Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20161109_220717_741
Start time	2016-11-09 22:07:17
Run time	01:07:13.833
Tasks executed	2
Tasks failed	1
Tasks failed names	markdup_bam_picard ctl1
Arguments*	[-title, SRR1370884_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370884_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

Thread ID	Parent	Tasks
thread_Root	None
thread_42	thread_Root	chipseq.bds.20161109_220717_741_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_11
thread_41	thread_Root	chipseq.bds.20161109_220717_741_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_10

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.align_bwa.bwa_sam_rep1.line_140.id_10
Name	bwa_sam rep1
Thread	thread_41
PID	6448

OK	false
Exit Code	0
Retries
State	RUNNING
Dep.	WAIT
Cpus	1
Mem

Start	2016-11-09 22:07:21
End	2016-11-09 22:07:21
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370884_1.fastq.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_1.sai
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_1.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/qc/rep1/SRR1370884_1.flagstat.qc
Dependencies

 
# SYS command. line 142

 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 147

 bwa samse /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_1.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370884_1.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_1.bam

# SYS command. line 149

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/rep1/SRR1370884_1.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/qc/rep1/SRR1370884_1.flagstat.qc

# SYS command. line 151

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
1782 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.50 sec
[bwa_aln_core] refine gapped alignments... 2.09 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences.
0.96 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.34 sec
[bwa_aln_core] refine gapped alignments... 2.53 sec
[bwa_aln_core] print alignments... 1.01 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.66 sec
[bwa_aln_core] refine gapped alignments... 1.34 sec
[bwa_aln_core] print alignments... 0.89 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.96 sec
[bwa_aln_core] refine gapped alignments... 0.89 sec
[bwa_aln_core] print alignments... 0.91 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.37 sec
[bwa_aln_core] refine gapped alignments... 0.81 sec
[bwa_aln_core] print alignments... 0.90 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.53 sec
[bwa_aln_core] refine gapped alignments... 0.76 sec
[bwa_aln_core] print alignments... 0.93 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.51 sec
[bwa_aln_core] refine gapped alignments... 2.58 sec
[bwa_aln_core] print alignments... 0.98 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.98 sec
[bwa_aln_core] refine gapped alignments... 0.90 sec
[bwa_aln_core] print alignments... 1.04 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.89 sec
[bwa_aln_core] refine gapped alignments... 0.81 sec
[bwa_aln_core] print alignments... 0.91 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.01 sec
[bwa_aln_core] refine gapped alignments... 0.81 sec
[bwa_aln_core] print alignments... 0.97 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.49 sec
[bwa_aln_core] refine gapped alignments... 2.23 sec
[bwa_aln_core] print alignments... 0.89 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.98 sec
[bwa_aln_core] refine gapped alignments... 2.00 sec
[bwa_aln_core] print alignments... 0.91 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.67 sec
[bwa_aln_core] refine gapped alignments... 2.12 sec
[bwa_aln_core] print alignments... 0.92 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.49 sec
[bwa_aln_core] refine gapped alignments... 2.03 sec
[bwa_aln_core] print alignments... 0.87 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.50 sec
[bwa_aln_core] refine gapped alignments... 2.64 sec
[bwa_aln_core] print alignments... 0.90 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.27 sec
[bwa_aln_core] refine gapped alignments... 1.74 sec
[bwa_aln_core] print alignments... 0.92 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.44 sec
[bwa_aln_core] refine gapped alignments... 1.00 sec
[bwa_aln_core] print alignments... 0.97 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.22 sec
[bwa_aln_core] refine gapped alignments... 0.89 sec
[bwa_aln_core] print alignments... 0.88 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.48 sec
[bwa_aln_core] refine gapped alignments... 1.90 sec
[bwa_aln_core] print alignments... 0.87 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.49 sec
[bwa_aln_core] refine gapped alignments... 0.89 sec
[bwa_aln_core] print alignments... 0.90 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.23 sec
[bwa_aln_core] refine gapped alignments... 1.92 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.61 sec
[bwa_aln_core] refine gapped alignments... 0.89 sec
[bwa_aln_core] print alignments... 0.86 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.07 sec
[bwa_aln_core] refine gapped alignments... 2.21 sec
[bwa_aln_core] print alignments... 0.87 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.45 sec
[bwa_aln_core] refine gapped alignments... 0.91 sec
[bwa_aln_core] print alignments... 0.96 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.91 sec
[bwa_aln_core] refine gapped alignments... 0.90 sec
[bwa_aln_core] print alignments... 0.85 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.36 sec
[bwa_aln_core] refine gapped alignments... 1.00 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.80 sec
[bwa_aln_core] refine gapped alignments... 0.90 sec
[bwa_aln_core] print alignments... 0.95 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.16 sec
[bwa_aln_core] refine gapped alignments... 0.92 sec
[bwa_aln_core] print alignments... 0.92 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.20 sec
[bwa_aln_core] refine gapped alignments... 0.94 sec
[bwa_aln_core] print alignments... 0.95 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.71 sec
[bwa_aln_core] refine gapped alignments... 0.90 sec
[bwa_aln_core] print alignments... 0.88 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.56 sec
[bwa_aln_core] refine gapped alignments... 1.06 sec
[bwa_aln_core] print alignments... 0.88 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.94 sec
[bwa_aln_core] refine gapped alignments... 0.92 sec
[bwa_aln_core] print alignments... 0.90 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.13 sec
[bwa_aln_core] refine gapped alignments... 1.58 sec
[bwa_aln_core] print alignments... 0.92 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.33 sec
[bwa_aln_core] refine gapped alignments... 1.00 sec
[bwa_aln_core] print alignments... 0.96 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.43 sec
[bwa_aln_core] refine gapped alignments... 0.95 sec
[bwa_aln_core] print alignments... 0.91 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.19 sec
[bwa_aln_core] refine gapped alignments... 0.81 sec
[bwa_aln_core] print alignments... 0.97 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.37 sec
[bwa_aln_core] refine gapped alignments... 0.81 sec
[bwa_aln_core] print alignments... 0.88 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.41 sec
[bwa_aln_core] refine gapped alignments... 3.07 sec
[bwa_aln_core] print alignments... 1.22 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.52 sec
[bwa_aln_core] refine gapped alignments... 1.21 sec
[bwa_aln_core] print alignments... 1.11 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.20 sec
[bwa_aln_core] refine gapped alignments...

Num	2
ID	task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_11
Name	markdup_bam_picard ctl1
Thread	thread_42
PID	6449

OK	false
Exit Code	1
Retries
State	ERROR
Dep.	ERROR
Cpus	1
Mem

Start	2016-11-09 22:07:21
End	2016-11-09 22:07:21
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_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/SRR1370884_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_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/SRR1370884_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_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--------------------
21859 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Wed Nov 09 22:38:32 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370884_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 22:38:32 PST 2016] Executing as imk1@surya on Linux 4.4.0-45-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-11-09 22:38:32	MarkDuplicates	Start of doWork freeMemory: 254879200; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-11-09 22:38:32	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-11-09 22:38:32	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-11-09 22:38:40	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:07s.  Time for last 1,000,000:    7s.  Last read position: chr1:22,298,551
INFO	2016-11-09 22:38:40	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:38:47	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:14s.  Time for last 1,000,000:    7s.  Last read position: chr1:41,895,424
INFO	2016-11-09 22:38:47	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 22:38:54	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:21s.  Time for last 1,000,000:    7s.  Last read position: chr1:63,396,527
INFO	2016-11-09 22:38:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:39:03	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:30s.  Time for last 1,000,000:    8s.  Last read position: chr1:89,147,707
INFO	2016-11-09 22:39:03	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:39:12	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:40s.  Time for last 1,000,000:    9s.  Last read position: chr1:115,615,553
INFO	2016-11-09 22:39:12	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:39:22	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:50s.  Time for last 1,000,000:    9s.  Last read position: chr1:164,468,682
INFO	2016-11-09 22:39:22	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-09 22:39:33	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:01:00s.  Time for last 1,000,000:   10s.  Last read position: chr1:189,102,252
INFO	2016-11-09 22:39:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:39:39	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:01:07s.  Time for last 1,000,000:    6s.  Last read position: chr1:213,979,760
INFO	2016-11-09 22:39:39	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:39:45	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:01:13s.  Time for last 1,000,000:    6s.  Last read position: chr1:231,814,268
INFO	2016-11-09 22:39:45	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:39:52	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:01:20s.  Time for last 1,000,000:    6s.  Last read position: chr2:3,652,468
INFO	2016-11-09 22:39:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:40:01	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:29s.  Time for last 1,000,000:    9s.  Last read position: chr2:39,505,122
INFO	2016-11-09 22:40:01	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:40:08	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:35s.  Time for last 1,000,000:    6s.  Last read position: chr2:73,561,393
INFO	2016-11-09 22:40:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:40:15	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:43s.  Time for last 1,000,000:    7s.  Last read position: chr2:120,526,571
INFO	2016-11-09 22:40:15	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:40:23	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:50s.  Time for last 1,000,000:    7s.  Last read position: chr2:160,316,783
INFO	2016-11-09 22:40:23	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:40:43	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:02:11s.  Time for last 1,000,000:   20s.  Last read position: chr2:195,549,735
INFO	2016-11-09 22:40:43	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:40:51	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:02:19s.  Time for last 1,000,000:    7s.  Last read position: chr2:230,358,034
INFO	2016-11-09 22:40:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:40:59	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:02:27s.  Time for last 1,000,000:    8s.  Last read position: chr3:16,305,780
INFO	2016-11-09 22:40:59	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-09 22:41:05	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:02:32s.  Time for last 1,000,000:    5s.  Last read position: chr3:49,251,279
INFO	2016-11-09 22:41:05	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:41:11	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:02:39s.  Time for last 1,000,000:    6s.  Last read position: chr3:84,621,225
INFO	2016-11-09 22:41:11	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:41:19	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:02:47s.  Time for last 1,000,000:    7s.  Last read position: chr3:128,121,129
INFO	2016-11-09 22:41:19	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:41:26	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:02:54s.  Time for last 1,000,000:    7s.  Last read position: chr3:165,373,238
INFO	2016-11-09 22:41:26	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:41:36	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:03:03s.  Time for last 1,000,000:    9s.  Last read position: chr3:195,333,247
INFO	2016-11-09 22:41:36	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:41:41	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:03:08s.  Time for last 1,000,000:    5s.  Last read position: chr4:37,752,582
INFO	2016-11-09 22:41:41	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:41:46	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:03:14s.  Time for last 1,000,000:    5s.  Last read position: chr4:81,286,306
INFO	2016-11-09 22:41:46	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:41:55	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:03:23s.  Time for last 1,000,000:    9s.  Last read position: chr4:119,339,736
INFO	2016-11-09 22:41:55	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:42:01	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:03:29s.  Time for last 1,000,000:    6s.  Last read position: chr4:158,818,783
INFO	2016-11-09 22:42:01	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 22:42:07	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:03:35s.  Time for last 1,000,000:    5s.  Last read position: chr5:6,447,551
INFO	2016-11-09 22:42:07	MarkDuplicates	Tracking 16 as yet unmatched pairs. 16 records in RAM.
INFO	2016-11-09 22:42:15	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:03:42s.  Time for last 1,000,000:    7s.  Last read position: chr5:33,219,021
INFO	2016-11-09 22:42:15	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-09 22:42:21	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:03:49s.  Time for last 1,000,000:    6s.  Last read position: chr5:60,694,078
INFO	2016-11-09 22:42:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:42:50	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:04:18s.  Time for last 1,000,000:   28s.  Last read position: chr5:86,336,676
INFO	2016-11-09 22:42:50	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:42:57	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:04:24s.  Time for last 1,000,000:    6s.  Last read position: chr5:112,930,184
INFO	2016-11-09 22:42:57	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:43:04	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:04:32s.  Time for last 1,000,000:    7s.  Last read position: chr5:136,852,889
INFO	2016-11-09 22:43:04	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:43:13	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:04:41s.  Time for last 1,000,000:    9s.  Last read position: chr5:160,271,193
INFO	2016-11-09 22:43:13	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:43:21	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:04:48s.  Time for last 1,000,000:    7s.  Last read position: chr6:4,126,386
INFO	2016-11-09 22:43:21	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-09 22:43:29	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:04:57s.  Time for last 1,000,000:    8s.  Last read position: chr6:28,666,579
INFO	2016-11-09 22:43:29	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:43:36	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:05:03s.  Time for last 1,000,000:    6s.  Last read position: chr6:49,527,281
INFO	2016-11-09 22:43:36	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:43:41	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:05:09s.  Time for last 1,000,000:    5s.  Last read position: chr6:81,728,195
INFO	2016-11-09 22:43:41	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:43:49	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:05:17s.  Time for last 1,000,000:    8s.  Last read position: chr6:107,535,760
INFO	2016-11-09 22:43:49	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:43:55	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:05:23s.  Time for last 1,000,000:    5s.  Last read position: chr6:132,364,408
INFO	2016-11-09 22:43:55	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 22:44:03	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:05:31s.  Time for last 1,000,000:    8s.  Last read position: chr6:156,918,595
INFO	2016-11-09 22:44:03	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:44:11	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:05:39s.  Time for last 1,000,000:    8s.  Last read position: chr7:18,636,743
INFO	2016-11-09 22:44:11	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:44:19	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:05:47s.  Time for last 1,000,000:    7s.  Last read position: chr7:53,850,313
INFO	2016-11-09 22:44:19	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:44:25	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:05:53s.  Time for last 1,000,000:    6s.  Last read position: chr7:96,503,433
INFO	2016-11-09 22:44:25	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:44:32	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:05:59s.  Time for last 1,000,000:    6s.  Last read position: chr7:120,651,846
INFO	2016-11-09 22:44:32	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:44:45	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:06:12s.  Time for last 1,000,000:   12s.  Last read position: chr7:146,401,497
INFO	2016-11-09 22:44:45	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:44:51	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:06:19s.  Time for last 1,000,000:    6s.  Last read position: chr8:17,030,519
INFO	2016-11-09 22:44:51	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:44:57	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:06:25s.  Time for last 1,000,000:    6s.  Last read position: chr8:42,750,671
INFO	2016-11-09 22:44:57	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:45:05	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:06:32s.  Time for last 1,000,000:    7s.  Last read position: chr8:85,385,487
INFO	2016-11-09 22:45:05	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:45:11	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:06:38s.  Time for last 1,000,000:    6s.  Last read position: chr8:124,358,985
INFO	2016-11-09 22:45:11	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:45:17	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:06:45s.  Time for last 1,000,000:    6s.  Last read position: chr9:18,183,883
INFO	2016-11-09 22:45:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:45:26	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:06:53s.  Time for last 1,000,000:    8s.  Last read position: chr9:84,163,983
INFO	2016-11-09 22:45:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:45:33	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:07:00s.  Time for last 1,000,000:    6s.  Last read position: chr9:119,875,535
INFO	2016-11-09 22:45:33	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:45:38	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:07:06s.  Time for last 1,000,000:    5s.  Last read position: chr10:5,661,683
INFO	2016-11-09 22:45:38	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 22:45:47	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:07:15s.  Time for last 1,000,000:    9s.  Last read position: chr10:29,748,948
INFO	2016-11-09 22:45:47	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:45:56	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:07:23s.  Time for last 1,000,000:    8s.  Last read position: chr10:61,280,221
INFO	2016-11-09 22:45:56	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:46:03	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:07:31s.  Time for last 1,000,000:    7s.  Last read position: chr10:85,305,552
INFO	2016-11-09 22:46:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:46:09	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:07:37s.  Time for last 1,000,000:    5s.  Last read position: chr10:108,129,202
INFO	2016-11-09 22:46:09	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:46:17	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:07:45s.  Time for last 1,000,000:    7s.  Last read position: chr10:132,730,123
INFO	2016-11-09 22:46:17	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:46:36	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:08:04s.  Time for last 1,000,000:   18s.  Last read position: chr11:35,359,267
INFO	2016-11-09 22:46:36	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:46:43	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:08:10s.  Time for last 1,000,000:    6s.  Last read position: chr11:75,696,431
INFO	2016-11-09 22:46:43	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:46:48	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:08:16s.  Time for last 1,000,000:    5s.  Last read position: chr11:114,414,621
INFO	2016-11-09 22:46:48	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-09 22:46:54	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:08:22s.  Time for last 1,000,000:    6s.  Last read position: chr12:8,900,276
INFO	2016-11-09 22:46:54	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 22:47:01	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:08:29s.  Time for last 1,000,000:    6s.  Last read position: chr12:38,863,889
INFO	2016-11-09 22:47:01	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:47:07	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:08:35s.  Time for last 1,000,000:    5s.  Last read position: chr12:60,598,824
INFO	2016-11-09 22:47:07	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:47:13	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:08:40s.  Time for last 1,000,000:    5s.  Last read position: chr12:88,520,538
INFO	2016-11-09 22:47:13	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-09 22:47:20	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:08:47s.  Time for last 1,000,000:    6s.  Last read position: chr12:112,268,437
INFO	2016-11-09 22:47:20	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:47:26	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:08:54s.  Time for last 1,000,000:    6s.  Last read position: chr13:23,999,632
INFO	2016-11-09 22:47:26	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:47:33	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:09:00s.  Time for last 1,000,000:    6s.  Last read position: chr13:51,165,870
INFO	2016-11-09 22:47:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:47:39	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:09:07s.  Time for last 1,000,000:    6s.  Last read position: chr13:88,986,369
INFO	2016-11-09 22:47:39	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:47:48	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:09:15s.  Time for last 1,000,000:    8s.  Last read position: chr14:23,149,367
INFO	2016-11-09 22:47:48	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 22:47:55	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:09:23s.  Time for last 1,000,000:    7s.  Last read position: chr14:58,140,905
INFO	2016-11-09 22:47:55	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:48:02	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:09:30s.  Time for last 1,000,000:    6s.  Last read position: chr14:91,912,553
INFO	2016-11-09 22:48:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:48:10	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:09:38s.  Time for last 1,000,000:    8s.  Last read position: chr15:38,895,095
INFO	2016-11-09 22:48:10	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:48:23	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:09:51s.  Time for last 1,000,000:   13s.  Last read position: chr15:68,188,367
INFO	2016-11-09 22:48:23	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 22:48:31	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:09:58s.  Time for last 1,000,000:    7s.  Last read position: chr15:87,921,272
INFO	2016-11-09 22:48:31	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:48:37	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:10:05s.  Time for last 1,000,000:    6s.  Last read position: chr16:11,143,813
INFO	2016-11-09 22:48:37	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:48:44	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:10:11s.  Time for last 1,000,000:    6s.  Last read position: chr16:51,391,437
INFO	2016-11-09 22:48:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:48:52	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:10:20s.  Time for last 1,000,000:    8s.  Last read position: chr16:84,928,458
INFO	2016-11-09 22:48:52	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:48:59	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:10:27s.  Time for last 1,000,000:    6s.  Last read position: chr17:18,368,935
INFO	2016-11-09 22:48:59	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:49:05	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:10:32s.  Time for last 1,000,000:    5s.  Last read position: chr17:44,246,522
INFO	2016-11-09 22:49:05	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:49:11	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:10:39s.  Time for last 1,000,000:    6s.  Last read position: chr17:66,172,158
INFO	2016-11-09 22:49:11	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-11-09 22:49:17	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:10:44s.  Time for last 1,000,000:    5s.  Last read position: chr18:5,619,614
INFO	2016-11-09 22:49:17	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-1

BigDataScript report: chipseq.bds

Timeline

Task Graph

Parallel (threads) details

Task details