BigDataScript report: chipseq.bds

Script file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20161110_170941_367
Start time 2016-11-10 17:09:41
Run time 07:40:00.048
Tasks executed 11
Tasks failed 0
Tasks failed names 
 

		
  Arguments*  [-title, SRR1370874_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370874_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.20161110_170941_367/task.graphviz.report.line_97.id_19
chipseq.bds.20161110_170941_367/task.report.pdf2png.line_324.id_24
 
 		 

	
  thread_41   thread_Root 	 
 chipseq.bds.20161110_170941_367_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_11
chipseq.bds.20161110_170941_367_parallel_41/task.postalign_bam.bam_to_tag_rep1.line_505.id_12
chipseq.bds.20161110_170941_367_parallel_41/task.postalign_bed.subsample_tag_rep1.line_45.id_14
chipseq.bds.20161110_170941_367_parallel_41/task.postalign_bed.spr_rep1.line_255.id_15
chipseq.bds.20161110_170941_367_parallel_41/task.postalign_bed.xcor_rep1.line_212.id_16
 
 		 

	
  thread_42   thread_Root 	 
 chipseq.bds.20161110_170941_367_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_10
chipseq.bds.20161110_170941_367_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_13
chipseq.bds.20161110_170941_367_parallel_42/task.postalign_bam.dedup_bam_2_ctl1.line_144.id_17
chipseq.bds.20161110_170941_367_parallel_42/task.postalign_bam.bam_to_tag_ctl1.line_505.id_18
 
 		 

	






	
 Task details 

	

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

    
  
 
  Num   1  
 
  ID   task.postalign_bam.dedup_bam_1_ctl1.line_95.id_10  
 
  Name   dedup_bam_1 ctl1 
 
  Thread   thread_42  
 
  PID   6875  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus    4 
 
  Mem    
 
 		  
 
  Start   2016-11-10 17:09:43  
 
  End   2016-11-10 17:36:03  
 
  Elapsed   00:26:19  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam
  
 
  Dependencies     
 
 		  
 
# SYS command. line 97

 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 105

 if [[ 0 > 0 ]]; then \
				sambamba sort -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
				samtools view -F 1804 -Su /dev/stdin | \
				sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam | \
			    	sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam; \
			    fi

# SYS command. line 116

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
15322 (process ID) old priority 0, new priority 10

  
 		 

    
  
 
  Num   2  
 
  ID   task.postalign_bam.dedup_bam_2_rep1.line_144.id_11  
 
  Name   dedup_bam_2 rep1 
 
  Thread   thread_41  
 
  PID   6876  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-11-10 17:09:44  
 
  End   2016-11-10 17:15:05  
 
  Elapsed   00:05:20  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/rep1/SRR1370874_1.dupmark.bam
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/rep1/SRR1370874_1.nodup.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/qc/rep1/SRR1370874_1.nodup.flagstat.qc
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/qc/rep1/SRR1370874_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/SRR1370874_1/out/align/rep1/SRR1370874_1.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/rep1/SRR1370874_1.nodup.bam

# SYS command. line 153

 sambamba index -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/rep1/SRR1370874_1.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/rep1/SRR1370874_1.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/qc/rep1/SRR1370874_1.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/rep1/SRR1370874_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/SRR1370874_1/out/qc/rep1/SRR1370874_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--------------------
29434 (process ID) old priority 0, new priority 10

  
 		 

    
  
 
  Num   3  
 
  ID   task.postalign_bam.bam_to_tag_rep1.line_505.id_12  
 
  Name   bam_to_tag rep1 
 
  Thread   thread_41  
 
  PID   7144  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-11-10 17:15:06  
 
  End   2016-11-10 19:39:50  
 
  Elapsed   02:24:43  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/rep1/SRR1370874_1.nodup.bam
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/rep1/SRR1370874_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/SRR1370874_1/out/align/rep1/SRR1370874_1.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/rep1/SRR1370874_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--------------------
20162 (process ID) old priority 0, new priority 10

Waiting for 13 seconds.

  
 		 

    
  
 
  Num   4  
 
  ID   task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_13  
 
  Name   markdup_bam_picard ctl1 
 
  Thread   thread_42  
 
  PID   7156  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus    1 
 
  Mem    
 
 		  
 
  Start   2016-11-10 17:36:05  
 
  End   2016-11-10 21:21:49  
 
  Elapsed   03:45:44  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc
  
 
  Dependencies     
 
 		  
 
# SYS command. line 350

 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 354

 export _JAVA_OPTIONS="-Xms256M -Xmx12G -XX:ParallelGCThreads=1"

# SYS command. line 360

 if [ -f "${PICARDROOT}/picard.jar" ]; then \
		      MARKDUP="${PICARDROOT}/picard.jar MarkDuplicates"; \
		    elif [ -f "${PICARDROOT}/MarkDuplicates.jar" ]; then \
		      MARKDUP="${PICARDROOT}/MarkDuplicates.jar"; \
		    elif [ $(which picard 2> /dev/null | wc -l || echo) == "1" ]; then \
		      MARKDUP="$(ls $(dirname $(which picard))/../share/picard*/MarkDuplicates.jar 2> /dev/null || echo)"; \
		    fi

# SYS command. line 369

 if [ -f "${MARKDUP}" ]; then \
			java -Xmx4G -jar ${MARKDUP} \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
		    else \
			picard MarkDuplicates \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
			fi

# SYS command. line 381

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
47426 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1
[Thu Nov 10 19:51:32 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Thu Nov 10 19:51:32 PST 2016] Executing as imk1@nandi on Linux 4.4.0-38-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-11-10 19:51:32	MarkDuplicates	Start of doWork freeMemory: 254879200; totalMemory: 257425408; maxMemory: 11453595648
INFO	2016-11-10 19:51:32	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-11-10 19:51:32	MarkDuplicates	Will retain up to 44052290 data points before spilling to disk.
INFO	2016-11-10 19:51:45	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:11s.  Time for last 1,000,000:   11s.  Last read position: chr1:22,298,551
INFO	2016-11-10 19:51:45	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:51:53	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:18s.  Time for last 1,000,000:    7s.  Last read position: chr1:41,895,424
INFO	2016-11-10 19:51:53	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:52:00	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:25s.  Time for last 1,000,000:    7s.  Last read position: chr1:63,396,527
INFO	2016-11-10 19:52:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:52:09	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:34s.  Time for last 1,000,000:    9s.  Last read position: chr1:89,147,707
INFO	2016-11-10 19:52:09	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:52:18	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:43s.  Time for last 1,000,000:    8s.  Last read position: chr1:115,615,553
INFO	2016-11-10 19:52:18	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:52:27	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:52s.  Time for last 1,000,000:    9s.  Last read position: chr1:164,468,682
INFO	2016-11-10 19:52:27	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:52:36	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:01:01s.  Time for last 1,000,000:    8s.  Last read position: chr1:189,102,252
INFO	2016-11-10 19:52:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:52:44	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:01:09s.  Time for last 1,000,000:    7s.  Last read position: chr1:213,979,760
INFO	2016-11-10 19:52:44	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:52:57	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:01:22s.  Time for last 1,000,000:   13s.  Last read position: chr1:231,814,268
INFO	2016-11-10 19:52:57	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:53:01	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:01:26s.  Time for last 1,000,000:    3s.  Last read position: chr2:3,652,468
INFO	2016-11-10 19:53:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:53:07	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:32s.  Time for last 1,000,000:    6s.  Last read position: chr2:39,505,122
INFO	2016-11-10 19:53:07	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:53:15	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:41s.  Time for last 1,000,000:    8s.  Last read position: chr2:73,561,393
INFO	2016-11-10 19:53:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:53:20	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:45s.  Time for last 1,000,000:    4s.  Last read position: chr2:120,526,571
INFO	2016-11-10 19:53:20	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:53:27	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:52s.  Time for last 1,000,000:    7s.  Last read position: chr2:160,316,783
INFO	2016-11-10 19:53:27	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:53:32	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:57s.  Time for last 1,000,000:    5s.  Last read position: chr2:195,549,735
INFO	2016-11-10 19:53:32	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:53:38	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:02:03s.  Time for last 1,000,000:    5s.  Last read position: chr2:230,358,034
INFO	2016-11-10 19:53:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:53:42	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:02:07s.  Time for last 1,000,000:    3s.  Last read position: chr3:16,305,780
INFO	2016-11-10 19:53:42	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:53:51	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:02:16s.  Time for last 1,000,000:    8s.  Last read position: chr3:49,251,279
INFO	2016-11-10 19:53:51	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:53:56	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:02:22s.  Time for last 1,000,000:    5s.  Last read position: chr3:84,621,225
INFO	2016-11-10 19:53:56	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:54:02	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:02:27s.  Time for last 1,000,000:    5s.  Last read position: chr3:128,121,129
INFO	2016-11-10 19:54:02	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:54:06	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:02:31s.  Time for last 1,000,000:    3s.  Last read position: chr3:165,373,238
INFO	2016-11-10 19:54:06	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:54:16	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:02:41s.  Time for last 1,000,000:   10s.  Last read position: chr3:195,333,247
INFO	2016-11-10 19:54:16	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:54:23	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:02:48s.  Time for last 1,000,000:    6s.  Last read position: chr4:37,752,582
INFO	2016-11-10 19:54:23	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:54:28	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:02:54s.  Time for last 1,000,000:    5s.  Last read position: chr4:81,286,306
INFO	2016-11-10 19:54:28	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:54:32	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:02:57s.  Time for last 1,000,000:    3s.  Last read position: chr4:119,339,736
INFO	2016-11-10 19:54:32	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:54:42	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:03:07s.  Time for last 1,000,000:    9s.  Last read position: chr4:158,818,783
INFO	2016-11-10 19:54:42	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:54:46	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:03:12s.  Time for last 1,000,000:    4s.  Last read position: chr5:6,447,551
INFO	2016-11-10 19:54:46	MarkDuplicates	Tracking 16 as yet unmatched pairs. 16 records in RAM.
INFO	2016-11-10 19:54:52	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:03:17s.  Time for last 1,000,000:    5s.  Last read position: chr5:33,219,021
INFO	2016-11-10 19:54:52	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:54:55	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:03:21s.  Time for last 1,000,000:    3s.  Last read position: chr5:60,694,078
INFO	2016-11-10 19:54:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:55:04	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:03:29s.  Time for last 1,000,000:    8s.  Last read position: chr5:86,336,676
INFO	2016-11-10 19:55:04	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:55:15	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:03:40s.  Time for last 1,000,000:   10s.  Last read position: chr5:112,930,184
INFO	2016-11-10 19:55:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:55:20	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:03:45s.  Time for last 1,000,000:    5s.  Last read position: chr5:136,852,889
INFO	2016-11-10 19:55:20	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:55:25	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:03:50s.  Time for last 1,000,000:    4s.  Last read position: chr5:160,271,193
INFO	2016-11-10 19:55:25	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:55:29	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:03:54s.  Time for last 1,000,000:    4s.  Last read position: chr6:4,126,386
INFO	2016-11-10 19:55:29	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:55:33	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:03:58s.  Time for last 1,000,000:    4s.  Last read position: chr6:28,666,579
INFO	2016-11-10 19:55:33	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:55:37	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:04:02s.  Time for last 1,000,000:    3s.  Last read position: chr6:49,527,281
INFO	2016-11-10 19:55:37	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:55:51	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:04:16s.  Time for last 1,000,000:   13s.  Last read position: chr6:81,728,195
INFO	2016-11-10 19:55:51	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:55:59	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:04:24s.  Time for last 1,000,000:    8s.  Last read position: chr6:107,535,760
INFO	2016-11-10 19:55:59	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:56:05	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:04:30s.  Time for last 1,000,000:    5s.  Last read position: chr6:132,364,408
INFO	2016-11-10 19:56:05	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:56:08	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:04:33s.  Time for last 1,000,000:    3s.  Last read position: chr6:156,918,595
INFO	2016-11-10 19:56:08	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:56:14	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:04:39s.  Time for last 1,000,000:    5s.  Last read position: chr7:18,636,743
INFO	2016-11-10 19:56:14	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:56:27	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:04:52s.  Time for last 1,000,000:   12s.  Last read position: chr7:53,850,313
INFO	2016-11-10 19:56:27	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:56:31	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:04:57s.  Time for last 1,000,000:    4s.  Last read position: chr7:96,503,433
INFO	2016-11-10 19:56:31	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:56:39	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:05:05s.  Time for last 1,000,000:    7s.  Last read position: chr7:120,651,846
INFO	2016-11-10 19:56:39	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:57:22	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:05:47s.  Time for last 1,000,000:   42s.  Last read position: chr7:146,401,497
INFO	2016-11-10 19:57:22	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:57:27	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:05:52s.  Time for last 1,000,000:    4s.  Last read position: chr8:17,030,519
INFO	2016-11-10 19:57:27	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:57:33	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:05:58s.  Time for last 1,000,000:    6s.  Last read position: chr8:42,750,671
INFO	2016-11-10 19:57:33	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:57:39	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:06:04s.  Time for last 1,000,000:    5s.  Last read position: chr8:85,385,487
INFO	2016-11-10 19:57:39	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:57:45	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:06:10s.  Time for last 1,000,000:    6s.  Last read position: chr8:124,358,985
INFO	2016-11-10 19:57:45	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:57:50	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:06:15s.  Time for last 1,000,000:    5s.  Last read position: chr9:18,183,883
INFO	2016-11-10 19:57:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:58:00	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:06:25s.  Time for last 1,000,000:   10s.  Last read position: chr9:84,163,983
INFO	2016-11-10 19:58:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:58:04	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:06:29s.  Time for last 1,000,000:    4s.  Last read position: chr9:119,875,535
INFO	2016-11-10 19:58:04	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:58:08	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:06:33s.  Time for last 1,000,000:    3s.  Last read position: chr10:5,661,683
INFO	2016-11-10 19:58:08	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:58:12	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:06:37s.  Time for last 1,000,000:    4s.  Last read position: chr10:29,748,948
INFO	2016-11-10 19:58:12	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:58:23	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:06:48s.  Time for last 1,000,000:   10s.  Last read position: chr10:61,280,221
INFO	2016-11-10 19:58:23	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:58:30	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:06:55s.  Time for last 1,000,000:    6s.  Last read position: chr10:85,305,552
INFO	2016-11-10 19:58:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 19:58:41	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:07:06s.  Time for last 1,000,000:   11s.  Last read position: chr10:108,129,202
INFO	2016-11-10 19:58:41	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:58:46	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:07:11s.  Time for last 1,000,000:    4s.  Last read position: chr10:132,730,123
INFO	2016-11-10 19:58:46	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:58:49	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:07:14s.  Time for last 1,000,000:    3s.  Last read position: chr11:35,359,267
INFO	2016-11-10 19:58:49	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:59:02	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:07:27s.  Time for last 1,000,000:   12s.  Last read position: chr11:75,696,431
INFO	2016-11-10 19:59:02	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:59:13	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:07:38s.  Time for last 1,000,000:   10s.  Last read position: chr11:114,414,621
INFO	2016-11-10 19:59:13	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:59:18	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:07:43s.  Time for last 1,000,000:    4s.  Last read position: chr12:8,900,276
INFO	2016-11-10 19:59:18	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 19:59:24	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:07:49s.  Time for last 1,000,000:    6s.  Last read position: chr12:38,863,889
INFO	2016-11-10 19:59:24	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 19:59:31	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:07:56s.  Time for last 1,000,000:    6s.  Last read position: chr12:60,598,824
INFO	2016-11-10 19:59:31	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 19:59:43	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:08:08s.  Time for last 1,000,000:   11s.  Last read position: chr12:88,520,538
INFO	2016-11-10 19:59:43	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 19:59:50	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:08:15s.  Time for last 1,000,000:    7s.  Last read position: chr12:112,268,437
INFO	2016-11-10 19:59:50	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 20:00:03	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:08:28s.  Time for last 1,000,000:   12s.  Last read position: chr13:23,999,632
INFO	2016-11-10 20:00:03	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 20:00:07	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:08:32s.  Time for last 1,000,000:    4s.  Last read position: chr13:51,165,870
INFO	2016-11-10 20:00:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 20:00:11	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:08:36s.  Time for last 1,000,000:    4s.  Last read position: chr13:88,986,369
INFO	2016-11-10 20:00:11	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 20:00:19	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:08:44s.  Time for last 1,000,000:    7s.  Last read position: chr14:23,149,367
INFO	2016-11-10 20:00:19	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 20:00:25	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:08:50s.  Time for last 1,000,000:    5s.  Last read position: chr14:58,140,905
INFO	2016-11-10 20:00:25	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 20:00:30	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:08:55s.  Time for last 1,000,000:    4s.  Last read position: chr14:91,912,553
INFO	2016-11-10 20:00:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 20:00:37	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:09:02s.  Time for last 1,000,000:    7s.  Last read position: chr15:38,895,095
INFO	2016-11-10 20:00:37	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 20:00:41	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:09:06s.  Time for last 1,000,000:    3s.  Last read position: chr15:68,188,367
INFO	2016-11-10 20:00:41	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 20:00:57	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:09:23s.  Time for last 1,000,000:   16s.  Last read position: chr15:87,921,272
INFO	2016-11-10 20:00:57	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 20:01:06	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:09:32s.  Time for last 1,000,000:    9s.  Last read position: chr16:11,143,813
INFO	2016-11-10 20:01:06	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 20:01:12	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:09:37s.  Time for last 1,000,000:    5s.  Last read position: chr16:51,391,437
INFO	2016-11-10 20:01:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 20:01:17	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:09:42s.  Time for last 1,000,000:    4s.  Last read position: chr16:84,928,458
INFO	2016-11-10 20:01:17	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 20:01:21	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:09:46s.  Time for last 1,000,000:    4s.  Last read position: chr17:18,368,935
INFO	2016-11-10 20:01:21	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 20:01:26	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:09:51s.  Time for last 1,000,000:    4s.  Last read position: chr17:44,246,522
INFO	2016-11-10 20:01:26	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 20:01:30	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:09:55s.  Time for last 1,000,000:    4s.  Last read position: chr17:66,172,158
INFO	2016-11-10 20:01:30	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-11-10 20:01:37	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:10:02s.  Time for last 1,000,000:    6s.  Last read position: chr18:5,619,614
INFO	2016-11-10 20:01:37	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 20:01:53	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:10:18s.  Time for last 1,000,000:   16s.  Last read position: chr18:46,152,631
INFO	2016-11-10 20:01:53	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 20:02:01	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:10:27s.  Time for last 1,000,000:    8s.  Last read position: chr19:1,328,731
INFO	2016-11-10 20:02:01	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 20:02:10	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:10:35s.  Time for last 1,000,000:    8s.  Last read position: chr19:28,148,444
INFO	2016-11-10 20:02:10	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 20:02:16	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:10:41s.  Time for last 1,000,000:    5s.  Last read position: chr19:40,341,579
INFO	2016-11-10 20:02:16	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 20:02:26	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:10:51s.  Time for last 1,000,000:   10s.  Last read position: chr20:3,222,035
INFO	2016-11-10 20:02:26	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 20:02:34	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:10:59s.  Time for last 1,000,000:    7s.  Last read position: chr20:37,218,903
INFO	2016-11-10 20:02:34	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 20:03:09	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:11:34s.  Time for last 1,000,000:   35s.  Last read position: chr20:62,871,367
INFO	2016-11-10 20:03:09	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-11-10 20:03:14	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:11:39s.  Time for last 1,000,000:    4s.  Last read position: chr21:39,474,524
INFO	2016-11-10 20:03:14	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 20:03:18	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:11:44s.  Time for last 1,000,000:    4s.  Last read position: chr22:31,346,944
INFO	2016-11-10 20:03:18	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 20:03:24	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:11:49s.  Time for last 1,000,000:    5s.  Last read position: chrX:6,235,951
INFO	2016-11-10 20:03:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 20:03:31	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:11:56s.  Time for last 1,000,000:    6s.  Last read position: chrX:38,820,975
INFO	2016-11-10 20:03:31	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 20:03:39	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:12:04s.  Time for last 1,000,000:    8s.  Last read position: chrX:69,473,954
INFO	2016-11-10 20:03:39	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 20:03:44	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:12:09s.  Time for last 1,000,000:    4s.  Last read position: chrX:92,683,143
INFO	2016-11-10 20:03:44	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 20:03:48	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:12:13s.  Time for last 1,000,000:    4s.  Last read position: chrX:118,447,518
INFO	2016-11-10 20:03:48	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 20:03:52	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:12:18s.  Time for last 1,000,000:    4s.  Last read position: chrX:142,819,613
INFO	2016-11-10 20:03:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 20:03:56	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:12:21s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,995
INFO	2016-11-10 20:03:56	MarkDuplicates	Tracking 7472 as yet unmatched pairs. 7472 records in RAM.
INFO	2016-11-10 20:04:00	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:12:25s.  Time for last 1,000,000:    4s.  Last read position: chrM:11,775
INFO	2016-11-10 20:04:00	MarkDuplicates	Tracking 14000 as yet unmatched pairs. 14000 records in RAM.
INFO	2016-11-10 20:04:04	MarkDuplicates	Read 99989486 records. 0 pairs never matched.
INFO	2016-11-10 20:04:10	MarkDuplicates	After buildSortedReadEndLists freeMemory: 5734654992; totalMemory: 5814353920; maxMemory: 11453595648
INFO	2016-11-10 20:04:10	MarkDuplicates	Will retain up to 357924864 duplicate indices before spilling to disk.
INFO	2016-11-10 20:04:11	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-11-10 20:04:32	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-11-10 20:04:54	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-11-10 20:04:55	MarkDuplicates	After generateDuplicateIndexes freeMemory: 5729416808; totalMemory: 8670674944; maxMemory: 11453595648
INFO	2016-11-10 20:04:55	MarkDuplicates	Marking 496224 records as duplicates.
INFO	2016-11-10 20:04:55	MarkDuplicates	Found 42648 optical duplicate clusters.
INFO	2016-11-10 20:08:03	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:02:38s.  Time for last 10,000,000:  158s.  Last read position: chr2:3,652,468
INFO	2016-11-10 20:11:40	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:06:15s.  Time for last 10,000,000:  216s.  Last read position: chr3:128,121,129
INFO	2016-11-10 20:15:19	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:09:53s.  Time for last 10,000,000:  218s.  Last read position: chr5:86,336,676
INFO	2016-11-10 20:23:06	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:17:41s.  Time for last 10,000,000:  467s.  Last read position: chr6:156,918,595
INFO	2016-11-10 20:30:14	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:24:48s.  Time for last 10,000,000:  427s.  Last read position: chr9:18,183,883
INFO	2016-11-10 20:40:20	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:34:55s.  Time for last 10,000,000:  606s.  Last read position: chr11:75,696,431
INFO	2016-11-10 20:52:14	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:46:49s.  Time for last 10,000,000:  713s.  Last read position: chr14:23,149,367
INFO	2016-11-10 20:59:04	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:53:38s.  Time for last 10,000,000:  409s.  Last read position: chr17:44,246,522
INFO	2016-11-10 21:13:33	MarkDuplicates	Written    90,000,000 records.  Elapsed time: 01:08:08s.  Time for last 10,000,000:  869s.  Last read position: chr21:39,474,524
INFO	2016-11-10 21:20:38	MarkDuplicates	Before output close freeMemory: 8660010552; totalMemory: 8744599552; maxMemory: 11453595648
INFO	2016-11-10 21:21:09	MarkDuplicates	After output close freeMemory: 8657388056; totalMemory: 8741978112; maxMemory: 11453595648
[Thu Nov 10 21:21:11 PST 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 89.66 minutes.
Runtime.totalMemory()=8741978112

 
 		 

    
  
 
  Num   5  
 
  ID   task.postalign_bed.subsample_tag_rep1.line_45.id_14  
 
  Name   subsample_tag rep1 
 
  Thread   thread_41  
 
  PID   7293  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-11-10 19:39:51  
 
  End   2016-11-10 20:46:02  
 
  Elapsed   01:06:10  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/rep1/SRR1370874_1.nodup.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/rep1/SRR1370874_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/SRR1370874_1/out/align/rep1/SRR1370874_1.nodup.tagAlign.gz | \
			grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/rep1/SRR1370874_1.nodup.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/rep1/SRR1370874_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--------------------
23055 (process ID) old priority 0, new priority 10

  
 		 

    
  
 
  Num   6  
 
  ID   task.postalign_bed.spr_rep1.line_255.id_15  
 
  Name   spr rep1 
 
  Thread   thread_41  
 
  PID   7294  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-11-10 19:39:52  
 
  End   2016-11-10 20:45:54  
 
  Elapsed   01:06:01  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/rep1/SRR1370874_1.nodup.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/pseudo_reps/rep1/pr1/SRR1370874_1.nodup.pr1.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/pseudo_reps/rep1/pr2/SRR1370874_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/SRR1370874_1/out/align/rep1/SRR1370874_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/SRR1370874_1/out/align/rep1/SRR1370874_1.nodup.tagAlign.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/rep1/SRR1370874_1.nodup.tagAlign.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/pseudo_reps/rep1/pr1/SRR1370874_1.nodup.

# SYS command. line 268

 gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/pseudo_reps/rep1/pr1/SRR1370874_1.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/pseudo_reps/rep1/pr1/SRR1370874_1.nodup.pr1.tagAlign.gz

# SYS command. line 269

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/pseudo_reps/rep1/pr1/SRR1370874_1.nodup.00

# SYS command. line 270

 gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/pseudo_reps/rep1/pr1/SRR1370874_1.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/pseudo_reps/rep1/pr2/SRR1370874_1.nodup.pr2.tagAlign.gz

# SYS command. line 271

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/pseudo_reps/rep1/pr1/SRR1370874_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--------------------
45156 (process ID) old priority 0, new priority 10
Waiting for 19 seconds.

  
 		 

    
  
 
  Num   7  
 
  ID   task.postalign_bed.xcor_rep1.line_212.id_16  
 
  Name   xcor rep1 
 
  Thread   thread_41  
 
  PID   7383  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-11-10 20:46:03  
 
  End   2016-11-10 21:53:47  
 
  Elapsed   01:07:43  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/rep1/SRR1370874_1.nodup.15M.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/qc/rep1/SRR1370874_1.nodup.15M.cc.qc
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/qc/rep1/SRR1370874_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/SRR1370874_1/out/align/rep1/SRR1370874_1.nodup.15M.tagAlign.gz -p=1 \
			-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/qc/rep1/SRR1370874_1.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/qc/rep1/SRR1370874_1.nodup.15M.cc.qc 

# SYS command. line 226

 sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/qc/rep1/SRR1370874_1.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/qc/rep1/SRR1370874_1.nodup.15M.cc.qc.tmp

# SYS command. line 227

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/qc/rep1/SRR1370874_1.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/qc/rep1/SRR1370874_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--------------------
20376 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/rep1/SRR1370874_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/SRR1370874_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/SRR1370874_1/out/qc/rep1/SRR1370874_1.nodup.15M.cc.plot.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/qc/rep1/SRR1370874_1.nodup.15M.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/rep1/SRR1370874_1.nodup.15M.tagAlign.gz 
opened /tmp/7383.1.q/Rtmp1X01A2/SRR1370874_1.nodup.15M.tagAlign5015281b1865
done. read 13213324 fragments
ChIP data read length 69 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1496215 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.203358157666487 
Top 3 estimates for fragment length 145 
Window half size 285 
Phantom peak location 75 
Phantom peak Correlation 0.1888174 
Normalized Strand cross-correlation coefficient (NSC) 1.359151 
Relative Strand cross-correlation Coefficient (RSC) 1.370977 
Phantom Peak Quality Tag 1 
null device 
          1 

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

 
 		 

    
  
 
  Num   8  
 
  ID   task.postalign_bam.dedup_bam_2_ctl1.line_144.id_17  
 
  Name   dedup_bam_2 ctl1 
 
  Thread   thread_42  
 
  PID   7425  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus    4 
 
  Mem    
 
 		  
 
  Start   2016-11-10 21:21:51  
 
  End   2016-11-11 00:38:18  
 
  Elapsed   03:16:27  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/qc/ctl1/ss_50M_2000_GRCh38.nodup.flagstat.qc
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/qc/ctl1/ss_50M_2000_GRCh38.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/SRR1370874_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam

# SYS command. line 153

 sambamba index -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/qc/ctl1/ss_50M_2000_GRCh38.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/ctl1/ss_50M_2000_GRCh38.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/SRR1370874_1/out/qc/ctl1/ss_50M_2000_GRCh38.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--------------------
43887 (process ID) old priority 0, new priority 10

  
 		 

    
  
 
  Num   9  
 
  ID   task.postalign_bam.bam_to_tag_ctl1.line_505.id_18  
 
  Name   bam_to_tag ctl1 
 
  Thread   thread_42  
 
  PID   7957  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-11-11 00:38:21  
 
  End   2016-11-11 00:49:26  
 
  Elapsed   00:11:05  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/ctl1/ss_50M_2000_GRCh38.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/SRR1370874_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/ctl1/ss_50M_2000_GRCh38.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--------------------
29790 (process ID) old priority 0, new priority 10


  
 		 

    
  
 
  Num   10  
 
  ID   task.graphviz.report.line_97.id_19  
 
  Name   report 
 
  Thread   thread_Root  
 
  PID   17372  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-11-11 00:49:27  
 
  End   2016-11-11 00:49:41  
 
  Elapsed   00:00:13  
 
  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/SRR1370874_1/out/report/SRR1370874_1_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/report/SRR1370874_1_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/report/SRR1370874_1_workflow.svg" # to suppress dot font error (exit code=1)
 
 
   
--------------------Stdout--------------------
17376 (process ID) old priority 0, new priority 10

  
 		 

    
  
 
  Num   11  
 
  ID   task.report.pdf2png.line_324.id_24  
 
  Name   pdf2png 
 
  Thread   thread_Root  
 
  PID   17413  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2016-11-11 00:49:28  
 
  End   2016-11-11 00:49:40  
 
  Elapsed   00:00:11  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/qc/rep1/SRR1370874_1.nodup.15M.cc.plot.pdf
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/qc/rep1/SRR1370874_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/SRR1370874_1/out/qc/rep1/SRR1370874_1.nodup.15M.cc.plot.png \
			-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/qc/rep1/SRR1370874_1.nodup.15M.cc.plot.pdf
 
 
   
--------------------Stdout--------------------
17417 (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, SRR1370874_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370874_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  /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  

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

	
  string  PERL_LOCAL_LIB_ROOT  /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/SRR1370874_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/SRR1370874_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  28373.SRR1370874_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