BigDataScript report: atac.bds

Script file /srv/scratch/annashch/bds_atac/atac.bds
Program ID atac.bds.20160516_125342_181
Start time 2016-05-16 12:53:42
Run time 00:02:02.636
Tasks executed 2
Tasks failed 0
Tasks failed names 
 

		
  Arguments*  [-out_dir, /srv/scratch/annashch/sundari/output, -fastq1_1, output/align/rep1/160429-BW-1_R1.trim.fastq.gz, -fastq1_2, output/align/rep1/160429-BW-1_R2.trim.fastq.gz, -fastq2_1, output/align/rep2/160429-BW-2_R1.trim.fastq.gz, -fastq2_2, output/align/rep2/160429-BW-2_R2.trim.fastq.gz, -species, hg19, -pseudorep, -idr, -blacklist, /srv/scratch/annashch/refs/wgEncodeDacMapabilityConsensusExcludable.bed, -par_lvl, 5, -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.20160516_125342_181_parallel_21/task.align_bowtie2.bowtie2_PE_rep2.line_128.id_7
 
 		 

	
  thread_20   thread_Root 	 
 atac.bds.20160516_125342_181_parallel_20/task.align_bowtie2.bowtie2_PE_rep1.line_128.id_6
 
 		 

	






	
 Task details 

	

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

    
  
 
  Num   1  
 
  ID   task.align_bowtie2.bowtie2_PE_rep2.line_128.id_7  
 
  Name   bowtie2_PE rep2 
 
  Thread   thread_21  
 
  PID   40670  
 
 		  
 
  OK   false   
 
  Exit Code   0   
 
  Retries    
 
  State   RUNNING  
 
  Dep.   WAIT  
 
  Cpus    2 
 
  Mem    
 
 		  
 
  Start   2016-05-16 12:53:43  
 
  End   2016-05-16 12:53:43  
 
  Elapsed   00:00:00  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/annashch/sundari/output/align/rep2/160429-BW-2_R1.trim.fastq.gz
/srv/scratch/annashch/sundari/output/align/rep2/160429-BW-2_R2.trim.fastq.gz
   
 
  Output files   /srv/scratch/annashch/sundari/output/align/rep2/160429-BW-2_R1.trim.PE2SE.bam
/srv/scratch/annashch/sundari/output/qc/rep2/160429-BW-2_R1.trim.PE2SE.align.log
  
 
  Dependencies     
 
 		  
 
# SYS command. line 130

 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 134

 bowtie2 -X2000 --mm --threads 2 -x /mnt/data/annotations/indexes/bowtie2_indexes/bowtie2/ENCODEHg19_male \
			-1 /srv/scratch/annashch/sundari/output/align/rep2/160429-BW-2_R1.trim.fastq.gz -2 /srv/scratch/annashch/sundari/output/align/rep2/160429-BW-2_R2.trim.fastq.gz 2>/srv/scratch/annashch/sundari/output/qc/rep2/160429-BW-2_R1.trim.PE2SE.align.log | samtools view -bS - | samtools sort - /srv/scratch/annashch/sundari/output/align/rep2/160429-BW-2_R1.trim.PE2SE

# SYS command. line 137

 samtools index /srv/scratch/annashch/sundari/output/align/rep2/160429-BW-2_R1.trim.PE2SE.bam
 
 
    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

 
 		 

    
  
 
  Num   2  
 
  ID   task.align_bowtie2.bowtie2_PE_rep1.line_128.id_6  
 
  Name   bowtie2_PE rep1 
 
  Thread   thread_20  
 
  PID   40675  
 
 		  
 
  OK   false   
 
  Exit Code   0   
 
  Retries    
 
  State   RUNNING  
 
  Dep.   WAIT  
 
  Cpus    2 
 
  Mem    
 
 		  
 
  Start   2016-05-16 12:53:43  
 
  End   2016-05-16 12:53:43  
 
  Elapsed   00:00:00  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/annashch/sundari/output/align/rep1/160429-BW-1_R1.trim.fastq.gz
/srv/scratch/annashch/sundari/output/align/rep1/160429-BW-1_R2.trim.fastq.gz
   
 
  Output files   /srv/scratch/annashch/sundari/output/align/rep1/160429-BW-1_R1.trim.PE2SE.bam
/srv/scratch/annashch/sundari/output/qc/rep1/160429-BW-1_R1.trim.PE2SE.align.log
  
 
  Dependencies     
 
 		  
 
# SYS command. line 130

 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 134

 bowtie2 -X2000 --mm --threads 2 -x /mnt/data/annotations/indexes/bowtie2_indexes/bowtie2/ENCODEHg19_male \
			-1 /srv/scratch/annashch/sundari/output/align/rep1/160429-BW-1_R1.trim.fastq.gz -2 /srv/scratch/annashch/sundari/output/align/rep1/160429-BW-1_R2.trim.fastq.gz 2>/srv/scratch/annashch/sundari/output/qc/rep1/160429-BW-1_R1.trim.PE2SE.align.log | samtools view -bS - | samtools sort - /srv/scratch/annashch/sundari/output/align/rep1/160429-BW-1_R1.trim.PE2SE

# SYS command. line 137

 samtools index /srv/scratch/annashch/sundari/output/align/rep1/160429-BW-1_R1.trim.PE2SE.bam
 
 
    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

 
 		 

	






	
 Global scope 

	Note: Global scope when program finished execution.
	

	
  Type  Name  Value