BigDataScript report: chipseq.bds

Script file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20161113_215853_058
Start time 2016-11-13 21:58:53
Run time 01:52:26.585
Tasks executed 7
Tasks failed 0
Tasks failed names 
 

		
  Arguments*  [-title, SRR1370888_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370888_1.fastq.gz, -ctl_bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam, -final_stage, xcor, $] 

		
  System*  sge 

		
  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 	 
 chipseq.bds.20161113_215853_058/task.graphviz.report.line_97.id_15
chipseq.bds.20161113_215853_058/task.report.pdf2png.line_324.id_20
 
 		 

	
  thread_41   thread_Root 	 
 chipseq.bds.20161113_215853_058_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_10
chipseq.bds.20161113_215853_058_parallel_41/task.postalign_bam.bam_to_tag_rep1.line_505.id_11
chipseq.bds.20161113_215853_058_parallel_41/task.postalign_bed.subsample_tag_rep1.line_45.id_12
chipseq.bds.20161113_215853_058_parallel_41/task.postalign_bed.spr_rep1.line_255.id_13
chipseq.bds.20161113_215853_058_parallel_41/task.postalign_bed.xcor_rep1.line_212.id_14
 
 		 

	
  thread_42   thread_Root 	 
  
 		 

	






	
 Task details 

	

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

    
  
 
  Num   1  
 
  ID   task.postalign_bam.dedup_bam_2_rep1.line_144.id_10  
 
  Name   dedup_bam_2 rep1 
 
  Thread   thread_41  
 
  PID   10241  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-11-13 21:58:57  
 
  End   2016-11-13 22:04:24  
 
  Elapsed   00:05:26  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.dupmark.bam
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.nodup.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/qc/rep1/SRR1370888_1.nodup.flagstat.qc
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/qc/rep1/SRR1370888_1.nodup.pbc.qc
  
 
  Dependencies     
 
 		  
 
# SYS command. line 146

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 150

 samtools view -F 1804 -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.nodup.bam

# SYS command. line 153

 sambamba index -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/qc/rep1/SRR1370888_1.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.dupmark.bam | \
				awk 'BEGIN{OFS="\t"}{print $1,$2,$3,$6}' | \
				grep -v 'chrM' | sort | uniq -c | \
				awk 'BEGIN{mt=0;m0=0;m1=0;m2=0} ($1==1){m1=m1+1} ($1==2){m2=m2+1} {m0=m0+1} {mt=mt+$1} END{m1_m2=-1.0; if(m2>0) m1_m2=m1/m2; printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1_m2}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/qc/rep1/SRR1370888_1.nodup.pbc.qc

# SYS command. line 169

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
14904 (process ID) old priority 0, new priority 10

  
 		 

    
  
 
  Num   2  
 
  ID   task.postalign_bam.bam_to_tag_rep1.line_505.id_11  
 
  Name   bam_to_tag rep1 
 
  Thread   thread_41  
 
  PID   10451  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-11-13 22:04:26  
 
  End   2016-11-13 22:27:51  
 
  Elapsed   00:23:25  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.nodup.bam
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.nodup.tagAlign.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 507

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 510

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.nodup.tagAlign.gz

# SYS command. line 512

 echo

# SYS command. line 514

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
5431 (process ID) old priority 0, new priority 10

Waiting for 20 seconds.

  
 		 

    
  
 
  Num   3  
 
  ID   task.postalign_bed.subsample_tag_rep1.line_45.id_12  
 
  Name   subsample_tag rep1 
 
  Thread   thread_41  
 
  PID   10527  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-11-13 22:27:52  
 
  End   2016-11-13 22:48:02  
 
  Elapsed   00:20:09  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.nodup.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.nodup.15M.tagAlign.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 47

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 50

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.nodup.tagAlign.gz | \
			grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.nodup.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.nodup.15M.tagAlign.gz

# SYS command. line 53

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
17772 (process ID) old priority 0, new priority 10
Waiting for 13 seconds.

  
 		 

    
  
 
  Num   4  
 
  ID   task.postalign_bed.spr_rep1.line_255.id_13  
 
  Name   spr rep1 
 
  Thread   thread_41  
 
  PID   10528  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-11-13 22:27:54  
 
  End   2016-11-13 22:48:10  
 
  Elapsed   00:20:15  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.nodup.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.pr1.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/pseudo_reps/rep1/pr2/SRR1370888_1.nodup.pr2.tagAlign.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 257

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 260

 nlines=$( zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.nodup.tagAlign.gz | wc -l )

# SYS command. line 261

 nlines=$(( (nlines + 1) / 2 ))

# SYS command. line 265

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.nodup.tagAlign.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.nodup.tagAlign.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.

# SYS command. line 268

 gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.pr1.tagAlign.gz

# SYS command. line 269

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.00

# SYS command. line 270

 gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/pseudo_reps/rep1/pr2/SRR1370888_1.nodup.pr2.tagAlign.gz

# SYS command. line 271

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/pseudo_reps/rep1/pr1/SRR1370888_1.nodup.01

# SYS command. line 273

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
5628 (process ID) old priority 0, new priority 10
Waiting for 3 seconds.

  
 		 

    
  
 
  Num   5  
 
  ID   task.postalign_bed.xcor_rep1.line_212.id_14  
 
  Name   xcor rep1 
 
  Thread   thread_41  
 
  PID   10596  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-11-13 22:48:12  
 
  End   2016-11-13 23:51:06  
 
  Elapsed   01:02:53  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.nodup.15M.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/qc/rep1/SRR1370888_1.nodup.15M.cc.qc
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/qc/rep1/SRR1370888_1.nodup.15M.cc.plot.pdf
  
 
  Dependencies     
 
 		  
 
# SYS command. line 214

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 217

 if [[ $(which run_spp_nodups.R 2> /dev/null | wc -l || echo) == "1" ]]; then RUN_SPP=$(which run_spp_nodups.R); \
		    else RUN_SPP=$(which run_spp.R); \
		    fi

# SYS command. line 223

 Rscript ${RUN_SPP} -rf \
			-c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.nodup.15M.tagAlign.gz -p=1 \
			-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/qc/rep1/SRR1370888_1.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/qc/rep1/SRR1370888_1.nodup.15M.cc.qc 

# SYS command. line 226

 sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/qc/rep1/SRR1370888_1.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/qc/rep1/SRR1370888_1.nodup.15M.cc.qc.tmp

# SYS command. line 227

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/qc/rep1/SRR1370888_1.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/qc/rep1/SRR1370888_1.nodup.15M.cc.qc

# SYS command. line 229

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
27878 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.nodup.15M.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/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1 
narrowPeak output file name: NA 
regionPeak output file name: NA 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/qc/rep1/SRR1370888_1.nodup.15M.cc.plot.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/qc/rep1/SRR1370888_1.nodup.15M.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/align/rep1/SRR1370888_1.nodup.15M.tagAlign.gz 
opened /tmp/10596.1.amd.q/RtmpaXTDff/SRR1370888_1.nodup.15M.tagAlign6de53b15ae10
done. read 15000000 fragments
ChIP data read length 50 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1736222 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.17947925435286,0.1754406796734,0.174836983999373 
Top 3 estimates for fragment length 150,225,280 
Window half size 205 
Phantom peak location 50 
Phantom peak Correlation 0.1763492 
Normalized Strand cross-correlation coefficient (NSC) 1.033734 
Relative Strand cross-correlation Coefficient (RSC) 2.147836 
Phantom Peak Quality Tag 2 
null device 
          1 

 
--------------------Stderr--------------------
Loading required package: caTools
Warning message:
package ‘caTools’ was built under R version 3.2.3 

 
 		 

    
  
 
  Num   6  
 
  ID   task.graphviz.report.line_97.id_15  
 
  Name   report 
 
  Thread   thread_Root  
 
  PID   8924  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-11-13 23:51:07  
 
  End   2016-11-13 23:51:19  
 
  Elapsed   00:00:12  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files     
 
  Output files     
 
  Dependencies     
 
 		  
 
# SYS command. line 98

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 99

 dot -Tsvg /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/report/SRR1370888_1_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/report/SRR1370888_1_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/report/SRR1370888_1_workflow.svg" # to suppress dot font error (exit code=1)
 
 
   
--------------------Stdout--------------------
8928 (process ID) old priority 0, new priority 10

  
 		 

    
  
 
  Num   7  
 
  ID   task.report.pdf2png.line_324.id_20  
 
  Name   pdf2png 
 
  Thread   thread_Root  
 
  PID   8976  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-11-13 23:51:08  
 
  End   2016-11-13 23:51:19  
 
  Elapsed   00:00:11  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/qc/rep1/SRR1370888_1.nodup.15M.cc.plot.pdf
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/qc/rep1/SRR1370888_1.nodup.15M.cc.plot.png
  
 
  Dependencies     
 
 		  
 
# SYS command. line 325

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 326

 gs -dFirstPage=1 -dLastPage=1 -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -r110x110 \
			-dUseCropBox -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -sDEVICE=png16m \
			-sOutputFile=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/qc/rep1/SRR1370888_1.nodup.15M.cc.plot.png \
			-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out/qc/rep1/SRR1370888_1.nodup.15M.cc.plot.pdf
 
 
   
--------------------Stdout--------------------
8980 (process ID) old priority 0, new priority 10

  
 		 

	






	
 Global scope 

	Note: Global scope when program finished execution.
	

	
  Type  Name  Value  

	
  string  _  /usr/bin/bds  

	
  string  _LMFILES_  /software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/sratoolkit/2.5.2:/software/modulefiles/ascp/3.5.6  

	
  bool  allowEmpty  false  

	
  string[]  args  [-title, SRR1370888_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370888_1.fastq.gz, -ctl_bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam, -final_stage, xcor, $]  

	
  string  ASCPKEY  /software/ascp/etc/asperaweb_id_dsa.openssh  

	
  bool  canFail  false  

	
  int  cpus  -1  

	
  int  cpusLocal  56  

	
  int  day  86400  

	
  string  DEEPLIFT_DIR  /srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift  

	
  string  DERBY_HOME  /usr/lib/jvm/java-8-oracle/db  

	
  string  DISPLAY  localhost:12.0  

	
  real  E  2.718281828459045  

	
  string  ENHANCER_SCRIPTS_DIR  /srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/  

	
  int  G  1073741824  

	
  string  HOME  /users/imk1/  

	
  int  hour  3600  

	
  string  J2REDIR  /usr/lib/jvm/java-8-oracle/jre  

	
  string  J2SDKDIR  /usr/lib/jvm/java-8-oracle  

	
  string  JAVA_HOME  /usr/lib/jvm/java-8-oracle  

	
  int  K  1024  

	
  string  KERAS_DIR  /users/imk1/.local/lib/python2.7/site-packages/keras/  

	
  string  KRB5CCNAME  FILE:/tmp/krb5cc_1048_N5SeQf  

	
  string  LANG  en_US.UTF-8  

	
  string  LOADEDMODULES  modsappsdir/modsappsdir:sratoolkit/2.5.2:ascp/3.5.6  

	
  string  LOGNAME  imk1  

	
  int  M  1048576  

	
  string  MAIL  /var/mail/imk1  

	
  int  mem  -1  

	
  int  minute  60  

	
  string  MODULE_VERSION  3.2.10  

	
  string  MODULE_VERSION_STACK  3.2.10  

	
  string  MODULEPATH  /usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles  

	
  string  MODULESAPPSDIR  /software  

	
  string  MODULESHOME  /software/env_module/3.2.10  

	
  string  NLSPATH  /usr/dt/lib/nls/msg/%L/%N.cat  

	
  string  node    

	
  int  P  1125899906842624  

	
  string  PATH  /users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/srv/scratch/imk1/TFBindingPredictionProject/src/R-3.2.3/bin:/users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/srv/scratch/imk1/TFBindingPredictionProject/src/R-3.2.3/bin:/software/ascp/:/software/sratoolkit/2.5.2/bin/:/users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/srv/scratch/imk1/TFBindingPredictionProject/src/R-3.2.3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/users/imk1/edirect:/users/imk1/edirect:/users/imk1/edirect:/users/imk1/edirect  

	
  string  PERL5LIB  /users/imk1/perl5/lib/perl5:/users/imk1/perl5/lib/perl5:/users/imk1/perl5/lib/perl5  

	
  string  PERL_LOCAL_LIB_ROOT  /users/imk1/perl5:/users/imk1/perl5:/users/imk1/perl5  

	
  string  PERL_MB_OPT  --install_base \"/users/imk1/perl5\"  

	
  string  PERL_MM_OPT  INSTALL_BASE=/users/imk1/perl5  

	
  real  PI  3.141592653589793  

	
  string  ppwd  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1  

	
  string  programName  chipseq.bds  

	
  string  programPath  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds  

	
  string  PWD  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370888_1  

	
  string  PYTHONPATH  /users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/  

	
  string  queue    

	
  int  retry  0  

	
  string  RULEFITBASE  /srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/  

	
  string  SHELL  /bin/bash  

	
  string  SHLVL  3  

	
  string  SSH_CLIENT  171.65.77.8 55144 22  

	
  string  SSH_CONNECTION  171.65.77.8 55144 171.65.76.63 22  

	
  string  SSH_TTY  /dev/pts/4  

	
  string  STY  12879.SRR1370888_1.BDS  

	
  string  system  sge  

	
  int  T  1099511627776  

	
  string  TERM  screen  

	
  string  TERMCAP  SC|screen|VT 100/ANSI X3.64 virtual terminal:\\\n\t:DO=\\E[%dB:LE=\\E[%dD:RI=\\E[%dC:UP=\\E[%dA:bs:bt=\\E[Z:\\\n\t:cd=\\E[J:ce=\\E[K:cl=\\E[H\\E[J:cm=\\E[%i%d;%dH:ct=\\E[3g:\\\n\t:do=^J:nd=\\E[C:pt:rc=\\E8:rs=\\Ec:sc=\\E7:st=\\EH:up=\\EM:\\\n\t:le=^H:bl=^G:cr=^M:it#8:ho=\\E[H:nw=\\EE:ta=^I:is=\\E)0:\\\n\t:li#24:co#80:am:xn:xv:LP:sr=\\EM:al=\\E[L:AL=\\E[%dL:\\\n\t:cs=\\E[%i%d;%dr:dl=\\E[M:DL=\\E[%dM:dc=\\E[P:DC=\\E[%dP:\\\n\t:im=\\E[4h:ei=\\E[4l:mi:IC=\\E[%d@:ks=\\E[?1h\\E=:\\\n\t:ke=\\E[?1l\\E>:vi=\\E[?25l:ve=\\E[34h\\E[?25h:vs=\\E[34l:\\\n\t:ti=\\E[?1049h:te=\\E[?1049l:Km=\\E[M:k0=\\E[10~:k1=\\EOP:\\\n\t:k2=\\EOQ:k3=\\EOR:k4=\\EOS:k5=\\E[15~:k6=\\E[17~:k7=\\E[18~:\\\n\t:k8=\\E[19~:k9=\\E[20~:k;=\\E[21~:F1=\\E[23~:F2=\\E[24~:\\\n\t:kh=\\E[1~:@1=\\E[1~:kH=\\E[4~:@7=\\E[4~:kN=\\E[6~:kP=\\E[5~:\\\n\t:kI=\\E[2~:kD=\\E[3~:ku=\\EOA:kd=\\EOB:kr=\\EOC:kl=\\EOD:  

	
  int  timeout  -1  

	
  string  USER  imk1  

	
  string  UTIL_SCRIPTS_DIR  /srv/scratch/imk1/TFBindingPredictionProject/src/av_scripts/  

	
  int  walltimeout  8640000  

	
  int  week  604800  

	
  string  WINDOW  0  

	
  string  XDG_RUNTIME_DIR  /run/user/1048  

	
  string  XDG_SESSION_ID  20  

	
  string  XFILESEARCHPATH  /usr/dt/app-defaults/%L/Dt