BigDataScript report: chipseq.bds

Script file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20161103_140610_672
Start time 2016-11-03 14:06:10
Run time 00:20:25.252
Tasks executed 4
Tasks failed 0
Tasks failed names 
 

		
  Arguments*  [-title, SRR372712_SRR372713, -nth, 5, -macs2_for_pooled_rep_only, -species, mm10, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/SRR372712_SRR372713.fastq.gz, -ctl_fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.fastq.gz, $] 

		
  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.20161103_140610_672/task.callpeak_spp.spp_rep1.line_54.id_11
chipseq.bds.20161103_140610_672/task.callpeak_spp.spp_rep1_pr1.line_54.id_12
chipseq.bds.20161103_140610_672/task.callpeak_spp.spp_rep1_pr2.line_54.id_13
 
 		 

	
  thread_41   thread_Root 	 
 chipseq.bds.20161103_140610_672_parallel_41/task.postalign_bed.xcor_rep1.line_205.id_10
 
 		 

	
  thread_42   thread_Root 	 
  
 		 

	






	
 Task details 

	

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

    
  
 
  Num   1  
 
  ID   task.postalign_bed.xcor_rep1.line_205.id_10  
 
  Name   xcor rep1 
 
  Thread   thread_41  
 
  PID   3396  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus    2 
 
  Mem    
 
 		  
 
  Start   2016-11-03 14:06:14  
 
  End   2016-11-03 14:14:17  
 
  Elapsed   00:08:02  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/align/rep1/SRR372712_SRR372713.nodup.15M.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/qc/rep1/SRR372712_SRR372713.nodup.15M.cc.qc
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/qc/rep1/SRR372712_SRR372713.nodup.15M.cc.plot.pdf
  
 
  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 210

 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 216

 Rscript ${RUN_SPP} -rf \
			-c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/align/rep1/SRR372712_SRR372713.nodup.15M.tagAlign.gz -p=2 \
			-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/qc/rep1/SRR372712_SRR372713.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/qc/rep1/SRR372712_SRR372713.nodup.15M.cc.qc 

# SYS command. line 219

 sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/qc/rep1/SRR372712_SRR372713.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/qc/rep1/SRR372712_SRR372713.nodup.15M.cc.qc.tmp

# SYS command. line 220

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/qc/rep1/SRR372712_SRR372713.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/qc/rep1/SRR372712_SRR372713.nodup.15M.cc.qc

# SYS command. line 222

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
11370 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/align/rep1/SRR372712_SRR372713.nodup.15M.tagAlign.gz 
Control data: NA 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift NA 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 2 
FDR threshold: 0.01 
NumPeaks Threshold: NA 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/align/rep1 
narrowPeak output file name: NA 
regionPeak output file name: NA 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/qc/rep1/SRR372712_SRR372713.nodup.15M.cc.plot.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/qc/rep1/SRR372712_SRR372713.nodup.15M.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/align/rep1/SRR372712_SRR372713.nodup.15M.tagAlign.gz 
opened /tmp/3396.1.q/RtmpLP9BP3/SRR372712_SRR372713.nodup.15M.tagAlign2ca93ff334b6
done. read 14853122 fragments
ChIP data read length 36 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1449979 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.506223487196022 
Top 3 estimates for fragment length 95 
Window half size 195 
Phantom peak location 40 
Phantom peak Correlation 0.368976 
Normalized Strand cross-correlation coefficient (NSC) 3.491246 
Relative Strand cross-correlation Coefficient (RSC) 1.612772 
Phantom Peak Quality Tag 2 
null device 
          1 

 
--------------------Stderr--------------------
Loading required package: caTools
Warning message:
package ‘caTools’ was built under R version 3.2.3 

 
 		 

    
  
 
  Num   2  
 
  ID   task.callpeak_spp.spp_rep1.line_54.id_11  
 
  Name   spp rep1 
 
  Thread   thread_Root  
 
  PID   3397  
 
 		  
 
  OK   false   
 
  Exit Code   0   
 
  Retries    
 
  State   RUNNING  
 
  Dep.   WAIT  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-11-03 14:14:18  
 
  End   2016-11-03 14:14:18  
 
  Elapsed   00:00:00  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/align/rep1/SRR372712_SRR372713.nodup.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/peak/spp/rep1/SRR372712_SRR372713.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/peak/spp/rep1/SRR372712_SRR372713.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.ccscore
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/peak/spp/rep1/SRR372712_SRR372713.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/SRR372712_SRR372713/out/align/rep1/SRR372712_SRR372713.nodup.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz \
			-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/peak/spp/rep1 -speak=95 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/peak/spp/rep1/SRR372712_SRR372713.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.ccscore

# SYS command. line 67

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/peak/spp/rep1/SRR372712_SRR372713.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/SRR372712_SRR372713/out/peak/spp/rep1/SRR372712_SRR372713.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/SRR372712_SRR372713/out/peak/spp/rep1/SRR372712_SRR372713.nodup.tagAlign_VS_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz

# SYS command. line 71

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/peak/spp/rep1/SRR372712_SRR372713.nodup.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/peak/spp/rep1/SRR372712_SRR372713.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pdf

# SYS command. line 74

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/peak/spp/rep1/SRR372712_SRR372713.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/SRR372712_SRR372713/out/peak/spp/rep1/SRR372712_SRR372713.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/SRR372712_SRR372713/out/peak/spp/rep1/SRR372712_SRR372713.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--------------------
11547 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/align/rep1/SRR372712_SRR372713.nodup.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 95 
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/SRR372712_SRR372713/out/peak/spp/rep1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/peak/spp/rep1/SRR372712_SRR372713.nodup.tagAlign_VS_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/peak/spp/rep1/SRR372712_SRR372713.nodup.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/peak/spp/rep1/SRR372712_SRR372713.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/SRR372712_SRR372713/out/align/rep1/SRR372712_SRR372713.nodup.tagAlign.gz 
opened /tmp/3397.1.q/RtmpgSglMw/SRR372712_SRR372713.nodup.tagAlign2dd465681afd
done. read 14854728 fragments
ChIP data read length 36 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz 
opened /tmp/3397.1.q/RtmpgSglMw/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign2dd42c34e5b3
done. read 3384182 fragments
Control data read length 50 
Calculating peak characteristics

 
--------------------Stderr--------------------
Loading required package: caTools
Warning message:
package ‘caTools’ was built under R version 3.2.3 

 
 		 

    
  
 
  Num   3  
 
  ID   task.callpeak_spp.spp_rep1_pr1.line_54.id_12  
 
  Name   spp rep1-pr1 
 
  Thread   thread_Root  
 
  PID   3398  
 
 		  
 
  OK   false   
 
  Exit Code   0   
 
  Retries    
 
  State   RUNNING  
 
  Dep.   WAIT  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-11-03 14:14:19  
 
  End   2016-11-03 14:14:19  
 
  Elapsed   00:00:00  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/align/pseudo_reps/rep1/pr1/SRR372712_SRR372713.nodup.pr1.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/peak/spp/pseudo_reps/rep1/pr1/SRR372712_SRR372713.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/peak/spp/pseudo_reps/rep1/pr1/SRR372712_SRR372713.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.ccscore
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/peak/spp/pseudo_reps/rep1/pr1/SRR372712_SRR372713.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/SRR372712_SRR372713/out/align/pseudo_reps/rep1/pr1/SRR372712_SRR372713.nodup.pr1.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz \
			-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/peak/spp/pseudo_reps/rep1/pr1 -speak=95 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/peak/spp/pseudo_reps/rep1/pr1/SRR372712_SRR372713.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.ccscore

# SYS command. line 67

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/peak/spp/pseudo_reps/rep1/pr1/SRR372712_SRR372713.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/SRR372712_SRR372713/out/peak/spp/pseudo_reps/rep1/pr1/SRR372712_SRR372713.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/SRR372712_SRR372713/out/peak/spp/pseudo_reps/rep1/pr1/SRR372712_SRR372713.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/SRR372712_SRR372713/out/peak/spp/pseudo_reps/rep1/pr1/SRR372712_SRR372713.nodup.pr1.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/peak/spp/pseudo_reps/rep1/pr1/SRR372712_SRR372713.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/SRR372712_SRR372713/out/peak/spp/pseudo_reps/rep1/pr1/SRR372712_SRR372713.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/SRR372712_SRR372713/out/peak/spp/pseudo_reps/rep1/pr1/SRR372712_SRR372713.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/SRR372712_SRR372713/out/peak/spp/pseudo_reps/rep1/pr1/SRR372712_SRR372713.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--------------------
11546 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/align/pseudo_reps/rep1/pr1/SRR372712_SRR372713.nodup.pr1.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 95 
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/SRR372712_SRR372713/out/peak/spp/pseudo_reps/rep1/pr1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/peak/spp/pseudo_reps/rep1/pr1/SRR372712_SRR372713.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/SRR372712_SRR372713/out/peak/spp/pseudo_reps/rep1/pr1/SRR372712_SRR372713.nodup.pr1.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/peak/spp/pseudo_reps/rep1/pr1/SRR372712_SRR372713.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/SRR372712_SRR372713/out/align/pseudo_reps/rep1/pr1/SRR372712_SRR372713.nodup.pr1.tagAlign.gz 
opened /tmp/3398.1.q/Rtmp685BWL/SRR372712_SRR372713.nodup.pr1.tagAlign2df8422b722d
done. read 7427364 fragments
ChIP data read length 36 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz 
opened /tmp/3398.1.q/Rtmp685BWL/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign2df884322d
done. read 3384182 fragments
Control data read length 50 
Calculating peak characteristics
Minimum cross-correlation value 0.09418589 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.328774587622481 
Top 3 estimates for fragment length 95 
Window half size 195 
Phantom peak location 40 
Phantom peak Correlation 0.239462 
Normalized Strand cross-correlation coefficient (NSC) 3.490699 
Relative Strand cross-correlation Coefficient (RSC) 1.614778 
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= 0.6291038  
 
--------------------Stderr--------------------
Loading required package: caTools
Warning message:
package ‘caTools’ was built under R version 3.2.3 

 
 		 

    
  
 
  Num   4  
 
  ID   task.callpeak_spp.spp_rep1_pr2.line_54.id_13  
 
  Name   spp rep1-pr2 
 
  Thread   thread_Root  
 
  PID   3399  
 
 		  
 
  OK   false   
 
  Exit Code   0   
 
  Retries    
 
  State   RUNNING  
 
  Dep.   WAIT  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-11-03 14:14:20  
 
  End   2016-11-03 14:14:20  
 
  Elapsed   00:00:00  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/align/pseudo_reps/rep1/pr2/SRR372712_SRR372713.nodup.pr2.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/peak/spp/pseudo_reps/rep1/pr2/SRR372712_SRR372713.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/peak/spp/pseudo_reps/rep1/pr2/SRR372712_SRR372713.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.ccscore
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/peak/spp/pseudo_reps/rep1/pr2/SRR372712_SRR372713.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/SRR372712_SRR372713/out/align/pseudo_reps/rep1/pr2/SRR372712_SRR372713.nodup.pr2.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz \
			-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/peak/spp/pseudo_reps/rep1/pr2 -speak=95 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/peak/spp/pseudo_reps/rep1/pr2/SRR372712_SRR372713.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.ccscore

# SYS command. line 67

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/peak/spp/pseudo_reps/rep1/pr2/SRR372712_SRR372713.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/SRR372712_SRR372713/out/peak/spp/pseudo_reps/rep1/pr2/SRR372712_SRR372713.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/SRR372712_SRR372713/out/peak/spp/pseudo_reps/rep1/pr2/SRR372712_SRR372713.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/SRR372712_SRR372713/out/peak/spp/pseudo_reps/rep1/pr2/SRR372712_SRR372713.nodup.pr2.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/peak/spp/pseudo_reps/rep1/pr2/SRR372712_SRR372713.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/SRR372712_SRR372713/out/peak/spp/pseudo_reps/rep1/pr2/SRR372712_SRR372713.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/SRR372712_SRR372713/out/peak/spp/pseudo_reps/rep1/pr2/SRR372712_SRR372713.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/SRR372712_SRR372713/out/peak/spp/pseudo_reps/rep1/pr2/SRR372712_SRR372713.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--------------------
11548 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/align/pseudo_reps/rep1/pr2/SRR372712_SRR372713.nodup.pr2.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 95 
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/SRR372712_SRR372713/out/peak/spp/pseudo_reps/rep1/pr2 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/peak/spp/pseudo_reps/rep1/pr2/SRR372712_SRR372713.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/SRR372712_SRR372713/out/peak/spp/pseudo_reps/rep1/pr2/SRR372712_SRR372713.nodup.pr2.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/peak/spp/pseudo_reps/rep1/pr2/SRR372712_SRR372713.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/SRR372712_SRR372713/out/align/pseudo_reps/rep1/pr2/SRR372712_SRR372713.nodup.pr2.tagAlign.gz 
opened /tmp/3399.1.q/Rtmp1PdZxC/SRR372712_SRR372713.nodup.pr2.tagAlign2de538d080ed
done. read 7427364 fragments
ChIP data read length 36 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz 
opened /tmp/3399.1.q/Rtmp1PdZxC/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign2de57ddbe266
done. read 3384182 fragments
Control data read length 50 
Calculating peak characteristics
Minimum cross-correlation value 0.09440047 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.328348244377004 
Top 3 estimates for fragment length 95 
Window half size 195 
Phantom peak location 40 
Phantom peak Correlation 0.2400284 
Normalized Strand cross-correlation coefficient (NSC) 3.478248 
Relative Strand cross-correlation Coefficient (RSC) 1.606476 
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= 0.6291337  
 
--------------------Stderr--------------------
Loading required package: caTools
Warning message:
package ‘caTools’ was built under R version 3.2.3 

 
 		 

	






	
 Global scope 

	Note: Global scope when program finished execution.
	

	
  Type  Name  Value  

	
  string{}  fraglen  {1=95}  

	
  string  fraglen_mean  95  

	
  string  fraglen_ppr1    

	
  string  fraglen_ppr2    

	
  string{}  fraglen_pr1  {1=95}  

	
  string{}  fraglen_pr2  {1=95}  

	
  real  fraglen_sum  95.0  

	
  string  macs2_o_dir  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/peak/macs2  

	
  string  macs2_sig_o_dir  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/signal/macs2  

	
  int  nth_other  1  

	
  int  nth_pooled  2  

	
  real  num_rep_real  1.0  

	
  string  spp_o_dir  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/peak/spp  

	
  string{}  tag_ctl  {1=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz, pooled=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz}  

	
  string{}  tag_ctl_label  {}  

	
  string[]  tags  [/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/align/rep1/SRR372712_SRR372713.nodup.tagAlign.gz]  

	
  string[]  tags_ctl  [/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz]  

	
  string[]  tags_pr1  [/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/align/pseudo_reps/rep1/pr1/SRR372712_SRR372713.nodup.pr1.tagAlign.gz]  

	
  string[]  tags_pr2  [/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/align/pseudo_reps/rep1/pr2/SRR372712_SRR372713.nodup.pr2.tagAlign.gz]  

	
  string  tmp  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR372712_SRR372713/out/peak/spp/pseudo_reps/rep1/pr2/SRR372712_SRR372713.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.ccscore