BigDataScript report: chipseq.bds

Script file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20161110_115537_143
Start time 2016-11-10 11:55:37
Run time 00:26:29.471
Tasks executed 2
Tasks failed 2
Tasks failed names 
bwa_aln rep1
markdup_bam_picard ctl1
Arguments* [-title, SRR1370900_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370900_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370900_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_41 thread_Root 
 chipseq.bds.20161110_115537_143_parallel_41/task.align_bwa.bwa_aln_rep1.line_108.id_10
thread_42 thread_Root 
 chipseq.bds.20161110_115537_143_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_11

Task details

Task Execution Time Dependencies Task program, Errors, StdOut / StdErr
Num 1
ID task.align_bwa.bwa_aln_rep1.line_108.id_10
Name bwa_aln rep1
Thread thread_41
PID 6631
OK false
Exit Code 3
Retries
State KILLED
Dep. ERROR
Cpus
Mem
Start 2016-11-10 11:55:38
End 2016-11-10 12:00:43
Elapsed 00:05:04
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370900_1.fastq.gz
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370900_1/out/align/rep1/SRR1370900_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/SRR1370900_1.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370900_1/out/align/rep1/SRR1370900_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--------------------
12989 (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] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 174.07 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 7.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 170.91 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 9.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 189.72 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 14.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 157.12 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 18.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 129.96 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 20.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.41 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 20.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.61 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 19.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.95 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 19.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 124.97 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 7.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 187.98 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 10.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate...
Num 2
ID task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_11
Name markdup_bam_picard ctl1
Thread thread_42
PID 6634
OK false
Exit Code 3
Retries
State RUNNING
Dep. WAIT
Cpus 1
Mem
Start 2016-11-10 11:55:40
End 2016-11-10 11:55:40
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370900_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370900_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370900_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/SRR1370900_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370900_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370900_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/SRR1370900_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370900_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370900_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--------------------
43373 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Thu Nov 10 11:55:49 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370900_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370900_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370900_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Thu Nov 10 11:55:49 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	2016-11-10 11:55:49	MarkDuplicates	Start of doWork freeMemory: 254879200; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-11-10 11:55:49	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-11-10 11:55:49	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-11-10 11:56:04	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:12s.  Time for last 1,000,000:   12s.  Last read position: chr1:22,298,551
INFO	2016-11-10 11:56:04	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 11:56:14	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:22s.  Time for last 1,000,000:    9s.  Last read position: chr1:41,895,424
INFO	2016-11-10 11:56:14	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 11:56:24	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:32s.  Time for last 1,000,000:    9s.  Last read position: chr1:63,396,527
INFO	2016-11-10 11:56:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 11:56:34	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:42s.  Time for last 1,000,000:    9s.  Last read position: chr1:89,147,707
INFO	2016-11-10 11:56:34	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 11:56:52	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:01:00s.  Time for last 1,000,000:   17s.  Last read position: chr1:115,615,553
INFO	2016-11-10 11:56:52	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 11:57:05	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:01:13s.  Time for last 1,000,000:   13s.  Last read position: chr1:164,468,682
INFO	2016-11-10 11:57:05	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 11:57:17	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:01:25s.  Time for last 1,000,000:   11s.  Last read position: chr1:189,102,252
INFO	2016-11-10 11:57:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 11:57:35	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:01:43s.  Time for last 1,000,000:   17s.  Last read position: chr1:213,979,760
INFO	2016-11-10 11:57:35	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 11:57:44	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:01:52s.  Time for last 1,000,000:    8s.  Last read position: chr1:231,814,268
INFO	2016-11-10 11:57:44	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 11:57:57	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:02:05s.  Time for last 1,000,000:   13s.  Last read position: chr2:3,652,468
INFO	2016-11-10 11:57:57	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 11:58:07	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:02:15s.  Time for last 1,000,000:    9s.  Last read position: chr2:39,505,122
INFO	2016-11-10 11:58:07	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 11:58:16	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:02:24s.  Time for last 1,000,000:    9s.  Last read position: chr2:73,561,393
INFO	2016-11-10 11:58:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 11:58:30	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:02:38s.  Time for last 1,000,000:   14s.  Last read position: chr2:120,526,571
INFO	2016-11-10 11:58:30	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 11:58:42	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:02:50s.  Time for last 1,000,000:   12s.  Last read position: chr2:160,316,783
INFO	2016-11-10 11:58:42	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 11:59:07	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:03:15s.  Time for last 1,000,000:   24s.  Last read position: chr2:195,549,735
INFO	2016-11-10 11:59:07	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 11:59:22	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:03:30s.  Time for last 1,000,000:   15s.  Last read position: chr2:230,358,034
INFO	2016-11-10 11:59:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 11:59:30	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:03:38s.  Time for last 1,000,000:    7s.  Last read position: chr3:16,305,780
INFO	2016-11-10 11:59:30	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 11:59:41	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:03:49s.  Time for last 1,000,000:   10s.  Last read position: chr3:49,251,279
INFO	2016-11-10 11:59:41	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:00:03	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:04:11s.  Time for last 1,000,000:   21s.  Last read position: chr3:84,621,225
INFO	2016-11-10 12:00:03	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:00:15	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:04:23s.  Time for last 1,000,000:   12s.  Last read position: chr3:128,121,129
INFO	2016-11-10 12:00:15	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:00:26	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:04:34s.  Time for last 1,000,000:   11s.  Last read position: chr3:165,373,238
INFO	2016-11-10 12:00:26	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:00:37	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:04:45s.  Time for last 1,000,000:   10s.  Last read position: chr3:195,333,247
INFO	2016-11-10 12:00:37	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:00:48	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:04:56s.  Time for last 1,000,000:   10s.  Last read position: chr4:37,752,582
INFO	2016-11-10 12:00:48	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:01:07	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:05:15s.  Time for last 1,000,000:   18s.  Last read position: chr4:81,286,306
INFO	2016-11-10 12:01:07	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:01:16	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:05:24s.  Time for last 1,000,000:    9s.  Last read position: chr4:119,339,736
INFO	2016-11-10 12:01:16	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:01:26	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:05:34s.  Time for last 1,000,000:   10s.  Last read position: chr4:158,818,783
INFO	2016-11-10 12:01:26	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 12:01:43	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:05:51s.  Time for last 1,000,000:   17s.  Last read position: chr5:6,447,551
INFO	2016-11-10 12:01:43	MarkDuplicates	Tracking 16 as yet unmatched pairs. 16 records in RAM.
INFO	2016-11-10 12:01:57	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:06:05s.  Time for last 1,000,000:   13s.  Last read position: chr5:33,219,021
INFO	2016-11-10 12:01:57	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 12:02:07	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:06:15s.  Time for last 1,000,000:    9s.  Last read position: chr5:60,694,078
INFO	2016-11-10 12:02:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 12:02:30	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:06:38s.  Time for last 1,000,000:   23s.  Last read position: chr5:86,336,676
INFO	2016-11-10 12:02:30	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:02:39	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:06:47s.  Time for last 1,000,000:    8s.  Last read position: chr5:112,930,184
INFO	2016-11-10 12:02:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 12:02:55	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:07:03s.  Time for last 1,000,000:   16s.  Last read position: chr5:136,852,889
INFO	2016-11-10 12:02:55	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:03:06	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:07:14s.  Time for last 1,000,000:   10s.  Last read position: chr5:160,271,193
INFO	2016-11-10 12:03:06	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:03:17	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:07:25s.  Time for last 1,000,000:   11s.  Last read position: chr6:4,126,386
INFO	2016-11-10 12:03:17	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 12:03:27	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:07:35s.  Time for last 1,000,000:    9s.  Last read position: chr6:28,666,579
INFO	2016-11-10 12:03:27	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:03:35	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:07:43s.  Time for last 1,000,000:    8s.  Last read position: chr6:49,527,281
INFO	2016-11-10 12:03:35	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:03:47	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:07:55s.  Time for last 1,000,000:   12s.  Last read position: chr6:81,728,195
INFO	2016-11-10 12:03:47	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:04:02	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:08:10s.  Time for last 1,000,000:   14s.  Last read position: chr6:107,535,760
INFO	2016-11-10 12:04:02	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:04:18	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:08:26s.  Time for last 1,000,000:   15s.  Last read position: chr6:132,364,408
INFO	2016-11-10 12:04:18	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 12:04:31	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:08:39s.  Time for last 1,000,000:   13s.  Last read position: chr6:156,918,595
INFO	2016-11-10 12:04:31	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:04:48	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:08:56s.  Time for last 1,000,000:   16s.  Last read position: chr7:18,636,743
INFO	2016-11-10 12:04:48	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:04:58	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:09:06s.  Time for last 1,000,000:    9s.  Last read position: chr7:53,850,313
INFO	2016-11-10 12:04:58	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:05:05	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:09:13s.  Time for last 1,000,000:    7s.  Last read position: chr7:96,503,433
INFO	2016-11-10 12:05:05	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:05:15	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:09:23s.  Time for last 1,000,000:    9s.  Last read position: chr7:120,651,846
INFO	2016-11-10 12:05:15	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:05:30	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:09:38s.  Time for last 1,000,000:   14s.  Last read position: chr7:146,401,497
INFO	2016-11-10 12:05:30	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:05:40	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:09:48s.  Time for last 1,000,000:   10s.  Last read position: chr8:17,030,519
INFO	2016-11-10 12:05:40	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:05:53	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:10:01s.  Time for last 1,000,000:   12s.  Last read position: chr8:42,750,671
INFO	2016-11-10 12:05:53	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:06:04	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:10:12s.  Time for last 1,000,000:   10s.  Last read position: chr8:85,385,487
INFO	2016-11-10 12:06:04	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:06:17	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:10:25s.  Time for last 1,000,000:   13s.  Last read position: chr8:124,358,985
INFO	2016-11-10 12:06:17	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:06:29	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:10:37s.  Time for last 1,000,000:   12s.  Last read position: chr9:18,183,883
INFO	2016-11-10 12:06:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 12:06:41	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:10:49s.  Time for last 1,000,000:   12s.  Last read position: chr9:84,163,983
INFO	2016-11-10 12:06:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 12:06:58	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:11:06s.  Time for last 1,000,000:   16s.  Last read position: chr9:119,875,535
INFO	2016-11-10 12:06:58	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:07:08	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:11:16s.  Time for last 1,000,000:    9s.  Last read position: chr10:5,661,683
INFO	2016-11-10 12:07:08	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 12:07:17	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:11:25s.  Time for last 1,000,000:    9s.  Last read position: chr10:29,748,948
INFO	2016-11-10 12:07:17	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:07:29	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:11:37s.  Time for last 1,000,000:   11s.  Last read position: chr10:61,280,221
INFO	2016-11-10 12:07:29	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:07:41	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:11:49s.  Time for last 1,000,000:   12s.  Last read position: chr10:85,305,552
INFO	2016-11-10 12:07:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 12:07:51	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:11:59s.  Time for last 1,000,000:    9s.  Last read position: chr10:108,129,202
INFO	2016-11-10 12:07:51	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:08:05	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:12:13s.  Time for last 1,000,000:   14s.  Last read position: chr10:132,730,123
INFO	2016-11-10 12:08:05	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:08:27	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:12:35s.  Time for last 1,000,000:   21s.  Last read position: chr11:35,359,267
INFO	2016-11-10 12:08:27	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:08:38	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:12:46s.  Time for last 1,000,000:   11s.  Last read position: chr11:75,696,431
INFO	2016-11-10 12:08:38	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:08:57	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:13:05s.  Time for last 1,000,000:   18s.  Last read position: chr11:114,414,621
INFO	2016-11-10 12:08:57	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 12:09:08	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:13:16s.  Time for last 1,000,000:   10s.  Last read position: chr12:8,900,276
INFO	2016-11-10 12:09:08	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 12:09:17	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:13:25s.  Time for last 1,000,000:    8s.  Last read position: chr12:38,863,889
INFO	2016-11-10 12:09:17	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:09:29	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:13:37s.  Time for last 1,000,000:   12s.  Last read position: chr12:60,598,824
INFO	2016-11-10 12:09:29	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:09:40	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:13:48s.  Time for last 1,000,000:   10s.  Last read position: chr12:88,520,538
INFO	2016-11-10 12:09:40	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 12:09:47	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:13:55s.  Time for last 1,000,000:    7s.  Last read position: chr12:112,268,437
INFO	2016-11-10 12:09:47	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:09:58	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:14:06s.  Time for last 1,