Script file	/users/pangwei/bds_atac/atac.bds
Program ID	atac.bds.20160515_230834_898
Start time	2016-05-15 23:08:34
Run time	20:01:35.113
Tasks executed	13
Tasks failed	0
Tasks failed names
Arguments*	[-out_dir, /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12, -num_rep, 2, -fastq1_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC11/ATAC11-trimmed-pair1.fastq.gz, -fastq1_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC11/ATAC11-trimmed-pair2.fastq.gz, -fastq2_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC12/ATAC12-trimmed-pair1.fastq.gz, -fastq2_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC12/ATAC12-trimmed-pair2.fastq.gz, -subsample, 17500000, -true_rep, -species, hg19]
System*	local
Cpus*	1
Exit value	0

Thread ID	Parent	Tasks
thread_Root	None
thread_21	thread_Root	atac.bds.20160515_230834_898_parallel_21/task.align_bowtie2.bowtie2_PE_rep2.line_133.id_7 atac.bds.20160515_230834_898_parallel_21/task.postalign_bam.dedup_bam_PE_rep2.line_215.id_8 atac.bds.20160515_230834_898_parallel_21/task.postalign_bam.nmsrt_bam_rep2.line_321.id_9 atac.bds.20160515_230834_898_parallel_21/task.postalign_bam.bam_to_bedpe_rep2.line_425.id_10 atac.bds.20160515_230834_898_parallel_21/task.postalign_bed.subsample_bedpe_rep2.line_116.id_11 atac.bds.20160515_230834_898_parallel_21/task.postalign_bam.bedpe_to_tag_rep2.line_465.id_12 atac.bds.20160515_230834_898_parallel_21/task.postalign_bed.shift_tag_rep2.line_140.id_13 atac.bds.20160515_230834_898_parallel_21/task.postalign_bed.subsample_bedpe2tagrep2.line_89.id_14 atac.bds.20160515_230834_898_parallel_21/task.postalign_bed.xcor_rep2.line_165.id_15 atac.bds.20160515_230834_898_parallel_21/task.callpeak_macs2.macs2_atac_rep2.pval0.1.line_192.id_16 atac.bds.20160515_230834_898_parallel_21/task.callpeak_macs2.macs2_atac_rep2.line_192.id_17
thread_20	thread_Root	atac.bds.20160515_230834_898_parallel_20/task.align_bowtie2.bowtie2_PE_rep1.line_133.id_6 atac.bds.20160515_230834_898_parallel_20/task.postalign_bam.dedup_bam_PE_rep1.line_215.id_18

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_20
PID	88427

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

Start	2016-05-15 23:08:36
End	2016-05-16 15:37:04
Elapsed	16:28:28
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-trimmed-pair1.trim.fastq.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-trimmed-pair2.trim.fastq.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/qc/rep1/ATAC11-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/ATAC11+12/align/rep1/ATAC11-trimmed-pair1.trim.fastq.gz -2 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-trimmed-pair2.trim.fastq.gz 2>/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/qc/rep1/ATAC11-trimmed-pair1.trim.PE2SE.align.log | samtools view -bS - | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-trimmed-pair1.trim.PE2SE

# SYS command. line 142

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-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 134 files...

Num	2
ID	task.align_bowtie2.bowtie2_PE_rep2.line_133.id_7
Name	bowtie2_PE rep2
Thread	thread_21
PID	88432

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

Start	2016-05-15 23:08:36
End	2016-05-16 06:32:54
Elapsed	07:24:17
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.fastq.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair2.trim.fastq.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/qc/rep2/ATAC12-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/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.fastq.gz -2 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair2.trim.fastq.gz 2>/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/qc/rep2/ATAC12-trimmed-pair1.trim.PE2SE.align.log | samtools view -bS - | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE

# SYS command. line 142

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-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 57 files...

Num	3
ID	task.postalign_bam.dedup_bam_PE_rep2.line_215.id_8
Name	dedup_bam_PE rep2
Thread	thread_21
PID	99280

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

Start	2016-05-16 06:32:55
End	2016-05-16 08:40:02
Elapsed	02:07:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/qc/rep2/ATAC12-trimmed-pair1.trim.PE2SE.dup.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/qc/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/qc/rep2/ATAC12-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/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-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/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-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/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.filt

# SYS command. line 239

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-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/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/qc/rep2/ATAC12-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/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/qc/rep2/ATAC12-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/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-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/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.filt.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 269

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 271

 if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.bai" ]; then \
			cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.bai; \
			fi

# SYS command. line 275

 samtools flagstat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/qc/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc

# SYS command. line 286

 samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.filt.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.filt.bam.tmp

# SYS command. line 287

 bedtools bamtobed -bedpe -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-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/ATAC11+12/qc/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.pbc.qc

# SYS command. line 291

 rm /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam

# SYS command. line 293

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.filt.bam

# SYS command. line 294

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-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 32 files...
[bam_sort_core] merging from 32 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Mon May 16 07:41:25 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/qc/rep2/ATAC12-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
[Mon May 16 07:41:25 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	2016-05-16 07:41:25	MarkDuplicates	Start of doWork freeMemory: 254889800; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-16 07:41:25	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-05-16 07:41:25	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-05-16 07:41:31	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:05s.  Time for last 1,000,000:    5s.  Last read position: chr11:13,299,087
INFO	2016-05-16 07:41:31	MarkDuplicates	Tracking 32 as yet unmatched pairs. 32 records in RAM.
INFO	2016-05-16 07:41:35	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:10s.  Time for last 1,000,000:    4s.  Last read position: chr12:16,257,490
INFO	2016-05-16 07:41:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 07:41:40	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:15s.  Time for last 1,000,000:    4s.  Last read position: chr13:61,954,243
INFO	2016-05-16 07:41:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 07:41:45	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:19s.  Time for last 1,000,000:    4s.  Last read position: chr15:41,057,219
INFO	2016-05-16 07:41:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 07:41:51	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:25s.  Time for last 1,000,000:    6s.  Last read position: chr16:87,886,903
INFO	2016-05-16 07:41:51	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 07:41:57	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:31s.  Time for last 1,000,000:    6s.  Last read position: chr18:52,044,723
INFO	2016-05-16 07:41:57	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 07:42:02	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:36s.  Time for last 1,000,000:    4s.  Last read position: chr1:4,755,733
INFO	2016-05-16 07:42:02	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 07:42:09	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:44s.  Time for last 1,000,000:    7s.  Last read position: chr1:160,651,456
INFO	2016-05-16 07:42:09	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 07:42:13	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:47s.  Time for last 1,000,000:    3s.  Last read position: chr20:58,331,428
INFO	2016-05-16 07:42:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 07:42:22	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:56s.  Time for last 1,000,000:    8s.  Last read position: chr2:55,315,294
INFO	2016-05-16 07:42:22	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 07:42:26	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:00s.  Time for last 1,000,000:    3s.  Last read position: chr2:223,725,733
INFO	2016-05-16 07:42:26	MarkDuplicates	Tracking 32 as yet unmatched pairs. 32 records in RAM.
INFO	2016-05-16 07:42:30	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:04s.  Time for last 1,000,000:    3s.  Last read position: chr3:133,983,856
INFO	2016-05-16 07:42:30	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 07:42:33	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:08s.  Time for last 1,000,000:    3s.  Last read position: chr4:103,749,428
INFO	2016-05-16 07:42:33	MarkDuplicates	Tracking 26 as yet unmatched pairs. 26 records in RAM.
INFO	2016-05-16 07:42:40	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:14s.  Time for last 1,000,000:    6s.  Last read position: chr5:96,614,716
INFO	2016-05-16 07:42:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 07:42:55	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:30s.  Time for last 1,000,000:   15s.  Last read position: chr6:29,039,977
INFO	2016-05-16 07:42:55	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 07:43:00	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:34s.  Time for last 1,000,000:    4s.  Last read position: chr7:13,784,834
INFO	2016-05-16 07:43:00	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 07:43:05	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:01:40s.  Time for last 1,000,000:    5s.  Last read position: chr8:14,567,723
INFO	2016-05-16 07:43:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 07:43:12	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:01:46s.  Time for last 1,000,000:    6s.  Last read position: chr9:28,568,044
INFO	2016-05-16 07:43:12	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 07:43:15	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:01:50s.  Time for last 1,000,000:    3s.  Last read position: chrM:85
INFO	2016-05-16 07:43:15	MarkDuplicates	Tracking 42250 as yet unmatched pairs. 42250 records in RAM.
INFO	2016-05-16 07:43:19	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:01:53s.  Time for last 1,000,000:    3s.  Last read position: chrM:438
INFO	2016-05-16 07:43:19	MarkDuplicates	Tracking 20624 as yet unmatched pairs. 20624 records in RAM.
INFO	2016-05-16 07:43:23	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:01:57s.  Time for last 1,000,000:    3s.  Last read position: chrM:683
INFO	2016-05-16 07:43:23	MarkDuplicates	Tracking 67654 as yet unmatched pairs. 67654 records in RAM.
INFO	2016-05-16 07:43:28	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:02:03s.  Time for last 1,000,000:    5s.  Last read position: chrM:895
INFO	2016-05-16 07:43:28	MarkDuplicates	Tracking 44480 as yet unmatched pairs. 44480 records in RAM.
INFO	2016-05-16 07:43:33	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:02:08s.  Time for last 1,000,000:    4s.  Last read position: chrM:1,341
INFO	2016-05-16 07:43:33	MarkDuplicates	Tracking 114998 as yet unmatched pairs. 114998 records in RAM.
INFO	2016-05-16 07:43:38	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:02:12s.  Time for last 1,000,000:    4s.  Last read position: chrM:1,608
INFO	2016-05-16 07:43:38	MarkDuplicates	Tracking 62290 as yet unmatched pairs. 62290 records in RAM.
INFO	2016-05-16 07:43:43	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:02:17s.  Time for last 1,000,000:    4s.  Last read position: chrM:1,990
INFO	2016-05-16 07:43:43	MarkDuplicates	Tracking 49250 as yet unmatched pairs. 49250 records in RAM.
INFO	2016-05-16 07:43:48	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:02:22s.  Time for last 1,000,000:    4s.  Last read position: chrM:2,369
INFO	2016-05-16 07:43:48	MarkDuplicates	Tracking 13978 as yet unmatched pairs. 13978 records in RAM.
INFO	2016-05-16 07:43:56	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:02:30s.  Time for last 1,000,000:    8s.  Last read position: chrM:2,649
INFO	2016-05-16 07:43:56	MarkDuplicates	Tracking 126518 as yet unmatched pairs. 126518 records in RAM.
INFO	2016-05-16 07:44:02	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:02:36s.  Time for last 1,000,000:    5s.  Last read position: chrM:2,825
INFO	2016-05-16 07:44:02	MarkDuplicates	Tracking 62748 as yet unmatched pairs. 62748 records in RAM.
INFO	2016-05-16 07:44:10	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:02:44s.  Time for last 1,000,000:    7s.  Last read position: chrM:2,998
INFO	2016-05-16 07:44:10	MarkDuplicates	Tracking 98502 as yet unmatched pairs. 98502 records in RAM.
INFO	2016-05-16 07:44:26	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:03:00s.  Time for last 1,000,000:   16s.  Last read position: chrM:3,194
INFO	2016-05-16 07:44:26	MarkDuplicates	Tracking 86904 as yet unmatched pairs. 86904 records in RAM.
INFO	2016-05-16 07:44:31	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:03:06s.  Time for last 1,000,000:    5s.  Last read position: chrM:3,344
INFO	2016-05-16 07:44:31	MarkDuplicates	Tracking 124734 as yet unmatched pairs. 124734 records in RAM.
INFO	2016-05-16 07:44:37	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:03:11s.  Time for last 1,000,000:    5s.  Last read position: chrM:3,450
INFO	2016-05-16 07:44:37	MarkDuplicates	Tracking 61828 as yet unmatched pairs. 61828 records in RAM.
INFO	2016-05-16 07:44:43	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:03:18s.  Time for last 1,000,000:    6s.  Last read position: chrM:3,630
INFO	2016-05-16 07:44:43	MarkDuplicates	Tracking 150526 as yet unmatched pairs. 150526 records in RAM.
INFO	2016-05-16 07:44:48	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:03:22s.  Time for last 1,000,000:    4s.  Last read position: chrM:3,758
INFO	2016-05-16 07:44:48	MarkDuplicates	Tracking 95840 as yet unmatched pairs. 95840 records in RAM.
INFO	2016-05-16 07:44:52	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:03:26s.  Time for last 1,000,000:    4s.  Last read position: chrM:3,903
INFO	2016-05-16 07:44:52	MarkDuplicates	Tracking 141312 as yet unmatched pairs. 141312 records in RAM.
INFO	2016-05-16 07:44:56	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:03:30s.  Time for last 1,000,000:    3s.  Last read position: chrM:4,442
INFO	2016-05-16 07:44:56	MarkDuplicates	Tracking 7196 as yet unmatched pairs. 7196 records in RAM.
INFO	2016-05-16 07:44:59	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:03:34s.  Time for last 1,000,000:    3s.  Last read position: chrM:4,973
INFO	2016-05-16 07:44:59	MarkDuplicates	Tracking 62800 as yet unmatched pairs. 62800 records in RAM.
INFO	2016-05-16 07:45:04	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:03:39s.  Time for last 1,000,000:    4s.  Last read position: chrM:5,386
INFO	2016-05-16 07:45:04	MarkDuplicates	Tracking 38652 as yet unmatched pairs. 38652 records in RAM.
INFO	2016-05-16 07:45:08	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:03:42s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,159
INFO	2016-05-16 07:45:08	MarkDuplicates	Tracking 53028 as yet unmatched pairs. 53028 records in RAM.
INFO	2016-05-16 07:45:11	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:03:45s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,323
INFO	2016-05-16 07:45:11	MarkDuplicates	Tracking 36856 as yet unmatched pairs. 36856 records in RAM.
INFO	2016-05-16 07:45:16	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:03:50s.  Time for last 1,000,000:    4s.  Last read position: chrM:6,495
INFO	2016-05-16 07:45:16	MarkDuplicates	Tracking 37614 as yet unmatched pairs. 37614 records in RAM.
INFO	2016-05-16 07:45:21	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:03:55s.  Time for last 1,000,000:    5s.  Last read position: chrM:6,896
INFO	2016-05-16 07:45:21	MarkDuplicates	Tracking 69798 as yet unmatched pairs. 69798 records in RAM.
INFO	2016-05-16 07:45:31	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:04:05s.  Time for last 1,000,000:    9s.  Last read position: chrM:7,247
INFO	2016-05-16 07:45:31	MarkDuplicates	Tracking 66724 as yet unmatched pairs. 66724 records in RAM.
INFO	2016-05-16 07:45:35	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:04:09s.  Time for last 1,000,000:    4s.  Last read position: chrM:7,836
INFO	2016-05-16 07:45:35	MarkDuplicates	Tracking 55652 as yet unmatched pairs. 55652 records in RAM.
INFO	2016-05-16 07:45:44	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:04:19s.  Time for last 1,000,000:    9s.  Last read position: chrM:8,145
INFO	2016-05-16 07:45:44	MarkDuplicates	Tracking 42088 as yet unmatched pairs. 42088 records in RAM.
INFO	2016-05-16 07:45:50	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:04:24s.  Time for last 1,000,000:    5s.  Last read position: chrM:8,690
INFO	2016-05-16 07:45:50	MarkDuplicates	Tracking 8742 as yet unmatched pairs. 8742 records in RAM.
INFO	2016-05-16 07:45:55	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:04:29s.  Time for last 1,000,000:    5s.  Last read position: chrM:9,257
INFO	2016-05-16 07:45:55	MarkDuplicates	Tracking 56714 as yet unmatched pairs. 56714 records in RAM.
INFO	2016-05-16 07:46:00	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:04:35s.  Time for last 1,000,000:    5s.  Last read position: chrM:9,715
INFO	2016-05-16 07:46:00	MarkDuplicates	Tracking 69368 as yet unmatched pairs. 69368 records in RAM.
INFO	2016-05-16 07:46:06	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:04:40s.  Time for last 1,000,000:    5s.  Last read position: chrM:9,922
INFO	2016-05-16 07:46:06	MarkDuplicates	Tracking 69154 as yet unmatched pairs. 69154 records in RAM.
INFO	2016-05-16 07:46:14	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:04:48s.  Time for last 1,000,000:    8s.  Last read position: chrM:10,206
INFO	2016-05-16 07:46:14	MarkDuplicates	Tracking 81948 as yet unmatched pairs. 81948 records in RAM.
INFO	2016-05-16 07:46:19	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:04:54s.  Time for last 1,000,000:    5s.  Last read position: chrM:10,490
INFO	2016-05-16 07:46:19	MarkDuplicates	Tracking 11110 as yet unmatched pairs. 11110 records in RAM.
INFO	2016-05-16 07:46:25	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:04:59s.  Time for last 1,000,000:    5s.  Last read position: chrM:10,691
INFO	2016-05-16 07:46:25	MarkDuplicates	Tracking 42420 as yet unmatched pairs. 42420 records in RAM.
INFO	2016-05-16 07:46:30	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:05:04s.  Time for last 1,000,000:    5s.  Last read position: chrM:11,177
INFO	2016-05-16 07:46:30	MarkDuplicates	Tracking 42248 as yet unmatched pairs. 42248 records in RAM.
INFO	2016-05-16 07:46:33	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:05:08s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,381
INFO	2016-05-16 07:46:33	MarkDuplicates	Tracking 10882 as yet unmatched pairs. 10882 records in RAM.
INFO	2016-05-16 07:46:37	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:05:11s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,768
INFO	2016-05-16 07:46:37	MarkDuplicates	Tracking 41338 as yet unmatched pairs. 41338 records in RAM.
INFO	2016-05-16 07:46:43	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:05:17s.  Time for last 1,000,000:    6s.  Last read position: chrM:12,024
INFO	2016-05-16 07:46:43	MarkDuplicates	Tracking 37870 as yet unmatched pairs. 37870 records in RAM.
INFO	2016-05-16 07:46:47	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:05:21s.  Time for last 1,000,000:    4s.  Last read position: chrM:12,353
INFO	2016-05-16 07:46:47	MarkDuplicates	Tracking 37896 as yet unmatched pairs. 37896 records in RAM.
INFO	2016-05-16 07:46:52	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:05:26s.  Time for last 1,000,000:    5s.  Last read position: chrM:12,568
INFO	2016-05-16 07:46:52	MarkDuplicates	Tracking 78630 as yet unmatched pairs. 78630 records in RAM.
INFO	2016-05-16 07:47:08	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:05:42s.  Time for last 1,000,000:   15s.  Last read position: chrM:12,764
INFO	2016-05-16 07:47:08	MarkDuplicates	Tracking 28364 as yet unmatched pairs. 28364 records in RAM.
INFO	2016-05-16 07:47:12	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:05:46s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,089
INFO	2016-05-16 07:47:12	MarkDuplicates	Tracking 81704 as yet unmatched pairs. 81704 records in RAM.
INFO	2016-05-16 07:47:18	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:05:53s.  Time for last 1,000,000:    6s.  Last read position: chrM:13,272
INFO	2016-05-16 07:47:18	MarkDuplicates	Tracking 54348 as yet unmatched pairs. 54348 records in RAM.
INFO	2016-05-16 07:47:23	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:05:57s.  Time for last 1,000,000:    4s.  Last read position: chrM:13,473
INFO	2016-05-16 07:47:23	MarkDuplicates	Tracking 77578 as yet unmatched pairs. 77578 records in RAM.
INFO	2016-05-16 07:47:28	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:06:03s.  Time for last 1,000,000:    5s.  Last read position: chrM:13,764
INFO	2016-05-16 07:47:28	MarkDuplicates	Tracking 19060 as yet unmatched pairs. 19060 records in RAM.
INFO	2016-05-16 07:47:32	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:06:06s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,962
INFO	2016-05-16 07:47:32	MarkDuplicates	Tracking 35284 as yet unmatched pairs. 35284 records in RAM.
INFO	2016-05-16 07:47:35	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:06:09s.  Time for last 1,000,000:    3s.  Last read position: chrM:14,306
INFO	2016-05-16 07:47:35	MarkDuplicates	Tracking 18340 as yet unmatched pairs. 18340 records in RAM.
INFO	2016-05-16 07:47:38	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:06:12s.  Time for last 1,000,000:    2s.  Last read position: chrM:14,644
INFO	2016-05-16 07:47:38	MarkDuplicates	Tracking 9594 as yet unmatched pairs. 9594 records in RAM.
INFO	2016-05-16 07:47:41	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:06:15s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,022
INFO	2016-05-16 07:47:41	MarkDuplicates	Tracking 95270 as yet unmatched pairs. 95270 records in RAM.
INFO	2016-05-16 07:47:44	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:06:19s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,145
INFO	2016-05-16 07:47:44	MarkDuplicates	Tracking 113020 as yet unmatched pairs. 113020 records in RAM.
INFO	2016-05-16 07:47:48	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:06:22s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,308
INFO	2016-05-16 07:47:48	MarkDuplicates	Tracking 46402 as yet unmatched pairs. 46402 records in RAM.
INFO	2016-05-16 07:47:54	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:06:28s.  Time for last 1,000,000:    6s.  Last read position: chrM:15,461
INFO	2016-05-16 07:47:54	MarkDuplicates	Tracking 56492 as yet unmatched pairs. 56492 records in RAM.
INFO	2016-05-16 07:47:58	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:06:33s.  Time for last 1,000,000:    4s.  Last read position: chrM:15,625
INFO	2016-05-16 07:47:58	MarkDuplicates	Tracking 85616 as yet unmatched pairs. 85616 records in RAM.
INFO	2016-05-16 07:48:03	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:06:37s.  Time for last 1,000,000:    4s.  Last read position: chrM:15,747
INFO	2016-05-16 07:48:03	MarkDuplicates	Tracking 104894 as yet unmatched pairs. 104894 records in RAM.
INFO	2016-05-16 07:48:09	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:06:43s.  Time for last 1,000,000:    5s.  Last read position: chrM:15,898
INFO	2016-05-16 07:48:09	MarkDuplicates	Tracking 123524 as yet unmatched pairs. 123524 records in RAM.
INFO	2016-05-16 07:48:18	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:06:52s.  Time for last 1,000,000:    9s.  Last read position: chrM:16,230
INFO	2016-05-16 07:48:18	MarkDuplicates	Tracking 25508 as yet unmatched pairs. 25508 records in RAM.
INFO	2016-05-16 07:48:23	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:06:58s.  Time for last 1,000,000:    5s.  Last read position: chrM:16,368
INFO	2016-05-16 07:48:23	MarkDuplicates	Tracking 77740 as yet unmatched pairs. 77740 records in RAM.
INFO	2016-05-16 07:48:29	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:07:03s.  Time for last 1,000,000:    5s.  Last read position: chrM:16,492
INFO	2016-05-16 07:48:29	MarkDuplicates	Tracking 20442 as yet unmatched pairs. 20442 records in RAM.
INFO	2016-05-16 07:48:34	MarkDuplicates	Read 76906720 records. 0 pairs never matched.
INFO	2016-05-16 07:48:40	MarkDuplicates	After buildSortedReadEndLists freeMemory: 3150157912; totalMemory: 3177185280; maxMemory: 3817865216
INFO	2016-05-16 07:48:40	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-05-16 07:48:40	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-05-16 07:49:14	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-05-16 07:49:31	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-05-16 07:49:35	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2253861864; totalMemory: 3234856960; maxMemory: 3817865216
INFO	2016-05-16 07:49:35	MarkDuplicates	Marking 63435090 records as duplicates.
INFO	2016-05-16 07:49:35	MarkDuplicates	Found 21349217 optical duplicate clusters.
INFO	2016-05-16 07:51:06	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:30s.  Time for last 10,000,000:   90s.  Last read position: chr2:55,315,294
INFO	2016-05-16 07:52:37	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:03:01s.  Time for last 10,000,000:   91s.  Last read position: chrM:438
INFO	2016-05-16 07:53:58	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:04:22s.  Time for last 10,000,000:   80s.  Last read position: chrM:3,194
INFO	2016-05-16 07:55:17	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:05:41s.  Time for last 10,000,000:   79s.  Last read position: chrM:6,323
INFO	2016-05-16 07:56:35	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:06:59s.  Time for last 10,000,000:   77s.  Last read position: chrM:10,206
INFO	2016-05-16 07:58:09	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:08:32s.  Time for last 10,000,000:   93s.  Last read position: chrM:13,089
INFO	2016-05-16 08:00:10	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:10:34s.  Time for last 10,000,000:  121s.  Last read position: chrM:15,461
INFO	2016-05-16 08:01:36	MarkDuplicates	Before output close freeMemory: 3301225296; totalMemory: 3331325952; maxMemory: 3817865216
INFO	2016-05-16 08:01:36	MarkDuplicates	After output close freeMemory: 3301224240; totalMemory: 3331325952; maxMemory: 3817865216
[Mon May 16 08:01:36 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 20.19 minutes.
Runtime.totalMemory()=3331325952
[bam_sort_core] merging from 32 files...

Num	4
ID	task.postalign_bam.nmsrt_bam_rep2.line_321.id_9
Name	nmsrt_bam rep2
Thread	thread_21
PID	101986

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

Start	2016-05-16 08:40:02
End	2016-05-16 08:45:25
Elapsed	00:05:23
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-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/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-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 6 files...

Num	5
ID	task.postalign_bam.bam_to_bedpe_rep2.line_425.id_10
Name	bam_to_bedpe rep2
Thread	thread_21
PID	102473

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

Start	2016-05-16 08:45:26
End	2016-05-16 08:46:12
Elapsed	00:00:46
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-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/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-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_21
PID	102534

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

Start	2016-05-16 08:46:13
End	2016-05-16 08:46:44
Elapsed	00:00:30
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-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/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | grep -v "chrM" | shuf -n 17500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-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_21
PID	102597

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

Start	2016-05-16 08:46:45
End	2016-05-16 08:47:16
Elapsed	00:00:31
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-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/ATAC11+12/align/rep2/ATAC12-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/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz

# SYS command. line 472

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz | grep -P -v 'chrM' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz; mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-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_21
PID	102662

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

Start	2016-05-16 08:47:17
End	2016-05-16 08:47:42
Elapsed	00:00:25
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-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/ATAC11+12/align/rep2/ATAC12-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/ATAC11+12/align/rep2/ATAC12-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_21
PID	102722

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

Start	2016-05-16 08:47:43
End	2016-05-16 08:47:57
Elapsed	00:00:14
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-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/ATAC11+12/align/rep2/ATAC12-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/ATAC11+12/align/rep2/ATAC12-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_21
PID	102782

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

Start	2016-05-16 08:47:57
End	2016-05-16 08:55:45
Elapsed	00:07:47
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/qc/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/qc/rep2/ATAC12-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/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz -p=1 \
			-filtchr=chrM -savp=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/qc/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf -out=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/qc/rep2/ATAC12-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/ATAC11+12/qc/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/qc/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp

# SYS command. line 175

 mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/qc/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/qc/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc

   
--------------------Stdout--------------------
################
ChIP data: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-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/ATAC11+12/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/ATAC11+12/qc/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf 
result filename: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/qc/rep2/ATAC12-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/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz 
opened /tmp/RtmprfO7Q6/ATAC12-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign192273c613f2a
done. read 5747364 fragments
ChIP data read length 74 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.06615897 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.132741128658081 
Top 3 estimates for fragment length 0 
Window half size 455 
Phantom peak location 65 
Phantom peak Correlation 0.1433236 
Normalized Strand cross-correlation coefficient (NSC) 2.006397 
Relative Strand Cross correlation Coefficient (RSC) 0.8628581 
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_21
PID	102784

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

Start	2016-05-16 08:47:58
End	2016-05-16 08:56:49
Elapsed	00:08:51
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/signal/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/signal/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-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
INFO  @ Mon, 16 May 2016 08:48:00: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 --broad --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-01
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is on
 
INFO  @ Mon, 16 May 2016 08:48:00: #1 read tag files... 
INFO  @ Mon, 16 May 2016 08:48:00: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 08:48:02:  1000000 
INFO  @ Mon, 16 May 2016 08:48:04:  2000000 
INFO  @ Mon, 16 May 2016 08:48:05:  3000000 
INFO  @ Mon, 16 May 2016 08:48:07:  4000000 
INFO  @ Mon, 16 May 2016 08:48:08:  5000000 
INFO  @ Mon, 16 May 2016 08:48:10:  6000000 
INFO  @ Mon, 16 May 2016 08:48:11:  7000000 
INFO  @ Mon, 16 May 2016 08:48:13:  8000000 
INFO  @ Mon, 16 May 2016 08:48:15:  9000000 
INFO  @ Mon, 16 May 2016 08:48:16:  10000000 
INFO  @ Mon, 16 May 2016 08:48:18:  11000000 
INFO  @ Mon, 16 May 2016 08:48:19: #1 tag size is determined as 64 bps 
INFO  @ Mon, 16 May 2016 08:48:19: #1 tag size = 64 
INFO  @ Mon, 16 May 2016 08:48:19: #1  total tags in treatment: 11494728 
INFO  @ Mon, 16 May 2016 08:48:19: #1 finished! 
INFO  @ Mon, 16 May 2016 08:48:19: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 08:48:19: #2 Skipped... 
INFO  @ Mon, 16 May 2016 08:48:19: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 08:48:19: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 08:48:19: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 08:48:19: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Mon, 16 May 2016 08:48:19: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 08:48:41: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 08:49:52: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls 
INFO  @ Mon, 16 May 2016 08:49:58: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Mon, 16 May 2016 08:50:01: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Mon, 16 May 2016 08:50:05: Done! 
INFO  @ Mon, 16 May 2016 08:50:17: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-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
# ARGUMENTS LIST:
# name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Mon, 16 May 2016 08:50:17: #1 read tag files... 
INFO  @ Mon, 16 May 2016 08:50:17: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 08:50:19:  1000000 
INFO  @ Mon, 16 May 2016 08:50:20:  2000000 
INFO  @ Mon, 16 May 2016 08:50:22:  3000000 
INFO  @ Mon, 16 May 2016 08:50:24:  4000000 
INFO  @ Mon, 16 May 2016 08:50:25:  5000000 
INFO  @ Mon, 16 May 2016 08:50:27:  6000000 
INFO  @ Mon, 16 May 2016 08:50:28:  7000000 
INFO  @ Mon, 16 May 2016 08:50:30:  8000000 
INFO  @ Mon, 16 May 2016 08:50:31:  9000000 
INFO  @ Mon, 16 May 2016 08:50:33:  10000000 
INFO  @ Mon, 16 May 2016 08:50:35:  11000000 
INFO  @ Mon, 16 May 2016 08:50:36: #1 tag size is determined as 64 bps 
INFO  @ Mon, 16 May 2016 08:50:36: #1 tag size = 64 
INFO  @ Mon, 16 May 2016 08:50:36: #1  total tags in treatment: 11494728 
INFO  @ Mon, 16 May 2016 08:50:36: #1 finished! 
INFO  @ Mon, 16 May 2016 08:50:36: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 08:50:36: #2 Skipped... 
INFO  @ Mon, 16 May 2016 08:50:36: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 08:50:36: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 08:50:36: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 08:50:36: #3 Going to call summits inside each peak ... 
INFO  @ Mon, 16 May 2016 08:50:36: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Mon, 16 May 2016 08:50:36: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 08:50:58: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Mon, 16 May 2016 08:50:58: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Mon, 16 May 2016 08:50:58: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Mon, 16 May 2016 08:50:58: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Mon, 16 May 2016 08:50:58: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 08:56:32: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls 
INFO  @ Mon, 16 May 2016 08:56:38: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Mon, 16 May 2016 08:56:42: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_summits.bed 
INFO  @ Mon, 16 May 2016 08:56:44: Done!

Num	12
ID	task.callpeak_macs2.macs2_atac_rep2.line_192.id_17
Name	macs2_atac rep2
Thread	thread_21
PID	102795

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

Start	2016-05-16 08:47:58
End	2016-05-16 09:02:12
Elapsed	00:14:13
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.gappedPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/signal/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/signal/macs2/rep2/ATAC12-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/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/signal/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/signal/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-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/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-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
INFO  @ Mon, 16 May 2016 08:48:00: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf -g hs -p 0.01 --nomodel --shift -75 --extsize 150 --broad --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is on
 
INFO  @ Mon, 16 May 2016 08:48:00: #1 read tag files... 
INFO  @ Mon, 16 May 2016 08:48:00: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 08:48:02:  1000000 
INFO  @ Mon, 16 May 2016 08:48:04:  2000000 
INFO  @ Mon, 16 May 2016 08:48:05:  3000000 
INFO  @ Mon, 16 May 2016 08:48:07:  4000000 
INFO  @ Mon, 16 May 2016 08:48:09:  5000000 
INFO  @ Mon, 16 May 2016 08:48:10:  6000000 
INFO  @ Mon, 16 May 2016 08:48:12:  7000000 
INFO  @ Mon, 16 May 2016 08:48:14:  8000000 
INFO  @ Mon, 16 May 2016 08:48:15:  9000000 
INFO  @ Mon, 16 May 2016 08:48:17:  10000000 
INFO  @ Mon, 16 May 2016 08:48:19:  11000000 
INFO  @ Mon, 16 May 2016 08:48:20: #1 tag size is determined as 64 bps 
INFO  @ Mon, 16 May 2016 08:48:20: #1 tag size = 64 
INFO  @ Mon, 16 May 2016 08:48:20: #1  total tags in treatment: 11494728 
INFO  @ Mon, 16 May 2016 08:48:20: #1 finished! 
INFO  @ Mon, 16 May 2016 08:48:20: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 08:48:20: #2 Skipped... 
INFO  @ Mon, 16 May 2016 08:48:20: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 08:48:20: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 08:48:20: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 08:48:20: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Mon, 16 May 2016 08:48:20: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 08:48:44: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 08:49:46: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls 
INFO  @ Mon, 16 May 2016 08:49:50: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.broadPeak 
INFO  @ Mon, 16 May 2016 08:49:53: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.gappedPeak 
INFO  @ Mon, 16 May 2016 08:49:55: Done! 
INFO  @ Mon, 16 May 2016 08:50:08: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-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
# ARGUMENTS LIST:
# name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Mon, 16 May 2016 08:50:08: #1 read tag files... 
INFO  @ Mon, 16 May 2016 08:50:08: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 08:50:10:  1000000 
INFO  @ Mon, 16 May 2016 08:50:11:  2000000 
INFO  @ Mon, 16 May 2016 08:50:13:  3000000 
INFO  @ Mon, 16 May 2016 08:50:15:  4000000 
INFO  @ Mon, 16 May 2016 08:50:16:  5000000 
INFO  @ Mon, 16 May 2016 08:50:18:  6000000 
INFO  @ Mon, 16 May 2016 08:50:19:  7000000 
INFO  @ Mon, 16 May 2016 08:50:21:  8000000 
INFO  @ Mon, 16 May 2016 08:50:22:  9000000 
INFO  @ Mon, 16 May 2016 08:50:24:  10000000 
INFO  @ Mon, 16 May 2016 08:50:26:  11000000 
INFO  @ Mon, 16 May 2016 08:50:27: #1 tag size is determined as 64 bps 
INFO  @ Mon, 16 May 2016 08:50:27: #1 tag size = 64 
INFO  @ Mon, 16 May 2016 08:50:27: #1  total tags in treatment: 11494728 
INFO  @ Mon, 16 May 2016 08:50:27: #1 finished! 
INFO  @ Mon, 16 May 2016 08:50:27: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 08:50:27: #2 Skipped... 
INFO  @ Mon, 16 May 2016 08:50:27: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 08:50:27: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 08:50:27: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 08:50:27: #3 Going to call summits inside each peak ... 
INFO  @ Mon, 16 May 2016 08:50:27: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Mon, 16 May 2016 08:50:27: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 08:50:49: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Mon, 16 May 2016 08:50:49: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_treat_pileup.bdg 
INFO  @ Mon, 16 May 2016 08:50:49: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_control_lambda.bdg 
INFO  @ Mon, 16 May 2016 08:50:49: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Mon, 16 May 2016 08:50:49: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 08:53:23: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls 
INFO  @ Mon, 16 May 2016 08:53:24: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.narrowPeak 
INFO  @ Mon, 16 May 2016 08:53:26: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_summits.bed 
INFO  @ Mon, 16 May 2016 08:53:27: Done! 
INFO  @ Mon, 16 May 2016 08:53:30: Read and build treatment bedGraph... 
INFO  @ Mon, 16 May 2016 08:53:51: Read and build control bedGraph... 
INFO  @ Mon, 16 May 2016 08:54:01: Build scoreTrackII... 
INFO  @ Mon, 16 May 2016 08:54:10: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Mon, 16 May 2016 08:55:24: Write bedGraph of scores... 
INFO  @ Mon, 16 May 2016 08:56:01: Finished 'FE'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_FE.bdg'! 
INFO  @ Mon, 16 May 2016 08:57:33: Read and build treatment bedGraph... 
INFO  @ Mon, 16 May 2016 08:57:55: Read and build control bedGraph... 
INFO  @ Mon, 16 May 2016 08:58:12: Build scoreTrackII... 
INFO  @ Mon, 16 May 2016 08:58:21: Values in your input bedGraph files will be multiplied by 11.494728 ... 
INFO  @ Mon, 16 May 2016 08:59:44: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Mon, 16 May 2016 08:59:54: Write bedGraph of scores... 
INFO  @ Mon, 16 May 2016 09:00:48: Finished 'ppois'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/peak/macs2/rep2/ATAC12-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_ppois.bdg'!

Num	13
ID	task.postalign_bam.dedup_bam_PE_rep1.line_215.id_18
Name	dedup_bam_PE rep1
Thread	thread_20
PID	120032

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

Start	2016-05-16 15:37:05
End	2016-05-16 15:37:05
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-trimmed-pair1.trim.PE2SE.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/qc/rep1/ATAC11-trimmed-pair1.trim.PE2SE.dup.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/qc/rep1/ATAC11-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/qc/rep1/ATAC11-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/ATAC11+12/align/rep1/ATAC11-trimmed-pair1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-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/ATAC11+12/align/rep1/ATAC11-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-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/ATAC11+12/align/rep1/ATAC11-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-trimmed-pair1.trim.PE2SE.filt

# SYS command. line 239

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-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/ATAC11+12/align/rep1/ATAC11-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/qc/rep1/ATAC11-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/ATAC11+12/align/rep1/ATAC11-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/qc/rep1/ATAC11-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/ATAC11+12/align/rep1/ATAC11-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-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/ATAC11+12/align/rep1/ATAC11-trimmed-pair1.trim.PE2SE.filt.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 269

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 271

 if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-trimmed-pair1.trim.PE2SE.nodup.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-trimmed-pair1.trim.PE2SE.nodup.bai" ]; then \
			cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-trimmed-pair1.trim.PE2SE.nodup.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-trimmed-pair1.trim.PE2SE.nodup.bai; \
			fi

# SYS command. line 275

 samtools flagstat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-trimmed-pair1.trim.PE2SE.nodup.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/qc/rep1/ATAC11-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc

# SYS command. line 286

 samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-trimmed-pair1.trim.PE2SE.filt.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-trimmed-pair1.trim.PE2SE.filt.bam.tmp

# SYS command. line 287

 bedtools bamtobed -bedpe -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-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/ATAC11+12/qc/rep1/ATAC11-trimmed-pair1.trim.PE2SE.nodup.pbc.qc

# SYS command. line 291

 rm /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam

# SYS command. line 293

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-trimmed-pair1.trim.PE2SE.filt.bam

# SYS command. line 294

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-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 74 files...
[bam_sort_core] merging from 74 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Mon May 16 18:41:44 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-trimmed-pair1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-trimmed-pair1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/qc/rep1/ATAC11-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
[Mon May 16 18:41:44 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	2016-05-16 18:41:45	MarkDuplicates	Start of doWork freeMemory: 254889656; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-16 18:41:45	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-05-16 18:41:45	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-05-16 18:41:52	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:06s.  Time for last 1,000,000:    6s.  Last read position: chr10:70,883,539
INFO	2016-05-16 18:41:52	MarkDuplicates	Tracking 26 as yet unmatched pairs. 26 records in RAM.
INFO	2016-05-16 18:41:57	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:11s.  Time for last 1,000,000:    4s.  Last read position: chr10:122,848,219
INFO	2016-05-16 18:41:57	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 18:42:02	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:15s.  Time for last 1,000,000:    4s.  Last read position: chr11:39,192,752
INFO	2016-05-16 18:42:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 18:42:06	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:20s.  Time for last 1,000,000:    4s.  Last read position: chr11:87,091,127
INFO	2016-05-16 18:42:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 18:42:10	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:23s.  Time for last 1,000,000:    3s.  Last read position: chr12:6,308,765
INFO	2016-05-16 18:42:10	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-05-16 18:42:14	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:28s.  Time for last 1,000,000:    4s.  Last read position: chr12:64,832,635
INFO	2016-05-16 18:42:14	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 18:42:18	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:32s.  Time for last 1,000,000:    3s.  Last read position: chr12:124,790,310
INFO	2016-05-16 18:42:18	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-05-16 18:42:22	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:36s.  Time for last 1,000,000:    4s.  Last read position: chr13:78,052,414
INFO	2016-05-16 18:42:22	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-16 18:42:26	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:40s.  Time for last 1,000,000:    3s.  Last read position: chr14:45,458,565
INFO	2016-05-16 18:42:26	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 18:42:31	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:45s.  Time for last 1,000,000:    5s.  Last read position: chr14:101,288,904
INFO	2016-05-16 18:42:31	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 18:42:35	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:49s.  Time for last 1,000,000:    3s.  Last read position: chr15:73,321,241
INFO	2016-05-16 18:42:35	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 18:42:39	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:00:53s.  Time for last 1,000,000:    3s.  Last read position: chr16:23,312,045
INFO	2016-05-16 18:42:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 18:42:44	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:00:58s.  Time for last 1,000,000:    5s.  Last read position: chr16:86,039,278
INFO	2016-05-16 18:42:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 18:42:48	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:02s.  Time for last 1,000,000:    3s.  Last read position: chr17:42,388,139
INFO	2016-05-16 18:42:48	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-16 18:43:03	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:17s.  Time for last 1,000,000:   14s.  Last read position: chr18:6,930,569
INFO	2016-05-16 18:43:03	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 18:43:08	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:22s.  Time for last 1,000,000:    4s.  Last read position: chr18:72,722,570
INFO	2016-05-16 18:43:08	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 18:43:11	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:01:25s.  Time for last 1,000,000:    3s.  Last read position: chr19:37,178,351
INFO	2016-05-16 18:43:11	MarkDuplicates	Tracking 12 as yet unmatched pairs. 12 records in RAM.
INFO	2016-05-16 18:43:15	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:01:29s.  Time for last 1,000,000:    3s.  Last read position: chr1:569,914
INFO	2016-05-16 18:43:15	MarkDuplicates	Tracking 16608 as yet unmatched pairs. 16608 records in RAM.
INFO	2016-05-16 18:43:18	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:01:32s.  Time for last 1,000,000:    3s.  Last read position: chr1:36,004,946
INFO	2016-05-16 18:43:18	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 18:43:23	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:01:37s.  Time for last 1,000,000:    4s.  Last read position: chr1:91,852,955
INFO	2016-05-16 18:43:23	MarkDuplicates	Tracking 1460 as yet unmatched pairs. 1460 records in RAM.
INFO	2016-05-16 18:43:27	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:01:41s.  Time for last 1,000,000:    3s.  Last read position: chr1:170,101,971
INFO	2016-05-16 18:43:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 18:43:31	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:01:45s.  Time for last 1,000,000:    3s.  Last read position: chr1:227,587,889
INFO	2016-05-16 18:43:31	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-16 18:43:36	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:01:50s.  Time for last 1,000,000:    5s.  Last read position: chr20:34,042,589
INFO	2016-05-16 18:43:36	MarkDuplicates	Tracking 12 as yet unmatched pairs. 12 records in RAM.
INFO	2016-05-16 18:43:40	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:01:54s.  Time for last 1,000,000:    3s.  Last read position: chr21:35,173,970
INFO	2016-05-16 18:43:40	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 18:43:44	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:01:58s.  Time for last 1,000,000:    3s.  Last read position: chr22:48,972,594
INFO	2016-05-16 18:43:44	MarkDuplicates	Tracking 12 as yet unmatched pairs. 12 records in RAM.
INFO	2016-05-16 18:43:48	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:02:02s.  Time for last 1,000,000:    3s.  Last read position: chr2:51,625,313
INFO	2016-05-16 18:43:48	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 18:43:54	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:02:08s.  Time for last 1,000,000:    6s.  Last read position: chr2:118,944,031
INFO	2016-05-16 18:43:54	MarkDuplicates	Tracking 12 as yet unmatched pairs. 12 records in RAM.
INFO	2016-05-16 18:43:58	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:02:12s.  Time for last 1,000,000:    3s.  Last read position: chr2:181,645,905
INFO	2016-05-16 18:43:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 18:44:02	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:02:16s.  Time for last 1,000,000:    3s.  Last read position: chr2:240,319,965
INFO	2016-05-16 18:44:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 18:44:14	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:02:28s.  Time for last 1,000,000:   12s.  Last read position: chr3:49,843,879
INFO	2016-05-16 18:44:14	MarkDuplicates	Tracking 16 as yet unmatched pairs. 16 records in RAM.
INFO	2016-05-16 18:44:18	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:02:32s.  Time for last 1,000,000:    3s.  Last read position: chr3:118,457,972
INFO	2016-05-16 18:44:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 18:44:22	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:02:36s.  Time for last 1,000,000:    4s.  Last read position: chr3:179,145,102
INFO	2016-05-16 18:44:22	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 18:44:26	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:02:40s.  Time for last 1,000,000:    3s.  Last read position: chr4:35,627,899
INFO	2016-05-16 18:44:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 18:44:30	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:02:44s.  Time for last 1,000,000:    3s.  Last read position: chr4:104,707,794
INFO	2016-05-16 18:44:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 18:44:33	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:02:47s.  Time for last 1,000,000:    3s.  Last read position: chr4:173,986,947
INFO	2016-05-16 18:44:33	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 18:44:37	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:02:51s.  Time for last 1,000,000:    3s.  Last read position: chr5:50,720,214
INFO	2016-05-16 18:44:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 18:44:42	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:02:56s.  Time for last 1,000,000:    5s.  Last read position: chr5:117,295,903
INFO	2016-05-16 18:44:42	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 18:44:45	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:02:59s.  Time for last 1,000,000:    3s.  Last read position: chr5:142,259,145
INFO	2016-05-16 18:44:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 18:44:49	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:03:03s.  Time for last 1,000,000:    3s.  Last read position: chr6:16,333,012
INFO	2016-05-16 18:44:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 18:44:53	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:03:07s.  Time for last 1,000,000:    3s.  Last read position: chr6:77,584,470
INFO	2016-05-16 18:44:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 18:44:56	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:03:10s.  Time for last 1,000,000:    3s.  Last read position: chr6:141,339,636
INFO	2016-05-16 18:44:56	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 18:45:02	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:03:16s.  Time for last 1,000,000:    5s.  Last read position: chr7:25,165,063
INFO	2016-05-16 18:45:02	MarkDuplicates	Tracking 44 as yet unmatched pairs. 44 records in RAM.
INFO	2016-05-16 18:45:06	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:03:20s.  Time for last 1,000,000:    3s.  Last read position: chr7:90,893,507
INFO	2016-05-16 18:45:06	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-05-16 18:45:09	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:03:23s.  Time for last 1,000,000:    3s.  Last read position: chr7:147,418,833
INFO	2016-05-16 18:45:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 18:45:17	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:03:31s.  Time for last 1,000,000:    7s.  Last read position: chr8:49,274,376
INFO	2016-05-16 18:45:17	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 18:45:20	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:03:34s.  Time for last 1,000,000:    3s.  Last read position: chr8:109,818,145
INFO	2016-05-16 18:45:20	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 18:45:24	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:03:38s.  Time for last 1,000,000:    3s.  Last read position: chr9:21,557,327
INFO	2016-05-16 18:45:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 18:45:29	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:03:43s.  Time for last 1,000,000:    5s.  Last read position: chr9:110,744,448
INFO	2016-05-16 18:45:29	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 18:45:32	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:03:46s.  Time for last 1,000,000:    3s.  Last read position: chrM:19
INFO	2016-05-16 18:45:32	MarkDuplicates	Tracking 51818 as yet unmatched pairs. 51818 records in RAM.
INFO	2016-05-16 18:45:36	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:03:50s.  Time for last 1,000,000:    3s.  Last read position: chrM:122
INFO	2016-05-16 18:45:36	MarkDuplicates	Tracking 126448 as yet unmatched pairs. 126448 records in RAM.
INFO	2016-05-16 18:45:40	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:03:54s.  Time for last 1,000,000:    3s.  Last read position: chrM:266
INFO	2016-05-16 18:45:40	MarkDuplicates	Tracking 19932 as yet unmatched pairs. 19932 records in RAM.
INFO	2016-05-16 18:45:43	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:03:57s.  Time for last 1,000,000:    3s.  Last read position: chrM:421
INFO	2016-05-16 18:45:43	MarkDuplicates	Tracking 76558 as yet unmatched pairs. 76558 records in RAM.
INFO	2016-05-16 18:45:50	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:04:04s.  Time for last 1,000,000:    6s.  Last read position: chrM:506
INFO	2016-05-16 18:45:50	MarkDuplicates	Tracking 34786 as yet unmatched pairs. 34786 records in RAM.
INFO	2016-05-16 18:45:53	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:04:07s.  Time for last 1,000,000:    3s.  Last read position: chrM:621
INFO	2016-05-16 18:45:53	MarkDuplicates	Tracking 92732 as yet unmatched pairs. 92732 records in RAM.
INFO	2016-05-16 18:45:57	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:04:11s.  Time for last 1,000,000:    3s.  Last read position: chrM:728
INFO	2016-05-16 18:45:57	MarkDuplicates	Tracking 117038 as yet unmatched pairs. 117038 records in RAM.
INFO	2016-05-16 18:46:01	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:04:15s.  Time for last 1,000,000:    3s.  Last read position: chrM:806
INFO	2016-05-16 18:46:01	MarkDuplicates	Tracking 76800 as yet unmatched pairs. 76800 records in RAM.
INFO	2016-05-16 18:46:04	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:04:18s.  Time for last 1,000,000:    3s.  Last read position: chrM:935
INFO	2016-05-16 18:46:04	MarkDuplicates	Tracking 145056 as yet unmatched pairs. 145056 records in RAM.
INFO	2016-05-16 18:46:08	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:04:22s.  Time for last 1,000,000:    3s.  Last read position: chrM:1,244
INFO	2016-05-16 18:46:08	MarkDuplicates	Tracking 122062 as yet unmatched pairs. 122062 records in RAM.
INFO	2016-05-16 18:46:19	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:04:33s.  Time for last 1,000,000:   11s.  Last read position: chrM:1,342
INFO	2016-05-16 18:46:19	MarkDuplicates	Tracking 278588 as yet unmatched pairs. 278588 records in RAM.
INFO	2016-05-16 18:46:29	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:04:43s.  Time for last 1,000,000:    9s.  Last read position: chrM:1,474
INFO	2016-05-16 18:46:29	MarkDuplicates	Tracking 99380 as yet unmatched pairs. 99380 records in RAM.
INFO	2016-05-16 18:46:33	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:04:47s.  Time for last 1,000,000:    3s.  Last read position: chrM:1,601
INFO	2016-05-16 18:46:33	MarkDuplicates	Tracking 149618 as yet unmatched pairs. 149618 records in RAM.
INFO	2016-05-16 18:46:36	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:04:50s.  Time for last 1,000,000:    3s.  Last read position: chrM:1,728
INFO	2016-05-16 18:46:36	MarkDuplicates	Tracking 35912 as yet unmatched pairs. 35912 records in RAM.
INFO	2016-05-16 18:46:40	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:04:54s.  Time for last 1,000,000:    3s.  Last read position: chrM:1,950
INFO	2016-05-16 18:46:40	MarkDuplicates	Tracking 89994 as yet unmatched pairs. 89994 records in RAM.
INFO	2016-05-16 18:46:43	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:04:57s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,109
INFO	2016-05-16 18:46:43	MarkDuplicates	Tracking 113002 as yet unmatched pairs. 113002 records in RAM.
INFO	2016-05-16 18:46:47	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:05:01s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,253
INFO	2016-05-16 18:46:47	MarkDuplicates	Tracking 85488 as yet unmatched pairs. 85488 records in RAM.
INFO	2016-05-16 18:46:53	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:05:07s.  Time for last 1,000,000:    5s.  Last read position: chrM:2,525
INFO	2016-05-16 18:46:53	MarkDuplicates	Tracking 55432 as yet unmatched pairs. 55432 records in RAM.
INFO	2016-05-16 18:46:56	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:05:10s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,600
INFO	2016-05-16 18:46:56	MarkDuplicates	Tracking 154564 as yet unmatched pairs. 154564 records in RAM.
INFO	2016-05-16 18:47:00	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:05:14s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,684
INFO	2016-05-16 18:47:00	MarkDuplicates	Tracking 251152 as yet unmatched pairs. 251152 records in RAM.
INFO	2016-05-16 18:47:04	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:05:18s.  Time for last 1,000,000:    4s.  Last read position: chrM:2,760
INFO	2016-05-16 18:47:04	MarkDuplicates	Tracking 443520 as yet unmatched pairs. 443520 records in RAM.
INFO	2016-05-16 18:47:08	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:05:22s.  Time for last 1,000,000:    4s.  Last read position: chrM:2,834
INFO	2016-05-16 18:47:08	MarkDuplicates	Tracking 166578 as yet unmatched pairs. 166578 records in RAM.
INFO	2016-05-16 18:47:15	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:05:29s.  Time for last 1,000,000:    6s.  Last read position: chrM:2,884
INFO	2016-05-16 18:47:15	MarkDuplicates	Tracking 277906 as yet unmatched pairs. 277906 records in RAM.
INFO	2016-05-16 18:47:19	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:05:33s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,991
INFO	2016-05-16 18:47:19	MarkDuplicates	Tracking 187966 as yet unmatched pairs. 187966 records in RAM.
INFO	2016-05-16 18:47:23	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:05:37s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,073
INFO	2016-05-16 18:47:23	MarkDuplicates	Tracking 229578 as yet unmatched pairs. 229578 records in RAM.
INFO	2016-05-16 18:47:31	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:05:45s.  Time for last 1,000,000:    8s.  Last read position: chrM:3,149
INFO	2016-05-16 18:47:31	MarkDuplicates	Tracking 126858 as yet unmatched pairs. 126858 records in RAM.
INFO	2016-05-16 18:47:34	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:05:48s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,243
INFO	2016-05-16 18:47:34	MarkDuplicates	Tracking 352520 as yet unmatched pairs. 352520 records in RAM.
INFO	2016-05-16 18:47:38	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:05:52s.  Time for last 1,000,000:    4s.  Last read position: chrM:3,321
INFO	2016-05-16 18:47:38	MarkDuplicates	Tracking 303578 as yet unmatched pairs. 303578 records in RAM.
INFO	2016-05-16 18:47:42	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:05:56s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,363
INFO	2016-05-16 18:47:42	MarkDuplicates	Tracking 350344 as yet unmatched pairs. 350344 records in RAM.
INFO	2016-05-16 18:47:49	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:06:03s.  Time for last 1,000,000:    6s.  Last read position: chrM:3,415
INFO	2016-05-16 18:47:49	MarkDuplicates	Tracking 217312 as yet unmatched pairs. 217312 records in RAM.
INFO	2016-05-16 18:47:52	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:06:06s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,463
INFO	2016-05-16 18:47:52	MarkDuplicates	Tracking 116254 as yet unmatched pairs. 116254 records in RAM.
INFO	2016-05-16 18:47:56	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:06:10s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,574
INFO	2016-05-16 18:47:56	MarkDuplicates	Tracking 51018 as yet unmatched pairs. 51018 records in RAM.
INFO	2016-05-16 18:47:59	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:06:13s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,630
INFO	2016-05-16 18:47:59	MarkDuplicates	Tracking 198432 as yet unmatched pairs. 198432 records in RAM.
INFO	2016-05-16 18:48:03	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:06:17s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,679
INFO	2016-05-16 18:48:03	MarkDuplicates	Tracking 274198 as yet unmatched pairs. 274198 records in RAM.
INFO	2016-05-16 18:48:07	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:06:21s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,732
INFO	2016-05-16 18:48:07	MarkDuplicates	Tracking 247156 as yet unmatched pairs. 247156 records in RAM.
INFO	2016-05-16 18:48:10	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:06:24s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,808
INFO	2016-05-16 18:48:10	MarkDuplicates	Tracking 237654 as yet unmatched pairs. 237654 records in RAM.
INFO	2016-05-16 18:48:18	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:06:32s.  Time for last 1,000,000:    7s.  Last read position: chrM:3,875
INFO	2016-05-16 18:48:18	MarkDuplicates	Tracking 287772 as yet unmatched pairs. 287772 records in RAM.
INFO	2016-05-16 18:48:22	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:06:36s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,997
INFO	2016-05-16 18:48:22	MarkDuplicates	Tracking 79882 as yet unmatched pairs. 79882 records in RAM.
INFO	2016-05-16 18:48:25	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:06:39s.  Time for last 1,000,000:    3s.  Last read position: chrM:4,245
INFO	2016-05-16 18:48:25	MarkDuplicates	Tracking 104094 as yet unmatched pairs. 104094 records in RAM.
INFO	2016-05-16 18:48:29	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:06:43s.  Time for last 1,000,000:    3s.  Last read position: chrM:4,670
INFO	2016-05-16 18:48:29	MarkDuplicates	Tracking 12576 as yet unmatched pairs. 12576 records in RAM.
INFO	2016-05-16 18:48:45	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:06:59s.  Time for last 1,000,000:   15s.  Last read position: chrM:4,885
INFO	2016-05-16 18:48:45	MarkDuplicates	Tracking 96476 as yet unmatched pairs. 96476 records in RAM.
INFO	2016-05-16 18:48:49	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:07:03s.  Time for last 1,000,000:    3s.  Last read position: chrM:4,963
INFO	2016-05-16 18:48:49	MarkDuplicates	Tracking 144888 as yet unmatched pairs. 144888 records in RAM.
INFO	2016-05-16 18:48:53	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:07:07s.  Time for last 1,000,000:    3s.  Last read position: chrM:5,114
INFO	2016-05-16 18:48:53	MarkDuplicates	Tracking 46680 as yet unmatched pairs. 46680 records in RAM.
INFO	2016-05-16 18:48:57	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:07:11s.  Time for last 1,000,000:    4s.  Last read position: chrM:5,353
INFO	2016-05-16 18:48:57	MarkDuplicates	Tracking 95746 as yet unmatched pairs. 95746 records in RAM.
INFO	2016-05-16 18:49:00	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:07:14s.  Time for last 1,000,000:    3s.  Last read position: chrM:5,471
INFO	2016-05-16 18:49:00	MarkDuplicates	Tracking 73850 as yet unmatched pairs. 73850 records in RAM.
INFO	2016-05-16 18:49:06	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:07:20s.  Time for last 1,000,000:    5s.  Last read position: chrM:5,986
INFO	2016-05-16 18:49:06	MarkDuplicates	Tracking 50676 as yet unmatched pairs. 50676 records in RAM.
INFO	2016-05-16 18:49:10	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:07:24s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,200
INFO	2016-05-16 18:49:10	MarkDuplicates	Tracking 131118 as yet unmatched pairs. 131118 records in RAM.
INFO	2016-05-16 18:49:14	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:07:28s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,253
INFO	2016-05-16 18:49:14	MarkDuplicates	Tracking 133516 as yet unmatched pairs. 133516 records in RAM.
INFO	2016-05-16 18:49:18	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:07:31s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,330
INFO	2016-05-16 18:49:18	MarkDuplicates	Tracking 141528 as yet unmatched pairs. 141528 records in RAM.
INFO	2016-05-16 18:49:21	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:07:35s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,427
INFO	2016-05-16 18:49:21	MarkDuplicates	Tracking 107762 as yet unmatched pairs. 107762 records in RAM.
INFO	2016-05-16 18:49:25	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:07:39s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,491
INFO	2016-05-16 18:49:25	MarkDuplicates	Tracking 88388 as yet unmatched pairs. 88388 records in RAM.
INFO	2016-05-16 18:49:29	MarkDuplicates	Read   100,000,000 records.  Elapsed time: 00:07:43s.  Time for last 1,000,000:    4s.  Last read position: chrM:6,589
INFO	2016-05-16 18:49:29	MarkDuplicates	Tracking 128508 as yet unmatched pairs. 128508 records in RAM.
INFO	2016-05-16 18:49:33	MarkDuplicates	Read   101,000,000 records.  Elapsed time: 00:07:47s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,791
INFO	2016-05-16 18:49:33	MarkDuplicates	Tracking 24950 as yet unmatched pairs. 24950 records in RAM.
INFO	2016-05-16 18:49:37	MarkDuplicates	Read   102,000,000 records.  Elapsed time: 00:07:51s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,988
INFO	2016-05-16 18:49:37	MarkDuplicates	Tracking 68352 as yet unmatched pairs. 68352 records in RAM.
INFO	2016-05-16 18:49:47	MarkDuplicates	Read   103,000,000 records.  Elapsed time: 00:08:01s.  Time for last 1,000,000:   10s.  Last read position: chrM:7,191
INFO	2016-05-16 18:49:47	MarkDuplicates	Tracking 41376 as yet unmatched pairs. 41376 records in RAM.
INFO	2016-05-16 18:49:51	MarkDuplicates	Read   104,000,000 records.  Elapsed time: 00:08:05s.  Time for last 1,000,000:    3s.  Last read position: chrM:7,487
INFO	2016-05-16 18:49:51	MarkDuplicates	Tracking 50064 as yet unmatched pairs. 50064 records in RAM.
INFO	2016-05-16 18:49:54	MarkDuplicates	Read   105,000,000 records.  Elapsed time: 00:08:08s.  Time for last 1,000,000:    3s.  Last read position: chrM:7,731
INFO	2016-05-16 18:49:54	MarkDuplicates	Tracking 48094 as yet unmatched pairs. 48094 records in RAM.
INFO	2016-05-16 18:49:57	MarkDuplicates	Read   106,000,000 records.  Elapsed time: 00:08:11s.  Time for last 1,000,000:    3s.  Last read position: chrM:7,853
INFO	2016-05-16 18:49:57	MarkDuplicates	Tracking 103082 as yet unmatched pairs. 103082 records in RAM.
INFO	2016-05-16 18:50:01	MarkDuplicates	Read   107,000,000 records.  Elapsed time: 00:08:15s.  Time for last 1,000,000:    3s.  Last read position: chrM:7,998
INFO	2016-05-16 18:50:01	MarkDuplicates	Tracking 104448 as yet unmatched pairs. 104448 records in RAM.
INFO	2016-05-16 18:50:04	MarkDuplicates	Read   108,000,000 records.  Elapsed time: 00:08:18s.  Time for last 1,000,000:    3s.  Last read position: chrM:8,142
INFO	2016-05-16 18:50:04	MarkDuplicates	Tracking 72264 as yet unmatched pairs. 72264 records in RAM.
INFO	2016-05-16 18:50:07	MarkDuplicates	Read   109,000,000 records.  Elapsed time: 00:08:21s.  Time for last 1,000,000:    3s.  Last read position: chrM:8,402
INFO	2016-05-16 18:50:07	MarkDuplicates	Tracking 54792 as yet unmatched pairs. 54792 records in RAM.
INFO	2016-05-16 18:50:11	MarkDuplicates	Read   110,000,000 records.  Elapsed time: 00:08:24s.  Time for last 1,000,000:    3s.  Last read position: chrM:8,613
INFO	2016-05-16 18:50:11	MarkDuplicates	Tracking 31842 as yet unmatched pairs. 31842 records in RAM.
INFO	2016-05-16 18:50:14	MarkDuplicates	Read   111,000,000 records.  Elapsed time: 00:08:28s.  Time for last 1,000,000:    3s.  Last read position: chrM:9,046
INFO	2016-05-16 18:50:14	MarkDuplicates	Tracking 22186 as yet unmatched pairs. 22186 records in RAM.
INFO	2016-05-16 18:50:17	MarkDuplicates	Read   112,000,000 records.  Elapsed time: 00:08:31s.  Time for last 1,000,000:    3s.  Last read position: chrM:9,214
INFO	2016-05-16 18:50:17	MarkDuplicates	Tracking 89662 as yet unmatched pairs. 89662 records in RAM.
INFO	2016-05-16 18:50:23	MarkDuplicates	Read   113,000,000 records.  Elapsed time: 00:08:37s.  Time for last 1,000,000:    6s.  Last read position: chrM:9,290
INFO	2016-05-16 18:50:23	MarkDuplicates	Tracking 90966 as yet unmatched pairs. 90966 records in RAM.
INFO	2016-05-16 18:50:26	MarkDuplicates	Read   114,000,000 records.  Elapsed time: 00:08:40s.  Time for last 1,000,000:    3s.  Last read position: chrM:9,583
INFO	2016-05-16 18:50:26	MarkDuplicates	Tracking 32944 as yet unmatched pairs. 32944 records in RAM.
INFO	2016-05-16 18:50:30	MarkDuplicates	Read   115,000,000 records.  Elapsed time: 00:08:44s.  Time for last 1,000,000:    3s.  Last read position: chrM:9,732
INFO	2016-05-16 18:50:30	MarkDuplicates	Tracking 239980 as yet unmatched pairs. 239980 records in RAM.
INFO	2016-05-16 18:50:33	MarkDuplicates	Read   116,000,000 records.  Elapsed time: 00:08:47s.  Time for last 1,000,000:    3s.  Last read position: chrM:9,813
INFO	2016-05-16 18:50:33	MarkDuplicates	Tracking 222242 as yet unmatched pairs. 222242 records in RAM.
INFO	2016-05-16 18:50:37	MarkDuplicates	Read   117,000,000 records.  Elapsed time: 00:08:51s.  Time for last 1,000,000:    3s.  Last read position: chrM:9,907
INFO	2016-05-16 18:50:37	MarkDuplicates	Tracking 191448 as yet unmatched pairs. 191448 records in RAM.
INFO	2016-05-16 18:50:52	MarkDuplicates	Read   118,000,000 records.  Elapsed time: 00:09:06s.  Time for last 1,000,000:   15s.  Last read position: chrM:10,026
INFO	2016-05-16 18:50:52	MarkDuplicates	Tracking 316342 as yet unmatched pairs. 316342 records in RAM.
INFO	2016-05-16 18:50:56	MarkDuplicates	Read   119,000,000 records.  Elapsed time: 00:09:10s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,140
INFO	2016-05-16 18:50:56	MarkDuplicates	Tracking 84822 as yet unmatched pairs. 84822 records in RAM.
INFO	2016-05-16 18:50:59	MarkDuplicates	Read   120,000,000 records.  Elapsed time: 00:09:13s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,245
INFO	2016-05-16 18:50:59	MarkDuplicates	Tracking 119318 as yet unmatched pairs. 119318 records in RAM.
INFO	2016-05-16 18:51:03	MarkDuplicates	Read   121,000,000 records.  Elapsed time: 00:09:17s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,341
INFO	2016-05-16 18:51:03	MarkDuplicates	Tracking 77232 as yet unmatched pairs. 77232 records in RAM.
INFO	2016-05-16 18:51:06	MarkDuplicates	Read   122,000,000 records.  Elapsed time: 00:09:20s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,503
INFO	2016-05-16 18:51:06	MarkDuplicates	Tracking 23976 as yet unmatched pairs. 23976 records in RAM.
INFO	2016-05-16 18:51:11	MarkDuplicates	Read   123,000,000 records.  Elapsed time: 00:09:25s.  Time for last 1,000,000:    4s.  Last read position: chrM:10,621
INFO	2016-05-16 18:51:11	MarkDuplicates	Tracking 188276 as yet unmatched pairs. 188276 records in RAM.
INFO	2016-05-16 18:51:14	MarkDuplicates	Read   124,000,000 records.  Elapsed time: 00:09:28s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,673
INFO	2016-05-16 18:51:14	MarkDuplicates	Tracking 63434 as yet unmatched pairs. 63434 records in RAM.
INFO	2016-05-16 18:51:18	MarkDuplicates	Read   125,000,000 records.  Elapsed time: 00:09:32s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,887
INFO	2016-05-16 18:51:18	MarkDuplicates	Tracking 7040 as yet unmatched pairs. 7040 records in RAM.
INFO	2016-05-16 18:51:21	MarkDuplicates	Read   126,000,000 records.  Elapsed time: 00:09:35s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,139
INFO	2016-05-16 18:51:21	MarkDuplicates	Tracking 131732 as yet unmatched pairs. 131732 records in RAM.
INFO	2016-05-16 18:51:24	MarkDuplicates	Read   127,000,000 records.  Elapsed time: 00:09:38s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,218
INFO	2016-05-16 18:51:24	MarkDuplicates	Tracking 104886 as yet unmatched pairs. 104886 records in RAM.
INFO	2016-05-16 18:51:27	MarkDuplicates	Read   128,000,000 records.  Elapsed time: 00:09:41s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,323
INFO	2016-05-16 18:51:27	MarkDuplicates	Tracking 101054 as yet unmatched pairs. 101054 records in RAM.
INFO	2016-05-16 18:51:31	MarkDuplicates	Read   129,000,000 records.  Elapsed time: 00:09:45s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,485
INFO	2016-05-16 18:51:31	MarkDuplicates	Tracking 51764 as yet unmatched pairs. 51764 records in RAM.
INFO	2016-05-16 18:51:35	MarkDuplicates	Read   130,000,000 records.  Elapsed time: 00:09:49s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,571
INFO	2016-05-16 18:51:35	MarkDuplicates	Tracking 93640 as yet unmatched pairs. 93640 records in RAM.
INFO	2016-05-16 18:51:38	MarkDuplicates	Read   131,000,000 records.  Elapsed time: 00:09:52s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,771
INFO	2016-05-16 18:51:38	MarkDuplicates	Tracking 77586 as yet unmatched pairs. 77586 records in RAM.
INFO	2016-05-16 18:51:41	MarkDuplicates	Read   132,000,000 records.  Elapsed time: 00:09:55s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,931
INFO	2016-05-16 18:51:41	MarkDuplicates	Tracking 22452 as yet unmatched pairs. 22452 records in RAM.
INFO	2016-05-16 18:51:48	MarkDuplicates	Read   133,000,000 records.  Elapsed time: 00:10:02s.  Time for last 1,000,000:    7s.  Last read position: chrM:12,021
INFO	2016-05-16 18:51:48	MarkDuplicates	Tracking 74160 as yet unmatched pairs. 74160 records in RAM.
INFO	2016-05-16 18:51:53	MarkDuplicates	Read   134,000,000 records.  Elapsed time: 00:10:07s.  Time for last 1,000,000:    4s.  Last read position: chrM:12,139
INFO	2016-05-16 18:51:53	MarkDuplicates	Tracking 110920 as yet unmatched pairs. 110920 records in RAM.
INFO	2016-05-16 18:51:57	MarkDuplicates	Read   135,000,000 records.  Elapsed time: 00:10:11s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,347
INFO	2016-05-16 18:51:57	MarkDuplicates	Tracking 25060 as yet unmatched pairs. 25060 records in RAM.
INFO	2016-05-16 18:52:00	MarkDuplicates	Read   136,000,000 records.  Elapsed time: 00:10:14s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,465
INFO	2016-05-16 18:52:00	MarkDuplicates	Tracking 116620 as yet unmatched pairs. 116620 records in RAM.
INFO	2016-05-16 18:52:04	MarkDuplicates	Read   137,000,000 records.  Elapsed time: 00:10:18s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,549
INFO	2016-05-16 18:52:04	MarkDuplicates	Tracking 168524 as yet unmatched pairs. 168524 records in RAM.
INFO	2016-05-16 18:52:07	MarkDuplicates	Read   138,000,000 records.  Elapsed time: 00:10:21s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,615
INFO	2016-05-16 18:52:07	MarkDuplicates	Tracking 216066 as yet unmatched pairs. 216066 records in RAM.
INFO	2016-05-16 18:52:11	MarkDuplicates	Read   139,000,000 records.  Elapsed time: 00:10:25s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,705
INFO	2016-05-16 18:52:11	MarkDuplicates	Tracking 149784 as yet unmatched pairs. 149784 records in RAM.
INFO	2016-05-16 18:52:14	MarkDuplicates	Read   140,000,000 records.  Elapsed time: 00:10:28s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,864
INFO	2016-05-16 18:52:14	MarkDuplicates	Tracking 29900 as yet unmatched pairs. 29900 records in RAM.
INFO	2016-05-16 18:52:18	MarkDuplicates	Read   141,000,000 records.  Elapsed time: 00:10:32s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,011
INFO	2016-05-16 18:52:18	MarkDuplicates	Tracking 15068 as yet unmatched pairs. 15068 records in RAM.
INFO	2016-05-16 18:52:21	MarkDuplicates	Read   142,000,000 records.  Elapsed time: 00:10:35s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,099
INFO	2016-05-16 18:52:21	MarkDuplicates	Tracking 138558 as yet unmatched pairs. 138558 records in RAM.
INFO	2016-05-16 18:52:25	MarkDuplicates	Read   143,000,000 records.  Elapsed time: 00:10:38s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,179
INFO	2016-05-16 18:52:25	MarkDuplicates	Tracking 169240 as yet unmatched pairs. 169240 records in RAM.
INFO	2016-05-16 18:52:32	MarkDuplicates	Read   144,000,000 records.  Elapsed time: 00:10:46s.  Time for last 1,000,000:    7s.  Last read position: chrM:13,270
INFO	2016-05-16 18:52:32	MarkDuplicates	Tracking 112190 as yet unmatched pairs. 112190 records in RAM.
INFO	2016-05-16 18:52:35	MarkDuplicates	Read   145,000,000 records.  Elapsed time: 00:10:49s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,368
INFO	2016-05-16 18:52:35	MarkDuplicates	Tracking 148274 as yet unmatched pairs. 148274 records in RAM.
INFO	2016-05-16 18:52:38	MarkDuplicates	Read   146,000,000 records.  Elapsed time: 00:10:52s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,459
INFO	2016-05-16 18:52:38	MarkDuplicates	Tracking 153034 as yet unmatched pairs. 153034 records in RAM.
INFO	2016-05-16 18:52:53	MarkDuplicates	Read   147,000,000 records.  Elapsed time: 00:11:07s.  Time for last 1,000,000:   15s.  Last read position: chrM:13,564
INFO	2016-05-16 18:52:53	MarkDuplicates	Tracking 93660 as yet unmatched pairs. 93660 records in RAM.
INFO	2016-05-16 18:52:57	MarkDuplicates	Read   148,000,000 records.  Elapsed time: 00:11:11s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,676
INFO	2016-05-16 18:52:57	MarkDuplicates	Tracking 88726 as yet unmatched pairs. 88726 records in RAM.
INFO	2016-05-16 18:53:00	MarkDuplicates	Read   149,000,000 records.  Elapsed time: 00:11:14s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,814
INFO	2016-05-16 18:53:00	MarkDuplicates	Tracking 107138 as yet unmatched pairs. 107138 records in RAM.
INFO	2016-05-16 18:53:04	MarkDuplicates	Read   150,000,000 records.  Elapsed time: 00:11:18s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,918
INFO	2016-05-16 18:53:04	MarkDuplicates	Tracking 99686 as yet unmatched pairs. 99686 records in RAM.
INFO	2016-05-16 18:53:07	MarkDuplicates	Read   151,000,000 records.  Elapsed time: 00:11:21s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,988
INFO	2016-05-16 18:53:07	MarkDuplicates	Tracking 101710 as yet unmatched pairs. 101710 records in RAM.
INFO	2016-05-16 18:53:10	MarkDuplicates	Read   152,000,000 records.  Elapsed time: 00:11:24s.  Time for last 1,000,000:    3s.  Last read position: chrM:14,083
INFO	2016-05-16 18:53:10	MarkDuplicates	Tracking 13964 as yet unmatched pairs. 13964 records in RAM.
INFO	2016-05-16 18:53:14	MarkDuplicates	Read   153,000,000 records.  Elapsed time: 00:11:28s.  Time for last 1,000,000:    3s.  Last read position: chrM:14,302
INFO	2016-05-16 18:53:14	MarkDuplicates	Tracking 45550 as yet unmatched pairs. 45550 records in RAM.
INFO	2016-05-16 18:53:17	MarkDuplicates	Read   154,000,000 records.  Elapsed time: 00:11:31s.  Time for last 1,000,000:    3s.  Last read position: chrM:14,414
INFO	2016-05-16 18:53:17	MarkDuplicates	Tracking 28948 as yet unmatched pairs. 28948 records in RAM.
INFO	2016-05-16 18:53:21	MarkDuplicates	Read   155,000,000 records.  Elapsed time: 00:11:35s.  Time for last 1,000,000:    3s.  Last read position: chrM:14,608
INFO	2016-05-16 18:53:21	MarkDuplicates	Tracking 54308 as yet unmatched pairs. 54308 records in RAM.
INFO	2016-05-16 18:53:26	MarkDuplicates	Read   156,000,000 records.  Elapsed time: 00:11:40s.  Time for last 1,000,000:    5s.  Last read position: chrM:14,826
INFO	2016-05-16 18:53:26	MarkDuplicates	Tracking 43954 as yet unmatched pairs. 43954 records in RAM.
INFO	2016-05-16 18:53:29	MarkDuplicates	Read   157,000,000 records.  Elapsed time: 00:11:43s.  Time for last 1,000,000:    3s.  Last read position: chrM:14,977
INFO	2016-05-16 18:53:29	MarkDuplicates	Tracking 162238 as yet unmatched pairs. 162238 records in RAM.
INFO	2016-05-16 18:53:33	MarkDuplicates	Read   158,000,000 records.  Elapsed time: 00:11:47s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,043
INFO	2016-05-16 18:53:33	MarkDuplicates	Tracking 304582 as yet unmatched pairs. 304582 records in RAM.
INFO	2016-05-16 18:53:36	MarkDuplicates	Read   159,000,000 records.  Elapsed time: 00:11:50s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,097
INFO	2016-05-16 18:53:36	MarkDuplicates	Tracking 202550 as yet unmatched pairs. 202550 records in RAM.
INFO	2016-05-16 18:53:40	MarkDuplicates	Read   160,000,000 records.  Elapsed time: 00:11:54s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,160
INFO	2016-05-16 18:53:40	MarkDuplicates	Tracking 222340 as yet unmatched pairs. 222340 records in RAM.
INFO	2016-05-16 18:53:43	MarkDuplicates	Read   161,000,000 records.  Elapsed time: 00:11:57s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,222
INFO	2016-05-16 18:53:43	MarkDuplicates	Tracking 107908 as yet unmatched pairs. 107908 records in RAM.
INFO	2016-05-16 18:53:51	MarkDuplicates	Read   162,000,000 records.  Elapsed time: 00:12:05s.  Time for last 1,000,000:    7s.  Last read position: chrM:15,307
INFO	2016-05-16 18:53:51	MarkDuplicates	Tracking 86756 as yet unmatched pairs. 86756 records in RAM.
INFO	2016-05-16 18:53:54	MarkDuplicates	Read   163,000,000 records.  Elapsed time: 00:12:08s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,392
INFO	2016-05-16 18:53:54	MarkDuplicates	Tracking 197274 as yet unmatched pairs. 197274 records in RAM.
INFO	2016-05-16 18:53:57	MarkDuplicates	Read   164,000,000 records.  Elapsed time: 00:12:11s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,444
INFO	2016-05-16 18:53:57	MarkDuplicates	Tracking 185138 as yet unmatched pairs. 185138 records in RAM.
INFO	2016-05-16 18:54:01	MarkDuplicates	Read   165,000,000 records.  Elapsed time: 00:12:15s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,512
INFO	2016-05-16 18:54:01	MarkDuplicates	Tracking 155996 as yet unmatched pairs. 155996 records in RAM.
INFO	2016-05-16 18:54:04	MarkDuplicates	Read   166,000,000 records.  Elapsed time: 00:12:18s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,588
INFO	2016-05-16 18:54:04	MarkDuplicates	Tracking 152518 as yet unmatched pairs. 152518 records in RAM.
INFO	2016-05-16 18:54:11	MarkDuplicates	Read   167,000,000 records.  Elapsed time: 00:12:25s.  Time for last 1,000,000:    6s.  Last read position: chrM:15,652
INFO	2016-05-16 18:54:11	MarkDuplicates	Tracking 237900 as yet unmatched pairs. 237900 records in RAM.
INFO	2016-05-16 18:54:14	MarkDuplicates	Read   168,000,000 records.  Elapsed time: 00:12:28s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,717
INFO	2016-05-16 18:54:14	MarkDuplicates	Tracking 218604 as yet unmatched pairs. 218604 records in RAM.
INFO	2016-05-16 18:54:18	MarkDuplicates	Read   169,000,000 records.  Elapsed time: 00:12:32s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,771
INFO	2016-05-16 18:54:18	MarkDuplicates	Tracking 209396 as yet unmatched pairs. 209396 records in RAM.
INFO	2016-05-16 18:54:21	MarkDuplicates	Read   170,000,000 records.  Elapsed time: 00:12:35s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,823
INFO	2016-05-16 18:54:21	MarkDuplicates	Tracking 349994 as yet unmatched pairs. 349994 records in RAM.
INFO	2016-05-16 18:54:25	MarkDuplicates	Read   171,000,000 records.  Elapsed time: 00:12:39s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,903
INFO	2016-05-16 18:54:25	MarkDuplicates	Tracking 310018 as yet unmatched pairs. 310018 records in RAM.
INFO	2016-05-16 18:54:28	MarkDuplicates	Read   172,000,000 records.  Elapsed time: 00:12:42s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,989
INFO	2016-05-16 18:54:28	MarkDuplicates	Tracking 222442 as yet unmatched pairs. 222442 records in RAM.
INFO	2016-05-16 18:54:32	MarkDuplicates	Read   173,000,000 records.  Elapsed time: 00:12:45s.  Time for last 1,000,000:    3s.  Last read position: chrM:16,094
INFO	2016-05-16 18:54:32	MarkDuplicates	Tracking 83942 as yet unmatched pairs. 83942 records in RAM.
INFO	2016-05-16 18:54:35	MarkDuplicates	Read   174,000,000 records.  Elapsed time: 00:12:49s.  Time for last 1,000,000:    3s.  Last read position: chrM:16,273
INFO	2016-05-16 18:54:35	MarkDuplicates	Tracking 116406 as yet unmatched pairs. 116406 records in RAM.
INFO	2016-05-16 18:54:38	MarkDuplicates	Read   175,000,000 records.  Elapsed time: 00:12:52s.  Time for last 1,000,000:    3s.  Last read position: chrM:16,337
INFO	2016-05-16 18:54:38	MarkDuplicates	Tracking 180842 as yet unmatched pairs. 180842 records in RAM.
INFO	2016-05-16 18:54:42	MarkDuplicates	Read   176,000,000 records.  Elapsed time: 00:12:56s.  Time for last 1,000,000:    3s.  Last read position: chrM:16,386
INFO	2016-05-16 18:54:42	MarkDuplicates	Tracking 189210 as yet unmatched pairs. 189210 records in RAM.
INFO	2016-05-16 18:54:58	MarkDuplicates	Read   177,000,000 records.  Elapsed time: 00:13:12s.  Time for last 1,000,000:   15s.  Last read position: chrM:16,439
INFO	2016-05-16 18:54:58	MarkDuplicates	Tracking 176236 as yet unmatched pairs. 176236 records in RAM.
INFO	2016-05-16 18:55:01	MarkDuplicates	Read   178,000,000 records.  Elapsed time: 00:13:15s.  Time for last 1,000,000:    3s.  Last read position: chrM:16,509
INFO	2016-05-16 18:55:01	MarkDuplicates	Tracking 2804 as yet unmatched pairs. 2804 records in RAM.
INFO	2016-05-16 18:55:04	MarkDuplicates	Read   179,000,000 records.  Elapsed time: 00:13:18s.  Time for last 1,000,000:    3s.  Last read position: chrX:62,537,485
INFO	2016-05-16 18:55:04	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 18:55:09	MarkDuplicates	Read   180,000,000 records.  Elapsed time: 00:13:23s.  Time for last 1,000,000:    4s.  Last read position: chrX:133,965,902
INFO	2016-05-16 18:55:09	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 18:55:10	MarkDuplicates	Read 180344434 records. 0 pairs never matched.
INFO	2016-05-16 18:55:12	MarkDuplicates	After buildSortedReadEndLists freeMemory: 3236521480; totalMemory: 3263168512; maxMemory: 3817865216
INFO	2016-05-16 18:55:12	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-05-16 18:55:12	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-05-16 18:57:24	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-05-16 18:58:12	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-05-16 18:58:15	MarkDuplicates	After generateDuplicateIndexes freeMemory: 3286796016; totalMemory: 3315597312; maxMemory: 3817865216
INFO	2016-05-16 18:58:15	MarkDuplicates	Marking 159785066 records as duplicates.
INFO	2016-05-16 18:58:15	MarkDuplicates	Found 55413083 optical duplicate clusters.
INFO	2016-05-16 18:59:43	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:25s.  Time for last 10,000,000:   85s.  Last read position: chr14:101,288,904
INFO	2016-05-16 19:01:12	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:02:54s.  Time for last 10,000,000:   88s.  Last read position: chr1:91,852,955
INFO	2016-05-16 19:02:42	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:04:24s.  Time for last 10,000,000:   90s.  Last read position: chr3:49,843,879
INFO	2016-05-16 19:04:10	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:05:52s.  Time for last 10,000,000:   87s.  Last read position: chr6:77,584,470
INFO	2016-05-16 19:05:38	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:07:20s.  Time for last 10,000,000:   88s.  Last read position: chrM:122
INFO	2016-05-16 19:07:00	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:08:42s.  Time for last 10,000,000:   81s.  Last read position: chrM:1,474
INFO	2016-05-16 19:08:20	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:10:02s.  Time for last 10,000,000:   80s.  Last read position: chrM:2,834
INFO	2016-05-16 19:09:42	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:11:24s.  Time for last 10,000,000:   81s.  Last read position: chrM:3,574

BigDataScript report: atac.bds

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