BigDataScript report: atac.bds

Script file /users/pangwei/bds_atac/atac.bds
Program ID atac.bds.20160516_120116_707
Start time 2016-05-16 12:01:16
Run time 07:08:17.398
Tasks executed 4
Tasks failed 0
Tasks failed names 
 

		
  Arguments*  [-out_dir, /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6, -num_rep, 2, -fastq1_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC5/ATAC5-trimmed-pair1.fastq.gz, -fastq1_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC5/ATAC5-trimmed-pair2.fastq.gz, -fastq2_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC6/ATAC6-trimmed-pair1.fastq.gz, -fastq2_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC6/ATAC6-trimmed-pair2.fastq.gz, -subsample, 17500000, -true_rep, -species, hg19] 

		
  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_20   thread_Root 	 
 atac.bds.20160516_120116_707_parallel_20/task.align_etc.trim_adapters_PE_rep1.line_57.id_6
atac.bds.20160516_120116_707_parallel_20/task.align_bowtie2.bowtie2_PE_rep1.line_133.id_9
 
 		 

	
  thread_21   thread_Root 	 
 atac.bds.20160516_120116_707_parallel_21/task.align_etc.trim_adapters_PE_rep2.line_57.id_7
atac.bds.20160516_120116_707_parallel_21/task.align_bowtie2.bowtie2_PE_rep2.line_133.id_8
 
 		 

	






	
 Task details 

	

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

    
  
 
  Num   1  
 
  ID   task.align_etc.trim_adapters_PE_rep1.line_57.id_6  
 
  Name   trim_adapters_PE rep1 
 
  Thread   thread_20  
 
  PID   109758  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus    1 
 
  Mem    
 
 		  
 
  Start   2016-05-16 12:01:16  
 
  End   2016-05-16 13:48:20  
 
  Elapsed   01:47:04  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC5/ATAC5-trimmed-pair1.fastq.gz
/srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC5/ATAC5-trimmed-pair2.fastq.gz
   
 
  Output files   /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.fastq.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair2.trim.fastq.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 59

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

# SYS command. line 61

 cd /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1

# SYS command. line 62

 $(which trimAdapters.py) -a /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC5/ATAC5-trimmed-pair1.fastq.gz -b /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC5/ATAC5-trimmed-pair2.fastq.gz

# SYS command. line 63

 gzip /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.fastq

# SYS command. line 64

 gzip /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair2.trim.fastq
 
 
   
--------------------Stdout--------------------
ATAC5-trimmed-pair1.trim.fastq
ATAC5-trimmed-pair2.trim.fastq

 
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
64562670 sequences total
25701696 sequences trimmed with 0 mismatches
1971652 sequences trimmed with 1 mismatch
21 mean number of bases trimmed for reads requiring trimming

 
 		 

    
  
 
  Num   2  
 
  ID   task.align_etc.trim_adapters_PE_rep2.line_57.id_7  
 
  Name   trim_adapters_PE rep2 
 
  Thread   thread_21  
 
  PID   109764  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus    1 
 
  Mem    
 
 		  
 
  Start   2016-05-16 12:01:17  
 
  End   2016-05-16 13:43:22  
 
  Elapsed   01:42:05  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC6/ATAC6-trimmed-pair1.fastq.gz
/srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC6/ATAC6-trimmed-pair2.fastq.gz
   
 
  Output files   /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.fastq.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair2.trim.fastq.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 59

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

# SYS command. line 61

 cd /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2

# SYS command. line 62

 $(which trimAdapters.py) -a /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC6/ATAC6-trimmed-pair1.fastq.gz -b /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC6/ATAC6-trimmed-pair2.fastq.gz

# SYS command. line 63

 gzip /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.fastq

# SYS command. line 64

 gzip /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair2.trim.fastq
 
 
   
--------------------Stdout--------------------
ATAC6-trimmed-pair1.trim.fastq
ATAC6-trimmed-pair2.trim.fastq

 
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
64401027 sequences total
28474078 sequences trimmed with 0 mismatches
2588823 sequences trimmed with 1 mismatch
22 mean number of bases trimmed for reads requiring trimming

 
 		 

    
  
 
  Num   3  
 
  ID   task.align_bowtie2.bowtie2_PE_rep2.line_133.id_8  
 
  Name   bowtie2_PE rep2 
 
  Thread   thread_21  
 
  PID   113314  
 
 		  
 
  OK   false   
 
  Exit Code   0   
 
  Retries    
 
  State   RUNNING  
 
  Dep.   WAIT  
 
  Cpus    2 
 
  Mem    
 
 		  
 
  Start   2016-05-16 13:43:23  
 
  End   2016-05-16 13:43:23  
 
  Elapsed   00:00:00  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.fastq.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair2.trim.fastq.gz
   
 
  Output files   /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.bam
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep2/ATAC6-trimmed-pair1.trim.PE2SE.align.log
  
 
  Dependencies     
 
 		  
 
# SYS command. line 135

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

# SYS command. line 139

 bowtie2  -X2000 --mm --threads 2 -x /mnt/data/annotations/indexes/bowtie2_indexes/bowtie2/ENCODEHg19_male \
			-1 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.fastq.gz -2 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair2.trim.fastq.gz 2>/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep2/ATAC6-trimmed-pair1.trim.PE2SE.align.log | samtools view -bS - | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE

# SYS command. line 142

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.bam
 
 
    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH

 
 		 

    
  
 
  Num   4  
 
  ID   task.align_bowtie2.bowtie2_PE_rep1.line_133.id_9  
 
  Name   bowtie2_PE rep1 
 
  Thread   thread_20  
 
  PID   113507  
 
 		  
 
  OK   false   
 
  Exit Code   0   
 
  Retries    
 
  State   RUNNING  
 
  Dep.   WAIT  
 
  Cpus    2 
 
  Mem    
 
 		  
 
  Start   2016-05-16 13:48:21  
 
  End   2016-05-16 13:48:21  
 
  Elapsed   00:00:00  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.fastq.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair2.trim.fastq.gz
   
 
  Output files   /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.bam
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep1/ATAC5-trimmed-pair1.trim.PE2SE.align.log
  
 
  Dependencies     
 
 		  
 
# SYS command. line 135

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

# SYS command. line 139

 bowtie2  -X2000 --mm --threads 2 -x /mnt/data/annotations/indexes/bowtie2_indexes/bowtie2/ENCODEHg19_male \
			-1 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.fastq.gz -2 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair2.trim.fastq.gz 2>/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep1/ATAC5-trimmed-pair1.trim.PE2SE.align.log | samtools view -bS - | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE

# SYS command. line 142

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.bam
 
 
    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH

 
 		 

	






	
 Global scope 

	Note: Global scope when program finished execution.
	

	
  Type  Name  Value