BigDataScript report: chipseq.bds

Script file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20170407_175545_311
Start time 2017-04-07 17:55:45
Run time 00:05:08.123
Tasks executed 2
Tasks failed 0
Tasks failed names 
 

		
  Arguments*  [-title, ZIC2_MACS2, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/leepc12/imk_chipseq/ZIC2_MACS2/out, -filt_bam1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.bam, -filt_bam2, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.bam, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz, -pe, $] 

		
  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 	 
  
 		 

	
  thread_41   thread_Root 	 
 chipseq.bds.20170407_175545_311_parallel_41/task.postalign_bam.nmsrt_bam_rep1.line_495.id_10
 
 		 

	
  thread_42   thread_Root 	 
 chipseq.bds.20170407_175545_311_parallel_42/task.postalign_bam.nmsrt_bam_rep2.line_495.id_11
 
 		 

	
  thread_43   thread_Root 	 
  
 		 

	






	
 Task details 

	

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

    
  
 
  Num   1  
 
  ID   task.postalign_bam.nmsrt_bam_rep1.line_495.id_10  
 
  Name   nmsrt_bam rep1 
 
  Thread   thread_41  
 
  PID   46366  
 
 		  
 
  OK   false   
 
  Exit Code   0   
 
  Retries    
 
  State   RUNNING  
 
  Dep.   WAIT  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-07 17:55:48  
 
  End   2017-04-07 17:55:48  
 
  Elapsed   00:00:00  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.bam
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.nmsrt.bam
  
 
  Dependencies     
 
 		  
 
# SYS command. line 497

 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 500

 sambamba sort -t 1 -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.bam -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.nmsrt.bam

# SYS command. line 502

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
5218 (process ID) old priority 0, new priority 19

  
 		 

    
  
 
  Num   2  
 
  ID   task.postalign_bam.nmsrt_bam_rep2.line_495.id_11  
 
  Name   nmsrt_bam rep2 
 
  Thread   thread_42  
 
  PID   46367  
 
 		  
 
  OK   false   
 
  Exit Code   0   
 
  Retries    
 
  State   RUNNING  
 
  Dep.   WAIT  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-04-07 17:55:48  
 
  End   2017-04-07 17:55:48  
 
  Elapsed   00:00:00  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.bam
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.nmsrt.bam
  
 
  Dependencies     
 
 		  
 
# SYS command. line 497

 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 500

 sambamba sort -t 1 -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.bam -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.nmsrt.bam

# SYS command. line 502

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
5219 (process ID) old priority 0, new priority 19

  
 		 

	






	
 Global scope 

	Note: Global scope when program finished execution.
	

	
  Type  Name  Value  

	
  int{}  filesize  {rep2=5040284283, rep1=5167121946, ctl1=3103781745}  

	
  int{}  nth_rep  {rep2=2, rep1=2, ctl1=1}