BigDataScript report: chipseq.bds

Script file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20170413_183759_527
Start time 2017-04-13 18:37:59
Run time 00:09:44.848
Tasks executed 7
Tasks failed 0
Tasks failed names 
 

		
  Arguments*  [-title, ZNF467_MACS2, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF467_MACS2/out, -tag1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/align/rep1/SRR1370886_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_183759_527/task.callpeak_macs2.macs2_g_b_rep1.line_155.id_10
chipseq.bds.20170413_183759_527/task.callpeak_macs2.macs2_g_b_rep1_pr1.line_155.id_11
chipseq.bds.20170413_183759_527/task.callpeak_macs2.macs2_g_b_rep1_pr2.line_155.id_12
chipseq.bds.20170413_183759_527/task.callpeak_naive_overlap.naive_overlap.line_59.id_13
chipseq.bds.20170413_183759_527/task.callpeak_naive_overlap.naive_overlap.line_59.id_14
chipseq.bds.20170413_183759_527/task.report.peak2hammock.line_361.id_17
chipseq.bds.20170413_183759_527/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   46997  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 18:38:07  
 
  End   2017-04-13 18:45:59  
 
  Elapsed   00:07:51  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/align/rep1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_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/ZNF467/out/align/rep1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all

# SYS command. line 166

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 170

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_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--------------------
14927 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 18:38:31: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/align/rep1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/align/rep1/SRR1370886_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 18:38:31: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 18:38:31: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 18:38:33:  1000000 
INFO  @ Thu, 13 Apr 2017 18:38:35:  2000000 
INFO  @ Thu, 13 Apr 2017 18:38:37:  3000000 
INFO  @ Thu, 13 Apr 2017 18:38:39:  4000000 
INFO  @ Thu, 13 Apr 2017 18:38:41:  5000000 
INFO  @ Thu, 13 Apr 2017 18:38:42:  6000000 
INFO  @ Thu, 13 Apr 2017 18:38:44:  7000000 
INFO  @ Thu, 13 Apr 2017 18:38:46:  8000000 
INFO  @ Thu, 13 Apr 2017 18:38:47:  9000000 
INFO  @ Thu, 13 Apr 2017 18:38:49:  10000000 
INFO  @ Thu, 13 Apr 2017 18:38:51:  11000000 
INFO  @ Thu, 13 Apr 2017 18:38:53:  12000000 
INFO  @ Thu, 13 Apr 2017 18:38:54:  13000000 
INFO  @ Thu, 13 Apr 2017 18:38:56:  14000000 
INFO  @ Thu, 13 Apr 2017 18:38:58:  15000000 
INFO  @ Thu, 13 Apr 2017 18:38:59:  16000000 
INFO  @ Thu, 13 Apr 2017 18:39:01:  17000000 
INFO  @ Thu, 13 Apr 2017 18:39:03:  18000000 
INFO  @ Thu, 13 Apr 2017 18:39:04: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 18:39:06:  1000000 
INFO  @ Thu, 13 Apr 2017 18:39:07:  2000000 
INFO  @ Thu, 13 Apr 2017 18:39:09:  3000000 
INFO  @ Thu, 13 Apr 2017 18:39:11:  4000000 
INFO  @ Thu, 13 Apr 2017 18:39:12:  5000000 
INFO  @ Thu, 13 Apr 2017 18:39:14:  6000000 
INFO  @ Thu, 13 Apr 2017 18:39:16:  7000000 
INFO  @ Thu, 13 Apr 2017 18:39:18:  8000000 
INFO  @ Thu, 13 Apr 2017 18:39:19:  9000000 
INFO  @ Thu, 13 Apr 2017 18:39:21:  10000000 
INFO  @ Thu, 13 Apr 2017 18:39:23:  11000000 
INFO  @ Thu, 13 Apr 2017 18:39:24:  12000000 
INFO  @ Thu, 13 Apr 2017 18:39:26:  13000000 
INFO  @ Thu, 13 Apr 2017 18:39:28:  14000000 
INFO  @ Thu, 13 Apr 2017 18:39:30:  15000000 
INFO  @ Thu, 13 Apr 2017 18:39:31:  16000000 
INFO  @ Thu, 13 Apr 2017 18:39:33:  17000000 
INFO  @ Thu, 13 Apr 2017 18:39:35:  18000000 
INFO  @ Thu, 13 Apr 2017 18:39:36:  19000000 
INFO  @ Thu, 13 Apr 2017 18:39:38:  20000000 
INFO  @ Thu, 13 Apr 2017 18:39:40:  21000000 
INFO  @ Thu, 13 Apr 2017 18:39:42:  22000000 
INFO  @ Thu, 13 Apr 2017 18:39:43:  23000000 
INFO  @ Thu, 13 Apr 2017 18:39:45:  24000000 
INFO  @ Thu, 13 Apr 2017 18:39:48:  25000000 
INFO  @ Thu, 13 Apr 2017 18:39:50:  26000000 
INFO  @ Thu, 13 Apr 2017 18:39:52:  27000000 
INFO  @ Thu, 13 Apr 2017 18:39:53:  28000000 
INFO  @ Thu, 13 Apr 2017 18:39:55:  29000000 
INFO  @ Thu, 13 Apr 2017 18:39:57:  30000000 
INFO  @ Thu, 13 Apr 2017 18:39:59:  31000000 
INFO  @ Thu, 13 Apr 2017 18:40:00:  32000000 
INFO  @ Thu, 13 Apr 2017 18:40:02:  33000000 
INFO  @ Thu, 13 Apr 2017 18:40:04:  34000000 
INFO  @ Thu, 13 Apr 2017 18:40:06:  35000000 
INFO  @ Thu, 13 Apr 2017 18:40:07:  36000000 
INFO  @ Thu, 13 Apr 2017 18:40:09:  37000000 
INFO  @ Thu, 13 Apr 2017 18:40:11:  38000000 
INFO  @ Thu, 13 Apr 2017 18:40:13:  39000000 
INFO  @ Thu, 13 Apr 2017 18:40:14:  40000000 
INFO  @ Thu, 13 Apr 2017 18:40:16:  41000000 
INFO  @ Thu, 13 Apr 2017 18:40:18:  42000000 
INFO  @ Thu, 13 Apr 2017 18:40:20:  43000000 
INFO  @ Thu, 13 Apr 2017 18:40:21:  44000000 
INFO  @ Thu, 13 Apr 2017 18:40:23:  45000000 
INFO  @ Thu, 13 Apr 2017 18:40:25:  46000000 
INFO  @ Thu, 13 Apr 2017 18:40:27:  47000000 
INFO  @ Thu, 13 Apr 2017 18:40:28:  48000000 
INFO  @ Thu, 13 Apr 2017 18:40:30:  49000000 
INFO  @ Thu, 13 Apr 2017 18:40:32:  50000000 
INFO  @ Thu, 13 Apr 2017 18:40:34: #1 tag size is determined as 49 bps 
INFO  @ Thu, 13 Apr 2017 18:40:34: #1 tag size = 49 
INFO  @ Thu, 13 Apr 2017 18:40:34: #1  total tags in treatment: 18384762 
INFO  @ Thu, 13 Apr 2017 18:40:34: #1  total tags in control: 50000000 
INFO  @ Thu, 13 Apr 2017 18:40:34: #1 finished! 
INFO  @ Thu, 13 Apr 2017 18:40:34: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 18:40:34: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 18:40:34: #2 Use 145 as fragment length 
INFO  @ Thu, 13 Apr 2017 18:40:34: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 18:40:34: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 13 Apr 2017 18:40:34: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 18:43:10: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 18:45:37: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 18:45:42: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Thu, 13 Apr 2017 18:45:46: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 13 Apr 2017 18:45:49: 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   46999  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 18:38:11  
 
  End   2017-04-13 18:45:55  
 
  Elapsed   00:07:44  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/align/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467_MACS2/out/align/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all

# SYS command. line 166

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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--------------------
14928 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 18:38:31: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/align/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/align/pseudo_reps/rep1/pr1/SRR1370886_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 18:38:31: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 18:38:31: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 18:38:33:  1000000 
INFO  @ Thu, 13 Apr 2017 18:38:35:  2000000 
INFO  @ Thu, 13 Apr 2017 18:38:37:  3000000 
INFO  @ Thu, 13 Apr 2017 18:38:39:  4000000 
INFO  @ Thu, 13 Apr 2017 18:38:41:  5000000 
INFO  @ Thu, 13 Apr 2017 18:38:43:  6000000 
INFO  @ Thu, 13 Apr 2017 18:38:44:  7000000 
INFO  @ Thu, 13 Apr 2017 18:38:46:  8000000 
INFO  @ Thu, 13 Apr 2017 18:38:48:  9000000 
INFO  @ Thu, 13 Apr 2017 18:38:49: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 18:38:51:  1000000 
INFO  @ Thu, 13 Apr 2017 18:38:53:  2000000 
INFO  @ Thu, 13 Apr 2017 18:38:54:  3000000 
INFO  @ Thu, 13 Apr 2017 18:38:56:  4000000 
INFO  @ Thu, 13 Apr 2017 18:38:58:  5000000 
INFO  @ Thu, 13 Apr 2017 18:39:00:  6000000 
INFO  @ Thu, 13 Apr 2017 18:39:02:  7000000 
INFO  @ Thu, 13 Apr 2017 18:39:03:  8000000 
INFO  @ Thu, 13 Apr 2017 18:39:05:  9000000 
INFO  @ Thu, 13 Apr 2017 18:39:07:  10000000 
INFO  @ Thu, 13 Apr 2017 18:39:09:  11000000 
INFO  @ Thu, 13 Apr 2017 18:39:11:  12000000 
INFO  @ Thu, 13 Apr 2017 18:39:13:  13000000 
INFO  @ Thu, 13 Apr 2017 18:39:14:  14000000 
INFO  @ Thu, 13 Apr 2017 18:39:16:  15000000 
INFO  @ Thu, 13 Apr 2017 18:39:18:  16000000 
INFO  @ Thu, 13 Apr 2017 18:39:20:  17000000 
INFO  @ Thu, 13 Apr 2017 18:39:22:  18000000 
INFO  @ Thu, 13 Apr 2017 18:39:23:  19000000 
INFO  @ Thu, 13 Apr 2017 18:39:25:  20000000 
INFO  @ Thu, 13 Apr 2017 18:39:27:  21000000 
INFO  @ Thu, 13 Apr 2017 18:39:29:  22000000 
INFO  @ Thu, 13 Apr 2017 18:39:30:  23000000 
INFO  @ Thu, 13 Apr 2017 18:39:32:  24000000 
INFO  @ Thu, 13 Apr 2017 18:39:34:  25000000 
INFO  @ Thu, 13 Apr 2017 18:39:36:  26000000 
INFO  @ Thu, 13 Apr 2017 18:39:38:  27000000 
INFO  @ Thu, 13 Apr 2017 18:39:39:  28000000 
INFO  @ Thu, 13 Apr 2017 18:39:41:  29000000 
INFO  @ Thu, 13 Apr 2017 18:39:43:  30000000 
INFO  @ Thu, 13 Apr 2017 18:39:45:  31000000 
INFO  @ Thu, 13 Apr 2017 18:39:47:  32000000 
INFO  @ Thu, 13 Apr 2017 18:39:50:  33000000 
INFO  @ Thu, 13 Apr 2017 18:39:52:  34000000 
INFO  @ Thu, 13 Apr 2017 18:39:53:  35000000 
INFO  @ Thu, 13 Apr 2017 18:39:55:  36000000 
INFO  @ Thu, 13 Apr 2017 18:39:57:  37000000 
INFO  @ Thu, 13 Apr 2017 18:39:59:  38000000 
INFO  @ Thu, 13 Apr 2017 18:40:00:  39000000 
INFO  @ Thu, 13 Apr 2017 18:40:02:  40000000 
INFO  @ Thu, 13 Apr 2017 18:40:04:  41000000 
INFO  @ Thu, 13 Apr 2017 18:40:06:  42000000 
INFO  @ Thu, 13 Apr 2017 18:40:07:  43000000 
INFO  @ Thu, 13 Apr 2017 18:40:09:  44000000 
INFO  @ Thu, 13 Apr 2017 18:40:11:  45000000 
INFO  @ Thu, 13 Apr 2017 18:40:13:  46000000 
INFO  @ Thu, 13 Apr 2017 18:40:15:  47000000 
INFO  @ Thu, 13 Apr 2017 18:40:16:  48000000 
INFO  @ Thu, 13 Apr 2017 18:40:18:  49000000 
INFO  @ Thu, 13 Apr 2017 18:40:20:  50000000 
INFO  @ Thu, 13 Apr 2017 18:40:22: #1 tag size is determined as 50 bps 
INFO  @ Thu, 13 Apr 2017 18:40:22: #1 tag size = 50 
INFO  @ Thu, 13 Apr 2017 18:40:22: #1  total tags in treatment: 9192381 
INFO  @ Thu, 13 Apr 2017 18:40:22: #1  total tags in control: 50000000 
INFO  @ Thu, 13 Apr 2017 18:40:22: #1 finished! 
INFO  @ Thu, 13 Apr 2017 18:40:22: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 18:40:22: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 18:40:22: #2 Use 145 as fragment length 
INFO  @ Thu, 13 Apr 2017 18:40:22: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 18:40:22: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 13 Apr 2017 18:40:22: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 18:42:52: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 18:45:26: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 18:45:32: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Thu, 13 Apr 2017 18:45:37: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 13 Apr 2017 18:45:42: 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   47000  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 18:38:11  
 
  End   2017-04-13 18:45:45  
 
  Elapsed   00:07:33  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/align/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467_MACS2/out/align/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all

# SYS command. line 166

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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--------------------
25187 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 18:38:32: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/align/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/align/pseudo_reps/rep1/pr2/SRR1370886_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 18:38:32: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 18:38:32: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 18:38:34:  1000000 
INFO  @ Thu, 13 Apr 2017 18:38:35:  2000000 
INFO  @ Thu, 13 Apr 2017 18:38:37:  3000000 
INFO  @ Thu, 13 Apr 2017 18:38:39:  4000000 
INFO  @ Thu, 13 Apr 2017 18:38:40:  5000000 
INFO  @ Thu, 13 Apr 2017 18:38:42:  6000000 
INFO  @ Thu, 13 Apr 2017 18:38:43:  7000000 
INFO  @ Thu, 13 Apr 2017 18:38:45:  8000000 
INFO  @ Thu, 13 Apr 2017 18:38:47:  9000000 
INFO  @ Thu, 13 Apr 2017 18:38:47: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 18:38:49:  1000000 
INFO  @ Thu, 13 Apr 2017 18:38:51:  2000000 
INFO  @ Thu, 13 Apr 2017 18:38:52:  3000000 
INFO  @ Thu, 13 Apr 2017 18:38:54:  4000000 
INFO  @ Thu, 13 Apr 2017 18:38:55:  5000000 
INFO  @ Thu, 13 Apr 2017 18:38:57:  6000000 
INFO  @ Thu, 13 Apr 2017 18:38:58:  7000000 
INFO  @ Thu, 13 Apr 2017 18:39:00:  8000000 
INFO  @ Thu, 13 Apr 2017 18:39:02:  9000000 
INFO  @ Thu, 13 Apr 2017 18:39:03:  10000000 
INFO  @ Thu, 13 Apr 2017 18:39:05:  11000000 
INFO  @ Thu, 13 Apr 2017 18:39:06:  12000000 
INFO  @ Thu, 13 Apr 2017 18:39:08:  13000000 
INFO  @ Thu, 13 Apr 2017 18:39:09:  14000000 
INFO  @ Thu, 13 Apr 2017 18:39:11:  15000000 
INFO  @ Thu, 13 Apr 2017 18:39:13:  16000000 
INFO  @ Thu, 13 Apr 2017 18:39:14:  17000000 
INFO  @ Thu, 13 Apr 2017 18:39:16:  18000000 
INFO  @ Thu, 13 Apr 2017 18:39:17:  19000000 
INFO  @ Thu, 13 Apr 2017 18:39:19:  20000000 
INFO  @ Thu, 13 Apr 2017 18:39:20:  21000000 
INFO  @ Thu, 13 Apr 2017 18:39:22:  22000000 
INFO  @ Thu, 13 Apr 2017 18:39:23:  23000000 
INFO  @ Thu, 13 Apr 2017 18:39:25:  24000000 
INFO  @ Thu, 13 Apr 2017 18:39:26:  25000000 
INFO  @ Thu, 13 Apr 2017 18:39:28:  26000000 
INFO  @ Thu, 13 Apr 2017 18:39:29:  27000000 
INFO  @ Thu, 13 Apr 2017 18:39:30:  28000000 
INFO  @ Thu, 13 Apr 2017 18:39:32:  29000000 
INFO  @ Thu, 13 Apr 2017 18:39:33:  30000000 
INFO  @ Thu, 13 Apr 2017 18:39:35:  31000000 
INFO  @ Thu, 13 Apr 2017 18:39:36:  32000000 
INFO  @ Thu, 13 Apr 2017 18:39:38:  33000000 
INFO  @ Thu, 13 Apr 2017 18:39:39:  34000000 
INFO  @ Thu, 13 Apr 2017 18:39:41:  35000000 
INFO  @ Thu, 13 Apr 2017 18:39:42:  36000000 
INFO  @ Thu, 13 Apr 2017 18:39:44:  37000000 
INFO  @ Thu, 13 Apr 2017 18:39:45:  38000000 
INFO  @ Thu, 13 Apr 2017 18:39:47:  39000000 
INFO  @ Thu, 13 Apr 2017 18:39:48:  40000000 
INFO  @ Thu, 13 Apr 2017 18:39:50:  41000000 
INFO  @ Thu, 13 Apr 2017 18:39:52:  42000000 
INFO  @ Thu, 13 Apr 2017 18:39:53:  43000000 
INFO  @ Thu, 13 Apr 2017 18:39:55:  44000000 
INFO  @ Thu, 13 Apr 2017 18:39:56:  45000000 
INFO  @ Thu, 13 Apr 2017 18:39:58:  46000000 
INFO  @ Thu, 13 Apr 2017 18:39:59:  47000000 
INFO  @ Thu, 13 Apr 2017 18:40:01:  48000000 
INFO  @ Thu, 13 Apr 2017 18:40:03:  49000000 
INFO  @ Thu, 13 Apr 2017 18:40:04:  50000000 
INFO  @ Thu, 13 Apr 2017 18:40:06: #1 tag size is determined as 50 bps 
INFO  @ Thu, 13 Apr 2017 18:40:06: #1 tag size = 50 
INFO  @ Thu, 13 Apr 2017 18:40:06: #1  total tags in treatment: 9192381 
INFO  @ Thu, 13 Apr 2017 18:40:06: #1  total tags in control: 50000000 
INFO  @ Thu, 13 Apr 2017 18:40:06: #1 finished! 
INFO  @ Thu, 13 Apr 2017 18:40:06: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 18:40:06: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 18:40:06: #2 Use 145 as fragment length 
INFO  @ Thu, 13 Apr 2017 18:40:06: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 18:40:06: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 13 Apr 2017 18:40:06: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 18:42:38: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 18:45:03: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 18:45:15: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Thu, 13 Apr 2017 18:45:24: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 13 Apr 2017 18:45:30: Done! 

 
 		 

    
  
 
  Num   4  
 
  ID   task.callpeak_naive_overlap.naive_overlap.line_59.id_13  
 
  Name   naive_overlap  
 
  Thread   thread_Root  
 
  PID   47003  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 18:46:02  
 
  End   2017-04-13 18:47:16  
 
  Elapsed   00:01:14  
 
  Timeout  01:00:00 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/overlap/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/overlap/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.gappedPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/overlap/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.gappedPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/overlap/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/overlap/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/overlap/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/overlap/SRR1370886_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--------------------
30360 (process ID) old priority 0, new priority 19
Waiting for 34 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KN196484.1	180131	180402	Peak_5857	258	.	180131	180402	0	2	1,1	0,270	13.46512	28.37284	25.81515

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KN196484.1	180131	180402	Peak_5857	258	.	180131	180402	0	2	1,1	0,270	13.46512	28.37284	25.81515

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270853.1	1824494	1824639	Peak_8181	200	.	1824494	1824639	0	2	1,1	0,144	12.72039	23.11344	20.03491

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270853.1	1824494	1824639	Peak_8181	200	.	1824494	1824639	0	2	1,1	0,144	12.72039	23.11344	20.03491

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL000195.1	136213	137901	Peak_300462	2	.	136213	137901	0	3	1,298,1	0,1300,1687	1.22427	1.00537	0.24478

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL000195.1	136213	137901	Peak_300462	2	.	136213	137901	0	3	1,298,1	0,1300,1687	1.22427	1.00537	0.24478


 
 		 

    
  
 
  Num   5  
 
  ID   task.callpeak_naive_overlap.naive_overlap.line_59.id_14  
 
  Name   naive_overlap  
 
  Thread   thread_Root  
 
  PID   47004  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 18:46:03  
 
  End   2017-04-13 18:47:15  
 
  Elapsed   00:01:12  
 
  Timeout  01:00:00 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/overlap/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/overlap/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.broadPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/overlap/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.broadPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/overlap/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/overlap/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/overlap/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/overlap/SRR1370886_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--------------------
15194 (process ID) old priority 0, new priority 19
Waiting for 43 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KN196484.1	180131	180402	Peak_5857	258	.	13.46512	28.37284	25.81515

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KN196484.1	180131	180402	Peak_5857	258	.	13.46512	28.37284	25.81515

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270853.1	1824494	1824639	Peak_8181	200	.	12.72039	23.11344	20.03491

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270853.1	1824494	1824639	Peak_8181	200	.	12.72039	23.11344	20.03491

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL000195.1	136213	137901	Peak_300462	2	.	1.22427	1.00537	0.24478

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL000195.1	136213	137901	Peak_300462	2	.	1.22427	1.00537	0.24478


 
 		 

    
  
 
  Num   6  
 
  ID   task.report.peak2hammock.line_361.id_17  
 
  Name   peak2hammock 
 
  Thread   thread_Root  
 
  PID   13455  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 18:47:18  
 
  End   2017-04-13 18:47:35  
 
  Elapsed   00:00:17  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/overlap/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.gappedPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/overlap/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/overlap/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/overlap/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/overlap/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.gappedPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/peak/macs2/overlap/SRR1370886_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/ZNF467_MACS2/out/peak/macs2/overlap/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.gappedPeak.tmp
 
 
   
--------------------Stdout--------------------
13460 (process ID) old priority 0, new priority 19

  
 		 

    
  
 
  Num   7  
 
  ID   task.graphviz.report.line_97.id_18  
 
  Name   report 
 
  Thread   thread_Root  
 
  PID   14262  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-13 18:47:36  
 
  End   2017-04-13 18:47:44  
 
  Elapsed   00:00:08  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files     
 
  Output files     
 
  Dependencies     
 
 		  
 
# SYS command. line 98

 if [[ -f $(which /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/ZNF467_MACS2/out/report/ZNF467_MACS2_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/report/ZNF467_MACS2_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467_MACS2/out/report/ZNF467_MACS2_workflow.svg" # to suppress dot font error (exit code=1)
 
 
   
--------------------Stdout--------------------
14266 (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, ZNF467_MACS2, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF467_MACS2/out, -tag1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/align/rep1/SRR1370886_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/ZNF467_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/ZNF467_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  47912.ZNF467_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