup.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/rep1/SRR1370902_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/MZF1/out/align/rep1/SRR1370902_1.nodup.tagAlign.gz 
opened /tmp/18055.1.q/Rtmp5s2Ras/SRR1370902_1.nodup.tagAlign479025d3f8c1
done. read 18853429 fragments
ChIP data read length 69 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
opened /tmp/18055.1.q/Rtmp5s2Ras/input15MReadsNSCLess1.05.50MSubsample.tagAlign479017377689
done. read 50000000 fragments
Control data read length 68 
Calculating peak characteristics
Minimum cross-correlation value 0.2089171 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.223033206130548 
Top 3 estimates for fragment length 145 
Window half size 180 
Phantom peak location 70 
Phantom peak Correlation 0.2141388 
Normalized Strand cross-correlation coefficient (NSC) 1.067568 
Relative Strand Cross correlation Coefficient (RSC) 2.703333 
Phantom Peak Quality Tag 2 
null device 
          1 
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 2.659544  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.3760044  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000057 
Detected 621121 peaks 

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
Loading required package: caTools
There were 50 or more warnings (use warnings() to see the first 50)

 
 		 

    
  
 
  Num   2  
 
  ID   task.callpeak_spp.spp_rep1_pr1.line_54.id_11  
 
  Name   spp rep1-pr1 
 
  Thread   thread_Root  
 
  PID   18056  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-12-13 08:14:08  
 
  End   2016-12-13 21:55:46  
 
  Elapsed   13:41:38  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/pseudo_reps/rep1/pr1/SRR1370902_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/MZF1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf
  
 
  Dependencies     
 
 		  
 
# SYS command. line 56

 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 59

 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 63

 Rscript ${RUN_SPP} -c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/pseudo_reps/rep1/pr1/SRR1370902_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/MZF1/out/peak/spp/pseudo_reps/rep1/pr1 -speak=145 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore

# SYS command. line 67

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370902_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/MZF1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 69

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.pr1.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 71

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.pr1.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf

# SYS command. line 74

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370902_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/MZF1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz; fi

# SYS command. line 77

 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi

# SYS command. line 79

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
18103 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/pseudo_reps/rep1/pr1/SRR1370902_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 145 
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/MZF1/out/peak/spp/pseudo_reps/rep1/pr1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.pr1.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.pr1.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370902_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/MZF1/out/align/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.pr1.tagAlign.gz 
opened /tmp/18056.1.q/RtmpERrjas/SRR1370902_1.nodup.pr1.tagAlign479160b12cc1
done. read 9426715 fragments
ChIP data read length 69 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
opened /tmp/18056.1.q/RtmpERrjas/input15MReadsNSCLess1.05.50MSubsample.tagAlign479116e4adb2
done. read 50000000 fragments
Control data read length 68 
Calculating peak characteristics
Minimum cross-correlation value 0.117472 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.125343112019051 
Top 3 estimates for fragment length 145 
Window half size 180 
Phantom peak location 70 
Phantom peak Correlation 0.1204181 
Normalized Strand cross-correlation coefficient (NSC) 1.067004 
Relative Strand Cross correlation Coefficient (RSC) 2.671743 
Phantom Peak Quality Tag 2 
null device 
          1 
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 5.311762  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.1882614  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000469 
Detected 219939 peaks 

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
Loading required package: caTools
There were 50 or more warnings (use warnings() to see the first 50)

 
 		 

    
  
 
  Num   3  
 
  ID   task.callpeak_spp.spp_rep1_pr2.line_54.id_12  
 
  Name   spp rep1-pr2 
 
  Thread   thread_Root  
 
  PID   18057  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-12-13 08:14:09  
 
  End   2016-12-13 21:35:44  
 
  Elapsed   13:21:35  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/pseudo_reps/rep1/pr2/SRR1370902_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/MZF1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370902_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370902_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370902_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf
  
 
  Dependencies     
 
 		  
 
# SYS command. line 56

 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 59

 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 63

 Rscript ${RUN_SPP} -c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/pseudo_reps/rep1/pr2/SRR1370902_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/MZF1/out/peak/spp/pseudo_reps/rep1/pr2 -speak=145 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370902_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore

# SYS command. line 67

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370902_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/MZF1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370902_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 69

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370902_1.nodup.pr2.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 71

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370902_1.nodup.pr2.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370902_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf

# SYS command. line 74

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370902_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/MZF1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370902_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz; fi

# SYS command. line 77

 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370902_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi

# SYS command. line 79

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
18102 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/pseudo_reps/rep1/pr2/SRR1370902_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 145 
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/MZF1/out/peak/spp/pseudo_reps/rep1/pr2 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370902_1.nodup.pr2.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370902_1.nodup.pr2.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370902_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/MZF1/out/align/pseudo_reps/rep1/pr2/SRR1370902_1.nodup.pr2.tagAlign.gz 
opened /tmp/18057.1.q/RtmphMovas/SRR1370902_1.nodup.pr2.tagAlign4792486446bf
done. read 9426714 fragments
ChIP data read length 69 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
opened /tmp/18057.1.q/RtmphMovas/input15MReadsNSCLess1.05.50MSubsample.tagAlign47923d96964
done. read 50000000 fragments
Control data read length 68 
Calculating peak characteristics
Minimum cross-correlation value 0.1172777 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.12529881447101 
Top 3 estimates for fragment length 145 
Window half size 180 
Phantom peak location 70 
Phantom peak Correlation 0.1202717 
Normalized Strand cross-correlation coefficient (NSC) 1.068394 
Relative Strand Cross correlation Coefficient (RSC) 2.679067 
Phantom Peak Quality Tag 2 
null device 
          1 
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 5.311699  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.1882637  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000474 
Detected 220893 peaks 

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
Loading required package: caTools
There were 50 or more warnings (use warnings() to see the first 50)

 
 		 

    
  
 
  Num   4  
 
  ID   task.callpeak_naive_overlap.naive_overlap_thresh.line_47.id_13  
 
  Name   naive_overlap_thresh  
 
  Thread   thread_Root  
 
  PID   18467  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-12-13 23:30:03  
 
  End   2016-12-14 18:21:49  
 
  Elapsed   18:51:45  
 
  Timeout  01:00:00 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/rep1/SRR1370902_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370902_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/overlap/SRR1370902_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 49

 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 52

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/rep1/SRR1370902_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370902_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/MZF1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370902_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/MZF1/out/peak/spp/overlap/SRR1370902_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz

# SYS command. line 58

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/overlap/SRR1370902_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/overlap/SRR1370902_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz

# SYS command. line 60

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/overlap/SRR1370902_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz

# SYS command. line 62

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
34263 (process ID) old priority 0, new priority 10
Waiting for 55 seconds.

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270467.1	3314	3494	.	0	.	20.6241197215505	-1	3.89658132750573	90

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270467.1	3314	3494	.	0	.	20.6241197215505	-1	3.89658132750573	90

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KN196487.1	2603	2783	.	0	.	13.8826993474464	-1	3.26185448752219	90

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KN196487.1	2603	2783	.	0	.	13.8826993474464	-1	3.26185448752219	90


 
 		 

    
  
 
  Num   5  
 
  ID   task.callpeak_idr.idr2_rep1_pr.line_70.id_14  
 
  Name   idr2 rep1-pr 
 
  Thread   thread_Root  
 
  PID   18509  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-12-14 18:21:50  
 
  End   2016-12-15 17:39:06  
 
  Elapsed   23:17:16  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370902_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/rep1/SRR1370902_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/idr/pseudo_reps/rep1/MZF1_rep1-pr.IDR0.05.filt.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/idr/pseudo_reps/rep1/MZF1_rep1-pr.unthresholded-peaks.txt.png
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/idr/pseudo_reps/rep1/MZF1_rep1-pr.unthresholded-peaks.txt.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/idr/pseudo_reps/rep1/MZF1_rep1-pr.IDR0.05.filt.12-col.bed.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 72

 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 74

 idr --samples /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370902_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/rep1/SRR1370902_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/idr/pseudo_reps/rep1/MZF1_rep1-pr.unthresholded-peaks.txt --rank signal.value --soft-idr-threshold 0.05 \
			--plot --use-best-multisummit-IDR

# SYS command. line 78

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

# SYS command. line 81

 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/MZF1/out/peak/idr/pseudo_reps/rep1/MZF1_rep1-pr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/idr/pseudo_reps/rep1/MZF1_rep1-pr.IDR0.05.13-col.bed.gz

# SYS command. line 84

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/idr/pseudo_reps/rep1/MZF1_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/MZF1/out/peak/idr/pseudo_reps/rep1/MZF1_rep1-pr.IDR0.05.narrowPeak.gz

# SYS command. line 85

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/idr/pseudo_reps/rep1/MZF1_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/MZF1/out/peak/idr/pseudo_reps/rep1/MZF1_rep1-pr.IDR0.05.12-col.bed.gz

# SYS command. line 87

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/idr/pseudo_reps/rep1/MZF1_rep1-pr.IDR0.05.13-col.bed.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/idr/pseudo_reps/rep1/MZF1_rep1-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 88

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/idr/pseudo_reps/rep1/MZF1_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/MZF1/out/peak/idr/pseudo_reps/rep1/MZF1_rep1-pr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 89

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/idr/pseudo_reps/rep1/MZF1_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/MZF1/out/peak/idr/pseudo_reps/rep1/MZF1_rep1-pr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 91

 gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/idr/pseudo_reps/rep1/MZF1_rep1-pr.unthresholded-peaks.txt

# SYS command. line 92

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/idr/pseudo_reps/rep1/MZF1_rep1-pr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/idr/pseudo_reps/rep1/MZF1_rep1-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 94

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
17467 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq_py3/bin to PATH
Initial parameter values: [0.10 1.00 0.20 0.50]
Final parameter values: [1.20 1.21 0.76 0.36]
Number of reported peaks - 27583/27583 (100.0%)

Number of peaks passing IDR cutoff of 0.05 - 3830/27583 (13.9%)


 
 		 

    
  
 
  Num   6  
 
  ID   task.callpeak_idr.idr_final_qc.line_205.id_17  
 
  Name   idr final qc 
 
  Thread   thread_Root  
 
  PID   18551  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-12-15 17:39:07  
 
  End   2016-12-16 16:30:04  
 
  Elapsed   22:50:57  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/idr/pseudo_reps/rep1/MZF1_rep1-pr.IDR0.05.filt.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/qc/MZF1_IDR_final.qc
  
 
  Dependencies     
 
 		  
 
# SYS command. line 207

 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 209

 echo -e "Nt\tN1	""Np\tconservative_set\toptimal_set\trescue_ratio\tself_consistency_ratio\treproducibility" > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/qc/MZF1_IDR_final.qc

# SYS command. line 210

 echo -e "0\t3814	""0\tN/A\tN/A\tNaN\t1.0\t1" >> /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/qc/MZF1_IDR_final.qc

# SYS command. line 212

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
10424 (process ID) old priority 0, new priority 10
Waiting for 59 seconds.

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH

 
 		 

    
  
 
  Num   7  
 
  ID   task.report.peak2hammock.line_357.id_18  
 
  Name   peak2hammock 
 
  Thread   thread_Root  
 
  PID   10492  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-12-16 16:30:05  
 
  End   2016-12-16 16:30:13  
 
  Elapsed   00:00:08  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/overlap/SRR1370902_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/overlap/SRR1370902_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.hammock.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 359

 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 360

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/overlap/SRR1370902_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/overlap/SRR1370902_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.tmp

# SYS command. line 362

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/overlap/SRR1370902_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/overlap/SRR1370902_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.hammock

# SYS command. line 363

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/spp/overlap/SRR1370902_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.tmp
 
 
   
--------------------Stdout--------------------
10496 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH

 
 		 

    
  
 
  Num   8  
 
  ID   task.report.peak2hammock.line_357.id_19  
 
  Name   peak2hammock 
 
  Thread   thread_Root  
 
  PID   10885  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-12-16 16:30:14  
 
  End   2016-12-16 16:30:21  
 
  Elapsed   00:00:07  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/idr/pseudo_reps/rep1/MZF1_rep1-pr.IDR0.05.filt.12-col.bed.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/idr/pseudo_reps/rep1/MZF1_rep1-pr.IDR0.05.filt.12-col.bed.hammock.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 359

 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 360

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/idr/pseudo_reps/rep1/MZF1_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/MZF1/out/peak/idr/pseudo_reps/rep1/MZF1_rep1-pr.IDR0.05.filt.12-col.bed.tmp

# SYS command. line 362

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/idr/pseudo_reps/rep1/MZF1_rep1-pr.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/idr/pseudo_reps/rep1/MZF1_rep1-pr.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 363

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/peak/idr/pseudo_reps/rep1/MZF1_rep1-pr.IDR0.05.filt.12-col.bed.tmp
 
 
   
--------------------Stdout--------------------
10890 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH

 
 		 

    
  
 
  Num   9  
 
  ID   task.graphviz.report.line_97.id_20  
 
  Name   report 
 
  Thread   thread_Root  
 
  PID   11310  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-12-16 16:30:22  
 
  End   2016-12-16 16:30:30  
 
  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/MZF1/out/report/MZF1_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/report/MZF1_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/report/MZF1_workflow.svg" # to suppress dot font error (exit code=1)
 
 
   
--------------------Stdout--------------------
11314 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH

 
 		 

	






	
 Global scope 

	Note: Global scope when program finished execution.
	

	
  Type  Name  Value  

	
  string  _  /usr/bin/bds  

	
  bool  allowEmpty  false  

	
  string[]  args  [-title, MZF1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/MZF1/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1/out/align/rep1/SRR1370902_1.bam, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz, -final_stage, idr, $]  

	
  bool  canFail  false  

	
  int  cpus  -1  

	
  int  cpusLocal  56  

	
  int  day  86400  

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

	
  string  DISPLAY  localhost:20.0  

	
  real  E  2.718281828459045  

	
  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  KRB5CCNAME  FILE:/tmp/krb5cc_1048_iC24uZ  

	
  string  LANG  en_US.UTF-8  

	
  string  LOADEDMODULES    

	
  string  LOGNAME  imk1  

	
  int  M  1048576  

	
  string  MAIL  /var/mail/imk1  

	
  int  mem  -1  

	
  int  minute  60  

	
  string  MODULE_VERSION  3.2.10  

	
  string  MODULE_VERSION_STACK  3.2.10  

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

	
  string  MODULESHOME  /software/env_module/3.2.10  

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

	
  string  node    

	
  int  P  1125899906842624  

	
  string  PATH  /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  

	
  real  PI  3.141592653589793  

	
  string  ppwd  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/MZF1  

	
  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/MZF1  

	
  string  queue    

	
  int  retry  0  

	
  string  SHELL  /bin/bash  

	
  string  SHLVL  3  

	
  string  SSH_CLIENT  171.66.30.179 56488 22  

	
  string  SSH_CONNECTION  171.66.30.179 56488 171.65.76.63 22  

	
  string  SSH_TTY  /dev/pts/33  

	
  string  STY  15988.MZF1.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  

	
  int  walltimeout  8640000  

	
  int  week  604800  

	
  string  WINDOW  0  

	
  string  XDG_RUNTIME_DIR  /run/user/1048  

	
  string  XDG_SESSION_ID  7890  

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