BigDataScript report: chipseq.bds

Script file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20170413_183753_598
Start time 2017-04-13 18:37:53
Run time 00:12:25.757
Tasks executed 7
Tasks failed 0
Tasks failed names 
 

		
  Arguments*  [-title, KLF14_MACS2, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/KLF14_MACS2/out, -tag1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/align/rep1/SRR1370885_1.nodup.tagAlign.gz, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz, -histone, $] 

		
  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.20170413_183753_598/task.callpeak_macs2.macs2_g_b_rep1.line_155.id_10
chipseq.bds.20170413_183753_598/task.callpeak_macs2.macs2_g_b_rep1_pr1.line_155.id_11
chipseq.bds.20170413_183753_598/task.callpeak_macs2.macs2_g_b_rep1_pr2.line_155.id_12
chipseq.bds.20170413_183753_598/task.callpeak_naive_overlap.naive_overlap.line_59.id_13
chipseq.bds.20170413_183753_598/task.callpeak_naive_overlap.naive_overlap.line_59.id_14
chipseq.bds.20170413_183753_598/task.report.peak2hammock.line_361.id_17
chipseq.bds.20170413_183753_598/task.graphviz.report.line_97.id_18
 
 		 

	
  thread_41   thread_Root 	 
  
 		 

	
  thread_42   thread_Root 	 
  
 		 

	






	
 Task details 

	

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

    
  
 
  Num   1  
 
  ID   task.callpeak_macs2.macs2_g_b_rep1.line_155.id_10  
 
  Name   macs2 g/b rep1 
 
  Thread   thread_Root  
 
  PID   46989  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 18:37:59  
 
  End   2017-04-13 18:48:06  
 
  Elapsed   00:10:06  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/align/rep1/SRR1370885_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/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 157

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 158

 export LC_COLLATE=C

# SYS command. line 163

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/align/rep1/SRR1370885_1.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all

# SYS command. line 166

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz

# SYS command. line 167

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 170

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 175

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
14319 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 18:38:16: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/align/rep1/SRR1370885_1.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/align/rep1/SRR1370885_1.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Thu, 13 Apr 2017 18:38:16: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 18:38:16: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 18:38:18:  1000000 
INFO  @ Thu, 13 Apr 2017 18:38:20:  2000000 
INFO  @ Thu, 13 Apr 2017 18:38:22:  3000000 
INFO  @ Thu, 13 Apr 2017 18:38:23:  4000000 
INFO  @ Thu, 13 Apr 2017 18:38:25:  5000000 
INFO  @ Thu, 13 Apr 2017 18:38:26:  6000000 
INFO  @ Thu, 13 Apr 2017 18:38:28:  7000000 
INFO  @ Thu, 13 Apr 2017 18:38:30:  8000000 
INFO  @ Thu, 13 Apr 2017 18:38:31:  9000000 
INFO  @ Thu, 13 Apr 2017 18:38:33:  10000000 
INFO  @ Thu, 13 Apr 2017 18:38:34:  11000000 
INFO  @ Thu, 13 Apr 2017 18:38:36:  12000000 
INFO  @ Thu, 13 Apr 2017 18:38:37:  13000000 
INFO  @ Thu, 13 Apr 2017 18:38:39:  14000000 
INFO  @ Thu, 13 Apr 2017 18:38:40: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 18:38:41:  1000000 
INFO  @ Thu, 13 Apr 2017 18:38:43:  2000000 
INFO  @ Thu, 13 Apr 2017 18:38:44:  3000000 
INFO  @ Thu, 13 Apr 2017 18:38:46:  4000000 
INFO  @ Thu, 13 Apr 2017 18:38:48:  5000000 
INFO  @ Thu, 13 Apr 2017 18:38:49:  6000000 
INFO  @ Thu, 13 Apr 2017 18:38:51:  7000000 
INFO  @ Thu, 13 Apr 2017 18:38:52:  8000000 
INFO  @ Thu, 13 Apr 2017 18:38:54:  9000000 
INFO  @ Thu, 13 Apr 2017 18:38:55:  10000000 
INFO  @ Thu, 13 Apr 2017 18:38:57:  11000000 
INFO  @ Thu, 13 Apr 2017 18:38:58:  12000000 
INFO  @ Thu, 13 Apr 2017 18:39:00:  13000000 
INFO  @ Thu, 13 Apr 2017 18:39:01:  14000000 
INFO  @ Thu, 13 Apr 2017 18:39:03:  15000000 
INFO  @ Thu, 13 Apr 2017 18:39:05:  16000000 
INFO  @ Thu, 13 Apr 2017 18:39:06:  17000000 
INFO  @ Thu, 13 Apr 2017 18:39:08:  18000000 
INFO  @ Thu, 13 Apr 2017 18:39:09:  19000000 
INFO  @ Thu, 13 Apr 2017 18:39:11:  20000000 
INFO  @ Thu, 13 Apr 2017 18:39:12:  21000000 
INFO  @ Thu, 13 Apr 2017 18:39:14:  22000000 
INFO  @ Thu, 13 Apr 2017 18:39:15:  23000000 
INFO  @ Thu, 13 Apr 2017 18:39:17:  24000000 
INFO  @ Thu, 13 Apr 2017 18:39:18:  25000000 
INFO  @ Thu, 13 Apr 2017 18:39:20:  26000000 
INFO  @ Thu, 13 Apr 2017 18:39:21:  27000000 
INFO  @ Thu, 13 Apr 2017 18:39:23:  28000000 
INFO  @ Thu, 13 Apr 2017 18:39:24:  29000000 
INFO  @ Thu, 13 Apr 2017 18:39:26:  30000000 
INFO  @ Thu, 13 Apr 2017 18:39:27:  31000000 
INFO  @ Thu, 13 Apr 2017 18:39:29:  32000000 
INFO  @ Thu, 13 Apr 2017 18:39:31:  33000000 
INFO  @ Thu, 13 Apr 2017 18:39:32:  34000000 
INFO  @ Thu, 13 Apr 2017 18:39:34:  35000000 
INFO  @ Thu, 13 Apr 2017 18:39:35:  36000000 
INFO  @ Thu, 13 Apr 2017 18:39:37:  37000000 
INFO  @ Thu, 13 Apr 2017 18:39:38:  38000000 
INFO  @ Thu, 13 Apr 2017 18:39:40:  39000000 
INFO  @ Thu, 13 Apr 2017 18:39:41:  40000000 
INFO  @ Thu, 13 Apr 2017 18:39:43:  41000000 
INFO  @ Thu, 13 Apr 2017 18:39:44:  42000000 
INFO  @ Thu, 13 Apr 2017 18:39:46:  43000000 
INFO  @ Thu, 13 Apr 2017 18:39:47:  44000000 
INFO  @ Thu, 13 Apr 2017 18:39:49:  45000000 
INFO  @ Thu, 13 Apr 2017 18:39:50:  46000000 
INFO  @ Thu, 13 Apr 2017 18:39:52:  47000000 
INFO  @ Thu, 13 Apr 2017 18:39:53:  48000000 
INFO  @ Thu, 13 Apr 2017 18:39:55:  49000000 
INFO  @ Thu, 13 Apr 2017 18:39:56:  50000000 
INFO  @ Thu, 13 Apr 2017 18:39:58: #1 tag size is determined as 68 bps 
INFO  @ Thu, 13 Apr 2017 18:39:58: #1 tag size = 68 
INFO  @ Thu, 13 Apr 2017 18:39:58: #1  total tags in treatment: 14380722 
INFO  @ Thu, 13 Apr 2017 18:39:58: #1  total tags in control: 50000000 
INFO  @ Thu, 13 Apr 2017 18:39:58: #1 finished! 
INFO  @ Thu, 13 Apr 2017 18:39:58: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 18:39:58: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 18:39:58: #2 Use 150 as fragment length 
INFO  @ Thu, 13 Apr 2017 18:39:58: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 18:39:58: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 13 Apr 2017 18:39:58: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 18:44:13: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 18:47:40: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 18:47:45: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Thu, 13 Apr 2017 18:47:48: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 13 Apr 2017 18:47:53: Done! 

 
 		 

    
  
 
  Num   2  
 
  ID   task.callpeak_macs2.macs2_g_b_rep1_pr1.line_155.id_11  
 
  Name   macs2 g/b rep1-pr1 
 
  Thread   thread_Root  
 
  PID   46992  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 18:38:01  
 
  End   2017-04-13 18:47:29  
 
  Elapsed   00:09:27  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/align/pseudo_reps/rep1/pr1/SRR1370885_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/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 157

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 158

 export LC_COLLATE=C

# SYS command. line 163

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/align/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all

# SYS command. line 166

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz

# SYS command. line 167

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 170

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 175

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
14329 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 18:38:16: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/align/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/align/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Thu, 13 Apr 2017 18:38:16: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 18:38:16: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 18:38:18:  1000000 
INFO  @ Thu, 13 Apr 2017 18:38:20:  2000000 
INFO  @ Thu, 13 Apr 2017 18:38:22:  3000000 
INFO  @ Thu, 13 Apr 2017 18:38:23:  4000000 
INFO  @ Thu, 13 Apr 2017 18:38:25:  5000000 
INFO  @ Thu, 13 Apr 2017 18:38:27:  6000000 
INFO  @ Thu, 13 Apr 2017 18:38:28:  7000000 
INFO  @ Thu, 13 Apr 2017 18:38:29: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 18:38:31:  1000000 
INFO  @ Thu, 13 Apr 2017 18:38:32:  2000000 
INFO  @ Thu, 13 Apr 2017 18:38:34:  3000000 
INFO  @ Thu, 13 Apr 2017 18:38:37:  4000000 
INFO  @ Thu, 13 Apr 2017 18:38:38:  5000000 
INFO  @ Thu, 13 Apr 2017 18:38:40:  6000000 
INFO  @ Thu, 13 Apr 2017 18:38:41:  7000000 
INFO  @ Thu, 13 Apr 2017 18:38:43:  8000000 
INFO  @ Thu, 13 Apr 2017 18:38:44:  9000000 
INFO  @ Thu, 13 Apr 2017 18:38:46:  10000000 
INFO  @ Thu, 13 Apr 2017 18:38:47:  11000000 
INFO  @ Thu, 13 Apr 2017 18:38:49:  12000000 
INFO  @ Thu, 13 Apr 2017 18:38:51:  13000000 
INFO  @ Thu, 13 Apr 2017 18:38:52:  14000000 
INFO  @ Thu, 13 Apr 2017 18:38:54:  15000000 
INFO  @ Thu, 13 Apr 2017 18:38:55:  16000000 
INFO  @ Thu, 13 Apr 2017 18:38:57:  17000000 
INFO  @ Thu, 13 Apr 2017 18:38:59:  18000000 
INFO  @ Thu, 13 Apr 2017 18:39:00:  19000000 
INFO  @ Thu, 13 Apr 2017 18:39:02:  20000000 
INFO  @ Thu, 13 Apr 2017 18:39:03:  21000000 
INFO  @ Thu, 13 Apr 2017 18:39:05:  22000000 
INFO  @ Thu, 13 Apr 2017 18:39:06:  23000000 
INFO  @ Thu, 13 Apr 2017 18:39:08:  24000000 
INFO  @ Thu, 13 Apr 2017 18:39:10:  25000000 
INFO  @ Thu, 13 Apr 2017 18:39:11:  26000000 
INFO  @ Thu, 13 Apr 2017 18:39:13:  27000000 
INFO  @ Thu, 13 Apr 2017 18:39:14:  28000000 
INFO  @ Thu, 13 Apr 2017 18:39:16:  29000000 
INFO  @ Thu, 13 Apr 2017 18:39:18:  30000000 
INFO  @ Thu, 13 Apr 2017 18:39:19:  31000000 
INFO  @ Thu, 13 Apr 2017 18:39:21:  32000000 
INFO  @ Thu, 13 Apr 2017 18:39:22:  33000000 
INFO  @ Thu, 13 Apr 2017 18:39:24:  34000000 
INFO  @ Thu, 13 Apr 2017 18:39:26:  35000000 
INFO  @ Thu, 13 Apr 2017 18:39:27:  36000000 
INFO  @ Thu, 13 Apr 2017 18:39:29:  37000000 
INFO  @ Thu, 13 Apr 2017 18:39:30:  38000000 
INFO  @ Thu, 13 Apr 2017 18:39:32:  39000000 
INFO  @ Thu, 13 Apr 2017 18:39:33:  40000000 
INFO  @ Thu, 13 Apr 2017 18:39:35:  41000000 
INFO  @ Thu, 13 Apr 2017 18:39:36:  42000000 
INFO  @ Thu, 13 Apr 2017 18:39:38:  43000000 
INFO  @ Thu, 13 Apr 2017 18:39:40:  44000000 
INFO  @ Thu, 13 Apr 2017 18:39:41:  45000000 
INFO  @ Thu, 13 Apr 2017 18:39:43:  46000000 
INFO  @ Thu, 13 Apr 2017 18:39:44:  47000000 
INFO  @ Thu, 13 Apr 2017 18:39:46:  48000000 
INFO  @ Thu, 13 Apr 2017 18:39:47:  49000000 
INFO  @ Thu, 13 Apr 2017 18:39:49:  50000000 
INFO  @ Thu, 13 Apr 2017 18:39:51: #1 tag size is determined as 67 bps 
INFO  @ Thu, 13 Apr 2017 18:39:51: #1 tag size = 67 
INFO  @ Thu, 13 Apr 2017 18:39:51: #1  total tags in treatment: 7190361 
INFO  @ Thu, 13 Apr 2017 18:39:51: #1  total tags in control: 50000000 
INFO  @ Thu, 13 Apr 2017 18:39:51: #1 finished! 
INFO  @ Thu, 13 Apr 2017 18:39:51: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 18:39:51: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 18:39:51: #2 Use 150 as fragment length 
INFO  @ Thu, 13 Apr 2017 18:39:51: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 18:39:51: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 13 Apr 2017 18:39:51: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 18:43:35: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 18:46:54: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 18:47:02: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Thu, 13 Apr 2017 18:47:08: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 13 Apr 2017 18:47:12: Done! 

 
 		 

    
  
 
  Num   3  
 
  ID   task.callpeak_macs2.macs2_g_b_rep1_pr2.line_155.id_12  
 
  Name   macs2 g/b rep1-pr2 
 
  Thread   thread_Root  
 
  PID   46994  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 18:38:02  
 
  End   2017-04-13 18:48:28  
 
  Elapsed   00:10:25  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/align/pseudo_reps/rep1/pr2/SRR1370885_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/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 157

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 158

 export LC_COLLATE=C

# SYS command. line 163

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/align/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all

# SYS command. line 166

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz

# SYS command. line 167

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 170

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 175

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
14330 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 18:38:16: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/align/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/align/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Thu, 13 Apr 2017 18:38:16: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 18:38:16: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 18:38:18:  1000000 
INFO  @ Thu, 13 Apr 2017 18:38:20:  2000000 
INFO  @ Thu, 13 Apr 2017 18:38:22:  3000000 
INFO  @ Thu, 13 Apr 2017 18:38:24:  4000000 
INFO  @ Thu, 13 Apr 2017 18:38:26:  5000000 
INFO  @ Thu, 13 Apr 2017 18:38:27:  6000000 
INFO  @ Thu, 13 Apr 2017 18:38:29:  7000000 
INFO  @ Thu, 13 Apr 2017 18:38:30: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 18:38:31:  1000000 
INFO  @ Thu, 13 Apr 2017 18:38:33:  2000000 
INFO  @ Thu, 13 Apr 2017 18:38:35:  3000000 
INFO  @ Thu, 13 Apr 2017 18:38:36:  4000000 
INFO  @ Thu, 13 Apr 2017 18:38:38:  5000000 
INFO  @ Thu, 13 Apr 2017 18:38:39:  6000000 
INFO  @ Thu, 13 Apr 2017 18:38:41:  7000000 
INFO  @ Thu, 13 Apr 2017 18:38:42:  8000000 
INFO  @ Thu, 13 Apr 2017 18:38:44:  9000000 
INFO  @ Thu, 13 Apr 2017 18:38:46:  10000000 
INFO  @ Thu, 13 Apr 2017 18:38:47:  11000000 
INFO  @ Thu, 13 Apr 2017 18:38:49:  12000000 
INFO  @ Thu, 13 Apr 2017 18:38:50:  13000000 
INFO  @ Thu, 13 Apr 2017 18:38:52:  14000000 
INFO  @ Thu, 13 Apr 2017 18:38:54:  15000000 
INFO  @ Thu, 13 Apr 2017 18:38:55:  16000000 
INFO  @ Thu, 13 Apr 2017 18:38:57:  17000000 
INFO  @ Thu, 13 Apr 2017 18:38:58:  18000000 
INFO  @ Thu, 13 Apr 2017 18:39:00:  19000000 
INFO  @ Thu, 13 Apr 2017 18:39:01:  20000000 
INFO  @ Thu, 13 Apr 2017 18:39:03:  21000000 
INFO  @ Thu, 13 Apr 2017 18:39:05:  22000000 
INFO  @ Thu, 13 Apr 2017 18:39:06:  23000000 
INFO  @ Thu, 13 Apr 2017 18:39:08:  24000000 
INFO  @ Thu, 13 Apr 2017 18:39:09:  25000000 
INFO  @ Thu, 13 Apr 2017 18:39:11:  26000000 
INFO  @ Thu, 13 Apr 2017 18:39:12:  27000000 
INFO  @ Thu, 13 Apr 2017 18:39:14:  28000000 
INFO  @ Thu, 13 Apr 2017 18:39:15:  29000000 
INFO  @ Thu, 13 Apr 2017 18:39:17:  30000000 
INFO  @ Thu, 13 Apr 2017 18:39:19:  31000000 
INFO  @ Thu, 13 Apr 2017 18:39:20:  32000000 
INFO  @ Thu, 13 Apr 2017 18:39:22:  33000000 
INFO  @ Thu, 13 Apr 2017 18:39:23:  34000000 
INFO  @ Thu, 13 Apr 2017 18:39:25:  35000000 
INFO  @ Thu, 13 Apr 2017 18:39:26:  36000000 
INFO  @ Thu, 13 Apr 2017 18:39:28:  37000000 
INFO  @ Thu, 13 Apr 2017 18:39:30:  38000000 
INFO  @ Thu, 13 Apr 2017 18:39:31:  39000000 
INFO  @ Thu, 13 Apr 2017 18:39:33:  40000000 
INFO  @ Thu, 13 Apr 2017 18:39:34:  41000000 
INFO  @ Thu, 13 Apr 2017 18:39:36:  42000000 
INFO  @ Thu, 13 Apr 2017 18:39:37:  43000000 
INFO  @ Thu, 13 Apr 2017 18:39:39:  44000000 
INFO  @ Thu, 13 Apr 2017 18:39:41:  45000000 
INFO  @ Thu, 13 Apr 2017 18:39:42:  46000000 
INFO  @ Thu, 13 Apr 2017 18:39:44:  47000000 
INFO  @ Thu, 13 Apr 2017 18:39:45:  48000000 
INFO  @ Thu, 13 Apr 2017 18:39:47:  49000000 
INFO  @ Thu, 13 Apr 2017 18:39:48:  50000000 
INFO  @ Thu, 13 Apr 2017 18:39:50: #1 tag size is determined as 68 bps 
INFO  @ Thu, 13 Apr 2017 18:39:50: #1 tag size = 68 
INFO  @ Thu, 13 Apr 2017 18:39:50: #1  total tags in treatment: 7190361 
INFO  @ Thu, 13 Apr 2017 18:39:50: #1  total tags in control: 50000000 
INFO  @ Thu, 13 Apr 2017 18:39:50: #1 finished! 
INFO  @ Thu, 13 Apr 2017 18:39:50: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 18:39:50: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 18:39:50: #2 Use 150 as fragment length 
INFO  @ Thu, 13 Apr 2017 18:39:50: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 18:39:50: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 13 Apr 2017 18:39:50: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 18:43:54: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 18:47:54: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 18:48:00: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Thu, 13 Apr 2017 18:48:05: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 13 Apr 2017 18:48:10: Done! 

 
 		 

    
  
 
  Num   4  
 
  ID   task.callpeak_naive_overlap.naive_overlap.line_59.id_13  
 
  Name   naive_overlap  
 
  Thread   thread_Root  
 
  PID   47007  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 18:48:30  
 
  End   2017-04-13 18:49:46  
 
  Elapsed   00:01:15  
 
  Timeout  01:00:00 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/overlap/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.gappedPeak.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 61

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 64

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz) | \
			awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$18-$17; if (($31/s1 >= 0.5) || ($31/s2 >= 0.5)) {print $0}}' | cut -f 1-15 | sort | uniq | \
			intersectBed  -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz) | \
			awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$18-$17; if (($31/s1 >= 0.5) || ($31/s2 >= 0.5)) {print $0}}' | cut -f 1-15 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/overlap/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.gappedPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/overlap/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.gappedPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/overlap/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.gappedPeak.gz

# SYS command. line 72

 bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/overlap/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.gappedPeak.gz) -b <(zcat -f /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz)  | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/overlap/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.gappedPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/overlap/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.gappedPeak.gz

# SYS command. line 76

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
18372 (process ID) old priority 0, new priority 19
Waiting for 22 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270733.1	140397	140547	Peak_953	74	.	140397	140547	0	2	1,1	0,149	6.53107	10.20611	7.44867

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270733.1	140397	140547	Peak_953	74	.	140397	140547	0	2	1,1	0,149	6.53107	10.20611	7.44867

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270905.1	1842373	1842523	Peak_7824	21	.	1842373	1842523	0	2	1,1	0,149	3.57280	4.41378	2.14729

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270905.1	1842373	1842523	Peak_7824	21	.	1842373	1842523	0	2	1,1	0,149	3.57280	4.41378	2.14729

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL000009.2	124703	124998	Peak_148643	2	.	124703	124998	0	3	1,285,1	0,9,294	1.45661	1.25423	0.24571

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL000009.2	124703	124998	Peak_148643	2	.	124703	124998	0	3	1,285,1	0,9,294	1.45661	1.25423	0.24571


 
 		 

    
  
 
  Num   5  
 
  ID   task.callpeak_naive_overlap.naive_overlap.line_59.id_14  
 
  Name   naive_overlap  
 
  Thread   thread_Root  
 
  PID   47008  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 18:48:31  
 
  End   2017-04-13 18:49:46  
 
  Elapsed   00:01:15  
 
  Timeout  01:00:00 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/overlap/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.broadPeak.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 61

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 64

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/rep1/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370885_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz) | \
			awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$12-$11; if (($19/s1 >= 0.5) || ($19/s2 >= 0.5)) {print $0}}' | cut -f 1-9 | sort | uniq | \
			intersectBed  -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370885_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz) | \
			awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$12-$11; if (($19/s1 >= 0.5) || ($19/s2 >= 0.5)) {print $0}}' | cut -f 1-9 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/overlap/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.broadPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/overlap/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.broadPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/overlap/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.broadPeak.gz

# SYS command. line 72

 bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/overlap/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.broadPeak.gz) -b <(zcat -f /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz)  | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/overlap/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.broadPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/overlap/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.broadPeak.gz

# SYS command. line 76

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
18381 (process ID) old priority 0, new priority 19
Waiting for 32 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270733.1	140397	140547	Peak_953	74	.	6.53107	10.20611	7.44867

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270733.1	140397	140547	Peak_953	74	.	6.53107	10.20611	7.44867

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270905.1	1842373	1842523	Peak_7824	21	.	3.57280	4.41378	2.14729

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270905.1	1842373	1842523	Peak_7824	21	.	3.57280	4.41378	2.14729

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL000009.2	124703	124998	Peak_148643	2	.	1.45661	1.25423	0.24571

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL000009.2	124703	124998	Peak_148643	2	.	1.45661	1.25423	0.24571


 
 		 

    
  
 
  Num   6  
 
  ID   task.report.peak2hammock.line_361.id_17  
 
  Name   peak2hammock 
 
  Thread   thread_Root  
 
  PID   19728  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 18:49:48  
 
  End   2017-04-13 18:50:09  
 
  Elapsed   00:00:21  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/overlap/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.gappedPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/overlap/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.gappedPeak.hammock.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 363

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 364

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/overlap/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.gappedPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/overlap/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.gappedPeak.tmp

# SYS command. line 366

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/gappedpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/overlap/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.gappedPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/overlap/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.gappedPeak.hammock

# SYS command. line 367

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/peak/macs2/overlap/SRR1370885_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.gappedPeak.tmp
 
 
   
--------------------Stdout--------------------
19732 (process ID) old priority 0, new priority 19

  
 		 

    
  
 
  Num   7  
 
  ID   task.graphviz.report.line_97.id_18  
 
  Name   report 
 
  Thread   thread_Root  
 
  PID   20735  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 18:50:10  
 
  End   2017-04-13 18:50:19  
 
  Elapsed   00:00:08  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files     
 
  Output files     
 
  Dependencies     
 
 		  
 
# SYS command. line 98

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 99

 dot -Tsvg /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/report/KLF14_MACS2_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/report/KLF14_MACS2_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2/out/report/KLF14_MACS2_workflow.svg" # to suppress dot font error (exit code=1)
 
 
   
--------------------Stdout--------------------
20739 (process ID) old priority 0, new priority 19

  
 		 

	






	
 Global scope 

	Note: Global scope when program finished execution.
	

	
  Type  Name  Value  

	
  string  _  /usr/bin/bds  

	
  bool  allowEmpty  false  

	
  string[]  args  [-title, KLF14_MACS2, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/KLF14_MACS2/out, -tag1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14/out/align/rep1/SRR1370885_1.nodup.tagAlign.gz, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz, -histone, $]  

	
  bool  canFail  false  

	
  string  CPATH  /users/imk1/anaconda2/pkgs/gsl-1.16-1/include  

	
  int  cpus  -1  

	
  int  cpusLocal  56  

	
  int  day  86400  

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

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

	
  string  DISPLAY  localhost:12.0  

	
  real  E  2.718281828459045  

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

	
  string  EVENT_NOEPOLL  1  

	
  int  G  1073741824  

	
  string  HOME  /users/imk1/  

	
  int  hour  3600  

	
  string  J2REDIR  /usr/lib/jvm/java-8-oracle/jre  

	
  string  J2SDKDIR  /usr/lib/jvm/java-8-oracle  

	
  string  JAVA_HOME  /usr/lib/jvm/java-8-oracle  

	
  int  K  1024  

	
  string  KERAS_DIR  /users/imk1/.local/lib/python2.7/site-packages/keras/  

	
  string  KRB5CCNAME  FILE:/tmp/krb5cc_1048_CCx82k  

	
  string  LANG  en_US.UTF-8  

	
  string  LIBRARY_PATH  /users/imk1/anaconda2/pkgs/gsl-1.16-1/lib  

	
  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  /users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/scratch/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:/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:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/av_scripts//exec:/users/imk1/edirect:/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  

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

	
  string  PERL_LOCAL_LIB_ROOT  /users/imk1/perl5  

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

	
  string  PERL_MM_OPT  INSTALL_BASE=/users/imk1/perl5  

	
  real  PI  3.141592653589793  

	
  string  ppwd  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/KLF14_MACS2  

	
  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/KLF14_MACS2  

	
  string  PYTHONPATH  /users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/  

	
  string  queue    

	
  int  retry  0  

	
  string  RULEFITBASE  /srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/  

	
  string  SHELL  /bin/bash  

	
  string  SHLVL  4  

	
  string  SSH_CLIENT  171.65.77.8 57066 22  

	
  string  SSH_CONNECTION  171.65.77.8 57067 171.65.76.63 22  

	
  string  SSH_TTY  /dev/pts/4  

	
  string  STY  47181.KLF14_MACS2.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  TMUX  /tmp/tmux-1048/default,43619,2  

	
  string  TMUX_PANE  %2  

	
  string  USER  imk1  

	
  string  UTIL_SCRIPTS_DIR  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/av_scripts/  

	
  int  walltimeout  8640000  

	
  int  week  604800  

	
  string  WINDOW  0  

	
  string  XDG_RUNTIME_DIR  /run/user/1048  

	
  string  XDG_SESSION_ID  67062  

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