BigDataScript report: chipseq.bds

Script file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20161109_220756_782
Start time 2016-11-09 22:07:56
Run time 14:00:37.646
Tasks executed 2
Tasks failed 2
Tasks failed names 
markdup_bam_picard ctl1
bwa_aln rep1
Arguments* [-title, SRR1370901_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370901_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370901_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_220756_782_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_11
thread_41 thread_Root 
 chipseq.bds.20161109_220756_782_parallel_41/task.align_bwa.bwa_aln_rep1.line_108.id_10

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 6462
OK false
Exit Code 3
Retries
State RUNNING
Dep. WAIT
Cpus 2
Mem
Start 2016-11-09 22:08:00
End 2016-11-09 22:08:00
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370901_1.fastq.gz
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370901_1/out/align/rep1/SRR1370901_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 2 /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370901_1.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370901_1/out/align/rep1/SRR1370901_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--------------------
28332 (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] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 106.70 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 96.82 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 101.49 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.41 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.18 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.97 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.60 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.69 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.68 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.72 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.20 sec
[bwa_aln_core] write to the disk... [fwrite] No space left on device
Num 2
ID task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_11
Name markdup_bam_picard ctl1
Thread thread_42
PID 6463
OK false
Exit Code 3
Retries
State KILLED
Dep. ERROR
Cpus 1
Mem
Start 2016-11-09 22:08:00
End 2016-11-09 22:15:08
Elapsed 00:07:07
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370901_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370901_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370901_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/SRR1370901_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370901_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370901_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/SRR1370901_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370901_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370901_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--------------------
40176 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Wed Nov 09 22:45:03 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370901_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370901_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370901_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 22:45:03 PST 2016] Executing as imk1@kali on Linux 3.19.0-64-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-11-09 22:45:04	MarkDuplicates	Start of doWork freeMemory: 254879200; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-11-09 22:45:04	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-11-09 22:45:04	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-11-09 22:45:18	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:13s.  Time for last 1,000,000:   13s.  Last read position: chr1:22,298,551
INFO	2016-11-09 22:45:18	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:45:37	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:32s.  Time for last 1,000,000:   18s.  Last read position: chr1:41,895,424
INFO	2016-11-09 22:45:37	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 22:45:51	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:46s.  Time for last 1,000,000:   14s.  Last read position: chr1:63,396,527
INFO	2016-11-09 22:45:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:46:07	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:01:02s.  Time for last 1,000,000:   15s.  Last read position: chr1:89,147,707
INFO	2016-11-09 22:46:07	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:46:18	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:01:13s.  Time for last 1,000,000:   11s.  Last read position: chr1:115,615,553
INFO	2016-11-09 22:46:18	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:46:29	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:01:24s.  Time for last 1,000,000:   10s.  Last read position: chr1:164,468,682
INFO	2016-11-09 22:46:29	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-09 22:46:41	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:01:36s.  Time for last 1,000,000:   11s.  Last read position: chr1:189,102,252
INFO	2016-11-09 22:46:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:46:49	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:01:44s.  Time for last 1,000,000:    7s.  Last read position: chr1:213,979,760
INFO	2016-11-09 22:46:49	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:47:01	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:01:56s.  Time for last 1,000,000:   12s.  Last read position: chr1:231,814,268
INFO	2016-11-09 22:47:01	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:47:11	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:02:06s.  Time for last 1,000,000:    9s.  Last read position: chr2:3,652,468
INFO	2016-11-09 22:47:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:47:23	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:02:18s.  Time for last 1,000,000:   11s.  Last read position: chr2:39,505,122
INFO	2016-11-09 22:47:23	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:47:34	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:02:29s.  Time for last 1,000,000:   11s.  Last read position: chr2:73,561,393
INFO	2016-11-09 22:47:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:47:45	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:02:40s.  Time for last 1,000,000:   10s.  Last read position: chr2:120,526,571
INFO	2016-11-09 22:47:45	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:47:56	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:02:51s.  Time for last 1,000,000:   11s.  Last read position: chr2:160,316,783
INFO	2016-11-09 22:47:56	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:48:27	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:03:22s.  Time for last 1,000,000:   30s.  Last read position: chr2:195,549,735
INFO	2016-11-09 22:48:27	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:48:39	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:03:34s.  Time for last 1,000,000:   11s.  Last read position: chr2:230,358,034
INFO	2016-11-09 22:48:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:48:50	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:03:45s.  Time for last 1,000,000:   11s.  Last read position: chr3:16,305,780
INFO	2016-11-09 22:48:50	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-09 22:49:01	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:03:56s.  Time for last 1,000,000:   11s.  Last read position: chr3:49,251,279
INFO	2016-11-09 22:49:01	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:49:13	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:04:08s.  Time for last 1,000,000:   11s.  Last read position: chr3:84,621,225
INFO	2016-11-09 22:49:13	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:49:23	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:04:18s.  Time for last 1,000,000:   10s.  Last read position: chr3:128,121,129
INFO	2016-11-09 22:49:23	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:49:31	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:04:26s.  Time for last 1,000,000:    7s.  Last read position: chr3:165,373,238
INFO	2016-11-09 22:49:31	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:49:42	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:04:37s.  Time for last 1,000,000:   10s.  Last read position: chr3:195,333,247
INFO	2016-11-09 22:49:42	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:49:48	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:04:43s.  Time for last 1,000,000:    6s.  Last read position: chr4:37,752,582
INFO	2016-11-09 22:49:48	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:49:55	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:04:50s.  Time for last 1,000,000:    7s.  Last read position: chr4:81,286,306
INFO	2016-11-09 22:49:55	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:50:04	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:04:59s.  Time for last 1,000,000:    9s.  Last read position: chr4:119,339,736
INFO	2016-11-09 22:50:04	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:50:18	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:05:13s.  Time for last 1,000,000:   13s.  Last read position: chr4:158,818,783
INFO	2016-11-09 22:50:18	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 22:50:26	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:05:21s.  Time for last 1,000,000:    8s.  Last read position: chr5:6,447,551
INFO	2016-11-09 22:50:26	MarkDuplicates	Tracking 16 as yet unmatched pairs. 16 records in RAM.
INFO	2016-11-09 22:50:35	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:05:30s.  Time for last 1,000,000:    8s.  Last read position: chr5:33,219,021
INFO	2016-11-09 22:50:35	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-09 22:50:50	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:05:45s.  Time for last 1,000,000:   14s.  Last read position: chr5:60,694,078
INFO	2016-11-09 22:50:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:51:09	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:06:04s.  Time for last 1,000,000:   18s.  Last read position: chr5:86,336,676
INFO	2016-11-09 22:51:09	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:51:22	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:06:17s.  Time for last 1,000,000:   13s.  Last read position: chr5:112,930,184
INFO	2016-11-09 22:51:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:51:31	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:06:26s.  Time for last 1,000,000:    9s.  Last read position: chr5:136,852,889
INFO	2016-11-09 22:51:31	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:51:43	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:06:38s.  Time for last 1,000,000:   11s.  Last read position: chr5:160,271,193
INFO	2016-11-09 22:51:43	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:51:55	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:06:50s.  Time for last 1,000,000:   11s.  Last read position: chr6:4,126,386
INFO	2016-11-09 22:51:55	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-09 22:52:02	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:06:57s.  Time for last 1,000,000:    7s.  Last read position: chr6:28,666,579
INFO	2016-11-09 22:52:02	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:52:11	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:07:06s.  Time for last 1,000,000:    9s.  Last read position: chr6:49,527,281
INFO	2016-11-09 22:52:11	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:52:19	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:07:14s.  Time for last 1,000,000:    7s.  Last read position: chr6:81,728,195
INFO	2016-11-09 22:52:19	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:52:26	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:07:21s.  Time for last 1,000,000:    7s.  Last read position: chr6:107,535,760
INFO	2016-11-09 22:52:26	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:52:36	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:07:31s.  Time for last 1,000,000:    9s.  Last read position: chr6:132,364,408
INFO	2016-11-09 22:52:36	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 22:52:48	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:07:43s.  Time for last 1,000,000:   12s.  Last read position: chr6:156,918,595
INFO	2016-11-09 22:52:48	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:52:59	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:07:54s.  Time for last 1,000,000:   10s.  Last read position: chr7:18,636,743
INFO	2016-11-09 22:52:59	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:53:12	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:08:07s.  Time for last 1,000,000:   13s.  Last read position: chr7:53,850,313
INFO	2016-11-09 22:53:12	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:53:25	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:08:20s.  Time for last 1,000,000:   12s.  Last read position: chr7:96,503,433
INFO	2016-11-09 22:53:25	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:53:35	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:08:30s.  Time for last 1,000,000:   10s.  Last read position: chr7:120,651,846
INFO	2016-11-09 22:53:35	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:53:50	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:08:45s.  Time for last 1,000,000:   14s.  Last read position: chr7:146,401,497
INFO	2016-11-09 22:53:50	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:54:01	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:08:56s.  Time for last 1,000,000:   11s.  Last read position: chr8:17,030,519
INFO	2016-11-09 22:54:01	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:54:07	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:09:02s.  Time for last 1,000,000:    5s.  Last read position: chr8:42,750,671
INFO	2016-11-09 22:54:07	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:54:14	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:09:09s.  Time for last 1,000,000:    7s.  Last read position: chr8:85,385,487
INFO	2016-11-09 22:54:14	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:54:21	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:09:16s.  Time for last 1,000,000:    7s.  Last read position: chr8:124,358,985
INFO	2016-11-09 22:54:21	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:54:28	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:09:23s.  Time for last 1,000,000:    6s.  Last read position: chr9:18,183,883
INFO	2016-11-09 22:54:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:54:36	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:09:31s.  Time for last 1,000,000:    8s.  Last read position: chr9:84,163,983
INFO	2016-11-09 22:54:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:54:45	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:09:40s.  Time for last 1,000,000:    8s.  Last read position: chr9:119,875,535
INFO	2016-11-09 22:54:45	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:54:54	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:09:49s.  Time for last 1,000,000:    8s.  Last read position: chr10:5,661,683
INFO	2016-11-09 22:54:54	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 22:55:00	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:09:55s.  Time for last 1,000,000:    6s.  Last read position: chr10:29,748,948
INFO	2016-11-09 22:55:00	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:55:08	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:10:03s.  Time for last 1,000,000:    8s.  Last read position: chr10:61,280,221
INFO	2016-11-09 22:55:08	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:55:14	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:10:09s.  Time for last 1,000,000:    5s.  Last read position: chr10:85,305,552
INFO	2016-11-09 22:55:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:55:24	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:10:19s.  Time for last 1,000,000:    9s.  Last read position: chr10:108,129,202
INFO	2016-11-09 22:55:24	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:55:30	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:10:25s.  Time for last 1,000,000:    5s.  Last read position: chr10:132,730,123
INFO	2016-11-09 22:55:30	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:55:48	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:10:43s.  Time for last 1,000,000:   18s.  Last read position: chr11:35,359,267
INFO	2016-11-09 22:55:48	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:55:54	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:10:49s.  Time for last 1,000,000:    6s.  Last read position: chr11:75,696,431
INFO	2016-11-09 22:55:54	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:56:01	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:10:56s.  Time for last 1,000,000:    6s.  Last read position: chr11:114,414,621
INFO	2016-11-09 22:56:01	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-09 22:56:10	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:11:05s.  Time for last 1,000,000:    9s.  Last read position: chr12:8,900,276
INFO	2016-11-09 22:56:10	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 22:56:22	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:11:17s.  Time for last 1,000,000:   11s.  Last read position: chr12:38,863,889
INFO	2016-11-09 22:56:22	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:56:28	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:11:23s.  Time for last 1,000,000:    5s.  Last read position: chr12:60,598,824
INFO	2016-11-09 22:56:28	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:56:33	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:11:28s.  Time for last 1,000,000:    5s.  Last read position: chr12:88,520,538
INFO	2016-11-09 22:56:33	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-09 22:56:39	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:11:34s.  Time for last 1,000,000:    5s.  Last read position: chr12:112,268,437
INFO	2016-11-09 22:56:39	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:56:46	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:11:41s.  Time for last 1,000,000:    6s.  Last read position: chr13:23,999,632
INFO	2016-11-09 22:56:46	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:56:55	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:11:50s.  Time for last 1,000,000:    9s.  Last read position: chr13:51,165,870
INFO	2016-11-09 22:56:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:57:02	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:11:57s.  Time for last 1,000,000:    6s.  Last read position: chr13:88,986,369
INFO	2016-11-09 22:57:02	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:57:12	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:12:07s.  Time for last 1,000,000:   10s.  Last read position: chr14:23,149,367
INFO	2016-11-09 22:57:12	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 22:57:20	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:12:15s.  Time for last 1,000,000:    7s.  Last read position: chr14:58,140,905
INFO	2016-11-09 22:57:20	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:57:28	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:12:23s.  Time for last 1,000,000:    8s.  Last read position: chr14:91,912,553
INFO	2016-11-09 22:57:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:57:35	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:12:30s.  Time for last 1,000,000:    7s.  Last read position: chr15:38,895,095
INFO	2016-11-09 22:57:35	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:57:48	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:12:43s.  Time for last 1,000,000:   12s.  Last read position: chr15:68,188,367
INFO	2016-11-09 22:57:48	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 22:58:00	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:12:55s.  Time for last 1,000,000:   11s.  Last read position: chr15:87,921,272
INFO	2016-11-09 22:58:00	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:58:08	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:13:03s.  Time for last 1,000,000:    8s.  Last read position: chr16:11,143,813
INFO	2016-11-09 22:58:08	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:58:17	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:13:12s.  Time for last 1,000,000:    8s.  Last read position: chr16:51,391,437
INFO	2016-11-09 22:58:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:58:26	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:13:21s.  Time for last 1,000,000:    9s.  Last read position: chr16:84,928,458
INFO	2016-11-09 22:58:26	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:58:37	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:13:32s.  Time for last 1,000,000:   10s.  Last read position: chr17:18,368,935
INFO	2016-11-09 22:58:37	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:58:42	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:13:37s.  Time for last 1,000,000:    5s.  Last read position: chr17:44,246,522
INFO	2016-11-09 22:58:42	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:58:49	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:13:44s.  Time for last 1,000,000:    7s.  Last read position: chr17:66,172,158
INFO	2016-11-09 22:58:49	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-11-09 22:58:57	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:13:52s.  Time for last 1,000,000:    7s.  Last read position: chr18:5,619,614
INFO	2016-11-09 22:58:57	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-