BigDataScript report: chipseq.bds

Script file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20161109_175134_792
Start time 2016-11-09 17:51:34
Run time 3 days 19:15:47.391
Tasks executed 3
Tasks failed 2
Tasks failed names 
bwa_aln rep1
markdup_bam_picard ctl1
Arguments* [-title, SRR1370905_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370905_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
thread_41 thread_Root 
 chipseq.bds.20161109_175134_792_parallel_41/task.align_bwa.bwa_aln_rep1.line_108.id_11
thread_42 thread_Root 
 chipseq.bds.20161109_175134_792_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_10
chipseq.bds.20161109_175134_792_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_12

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 6011
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus 4
Mem
Start 2016-11-09 17:51:38
End 2016-11-09 18:52:26
Elapsed 01:00:47
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/SRR1370905_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam
Dependencies 
 
# SYS command. line 97

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${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/SRR1370905_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_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/SRR1370905_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_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/SRR1370905_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--------------------
32708 (process ID) old priority 0, new priority 10
Num 2
ID task.align_bwa.bwa_aln_rep1.line_108.id_11
Name bwa_aln rep1
Thread thread_41
PID 6013
OK false
Exit Code 3
Retries
State KILLED
Dep. ERROR
Cpus
Mem
Start 2016-11-09 17:51:38
End 2016-11-09 21:13:07
Elapsed 03:21:28
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370905_1.fastq.gz
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.sai
Dependencies 
 
# SYS command. line 110

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

# SYS command. line 113

 bwa aln -q 5 -l 32 -k 2 -t 1 /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370905_1.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/rep1/SRR1370905_1.sai

# SYS command. line 115

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
   
--------------------Stdout--------------------
4055 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.41 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.54 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.03 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.97 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.61 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.78 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.48 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.43 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.35 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.74 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.94 sec
[bwa_aln_core] write to the disk... 0.11 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.87 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.89 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.08 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.94 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.00 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.37 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.37 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.60 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.10 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.23 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.13 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.02 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.18 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.25 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.70 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.10 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.23 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.45 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.88 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.78 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.63 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.59 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.30 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.74 sec
[bwa_aln_core] write to the disk... [fwrite] No space left on device
Num 3
ID task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_12
Name markdup_bam_picard ctl1
Thread thread_42
PID 6280
OK false
Exit Code 3
Retries
State RUNNING
Dep. WAIT
Cpus 1
Mem
Start 2016-11-09 18:52:28
End 2016-11-09 18:52:28
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc
Dependencies 
 
# SYS command. line 349

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

# SYS command. line 353

 export _JAVA_OPTIONS="-Xms256M -Xmx4G -XX:ParallelGCThreads=1"

# SYS command. line 354

 export MAX_JAVA_MEM="12G"

# SYS command. line 359

 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 368

 if [ -f "${MARKDUP}" ]; then \
			java -Xmx4G -jar ${MARKDUP} \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_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/SRR1370905_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
			fi

# SYS command. line 380

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
   
--------------------Stdout--------------------
40379 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Wed Nov 09 21:22:03 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370905_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
[Wed Nov 09 21:22:03 PST 2016] Executing as imk1@kali on Linux 3.19.0-64-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-11-09 21:22:04	MarkDuplicates	Start of doWork freeMemory: 254879344; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-11-09 21:22:04	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-11-09 21:22:04	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-11-09 21:22:27	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:21s.  Time for last 1,000,000:   21s.  Last read position: chr1:22,298,551
INFO	2016-11-09 21:22:27	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 21:22:50	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:43s.  Time for last 1,000,000:   22s.  Last read position: chr1:41,895,424
INFO	2016-11-09 21:22:50	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 21:23:02	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:56s.  Time for last 1,000,000:   12s.  Last read position: chr1:63,396,527
INFO	2016-11-09 21:23:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 21:23:12	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:01:06s.  Time for last 1,000,000:   10s.  Last read position: chr1:89,147,707
INFO	2016-11-09 21:23:12	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 21:23:26	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:01:20s.  Time for last 1,000,000:   14s.  Last read position: chr1:115,615,553
INFO	2016-11-09 21:23:26	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 21:23:38	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:01:31s.  Time for last 1,000,000:   11s.  Last read position: chr1:164,468,682
INFO	2016-11-09 21:23:38	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-09 21:23:54	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:01:48s.  Time for last 1,000,000:   16s.  Last read position: chr1:189,102,252
INFO	2016-11-09 21:23:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 21:24:07	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:02:01s.  Time for last 1,000,000:   13s.  Last read position: chr1:213,979,760
INFO	2016-11-09 21:24:07	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 21:24:22	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:02:16s.  Time for last 1,000,000:   14s.  Last read position: chr1:231,814,268
INFO	2016-11-09 21:24:22	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 21:24:37	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:02:31s.  Time for last 1,000,000:   15s.  Last read position: chr2:3,652,468
INFO	2016-11-09 21:24:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 21:24:53	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:02:47s.  Time for last 1,000,000:   16s.  Last read position: chr2:39,505,122
INFO	2016-11-09 21:24:53	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 21:25:13	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:03:06s.  Time for last 1,000,000:   19s.  Last read position: chr2:73,561,393
INFO	2016-11-09 21:25:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 21:25:32	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:03:26s.  Time for last 1,000,000:   19s.  Last read position: chr2:120,526,571
INFO	2016-11-09 21:25:32	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 21:25:50	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:03:44s.  Time for last 1,000,000:   17s.  Last read position: chr2:160,316,783
INFO	2016-11-09 21:25:50	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 21:26:19	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:04:12s.  Time for last 1,000,000:   28s.  Last read position: chr2:195,549,735
INFO	2016-11-09 21:26:19	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 21:26:39	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:04:32s.  Time for last 1,000,000:   20s.  Last read position: chr2:230,358,034
INFO	2016-11-09 21:26:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 21:26:56	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:04:49s.  Time for last 1,000,000:   16s.  Last read position: chr3:16,305,780
INFO	2016-11-09 21:26:56	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-09 21:27:17	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:05:11s.  Time for last 1,000,000:   21s.  Last read position: chr3:49,251,279
INFO	2016-11-09 21:27:17	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 21:27:38	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:05:31s.  Time for last 1,000,000:   20s.  Last read position: chr3:84,621,225
INFO	2016-11-09 21:27:38	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 21:27:58	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:05:52s.  Time for last 1,000,000:   20s.  Last read position: chr3:128,121,129
INFO	2016-11-09 21:27:58	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 21:28:16	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:06:10s.  Time for last 1,000,000:   18s.  Last read position: chr3:165,373,238
INFO	2016-11-09 21:28:16	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 21:28:43	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:06:37s.  Time for last 1,000,000:   26s.  Last read position: chr3:195,333,247
INFO	2016-11-09 21:28:43	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 21:28:59	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:06:52s.  Time for last 1,000,000:   15s.  Last read position: chr4:37,752,582
INFO	2016-11-09 21:28:59	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 21:29:21	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:07:14s.  Time for last 1,000,000:   21s.  Last read position: chr4:81,286,306
INFO	2016-11-09 21:29:21	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 21:29:41	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:07:35s.  Time for last 1,000,000:   20s.  Last read position: chr4:119,339,736
INFO	2016-11-09 21:29:41	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 21:30:07	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:08:00s.  Time for last 1,000,000:   25s.  Last read position: chr4:158,818,783
INFO	2016-11-09 21:30:07	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 21:30:37	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:08:30s.  Time for last 1,000,000:   29s.  Last read position: chr5:6,447,551
INFO	2016-11-09 21:30:37	MarkDuplicates	Tracking 16 as yet unmatched pairs. 16 records in RAM.
INFO	2016-11-09 21:30:56	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:08:49s.  Time for last 1,000,000:   18s.  Last read position: chr5:33,219,021
INFO	2016-11-09 21:30:56	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-09 21:31:20	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:09:14s.  Time for last 1,000,000:   24s.  Last read position: chr5:60,694,078
INFO	2016-11-09 21:31:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 21:31:57	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:09:51s.  Time for last 1,000,000:   37s.  Last read position: chr5:86,336,676
INFO	2016-11-09 21:31:57	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 21:32:29	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:10:23s.  Time for last 1,000,000:   31s.  Last read position: chr5:112,930,184
INFO	2016-11-09 21:32:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 21:32:57	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:10:51s.  Time for last 1,000,000:   28s.  Last read position: chr5:136,852,889
INFO	2016-11-09 21:32:57	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 21:33:21	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:11:14s.  Time for last 1,000,000:   23s.  Last read position: chr5:160,271,193
INFO	2016-11-09 21:33:21	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 21:33:52	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:11:46s.  Time for last 1,000,000:   31s.  Last read position: chr6:4,126,386
INFO	2016-11-09 21:33:52	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-09 21:34:15	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:12:08s.  Time for last 1,000,000:   22s.  Last read position: chr6:28,666,579
INFO	2016-11-09 21:34:15	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 21:34:39	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:12:33s.  Time for last 1,000,000:   24s.  Last read position: chr6:49,527,281
INFO	2016-11-09 21:34:39	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 21:35:06	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:13:00s.  Time for last 1,000,000:   27s.  Last read position: chr6:81,728,195
INFO	2016-11-09 21:35:06	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 21:35:31	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:13:25s.  Time for last 1,000,000:   25s.  Last read position: chr6:107,535,760
INFO	2016-11-09 21:35:31	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 21:36:00	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:13:53s.  Time for last 1,000,000:   28s.  Last read position: chr6:132,364,408
INFO	2016-11-09 21:36:00	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 21:36:22	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:14:16s.  Time for last 1,000,000:   22s.  Last read position: chr6:156,918,595
INFO	2016-11-09 21:36:22	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 21:36:53	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:14:46s.  Time for last 1,000,000:   30s.  Last read position: chr7:18,636,743
INFO	2016-11-09 21:36:53	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 21:37:33	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:15:27s.  Time for last 1,000,000:   40s.  Last read position: chr7:53,850,313
INFO	2016-11-09 21:37:33	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 21:38:13	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:16:07s.  Time for last 1,000,000:   39s.  Last read position: chr7:96,503,433
INFO	2016-11-09 21:38:13	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 21:38:42	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:16:35s.  Time for last 1,000,000:   28s.  Last read position: chr7:120,651,846
INFO	2016-11-09 21:38:42	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 21:39:13	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:17:06s.  Time for last 1,000,000:   31s.  Last read position: chr7:146,401,497
INFO	2016-11-09 21:39:13	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 21:39:44	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:17:38s.  Time for last 1,000,000:   31s.  Last read position: chr8:17,030,519
INFO	2016-11-09 21:39:44	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 21:40:17	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:18:11s.  Time for last 1,000,000:   33s.  Last read position: chr8:42,750,671
INFO	2016-11-09 21:40:17	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 21:40:43	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:18:37s.  Time for last 1,000,000:   25s.  Last read position: chr8:85,385,487
INFO	2016-11-09 21:40:43	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 21:41:03	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:18:57s.  Time for last 1,000,000:   20s.  Last read position: chr8:124,358,985
INFO	2016-11-09 21:41:03	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 21:41:27	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:19:21s.  Time for last 1,000,000:   23s.  Last read position: chr9:18,183,883
INFO	2016-11-09 21:41:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 21:41:53	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:19:47s.  Time for last 1,000,000:   26s.  Last read position: chr9:84,163,983
INFO	2016-11-09 21:41:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 21:42:22	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:20:16s.  Time for last 1,000,000:   29s.  Last read position: chr9:119,875,535
INFO	2016-11-09 21:42:22	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 21:42:41	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:20:35s.  Time for last 1,000,000:   18s.  Last read position: chr10:5,661,683
INFO	2016-11-09 21:42:41	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 21:43:08	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:21:02s.  Time for last 1,000,000:   26s.  Last read position: chr10:29,748,948
INFO	2016-11-09 21:43:08	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 21:43:29	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:21:23s.  Time for last 1,000,000:   21s.  Last read position: chr10:61,280,221
INFO	2016-11-09 21:43:29	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 21:43:56	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:21:49s.  Time for last 1,000,000:   26s.  Last read position: chr10:85,305,552
INFO	2016-11-09 21:43:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 21:44:12	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:22:06s.  Time for last 1,000,000:   16s.  Last read position: chr10:108,129,202
INFO	2016-11-09 21:44:12	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 21:44:34	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:22:28s.  Time for last 1,000,000:   22s.  Last read position: chr10:132,730,123
INFO	2016-11-09 21:44:34	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 21:45:00	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:22:53s.  Time for last 1,000,000:   25s.  Last read position: chr11:35,359,267
INFO	2016-11-09 21:45:00	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 21:45:20	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:23:14s.  Time for last 1,000,000:   20s.  Last read position: chr11:75,696,431
INFO	2016-11-09 21:45:20	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 21:45:34	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:23:28s.  Time for last 1,000,000:   14s.  Last read position: chr11:114,414,621
INFO	2016-11-09 21:45:34	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-09 21:46:02	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:23:55s.  Time for last 1,000,000:   27s.  Last read position: chr12:8,900,276
INFO	2016-11-09 21:46:02	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 21:46:18	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:24:11s.  Time for last 1,000,000:   16s.  Last read position: chr12:38,863,889
INFO	2016-11-09 21:46:18	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 21:46:35	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:24:29s.  Time for last 1,000,000:   17s.  Last read position: chr12:60,598,824
INFO	2016-11-09 21:46:35	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 21:46:52	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:24:46s.  Time for last 1,000,000:   17s.  Last read position: chr12:88,520,538
INFO	2016-11-09 21:46:52	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-09 21:47:08	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:25:02s.  Time for last 1,000,000:   15s.  Last read position: chr12:112,268,437
INFO	2016-11-09 21:47:08	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 21:47:24	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:25:18s.  Time for last 1,000,000:   16s.  Last read position: chr13:23,999,632
INFO	2016-11-09 21:47:24	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 21:47:48	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:25:42s.  Time for last 1,000,000:   24s.  Last read position: chr13:51,165,870
INFO	2016-11-09 21:47:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 21:48:12	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:26:05s.  Time for last 1,000,000:   23s.  Last read position: chr13:88,986,369
INFO	2016-11-09 21:48:12	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 21:48:36	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:26:29s.  Time for last 1,000,000:   23s.  Last read position: chr14:23,149,367
INFO	2016-11-09 21:48:36	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 21:49:00	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:26:54s.  Time for last 1,000,000:   24s.  Last read position: chr14:58,140,905
INFO	2016-11-09 21:49:00	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 21:49:21	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:27:15s.  Time for last 1,000,000:   20s.  Last read position: chr14:91,912,553
INFO	2016-11-09 21:49:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 21:49:40	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:27:33s.  Time for last 1,000,000:   18s.  Last read position: chr15:38,895,095
INFO	2016-11-09 21:49:40	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 21:50:03	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:27:57s.  Time for last 1,000,000:   23s.  Last read position: chr15:68,188,367
INFO	2016-11-09 21:50:03	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 21:50:33	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:28:27s.  Time for last 1,000,000:   29s.  Last read position: chr15:87,921,272
INFO	2016-11-09 21:50:33	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 21:51:00	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:28:54s.  Time for last 1,000,000:   27s.  Last read position: chr16:11,143,813
INFO	2016-11-09 21:51:00	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 21:51:25	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:29:19s.  Time for last 1,000,000:   25s.  Last read position: chr16:51,391,437
INFO	2016-11-09 21:51:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 21:51:50	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:29:44s.  Time for last 1,000,000:   24s.  Last read position: chr16:84,928,458
INFO	2016-11-09 21:51:50	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 21:52:14	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:30:07s.  Time for last 1,000,000:   23s.  Last read position: chr17:18,368,935
INFO	2016-11-09 21:52:14	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 21:52:43	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:30:36s.  Time for last 1,000,000:   29s.  Last read position: chr17:44,246,522
INFO	2016-11-09 21:52:43	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 21:53:07	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:31:00s.  Time for last 1,000,000:   23s.  Last read position: chr17:66,172,158
INFO	2016-11-09 21:53:07	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-11-09 21:53:57	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:31:51s.  Time for last 1,000,000:   50s.  Last read position: chr18:5,619,614
INFO	2016-11-09 21:53:57	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 21:54:19	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:32:13s.  Time for last 1,000,000:   21s.  Last read position: chr18:46,152,631
INFO	2016-11-09 21:54:19	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 21:54:46	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:32:39s.  Time for last 1,000,000:   26s.  Last read position: chr19:1,328,731
INFO	2016-11-09 21:54:46	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 21:55:08	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:33:01s.  Time for last 1,000,000:   22s.  Last read position: chr19:28,148,444
INFO	2016-11-09 21:55:08	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 21:55:37	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:33:30s.  Time for last 1,000,000:   28s.  Last read position: chr19:40,341,579
INFO	2016-11-09 21:55:37	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-09 21:55:57	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:33:50s.  Time for last 1,000,000:   19s.  Last read position: chr20:3,222,035
INFO	2016-11-09 21:55:57	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 21:56:17	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:34:11s.  Time for last 1,000,000:   20s.  Last read position: chr20:37,218,903
INFO	2016-11-09 21:56:17	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 21:56:44	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:34:38s.  Time for last 1,000,000:   27s.  Last read position: chr20:62,871,367
INFO	2016-11-09 21:56:44	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-11-09 21:57:08	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:35:02s.  Time for last 1,000,000:   23s.  Last read position: chr21:39,474,524
INFO	2016-11-09 21:57:08	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 21:57:31	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:35:24s.  Time for last 1,000,000:   22s.  Last read position: chr22:31,346,944
INFO	2016-11-09 21:57:31	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 21:57:55	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:35:48s.  Time for last 1,000,000:   24s.  Last read position: chrX:6,235,951
INFO	2016-11-09 21:57:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 21:58:14	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:36:08s.  Time for last 1,000,000:   19s.  Last read position: chrX:38,820,975
INFO	2016-11-09 21:58:14	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 21:58:35	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:36:29s.  Time for last 1,000,000:   20s.  Last read position: chrX:69,473,954
INFO	2016-11-09 21:58:35	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 21:58:50	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:36:44s.  Time for last 1,000,000:   14s.  Last read position: chrX:92,683,143
INFO	2016-11-09 21:58:50	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 21:59:11	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:37:05s.  Time for last 1,000,000:   21s.  Last read position: chrX:118,447,518
INFO	2016-11-09 21:59:11	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-09 21:59:27	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:37:20s.  Time for last 1,000,000:   15s.  Last read position: chrX:142,819,613
INFO	2016-11-09 21:59:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 21:59:55	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:37:49s.  Time for last 1,000,000:   28s.  Last read position: chrM:3,995
INFO	2016-11-09 21:59:55	MarkDuplicates	Tracking 7472 as yet unmatched pairs. 7472 records in RAM.
INFO	2016-11-09 22:00:17	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:38:11s.  Time for last 1,000,000:   21s.  Last read position: chrM:11,775
INFO	2016-11-09 22:00:17	MarkDuplicates	Tracking 14000 as yet unmatched pairs. 14000 records in RAM.
INFO	2016-11-09 22:00:37	MarkDuplicates	Read 99989486 records. 0 pairs never matched.
INFO	2016-11-09 22:00:44	MarkDuplicates	After buildSortedReadEndLists freeMemory: 2735793072; totalMemory: 2764046336; maxMemory: 3817865216
INFO	2016-11-09 22:00:44	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-11-09 22:00:44	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-11-09 22:01:02	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-11-09 22:01:29	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-11-09 22:01:29	MarkDuplicates	After generateDuplicateIndexes freeMemory: 1811748952; totalMemory: 2793930752; maxMemory: 3817865216
INFO	2016-11-09 22:01:29	MarkDuplicates	Marking 496224 records as duplicates.
INFO	2016-11-09 22:01:29	MarkDuplicates	Found 42648 optical duplicate clusters.
INFO	2016-11-09 22:05:14	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:03:40s.  Time for last 10,000,000:  220s.  Last read position: chr2:3,652,468
INFO	2016-11-09 22:08:21	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:06:47s.  Time for last 10,000,000:  186s.  Last read position: chr3:128,121,129
INFO	2016-11-09 22:11:13	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:09:39s.  Time for last 10,000,000:  172s.  Last read position: chr5:86,336,676
INFO	2016-11-09 22:14:31	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:12:57s.  Time for last 10,000,000:  198s.  Last read position: chr6:156,918,595
INFO	2016-11-09 22:18:09	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:16:35s.  Time for last 10,000,000:  218s.  Last read position: chr9:18,183,883
INFO	2016-11-09 22:21:10	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:19:36s.  Time for last 10,000,000:  180s.  Last read position: chr11:75,696,431
INFO	2016-11-09 22:24:27	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:22:53s.  Time for last 10,000,000:  197s.  Last read position: chr14:23,149,367
INFO	2016-11-09 22:27:38	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:26:04s.  Time for last 10,000,000:  190s.  Last read position: chr17:44,246,522
INFO	2016-11-09 22:30:46	MarkDuplicates	Written    90,000,000 records.  Elapsed time: 00:29:12s.  Time for last 10,000,000:  188s.  Last read position: chr21:39,474,524
INFO	2016-11-09 22:33:53	MarkDuplicates	Before output close freeMemory: 2830112304; totalMemory: 2861039616; maxMemory: 3817865216
INFO	2016-11-09 22:33:58	MarkDuplicates	After output close freeMemory: 2830111248; totalMemory: 2861039616; maxMemory: 3817865216
[Wed Nov 09 22:33:59 PST 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 71.94 minutes.
Runtime.totalMemory()=2861039616

Global scope

Note: Global scope when program finished execution.
Type Name Value
int{} filesize {rep1=2556569841, ctl1=11033042636}
int{} nth_rep {rep1=1, ctl1=4}