Script file	/users/pangwei/bds_atac/atac.bds
Program ID	atac.bds.20160513_182612_276
Start time	2016-05-13 18:26:12
Run time	1 day 14:17:24.291
Tasks executed	20
Tasks failed	2
Tasks failed names	macs2_atac rep2 macs2_atac rep2.pval0.1
Arguments*	[-out_dir, /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22, -num_rep, 2, -fastq1_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC21/ATAC21-trimmed-pair1.fastq.gz, -fastq1_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC21/ATAC21-trimmed-pair2.fastq.gz, -fastq2_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC22/ATAC22-trimmed-pair1.fastq.gz, -fastq2_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC22/ATAC22-trimmed-pair2.fastq.gz, -subsample, 17500000, -true_rep, -species, hg19]
System*	local
Cpus*	1
Exit value	1

Thread ID	Parent	Tasks
thread_Root	None
thread_21	thread_Root	atac.bds.20160513_182612_276_parallel_21/task.align_bowtie2.bowtie2_PE_rep1.line_133.id_6 atac.bds.20160513_182612_276_parallel_21/task.postalign_bam.dedup_bam_PE_rep1.line_215.id_18 atac.bds.20160513_182612_276_parallel_21/task.postalign_bam.nmsrt_bam_rep1.line_321.id_19 atac.bds.20160513_182612_276_parallel_21/task.postalign_bam.bam_to_bedpe_rep1.line_425.id_20 atac.bds.20160513_182612_276_parallel_21/task.postalign_bed.subsample_bedpe_rep1.line_116.id_21 atac.bds.20160513_182612_276_parallel_21/task.postalign_bam.bedpe_to_tag_rep1.line_465.id_22 atac.bds.20160513_182612_276_parallel_21/task.postalign_bed.shift_tag_rep1.line_140.id_23 atac.bds.20160513_182612_276_parallel_21/task.postalign_bed.subsample_bedpe2tagrep1.line_89.id_24 atac.bds.20160513_182612_276_parallel_21/task.postalign_bed.xcor_rep1.line_165.id_25
thread_22	thread_Root	atac.bds.20160513_182612_276_parallel_22/task.align_bowtie2.bowtie2_PE_rep2.line_133.id_7 atac.bds.20160513_182612_276_parallel_22/task.postalign_bam.dedup_bam_PE_rep2.line_215.id_8 atac.bds.20160513_182612_276_parallel_22/task.postalign_bam.nmsrt_bam_rep2.line_321.id_9 atac.bds.20160513_182612_276_parallel_22/task.postalign_bam.bam_to_bedpe_rep2.line_425.id_10 atac.bds.20160513_182612_276_parallel_22/task.postalign_bed.subsample_bedpe_rep2.line_116.id_11 atac.bds.20160513_182612_276_parallel_22/task.postalign_bam.bedpe_to_tag_rep2.line_465.id_12 atac.bds.20160513_182612_276_parallel_22/task.postalign_bed.shift_tag_rep2.line_140.id_13 atac.bds.20160513_182612_276_parallel_22/task.postalign_bed.subsample_bedpe2tagrep2.line_89.id_14 atac.bds.20160513_182612_276_parallel_22/task.postalign_bed.xcor_rep2.line_165.id_15 atac.bds.20160513_182612_276_parallel_22/task.callpeak_macs2.macs2_atac_rep2.pval0.1.line_192.id_16 atac.bds.20160513_182612_276_parallel_22/task.callpeak_macs2.macs2_atac_rep2.line_192.id_17

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.align_bowtie2.bowtie2_PE_rep1.line_133.id_6
Name	bowtie2_PE rep1
Thread	thread_21
PID	103682

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	2
Mem

Start	2016-05-13 18:26:13
End	2016-05-14 23:01:56
Elapsed	1 day 04:35:43
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.fastq.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair2.trim.fastq.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.align.log
Dependencies

 
# SYS command. line 135

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 139

 bowtie2  -X2000 --mm --threads 2 -x /mnt/data/annotations/indexes/bowtie2_indexes/bowtie2/ENCODEHg19_male \
			-1 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.fastq.gz -2 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair2.trim.fastq.gz 2>/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.align.log | samtools view -bS - | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE

# SYS command. line 142

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.bam

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 298 files...

Num	2
ID	task.align_bowtie2.bowtie2_PE_rep2.line_133.id_7
Name	bowtie2_PE rep2
Thread	thread_22
PID	103688

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	2
Mem

Start	2016-05-13 18:26:13
End	2016-05-14 08:52:45
Elapsed	14:26:32
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.fastq.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair2.trim.fastq.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep2/ATAC22-trimmed-pair1.trim.PE2SE.align.log
Dependencies

 
# SYS command. line 135

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 139

 bowtie2  -X2000 --mm --threads 2 -x /mnt/data/annotations/indexes/bowtie2_indexes/bowtie2/ENCODEHg19_male \
			-1 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.fastq.gz -2 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair2.trim.fastq.gz 2>/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep2/ATAC22-trimmed-pair1.trim.PE2SE.align.log | samtools view -bS - | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE

# SYS command. line 142

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.bam

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 125 files...

Num	3
ID	task.postalign_bam.dedup_bam_PE_rep2.line_215.id_8
Name	dedup_bam_PE rep2
Thread	thread_22
PID	19698

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-14 08:52:46
End	2016-05-14 12:49:35
Elapsed	03:56:49
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep2/ATAC22-trimmed-pair1.trim.PE2SE.dup.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.pbc.qc
Dependencies

 
# SYS command. line 217

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 228

 echo

# SYS command. line 229

 samtools view -F 1804 -f 2 -q 30 -u /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.dupmark

# SYS command. line 230

 echo

# SYS command. line 237

 samtools fixmate -r /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam

# SYS command. line 238

 samtools view -F 1804 -f 2 -u /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.filt

# SYS command. line 239

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam

# SYS command. line 243

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

# SYS command. line 244

 export MAX_JAVA_MEM="12G"

# SYS command. line 247

 if [ -f ${PICARDROOT}/MarkDuplicates.jar ]; then \
			java -Xmx4G -jar ${PICARDROOT}/MarkDuplicates.jar \
				INPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep2/ATAC22-trimmed-pair1.trim.PE2SE.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
			else \
			java -Xmx4G -jar ${PICARDROOT}/picard.jar MarkDuplicates \
				INPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep2/ATAC22-trimmed-pair1.trim.PE2SE.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
			fi

# SYS command. line 265

 mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.filt.bam

# SYS command. line 267

 samtools view -F 1804 -f 2 -b /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.filt.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 269

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 271

 if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.bai" ]; then \
			cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.bai; \
			fi

# SYS command. line 275

 samtools flagstat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc

# SYS command. line 286

 samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.filt.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.filt.bam.tmp

# SYS command. line 287

 bedtools bamtobed -bedpe -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam | \
			awk 'BEGIN{OFS="\t"}{print $1,$2,$4,$6,$9,$10}' | \
			grep -v 'chrM' | sort | uniq -c | \
			awk 'BEGIN{mt=0;m0=0;m1=0;m2=0} ($1==1){m1=m1+1} ($1==2){m2=m2+1} {m0=m0+1} {mt=mt+$1} END{printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1/m2}' > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.pbc.qc

# SYS command. line 291

 rm /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam

# SYS command. line 293

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.filt.bam

# SYS command. line 294

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.dupmark.bam

   
--------------------Stdout--------------------



 
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 90 files...
[bam_sort_core] merging from 92 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Sat May 14 10:53:55 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep2/ATAC22-trimmed-pair1.trim.PE2SE.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
[Sat May 14 10:53:55 PDT 2016] Executing as pangwei@mitra on Linux 3.16.0-70-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_45-b14; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-05-14 10:53:56	MarkDuplicates	Start of doWork freeMemory: 254889656; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-14 10:53:56	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-05-14 10:53:56	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-05-14 10:54:02	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:06s.  Time for last 1,000,000:    6s.  Last read position: chr10:33,624,337
INFO	2016-05-14 10:54:02	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 10:54:07	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:11s.  Time for last 1,000,000:    4s.  Last read position: chr10:73,781,092
INFO	2016-05-14 10:54:07	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 10:54:11	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:15s.  Time for last 1,000,000:    4s.  Last read position: chr10:103,520,526
INFO	2016-05-14 10:54:11	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 10:54:16	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:20s.  Time for last 1,000,000:    4s.  Last read position: chr10:132,286,472
INFO	2016-05-14 10:54:16	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 10:54:22	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:26s.  Time for last 1,000,000:    6s.  Last read position: chr11:23,657,230
INFO	2016-05-14 10:54:22	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 10:54:29	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:33s.  Time for last 1,000,000:    7s.  Last read position: chr11:62,243,844
INFO	2016-05-14 10:54:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:54:34	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:38s.  Time for last 1,000,000:    4s.  Last read position: chr11:86,047,256
INFO	2016-05-14 10:54:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:54:40	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:44s.  Time for last 1,000,000:    5s.  Last read position: chr11:119,842,215
INFO	2016-05-14 10:54:40	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 10:54:44	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:48s.  Time for last 1,000,000:    4s.  Last read position: chr12:12,421,411
INFO	2016-05-14 10:54:44	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 10:54:49	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:53s.  Time for last 1,000,000:    4s.  Last read position: chr12:51,927,525
INFO	2016-05-14 10:54:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:54:53	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:57s.  Time for last 1,000,000:    4s.  Last read position: chr12:85,306,440
INFO	2016-05-14 10:54:53	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-05-14 10:55:00	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:04s.  Time for last 1,000,000:    6s.  Last read position: chr12:116,554,569
INFO	2016-05-14 10:55:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:55:04	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:08s.  Time for last 1,000,000:    4s.  Last read position: chr13:29,825,729
INFO	2016-05-14 10:55:04	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:55:11	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:15s.  Time for last 1,000,000:    6s.  Last read position: chr13:68,131,684
INFO	2016-05-14 10:55:11	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 10:55:27	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:31s.  Time for last 1,000,000:   15s.  Last read position: chr13:107,603,388
INFO	2016-05-14 10:55:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:55:30	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:34s.  Time for last 1,000,000:    3s.  Last read position: chr14:46,959,987
INFO	2016-05-14 10:55:30	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 10:55:34	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:01:38s.  Time for last 1,000,000:    3s.  Last read position: chr14:77,591,121
INFO	2016-05-14 10:55:34	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 10:55:38	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:01:42s.  Time for last 1,000,000:    4s.  Last read position: chr14:105,437,132
INFO	2016-05-14 10:55:38	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 10:55:44	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:01:48s.  Time for last 1,000,000:    6s.  Last read position: chr15:56,036,257
INFO	2016-05-14 10:55:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:55:48	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:01:52s.  Time for last 1,000,000:    4s.  Last read position: chr15:82,458,858
INFO	2016-05-14 10:55:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:55:53	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:01:57s.  Time for last 1,000,000:    4s.  Last read position: chr16:6,232,634
INFO	2016-05-14 10:55:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:55:58	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:02:02s.  Time for last 1,000,000:    4s.  Last read position: chr16:49,716,586
INFO	2016-05-14 10:55:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:56:02	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:02:06s.  Time for last 1,000,000:    4s.  Last read position: chr16:79,146,911
INFO	2016-05-14 10:56:02	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 10:56:07	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:02:11s.  Time for last 1,000,000:    4s.  Last read position: chr17:11,113,374
INFO	2016-05-14 10:56:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:56:15	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:02:19s.  Time for last 1,000,000:    8s.  Last read position: chr17:40,953,390
INFO	2016-05-14 10:56:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:56:19	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:02:23s.  Time for last 1,000,000:    3s.  Last read position: chr17:68,161,964
INFO	2016-05-14 10:56:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:56:24	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:02:28s.  Time for last 1,000,000:    4s.  Last read position: chr18:11,127,890
INFO	2016-05-14 10:56:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:56:28	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:02:32s.  Time for last 1,000,000:    3s.  Last read position: chr18:48,129,878
INFO	2016-05-14 10:56:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:56:36	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:02:40s.  Time for last 1,000,000:    8s.  Last read position: chr19:2,253,308
INFO	2016-05-14 10:56:36	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-14 10:56:51	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:02:54s.  Time for last 1,000,000:   14s.  Last read position: chr19:28,242,566
INFO	2016-05-14 10:56:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:56:55	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:02:58s.  Time for last 1,000,000:    4s.  Last read position: chr19:50,939,735
INFO	2016-05-14 10:56:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:56:59	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:03:02s.  Time for last 1,000,000:    4s.  Last read position: chr1:9,818,015
INFO	2016-05-14 10:56:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:57:03	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:03:07s.  Time for last 1,000,000:    4s.  Last read position: chr1:31,932,771
INFO	2016-05-14 10:57:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:57:08	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:03:11s.  Time for last 1,000,000:    4s.  Last read position: chr1:56,894,247
INFO	2016-05-14 10:57:08	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 10:57:14	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:03:17s.  Time for last 1,000,000:    5s.  Last read position: chr1:92,363,900
INFO	2016-05-14 10:57:14	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 10:57:17	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:03:21s.  Time for last 1,000,000:    3s.  Last read position: chr1:151,139,210
INFO	2016-05-14 10:57:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:57:21	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:03:25s.  Time for last 1,000,000:    4s.  Last read position: chr1:180,195,283
INFO	2016-05-14 10:57:21	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 10:57:26	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:03:30s.  Time for last 1,000,000:    4s.  Last read position: chr1:212,379,133
INFO	2016-05-14 10:57:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:57:30	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:03:34s.  Time for last 1,000,000:    4s.  Last read position: chr1:244,201,576
INFO	2016-05-14 10:57:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:57:34	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:03:38s.  Time for last 1,000,000:    4s.  Last read position: chr20:26,249,330
INFO	2016-05-14 10:57:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:57:41	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:03:45s.  Time for last 1,000,000:    6s.  Last read position: chr20:52,884,757
INFO	2016-05-14 10:57:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:57:46	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:03:50s.  Time for last 1,000,000:    4s.  Last read position: chr21:34,125,852
INFO	2016-05-14 10:57:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:57:50	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:03:54s.  Time for last 1,000,000:    4s.  Last read position: chr22:28,212,378
INFO	2016-05-14 10:57:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:57:54	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:03:58s.  Time for last 1,000,000:    3s.  Last read position: chr22:50,343,696
INFO	2016-05-14 10:57:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:58:03	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:04:07s.  Time for last 1,000,000:    8s.  Last read position: chr2:27,891,412
INFO	2016-05-14 10:58:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:58:07	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:04:10s.  Time for last 1,000,000:    3s.  Last read position: chr2:61,765,808
INFO	2016-05-14 10:58:07	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-14 10:58:10	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:04:14s.  Time for last 1,000,000:    3s.  Last read position: chr2:100,217,354
INFO	2016-05-14 10:58:10	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 10:58:16	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:04:20s.  Time for last 1,000,000:    5s.  Last read position: chr2:134,733,820
INFO	2016-05-14 10:58:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:58:20	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:04:23s.  Time for last 1,000,000:    3s.  Last read position: chr2:173,524,446
INFO	2016-05-14 10:58:20	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 10:58:23	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:04:27s.  Time for last 1,000,000:    3s.  Last read position: chr2:210,634,207
INFO	2016-05-14 10:58:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:58:27	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:04:31s.  Time for last 1,000,000:    3s.  Last read position: chr2:240,687,697
INFO	2016-05-14 10:58:27	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 10:58:31	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:04:35s.  Time for last 1,000,000:    3s.  Last read position: chr3:28,307,660
INFO	2016-05-14 10:58:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:58:34	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:04:38s.  Time for last 1,000,000:    3s.  Last read position: chr3:55,954,780
INFO	2016-05-14 10:58:34	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 10:58:38	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:04:42s.  Time for last 1,000,000:    3s.  Last read position: chr3:98,060,441
INFO	2016-05-14 10:58:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:58:44	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:04:48s.  Time for last 1,000,000:    6s.  Last read position: chr3:132,003,853
INFO	2016-05-14 10:58:44	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 10:58:48	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:04:52s.  Time for last 1,000,000:    3s.  Last read position: chr3:167,994,379
INFO	2016-05-14 10:58:48	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 10:58:51	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:04:55s.  Time for last 1,000,000:    3s.  Last read position: chr4:1,834,834
INFO	2016-05-14 10:58:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:58:55	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:04:59s.  Time for last 1,000,000:    3s.  Last read position: chr4:35,404,631
INFO	2016-05-14 10:58:55	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 10:59:09	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:05:13s.  Time for last 1,000,000:   13s.  Last read position: chr4:79,145,978
INFO	2016-05-14 10:59:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:59:13	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:05:16s.  Time for last 1,000,000:    3s.  Last read position: chr4:118,544,853
INFO	2016-05-14 10:59:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:59:16	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:05:20s.  Time for last 1,000,000:    3s.  Last read position: chr4:158,488,082
INFO	2016-05-14 10:59:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:59:20	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:05:24s.  Time for last 1,000,000:    4s.  Last read position: chr5:4,411,919
INFO	2016-05-14 10:59:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:59:26	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:05:30s.  Time for last 1,000,000:    5s.  Last read position: chr5:43,312,679
INFO	2016-05-14 10:59:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:59:30	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:05:34s.  Time for last 1,000,000:    4s.  Last read position: chr5:85,713,177
INFO	2016-05-14 10:59:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:59:34	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:05:38s.  Time for last 1,000,000:    4s.  Last read position: chr5:125,343,613
INFO	2016-05-14 10:59:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:59:38	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:05:42s.  Time for last 1,000,000:    4s.  Last read position: chr5:148,378,014
INFO	2016-05-14 10:59:38	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 10:59:43	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:05:47s.  Time for last 1,000,000:    4s.  Last read position: chr5:177,993,958
INFO	2016-05-14 10:59:43	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 10:59:47	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:05:51s.  Time for last 1,000,000:    4s.  Last read position: chr6:27,045,581
INFO	2016-05-14 10:59:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:59:52	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:05:56s.  Time for last 1,000,000:    4s.  Last read position: chr6:52,908,953
INFO	2016-05-14 10:59:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 10:59:56	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:06:00s.  Time for last 1,000,000:    4s.  Last read position: chr6:96,333,869
INFO	2016-05-14 10:59:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 11:00:04	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:06:08s.  Time for last 1,000,000:    7s.  Last read position: chr6:133,055,769
INFO	2016-05-14 11:00:04	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 11:00:09	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:06:12s.  Time for last 1,000,000:    4s.  Last read position: chr6:165,968,735
INFO	2016-05-14 11:00:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 11:00:13	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:06:17s.  Time for last 1,000,000:    4s.  Last read position: chr7:25,730,443
INFO	2016-05-14 11:00:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 11:00:22	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:06:26s.  Time for last 1,000,000:    8s.  Last read position: chr7:64,190,167
INFO	2016-05-14 11:00:22	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 11:00:26	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:06:30s.  Time for last 1,000,000:    4s.  Last read position: chr7:100,289,402
INFO	2016-05-14 11:00:26	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 11:00:31	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:06:34s.  Time for last 1,000,000:    4s.  Last read position: chr7:134,224,285
INFO	2016-05-14 11:00:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 11:00:36	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:06:39s.  Time for last 1,000,000:    4s.  Last read position: chr8:6,722,926
INFO	2016-05-14 11:00:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 11:00:40	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:06:44s.  Time for last 1,000,000:    4s.  Last read position: chr8:38,853,694
INFO	2016-05-14 11:00:40	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-14 11:00:44	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:06:48s.  Time for last 1,000,000:    4s.  Last read position: chr8:77,912,991
INFO	2016-05-14 11:00:44	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-14 11:00:51	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:06:55s.  Time for last 1,000,000:    6s.  Last read position: chr8:114,566,376
INFO	2016-05-14 11:00:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 11:00:55	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:06:59s.  Time for last 1,000,000:    4s.  Last read position: chr8:144,592,782
INFO	2016-05-14 11:00:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 11:00:59	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:07:03s.  Time for last 1,000,000:    4s.  Last read position: chr9:34,043,638
INFO	2016-05-14 11:00:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 11:01:04	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:07:08s.  Time for last 1,000,000:    4s.  Last read position: chr9:96,993,696
INFO	2016-05-14 11:01:04	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 11:01:09	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:07:12s.  Time for last 1,000,000:    4s.  Last read position: chr9:127,483,632
INFO	2016-05-14 11:01:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 11:01:13	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:07:17s.  Time for last 1,000,000:    4s.  Last read position: chrM:80
INFO	2016-05-14 11:01:13	MarkDuplicates	Tracking 15336 as yet unmatched pairs. 15336 records in RAM.
INFO	2016-05-14 11:01:17	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:07:21s.  Time for last 1,000,000:    3s.  Last read position: chrM:490
INFO	2016-05-14 11:01:17	MarkDuplicates	Tracking 13016 as yet unmatched pairs. 13016 records in RAM.
INFO	2016-05-14 11:01:21	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:07:25s.  Time for last 1,000,000:    4s.  Last read position: chrM:759
INFO	2016-05-14 11:01:21	MarkDuplicates	Tracking 5556 as yet unmatched pairs. 5556 records in RAM.
INFO	2016-05-14 11:01:25	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:07:29s.  Time for last 1,000,000:    4s.  Last read position: chrM:1,315
INFO	2016-05-14 11:01:25	MarkDuplicates	Tracking 5162 as yet unmatched pairs. 5162 records in RAM.
INFO	2016-05-14 11:01:39	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:07:43s.  Time for last 1,000,000:   14s.  Last read position: chrM:1,716
INFO	2016-05-14 11:01:39	MarkDuplicates	Tracking 8410 as yet unmatched pairs. 8410 records in RAM.
INFO	2016-05-14 11:01:43	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:07:47s.  Time for last 1,000,000:    4s.  Last read position: chrM:2,243
INFO	2016-05-14 11:01:43	MarkDuplicates	Tracking 3776 as yet unmatched pairs. 3776 records in RAM.
INFO	2016-05-14 11:01:47	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:07:50s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,688
INFO	2016-05-14 11:01:47	MarkDuplicates	Tracking 18694 as yet unmatched pairs. 18694 records in RAM.
INFO	2016-05-14 11:01:50	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:07:54s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,973
INFO	2016-05-14 11:01:50	MarkDuplicates	Tracking 13166 as yet unmatched pairs. 13166 records in RAM.
INFO	2016-05-14 11:01:54	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:07:58s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,272
INFO	2016-05-14 11:01:54	MarkDuplicates	Tracking 9632 as yet unmatched pairs. 9632 records in RAM.
INFO	2016-05-14 11:01:57	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:08:01s.  Time for last 1,000,000:    2s.  Last read position: chrM:3,486
INFO	2016-05-14 11:01:57	MarkDuplicates	Tracking 21606 as yet unmatched pairs. 21606 records in RAM.
INFO	2016-05-14 11:02:00	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:08:04s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,690
INFO	2016-05-14 11:02:00	MarkDuplicates	Tracking 14078 as yet unmatched pairs. 14078 records in RAM.
INFO	2016-05-14 11:02:03	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:08:07s.  Time for last 1,000,000:    3s.  Last read position: chrM:4,060
INFO	2016-05-14 11:02:03	MarkDuplicates	Tracking 4558 as yet unmatched pairs. 4558 records in RAM.
INFO	2016-05-14 11:02:07	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:08:11s.  Time for last 1,000,000:    3s.  Last read position: chrM:4,918
INFO	2016-05-14 11:02:07	MarkDuplicates	Tracking 4500 as yet unmatched pairs. 4500 records in RAM.
INFO	2016-05-14 11:02:10	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:08:14s.  Time for last 1,000,000:    3s.  Last read position: chrM:5,393
INFO	2016-05-14 11:02:10	MarkDuplicates	Tracking 1714 as yet unmatched pairs. 1714 records in RAM.
INFO	2016-05-14 11:02:13	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:08:17s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,230
INFO	2016-05-14 11:02:13	MarkDuplicates	Tracking 13772 as yet unmatched pairs. 13772 records in RAM.
INFO	2016-05-14 11:02:20	MarkDuplicates	Read   100,000,000 records.  Elapsed time: 00:08:23s.  Time for last 1,000,000:    6s.  Last read position: chrM:6,472
INFO	2016-05-14 11:02:20	MarkDuplicates	Tracking 6486 as yet unmatched pairs. 6486 records in RAM.
INFO	2016-05-14 11:02:23	MarkDuplicates	Read   101,000,000 records.  Elapsed time: 00:08:27s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,977
INFO	2016-05-14 11:02:23	MarkDuplicates	Tracking 1694 as yet unmatched pairs. 1694 records in RAM.
INFO	2016-05-14 11:02:26	MarkDuplicates	Read   102,000,000 records.  Elapsed time: 00:08:30s.  Time for last 1,000,000:    2s.  Last read position: chrM:7,699
INFO	2016-05-14 11:02:26	MarkDuplicates	Tracking 5360 as yet unmatched pairs. 5360 records in RAM.
INFO	2016-05-14 11:02:35	MarkDuplicates	Read   103,000,000 records.  Elapsed time: 00:08:39s.  Time for last 1,000,000:    9s.  Last read position: chrM:8,093
INFO	2016-05-14 11:02:35	MarkDuplicates	Tracking 8088 as yet unmatched pairs. 8088 records in RAM.
INFO	2016-05-14 11:02:38	MarkDuplicates	Read   104,000,000 records.  Elapsed time: 00:08:42s.  Time for last 1,000,000:    3s.  Last read position: chrM:8,649
INFO	2016-05-14 11:02:38	MarkDuplicates	Tracking 3646 as yet unmatched pairs. 3646 records in RAM.
INFO	2016-05-14 11:02:42	MarkDuplicates	Read   105,000,000 records.  Elapsed time: 00:08:45s.  Time for last 1,000,000:    3s.  Last read position: chrM:9,382
INFO	2016-05-14 11:02:42	MarkDuplicates	Tracking 542 as yet unmatched pairs. 542 records in RAM.
INFO	2016-05-14 11:02:45	MarkDuplicates	Read   106,000,000 records.  Elapsed time: 00:08:49s.  Time for last 1,000,000:    3s.  Last read position: chrM:9,850
INFO	2016-05-14 11:02:45	MarkDuplicates	Tracking 13360 as yet unmatched pairs. 13360 records in RAM.
INFO	2016-05-14 11:02:48	MarkDuplicates	Read   107,000,000 records.  Elapsed time: 00:08:52s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,218
INFO	2016-05-14 11:02:48	MarkDuplicates	Tracking 6238 as yet unmatched pairs. 6238 records in RAM.
INFO	2016-05-14 11:02:52	MarkDuplicates	Read   108,000,000 records.  Elapsed time: 00:08:56s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,627
INFO	2016-05-14 11:02:52	MarkDuplicates	Tracking 1032 as yet unmatched pairs. 1032 records in RAM.
INFO	2016-05-14 11:02:56	MarkDuplicates	Read   109,000,000 records.  Elapsed time: 00:09:00s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,154
INFO	2016-05-14 11:02:56	MarkDuplicates	Tracking 6374 as yet unmatched pairs. 6374 records in RAM.
INFO	2016-05-14 11:02:59	MarkDuplicates	Read   110,000,000 records.  Elapsed time: 00:09:03s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,534
INFO	2016-05-14 11:02:59	MarkDuplicates	Tracking 1274 as yet unmatched pairs. 1274 records in RAM.
INFO	2016-05-14 11:03:02	MarkDuplicates	Read   111,000,000 records.  Elapsed time: 00:09:06s.  Time for last 1,000,000:    2s.  Last read position: chrM:11,972
INFO	2016-05-14 11:03:02	MarkDuplicates	Tracking 8100 as yet unmatched pairs. 8100 records in RAM.
INFO	2016-05-14 11:03:08	MarkDuplicates	Read   112,000,000 records.  Elapsed time: 00:09:12s.  Time for last 1,000,000:    5s.  Last read position: chrM:12,369
INFO	2016-05-14 11:03:08	MarkDuplicates	Tracking 8560 as yet unmatched pairs. 8560 records in RAM.
INFO	2016-05-14 11:03:11	MarkDuplicates	Read   113,000,000 records.  Elapsed time: 00:09:15s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,657
INFO	2016-05-14 11:03:11	MarkDuplicates	Tracking 13978 as yet unmatched pairs. 13978 records in RAM.
INFO	2016-05-14 11:03:14	MarkDuplicates	Read   114,000,000 records.  Elapsed time: 00:09:18s.  Time for last 1,000,000:    2s.  Last read position: chrM:13,043
INFO	2016-05-14 11:03:14	MarkDuplicates	Tracking 12994 as yet unmatched pairs. 12994 records in RAM.
INFO	2016-05-14 11:03:17	MarkDuplicates	Read   115,000,000 records.  Elapsed time: 00:09:21s.  Time for last 1,000,000:    2s.  Last read position: chrM:13,323
INFO	2016-05-14 11:03:17	MarkDuplicates	Tracking 11798 as yet unmatched pairs. 11798 records in RAM.
INFO	2016-05-14 11:03:20	MarkDuplicates	Read   116,000,000 records.  Elapsed time: 00:09:24s.  Time for last 1,000,000:    2s.  Last read position: chrM:13,625
INFO	2016-05-14 11:03:20	MarkDuplicates	Tracking 12128 as yet unmatched pairs. 12128 records in RAM.
INFO	2016-05-14 11:03:23	MarkDuplicates	Read   117,000,000 records.  Elapsed time: 00:09:27s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,946
INFO	2016-05-14 11:03:23	MarkDuplicates	Tracking 7982 as yet unmatched pairs. 7982 records in RAM.
INFO	2016-05-14 11:03:38	MarkDuplicates	Read   118,000,000 records.  Elapsed time: 00:09:42s.  Time for last 1,000,000:   15s.  Last read position: chrM:14,344
INFO	2016-05-14 11:03:38	MarkDuplicates	Tracking 3894 as yet unmatched pairs. 3894 records in RAM.
INFO	2016-05-14 11:03:41	MarkDuplicates	Read   119,000,000 records.  Elapsed time: 00:09:45s.  Time for last 1,000,000:    2s.  Last read position: chrM:14,811
INFO	2016-05-14 11:03:41	MarkDuplicates	Tracking 5514 as yet unmatched pairs. 5514 records in RAM.
INFO	2016-05-14 11:03:44	MarkDuplicates	Read   120,000,000 records.  Elapsed time: 00:09:47s.  Time for last 1,000,000:    2s.  Last read position: chrM:15,129
INFO	2016-05-14 11:03:44	MarkDuplicates	Tracking 18212 as yet unmatched pairs. 18212 records in RAM.
INFO	2016-05-14 11:03:46	MarkDuplicates	Read   121,000,000 records.  Elapsed time: 00:09:50s.  Time for last 1,000,000:    2s.  Last read position: chrM:15,375
INFO	2016-05-14 11:03:46	MarkDuplicates	Tracking 11676 as yet unmatched pairs. 11676 records in RAM.
INFO	2016-05-14 11:03:49	MarkDuplicates	Read   122,000,000 records.  Elapsed time: 00:09:53s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,628
INFO	2016-05-14 11:03:49	MarkDuplicates	Tracking 14400 as yet unmatched pairs. 14400 records in RAM.
INFO	2016-05-14 11:03:54	MarkDuplicates	Read   123,000,000 records.  Elapsed time: 00:09:58s.  Time for last 1,000,000:    4s.  Last read position: chrM:15,866
INFO	2016-05-14 11:03:54	MarkDuplicates	Tracking 14046 as yet unmatched pairs. 14046 records in RAM.
INFO	2016-05-14 11:03:57	MarkDuplicates	Read   124,000,000 records.  Elapsed time: 00:10:01s.  Time for last 1,000,000:    3s.  Last read position: chrM:16,333
INFO	2016-05-14 11:03:57	MarkDuplicates	Tracking 10426 as yet unmatched pairs. 10426 records in RAM.
INFO	2016-05-14 11:04:00	MarkDuplicates	Read   125,000,000 records.  Elapsed time: 00:10:04s.  Time for last 1,000,000:    3s.  Last read position: chrX:9,675,700
INFO	2016-05-14 11:04:00	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 11:04:04	MarkDuplicates	Read   126,000,000 records.  Elapsed time: 00:10:08s.  Time for last 1,000,000:    3s.  Last read position: chrX:45,575,309
INFO	2016-05-14 11:04:04	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 11:04:07	MarkDuplicates	Read   127,000,000 records.  Elapsed time: 00:10:11s.  Time for last 1,000,000:    3s.  Last read position: chrX:95,577,986
INFO	2016-05-14 11:04:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 11:04:11	MarkDuplicates	Read   128,000,000 records.  Elapsed time: 00:10:15s.  Time for last 1,000,000:    3s.  Last read position: chrX:133,405,457
INFO	2016-05-14 11:04:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 11:04:13	MarkDuplicates	Read 128586984 records. 0 pairs never matched.
INFO	2016-05-14 11:04:19	MarkDuplicates	After buildSortedReadEndLists freeMemory: 3054933896; totalMemory: 3082813440; maxMemory: 3817865216
INFO	2016-05-14 11:04:19	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-05-14 11:04:19	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-05-14 11:04:47	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-05-14 11:05:16	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-05-14 11:05:18	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2151947248; totalMemory: 3134193664; maxMemory: 3817865216
INFO	2016-05-14 11:05:18	MarkDuplicates	Marking 50097086 records as duplicates.
INFO	2016-05-14 11:05:18	MarkDuplicates	Found 21552384 optical duplicate clusters.
INFO	2016-05-14 11:06:59	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:38s.  Time for last 10,000,000:   98s.  Last read position: chr12:51,927,525
INFO	2016-05-14 11:08:40	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:03:19s.  Time for last 10,000,000:  101s.  Last read position: chr15:82,458,858
INFO	2016-05-14 11:10:19	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:04:59s.  Time for last 10,000,000:   99s.  Last read position: chr19:28,242,566
INFO	2016-05-14 11:11:58	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:06:38s.  Time for last 10,000,000:   98s.  Last read position: chr20:26,249,330
INFO	2016-05-14 11:13:39	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:08:18s.  Time for last 10,000,000:  100s.  Last read position: chr2:210,634,207
INFO	2016-05-14 11:15:21	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:10:00s.  Time for last 10,000,000:  102s.  Last read position: chr4:118,544,853
INFO	2016-05-14 11:17:02	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:11:42s.  Time for last 10,000,000:  101s.  Last read position: chr6:96,333,869
INFO	2016-05-14 11:18:44	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:13:23s.  Time for last 10,000,000:  101s.  Last read position: chr8:114,566,376
INFO	2016-05-14 11:20:11	MarkDuplicates	Written    90,000,000 records.  Elapsed time: 00:14:50s.  Time for last 10,000,000:   87s.  Last read position: chrM:2,243
INFO	2016-05-14 11:21:23	MarkDuplicates	Written   100,000,000 records.  Elapsed time: 00:16:02s.  Time for last 10,000,000:   71s.  Last read position: chrM:6,472
INFO	2016-05-14 11:22:32	MarkDuplicates	Written   110,000,000 records.  Elapsed time: 00:17:12s.  Time for last 10,000,000:   69s.  Last read position: chrM:11,534
INFO	2016-05-14 11:23:42	MarkDuplicates	Written   120,000,000 records.  Elapsed time: 00:18:21s.  Time for last 10,000,000:   69s.  Last read position: chrM:15,129
INFO	2016-05-14 11:24:53	MarkDuplicates	Before output close freeMemory: 3163474752; totalMemory: 3193962496; maxMemory: 3817865216
INFO	2016-05-14 11:24:54	MarkDuplicates	After output close freeMemory: 3163473696; totalMemory: 3193962496; maxMemory: 3817865216
[Sat May 14 11:24:54 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 30.97 minutes.
Runtime.totalMemory()=3193962496
[bam_sort_core] merging from 93 files...

Num	4
ID	task.postalign_bam.nmsrt_bam_rep2.line_321.id_9
Name	nmsrt_bam rep2
Thread	thread_22
PID	24478

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-14 12:49:36
End	2016-05-14 13:22:44
Elapsed	00:33:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam
Dependencies

 
# SYS command. line 323

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 325

 samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.nmsrt

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 56 files...

Num	5
ID	task.postalign_bam.bam_to_bedpe_rep2.line_425.id_10
Name	bam_to_bedpe rep2
Thread	thread_22
PID	24824

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-14 13:22:45
End	2016-05-14 13:26:46
Elapsed	00:04:01
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Dependencies	nmsrt_bam rep2 nmsrt_bam rep2

 
# SYS command. line 427

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 430

 bedtools bamtobed -bedpe -mate1 -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH

Num	6
ID	task.postalign_bed.subsample_bedpe_rep2.line_116.id_11
Name	subsample_bedpe rep2
Thread	thread_22
PID	24900

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-14 13:26:48
End	2016-05-14 13:28:50
Elapsed	00:02:02
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz
Dependencies

 
# SYS command. line 118

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 120

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | grep -v "chrM" | shuf -n 17500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH

Num	7
ID	task.postalign_bam.bedpe_to_tag_rep2.line_465.id_12
Name	bedpe_to_tag rep2
Thread	thread_22
PID	24969

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-14 13:28:51
End	2016-05-14 13:30:26
Elapsed	00:01:34
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
Dependencies

 
# SYS command. line 467

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 469

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz | awk 'BEGIN{OFS="\t"}{printf "%s\t%s\t%s\tN\t1000\t%s\n%s\t%s\t%s\tN\t1000\t%s\n",$1,$2,$3,$9,$4,$5,$6,$10}' | \
			gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz

# SYS command. line 472

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz | grep -P -v 'chrM' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz; mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH

Num	8
ID	task.postalign_bed.shift_tag_rep2.line_140.id_13
Name	shift_tag rep2
Thread	thread_22
PID	25037

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-14 13:30:27
End	2016-05-14 13:31:19
Elapsed	00:00:52
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Dependencies

 
# SYS command. line 142

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 144

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz | awk -F $'\t' 'BEGIN {OFS = FS}{ if ($6 == "+") {$2 = $2 + 4} else if ($6 == "-") {$3 = $3 - 5} print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH

Num	9
ID	task.postalign_bed.subsample_bedpe2tagrep2.line_89.id_14
Name	subsample_bedpe2tagrep2
Thread	thread_22
PID	25099

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-14 13:31:20
End	2016-05-14 13:32:38
Elapsed	00:01:17
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
Dependencies

 
# SYS command. line 91

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 95

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | \
			grep -v "chrM" | shuf -n 25000000 | \
			awk 'BEGIN{OFS="\t"}{print $1,$2,$3,"N","1000",$9}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH

Num	10
ID	task.postalign_bed.xcor_rep2.line_165.id_15
Name	xcor rep2
Thread	thread_22
PID	25167

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-14 13:32:38
End	2016-05-14 14:09:04
Elapsed	00:36:25
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf
Dependencies

 
# SYS command. line 167

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 171

 Rscript $(which run_spp_nodups.R) -rf \
			-c=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz -p=1 \
			-filtchr=chrM -savp=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf -out=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc -speak=0

# SYS command. line 174

 sed -r 's/,[^\t]+//g' /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp

# SYS command. line 175

 mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc

   
--------------------Stdout--------------------
################
ChIP data: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz 
Control data: NA 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 0 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: NA 
Output Directory: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2 
narrowPeak output file name: NA 
regionPeak output file name: NA 
Rdata filename: NA 
plot pdf filename: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf 
result filename: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz 
opened /tmp/RtmpdKEY4l/ATAC22-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign62f87bd360c8
done. read 25000000 fragments
ChIP data read length 64 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.248117 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.265206958283454 
Top 3 estimates for fragment length 0 
Window half size 475 
Phantom peak location 55 
Phantom peak Correlation 0.2671423 
Normalized Strand cross-correlation coefficient (NSC) 1.068879 
Relative Strand Cross correlation Coefficient (RSC) 0.8982756 
Phantom Peak Quality Tag 0 
null device 
          1 

 
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
Loading required package: caTools

Num	11
ID	task.callpeak_macs2.macs2_atac_rep2.pval0.1.line_192.id_16
Name	macs2_atac rep2.pval0.1
Thread	thread_22
PID	25169

OK	false
Exit Code	1
Retries
State	ERROR
Dep.	ERROR
Cpus	2
Mem

Start	2016-05-14 13:32:38
End	2016-05-14 13:32:38
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz
Dependencies

 
# SYS command. line 194

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 195

 LC_COLLATE=C

# SYS command. line 197

 macs2 callpeak \
			-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 --broad --keep-dup all

# SYS command. line 202

 sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.broadPeak.gz

# SYS command. line 203

 sort -k 14gr,14gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz

# SYS command. line 204

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.broadPeak

# SYS command. line 205

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.gappedPeak

# SYS command. line 207

 macs2 callpeak \
			-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits

# SYS command. line 212

 sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz

# SYS command. line 213

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.narrowPeak

# SYS command. line 214

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.xls

# SYS command. line 215

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_summits.bed

# SYS command. line 217

 if [[ false == "true" ]]; then \
			\
			macs2 bdgcmp -t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_FE.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/signal/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			\
			# sval counts the number of tags per million in the (compressed) BED file; \
			sval=$(wc -l <(zcat -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_ppois.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/signal/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			\
			fi

# SYS command. line 243

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
Traceback (most recent call last):
  File "/users/pangwei/anaconda3/envs/bds_atac/bin/macs2", line 4, in 
    __import__('pkg_resources').run_script('MACS2==2.1.0.20150731', 'macs2')
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/setuptools-20.7.0-py2.7.egg/pkg_resources/__init__.py", line 719, in run_script
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/setuptools-20.7.0-py2.7.egg/pkg_resources/__init__.py", line 1511, in run_script
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 614, in 
    
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 55, in main
    
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/callpeak_cmd.py", line 30, in 
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/OptValidator.py", line 27, in 
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/IO/Parser.py", line 7, in 
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/IO/Parser.py", line 6, in __bootstrap__
  File "__init__.pxd", line 155, in init MACS2.IO.Parser (MACS2/IO/Parser.c:24419)
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/numpy/__init__.py", line 180, in 
    from . import add_newdocs
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/numpy/add_newdocs.py", line 13, in 
    from numpy.lib import add_newdoc
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/numpy/lib/__init__.py", line 8, in 
    from .type_check import *
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/numpy/lib/type_check.py", line 11, in 
    import numpy.core.numeric as _nx
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/numpy/core/__init__.py", line 14, in 
    from . import multiarray
ImportError: libopenblasp-r0-39a31c03.2.18.so: cannot open shared object file: No such file or directory

Num	12
ID	task.callpeak_macs2.macs2_atac_rep2.line_192.id_17
Name	macs2_atac rep2
Thread	thread_22
PID	25182

OK	false
Exit Code	1
Retries
State	ERROR
Dep.	ERROR
Cpus	2
Mem

Start	2016-05-14 13:32:39
End	2016-05-14 13:32:39
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.gappedPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/signal/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/signal/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig
Dependencies

 
# SYS command. line 194

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 195

 LC_COLLATE=C

# SYS command. line 197

 macs2 callpeak \
			-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -g "hs" -p 0.01 \
			--nomodel --shift -75 --extsize 150 --broad --keep-dup all

# SYS command. line 202

 sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.broadPeak.gz

# SYS command. line 203

 sort -k 14gr,14gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.gappedPeak.gz

# SYS command. line 204

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.broadPeak

# SYS command. line 205

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.gappedPeak

# SYS command. line 207

 macs2 callpeak \
			-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -g "hs" -p 0.01 \
			--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits

# SYS command. line 212

 sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz

# SYS command. line 213

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.narrowPeak

# SYS command. line 214

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.xls

# SYS command. line 215

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_summits.bed

# SYS command. line 217

 if [[ true == "true" ]]; then \
			\
			macs2 bdgcmp -t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_FE.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/signal/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph; \
			\
			# sval counts the number of tags per million in the (compressed) BED file; \
			sval=$(wc -l <(zcat -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_ppois.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/signal/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph; \
			\
			fi

# SYS command. line 243

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
Traceback (most recent call last):
  File "/users/pangwei/anaconda3/envs/bds_atac/bin/macs2", line 4, in 
    __import__('pkg_resources').run_script('MACS2==2.1.0.20150731', 'macs2')
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/setuptools-20.7.0-py2.7.egg/pkg_resources/__init__.py", line 719, in run_script
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/setuptools-20.7.0-py2.7.egg/pkg_resources/__init__.py", line 1511, in run_script
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 614, in 
    
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 55, in main
    
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/callpeak_cmd.py", line 30, in 
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/OptValidator.py", line 27, in 
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/IO/Parser.py", line 7, in 
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/IO/Parser.py", line 6, in __bootstrap__
  File "__init__.pxd", line 155, in init MACS2.IO.Parser (MACS2/IO/Parser.c:24419)
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/numpy/__init__.py", line 180, in 
    from . import add_newdocs
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/numpy/add_newdocs.py", line 13, in 
    from numpy.lib import add_newdoc
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/numpy/lib/__init__.py", line 8, in 
    from .type_check import *
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/numpy/lib/type_check.py", line 11, in 
    import numpy.core.numeric as _nx
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/numpy/core/__init__.py", line 14, in 
    from . import multiarray
ImportError: libopenblasp-r0-39a31c03.2.18.so: cannot open shared object file: No such file or directory

Num	13
ID	task.postalign_bam.dedup_bam_PE_rep1.line_215.id_18
Name	dedup_bam_PE rep1
Thread	thread_21
PID	30565

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-14 23:01:57
End	2016-05-15 07:21:27
Elapsed	08:19:29
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.dup.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.pbc.qc
Dependencies

 
# SYS command. line 217

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 228

 echo

# SYS command. line 229

 samtools view -F 1804 -f 2 -q 30 -u /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.dupmark

# SYS command. line 230

 echo

# SYS command. line 237

 samtools fixmate -r /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam

# SYS command. line 238

 samtools view -F 1804 -f 2 -u /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.filt

# SYS command. line 239

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam

# SYS command. line 243

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

# SYS command. line 244

 export MAX_JAVA_MEM="12G"

# SYS command. line 247

 if [ -f ${PICARDROOT}/MarkDuplicates.jar ]; then \
			java -Xmx4G -jar ${PICARDROOT}/MarkDuplicates.jar \
				INPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
			else \
			java -Xmx4G -jar ${PICARDROOT}/picard.jar MarkDuplicates \
				INPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
			fi

# SYS command. line 265

 mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.filt.bam

# SYS command. line 267

 samtools view -F 1804 -f 2 -b /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.filt.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 269

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 271

 if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.bai" ]; then \
			cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.bai; \
			fi

# SYS command. line 275

 samtools flagstat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc

# SYS command. line 286

 samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.filt.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.filt.bam.tmp

# SYS command. line 287

 bedtools bamtobed -bedpe -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam | \
			awk 'BEGIN{OFS="\t"}{print $1,$2,$4,$6,$9,$10}' | \
			grep -v 'chrM' | sort | uniq -c | \
			awk 'BEGIN{mt=0;m0=0;m1=0;m2=0} ($1==1){m1=m1+1} ($1==2){m2=m2+1} {m0=m0+1} {mt=mt+$1} END{printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1/m2}' > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.pbc.qc

# SYS command. line 291

 rm /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam

# SYS command. line 293

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.filt.bam

# SYS command. line 294

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.dupmark.bam

   
--------------------Stdout--------------------



 
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 217 files...
[bam_sort_core] merging from 222 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Sun May 15 03:12:54 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.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
[Sun May 15 03:12:54 PDT 2016] Executing as pangwei@mitra on Linux 3.16.0-70-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_45-b14; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-05-15 03:12:54	MarkDuplicates	Start of doWork freeMemory: 254889656; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-15 03:12:54	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-05-15 03:12:54	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-05-15 03:12:59	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:05s.  Time for last 1,000,000:    5s.  Last read position: chr10:13,768,867
INFO	2016-05-15 03:12:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:13:04	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:09s.  Time for last 1,000,000:    4s.  Last read position: chr10:29,365,966
INFO	2016-05-15 03:13:04	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:13:08	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:13s.  Time for last 1,000,000:    4s.  Last read position: chr10:48,551,607
INFO	2016-05-15 03:13:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:13:13	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:19s.  Time for last 1,000,000:    5s.  Last read position: chr10:66,088,211
INFO	2016-05-15 03:13:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:13:19	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:24s.  Time for last 1,000,000:    5s.  Last read position: chr10:78,304,019
INFO	2016-05-15 03:13:19	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:13:23	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:28s.  Time for last 1,000,000:    4s.  Last read position: chr10:91,391,716
INFO	2016-05-15 03:13:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:13:28	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:33s.  Time for last 1,000,000:    4s.  Last read position: chr10:103,547,352
INFO	2016-05-15 03:13:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:13:31	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:37s.  Time for last 1,000,000:    3s.  Last read position: chr10:116,109,601
INFO	2016-05-15 03:13:31	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:13:35	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:41s.  Time for last 1,000,000:    4s.  Last read position: chr10:127,697,332
INFO	2016-05-15 03:13:35	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:13:40	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:45s.  Time for last 1,000,000:    4s.  Last read position: chr11:2,008,719
INFO	2016-05-15 03:13:40	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:13:46	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:51s.  Time for last 1,000,000:    6s.  Last read position: chr11:13,571,842
INFO	2016-05-15 03:13:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:13:50	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:00:55s.  Time for last 1,000,000:    4s.  Last read position: chr11:28,984,272
INFO	2016-05-15 03:13:50	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:13:54	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:00:59s.  Time for last 1,000,000:    3s.  Last read position: chr11:44,838,187
INFO	2016-05-15 03:13:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:14:00	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:05s.  Time for last 1,000,000:    6s.  Last read position: chr11:61,860,440
INFO	2016-05-15 03:14:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:14:15	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:20s.  Time for last 1,000,000:   15s.  Last read position: chr11:69,658,250
INFO	2016-05-15 03:14:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:14:18	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:24s.  Time for last 1,000,000:    3s.  Last read position: chr11:80,196,983
INFO	2016-05-15 03:14:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:14:23	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:01:28s.  Time for last 1,000,000:    4s.  Last read position: chr11:96,766,591
INFO	2016-05-15 03:14:23	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:14:27	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:01:33s.  Time for last 1,000,000:    4s.  Last read position: chr11:113,149,167
INFO	2016-05-15 03:14:27	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:14:33	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:01:39s.  Time for last 1,000,000:    5s.  Last read position: chr11:123,568,066
INFO	2016-05-15 03:14:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:14:37	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:01:43s.  Time for last 1,000,000:    3s.  Last read position: chr12:329,850
INFO	2016-05-15 03:14:37	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:14:41	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:01:46s.  Time for last 1,000,000:    3s.  Last read position: chr12:12,381,511
INFO	2016-05-15 03:14:41	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:14:44	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:01:50s.  Time for last 1,000,000:    3s.  Last read position: chr12:28,343,256
INFO	2016-05-15 03:14:44	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:14:48	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:01:53s.  Time for last 1,000,000:    3s.  Last read position: chr12:48,214,721
INFO	2016-05-15 03:14:48	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:14:53	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:01:59s.  Time for last 1,000,000:    5s.  Last read position: chr12:57,635,014
INFO	2016-05-15 03:14:53	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:14:57	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:02:02s.  Time for last 1,000,000:    3s.  Last read position: chr12:72,955,471
INFO	2016-05-15 03:14:57	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:15:00	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:02:06s.  Time for last 1,000,000:    3s.  Last read position: chr12:90,346,621
INFO	2016-05-15 03:15:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:15:04	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:02:09s.  Time for last 1,000,000:    3s.  Last read position: chr12:105,018,161
INFO	2016-05-15 03:15:04	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:15:10	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:02:15s.  Time for last 1,000,000:    6s.  Last read position: chr12:116,118,477
INFO	2016-05-15 03:15:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:15:13	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:02:19s.  Time for last 1,000,000:    3s.  Last read position: chr12:126,185,030
INFO	2016-05-15 03:15:13	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:15:25	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:02:30s.  Time for last 1,000,000:   11s.  Last read position: chr13:24,729,244
INFO	2016-05-15 03:15:25	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:15:28	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:02:34s.  Time for last 1,000,000:    3s.  Last read position: chr13:39,744,308
INFO	2016-05-15 03:15:28	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:15:33	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:02:39s.  Time for last 1,000,000:    4s.  Last read position: chr13:54,731,407
INFO	2016-05-15 03:15:33	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:15:39	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:02:44s.  Time for last 1,000,000:    5s.  Last read position: chr13:74,687,188
INFO	2016-05-15 03:15:39	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:15:44	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:02:50s.  Time for last 1,000,000:    5s.  Last read position: chr13:93,734,460
INFO	2016-05-15 03:15:44	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-05-15 03:15:48	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:02:53s.  Time for last 1,000,000:    3s.  Last read position: chr13:108,877,651
INFO	2016-05-15 03:15:48	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:15:51	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:02:57s.  Time for last 1,000,000:    3s.  Last read position: chr14:25,162,016
INFO	2016-05-15 03:15:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:15:55	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:03:01s.  Time for last 1,000,000:    3s.  Last read position: chr14:42,812,852
INFO	2016-05-15 03:15:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:15:59	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:03:04s.  Time for last 1,000,000:    3s.  Last read position: chr14:59,082,259
INFO	2016-05-15 03:15:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:16:02	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:03:08s.  Time for last 1,000,000:    3s.  Last read position: chr14:72,389,509
INFO	2016-05-15 03:16:02	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:16:06	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:03:12s.  Time for last 1,000,000:    3s.  Last read position: chr14:85,881,371
INFO	2016-05-15 03:16:06	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:16:12	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:03:17s.  Time for last 1,000,000:    5s.  Last read position: chr14:98,203,056
INFO	2016-05-15 03:16:12	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:16:15	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:03:20s.  Time for last 1,000,000:    3s.  Last read position: chr15:20,557,251
INFO	2016-05-15 03:16:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:16:18	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:03:24s.  Time for last 1,000,000:    3s.  Last read position: chr15:39,886,152
INFO	2016-05-15 03:16:18	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:16:22	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:03:27s.  Time for last 1,000,000:    3s.  Last read position: chr15:53,503,473
INFO	2016-05-15 03:16:22	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:16:28	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:03:34s.  Time for last 1,000,000:    6s.  Last read position: chr15:66,882,355
INFO	2016-05-15 03:16:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:16:32	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:03:37s.  Time for last 1,000,000:    3s.  Last read position: chr15:77,395,579
INFO	2016-05-15 03:16:32	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:16:35	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:03:41s.  Time for last 1,000,000:    3s.  Last read position: chr15:90,217,450
INFO	2016-05-15 03:16:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:16:40	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:03:46s.  Time for last 1,000,000:    5s.  Last read position: chr16:325,171
INFO	2016-05-15 03:16:40	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:16:44	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:03:49s.  Time for last 1,000,000:    3s.  Last read position: chr16:9,350,241
INFO	2016-05-15 03:16:44	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:16:47	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:03:53s.  Time for last 1,000,000:    3s.  Last read position: chr16:23,791,883
INFO	2016-05-15 03:16:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:16:50	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:03:56s.  Time for last 1,000,000:    3s.  Last read position: chr16:48,901,834
INFO	2016-05-15 03:16:50	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:16:54	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:03:59s.  Time for last 1,000,000:    3s.  Last read position: chr16:60,627,064
INFO	2016-05-15 03:16:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:16:57	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:04:03s.  Time for last 1,000,000:    3s.  Last read position: chr16:73,097,018
INFO	2016-05-15 03:16:57	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:17:01	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:04:06s.  Time for last 1,000,000:    3s.  Last read position: chr16:85,347,291
INFO	2016-05-15 03:17:01	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:17:07	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:04:12s.  Time for last 1,000,000:    6s.  Last read position: chr17:3,342,623
INFO	2016-05-15 03:17:07	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:17:10	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:04:16s.  Time for last 1,000,000:    3s.  Last read position: chr17:14,128,276
INFO	2016-05-15 03:17:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:17:14	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:04:19s.  Time for last 1,000,000:    3s.  Last read position: chr17:28,778,210
INFO	2016-05-15 03:17:14	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:17:17	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:04:23s.  Time for last 1,000,000:    3s.  Last read position: chr17:39,942,362
INFO	2016-05-15 03:17:17	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:17:28	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:04:34s.  Time for last 1,000,000:   11s.  Last read position: chr17:48,760,405
INFO	2016-05-15 03:17:28	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:17:32	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:04:37s.  Time for last 1,000,000:    3s.  Last read position: chr17:62,133,028
INFO	2016-05-15 03:17:32	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:17:35	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:04:41s.  Time for last 1,000,000:    3s.  Last read position: chr17:73,710,827
INFO	2016-05-15 03:17:35	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:17:38	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:04:44s.  Time for last 1,000,000:    3s.  Last read position: chr17:81,007,002
INFO	2016-05-15 03:17:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:17:43	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:04:49s.  Time for last 1,000,000:    4s.  Last read position: chr18:13,726,718
INFO	2016-05-15 03:17:43	MarkDuplicates	Tracking 18 as yet unmatched pairs. 18 records in RAM.
INFO	2016-05-15 03:17:47	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:04:52s.  Time for last 1,000,000:    3s.  Last read position: chr18:33,093,734
INFO	2016-05-15 03:17:47	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:17:50	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:04:56s.  Time for last 1,000,000:    3s.  Last read position: chr18:47,018,253
INFO	2016-05-15 03:17:50	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:17:54	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:04:59s.  Time for last 1,000,000:    3s.  Last read position: chr18:61,528,601
INFO	2016-05-15 03:17:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:17:57	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:05:03s.  Time for last 1,000,000:    3s.  Last read position: chr18:77,557,836
INFO	2016-05-15 03:17:57	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:18:01	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:05:06s.  Time for last 1,000,000:    3s.  Last read position: chr19:7,114,212
INFO	2016-05-15 03:18:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:18:04	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:05:09s.  Time for last 1,000,000:    3s.  Last read position: chr19:16,703,840
INFO	2016-05-15 03:18:04	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:18:07	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:05:13s.  Time for last 1,000,000:    3s.  Last read position: chr19:32,244,975
INFO	2016-05-15 03:18:07	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:18:10	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:05:16s.  Time for last 1,000,000:    3s.  Last read position: chr19:42,493,966
INFO	2016-05-15 03:18:10	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:18:17	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:05:22s.  Time for last 1,000,000:    6s.  Last read position: chr19:51,028,256
INFO	2016-05-15 03:18:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:18:20	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:05:25s.  Time for last 1,000,000:    3s.  Last read position: chr1:569,907
INFO	2016-05-15 03:18:20	MarkDuplicates	Tracking 22730 as yet unmatched pairs. 22730 records in RAM.
INFO	2016-05-15 03:18:27	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:05:32s.  Time for last 1,000,000:    6s.  Last read position: chr1:6,453,896
INFO	2016-05-15 03:18:27	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:18:30	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:05:36s.  Time for last 1,000,000:    3s.  Last read position: chr1:16,752,513
INFO	2016-05-15 03:18:30	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:18:34	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:05:39s.  Time for last 1,000,000:    3s.  Last read position: chr1:25,862,011
INFO	2016-05-15 03:18:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:18:37	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:05:43s.  Time for last 1,000,000:    3s.  Last read position: chr1:35,124,282
INFO	2016-05-15 03:18:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:18:41	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:05:46s.  Time for last 1,000,000:    3s.  Last read position: chr1:45,060,949
INFO	2016-05-15 03:18:41	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:18:44	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:05:50s.  Time for last 1,000,000:    3s.  Last read position: chr1:56,539,845
INFO	2016-05-15 03:18:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:18:48	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:05:53s.  Time for last 1,000,000:    3s.  Last read position: chr1:71,141,616
INFO	2016-05-15 03:18:48	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:18:54	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:05:59s.  Time for last 1,000,000:    5s.  Last read position: chr1:88,152,420
INFO	2016-05-15 03:18:54	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:18:57	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:06:03s.  Time for last 1,000,000:    3s.  Last read position: chr1:103,359,856
INFO	2016-05-15 03:18:57	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:19:01	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:06:06s.  Time for last 1,000,000:    3s.  Last read position: chr1:118,107,938
INFO	2016-05-15 03:19:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:19:04	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:06:09s.  Time for last 1,000,000:    3s.  Last read position: chr1:155,214,473
INFO	2016-05-15 03:19:04	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-05-15 03:19:07	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:06:13s.  Time for last 1,000,000:    3s.  Last read position: chr1:167,189,418
INFO	2016-05-15 03:19:07	MarkDuplicates	Tracking 12 as yet unmatched pairs. 12 records in RAM.
INFO	2016-05-15 03:19:11	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:06:16s.  Time for last 1,000,000:    3s.  Last read position: chr1:181,307,358
INFO	2016-05-15 03:19:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:19:14	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:06:20s.  Time for last 1,000,000:    3s.  Last read position: chr1:198,563,809
INFO	2016-05-15 03:19:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:19:18	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:06:23s.  Time for last 1,000,000:    3s.  Last read position: chr1:209,659,358
INFO	2016-05-15 03:19:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:19:30	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:06:35s.  Time for last 1,000,000:   12s.  Last read position: chr1:223,906,159
INFO	2016-05-15 03:19:30	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:19:34	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:06:39s.  Time for last 1,000,000:    3s.  Last read position: chr1:235,785,563
INFO	2016-05-15 03:19:34	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:19:38	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:06:44s.  Time for last 1,000,000:    4s.  Last read position: chr20:1,261,907
INFO	2016-05-15 03:19:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:19:42	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:06:47s.  Time for last 1,000,000:    3s.  Last read position: chr20:14,985,822
INFO	2016-05-15 03:19:42	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:19:45	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:06:51s.  Time for last 1,000,000:    3s.  Last read position: chr20:30,458,051
INFO	2016-05-15 03:19:45	MarkDuplicates	Tracking 14 as yet unmatched pairs. 14 records in RAM.
INFO	2016-05-15 03:19:49	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:06:54s.  Time for last 1,000,000:    3s.  Last read position: chr20:39,745,299
INFO	2016-05-15 03:19:49	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:19:52	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:06:58s.  Time for last 1,000,000:    3s.  Last read position: chr20:50,278,865
INFO	2016-05-15 03:19:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:19:56	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:07:01s.  Time for last 1,000,000:    3s.  Last read position: chr20:61,610,079
INFO	2016-05-15 03:19:56	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:19:59	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:07:05s.  Time for last 1,000,000:    3s.  Last read position: chr21:25,708,575
INFO	2016-05-15 03:19:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:20:03	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:07:08s.  Time for last 1,000,000:    3s.  Last read position: chr21:40,403,135
INFO	2016-05-15 03:20:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:20:06	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:07:11s.  Time for last 1,000,000:    3s.  Last read position: chr22:19,409,603
INFO	2016-05-15 03:20:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:20:10	MarkDuplicates	Read   100,000,000 records.  Elapsed time: 00:07:15s.  Time for last 1,000,000:    3s.  Last read position: chr22:30,116,749
INFO	2016-05-15 03:20:10	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:20:16	MarkDuplicates	Read   101,000,000 records.  Elapsed time: 00:07:21s.  Time for last 1,000,000:    6s.  Last read position: chr22:39,927,337
INFO	2016-05-15 03:20:16	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:20:19	MarkDuplicates	Read   102,000,000 records.  Elapsed time: 00:07:24s.  Time for last 1,000,000:    3s.  Last read position: chr22:49,027,605
INFO	2016-05-15 03:20:19	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:20:27	MarkDuplicates	Read   103,000,000 records.  Elapsed time: 00:07:32s.  Time for last 1,000,000:    7s.  Last read position: chr2:9,557,131
INFO	2016-05-15 03:20:27	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:20:30	MarkDuplicates	Read   104,000,000 records.  Elapsed time: 00:07:36s.  Time for last 1,000,000:    3s.  Last read position: chr2:22,089,086
INFO	2016-05-15 03:20:30	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:20:34	MarkDuplicates	Read   105,000,000 records.  Elapsed time: 00:07:39s.  Time for last 1,000,000:    3s.  Last read position: chr2:34,205,543
INFO	2016-05-15 03:20:34	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:20:38	MarkDuplicates	Read   106,000,000 records.  Elapsed time: 00:07:43s.  Time for last 1,000,000:    3s.  Last read position: chr2:47,790,925
INFO	2016-05-15 03:20:38	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:20:41	MarkDuplicates	Read   107,000,000 records.  Elapsed time: 00:07:47s.  Time for last 1,000,000:    3s.  Last read position: chr2:63,413,534
INFO	2016-05-15 03:20:41	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:20:45	MarkDuplicates	Read   108,000,000 records.  Elapsed time: 00:07:50s.  Time for last 1,000,000:    3s.  Last read position: chr2:75,827,442
INFO	2016-05-15 03:20:45	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:20:48	MarkDuplicates	Read   109,000,000 records.  Elapsed time: 00:07:54s.  Time for last 1,000,000:    3s.  Last read position: chr2:97,286,253
INFO	2016-05-15 03:20:48	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:20:52	MarkDuplicates	Read   110,000,000 records.  Elapsed time: 00:07:58s.  Time for last 1,000,000:    3s.  Last read position: chr2:112,505,603
INFO	2016-05-15 03:20:52	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:20:56	MarkDuplicates	Read   111,000,000 records.  Elapsed time: 00:08:01s.  Time for last 1,000,000:    3s.  Last read position: chr2:127,399,777
INFO	2016-05-15 03:20:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:21:02	MarkDuplicates	Read   112,000,000 records.  Elapsed time: 00:08:07s.  Time for last 1,000,000:    6s.  Last read position: chr2:141,855,890
INFO	2016-05-15 03:21:02	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:21:05	MarkDuplicates	Read   113,000,000 records.  Elapsed time: 00:08:11s.  Time for last 1,000,000:    3s.  Last read position: chr2:159,158,533
INFO	2016-05-15 03:21:05	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:21:09	MarkDuplicates	Read   114,000,000 records.  Elapsed time: 00:08:14s.  Time for last 1,000,000:    3s.  Last read position: chr2:174,768,786
INFO	2016-05-15 03:21:09	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:21:12	MarkDuplicates	Read   115,000,000 records.  Elapsed time: 00:08:18s.  Time for last 1,000,000:    3s.  Last read position: chr2:191,166,040
INFO	2016-05-15 03:21:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:21:15	MarkDuplicates	Read   116,000,000 records.  Elapsed time: 00:08:21s.  Time for last 1,000,000:    3s.  Last read position: chr2:206,950,336
INFO	2016-05-15 03:21:15	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-15 03:21:19	MarkDuplicates	Read   117,000,000 records.  Elapsed time: 00:08:24s.  Time for last 1,000,000:    3s.  Last read position: chr2:220,586,652
INFO	2016-05-15 03:21:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:21:30	MarkDuplicates	Read   118,000,000 records.  Elapsed time: 00:08:36s.  Time for last 1,000,000:   11s.  Last read position: chr2:234,433,362
INFO	2016-05-15 03:21:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:21:34	MarkDuplicates	Read   119,000,000 records.  Elapsed time: 00:08:39s.  Time for last 1,000,000:    3s.  Last read position: chr3:2,114,707
INFO	2016-05-15 03:21:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:21:37	MarkDuplicates	Read   120,000,000 records.  Elapsed time: 00:08:42s.  Time for last 1,000,000:    3s.  Last read position: chr3:14,154,423
INFO	2016-05-15 03:21:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:21:40	MarkDuplicates	Read   121,000,000 records.  Elapsed time: 00:08:46s.  Time for last 1,000,000:    3s.  Last read position: chr3:28,964,307
INFO	2016-05-15 03:21:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:21:44	MarkDuplicates	Read   122,000,000 records.  Elapsed time: 00:08:49s.  Time for last 1,000,000:    3s.  Last read position: chr3:42,746,745
INFO	2016-05-15 03:21:44	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:21:47	MarkDuplicates	Read   123,000,000 records.  Elapsed time: 00:08:53s.  Time for last 1,000,000:    3s.  Last read position: chr3:52,548,622
INFO	2016-05-15 03:21:47	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:21:52	MarkDuplicates	Read   124,000,000 records.  Elapsed time: 00:08:58s.  Time for last 1,000,000:    4s.  Last read position: chr3:66,300,652
INFO	2016-05-15 03:21:52	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:21:56	MarkDuplicates	Read   125,000,000 records.  Elapsed time: 00:09:01s.  Time for last 1,000,000:    3s.  Last read position: chr3:83,369,068
INFO	2016-05-15 03:21:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:21:59	MarkDuplicates	Read   126,000,000 records.  Elapsed time: 00:09:05s.  Time for last 1,000,000:    3s.  Last read position: chr3:105,601,275
INFO	2016-05-15 03:21:59	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:22:03	MarkDuplicates	Read   127,000,000 records.  Elapsed time: 00:09:08s.  Time for last 1,000,000:    3s.  Last read position: chr3:121,977,709
INFO	2016-05-15 03:22:03	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:22:06	MarkDuplicates	Read   128,000,000 records.  Elapsed time: 00:09:12s.  Time for last 1,000,000:    3s.  Last read position: chr3:133,449,351
INFO	2016-05-15 03:22:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:22:10	MarkDuplicates	Read   129,000,000 records.  Elapsed time: 00:09:15s.  Time for last 1,000,000:    3s.  Last read position: chr3:147,875,447
INFO	2016-05-15 03:22:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:22:13	MarkDuplicates	Read   130,000,000 records.  Elapsed time: 00:09:18s.  Time for last 1,000,000:    3s.  Last read position: chr3:163,949,866
INFO	2016-05-15 03:22:13	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:22:16	MarkDuplicates	Read   131,000,000 records.  Elapsed time: 00:09:22s.  Time for last 1,000,000:    3s.  Last read position: chr3:180,546,126
INFO	2016-05-15 03:22:16	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-15 03:22:20	MarkDuplicates	Read   132,000,000 records.  Elapsed time: 00:09:25s.  Time for last 1,000,000:    3s.  Last read position: chr3:193,942,904
INFO	2016-05-15 03:22:20	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:22:27	MarkDuplicates	Read   133,000,000 records.  Elapsed time: 00:09:33s.  Time for last 1,000,000:    7s.  Last read position: chr4:5,935,964
INFO	2016-05-15 03:22:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:22:31	MarkDuplicates	Read   134,000,000 records.  Elapsed time: 00:09:36s.  Time for last 1,000,000:    3s.  Last read position: chr4:18,943,597
INFO	2016-05-15 03:22:31	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:22:34	MarkDuplicates	Read   135,000,000 records.  Elapsed time: 00:09:40s.  Time for last 1,000,000:    3s.  Last read position: chr4:37,244,826
INFO	2016-05-15 03:22:34	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:22:40	MarkDuplicates	Read   136,000,000 records.  Elapsed time: 00:09:45s.  Time for last 1,000,000:    5s.  Last read position: chr4:56,679,197
INFO	2016-05-15 03:22:40	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:22:43	MarkDuplicates	Read   137,000,000 records.  Elapsed time: 00:09:48s.  Time for last 1,000,000:    3s.  Last read position: chr4:75,908,853
INFO	2016-05-15 03:22:43	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:22:46	MarkDuplicates	Read   138,000,000 records.  Elapsed time: 00:09:52s.  Time for last 1,000,000:    3s.  Last read position: chr4:91,332,056
INFO	2016-05-15 03:22:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:22:50	MarkDuplicates	Read   139,000,000 records.  Elapsed time: 00:09:55s.  Time for last 1,000,000:    3s.  Last read position: chr4:109,083,273
INFO	2016-05-15 03:22:50	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-15 03:22:53	MarkDuplicates	Read   140,000,000 records.  Elapsed time: 00:09:58s.  Time for last 1,000,000:    3s.  Last read position: chr4:126,245,560
INFO	2016-05-15 03:22:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:22:56	MarkDuplicates	Read   141,000,000 records.  Elapsed time: 00:10:02s.  Time for last 1,000,000:    3s.  Last read position: chr4:144,358,491
INFO	2016-05-15 03:22:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:23:00	MarkDuplicates	Read   142,000,000 records.  Elapsed time: 00:10:05s.  Time for last 1,000,000:    3s.  Last read position: chr4:160,403,088
INFO	2016-05-15 03:23:00	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:23:03	MarkDuplicates	Read   143,000,000 records.  Elapsed time: 00:10:08s.  Time for last 1,000,000:    3s.  Last read position: chr4:178,460,274
INFO	2016-05-15 03:23:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:23:06	MarkDuplicates	Read   144,000,000 records.  Elapsed time: 00:10:12s.  Time for last 1,000,000:    3s.  Last read position: chr5:1,829,078
INFO	2016-05-15 03:23:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:23:10	MarkDuplicates	Read   145,000,000 records.  Elapsed time: 00:10:15s.  Time for last 1,000,000:    3s.  Last read position: chr5:15,916,340
INFO	2016-05-15 03:23:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:23:13	MarkDuplicates	Read   146,000,000 records.  Elapsed time: 00:10:18s.  Time for last 1,000,000:    3s.  Last read position: chr5:34,577,659
INFO	2016-05-15 03:23:13	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:23:23	MarkDuplicates	Read   147,000,000 records.  Elapsed time: 00:10:29s.  Time for last 1,000,000:   10s.  Last read position: chr5:54,541,789
INFO	2016-05-15 03:23:23	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:23:26	MarkDuplicates	Read   148,000,000 records.  Elapsed time: 00:10:32s.  Time for last 1,000,000:    3s.  Last read position: chr5:71,850,497
INFO	2016-05-15 03:23:26	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:23:30	MarkDuplicates	Read   149,000,000 records.  Elapsed time: 00:10:35s.  Time for last 1,000,000:    3s.  Last read position: chr5:87,157,907
INFO	2016-05-15 03:23:30	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:23:33	MarkDuplicates	Read   150,000,000 records.  Elapsed time: 00:10:39s.  Time for last 1,000,000:    3s.  Last read position: chr5:104,447,068
INFO	2016-05-15 03:23:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:23:37	MarkDuplicates	Read   151,000,000 records.  Elapsed time: 00:10:42s.  Time for last 1,000,000:    3s.  Last read position: chr5:120,535,602
INFO	2016-05-15 03:23:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:23:39	MarkDuplicates	Read   152,000,000 records.  Elapsed time: 00:10:45s.  Time for last 1,000,000:    2s.  Last read position: chr5:134,259,871
INFO	2016-05-15 03:23:39	MarkDuplicates	Tracking 928 as yet unmatched pairs. 928 records in RAM.
INFO	2016-05-15 03:23:42	MarkDuplicates	Read   153,000,000 records.  Elapsed time: 00:10:48s.  Time for last 1,000,000:    2s.  Last read position: chr5:139,118,347
INFO	2016-05-15 03:23:42	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:23:45	MarkDuplicates	Read   154,000,000 records.  Elapsed time: 00:10:51s.  Time for last 1,000,000:    3s.  Last read position: chr5:150,937,724
INFO	2016-05-15 03:23:45	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:23:48	MarkDuplicates	Read   155,000,000 records.  Elapsed time: 00:10:54s.  Time for last 1,000,000:    3s.  Last read position: chr5:165,820,350
INFO	2016-05-15 03:23:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:23:51	MarkDuplicates	Read   156,000,000 records.  Elapsed time: 00:10:57s.  Time for last 1,000,000:    3s.  Last read position: chr5:176,896,264
INFO	2016-05-15 03:23:51	MarkDuplicates	Tracking 12 as yet unmatched pairs. 12 records in RAM.
INFO	2016-05-15 03:23:54	MarkDuplicates	Read   157,000,000 records.  Elapsed time: 00:11:00s.  Time for last 1,000,000:    3s.  Last read position: chr6:7,345,401
INFO	2016-05-15 03:23:54	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:23:58	MarkDuplicates	Read   158,000,000 records.  Elapsed time: 00:11:03s.  Time for last 1,000,000:    3s.  Last read position: chr6:21,374,904
INFO	2016-05-15 03:23:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:24:01	MarkDuplicates	Read   159,000,000 records.  Elapsed time: 00:11:06s.  Time for last 1,000,000:    3s.  Last read position: chr6:33,792,760
INFO	2016-05-15 03:24:01	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:24:04	MarkDuplicates	Read   160,000,000 records.  Elapsed time: 00:11:09s.  Time for last 1,000,000:    3s.  Last read position: chr6:43,543,052
INFO	2016-05-15 03:24:04	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-05-15 03:24:07	MarkDuplicates	Read   161,000,000 records.  Elapsed time: 00:11:12s.  Time for last 1,000,000:    3s.  Last read position: chr6:58,777,943
INFO	2016-05-15 03:24:07	MarkDuplicates	Tracking 14 as yet unmatched pairs. 14 records in RAM.
INFO	2016-05-15 03:24:13	MarkDuplicates	Read   162,000,000 records.  Elapsed time: 00:11:18s.  Time for last 1,000,000:    6s.  Last read position: chr6:80,425,328
INFO	2016-05-15 03:24:13	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:24:16	MarkDuplicates	Read   163,000,000 records.  Elapsed time: 00:11:22s.  Time for last 1,000,000:    3s.  Last read position: chr6:97,518,705
INFO	2016-05-15 03:24:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:24:21	MarkDuplicates	Read   164,000,000 records.  Elapsed time: 00:11:26s.  Time for last 1,000,000:    4s.  Last read position: chr6:112,946,422
INFO	2016-05-15 03:24:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:24:24	MarkDuplicates	Read   165,000,000 records.  Elapsed time: 00:11:29s.  Time for last 1,000,000:    3s.  Last read position: chr6:129,850,208
INFO	2016-05-15 03:24:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:24:27	MarkDuplicates	Read   166,000,000 records.  Elapsed time: 00:11:32s.  Time for last 1,000,000:    3s.  Last read position: chr6:145,290,866
INFO	2016-05-15 03:24:27	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:24:30	MarkDuplicates	Read   167,000,000 records.  Elapsed time: 00:11:35s.  Time for last 1,000,000:    3s.  Last read position: chr6:159,046,200
INFO	2016-05-15 03:24:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:24:33	MarkDuplicates	Read   168,000,000 records.  Elapsed time: 00:11:39s.  Time for last 1,000,000:    3s.  Last read position: chr7:491,904
INFO	2016-05-15 03:24:33	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-15 03:24:36	MarkDuplicates	Read   169,000,000 records.  Elapsed time: 00:11:42s.  Time for last 1,000,000:    3s.  Last read position: chr7:11,628,901
INFO	2016-05-15 03:24:36	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:24:39	MarkDuplicates	Read   170,000,000 records.  Elapsed time: 00:11:45s.  Time for last 1,000,000:    3s.  Last read position: chr7:27,539,639
INFO	2016-05-15 03:24:39	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:24:42	MarkDuplicates	Read   171,000,000 records.  Elapsed time: 00:11:48s.  Time for last 1,000,000:    3s.  Last read position: chr7:41,571,777
INFO	2016-05-15 03:24:42	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:24:45	MarkDuplicates	Read   172,000,000 records.  Elapsed time: 00:11:51s.  Time for last 1,000,000:    3s.  Last read position: chr7:55,563,396
INFO	2016-05-15 03:24:45	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:24:48	MarkDuplicates	Read   173,000,000 records.  Elapsed time: 00:11:54s.  Time for last 1,000,000:    3s.  Last read position: chr7:75,865,553
INFO	2016-05-15 03:24:48	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:24:52	MarkDuplicates	Read   174,000,000 records.  Elapsed time: 00:11:57s.  Time for last 1,000,000:    3s.  Last read position: chr7:93,015,132
INFO	2016-05-15 03:24:52	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:24:55	MarkDuplicates	Read   175,000,000 records.  Elapsed time: 00:12:00s.  Time for last 1,000,000:    3s.  Last read position: chr7:105,714,426
INFO	2016-05-15 03:24:55	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:24:58	MarkDuplicates	Read   176,000,000 records.  Elapsed time: 00:12:03s.  Time for last 1,000,000:    3s.  Last read position: chr7:122,500,308
INFO	2016-05-15 03:24:58	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:25:10	MarkDuplicates	Read   177,000,000 records.  Elapsed time: 00:12:15s.  Time for last 1,000,000:   11s.  Last read position: chr7:135,831,048
INFO	2016-05-15 03:25:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:25:13	MarkDuplicates	Read   178,000,000 records.  Elapsed time: 00:12:18s.  Time for last 1,000,000:    3s.  Last read position: chr7:150,530,042
INFO	2016-05-15 03:25:13	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:25:17	MarkDuplicates	Read   179,000,000 records.  Elapsed time: 00:12:22s.  Time for last 1,000,000:    4s.  Last read position: chr8:3,005,766
INFO	2016-05-15 03:25:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:25:21	MarkDuplicates	Read   180,000,000 records.  Elapsed time: 00:12:26s.  Time for last 1,000,000:    3s.  Last read position: chr8:19,430,197
INFO	2016-05-15 03:25:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:25:24	MarkDuplicates	Read   181,000,000 records.  Elapsed time: 00:12:29s.  Time for last 1,000,000:    3s.  Last read position: chr8:31,808,843
INFO	2016-05-15 03:25:24	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:25:27	MarkDuplicates	Read   182,000,000 records.  Elapsed time: 00:12:33s.  Time for last 1,000,000:    3s.  Last read position: chr8:49,580,010
INFO	2016-05-15 03:25:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:25:31	MarkDuplicates	Read   183,000,000 records.  Elapsed time: 00:12:36s.  Time for last 1,000,000:    3s.  Last read position: chr8:65,831,612
INFO	2016-05-15 03:25:31	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:25:34	MarkDuplicates	Read   184,000,000 records.  Elapsed time: 00:12:39s.  Time for last 1,000,000:    3s.  Last read position: chr8:81,528,082
INFO	2016-05-15 03:25:34	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-15 03:25:37	MarkDuplicates	Read   185,000,000 records.  Elapsed time: 00:12:43s.  Time for last 1,000,000:    3s.  Last read position: chr8:98,350,914
INFO	2016-05-15 03:25:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:25:41	MarkDuplicates	Read   186,000,000 records.  Elapsed time: 00:12:46s.  Time for last 1,000,000:    3s.  Last read position: chr8:112,908,837
INFO	2016-05-15 03:25:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:25:44	MarkDuplicates	Read   187,000,000 records.  Elapsed time: 00:12:50s.  Time for last 1,000,000:    3s.  Last read position: chr8:128,353,028
INFO	2016-05-15 03:25:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:25:48	MarkDuplicates	Read   188,000,000 records.  Elapsed time: 00:12:53s.  Time for last 1,000,000:    3s.  Last read position: chr8:141,630,401
INFO	2016-05-15 03:25:48	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:25:51	MarkDuplicates	Read   189,000,000 records.  Elapsed time: 00:12:56s.  Time for last 1,000,000:    3s.  Last read position: chr9:5,633,158
INFO	2016-05-15 03:25:51	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:25:54	MarkDuplicates	Read   190,000,000 records.  Elapsed time: 00:13:00s.  Time for last 1,000,000:    3s.  Last read position: chr9:22,059,701
INFO	2016-05-15 03:25:54	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:26:01	MarkDuplicates	Read   191,000,000 records.  Elapsed time: 00:13:06s.  Time for last 1,000,000:    6s.  Last read position: chr9:37,335,281
INFO	2016-05-15 03:26:01	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:26:05	MarkDuplicates	Read   192,000,000 records.  Elapsed time: 00:13:10s.  Time for last 1,000,000:    3s.  Last read position: chr9:83,090,294
INFO	2016-05-15 03:26:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:26:08	MarkDuplicates	Read   193,000,000 records.  Elapsed time: 00:13:13s.  Time for last 1,000,000:    3s.  Last read position: chr9:96,900,829
INFO	2016-05-15 03:26:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:26:13	MarkDuplicates	Read   194,000,000 records.  Elapsed time: 00:13:19s.  Time for last 1,000,000:    5s.  Last read position: chr9:110,842,724
INFO	2016-05-15 03:26:13	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-15 03:26:17	MarkDuplicates	Read   195,000,000 records.  Elapsed time: 00:13:22s.  Time for last 1,000,000:    3s.  Last read position: chr9:124,079,463
INFO	2016-05-15 03:26:17	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:26:20	MarkDuplicates	Read   196,000,000 records.  Elapsed time: 00:13:26s.  Time for last 1,000,000:    3s.  Last read position: chr9:132,977,462
INFO	2016-05-15 03:26:20	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:26:24	MarkDuplicates	Read   197,000,000 records.  Elapsed time: 00:13:29s.  Time for last 1,000,000:    3s.  Last read position: chr9:140,323,136
INFO	2016-05-15 03:26:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:26:26	MarkDuplicates	Read   198,000,000 records.  Elapsed time: 00:13:32s.  Time for last 1,000,000:    2s.  Last read position: chrM:118
INFO	2016-05-15 03:26:26	MarkDuplicates	Tracking 25370 as yet unmatched pairs. 25370 records in RAM.
INFO	2016-05-15 03:26:29	MarkDuplicates	Read   199,000,000 records.  Elapsed time: 00:13:35s.  Time for last 1,000,000:    3s.  Last read position: chrM:334
INFO	2016-05-15 03:26:29	MarkDuplicates	Tracking 26408 as yet unmatched pairs. 26408 records in RAM.
INFO	2016-05-15 03:26:32	MarkDuplicates	Read   200,000,000 records.  Elapsed time: 00:13:38s.  Time for last 1,000,000:    3s.  Last read position: chrM:475
INFO	2016-05-15 03:26:32	MarkDuplicates	Tracking 45088 as yet unmatched pairs. 45088 records in RAM.
INFO	2016-05-15 03:26:35	MarkDuplicates	Read   201,000,000 records.  Elapsed time: 00:13:41s.  Time for last 1,000,000:    2s.  Last read position: chrM:543
INFO	2016-05-15 03:26:35	MarkDuplicates	Tracking 43662 as yet unmatched pairs. 43662 records in RAM.
INFO	2016-05-15 03:26:38	MarkDuplicates	Read   202,000,000 records.  Elapsed time: 00:13:44s.  Time for last 1,000,000:    2s.  Last read position: chrM:683
INFO	2016-05-15 03:26:38	MarkDuplicates	Tracking 16400 as yet unmatched pairs. 16400 records in RAM.
INFO	2016-05-15 03:26:41	MarkDuplicates	Read   203,000,000 records.  Elapsed time: 00:13:47s.  Time for last 1,000,000:    2s.  Last read position: chrM:779
INFO	2016-05-15 03:26:41	MarkDuplicates	Tracking 19732 as yet unmatched pairs. 19732 records in RAM.
INFO	2016-05-15 03:26:44	MarkDuplicates	Read   204,000,000 records.  Elapsed time: 00:13:49s.  Time for last 1,000,000:    2s.  Last read position: chrM:912
INFO	2016-05-15 03:26:44	MarkDuplicates	Tracking 32446 as yet unmatched pairs. 32446 records in RAM.
INFO	2016-05-15 03:26:47	MarkDuplicates	Read   205,000,000 records.  Elapsed time: 00:13:52s.  Time for last 1,000,000:    2s.  Last read position: chrM:1,254
INFO	2016-05-15 03:26:47	MarkDuplicates	Tracking 31604 as yet unmatched pairs. 31604 records in RAM.
INFO	2016-05-15 03:26:59	MarkDuplicates	Read   206,000,000 records.  Elapsed time: 00:14:05s.  Time for last 1,000,000:   12s.  Last read position: chrM:1,384
INFO	2016-05-15 03:26:59	MarkDuplicates	Tracking 13120 as yet unmatched pairs. 13120 records in RAM.
INFO	2016-05-15 03:27:02	MarkDuplicates	Read   207,000,000 records.  Elapsed time: 00:14:07s.  Time for last 1,000,000:    2s.  Last read position: chrM:1,541
INFO	2016-05-15 03:27:02	MarkDuplicates	Tracking 27728 as yet unmatched pairs. 27728 records in RAM.
INFO	2016-05-15 03:27:05	MarkDuplicates	Read   208,000,000 records.  Elapsed time: 00:14:11s.  Time for last 1,000,000:    3s.  Last read position: chrM:1,712
INFO	2016-05-15 03:27:05	MarkDuplicates	Tracking 1064 as yet unmatched pairs. 1064 records in RAM.
INFO	2016-05-15 03:27:08	MarkDuplicates	Read   209,000,000 records.  Elapsed time: 00:14:14s.  Time for last 1,000,000:    3s.  Last read position: chrM:1,948
INFO	2016-05-15 03:27:08	MarkDuplicates	Tracking 12842 as yet unmatched pairs. 12842 records in RAM.
INFO	2016-05-15 03:27:13	MarkDuplicates	Read   210,000,000 records.  Elapsed time: 00:14:18s.  Time for last 1,000,000:    4s.  Last read position: chrM:2,139
INFO	2016-05-15 03:27:13	MarkDuplicates	Tracking 28492 as yet unmatched pairs. 28492 records in RAM.
INFO	2016-05-15 03:27:16	MarkDuplicates	Read   211,000,000 records.  Elapsed time: 00:14:21s.  Time for last 1,000,000:    2s.  Last read position: chrM:2,358
INFO	2016-05-15 03:27:16	MarkDuplicates	Tracking 6052 as yet unmatched pairs. 6052 records in RAM.
INFO	2016-05-15 03:27:19	MarkDuplicates	Read   212,000,000 records.  Elapsed time: 00:14:24s.  Time for last 1,000,000:    2s.  Last read position: chrM:2,555
INFO	2016-05-15 03:27:19	MarkDuplicates	Tracking 15706 as yet unmatched pairs. 15706 records in RAM.
INFO	2016-05-15 03:27:22	MarkDuplicates	Read   213,000,000 records.  Elapsed time: 00:14:27s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,660
INFO	2016-05-15 03:27:22	MarkDuplicates	Tracking 49726 as yet unmatched pairs. 49726 records in RAM.
INFO	2016-05-15 03:27:25	MarkDuplicates	Read   214,000,000 records.  Elapsed time: 00:14:30s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,766
INFO	2016-05-15 03:27:25	MarkDuplicates	Tracking 37658 as yet unmatched pairs. 37658 records in RAM.
INFO	2016-05-15 03:27:28	MarkDuplicates	Read   215,000,000 records.  Elapsed time: 00:14:33s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,871
INFO	2016-05-15 03:27:28	MarkDuplicates	Tracking 35470 as yet unmatched pairs. 35470 records in RAM.
INFO	2016-05-15 03:27:31	MarkDuplicates	Read   216,000,000 records.  Elapsed time: 00:14:37s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,999
INFO	2016-05-15 03:27:31	MarkDuplicates	Tracking 38428 as yet unmatched pairs. 38428 records in RAM.
INFO	2016-05-15 03:27:34	MarkDuplicates	Read   217,000,000 records.  Elapsed time: 00:14:40s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,098
INFO	2016-05-15 03:27:34	MarkDuplicates	Tracking 42300 as yet unmatched pairs. 42300 records in RAM.
INFO	2016-05-15 03:27:38	MarkDuplicates	Read   218,000,000 records.  Elapsed time: 00:14:43s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,216
INFO	2016-05-15 03:27:38	MarkDuplicates	Tracking 73614 as yet unmatched pairs. 73614 records in RAM.
INFO	2016-05-15 03:27:41	MarkDuplicates	Read   219,000,000 records.  Elapsed time: 00:14:46s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,334
INFO	2016-05-15 03:27:41	MarkDuplicates	Tracking 61154 as yet unmatched pairs. 61154 records in RAM.
INFO	2016-05-15 03:27:44	MarkDuplicates	Read   220,000,000 records.  Elapsed time: 00:14:49s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,414
INFO	2016-05-15 03:27:44	MarkDuplicates	Tracking 26952 as yet unmatched pairs. 26952 records in RAM.
INFO	2016-05-15 03:27:51	MarkDuplicates	Read   221,000,000 records.  Elapsed time: 00:14:57s.  Time for last 1,000,000:    7s.  Last read position: chrM:3,488
INFO	2016-05-15 03:27:51	MarkDuplicates	Tracking 34488 as yet unmatched pairs. 34488 records in RAM.
INFO	2016-05-15 03:27:54	MarkDuplicates	Read   222,000,000 records.  Elapsed time: 00:15:00s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,575
INFO	2016-05-15 03:27:54	MarkDuplicates	Tracking 99570 as yet unmatched pairs. 99570 records in RAM.
INFO	2016-05-15 03:27:57	MarkDuplicates	Read   223,000,000 records.  Elapsed time: 00:15:03s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,647
INFO	2016-05-15 03:27:57	MarkDuplicates	Tracking 30954 as yet unmatched pairs. 30954 records in RAM.
INFO	2016-05-15 03:28:01	MarkDuplicates	Read   224,000,000 records.  Elapsed time: 00:15:06s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,735
INFO	2016-05-15 03:28:01	MarkDuplicates	Tracking 35064 as yet unmatched pairs. 35064 records in RAM.
INFO	2016-05-15 03:28:04	MarkDuplicates	Read   225,000,000 records.  Elapsed time: 00:15:09s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,857
INFO	2016-05-15 03:28:04	MarkDuplicates	Tracking 29814 as yet unmatched pairs. 29814 records in RAM.
INFO	2016-05-15 03:28:09	MarkDuplicates	Read   226,000,000 records.  Elapsed time: 00:15:14s.  Time for last 1,000,000:    5s.  Last read position: chrM:4,044
INFO	2016-05-15 03:28:09	MarkDuplicates	Tracking 26782 as yet unmatched pairs. 26782 records in RAM.
INFO	2016-05-15 03:28:12	MarkDuplicates	Read   227,000,000 records.  Elapsed time: 00:15:17s.  Time for last 1,000,000:    2s.  Last read position: chrM:4,382
INFO	2016-05-15 03:28:12	MarkDuplicates	Tracking 8128 as yet unmatched pairs. 8128 records in RAM.
INFO	2016-05-15 03:28:15	MarkDuplicates	Read   228,000,000 records.  Elapsed time: 00:15:20s.  Time for last 1,000,000:    2s.  Last read position: chrM:4,837
INFO	2016-05-15 03:28:15	MarkDuplicates	Tracking 14424 as yet unmatched pairs. 14424 records in RAM.
INFO	2016-05-15 03:28:18	MarkDuplicates	Read   229,000,000 records.  Elapsed time: 00:15:23s.  Time for last 1,000,000:    2s.  Last read position: chrM:4,951
INFO	2016-05-15 03:28:18	MarkDuplicates	Tracking 14120 as yet unmatched pairs. 14120 records in RAM.
INFO	2016-05-15 03:28:21	MarkDuplicates	Read   230,000,000 records.  Elapsed time: 00:15:26s.  Time for last 1,000,000:    2s.  Last read position: chrM:5,137
INFO	2016-05-15 03:28:21	MarkDuplicates	Tracking 10802 as yet unmatched pairs. 10802 records in RAM.
INFO	2016-05-15 03:28:24	MarkDuplicates	Read   231,000,000 records.  Elapsed time: 00:15:29s.  Time for last 1,000,000:    2s.  Last read position: chrM:5,377
INFO	2016-05-15 03:28:24	MarkDuplicates	Tracking 5274 as yet unmatched pairs. 5274 records in RAM.
INFO	2016-05-15 03:28:27	MarkDuplicates	Read   232,000,000 records.  Elapsed time: 00:15:32s.  Time for last 1,000,000:    2s.  Last read position: chrM:5,758
INFO	2016-05-15 03:28:27	MarkDuplicates	Tracking 4784 as yet unmatched pairs. 4784 records in RAM.
INFO	2016-05-15 03:28:30	MarkDuplicates	Read   233,000,000 records.  Elapsed time: 00:15:35s.  Time for last 1,000,000:    2s.  Last read position: chrM:6,018
INFO	2016-05-15 03:28:30	MarkDuplicates	Tracking 8694 as yet unmatched pairs. 8694 records in RAM.
INFO	2016-05-15 03:28:33	MarkDuplicates	Read   234,000,000 records.  Elapsed time: 00:15:38s.  Time for last 1,000,000:    2s.  Last read position: chrM:6,248
INFO	2016-05-15 03:28:33	MarkDuplicates	Tracking 25280 as yet unmatched pairs. 25280 records in RAM.
INFO	2016-05-15 03:28:46	MarkDuplicates	Read   235,000,000 records.  Elapsed time: 00:15:51s.  Time for last 1,000,000:   12s.  Last read position: chrM:6,340
INFO	2016-05-15 03:28:46	MarkDuplicates	Tracking 13760 as yet unmatched pairs. 13760 records in RAM.
INFO	2016-05-15 03:28:49	MarkDuplicates	Read   236,000,000 records.  Elapsed time: 00:15:54s.  Time for last 1,000,000:    2s.  Last read position: chrM:6,434
INFO	2016-05-15 03:28:49	MarkDuplicates	Tracking 45760 as yet unmatched pairs. 45760 records in RAM.
INFO	2016-05-15 03:28:52	MarkDuplicates	Read   237,000,000 records.  Elapsed time: 00:15:57s.  Time for last 1,000,000:    2s.  Last read position: chrM:6,527
INFO	2016-05-15 03:28:52	MarkDuplicates	Tracking 23588 as yet unmatched pairs. 23588 records in RAM.
INFO	2016-05-15 03:28:55	MarkDuplicates	Read   238,000,000 records.  Elapsed time: 00:16:00s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,638
INFO	2016-05-15 03:28:55	MarkDuplicates	Tracking 34406 as yet unmatched pairs. 34406 records in RAM.
INFO	2016-05-15 03:28:58	MarkDuplicates	Read   239,000,000 records.  Elapsed time: 00:16:03s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,931
INFO	2016-05-15 03:28:58	MarkDuplicates	Tracking 11578 as yet unmatched pairs. 11578 records in RAM.
INFO	2016-05-15 03:29:01	MarkDuplicates	Read   240,000,000 records.  Elapsed time: 00:16:06s.  Time for last 1,000,000:    3s.  Last read position: chrM:7,192
INFO	2016-05-15 03:29:01	MarkDuplicates	Tracking 13322 as yet unmatched pairs. 13322 records in RAM.
INFO	2016-05-15 03:29:04	MarkDuplicates	Read   241,000,000 records.  Elapsed time: 00:16:09s.  Time for last 1,000,000:    3s.  Last read position: chrM:7,608
INFO	2016-05-15 03:29:04	MarkDuplicates	Tracking 17896 as yet unmatched pairs. 17896 records in RAM.
INFO	2016-05-15 03:29:07	MarkDuplicates	Read   242,000,000 records.  Elapsed time: 00:16:12s.  Time for last 1,000,000:    3s.  Last read position: chrM:7,798
INFO	2016-05-15 03:29:07	MarkDuplicates	Tracking 9874 as yet unmatched pairs. 9874 records in RAM.
INFO	2016-05-15 03:29:12	MarkDuplicates	Read   243,000,000 records.  Elapsed time: 00:16:17s.  Time for last 1,000,000:    4s.  Last read position: chrM:7,893
INFO	2016-05-15 03:29:12	MarkDuplicates	Tracking 36404 as yet unmatched pairs. 36404 records in RAM.
INFO	2016-05-15 03:29:15	MarkDuplicates	Read   244,000,000 records.  Elapsed time: 00:16:20s.  Time for last 1,000,000:    3s.  Last read position: chrM:8,061
INFO	2016-05-15 03:29:15	MarkDuplicates	Tracking 10896 as yet unmatched pairs. 10896 records in RAM.
INFO	2016-05-15 03:29:18	MarkDuplicates	Read   245,000,000 records.  Elapsed time: 00:16:23s.  Time for last 1,000,000:    2s.  Last read position: chrM:8,173
INFO	2016-05-15 03:29:18	MarkDuplicates	Tracking 8262 as yet unmatched pairs. 8262 records in RAM.
INFO	2016-05-15 03:29:21	MarkDuplicates	Read   246,000,000 records.  Elapsed time: 00:16:26s.  Time for last 1,000,000:    2s.  Last read position: chrM:8,461
INFO	2016-05-15 03:29:21	MarkDuplicates	Tracking 15598 as yet unmatched pairs. 15598 records in RAM.
INFO	2016-05-15 03:29:24	MarkDuplicates	Read   247,000,000 records.  Elapsed time: 00:16:29s.  Time for last 1,000,000:    3s.  Last read position: chrM:8,712
INFO	2016-05-15 03:29:24	MarkDuplicates	Tracking 12896 as yet unmatched pairs. 12896 records in RAM.
INFO	2016-05-15 03:29:27	MarkDuplicates	Read   248,000,000 records.  Elapsed time: 00:16:32s.  Time for last 1,000,000:    2s.  Last read position: chrM:9,144
INFO	2016-05-15 03:29:27	MarkDuplicates	Tracking 4326 as yet unmatched pairs. 4326 records in RAM.
INFO	2016-05-15 03:29:30	MarkDuplicates	Read   249,000,000 records.  Elapsed time: 00:16:35s.  Time for last 1,000,000:    2s.  Last read position: chrM:9,283
INFO	2016-05-15 03:29:30	MarkDuplicates	Tracking 26664 as yet unmatched pairs. 26664 records in RAM.
INFO	2016-05-15 03:29:36	MarkDuplicates	Read   250,000,000 records.  Elapsed time: 00:16:42s.  Time for last 1,000,000:    6s.  Last read position: chrM:9,522
INFO	2016-05-15 03:29:36	MarkDuplicates	Tracking 7634 as yet unmatched pairs. 7634 records in RAM.
INFO	2016-05-15 03:29:40	MarkDuplicates	Read   251,000,000 records.  Elapsed time: 00:16:45s.  Time for last 1,000,000:    3s.  Last read position: chrM:9,745
INFO	2016-05-15 03:29:40	MarkDuplicates	Tracking 43454 as yet unmatched pairs. 43454 records in RAM.
INFO	2016-05-15 03:29:43	MarkDuplicates	Read   252,000,000 records.  Elapsed time: 00:16:48s.  Time for last 1,000,000:    2s.  Last read position: chrM:9,856
INFO	2016-05-15 03:29:43	MarkDuplicates	Tracking 40368 as yet unmatched pairs. 40368 records in RAM.
INFO	2016-05-15 03:29:46	MarkDuplicates	Read   253,000,000 records.  Elapsed time: 00:16:51s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,006
INFO	2016-05-15 03:29:46	MarkDuplicates	Tracking 48328 as yet unmatched pairs. 48328 records in RAM.
INFO	2016-05-15 03:29:49	MarkDuplicates	Read   254,000,000 records.  Elapsed time: 00:16:54s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,185
INFO	2016-05-15 03:29:49	MarkDuplicates	Tracking 30522 as yet unmatched pairs. 30522 records in RAM.
INFO	2016-05-15 03:29:52	MarkDuplicates	Read   255,000,000 records.  Elapsed time: 00:16:57s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,308
INFO	2016-05-15 03:29:52	MarkDuplicates	Tracking 16276 as yet unmatched pairs. 16276 records in RAM.
INFO	2016-05-15 03:29:55	MarkDuplicates	Read   256,000,000 records.  Elapsed time: 00:17:00s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,523
INFO	2016-05-15 03:29:55	MarkDuplicates	Tracking 2170 as yet unmatched pairs. 2170 records in RAM.
INFO	2016-05-15 03:29:58	MarkDuplicates	Read   257,000,000 records.  Elapsed time: 00:17:03s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,640
INFO	2016-05-15 03:29:58	MarkDuplicates	Tracking 14442 as yet unmatched pairs. 14442 records in RAM.
INFO	2016-05-15 03:30:01	MarkDuplicates	Read   258,000,000 records.  Elapsed time: 00:17:06s.  Time for last 1,000,000:    2s.  Last read position: chrM:10,745
INFO	2016-05-15 03:30:01	MarkDuplicates	Tracking 33418 as yet unmatched pairs. 33418 records in RAM.
INFO	2016-05-15 03:30:04	MarkDuplicates	Read   259,000,000 records.  Elapsed time: 00:17:09s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,124
INFO	2016-05-15 03:30:04	MarkDuplicates	Tracking 6332 as yet unmatched pairs. 6332 records in RAM.
INFO	2016-05-15 03:30:10	MarkDuplicates	Read   260,000,000 records.  Elapsed time: 00:17:16s.  Time for last 1,000,000:    6s.  Last read position: chrM:11,219
INFO	2016-05-15 03:30:10	MarkDuplicates	Tracking 744 as yet unmatched pairs. 744 records in RAM.
INFO	2016-05-15 03:30:13	MarkDuplicates	Read   261,000,000 records.  Elapsed time: 00:17:19s.  Time for last 1,000,000:    2s.  Last read position: chrM:11,357
INFO	2016-05-15 03:30:13	MarkDuplicates	Tracking 4814 as yet unmatched pairs. 4814 records in RAM.
INFO	2016-05-15 03:30:16	MarkDuplicates	Read   262,000,000 records.  Elapsed time: 00:17:21s.  Time for last 1,000,000:    2s.  Last read position: chrM:11,539
INFO	2016-05-15 03:30:16	MarkDuplicates	Tracking 4232 as yet unmatched pairs. 4232 records in RAM.
INFO	2016-05-15 03:30:19	MarkDuplicates	Read   263,000,000 records.  Elapsed time: 00:17:24s.  Time for last 1,000,000:    2s.  Last read position: chrM:11,738
INFO	2016-05-15 03:30:19	MarkDuplicates	Tracking 7074 as yet unmatched pairs. 7074 records in RAM.
INFO	2016-05-15 03:30:21	MarkDuplicates	Read   264,000,000 records.  Elapsed time: 00:17:27s.  Time for last 1,000,000:    2s.  Last read position: chrM:11,919
INFO	2016-05-15 03:30:21	MarkDuplicates	Tracking 1580 as yet unmatched pairs. 1580 records in RAM.
INFO	2016-05-15 03:30:35	MarkDuplicates	Read   265,000,000 records.  Elapsed time: 00:17:40s.  Time for last 1,000,000:   13s.  Last read position: chrM:12,016
INFO	2016-05-15 03:30:35	MarkDuplicates	Tracking 22440 as yet unmatched pairs. 22440 records in RAM.
INFO	2016-05-15 03:30:38	MarkDuplicates	Read   266,000,000 records.  Elapsed time: 00:17:43s.  Time for last 1,000,000:    2s.  Last read position: chrM:12,147
INFO	2016-05-15 03:30:38	MarkDuplicates	Tracking 5172 as yet unmatched pairs. 5172 records in RAM.
INFO	2016-05-15 03:30:41	MarkDuplicates	Read   267,000,000 records.  Elapsed time: 00:17:46s.  Time for last 1,000,000:    2s.  Last read position: chrM:12,354
INFO	2016-05-15 03:30:41	MarkDuplicates	Tracking 40386 as yet unmatched pairs. 40386 records in RAM.
INFO	2016-05-15 03:30:44	MarkDuplicates	Read   268,000,000 records.  Elapsed time: 00:17:49s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,497
INFO	2016-05-15 03:30:44	MarkDuplicates	Tracking 16792 as yet unmatched pairs. 16792 records in RAM.
INFO	2016-05-15 03:30:47	MarkDuplicates	Read   269,000,000 records.  Elapsed time: 00:17:52s.  Time for last 1,000,000:    2s.  Last read position: chrM:12,599
INFO	2016-05-15 03:30:47	MarkDuplicates	Tracking 33534 as yet unmatched pairs. 33534 records in RAM.
INFO	2016-05-15 03:30:50	MarkDuplicates	Read   270,000,000 records.  Elapsed time: 00:17:55s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,720
INFO	2016-05-15 03:30:50	MarkDuplicates	Tracking 14432 as yet unmatched pairs. 14432 records in RAM.
INFO	2016-05-15 03:30:52	MarkDuplicates	Read   271,000,000 records.  Elapsed time: 00:17:58s.  Time for last 1,000,000:    2s.  Last read position: chrM:12,929
INFO	2016-05-15 03:30:52	MarkDuplicates	Tracking 1462 as yet unmatched pairs. 1462 records in RAM.
INFO	2016-05-15 03:30:55	MarkDuplicates	Read   272,000,000 records.  Elapsed time: 00:18:01s.  Time for last 1,000,000:    2s.  Last read position: chrM:13,028
INFO	2016-05-15 03:30:55	MarkDuplicates	Tracking 26084 as yet unmatched pairs. 26084 records in RAM.
INFO	2016-05-15 03:30:58	MarkDuplicates	Read   273,000,000 records.  Elapsed time: 00:18:04s.  Time for last 1,000,000:    2s.  Last read position: chrM:13,108
INFO	2016-05-15 03:30:58	MarkDuplicates	Tracking 46698 as yet unmatched pairs. 46698 records in RAM.
INFO	2016-05-15 03:31:03	MarkDuplicates	Read   274,000,000 records.  Elapsed time: 00:18:09s.  Time for last 1,000,000:    5s.  Last read position: chrM:13,206
INFO	2016-05-15 03:31:03	MarkDuplicates	Tracking 22552 as yet unmatched pairs. 22552 records in RAM.
INFO	2016-05-15 03:31:06	MarkDuplicates	Read   275,000,000 records.  Elapsed time: 00:18:12s.  Time for last 1,000,000:    2s.  Last read position: chrM:13,347
INFO	2016-05-15 03:31:06	MarkDuplicates	Tracking 14676 as yet unmatched pairs. 14676 records in RAM.
INFO	2016-05-15 03:31:10	MarkDuplicates	Read   276,000,000 records.  Elapsed time: 00:18:15s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,458
INFO	2016-05-15 03:31:10	MarkDuplicates	Tracking 21184 as yet unmatched pairs. 21184 records in RAM.
INFO	2016-05-15 03:31:13	MarkDuplicates	Read   277,000,000 records.  Elapsed time: 00:18:18s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,577
INFO	2016-05-15 03:31:13	MarkDuplicates	Tracking 19036 as yet unmatched pairs. 19036 records in RAM.
INFO	2016-05-15 03:31:16	MarkDuplicates	Read   278,000,000 records.  Elapsed time: 00:18:21s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,687
INFO	2016-05-15 03:31:16	MarkDuplicates	Tracking 43252 as yet unmatched pairs. 43252 records in RAM.
INFO	2016-05-15 03:31:23	MarkDuplicates	Read   279,000,000 records.  Elapsed time: 00:18:28s.  Time for last 1,000,000:    7s.  Last read position: chrM:13,838
INFO	2016-05-15 03:31:23	MarkDuplicates	Tracking 44372 as yet unmatched pairs. 44372 records in RAM.
INFO	2016-05-15 03:31:26	MarkDuplicates	Read   280,000,000 records.  Elapsed time: 00:18:32s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,954
INFO	2016-05-15 03:31:26	MarkDuplicates	Tracking 21642 as yet unmatched pairs. 21642 records in RAM.
INFO	2016-05-15 03:31:29	MarkDuplicates	Read   281,000,000 records.  Elapsed time: 00:18:35s.  Time for last 1,000,000:    3s.  Last read position: chrM:14,090
INFO	2016-05-15 03:31:29	MarkDuplicates	Tracking 1300 as yet unmatched pairs. 1300 records in RAM.
INFO	2016-05-15 03:31:32	MarkDuplicates	Read   282,000,000 records.  Elapsed time: 00:18:38s.  Time for last 1,000,000:    2s.  Last read position: chrM:14,309
INFO	2016-05-15 03:31:32	MarkDuplicates	Tracking 27992 as yet unmatched pairs. 27992 records in RAM.
INFO	2016-05-15 03:31:35	MarkDuplicates	Read   283,000,000 records.  Elapsed time: 00:18:41s.  Time for last 1,000,000:    2s.  Last read position: chrM:14,405
INFO	2016-05-15 03:31:35	MarkDuplicates	Tracking 15226 as yet unmatched pairs. 15226 records in RAM.
INFO	2016-05-15 03:31:38	MarkDuplicates	Read   284,000,000 records.  Elapsed time: 00:18:44s.  Time for last 1,000,000:    3s.  Last read position: chrM:14,602
INFO	2016-05-15 03:31:38	MarkDuplicates	Tracking 2254 as yet unmatched pairs. 2254 records in RAM.
INFO	2016-05-15 03:31:41	MarkDuplicates	Read   285,000,000 records.  Elapsed time: 00:18:47s.  Time for last 1,000,000:    2s.  Last read position: chrM:14,823
INFO	2016-05-15 03:31:41	MarkDuplicates	Tracking 4632 as yet unmatched pairs. 4632 records in RAM.
INFO	2016-05-15 03:31:44	MarkDuplicates	Read   286,000,000 records.  Elapsed time: 00:18:50s.  Time for last 1,000,000:    2s.  Last read position: chrM:14,991
INFO	2016-05-15 03:31:44	MarkDuplicates	Tracking 40740 as yet unmatched pairs. 40740 records in RAM.
INFO	2016-05-15 03:31:47	MarkDuplicates	Read   287,000,000 records.  Elapsed time: 00:18:53s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,094
INFO	2016-05-15 03:31:47	MarkDuplicates	Tracking 15400 as yet unmatched pairs. 15400 records in RAM.
INFO	2016-05-15 03:31:50	MarkDuplicates	Read   288,000,000 records.  Elapsed time: 00:18:56s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,181
INFO	2016-05-15 03:31:50	MarkDuplicates	Tracking 12676 as yet unmatched pairs. 12676 records in RAM.
INFO	2016-05-15 03:31:53	MarkDuplicates	Read   289,000,000 records.  Elapsed time: 00:18:58s.  Time for last 1,000,000:    2s.  Last read position: chrM:15,269
INFO	2016-05-15 03:31:53	MarkDuplicates	Tracking 17088 as yet unmatched pairs. 17088 records in RAM.
INFO	2016-05-15 03:31:56	MarkDuplicates	Read   290,000,000 records.  Elapsed time: 00:19:01s.  Time for last 1,000,000:    2s.  Last read position: chrM:15,376
INFO	2016-05-15 03:31:56	MarkDuplicates	Tracking 26682 as yet unmatched pairs. 26682 records in RAM.
INFO	2016-05-15 03:31:59	MarkDuplicates	Read   291,000,000 records.  Elapsed time: 00:19:04s.  Time for last 1,000,000:    2s.  Last read position: chrM:15,480
INFO	2016-05-15 03:31:59	MarkDuplicates	Tracking 34714 as yet unmatched pairs. 34714 records in RAM.
INFO	2016-05-15 03:32:02	MarkDuplicates	Read   292,000,000 records.  Elapsed time: 00:19:07s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,575
INFO	2016-05-15 03:32:02	MarkDuplicates	Tracking 45038 as yet unmatched pairs. 45038 records in RAM.
INFO	2016-05-15 03:32:09	MarkDuplicates	Read   293,000,000 records.  Elapsed time: 00:19:14s.  Time for last 1,000,000:    7s.  Last read position: chrM:15,665
INFO	2016-05-15 03:32:09	MarkDuplicates	Tracking 56854 as yet unmatched pairs. 56854 records in RAM.
INFO	2016-05-15 03:32:23	MarkDuplicates	Read   294,000,000 records.  Elapsed time: 00:19:28s.  Time for last 1,000,000:   14s.  Last read position: chrM:15,748
INFO	2016-05-15 03:32:23	MarkDuplicates	Tracking 38126 as yet unmatched pairs. 38126 records in RAM.
INFO	2016-05-15 03:32:26	MarkDuplicates	Read   295,000,000 records.  Elapsed time: 00:19:32s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,841
INFO	2016-05-15 03:32:26	MarkDuplicates	Tracking 39386 as yet unmatched pairs. 39386 records in RAM.
INFO	2016-05-15 03:32:29	MarkDuplicates	Read   296,000,000 records.  Elapsed time: 00:19:35s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,991
INFO	2016-05-15 03:32:29	MarkDuplicates	Tracking 34756 as yet unmatched pairs. 34756 records in RAM.
INFO	2016-05-15 03:32:33	MarkDuplicates	Read   297,000,000 records.  Elapsed time: 00:19:38s.  Time for last 1,000,000:    3s.  Last read position: chrM:16,255
INFO	2016-05-15 03:32:33	MarkDuplicates	Tracking 16788 as yet unmatched pairs. 16788 records in RAM.
INFO	2016-05-15 03:32:36	MarkDuplicates	Read   298,000,000 records.  Elapsed time: 00:19:41s.  Time for last 1,000,000:    3s.  Last read position: chrM:16,364
INFO	2016-05-15 03:32:36	MarkDuplicates	Tracking 15190 as yet unmatched pairs. 15190 records in RAM.
INFO	2016-05-15 03:32:39	MarkDuplicates	Read   299,000,000 records.  Elapsed time: 00:19:44s.  Time for last 1,000,000:    3s.  Last read position: chrM:16,439
INFO	2016-05-15 03:32:39	MarkDuplicates	Tracking 13942 as yet unmatched pairs. 13942 records in RAM.
INFO	2016-05-15 03:32:42	MarkDuplicates	Read   300,000,000 records.  Elapsed time: 00:19:47s.  Time for last 1,000,000:    3s.  Last read position: chrX:5,820,230
INFO	2016-05-15 03:32:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:32:46	MarkDuplicates	Read   301,000,000 records.  Elapsed time: 00:19:51s.  Time for last 1,000,000:    3s.  Last read position: chrX:19,998,042
INFO	2016-05-15 03:32:46	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:32:49	MarkDuplicates	Read   302,000,000 records.  Elapsed time: 00:19:55s.  Time for last 1,000,000:    3s.  Last read position: chrX:37,545,245
INFO	2016-05-15 03:32:49	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-15 03:32:55	MarkDuplicates	Read   303,000,000 records.  Elapsed time: 00:20:00s.  Time for last 1,000,000:    5s.  Last read position: chrX:51,985,699
INFO	2016-05-15 03:32:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:32:58	MarkDuplicates	Read   304,000,000 records.  Elapsed time: 00:20:04s.  Time for last 1,000,000:    3s.  Last read position: chrX:73,641,118
INFO	2016-05-15 03:32:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:33:02	MarkDuplicates	Read   305,000,000 records.  Elapsed time: 00:20:07s.  Time for last 1,000,000:    3s.  Last read position: chrX:96,647,676
INFO	2016-05-15 03:33:02	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:33:06	MarkDuplicates	Read   306,000,000 records.  Elapsed time: 00:20:11s.  Time for last 1,000,000:    3s.  Last read position: chrX:112,610,470
INFO	2016-05-15 03:33:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-15 03:33:09	MarkDuplicates	Read   307,000,000 records.  Elapsed time: 00:20:14s.  Time for last 1,000,000:    3s.  Last read position: chrX:129,255,119
INFO	2016-05-15 03:33:09	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-15 03:33:12	MarkDuplicates	Read   308,000,000 records.  Elapsed time: 00:20:18s.  Time for last 1,000,000:    3s.  Last read position: chrX:145,269,144
INFO	2016-05-15 03:33:12	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-15 03:33:18	MarkDuplicates	Read 308685482 records. 0 pairs never matched.
INFO	2016-05-15 03:33:21	MarkDuplicates	After buildSortedReadEndLists freeMemory: 4193245000; totalMemory: 4221042688; maxMemory: 4221042688
INFO	2016-05-15 03:33:21	MarkDuplicates	Will retain up to 131907584 duplicate indices before spilling to disk.
INFO	2016-05-15 03:33:21	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-05-15 03:35:07	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-05-15 03:36:18	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-05-15 03:36:19	MarkDuplicates	After generateDuplicateIndexes freeMemory: 4238866808; totalMemory: 4268752896; maxMemory: 4268752896
INFO	2016-05-15 03:36:19	MarkDuplicates	Marking 143101150 records as duplicates.
INFO	2016-05-15 03:36:19	MarkDuplicates	Found 62470578 optical duplicate clusters.
INFO	2016-05-15 03:37:47	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:24s.  Time for last 10,000,000:   84s.  Last read position: chr11:2,008,719
INFO	2016-05-15 03:39:13	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:02:50s.  Time for last 10,000,000:   85s.  Last read position: chr12:329,850
INFO	2016-05-15 03:40:38	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:04:15s.  Time for last 10,000,000:   85s.  Last read position: chr13:24,729,244
INFO	2016-05-15 03:42:03	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:05:40s.  Time for last 10,000,000:   84s.  Last read position: chr14:85,881,371
INFO	2016-05-15 03:43:26	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:07:03s.  Time for last 10,000,000:   82s.  Last read position: chr16:23,791,883
INFO	2016-05-15 03:44:48	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:08:25s.  Time for last 10,000,000:   82s.  Last read position: chr17:62,133,028
INFO	2016-05-15 03:46:13	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:09:50s.  Time for last 10,000,000:   84s.  Last read position: chr19:32,244,975
INFO	2016-05-15 03:47:38	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:11:15s.  Time for last 10,000,000:   85s.  Last read position: chr1:71,141,616
INFO	2016-05-15 03:49:07	MarkDuplicates	Written    90,000,000 records.  Elapsed time: 00:12:44s.  Time for last 10,000,000:   88s.  Last read position: chr1:235,785,563
INFO	2016-05-15 03:50:30	MarkDuplicates	Written   100,000,000 records.  Elapsed time: 00:14:07s.  Time for last 10,000,000:   83s.  Last read position: chr22:30,116,749
INFO	2016-05-15 03:51:53	MarkDuplicates	Written   110,000,000 records.  Elapsed time: 00:15:30s.  Time for last 10,000,000:   83s.  Last read position: chr2:112,505,603
INFO	2016-05-15 03:53:21	MarkDuplicates	Written   120,000,000 records.  Elapsed time: 00:16:58s.  Time for last 10,000,000:   87s.  Last read position: chr3:14,154,423
INFO	2016-05-15 03:54:50	MarkDuplicates	Written   130,000,000 records.  Elapsed time: 00:18:27s.  Time for last 10,000,000:   88s.  Last read position: chr3:163,949,866
INFO	2016-05-15 03:56:20	MarkDuplicates	Written   140,000,000 records.  Elapsed time: 00:19:57s.  Time for last 10,000,000:   89s.  Last read position: chr4:126,245,560
INFO	2016-05-15 03:57:47	MarkDuplicates	Written   150,000,000 records.  Elapsed time: 00:21:24s.  Time for last 10,000,000:   87s.  Last read position: chr5:104,447,068
INFO	2016-05-15 03:59:13	MarkDuplicates	Written   160,000,000 records.  Elapsed time: 00:22:50s.  Time for last 10,000,000:   86s.  Last read position: chr6:43,543,052
INFO	2016-05-15 04:00:41	MarkDuplicates	Written   170,000,000 records.  Elapsed time: 00:24:18s.  Time for last 10,000,000:   88s.  Last read position: chr7:27,539,639
INFO	2016-05-15 04:02:06	MarkDuplicates	Written   180,000,000 records.  Elapsed time: 00:25:43s.  Time for last 10,000,000:   84s.  Last read position: chr8:19,430,197
INFO	2016-05-15 04:03:31	MarkDuplicates	Written   190,000,000 records.  Elapsed time: 00:27:08s.  Time for last 10,000,000:   85s.  Last read position: chr9:22,059,701
INFO	2016-05-15 04:04:53	MarkDuplicates	Written   200,000,000 records.  Elapsed time: 00:28:30s.  Time for last 10,000,000:   82s.  Last read position: chrM:475
INFO	2016-05-15 04:06:00	MarkDuplicates	Written   210,000,000 records.  Elapsed time: 00:29:37s.  Time for last 10,000,000:   66s.  Last read position: chrM:2,139
INFO	2016-05-15 04:07:08	MarkDuplicates	Written   220,000,000 records.  Elapsed time: 00:30:45s.  Time for last 10,000,000:   67s.  Last read position: chrM:3,414
INFO	2016-05-15 04:08:19	MarkDuplicates	Written   230,000,000 records.  Elapsed time: 00:31:56s.  Time for last 10,000,000:   71s.  Last read position: chrM:5,137
INFO	2016-05-15 04:09:30	MarkDuplicates	Written   240,000,000 records.  Elapsed time: 00:33:07s.  Time for last 10,000,000:   70s.  Last read position: chrM:7,192
INFO	2016-05-15 04:10:41	MarkDuplicates	Written   250,000,000 records.  Elapsed time: 00:34:18s.  Time for last 10,000,000:   70s.  Last read position: chrM:9,522
INFO	2016-05-15 04:11:53	MarkDuplicates	Written   260,000,000 records.  Elapsed time: 00:35:31s.  Time for last 10,000,000:   72s.  Last read position: chrM:11,219
INFO	2016-05-15 04:13:05	MarkDuplicates	Written   270,000,000 records.  Elapsed time: 00:36:42s.  Time for last 10,000,000:   71s.  Last read position: chrM:12,720
INFO	2016-05-15 04:14:17	MarkDuplicates	Written   280,000,000 records.  Elapsed time: 00:37:54s.  Time for last 10,000,000:   71s.  Last read position: chrM:13,954
INFO	2016-05-15 04:15:28	MarkDuplicates	Written   290,000,000 records.  Elapsed time: 00:39:05s.  Time for last 10,000,000:   70s.  Last read position: chrM:15,376
INFO	2016-05-15 04:16:42	MarkDuplicates	Written   300,000,000 records.  Elapsed time: 00:40:19s.  Time for last 10,000,000:   74s.  Last read position: chrX:5,820,230
Could not delete file /tmp/pangwei/sortingcollection.7794319657344695769.tmp
Could not delete file /tmp/pangwei/sortingcollection.8237041381146091035.tmp
INFO	2016-05-15 04:18:04	MarkDuplicates	Before output close freeMemory: 4149171496; totalMemory: 4177002496; maxMemory: 4177002496
INFO	2016-05-15 04:18:04	MarkDuplicates	After output close freeMemory: 4149170680; totalMemory: 4177002496; maxMemory: 4177002496
[Sun May 15 04:18:04 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 65.17 minutes.
Runtime.totalMemory()=4177002496
[bam_sort_core] merging from 223 files...

Num	14
ID	task.postalign_bam.nmsrt_bam_rep1.line_321.id_19
Name	nmsrt_bam rep1
Thread	thread_21
PID	43191

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-15 07:21:27
End	2016-05-15 08:28:48
Elapsed	01:07:21
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam
Dependencies

 
# SYS command. line 323

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 325

 samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.nmsrt

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 119 files...

Num	15
ID	task.postalign_bam.bam_to_bedpe_rep1.line_425.id_20
Name	bam_to_bedpe rep1
Thread	thread_21
PID	43697

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-15 08:28:49
End	2016-05-15 08:37:21
Elapsed	00:08:32
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Dependencies	nmsrt_bam rep1 nmsrt_bam rep1

 
# SYS command. line 427

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 430

 bedtools bamtobed -bedpe -mate1 -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH

Num	16
ID	task.postalign_bed.subsample_bedpe_rep1.line_116.id_21
Name	subsample_bedpe rep1
Thread	thread_21
PID	43789

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-15 08:37:24
End	2016-05-15 08:39:30
Elapsed	00:02:05
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz
Dependencies

 
# SYS command. line 118

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 120

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | grep -v "chrM" | shuf -n 17500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH

Num	17
ID	task.postalign_bam.bedpe_to_tag_rep1.line_465.id_22
Name	bedpe_to_tag rep1
Thread	thread_21
PID	43857

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-15 08:39:31
End	2016-05-15 08:41:08
Elapsed	00:01:37
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
Dependencies

 
# SYS command. line 467

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 469

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz | awk 'BEGIN{OFS="\t"}{printf "%s\t%s\t%s\tN\t1000\t%s\n%s\t%s\t%s\tN\t1000\t%s\n",$1,$2,$3,$9,$4,$5,$6,$10}' | \
			gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz

# SYS command. line 472

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz | grep -P -v 'chrM' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz; mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH

Num	18
ID	task.postalign_bed.shift_tag_rep1.line_140.id_23
Name	shift_tag rep1
Thread	thread_21
PID	43926

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-15 08:41:09
End	2016-05-15 08:42:03
Elapsed	00:00:54
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Dependencies

 
# SYS command. line 142

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 144

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz | awk -F $'\t' 'BEGIN {OFS = FS}{ if ($6 == "+") {$2 = $2 + 4} else if ($6 == "-") {$3 = $3 - 5} print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH

Num	19
ID	task.postalign_bed.subsample_bedpe2tagrep1.line_89.id_24
Name	subsample_bedpe2tagrep1
Thread	thread_21
PID	43988

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-15 08:42:04
End	2016-05-15 08:43:36
Elapsed	00:01:31
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
Dependencies

 
# SYS command. line 91

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 95

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | \
			grep -v "chrM" | shuf -n 25000000 | \
			awk 'BEGIN{OFS="\t"}{print $1,$2,$3,"N","1000",$9}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH

Num	20
ID	task.postalign_bed.xcor_rep1.line_165.id_25
Name	xcor rep1
Thread	thread_21
PID

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

Start
End
Elapsed
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf
Dependencies

 
# SYS command. line 167

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 171

 Rscript $(which run_spp_nodups.R) -rf \
			-c=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz -p=1 \
			-filtchr=chrM -savp=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf -out=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc -speak=0

# SYS command. line 174

 sed -r 's/,[^\t]+//g' /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp

# SYS command. line 175

 mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc

Type	Name	Value
string	_	/usr/bin/bds
string	_LMFILES_	/software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/samtools/1.2:/software/modulefiles/bedtools/2.23.0:/software/modulefiles/rsem/1.2.21
string	_ZSH_TMUX_FIXED_CONFIG	/users/pangwei/.oh-my-zsh/plugins/tmux/tmux.extra.conf
bool	allowEmpty	false
string[]	args	[-out_dir, /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22, -num_rep, 2, -fastq1_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC21/ATAC21-trimmed-pair1.fastq.gz, -fastq1_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC21/ATAC21-trimmed-pair2.fastq.gz, -fastq2_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC22/ATAC22-trimmed-pair1.fastq.gz, -fastq2_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC22/ATAC22-trimmed-pair2.fastq.gz, -subsample, 17500000, -true_rep, -species, hg19]
string	C_INCLUDE_PATH	/software/samtools/samtools-1.2/include/htslib
bool	canFail	false
int	cpus	1
int	cpusLocal	48
int	day	86400
real	E	2.718281828459045
int	G	1073741824
string	HOME	/users/pangwei/
int	hour	3600
int	K	1024
string	LANG	en_US.UTF-8
string	LC_CTYPE	en_US.UTF-8
string	LD_LIBRARY_PATH	/software/samtools/samtools-1.2/lib:/usr/local/cudnn-3/lib64/:/usr/local/cudnn-3/lib64/
string	LESS	-R
string	LOADEDMODULES	modsappsdir/modsappsdir:samtools/1.2:bedtools/2.23.0:rsem/1.2.21
string	LOGNAME	pangwei
string	LSCOLORS	Gxfxcxdxbxegedabagacad
int	M	1048576
string	MAIL	/var/mail/pangwei
string	MANPATH	/software/samtools/samtools-1.2/share/man:/usr/share/man
int	mem	-1
int	minute	60
string	MODULE_VERSION	3.2.10
string	MODULE_VERSION_STACK	3.2.10
string	MODULEPATH	/usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles
string	MODULESAPPSDIR	/software
string	MODULESHOME	/software/env_module/3.2.10
string	node
string	OLDPWD	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4
int	P	1125899906842624
string	PAGER	less
string	PATH	/software/RSEM/rsem-1.2.21/:/software/bedtools/2.23.0/bin:/software/samtools/samtools-1.2/bin:/users/pangwei/anaconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
real	PI	3.141592653589793
string	ppwd	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata
string	programName	atac.bds
string	programPath	/users/pangwei/bds_atac/atac.bds
string	PWD	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata
string	PYTHONPATH	/home/jisraeli/src/caffe_atac/python/:/users/pangwei/stemcells:/home/jisraeli/src/caffe_atac/python/:/users/pangwei/stemcells:
string	queue
int	retry	0
string	SAMTOOLS_HOME	/software/samtools/samtools-1.2/bin
string	SHELL	/usr/bin/zsh
string	SHLVL	2
string	SSH_AUTH_SOCK	/tmp/ssh-5gr8qSU2WF/agent.74700
string	SSH_CLIENT	171.65.76.244 36245 22
string	SSH_CONNECTION	171.65.76.244 49273 171.65.76.236 22
string	SSH_TTY	/dev/pts/0
string	system	local
int	T	1099511627776
string	TERM	screen
string	THEANO_FLAGS	device=gpu6,floatX=float32,warn_float64=warn,optimizer_excluding=cudnn
int	timeout	-1
string	TMUX	/tmp/tmux-1077/default,106699,3
string	TMUX_PANE	%3
string	USER	pangwei
string	UTIL_SCRIPTS_DIR	/users/pangwei/av_scripts
int	walltimeout	8640000
int	week	604800
string	WWW	/srv/www/kundaje/pangwei
string	XDG_RUNTIME_DIR	/run/user/1077
string	XDG_SESSION_ID	1907
string	ZSH	/users/pangwei//.oh-my-zsh
string	ZSH_TMUX_TERM	screen

BigDataScript report: atac.bds

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