BigDataScript report: chipseq.bds

Script file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20161109_220703_371
Start time 2016-11-09 22:07:03
Run time 00:49:05.309
Tasks executed 2
Tasks failed 1
Tasks failed names 
dedup_bam_1 rep1
Arguments* [-title, SRR1370875_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370875_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370875_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 1
* Values in global scope when program finished execution.

Timeline

Task Graph

Parallel (threads) details

Thread ID Parent Tasks
thread_Root None
thread_42 thread_Root 
 chipseq.bds.20161109_220703_371_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_11
thread_41 thread_Root 
 chipseq.bds.20161109_220703_371_parallel_41/task.postalign_bam.dedup_bam_1_rep1.line_95.id_10

Task details

Task Execution Time Dependencies Task program, Errors, StdOut / StdErr
Num 1
ID task.postalign_bam.dedup_bam_1_rep1.line_95.id_10
Name dedup_bam_1 rep1
Thread thread_41
PID 6437
OK false
Exit Code 1
Retries
State ERROR
Dep. ERROR
Cpus
Mem
Start 2016-11-09 22:07:17
End 2016-11-09 22:07:17
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370875_1/out/align/rep1/SRR1370875_1.bam
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370875_1/out/align/rep1/SRR1370875_1.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 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370875_1/out/align/rep1/SRR1370875_1.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370875_1/out/align/rep1/SRR1370875_1.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370875_1/out/align/rep1/SRR1370875_1.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
				samtools view -F 1804 -Su /dev/stdin | \
				sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370875_1/out/align/rep1/SRR1370875_1.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370875_1/out/align/rep1/SRR1370875_1.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370875_1/out/align/rep1/SRR1370875_1.bam | \
			    	sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370875_1/out/align/rep1/SRR1370875_1.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
 
    
--------------------Stderr--------------------
sambamba-sort: Unable to write to stream

 
--------------------Post mortem info--------------------
==============================================================
job_number:                 6437
exec_file:                  job_scripts/6437
submission_time:            Wed Nov  9 22:07:17 2016
owner:                      imk1
uid:                        1048
group:                      users
gid:                        100
sge_o_home:                 /users/imk1/
sge_o_log_name:             imk1
sge_o_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
sge_o_shell:                /bin/bash
sge_o_workdir:              /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370875_1
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370875_1/chipseq.bds.20161109_220703_371_parallel_41/task.postalign_bam.dedup_bam_1_rep1.line_95.id_10.stderr.cluster
mail_list:                  imk1@surya
notify:                     FALSE
job_name:                   STDIN
stdout_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370875_1/chipseq.bds.20161109_220703_371_parallel_41/task.postalign_bam.dedup_bam_1_rep1.line_95.id_10.stdout.cluster
jobshare:                   0
env_list:                   MAIL=/var/mail/imk1,SSH_CLIENT=171.65.77.8 55144 22,USER=imk1,J2SDKDIR=/usr/lib/jvm/java-8-oracle,SHLVL=3,PERL_LOCAL_LIB_ROOT=/users/imk1/perl5,J2REDIR=/usr/lib/jvm/java-8-oracle/jre,HOME=/users/imk1/,DEEPLIFT_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift,SSH_TTY=/dev/pts/4,ASCPKEY=/software/ascp/etc/asperaweb_id_dsa.openssh,_LMFILES_=/software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/sratoolkit/2.5.2:/software/modulefiles/ascp/3.5.6,LOGNAME=imk1,_=/usr/bin/bds,XDG_SESSION_ID=20,TERM=screen,PERL_MB_OPT=--install_base "/users/imk1/perl5",KERAS_DIR=/users/imk1/.local/lib/python2.7/site-packages/keras/,SGE_ROOT=/var/lib/gridengine,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,DERBY_HOME=/usr/lib/jvm/java-8-oracle/db,PERL5LIB=/users/imk1/perl5/lib/perl5,XDG_RUNTIME_DIR=/run/user/1048,DISPLAY=localhost:12.0,SGE_CELL=default,STY=36979.SRR1370875_1.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,KRB5CCNAME=FILE:/tmp/krb5cc_1048_N5SeQf,XFILESEARCHPATH=/usr/dt/app-defaults/%L/Dt,RULEFITBASE=/srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/,PERL_MM_OPT=INSTALL_BASE=/users/imk1/perl5,UTIL_SCRIPTS_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/av_scripts/,MODULE_VERSION=3.2.10,MODULE_VERSION_STACK=3.2.10,WINDOW=0,NLSPATH=/usr/dt/lib/nls/msg/%L/%N.cat,PWD=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370875_1,JAVA_HOME=/usr/lib/jvm/java-8-oracle,LOADEDMODULES=modsappsdir/modsappsdir:sratoolkit/2.5.2:ascp/3.5.6,SSH_CONNECTION=171.65.77.8 55144 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,PYTHONPATH=/users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/,ENHANCER_SCRIPTS_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/,MODULEPATH=/usr/local/Modules/versions				:/usr/local/Modules/$MODULE_VERSION/modulefiles	:/modules/				:/software/modulefiles,MODULESAPPSDIR=/software,MODULESHOME=/software/env_module/3.2.10
script_file:                STDIN
usage    1:                 cpu=00:08:36, mem=569.97034 GBs, io=14.80324, vmem=796.062M, maxvmem=2.169G
scheduling info:            queue instance "amd.q@wotan" dropped because it is full
                            queue instance "q@nandi" dropped because it is full
                            queue instance "q@kadru" dropped because it is full
                            queue instance "q@kali" dropped because it is full
                            queue instance "q@surya" dropped because it is full
Num 2
ID task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_11
Name markdup_bam_picard ctl1
Thread thread_42
PID 6442
OK false
Exit Code 0
Retries
State RUNNING
Dep. WAIT
Cpus 1
Mem
Start 2016-11-09 22:07:18
End 2016-11-09 22:07:18
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370875_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370875_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370875_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/SRR1370875_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370875_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370875_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/SRR1370875_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370875_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370875_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--------------------
34997 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Wed Nov 09 22:36:48 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370875_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370875_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370875_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 22:36:48 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 22:36:48	MarkDuplicates	Start of doWork freeMemory: 254879200; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-11-09 22:36:48	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-11-09 22:36:48	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-11-09 22:37:20	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:30s.  Time for last 1,000,000:   30s.  Last read position: chr1:22,298,551
INFO	2016-11-09 22:37:20	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:37:45	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:56s.  Time for last 1,000,000:   25s.  Last read position: chr1:41,895,424
INFO	2016-11-09 22:37:45	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 22:38:06	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:01:16s.  Time for last 1,000,000:   20s.  Last read position: chr1:63,396,527
INFO	2016-11-09 22:38:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:38:20	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:01:31s.  Time for last 1,000,000:   14s.  Last read position: chr1:89,147,707
INFO	2016-11-09 22:38:20	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:38:36	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:01:47s.  Time for last 1,000,000:   15s.  Last read position: chr1:115,615,553
INFO	2016-11-09 22:38:36	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:38:55	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:02:05s.  Time for last 1,000,000:   18s.  Last read position: chr1:164,468,682
INFO	2016-11-09 22:38:55	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-09 22:39:12	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:02:22s.  Time for last 1,000,000:   17s.  Last read position: chr1:189,102,252
INFO	2016-11-09 22:39:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:39:22	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:02:32s.  Time for last 1,000,000:    9s.  Last read position: chr1:213,979,760
INFO	2016-11-09 22:39:22	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:39:35	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:02:46s.  Time for last 1,000,000:   13s.  Last read position: chr1:231,814,268
INFO	2016-11-09 22:39:35	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:39:45	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:02:55s.  Time for last 1,000,000:    9s.  Last read position: chr2:3,652,468
INFO	2016-11-09 22:39:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:39:58	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:03:09s.  Time for last 1,000,000:   13s.  Last read position: chr2:39,505,122
INFO	2016-11-09 22:39:58	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:40:15	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:03:26s.  Time for last 1,000,000:   17s.  Last read position: chr2:73,561,393
INFO	2016-11-09 22:40:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:40:30	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:03:40s.  Time for last 1,000,000:   14s.  Last read position: chr2:120,526,571
INFO	2016-11-09 22:40:30	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:40:45	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:03:55s.  Time for last 1,000,000:   15s.  Last read position: chr2:160,316,783
INFO	2016-11-09 22:40:45	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:41:09	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:04:20s.  Time for last 1,000,000:   24s.  Last read position: chr2:195,549,735
INFO	2016-11-09 22:41:09	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:41:19	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:04:29s.  Time for last 1,000,000:    9s.  Last read position: chr2:230,358,034
INFO	2016-11-09 22:41:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:41:32	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:04:43s.  Time for last 1,000,000:   13s.  Last read position: chr3:16,305,780
INFO	2016-11-09 22:41:32	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-09 22:41:43	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:04:54s.  Time for last 1,000,000:   10s.  Last read position: chr3:49,251,279
INFO	2016-11-09 22:41:43	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:41:51	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:05:02s.  Time for last 1,000,000:    8s.  Last read position: chr3:84,621,225
INFO	2016-11-09 22:41:51	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:42:01	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:05:11s.  Time for last 1,000,000:    9s.  Last read position: chr3:128,121,129
INFO	2016-11-09 22:42:01	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:42:15	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:05:26s.  Time for last 1,000,000:   14s.  Last read position: chr3:165,373,238
INFO	2016-11-09 22:42:15	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:42:23	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:05:33s.  Time for last 1,000,000:    7s.  Last read position: chr3:195,333,247
INFO	2016-11-09 22:42:23	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:42:33	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:05:44s.  Time for last 1,000,000:   10s.  Last read position: chr4:37,752,582
INFO	2016-11-09 22:42:33	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:42:53	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:06:04s.  Time for last 1,000,000:   19s.  Last read position: chr4:81,286,306
INFO	2016-11-09 22:42:53	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:43:04	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:06:14s.  Time for last 1,000,000:   10s.  Last read position: chr4:119,339,736
INFO	2016-11-09 22:43:04	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:43:20	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:06:31s.  Time for last 1,000,000:   16s.  Last read position: chr4:158,818,783
INFO	2016-11-09 22:43:20	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 22:43:32	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:06:42s.  Time for last 1,000,000:   11s.  Last read position: chr5:6,447,551
INFO	2016-11-09 22:43:32	MarkDuplicates	Tracking 16 as yet unmatched pairs. 16 records in RAM.
INFO	2016-11-09 22:43:40	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:06:50s.  Time for last 1,000,000:    8s.  Last read position: chr5:33,219,021
INFO	2016-11-09 22:43:40	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-09 22:43:58	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:07:09s.  Time for last 1,000,000:   18s.  Last read position: chr5:60,694,078
INFO	2016-11-09 22:43:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:44:19	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:07:29s.  Time for last 1,000,000:   20s.  Last read position: chr5:86,336,676
INFO	2016-11-09 22:44:19	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:44:30	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:07:40s.  Time for last 1,000,000:   11s.  Last read position: chr5:112,930,184
INFO	2016-11-09 22:44:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:44:42	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:07:53s.  Time for last 1,000,000:   12s.  Last read position: chr5:136,852,889
INFO	2016-11-09 22:44:42	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:44:55	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:08:06s.  Time for last 1,000,000:   12s.  Last read position: chr5:160,271,193
INFO	2016-11-09 22:44:55	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:45:02	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:08:13s.  Time for last 1,000,000:    6s.  Last read position: chr6:4,126,386
INFO	2016-11-09 22:45:02	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-09 22:45:10	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:08:20s.  Time for last 1,000,000:    7s.  Last read position: chr6:28,666,579
INFO	2016-11-09 22:45:10	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:45:16	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:08:27s.  Time for last 1,000,000:    6s.  Last read position: chr6:49,527,281
INFO	2016-11-09 22:45:16	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:45:27	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:08:38s.  Time for last 1,000,000:   10s.  Last read position: chr6:81,728,195
INFO	2016-11-09 22:45:27	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:45:36	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:08:46s.  Time for last 1,000,000:    8s.  Last read position: chr6:107,535,760
INFO	2016-11-09 22:45:36	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:45:49	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:08:59s.  Time for last 1,000,000:   12s.  Last read position: chr6:132,364,408
INFO	2016-11-09 22:45:49	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 22:46:02	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:09:13s.  Time for last 1,000,000:   13s.  Last read position: chr6:156,918,595
INFO	2016-11-09 22:46:02	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:46:17	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:09:27s.  Time for last 1,000,000:   14s.  Last read position: chr7:18,636,743
INFO	2016-11-09 22:46:17	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:46:24	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:09:35s.  Time for last 1,000,000:    7s.  Last read position: chr7:53,850,313
INFO	2016-11-09 22:46:24	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:46:35	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:09:46s.  Time for last 1,000,000:   10s.  Last read position: chr7:96,503,433
INFO	2016-11-09 22:46:35	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:46:45	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:09:56s.  Time for last 1,000,000:   10s.  Last read position: chr7:120,651,846
INFO	2016-11-09 22:46:45	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:46:58	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:10:08s.  Time for last 1,000,000:   12s.  Last read position: chr7:146,401,497
INFO	2016-11-09 22:46:58	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:47:09	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:10:19s.  Time for last 1,000,000:   11s.  Last read position: chr8:17,030,519
INFO	2016-11-09 22:47:09	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:47:21	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:10:31s.  Time for last 1,000,000:   11s.  Last read position: chr8:42,750,671
INFO	2016-11-09 22:47:21	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:47:30	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:10:40s.  Time for last 1,000,000:    8s.  Last read position: chr8:85,385,487
INFO	2016-11-09 22:47:30	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:47:36	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:10:47s.  Time for last 1,000,000:    6s.  Last read position: chr8:124,358,985
INFO	2016-11-09 22:47:36	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:47:47	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:10:58s.  Time for last 1,000,000:   10s.  Last read position: chr9:18,183,883
INFO	2016-11-09 22:47:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:47:59	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:11:10s.  Time for last 1,000,000:   12s.  Last read position: chr9:84,163,983
INFO	2016-11-09 22:47:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:48:08	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:11:19s.  Time for last 1,000,000:    8s.  Last read position: chr9:119,875,535
INFO	2016-11-09 22:48:08	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:48:21	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:11:31s.  Time for last 1,000,000:   12s.  Last read position: chr10:5,661,683
INFO	2016-11-09 22:48:21	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 22:48:39	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:11:49s.  Time for last 1,000,000:   17s.  Last read position: chr10:29,748,948
INFO	2016-11-09 22:48:39	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:48:49	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:11:59s.  Time for last 1,000,000:   10s.  Last read position: chr10:61,280,221
INFO	2016-11-09 22:48:49	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:49:01	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:12:11s.  Time for last 1,000,000:   11s.  Last read position: chr10:85,305,552
INFO	2016-11-09 22:49:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:49:09	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:12:20s.  Time for last 1,000,000:    8s.  Last read position: chr10:108,129,202
INFO	2016-11-09 22:49:09	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:49:19	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:12:29s.  Time for last 1,000,000:    9s.  Last read position: chr10:132,730,123
INFO	2016-11-09 22:49:19	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:49:41	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:12:52s.  Time for last 1,000,000:   22s.  Last read position: chr11:35,359,267
INFO	2016-11-09 22:49:41	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:49:47	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:12:58s.  Time for last 1,000,000:    6s.  Last read position: chr11:75,696,431
INFO	2016-11-09 22:49:47	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:49:56	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:13:06s.  Time for last 1,000,000:    8s.  Last read position: chr11:114,414,621
INFO	2016-11-09 22:49:56	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-09 22:50:04	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:13:15s.  Time for last 1,000,000:    8s.  Last read position: chr12:8,900,276
INFO	2016-11-09 22:50:04	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 22:50:15	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:13:26s.  Time for last 1,000,000:   10s.  Last read position: chr12:38,863,889
INFO	2016-11-09 22:50:15	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:50:24	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:13:35s.  Time for last 1,000,000:    9s.  Last read position: chr12:60,598,824
INFO	2016-11-09 22:50:24	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:50:31	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:13:41s.  Time for last 1,000,000:    6s.  Last read position: chr12:88,520,538
INFO	2016-11-09 22:50:31	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-09 22:50:38	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:13:49s.  Time for last 1,000,000:    7s.  Last read position: chr12:112,268,437
INFO	2016-11-09 22:50:38	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:50:51	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:14:01s.  Time for last 1,000,000:   12s.  Last read position: chr13:23,999,632
INFO	2016-11-09 22:50:51	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:51:00	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:14:11s.  Time for last 1,000,000:    9s.  Last read position: chr13:51,165,870
INFO	2016-11-09 22:51:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:51:11	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:14:22s.  Time for last 1,000,000:   10s.  Last read position: chr13:88,986,369
INFO	2016-11-09 22:51:11	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:51:22	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:14:33s.  Time for last 1,000,000:   11s.  Last read position: chr14:23,149,367
INFO	2016-11-09 22:51:22	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 22:51:32	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:14:43s.  Time for last 1,000,000:   10s.  Last read position: chr14:58,140,905
INFO	2016-11-09 22:51:32	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:51:46	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:14:57s.  Time for last 1,000,000:   13s.  Last read position: chr14:91,912,553
INFO	2016-11-09 22:51:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:51:59	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:15:09s.  Time for last 1,000,000:   12s.  Last read position: chr15:38,895,095
INFO	2016-11-09 22:51:59	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:52:11	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:15:22s.  Time for last 1,000,000:   12s.  Last read position: chr15:68,188,367
INFO	2016-11-09 22:52:11	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 22:52:18	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:15:29s.  Time for last 1,000,000:    6s.  Last read position: chr15:87,921,272
INFO	2016-11-09 22:52:18	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:52:26	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:15:37s.  Time for last 1,000,000:    7s.  Last read position: chr16:11,143,813
INFO	2016-11-09 22:52:26	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:52:34	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:15:45s.  Time for last 1,000,000:    7s.  Last read position: chr16:51,391,437
INFO	2016-11-09 22:52:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:52:42	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:15:53s.  Time for last 1,000,000:    8s.  Last read position: chr16:84,928,458
INFO	2016-11-09 22:52:42	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:52:49	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:16:00s.  Time for last 1,000,000:    7s.  Last read position: chr17:18,368,935
INFO	2016-11-09 22:52:49	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:52:59	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:16:10s.  Time for last 1,000,000:    9s.  Last read position: chr17:44,246,522
INFO	2016-11-09 22:52:59	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:53:17	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:16:27s.  Time for last 1,000,000:   17s.  Last read position: chr17:66,172,158
INFO	2016-11-09 22:53:17	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-11-09 22:53:27	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:16:37s.  Time for last 1,000,000:   10s.  Last read position: chr18:5,619,614
INFO	2016-11-09 22:53:27	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:53:38	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:16:49s.  Time for last 1,000,000:   11s.  Last read position: chr18:46,152,631
INFO	2016-11-09 22:53:38	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:53:49	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:17:00s.  Time for last 1,000,000:   10s.  Last read position: chr19:1,328,731
INFO	2016-11-09 22:53:49	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:53:58	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:17:08s.  Time for last 1,000,000:    8s.  Last read position: chr19:28,148,444
INFO	2016-11-09 22:53:58	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:54:05	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:17:15s.  Time for last 1,000,000:    6s.  Last read position: chr19:40,341,579
INFO	2016-11-09 22:54:05	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-09 22:54:16	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:17:27s.  Time for last 1,000,000:   11s.  Last read position: chr20:3,222,035
INFO	2016-11-09 22:54:16	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:54:23	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:17:34s.  Time for last 1,000,000:    7s.  Last read position: chr20:37,218,903
INFO	2016-11-09 22:54:23	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:54:42	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:17:52s.  Time for last 1,000,000:   18s.  Last read position: chr20:62,871,367
INFO	2016-11-09 22:54:42	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-11-09 22:54:52	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:18:03s.  Time for last 1,000,000:   10s.  Last read position: chr21:39,474,524
INFO	2016-11-09 22:54:52	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:54:59	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:18:09s.  Time for last 1,000,000:    6s.  Last read position: chr22:31,346,944
INFO	2016-11-09 22:54:59	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 22:55:05	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:18:15s.  Time for last 1,000,000:    5s.  Last read position: chrX:6,235,951
INFO	2016-11-09 22:55:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:55:13	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:18:23s.  Time for last 1,000,000:    7s.  Last read position: chrX:38,820,975
INFO	2016-11-09 22:55:13	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:55:21	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:18:31s.  Time for last 1,000,000:    8s.  Last read position: chrX:69,473,954
INFO	2016-11-09 22:55:21	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:55:27	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:18:37s.  Time for last 1,000,000:    5s.  Last read position: chrX:92,683,143
INFO	2016-11-09 22:55:27	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:55:32	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:18:43s.  Time for last 1,000,000:    5s.  Last read position: chrX:118,447,518
INFO	2016-11-09 22:55:32	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-09 22:55:40	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:18:51s.  Time for last 1,000,000:    7s.  Last read position: chrX:142,819,613
INFO	2016-11-09 22:55:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:55:47	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:18:58s.  Time for last 1,000,000:    7s.  Last read position: chrM:3,995
INFO	2016-11-09 22:55:47	MarkDuplicates	Tracking 7472 as yet unmatched pairs. 7472 records in RAM.
INFO	2016-11-09 22:55:53	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:19:03s.  Time for last 1,000,000:    5s.  Last read position: chrM:11,775
INFO	2016-11-09 22:55:53	MarkDuplicates	Tracking 14000 as yet unmatched pairs. 14000 records in RAM.
INFO	2016-11-09 22:56:01	MarkDuplicates	Read 99989486 records. 0 pairs never matched.

Global scope

Note: Global scope when program finished execution.
Type Name Value