BigDataScript report: chipseq.bds

Script file /users/pangwei/ENCODE_chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20150903_212210_274
Start time 2015-09-03 21:22:10
Run time 00:20:21.723
Tasks executed 1
Tasks failed 0
Tasks failed names 
 

		
  Arguments*  [-input, tag, -final_stage, xcor, -num_rep, 1, -tag1_PE, -tag1, /srv/scratch/pangwei/deepimpute/data/subsampled/test-test_subsample-20e4.tagAlign.gz, -sigtrk, aln2rawsig, -make_bw, -seq, /mnt/data/ENCODE/sequence/encodeHg19Male, -umap, /mnt/data/ENCODE/umap/hg19_allmappable/globalmap_k1tok1000/, -chrsz, /mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes, -kundaje_lab] 

		
  System*  local 

		
  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_9   thread_Root 	 
 chipseq.bds.20150903_212210_274_parallel_9/task.signal.tag_to_bdg_a2rs_rep1.line_63.id_1
 
 		 

	






	
 Task details 

	

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

    
  
 
  Num   1  
 
  ID   task.signal.tag_to_bdg_a2rs_rep1.line_63.id_1  
 
  Name   tag to bdg a2rs rep1 
 
  Thread   thread_9  
 
  PID   42313  
 
 		  
 
  OK   false   
 
  Exit Code   0   
 
  Retries    
 
  State   RUNNING  
 
  Dep.   WAIT  
 
  Cpus    1 
 
  Mem    
 
 		  
 
  Start   2015-09-03 21:22:10  
 
  End   2015-09-03 21:22:10  
 
  Elapsed   00:00:00  
 
  Timeout  06:00:00 
 
  Wall Timeout   1 day 
 
 		  
 
  Input files  /srv/scratch/pangwei/deepimpute/data/subsampled/test-test_subsample-20e4.tagAlign.gz
   
 
  Output files   /users/pangwei/deepimpute/out/align_rep1/test-test_subsample-20e4.bedgraph
  
 
  Dependencies     
 
 		  
 
# SYS command. line 67

 export PATH=/users/pangwei/ENCODE_chipseq_pipeline/.:/users/pangwei/ENCODE_chipseq_pipeline/..:/users/pangwei/ENCODE_chipseq_pipeline/modules:/users/pangwei/ENCODE_chipseq_pipeline/species:/bin:/usr/bin:${HOME}/.bds:${PATH};  . /etc/profile.d/modules.sh; module add bwa/0.7.3 samtools/0.1.19 bedtools/2.19.1 ucsc_tools/3.0.9 picard-tools/1.92; module add phantompeakqualtools/default idr/latest align2rawsignal/2.0 MACS2/2.1.0 java/latest r/2.15.1 gem/2.6 deepTools/latest; export PATH=${PATH}:/software/idrCode;  export _JAVA_OPTIONS='-Xms256M -Xmx512M -XX:ParallelGCThreads=1'; export MAX_JAVA_MEM='8G'; export MALLOC_ARENA_MAX=4

# SYS command. line 69

 align2rawsignal -i=/srv/scratch/pangwei/deepimpute/data/subsampled/test-test_subsample-20e4.tagAlign.gz -o=/users/pangwei/deepimpute/out/align_rep1/test-test_subsample-20e4.bedgraph -s=/mnt/data/ENCODE/sequence/encodeHg19Male -u=/mnt/data/ENCODE/umap/hg19_allmappable/globalmap_k1tok1000/ -of=bg -l=230 -mm=4
 
 
     
 		 

	






	
 Global scope 

	Note: Global scope when program finished execution.
	

	
  Type  Name  Value