BigDataScript report: atac.bds

Script file /srv/scratch/annashch/bds_atac/atac.bds
Program ID atac.bds.20160518_111203_327
Start time 2016-05-18 11:12:03
Run time 06:25:36.018
Tasks executed 2
Tasks failed 0
Tasks failed names 
 

		
  Arguments*  [-out_dir, 4x_experiments/baseChroms_noMultiMap_3hr, -fastq1_1, 4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.fastq.gz, -fastq1_2, 4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R2.trim.fastq.gz, -fastq2_1, 4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.fastq.gz, -fastq2_2, 4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R2.trim.fastq.gz, -bwt2_idx, /srv/scratch/annashch/refs/hg19_mm9_phix, -gensz, hs, -chrsz, /srv/scratch/annashch/refs/hg19_mm9_phix_chrom.sizes, -species, hg19, -pseudorep, -idr, -blacklist_idr, wgEncodeDacMapabilityConsensusExcludable.bed, -trimmed_fastq] 

		
  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_21   thread_Root 	 
 atac.bds.20160518_111203_327_parallel_21/task.align_bowtie2.bowtie2_PE_rep2.line_131.id_6
 
 		 

	
  thread_20   thread_Root 	 
 atac.bds.20160518_111203_327_parallel_20/task.align_bowtie2.bowtie2_PE_rep1.line_131.id_7
 
 		 

	






	
 Task details 

	

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

    
  
 
  Num   1  
 
  ID   task.align_bowtie2.bowtie2_PE_rep2.line_131.id_6  
 
  Name   bowtie2_PE rep2 
 
  Thread   thread_21  
 
  PID   1580  
 
 		  
 
  OK   false   
 
  Exit Code   0   
 
  Retries    
 
  State   RUNNING  
 
  Dep.   WAIT  
 
  Cpus    2 
 
  Mem    
 
 		  
 
  Start   2016-05-18 11:12:04  
 
  End   2016-05-18 11:12:04  
 
  Elapsed   00:00:00  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.fastq.gz
/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R2.trim.fastq.gz
   
 
  Output files   /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.bam
/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.align.log
  
 
  Dependencies     
 
 		  
 
# SYS command. line 133

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 135

 bowtie2  -X2000 --mm --threads 2 -x /srv/scratch/annashch/refs/hg19_mm9_phix \
			-1 /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.fastq.gz -2 /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R2.trim.fastq.gz 2>/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.align.log | \
			sambamba view -t 2 -S --format=bam /dev/stdin | sambamba sort /dev/stdin -t 2 -o /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.bam
 
 
     
 		 

    
  
 
  Num   2  
 
  ID   task.align_bowtie2.bowtie2_PE_rep1.line_131.id_7  
 
  Name   bowtie2_PE rep1 
 
  Thread   thread_20  
 
  PID   1585  
 
 		  
 
  OK   false   
 
  Exit Code   0   
 
  Retries    
 
  State   RUNNING  
 
  Dep.   WAIT  
 
  Cpus    2 
 
  Mem    
 
 		  
 
  Start   2016-05-18 11:12:04  
 
  End   2016-05-18 11:12:04  
 
  Elapsed   00:00:00  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.fastq.gz
/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R2.trim.fastq.gz
   
 
  Output files   /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.bam
/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.align.log
  
 
  Dependencies     
 
 		  
 
# SYS command. line 133

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 135

 bowtie2  -X2000 --mm --threads 2 -x /srv/scratch/annashch/refs/hg19_mm9_phix \
			-1 /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.fastq.gz -2 /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R2.trim.fastq.gz 2>/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.align.log | \
			sambamba view -t 2 -S --format=bam /dev/stdin | sambamba sort /dev/stdin -t 2 -o /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.bam
 
 
     
 		 

	






	
 Global scope 

	Note: Global scope when program finished execution.
	

	
  Type  Name  Value