BigDataScript report: chipseq.bds

Script file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20161007_171731_132
Start time 2016-10-07 17:17:31
Run time 20:30:17.547
Tasks executed 9
Tasks failed 0
Tasks failed names 
 

		
  Arguments*  [-title, ZF7, -nth, 5, -macs2_for_pooled_rep_only, -species, mm10, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out, -tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/rep1/ZF7_allReps.nodup.tagAlign.gz, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz, -gensz, mm, -chrsz, /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes, $] 

		
  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.20161007_171731_132/task.callpeak_spp.spp_rep1.line_54.id_10
chipseq.bds.20161007_171731_132/task.callpeak_spp.spp_rep1_pr1.line_54.id_11
chipseq.bds.20161007_171731_132/task.callpeak_spp.spp_rep1_pr2.line_54.id_12
chipseq.bds.20161007_171731_132/task.callpeak_naive_overlap.naive_overlap_thresh.line_32.id_13
chipseq.bds.20161007_171731_132/task.callpeak_idr.idr2_rep1_pr.line_70.id_14
chipseq.bds.20161007_171731_132/task.callpeak_idr.idr_final_qc.line_205.id_17
chipseq.bds.20161007_171731_132/task.report.peak2hammock.line_357.id_18
chipseq.bds.20161007_171731_132/task.report.peak2hammock.line_357.id_19
chipseq.bds.20161007_171731_132/task.graphviz.report.line_97.id_20
 
 		 

	
  thread_41   thread_Root 	 
  
 		 

	
  thread_42   thread_Root 	 
  
 		 

	






	
 Task details 

	

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

    
  
 
  Num   1  
 
  ID   task.callpeak_spp.spp_rep1.line_54.id_10  
 
  Name   spp rep1 
 
  Thread   thread_Root  
 
  PID   94  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-10-07 17:17:35  
 
  End   2016-10-08 13:31:10  
 
  Elapsed   20:13:34  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/rep1/ZF7_allReps.nodup.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/rep1/ZF7_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/rep1/ZF7_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.ccscore
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/rep1/ZF7_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pdf
  
 
  Dependencies     
 
 		  
 
# SYS command. line 56

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

# SYS command. line 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/MouseMutantData/ZF7/out/align/rep1/ZF7_allReps.nodup.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz \
			-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/rep1 -speak=160 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/rep1/ZF7_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.ccscore

# SYS command. line 67

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/rep1/ZF7_allReps.nodup.tagAlign_VS_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.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/MouseMutantData/ZF7/out/peak/spp/rep1/ZF7_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz

# SYS command. line 69

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/rep1/ZF7_allReps.nodup.tagAlign_VS_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz

# SYS command. line 71

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/rep1/ZF7_allReps.nodup.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/rep1/ZF7_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pdf

# SYS command. line 74

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/rep1/ZF7_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/rep1/ZF7_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz; fi

# SYS command. line 77

 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/rep1/ZF7_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.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--------------------
11187 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/rep1/ZF7_allReps.nodup.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 160 
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/MouseMutantData/ZF7/out/peak/spp/rep1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/rep1/ZF7_allReps.nodup.tagAlign_VS_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/rep1/ZF7_allReps.nodup.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/rep1/ZF7_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.ccscore 
Overwrite files?: TRUE

Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/rep1/ZF7_allReps.nodup.tagAlign.gz 
opened /tmp/94.1.q/RtmpXxtRqI/ZF7_allReps.nodup.tagAlign2e3c6ba0a71d
done. read 41454335 fragments
ChIP data read length 50 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz 
opened /tmp/94.1.q/RtmpXxtRqI/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign2e3c32c163d1
done. read 3384182 fragments
Control data read length 50 
Calculating peak characteristics
Minimum cross-correlation value 0.3990269 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.43484250254046 
Top 3 estimates for fragment length 160 
Window half size 565 
Phantom peak location 55 
Phantom peak Correlation 0.4216947 
Normalized Strand cross-correlation coefficient (NSC) 1.089757 
Relative Strand Cross correlation Coefficient (RSC) 1.580021 
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= 0.08569016  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 11.66995  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.00004 
Detected 2223303 peaks 

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
Loading required package: caTools
There were 36 warnings (use warnings() to see them)

 
 		 

    
  
 
  Num   2  
 
  ID   task.callpeak_spp.spp_rep1_pr1.line_54.id_11  
 
  Name   spp rep1-pr1 
 
  Thread   thread_Root  
 
  PID   97  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-10-07 17:17:36  
 
  End   2016-10-08 12:14:18  
 
  Elapsed   18:56:42  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/pseudo_reps/rep1/pr1/ZF7_allReps.nodup.pr1.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr1/ZF7_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr1/ZF7_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.ccscore
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr1/ZF7_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pdf
  
 
  Dependencies     
 
 		  
 
# SYS command. line 56

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

# SYS command. line 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/MouseMutantData/ZF7/out/align/pseudo_reps/rep1/pr1/ZF7_allReps.nodup.pr1.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz \
			-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr1 -speak=160 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr1/ZF7_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.ccscore

# SYS command. line 67

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr1/ZF7_allReps.nodup.pr1.tagAlign_VS_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.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/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr1/ZF7_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz

# SYS command. line 69

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr1/ZF7_allReps.nodup.pr1.tagAlign_VS_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz

# SYS command. line 71

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr1/ZF7_allReps.nodup.pr1.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr1/ZF7_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pdf

# SYS command. line 74

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr1/ZF7_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr1/ZF7_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz; fi

# SYS command. line 77

 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr1/ZF7_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.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--------------------
12002 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/pseudo_reps/rep1/pr1/ZF7_allReps.nodup.pr1.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 160 
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/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr1/ZF7_allReps.nodup.pr1.tagAlign_VS_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr1/ZF7_allReps.nodup.pr1.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr1/ZF7_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.ccscore 
Overwrite files?: TRUE

Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/pseudo_reps/rep1/pr1/ZF7_allReps.nodup.pr1.tagAlign.gz 
opened /tmp/97.1.q/RtmpimjJtG/ZF7_allReps.nodup.pr1.tagAlign300d41e83404
done. read 20727168 fragments
ChIP data read length 50 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz 
opened /tmp/97.1.q/RtmpimjJtG/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign300d20c3d7b1
done. read 3384182 fragments
Control data read length 50 
Calculating peak characteristics
Minimum cross-correlation value 0.2545881 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.277519304983176 
Top 3 estimates for fragment length 160 
Window half size 565 
Phantom peak location 55 
Phantom peak Correlation 0.269107 
Normalized Strand cross-correlation coefficient (NSC) 1.090072 
Relative Strand Cross correlation Coefficient (RSC) 1.579404 
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= 0.1706575  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 5.859688  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000176 
Detected 1409943 peaks 

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
Loading required package: caTools
There were 36 warnings (use warnings() to see them)

 
 		 

    
  
 
  Num   3  
 
  ID   task.callpeak_spp.spp_rep1_pr2.line_54.id_12  
 
  Name   spp rep1-pr2 
 
  Thread   thread_Root  
 
  PID   111  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-10-07 17:17:37  
 
  End   2016-10-08 13:38:01  
 
  Elapsed   20:20:23  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/pseudo_reps/rep1/pr2/ZF7_allReps.nodup.pr2.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr2/ZF7_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr2/ZF7_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.ccscore
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr2/ZF7_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pdf
  
 
  Dependencies     
 
 		  
 
# SYS command. line 56

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

# SYS command. line 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/MouseMutantData/ZF7/out/align/pseudo_reps/rep1/pr2/ZF7_allReps.nodup.pr2.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz \
			-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr2 -speak=160 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr2/ZF7_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.ccscore

# SYS command. line 67

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr2/ZF7_allReps.nodup.pr2.tagAlign_VS_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.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/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr2/ZF7_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz

# SYS command. line 69

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr2/ZF7_allReps.nodup.pr2.tagAlign_VS_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz

# SYS command. line 71

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr2/ZF7_allReps.nodup.pr2.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr2/ZF7_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pdf

# SYS command. line 74

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr2/ZF7_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr2/ZF7_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz; fi

# SYS command. line 77

 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr2/ZF7_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.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--------------------
11174 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/pseudo_reps/rep1/pr2/ZF7_allReps.nodup.pr2.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 160 
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/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr2 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr2/ZF7_allReps.nodup.pr2.tagAlign_VS_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr2/ZF7_allReps.nodup.pr2.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr2/ZF7_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.ccscore 
Overwrite files?: TRUE

Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/pseudo_reps/rep1/pr2/ZF7_allReps.nodup.pr2.tagAlign.gz 
opened /tmp/111.1.q/RtmpX1IWDS/ZF7_allReps.nodup.pr2.tagAlign2ea552f41e6
done. read 20727167 fragments
ChIP data read length 50 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz 
opened /tmp/111.1.q/RtmpX1IWDS/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign2ea549eb9955
done. read 3384182 fragments
Control data read length 50 
Calculating peak characteristics
Minimum cross-correlation value 0.2547185 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.277386308296189 
Top 3 estimates for fragment length 160 
Window half size 565 
Phantom peak location 55 
Phantom peak Correlation 0.2691429 
Normalized Strand cross-correlation coefficient (NSC) 1.088991 
Relative Strand Cross correlation Coefficient (RSC) 1.571493 
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= 0.1706896  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 5.858587  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.00013 
Detected 1409892 peaks 

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
Loading required package: caTools
There were 36 warnings (use warnings() to see them)

 
 		 

    
  
 
  Num   4  
 
  ID   task.callpeak_naive_overlap.naive_overlap_thresh.line_32.id_13  
 
  Name   naive_overlap_thresh  
 
  Thread   thread_Root  
 
  PID   144  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-10-08 13:38:02  
 
  End   2016-10-08 13:39:08  
 
  Elapsed   00:01:05  
 
  Timeout  01:00:00 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/rep1/ZF7_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr1/ZF7_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr2/ZF7_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/SPP/overlap/ZF7_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.naive_overlap.regionPeak.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 34

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

# SYS command. line 37

 intersectBed -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/rep1/ZF7_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr1/ZF7_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.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/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr2/ZF7_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.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 -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/SPP/overlap/ZF7_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.PooledInRep1AndRep2.regionPeak.gz

# SYS command. line 43

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/SPP/overlap/ZF7_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.PooledInRep1AndRep2.regionPeak.gz | sort | uniq | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/SPP/overlap/ZF7_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.naive_overlap.regionPeak.gz

# SYS command. line 45

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/SPP/overlap/ZF7_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.PooledInRep1AndRep2.regionPeak.gz

# SYS command. line 47

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
17899 (process ID) old priority 0, new priority 10
Waiting for 52 seconds.

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

 
 		 

    
  
 
  Num   5  
 
  ID   task.callpeak_idr.idr2_rep1_pr.line_70.id_14  
 
  Name   idr2 rep1-pr 
 
  Thread   thread_Root  
 
  PID   145  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-10-08 13:39:09  
 
  End   2016-10-08 13:46:27  
 
  Elapsed   00:07:17  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr1/ZF7_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr2/ZF7_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/rep1/ZF7_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/idr/pseudo_reps/rep1/ZF7_rep1-pr.IDR0.05.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/idr/pseudo_reps/rep1/ZF7_rep1-pr.unthresholded-peaks.txt.png
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/idr/pseudo_reps/rep1/ZF7_rep1-pr.unthresholded-peaks.txt.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/idr/pseudo_reps/rep1/ZF7_rep1-pr.IDR0.05.12-col.bed.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 72

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

# SYS command. line 74

 idr --samples /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr1/ZF7_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/pseudo_reps/rep1/pr2/ZF7_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/rep1/ZF7_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/idr/pseudo_reps/rep1/ZF7_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/MouseMutantData/ZF7/out/peak/idr/pseudo_reps/rep1/ZF7_rep1-pr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/idr/pseudo_reps/rep1/ZF7_rep1-pr.IDR0.05.13-col.bed.gz

# SYS command. line 84

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/idr/pseudo_reps/rep1/ZF7_rep1-pr.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/idr/pseudo_reps/rep1/ZF7_rep1-pr.IDR0.05.narrowPeak.gz

# SYS command. line 85

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/idr/pseudo_reps/rep1/ZF7_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 -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/idr/pseudo_reps/rep1/ZF7_rep1-pr.IDR0.05.12-col.bed.gz

# SYS command. line 87

 echo

# SYS command. line 88

 echo

# SYS command. line 89

 echo

# SYS command. line 91

 gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/idr/pseudo_reps/rep1/ZF7_rep1-pr.unthresholded-peaks.txt

# SYS command. line 92

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/idr/pseudo_reps/rep1/ZF7_rep1-pr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/idr/pseudo_reps/rep1/ZF7_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--------------------
18017 (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: [1.32 1.04 0.70 0.38]
Number of reported peaks - 163124/163124 (100.0%)

Number of peaks passing IDR cutoff of 0.05 - 27367/163124 (16.8%)


 
 		 

    
  
 
  Num   6  
 
  ID   task.callpeak_idr.idr_final_qc.line_205.id_17  
 
  Name   idr final qc 
 
  Thread   thread_Root  
 
  PID   148  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-10-08 13:46:28  
 
  End   2016-10-08 13:47:38  
 
  Elapsed   00:01:09  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/idr/pseudo_reps/rep1/ZF7_rep1-pr.IDR0.05.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/qc/ZF7_IDR_final.qc
  
 
  Dependencies     
 
 		  
 
# SYS command. line 207

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

# SYS command. line 209

 echo -e "Nt\tN1	""Np\tconservative_set\toptimal_set\trescue_ratio\tself_consistency_ratio\treproducibility" > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/qc/ZF7_IDR_final.qc

# SYS command. line 210

 echo -e "0\t27252	""0\tN/A\tN/A\tNaN\t1.0\t1" >> /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/qc/ZF7_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--------------------
18943 (process ID) old priority 0, new priority 10
Waiting for 60 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   19019  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-10-08 13:47:39  
 
  End   2016-10-08 13:47:43  
 
  Elapsed   00:00:03  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/SPP/overlap/ZF7_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.naive_overlap.regionPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/SPP/overlap/ZF7_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.naive_overlap.regionPeak.hammock.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 359

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

# SYS command. line 360

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/SPP/overlap/ZF7_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.naive_overlap.regionPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/SPP/overlap/ZF7_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.naive_overlap.regionPeak.tmp

# SYS command. line 362

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/SPP/overlap/ZF7_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.naive_overlap.regionPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/SPP/overlap/ZF7_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.naive_overlap.regionPeak.hammock

# SYS command. line 363

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/SPP/overlap/ZF7_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.naive_overlap.regionPeak.tmp
 
 
   
--------------------Stdout--------------------
19023 (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   19102  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-10-08 13:47:44  
 
  End   2016-10-08 13:47:46  
 
  Elapsed   00:00:02  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/idr/pseudo_reps/rep1/ZF7_rep1-pr.IDR0.05.12-col.bed.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/idr/pseudo_reps/rep1/ZF7_rep1-pr.IDR0.05.12-col.bed.hammock.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 359

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

# SYS command. line 360

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/idr/pseudo_reps/rep1/ZF7_rep1-pr.IDR0.05.12-col.bed.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/idr/pseudo_reps/rep1/ZF7_rep1-pr.IDR0.05.12-col.bed.tmp

# SYS command. line 362

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/idr/pseudo_reps/rep1/ZF7_rep1-pr.IDR0.05.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/idr/pseudo_reps/rep1/ZF7_rep1-pr.IDR0.05.12-col.bed.hammock

# SYS command. line 363

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/idr/pseudo_reps/rep1/ZF7_rep1-pr.IDR0.05.12-col.bed.tmp
 
 
   
--------------------Stdout--------------------
19106 (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   19183  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-10-08 13:47:47  
 
  End   2016-10-08 13:47:48  
 
  Elapsed   00:00:01  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files     
 
  Output files     
 
  Dependencies     
 
 		  
 
# SYS command. line 98

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

# SYS command. line 99

 dot -Tsvg /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/report/ZF7_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/report/ZF7_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/report/ZF7_workflow.svg" # to suppress dot font error (exit code=1)
 
 
   
--------------------Stdout--------------------
19187 (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, ZF7, -nth, 5, -macs2_for_pooled_rep_only, -species, mm10, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out, -tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/rep1/ZF7_allReps.nodup.tagAlign.gz, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz, -gensz, mm, -chrsz, /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes, $]  

	
  bool  canFail  false  

	
  int  cpus  -1  

	
  int  cpusLocal  56  

	
  int  day  86400  

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

	
  string  DISPLAY  localhost:12.0  

	
  real  E  2.718281828459045  

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

	
  int  G  1073741824  

	
  string  HOME  /users/imk1/  

	
  int  hour  3600  

	
  int  K  1024  

	
  string  KERAS_DIR  /srv/scratch/imk1/TFBindingPredictionProject/src/keras  

	
  string  KRB5CCNAME  FILE:/tmp/krb5cc_1048_rUZelg  

	
  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  node    

	
  int  P  1125899906842624  

	
  string  PATH  /users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/users/imk1/edirect:/users/imk1/edirect:/users/imk1/edirect  

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

	
  string  PERL_LOCAL_LIB_ROOT  /users/imk1/perl5:/users/imk1/perl5  

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

	
  string  PERL_MM_OPT  INSTALL_BASE=/users/imk1/perl5  

	
  real  PI  3.141592653589793  

	
  string  ppwd  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7  

	
  string  programName  chipseq.bds  

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

	
  string  PWD  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7  

	
  string  PYTHONPATH  /software/python_anaconda/2.2.0/bin/python:/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 51178 22  

	
  string  SSH_CONNECTION  171.65.77.8 51178 171.65.76.63 22  

	
  string  SSH_TTY  /dev/pts/18  

	
  string  STY  9841.ZF7.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