BigDataScript report: chipseq.bds

Script file /users/pangwei/ENCODE_chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20150903_230202_781
Start time 2015-09-03 23:02:02
Run time 01:12:04.244
Tasks executed 4
Tasks failed 0
Tasks failed names 
 

		
  Arguments*  [-out_dir, /srv/scratch/pangwei/deepimpute/data/bigWigs/GM12878-H3K36ME3_merged, -input, tag, -final_stage, xcor, -num_rep, 1, -tag1_PE, -tag1, /srv/scratch/pangwei/deepimpute/data/merged/GM12878-H3K36ME3_merged.tagAlign.gz, -sigtrk, aln2rawsig, -make_bw, -species, hg19_allmappable, -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_230202_781_parallel_9/task.align.subsample_tag_rep1.line_387.id_1
chipseq.bds.20150903_230202_781_parallel_9/task.align.xcor_rep1.line_438.id_2
chipseq.bds.20150903_230202_781_parallel_9/task.signal.tag_to_bdg_a2rs_rep1.line_63.id_3
chipseq.bds.20150903_230202_781_parallel_9/task.signal.bdg_to_bw_rep1.line_106.id_4
 
 		 

	






	
 Task details 

	

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

    
  
 
  Num   1  
 
  ID   task.align.subsample_tag_rep1.line_387.id_1  
 
  Name   _subsample_tag rep1 
 
  Thread   thread_9  
 
  PID   48648  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus    1 
 
  Mem    
 
 		  
 
  Start   2015-09-03 23:02:03  
 
  End   2015-09-03 23:03:21  
 
  Elapsed   00:01:18  
 
  Timeout  06:00:00 
 
  Wall Timeout   1 day 
 
 		  
 
  Input files  /srv/scratch/pangwei/deepimpute/data/merged/GM12878-H3K36ME3_merged.tagAlign.gz
   
 
  Output files   /srv/scratch/pangwei/deepimpute/data/bigWigs/GM12878-H3K36ME3_merged/align_rep1/GM12878-H3K36ME3_merged.15.tagAlign.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 391

 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 394

 zcat /srv/scratch/pangwei/deepimpute/data/merged/GM12878-H3K36ME3_merged.tagAlign.gz | \
			grep -v "chrM" | shuf -n 15000000 | gzip -c > /srv/scratch/pangwei/deepimpute/data/bigWigs/GM12878-H3K36ME3_merged/align_rep1/GM12878-H3K36ME3_merged.15.tagAlign.gz
 
 
     
 		 

    
  
 
  Num   2  
 
  ID   task.align.xcor_rep1.line_438.id_2  
 
  Name   xcor rep1 
 
  Thread   thread_9  
 
  PID   514  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus    1 
 
  Mem    
 
 		  
 
  Start   2015-09-03 23:03:22  
 
  End   2015-09-03 23:21:54  
 
  Elapsed   00:18:31  
 
  Timeout  06:00:00 
 
  Wall Timeout   1 day 
 
 		  
 
  Input files  /srv/scratch/pangwei/deepimpute/data/bigWigs/GM12878-H3K36ME3_merged/align_rep1/GM12878-H3K36ME3_merged.15.tagAlign.gz
   
 
  Output files   /srv/scratch/pangwei/deepimpute/data/bigWigs/GM12878-H3K36ME3_merged/align_rep1/GM12878-H3K36ME3_merged.15.cc.qc
/srv/scratch/pangwei/deepimpute/data/bigWigs/GM12878-H3K36ME3_merged/align_rep1/GM12878-H3K36ME3_merged.15.cc.plot.pdf
  
 
  Dependencies     
 
 		  
 
# SYS command. line 442

 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 446

 Rscript $(which run_spp_nodups.R) -rf \
			-c=/srv/scratch/pangwei/deepimpute/data/bigWigs/GM12878-H3K36ME3_merged/align_rep1/GM12878-H3K36ME3_merged.15.tagAlign.gz -p=1 \
			-filtchr=chrM -savp=/srv/scratch/pangwei/deepimpute/data/bigWigs/GM12878-H3K36ME3_merged/align_rep1/GM12878-H3K36ME3_merged.15.cc.plot.pdf -out=/srv/scratch/pangwei/deepimpute/data/bigWigs/GM12878-H3K36ME3_merged/align_rep1/GM12878-H3K36ME3_merged.15.cc.qc

# SYS command. line 449

 sed -r 's/,[^\t]+//g' /srv/scratch/pangwei/deepimpute/data/bigWigs/GM12878-H3K36ME3_merged/align_rep1/GM12878-H3K36ME3_merged.15.cc.qc > /srv/scratch/pangwei/deepimpute/data/bigWigs/GM12878-H3K36ME3_merged/align_rep1/GM12878-H3K36ME3_merged.15.cc.qc.tmp

# SYS command. line 450

 mv /srv/scratch/pangwei/deepimpute/data/bigWigs/GM12878-H3K36ME3_merged/align_rep1/GM12878-H3K36ME3_merged.15.cc.qc.tmp /srv/scratch/pangwei/deepimpute/data/bigWigs/GM12878-H3K36ME3_merged/align_rep1/GM12878-H3K36ME3_merged.15.cc.qc
 
 
   
--------------------Stdout--------------------
################
ChIP data: /srv/scratch/pangwei/deepimpute/data/bigWigs/GM12878-H3K36ME3_merged/align_rep1/GM12878-H3K36ME3_merged.15.tagAlign.gz 
Control data: NA 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift NA 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: NA 
Output Directory: /srv/scratch/pangwei/deepimpute/data/bigWigs/GM12878-H3K36ME3_merged/align_rep1 
narrowPeak output file name: NA 
regionPeak output file name: NA 
Rdata filename: NA 
plot pdf filename: /srv/scratch/pangwei/deepimpute/data/bigWigs/GM12878-H3K36ME3_merged/align_rep1/GM12878-H3K36ME3_merged.15.cc.plot.pdf 
result filename: /srv/scratch/pangwei/deepimpute/data/bigWigs/GM12878-H3K36ME3_merged/align_rep1/GM12878-H3K36ME3_merged.15.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/pangwei/deepimpute/data/bigWigs/GM12878-H3K36ME3_merged/align_rep1/GM12878-H3K36ME3_merged.15.tagAlign.gz 
opened /tmp/RtmpZMKjbH/GM12878-H3K36ME3_merged.15.tagAlign2116fdb9b76
done. read 15000000 fragments
ChIP data read length 101 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.2200816 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.232524812460232,0.230152957063746,0.226909229951439 
Top 3 estimates for fragment length 295,365,435 
Window half size 720 
Phantom peak location 105 
Phantom peak Correlation 0.2262479 
Normalized Strand cross-correlation coefficient (NSC) 1.056539 
Relative Strand Cross correlation Coefficient (RSC) 2.017919 
Phantom Peak Quality Tag 2 
null device 
          1 

 
--------------------Stderr--------------------
Loading required package: caTools

 
 		 

    
  
 
  Num   3  
 
  ID   task.signal.tag_to_bdg_a2rs_rep1.line_63.id_3  
 
  Name   tag to bdg a2rs rep1 
 
  Thread   thread_9  
 
  PID   1532  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus    1 
 
  Mem    
 
 		  
 
  Start   2015-09-03 23:21:55  
 
  End   2015-09-04 00:11:57  
 
  Elapsed   00:50:01  
 
  Timeout  06:00:00 
 
  Wall Timeout   1 day 
 
 		  
 
  Input files  /srv/scratch/pangwei/deepimpute/data/merged/GM12878-H3K36ME3_merged.tagAlign.gz
   
 
  Output files   /srv/scratch/pangwei/deepimpute/data/bigWigs/GM12878-H3K36ME3_merged/align_rep1/GM12878-H3K36ME3_merged.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/merged/GM12878-H3K36ME3_merged.tagAlign.gz -o=/srv/scratch/pangwei/deepimpute/data/bigWigs/GM12878-H3K36ME3_merged/align_rep1/GM12878-H3K36ME3_merged.bedgraph -s=/mnt/data/ENCODE/sequence/encodeHg19Male -u=/mnt/data/ENCODE/umap/hg19_allmappable/globalmap_k1tok1000 -of=bg -l=295 -mm=4
 
 
   
--------------------Stdout--------------------
Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /users/pangwei//java.log.1547

  
 		 

    
  
 
  Num   4  
 
  ID   task.signal.bdg_to_bw_rep1.line_106.id_4  
 
  Name   bdg to bw rep1 
 
  Thread   thread_9  
 
  PID   3777  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus    1 
 
  Mem    
 
 		  
 
  Start   2015-09-04 00:11:58  
 
  End   2015-09-04 00:14:06  
 
  Elapsed   00:02:08  
 
  Timeout  06:00:00 
 
  Wall Timeout   1 day 
 
 		  
 
  Input files  /srv/scratch/pangwei/deepimpute/data/bigWigs/GM12878-H3K36ME3_merged/align_rep1/GM12878-H3K36ME3_merged.bedgraph
   
 
  Output files   /srv/scratch/pangwei/deepimpute/data/bigWigs/GM12878-H3K36ME3_merged/align_rep1/GM12878-H3K36ME3_merged.bigwig
  
 
  Dependencies     
 
 		  
 
# SYS command. line 110

 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 112

 sort -k1,1 -k2,2n /srv/scratch/pangwei/deepimpute/data/bigWigs/GM12878-H3K36ME3_merged/align_rep1/GM12878-H3K36ME3_merged.bedgraph > /srv/scratch/pangwei/deepimpute/data/bigWigs/GM12878-H3K36ME3_merged/align_rep1/GM12878-H3K36ME3_merged.srt.bedgraph

# SYS command. line 114

 bedGraphToBigWig /srv/scratch/pangwei/deepimpute/data/bigWigs/GM12878-H3K36ME3_merged/align_rep1/GM12878-H3K36ME3_merged.srt.bedgraph /mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes /srv/scratch/pangwei/deepimpute/data/bigWigs/GM12878-H3K36ME3_merged/align_rep1/GM12878-H3K36ME3_merged.bigwig

# SYS command. line 115

 rm -f /srv/scratch/pangwei/deepimpute/data/bigWigs/GM12878-H3K36ME3_merged/align_rep1/GM12878-H3K36ME3_merged.srt.bedgraph
 
 
     
 		 

	






	
 Global scope 

	Note: Global scope when program finished execution.
	

	
  Type  Name  Value  

	
  string  _  /usr/bin/bds  

	
  string  _LMFILES_  /software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/samtools/1.2:/software/modulefiles/bedtools/2.23.0:/software/modulefiles/rsem/1.2.21  

	
  string  _ZSH_TMUX_FIXED_CONFIG  /users/pangwei/.oh-my-zsh/plugins/tmux/tmux.extra.conf  

	
  bool  allowEmpty  false  

	
  string[]  args  [-out_dir, /srv/scratch/pangwei/deepimpute/data/bigWigs/GM12878-H3K36ME3_merged, -input, tag, -final_stage, xcor, -num_rep, 1, -tag1_PE, -tag1, /srv/scratch/pangwei/deepimpute/data/merged/GM12878-H3K36ME3_merged.tagAlign.gz, -sigtrk, aln2rawsig, -make_bw, -species, hg19_allmappable, -kundaje_lab]  

	
  string  C_INCLUDE_PATH  /software/samtools/samtools-1.2/include/htslib  

	
  bool  canFail  false  

	
  int  cpus  1  

	
  int  cpusLocal  48  

	
  int  day  86400  

	
  real  E  2.718281828459045  

	
  int  G  1073741824  

	
  string  HOME  /users/pangwei/  

	
  int  hour  3600  

	
  int  K  1024  

	
  string  LANG  en_US.UTF-8  

	
  string  LC_CTYPE  en_US.UTF-8  

	
  string  LD_LIBRARY_PATH  /software/samtools/samtools-1.2/lib  

	
  string  LESS  -R  

	
  string  LOADEDMODULES  modsappsdir/modsappsdir:samtools/1.2:bedtools/2.23.0:rsem/1.2.21  

	
  string  LOGNAME  pangwei  

	
  string  LSCOLORS  Gxfxcxdxbxegedabagacad  

	
  int  M  1048576  

	
  string  MAIL  /var/mail/pangwei  

	
  string  MANPATH  /software/samtools/samtools-1.2/share/man:/usr/share/man  

	
  int  mem  -1  

	
  int  minute  60  

	
  string  MODULE_VERSION  3.2.10  

	
  string  MODULE_VERSION_STACK  3.2.10  

	
  string  MODULEPATH  /etc/environment-modules/modules:/usr/share/modules/versions:/usr/Modules/$MODULE_VERSION/modulefiles:/usr/share/modules/modulefiles:/software/modulefiles  

	
  string  MODULESAPPSDIR  /software  

	
  string  MODULESHOME  /usr/share/modules  

	
  string  node    

	
  int  P  1125899906842624  

	
  string  PAGER  less  

	
  string  PATH  /software/RSEM/rsem-1.2.21/:/software/bedtools/2.23.0/bin:/software/samtools/samtools-1.2/bin:/users/pangwei/anaconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games  

	
  real  PI  3.141592653589793  

	
  string  ppwd  /users/pangwei/deepimpute  

	
  string  programName  chipseq.bds  

	
  string  programPath  /users/pangwei/ENCODE_chipseq_pipeline/chipseq.bds  

	
  string  PWD  /users/pangwei/deepimpute  

	
  string  PYTHONPATH  /home/jisraeli/src/caffe_atac/python/:/home/jisraeli/src/caffe_atac/python/:  

	
  string  queue    

	
  int  retry  0  

	
  string  SAMTOOLS_HOME  /software/samtools/samtools-1.2/bin  

	
  string  SHELL  /usr/bin/zsh  

	
  string  SHLVL  3  

	
  string  SSH_AUTH_SOCK  /tmp/ssh-4dtHLfWUQO/agent.45548  

	
  string  SSH_CLIENT  171.65.76.244 60329 22  

	
  string  SSH_CONNECTION  171.65.76.244 60329 171.65.76.162 22  

	
  string  SSH_TTY  /dev/pts/51  

	
  string  system  local  

	
  int  T  1099511627776  

	
  string  TERM  screen  

	
  int  timeout  86400  

	
  string  TMUX  /tmp/tmux-1077/default,45610,0  

	
  string  TMUX_PANE  %0  

	
  string  USER  pangwei  

	
  int  walltimeout  86400  

	
  int  week  604800  

	
  string  XDG_RUNTIME_DIR  /run/user/1077  

	
  string  XDG_SESSION_ID  210  

	
  string  ZSH  /users/pangwei//.oh-my-zsh  

	
  string  ZSH_TMUX_TERM  screen