Script file	/users/pangwei/bds_atac/atac.bds
Program ID	atac.bds.20160513_182615_369
Start time	2016-05-13 18:26:15
Run time	23:58:49.259
Tasks executed	20
Tasks failed	2
Tasks failed names	macs2_atac rep2 macs2_atac rep2.pval0.1
Arguments*	[-out_dir, /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/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	1

Thread ID	Parent	Tasks
thread_Root	None
thread_21	thread_Root	atac.bds.20160513_182615_369_parallel_21/task.align_bowtie2.bowtie2_PE_rep2.line_133.id_7 atac.bds.20160513_182615_369_parallel_21/task.postalign_bam.dedup_bam_PE_rep2.line_215.id_8 atac.bds.20160513_182615_369_parallel_21/task.postalign_bam.nmsrt_bam_rep2.line_321.id_9 atac.bds.20160513_182615_369_parallel_21/task.postalign_bam.bam_to_bedpe_rep2.line_425.id_10 atac.bds.20160513_182615_369_parallel_21/task.postalign_bed.subsample_bedpe_rep2.line_116.id_11 atac.bds.20160513_182615_369_parallel_21/task.postalign_bam.bedpe_to_tag_rep2.line_465.id_12 atac.bds.20160513_182615_369_parallel_21/task.postalign_bed.shift_tag_rep2.line_140.id_13 atac.bds.20160513_182615_369_parallel_21/task.postalign_bed.subsample_bedpe2tagrep2.line_89.id_14 atac.bds.20160513_182615_369_parallel_21/task.postalign_bed.xcor_rep2.line_165.id_15 atac.bds.20160513_182615_369_parallel_21/task.callpeak_macs2.macs2_atac_rep2.pval0.1.line_192.id_16 atac.bds.20160513_182615_369_parallel_21/task.callpeak_macs2.macs2_atac_rep2.line_192.id_17
thread_20	thread_Root	atac.bds.20160513_182615_369_parallel_20/task.align_bowtie2.bowtie2_PE_rep1.line_133.id_6 atac.bds.20160513_182615_369_parallel_20/task.postalign_bam.dedup_bam_PE_rep1.line_215.id_18 atac.bds.20160513_182615_369_parallel_20/task.postalign_bam.nmsrt_bam_rep1.line_321.id_19 atac.bds.20160513_182615_369_parallel_20/task.postalign_bam.bam_to_bedpe_rep1.line_425.id_20 atac.bds.20160513_182615_369_parallel_20/task.postalign_bed.subsample_bedpe_rep1.line_116.id_21 atac.bds.20160513_182615_369_parallel_20/task.postalign_bam.bedpe_to_tag_rep1.line_465.id_22 atac.bds.20160513_182615_369_parallel_20/task.postalign_bed.shift_tag_rep1.line_140.id_23 atac.bds.20160513_182615_369_parallel_20/task.postalign_bed.subsample_bedpe2tagrep1.line_89.id_24 atac.bds.20160513_182615_369_parallel_20/task.postalign_bed.xcor_rep1.line_165.id_25

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	104169

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

Start	2016-05-13 18:26:16
End	2016-05-14 13:33:55
Elapsed	19:07:38
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	104174

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

Start	2016-05-13 18:26:16
End	2016-05-14 04:10:18
Elapsed	09:44:01
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	15852

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

Start	2016-05-14 04:10:19
End	2016-05-14 06:20:45
Elapsed	02:10:25
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.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
[Sat May 14 05:21:54 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
[Sat May 14 05:21:54 PDT 2016] Executing as pangwei@mitra on Linux 3.16.0-70-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_45-b14; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-05-14 05:21:54	MarkDuplicates	Start of doWork freeMemory: 254889800; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-14 05:21:54	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-05-14 05:21:54	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-05-14 05:22:00	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:06s.  Time for last 1,000,000:    6s.  Last read position: chr11:13,299,087
INFO	2016-05-14 05:22:00	MarkDuplicates	Tracking 32 as yet unmatched pairs. 32 records in RAM.
INFO	2016-05-14 05:22:06	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:12s.  Time for last 1,000,000:    6s.  Last read position: chr12:16,257,490
INFO	2016-05-14 05:22:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 05:22:12	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:17s.  Time for last 1,000,000:    5s.  Last read position: chr13:61,954,243
INFO	2016-05-14 05:22:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 05:22:18	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:24s.  Time for last 1,000,000:    6s.  Last read position: chr15:41,057,219
INFO	2016-05-14 05:22:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 05:22:23	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:29s.  Time for last 1,000,000:    5s.  Last read position: chr16:87,886,903
INFO	2016-05-14 05:22:23	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 05:22:30	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:36s.  Time for last 1,000,000:    6s.  Last read position: chr18:52,044,723
INFO	2016-05-14 05:22:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 05:22:36	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:41s.  Time for last 1,000,000:    5s.  Last read position: chr1:4,755,733
INFO	2016-05-14 05:22:36	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 05:22:41	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:46s.  Time for last 1,000,000:    4s.  Last read position: chr1:160,651,456
INFO	2016-05-14 05:22:41	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-14 05:22:46	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:51s.  Time for last 1,000,000:    4s.  Last read position: chr20:58,331,428
INFO	2016-05-14 05:22:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 05:22:51	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:57s.  Time for last 1,000,000:    5s.  Last read position: chr2:55,315,294
INFO	2016-05-14 05:22:51	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 05:22:56	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:02s.  Time for last 1,000,000:    4s.  Last read position: chr2:223,725,733
INFO	2016-05-14 05:22:56	MarkDuplicates	Tracking 32 as yet unmatched pairs. 32 records in RAM.
INFO	2016-05-14 05:23:00	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:06s.  Time for last 1,000,000:    3s.  Last read position: chr3:133,983,856
INFO	2016-05-14 05:23:00	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 05:23:04	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:09s.  Time for last 1,000,000:    3s.  Last read position: chr4:103,749,428
INFO	2016-05-14 05:23:04	MarkDuplicates	Tracking 26 as yet unmatched pairs. 26 records in RAM.
INFO	2016-05-14 05:23:07	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:13s.  Time for last 1,000,000:    3s.  Last read position: chr5:96,614,716
INFO	2016-05-14 05:23:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 05:23:25	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:31s.  Time for last 1,000,000:   17s.  Last read position: chr6:29,039,977
INFO	2016-05-14 05:23:25	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 05:23:29	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:34s.  Time for last 1,000,000:    3s.  Last read position: chr7:13,784,834
INFO	2016-05-14 05:23:29	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 05:23:32	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:01:38s.  Time for last 1,000,000:    3s.  Last read position: chr8:14,567,723
INFO	2016-05-14 05:23:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 05:23:37	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:01:42s.  Time for last 1,000,000:    4s.  Last read position: chr9:28,568,044
INFO	2016-05-14 05:23:37	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 05:23:43	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:01:48s.  Time for last 1,000,000:    5s.  Last read position: chrM:85
INFO	2016-05-14 05:23:43	MarkDuplicates	Tracking 42250 as yet unmatched pairs. 42250 records in RAM.
INFO	2016-05-14 05:23:46	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:01:52s.  Time for last 1,000,000:    3s.  Last read position: chrM:438
INFO	2016-05-14 05:23:46	MarkDuplicates	Tracking 20624 as yet unmatched pairs. 20624 records in RAM.
INFO	2016-05-14 05:23:50	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:01:56s.  Time for last 1,000,000:    3s.  Last read position: chrM:683
INFO	2016-05-14 05:23:50	MarkDuplicates	Tracking 67654 as yet unmatched pairs. 67654 records in RAM.
INFO	2016-05-14 05:23:54	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:01:59s.  Time for last 1,000,000:    3s.  Last read position: chrM:895
INFO	2016-05-14 05:23:54	MarkDuplicates	Tracking 44480 as yet unmatched pairs. 44480 records in RAM.
INFO	2016-05-14 05:24:00	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:02:05s.  Time for last 1,000,000:    5s.  Last read position: chrM:1,341
INFO	2016-05-14 05:24:00	MarkDuplicates	Tracking 114998 as yet unmatched pairs. 114998 records in RAM.
INFO	2016-05-14 05:24:04	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:02:09s.  Time for last 1,000,000:    3s.  Last read position: chrM:1,608
INFO	2016-05-14 05:24:04	MarkDuplicates	Tracking 62290 as yet unmatched pairs. 62290 records in RAM.
INFO	2016-05-14 05:24:07	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:02:13s.  Time for last 1,000,000:    3s.  Last read position: chrM:1,990
INFO	2016-05-14 05:24:07	MarkDuplicates	Tracking 49250 as yet unmatched pairs. 49250 records in RAM.
INFO	2016-05-14 05:24:12	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:02:17s.  Time for last 1,000,000:    4s.  Last read position: chrM:2,369
INFO	2016-05-14 05:24:12	MarkDuplicates	Tracking 13978 as yet unmatched pairs. 13978 records in RAM.
INFO	2016-05-14 05:24:16	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:02:22s.  Time for last 1,000,000:    4s.  Last read position: chrM:2,649
INFO	2016-05-14 05:24:16	MarkDuplicates	Tracking 126518 as yet unmatched pairs. 126518 records in RAM.
INFO	2016-05-14 05:24:25	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:02:31s.  Time for last 1,000,000:    8s.  Last read position: chrM:2,825
INFO	2016-05-14 05:24:25	MarkDuplicates	Tracking 62748 as yet unmatched pairs. 62748 records in RAM.
INFO	2016-05-14 05:24:30	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:02:35s.  Time for last 1,000,000:    4s.  Last read position: chrM:2,998
INFO	2016-05-14 05:24:30	MarkDuplicates	Tracking 98502 as yet unmatched pairs. 98502 records in RAM.
INFO	2016-05-14 05:24:46	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:02:51s.  Time for last 1,000,000:   15s.  Last read position: chrM:3,194
INFO	2016-05-14 05:24:46	MarkDuplicates	Tracking 86904 as yet unmatched pairs. 86904 records in RAM.
INFO	2016-05-14 05:24:50	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:02:56s.  Time for last 1,000,000:    4s.  Last read position: chrM:3,344
INFO	2016-05-14 05:24:50	MarkDuplicates	Tracking 124734 as yet unmatched pairs. 124734 records in RAM.
INFO	2016-05-14 05:24:55	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:03:01s.  Time for last 1,000,000:    5s.  Last read position: chrM:3,450
INFO	2016-05-14 05:24:55	MarkDuplicates	Tracking 61828 as yet unmatched pairs. 61828 records in RAM.
INFO	2016-05-14 05:25:01	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:03:07s.  Time for last 1,000,000:    6s.  Last read position: chrM:3,630
INFO	2016-05-14 05:25:01	MarkDuplicates	Tracking 150526 as yet unmatched pairs. 150526 records in RAM.
INFO	2016-05-14 05:25:06	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:03:11s.  Time for last 1,000,000:    4s.  Last read position: chrM:3,758
INFO	2016-05-14 05:25:06	MarkDuplicates	Tracking 95840 as yet unmatched pairs. 95840 records in RAM.
INFO	2016-05-14 05:25:10	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:03:16s.  Time for last 1,000,000:    4s.  Last read position: chrM:3,903
INFO	2016-05-14 05:25:10	MarkDuplicates	Tracking 141312 as yet unmatched pairs. 141312 records in RAM.
INFO	2016-05-14 05:25:15	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:03:21s.  Time for last 1,000,000:    4s.  Last read position: chrM:4,442
INFO	2016-05-14 05:25:15	MarkDuplicates	Tracking 7196 as yet unmatched pairs. 7196 records in RAM.
INFO	2016-05-14 05:25:19	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:03:25s.  Time for last 1,000,000:    3s.  Last read position: chrM:4,973
INFO	2016-05-14 05:25:19	MarkDuplicates	Tracking 62800 as yet unmatched pairs. 62800 records in RAM.
INFO	2016-05-14 05:25:24	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:03:30s.  Time for last 1,000,000:    5s.  Last read position: chrM:5,386
INFO	2016-05-14 05:25:24	MarkDuplicates	Tracking 38652 as yet unmatched pairs. 38652 records in RAM.
INFO	2016-05-14 05:25:28	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:03:33s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,159
INFO	2016-05-14 05:25:28	MarkDuplicates	Tracking 53028 as yet unmatched pairs. 53028 records in RAM.
INFO	2016-05-14 05:25:31	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:03:36s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,323
INFO	2016-05-14 05:25:31	MarkDuplicates	Tracking 36856 as yet unmatched pairs. 36856 records in RAM.
INFO	2016-05-14 05:25:34	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:03:39s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,495
INFO	2016-05-14 05:25:34	MarkDuplicates	Tracking 37614 as yet unmatched pairs. 37614 records in RAM.
INFO	2016-05-14 05:25:37	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:03:42s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,896
INFO	2016-05-14 05:25:37	MarkDuplicates	Tracking 69798 as yet unmatched pairs. 69798 records in RAM.
INFO	2016-05-14 05:25:40	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:03:45s.  Time for last 1,000,000:    3s.  Last read position: chrM:7,247
INFO	2016-05-14 05:25:40	MarkDuplicates	Tracking 66724 as yet unmatched pairs. 66724 records in RAM.
INFO	2016-05-14 05:25:43	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:03:49s.  Time for last 1,000,000:    3s.  Last read position: chrM:7,836
INFO	2016-05-14 05:25:43	MarkDuplicates	Tracking 55652 as yet unmatched pairs. 55652 records in RAM.
INFO	2016-05-14 05:25:53	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:03:59s.  Time for last 1,000,000:   10s.  Last read position: chrM:8,145
INFO	2016-05-14 05:25:53	MarkDuplicates	Tracking 42088 as yet unmatched pairs. 42088 records in RAM.
INFO	2016-05-14 05:25:56	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:04:02s.  Time for last 1,000,000:    3s.  Last read position: chrM:8,690
INFO	2016-05-14 05:25:56	MarkDuplicates	Tracking 8742 as yet unmatched pairs. 8742 records in RAM.
INFO	2016-05-14 05:25:59	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:04:05s.  Time for last 1,000,000:    3s.  Last read position: chrM:9,257
INFO	2016-05-14 05:25:59	MarkDuplicates	Tracking 56714 as yet unmatched pairs. 56714 records in RAM.
INFO	2016-05-14 05:26:02	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:04:08s.  Time for last 1,000,000:    3s.  Last read position: chrM:9,715
INFO	2016-05-14 05:26:02	MarkDuplicates	Tracking 69368 as yet unmatched pairs. 69368 records in RAM.
INFO	2016-05-14 05:26:06	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:04:11s.  Time for last 1,000,000:    3s.  Last read position: chrM:9,922
INFO	2016-05-14 05:26:06	MarkDuplicates	Tracking 69154 as yet unmatched pairs. 69154 records in RAM.
INFO	2016-05-14 05:26:09	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:04:15s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,206
INFO	2016-05-14 05:26:09	MarkDuplicates	Tracking 81948 as yet unmatched pairs. 81948 records in RAM.
INFO	2016-05-14 05:26:14	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:04:20s.  Time for last 1,000,000:    5s.  Last read position: chrM:10,490
INFO	2016-05-14 05:26:14	MarkDuplicates	Tracking 11110 as yet unmatched pairs. 11110 records in RAM.
INFO	2016-05-14 05:26:17	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:04:23s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,691
INFO	2016-05-14 05:26:17	MarkDuplicates	Tracking 42420 as yet unmatched pairs. 42420 records in RAM.
INFO	2016-05-14 05:26:20	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:04:26s.  Time for last 1,000,000:    2s.  Last read position: chrM:11,177
INFO	2016-05-14 05:26:20	MarkDuplicates	Tracking 42248 as yet unmatched pairs. 42248 records in RAM.
INFO	2016-05-14 05:26:23	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:04:29s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,381
INFO	2016-05-14 05:26:23	MarkDuplicates	Tracking 10882 as yet unmatched pairs. 10882 records in RAM.
INFO	2016-05-14 05:26:26	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:04:32s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,768
INFO	2016-05-14 05:26:26	MarkDuplicates	Tracking 41338 as yet unmatched pairs. 41338 records in RAM.
INFO	2016-05-14 05:26:30	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:04:35s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,024
INFO	2016-05-14 05:26:30	MarkDuplicates	Tracking 37870 as yet unmatched pairs. 37870 records in RAM.
INFO	2016-05-14 05:26:33	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:04:39s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,353
INFO	2016-05-14 05:26:33	MarkDuplicates	Tracking 37896 as yet unmatched pairs. 37896 records in RAM.
INFO	2016-05-14 05:26:37	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:04:43s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,568
INFO	2016-05-14 05:26:37	MarkDuplicates	Tracking 78630 as yet unmatched pairs. 78630 records in RAM.
INFO	2016-05-14 05:26:56	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:05:01s.  Time for last 1,000,000:   18s.  Last read position: chrM:12,764
INFO	2016-05-14 05:26:56	MarkDuplicates	Tracking 28364 as yet unmatched pairs. 28364 records in RAM.
INFO	2016-05-14 05:26:59	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:05:04s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,089
INFO	2016-05-14 05:26:59	MarkDuplicates	Tracking 81704 as yet unmatched pairs. 81704 records in RAM.
INFO	2016-05-14 05:27:02	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:05:08s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,272
INFO	2016-05-14 05:27:02	MarkDuplicates	Tracking 54348 as yet unmatched pairs. 54348 records in RAM.
INFO	2016-05-14 05:27:06	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:05:11s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,473
INFO	2016-05-14 05:27:06	MarkDuplicates	Tracking 77578 as yet unmatched pairs. 77578 records in RAM.
INFO	2016-05-14 05:27:09	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:05:15s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,764
INFO	2016-05-14 05:27:09	MarkDuplicates	Tracking 19060 as yet unmatched pairs. 19060 records in RAM.
INFO	2016-05-14 05:27:13	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:05:18s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,962
INFO	2016-05-14 05:27:13	MarkDuplicates	Tracking 35284 as yet unmatched pairs. 35284 records in RAM.
INFO	2016-05-14 05:27:16	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:05:22s.  Time for last 1,000,000:    3s.  Last read position: chrM:14,306
INFO	2016-05-14 05:27:16	MarkDuplicates	Tracking 18340 as yet unmatched pairs. 18340 records in RAM.
INFO	2016-05-14 05:27:20	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:05:25s.  Time for last 1,000,000:    3s.  Last read position: chrM:14,644
INFO	2016-05-14 05:27:20	MarkDuplicates	Tracking 9594 as yet unmatched pairs. 9594 records in RAM.
INFO	2016-05-14 05:27:25	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:05:30s.  Time for last 1,000,000:    5s.  Last read position: chrM:15,022
INFO	2016-05-14 05:27:25	MarkDuplicates	Tracking 95270 as yet unmatched pairs. 95270 records in RAM.
INFO	2016-05-14 05:27:28	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:05:34s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,145
INFO	2016-05-14 05:27:28	MarkDuplicates	Tracking 113020 as yet unmatched pairs. 113020 records in RAM.
INFO	2016-05-14 05:27:32	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:05:37s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,308
INFO	2016-05-14 05:27:32	MarkDuplicates	Tracking 46402 as yet unmatched pairs. 46402 records in RAM.
INFO	2016-05-14 05:27:35	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:05:41s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,461
INFO	2016-05-14 05:27:35	MarkDuplicates	Tracking 56492 as yet unmatched pairs. 56492 records in RAM.
INFO	2016-05-14 05:27:39	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:05:44s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,625
INFO	2016-05-14 05:27:39	MarkDuplicates	Tracking 85616 as yet unmatched pairs. 85616 records in RAM.
INFO	2016-05-14 05:27:42	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:05:47s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,747
INFO	2016-05-14 05:27:42	MarkDuplicates	Tracking 104894 as yet unmatched pairs. 104894 records in RAM.
INFO	2016-05-14 05:27:46	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:05:51s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,898
INFO	2016-05-14 05:27:46	MarkDuplicates	Tracking 123524 as yet unmatched pairs. 123524 records in RAM.
INFO	2016-05-14 05:27:54	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:06:00s.  Time for last 1,000,000:    8s.  Last read position: chrM:16,230
INFO	2016-05-14 05:27:54	MarkDuplicates	Tracking 25508 as yet unmatched pairs. 25508 records in RAM.
INFO	2016-05-14 05:27:59	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:06:05s.  Time for last 1,000,000:    4s.  Last read position: chrM:16,368
INFO	2016-05-14 05:27:59	MarkDuplicates	Tracking 77740 as yet unmatched pairs. 77740 records in RAM.
INFO	2016-05-14 05:28:03	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:06:08s.  Time for last 1,000,000:    3s.  Last read position: chrM:16,492
INFO	2016-05-14 05:28:03	MarkDuplicates	Tracking 20442 as yet unmatched pairs. 20442 records in RAM.
INFO	2016-05-14 05:28:05	MarkDuplicates	Read 76906720 records. 0 pairs never matched.
INFO	2016-05-14 05:28:11	MarkDuplicates	After buildSortedReadEndLists freeMemory: 2848790512; totalMemory: 2876243968; maxMemory: 3817865216
INFO	2016-05-14 05:28:11	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-05-14 05:28:11	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-05-14 05:28:46	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-05-14 05:29:05	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-05-14 05:29:08	MarkDuplicates	After generateDuplicateIndexes freeMemory: 1938259352; totalMemory: 2919235584; maxMemory: 3817865216
INFO	2016-05-14 05:29:08	MarkDuplicates	Marking 63435090 records as duplicates.
INFO	2016-05-14 05:29:08	MarkDuplicates	Found 21349217 optical duplicate clusters.
INFO	2016-05-14 05:30:39	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	2016-05-14 05:32:10	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:03:00s.  Time for last 10,000,000:   90s.  Last read position: chrM:438
INFO	2016-05-14 05:33:28	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:04:18s.  Time for last 10,000,000:   77s.  Last read position: chrM:3,194
INFO	2016-05-14 05:34:45	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:05:36s.  Time for last 10,000,000:   77s.  Last read position: chrM:6,323
INFO	2016-05-14 05:36:02	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:06:52s.  Time for last 10,000,000:   76s.  Last read position: chrM:10,206
INFO	2016-05-14 05:37:19	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:08:09s.  Time for last 10,000,000:   76s.  Last read position: chrM:13,089
INFO	2016-05-14 05:38:45	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:09:35s.  Time for last 10,000,000:   86s.  Last read position: chrM:15,461
INFO	2016-05-14 05:39:40	MarkDuplicates	Before output close freeMemory: 2985415392; totalMemory: 3015704576; maxMemory: 3817865216
INFO	2016-05-14 05:39:40	MarkDuplicates	After output close freeMemory: 2985414336; totalMemory: 3015704576; maxMemory: 3817865216
[Sat May 14 05:39:40 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 17.78 minutes.
Runtime.totalMemory()=3015704576
[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	17174

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

Start	2016-05-14 06:20:45
End	2016-05-14 06:26:24
Elapsed	00:05:39
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	17323

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

Start	2016-05-14 06:26:25
End	2016-05-14 06:27:14
Elapsed	00:00:49
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	17385

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

Start	2016-05-14 06:27:15
End	2016-05-14 06:27:46
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.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	17448

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

Start	2016-05-14 06:27:47
End	2016-05-14 06:28:21
Elapsed	00:00:34
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	17516

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

Start	2016-05-14 06:28:22
End	2016-05-14 06:28:43
Elapsed	00:00:21
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	17577

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

Start	2016-05-14 06:28:44
End	2016-05-14 06:29:01
Elapsed	00:00:17
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.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	17640

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

Start	2016-05-14 06:29:02
End	2016-05-14 06:38:14
Elapsed	00:09:11
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/Rtmpmqokud/ATAC12-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign4591258ada79
done. read 5747364 fragments
ChIP data read length 75 
[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	17642

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

Start	2016-05-14 06:29:02
End	2016-05-14 06:29:02
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/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
Traceback (most recent call last):
  File "/users/pangwei/anaconda3/envs/bds_atac/bin/macs2", line 4, in 
    __import__('pkg_resources').run_script('MACS2==2.1.0.20150731', 'macs2')
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/setuptools-20.7.0-py2.7.egg/pkg_resources/__init__.py", line 719, in run_script
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/setuptools-20.7.0-py2.7.egg/pkg_resources/__init__.py", line 1511, in run_script
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 614, in 
    
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 55, in main
    
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/callpeak_cmd.py", line 30, in 
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/OptValidator.py", line 27, in 
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/IO/Parser.py", line 7, in 
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/IO/Parser.py", line 6, in __bootstrap__
  File "__init__.pxd", line 155, in init MACS2.IO.Parser (MACS2/IO/Parser.c:24419)
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/numpy/__init__.py", line 180, in 
    from . import add_newdocs
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/numpy/add_newdocs.py", line 13, in 
    from numpy.lib import add_newdoc
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/numpy/lib/__init__.py", line 8, in 
    from .type_check import *
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/numpy/lib/type_check.py", line 11, in 
    import numpy.core.numeric as _nx
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/numpy/core/__init__.py", line 14, in 
    from . import multiarray
ImportError: libopenblasp-r0-39a31c03.2.18.so: cannot open shared object file: No such file or directory

Num	12
ID	task.callpeak_macs2.macs2_atac_rep2.line_192.id_17
Name	macs2_atac rep2
Thread	thread_21
PID	17653

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

Start	2016-05-14 06:29:02
End	2016-05-14 06:29:02
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/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
Traceback (most recent call last):
  File "/users/pangwei/anaconda3/envs/bds_atac/bin/macs2", line 4, in 
    __import__('pkg_resources').run_script('MACS2==2.1.0.20150731', 'macs2')
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/setuptools-20.7.0-py2.7.egg/pkg_resources/__init__.py", line 719, in run_script
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/setuptools-20.7.0-py2.7.egg/pkg_resources/__init__.py", line 1511, in run_script
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 614, in 
    
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 55, in main
    
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/callpeak_cmd.py", line 30, in 
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/OptValidator.py", line 27, in 
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/IO/Parser.py", line 7, in 
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/IO/Parser.py", line 6, in __bootstrap__
  File "__init__.pxd", line 155, in init MACS2.IO.Parser (MACS2/IO/Parser.c:24419)
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/numpy/__init__.py", line 180, in 
    from . import add_newdocs
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/numpy/add_newdocs.py", line 13, in 
    from numpy.lib import add_newdoc
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/numpy/lib/__init__.py", line 8, in 
    from .type_check import *
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/numpy/lib/type_check.py", line 11, in 
    import numpy.core.numeric as _nx
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/numpy/core/__init__.py", line 14, in 
    from . import multiarray
ImportError: libopenblasp-r0-39a31c03.2.18.so: cannot open shared object file: No such file or directory

Num	13
ID	task.postalign_bam.dedup_bam_PE_rep1.line_215.id_18
Name	dedup_bam_PE rep1
Thread	thread_20
PID	25350

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

Start	2016-05-14 13:33:56
End	2016-05-14 18:13:54
Elapsed	04:39:58
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
[Sat May 14 16:08:20 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
[Sat May 14 16:08:20 PDT 2016] Executing as pangwei@mitra on Linux 3.16.0-70-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_45-b14; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-05-14 16:08:20	MarkDuplicates	Start of doWork freeMemory: 254889656; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-14 16:08:20	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-05-14 16:08:20	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-05-14 16:08:26	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:05s.  Time for last 1,000,000:    5s.  Last read position: chr10:70,883,539
INFO	2016-05-14 16:08:26	MarkDuplicates	Tracking 26 as yet unmatched pairs. 26 records in RAM.
INFO	2016-05-14 16:08:30	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:10s.  Time for last 1,000,000:    4s.  Last read position: chr10:122,848,219
INFO	2016-05-14 16:08:30	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 16:08:35	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	2016-05-14 16:08:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 16:08:40	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:20s.  Time for last 1,000,000:    5s.  Last read position: chr11:87,091,127
INFO	2016-05-14 16:08:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 16:08:49	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:29s.  Time for last 1,000,000:    8s.  Last read position: chr12:6,308,765
INFO	2016-05-14 16:08:49	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-05-14 16:09:00	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:39s.  Time for last 1,000,000:   10s.  Last read position: chr12:64,832,635
INFO	2016-05-14 16:09:00	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-14 16:09:09	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:48s.  Time for last 1,000,000:    8s.  Last read position: chr12:124,790,310
INFO	2016-05-14 16:09:09	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-05-14 16:09:15	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:54s.  Time for last 1,000,000:    6s.  Last read position: chr13:78,052,414
INFO	2016-05-14 16:09:15	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-14 16:09:22	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:01:02s.  Time for last 1,000,000:    7s.  Last read position: chr14:45,458,565
INFO	2016-05-14 16:09:22	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-14 16:09:28	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:01:07s.  Time for last 1,000,000:    5s.  Last read position: chr14:101,288,904
INFO	2016-05-14 16:09:28	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 16:09:32	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:11s.  Time for last 1,000,000:    4s.  Last read position: chr15:73,321,241
INFO	2016-05-14 16:09:32	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 16:09:38	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:18s.  Time for last 1,000,000:    6s.  Last read position: chr16:23,312,045
INFO	2016-05-14 16:09:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 16:09:42	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:21s.  Time for last 1,000,000:    3s.  Last read position: chr16:86,039,278
INFO	2016-05-14 16:09:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 16:09:46	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:25s.  Time for last 1,000,000:    4s.  Last read position: chr17:42,388,139
INFO	2016-05-14 16:09:46	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-14 16:10:03	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:42s.  Time for last 1,000,000:   16s.  Last read position: chr18:6,930,569
INFO	2016-05-14 16:10:03	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 16:10:08	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:47s.  Time for last 1,000,000:    4s.  Last read position: chr18:72,722,570
INFO	2016-05-14 16:10:08	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-14 16:10:13	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:01:52s.  Time for last 1,000,000:    4s.  Last read position: chr19:37,178,351
INFO	2016-05-14 16:10:13	MarkDuplicates	Tracking 12 as yet unmatched pairs. 12 records in RAM.
INFO	2016-05-14 16:10:20	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:01:59s.  Time for last 1,000,000:    7s.  Last read position: chr1:569,914
INFO	2016-05-14 16:10:20	MarkDuplicates	Tracking 16608 as yet unmatched pairs. 16608 records in RAM.
INFO	2016-05-14 16:10:28	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:02:08s.  Time for last 1,000,000:    8s.  Last read position: chr1:36,004,946
INFO	2016-05-14 16:10:28	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-14 16:10:33	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:02:12s.  Time for last 1,000,000:    4s.  Last read position: chr1:91,852,955
INFO	2016-05-14 16:10:33	MarkDuplicates	Tracking 1460 as yet unmatched pairs. 1460 records in RAM.
INFO	2016-05-14 16:10:37	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:02:16s.  Time for last 1,000,000:    4s.  Last read position: chr1:170,101,971
INFO	2016-05-14 16:10:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 16:10:41	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:02:20s.  Time for last 1,000,000:    4s.  Last read position: chr1:227,587,889
INFO	2016-05-14 16:10:41	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-14 16:10:47	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:02:27s.  Time for last 1,000,000:    6s.  Last read position: chr20:34,042,589
INFO	2016-05-14 16:10:47	MarkDuplicates	Tracking 12 as yet unmatched pairs. 12 records in RAM.
INFO	2016-05-14 16:10:51	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:02:31s.  Time for last 1,000,000:    4s.  Last read position: chr21:35,173,970
INFO	2016-05-14 16:10:51	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-14 16:10:58	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:02:37s.  Time for last 1,000,000:    6s.  Last read position: chr22:48,972,594
INFO	2016-05-14 16:10:58	MarkDuplicates	Tracking 12 as yet unmatched pairs. 12 records in RAM.
INFO	2016-05-14 16:11:09	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:02:49s.  Time for last 1,000,000:   11s.  Last read position: chr2:51,625,313
INFO	2016-05-14 16:11:09	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 16:11:15	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:02:54s.  Time for last 1,000,000:    5s.  Last read position: chr2:118,944,031
INFO	2016-05-14 16:11:15	MarkDuplicates	Tracking 12 as yet unmatched pairs. 12 records in RAM.
INFO	2016-05-14 16:11:20	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:02:59s.  Time for last 1,000,000:    5s.  Last read position: chr2:181,645,905
INFO	2016-05-14 16:11:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 16:11:26	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:03:05s.  Time for last 1,000,000:    5s.  Last read position: chr2:240,319,965
INFO	2016-05-14 16:11:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 16:11:40	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:03:19s.  Time for last 1,000,000:   13s.  Last read position: chr3:49,843,879
INFO	2016-05-14 16:11:40	MarkDuplicates	Tracking 16 as yet unmatched pairs. 16 records in RAM.
INFO	2016-05-14 16:11:45	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:03:25s.  Time for last 1,000,000:    5s.  Last read position: chr3:118,457,972
INFO	2016-05-14 16:11:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 16:11:51	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:03:30s.  Time for last 1,000,000:    5s.  Last read position: chr3:179,145,102
INFO	2016-05-14 16:11:51	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 16:11:55	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:03:35s.  Time for last 1,000,000:    4s.  Last read position: chr4:35,627,899
INFO	2016-05-14 16:11:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 16:11:59	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:03:38s.  Time for last 1,000,000:    3s.  Last read position: chr4:104,707,794
INFO	2016-05-14 16:11:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 16:12:03	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:03:42s.  Time for last 1,000,000:    3s.  Last read position: chr4:173,986,947
INFO	2016-05-14 16:12:03	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-14 16:12:07	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:03:46s.  Time for last 1,000,000:    4s.  Last read position: chr5:50,720,214
INFO	2016-05-14 16:12:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 16:12:12	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:03:51s.  Time for last 1,000,000:    5s.  Last read position: chr5:117,295,903
INFO	2016-05-14 16:12:12	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 16:12:15	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:03:55s.  Time for last 1,000,000:    3s.  Last read position: chr5:142,259,145
INFO	2016-05-14 16:12:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 16:12:20	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:03:59s.  Time for last 1,000,000:    4s.  Last read position: chr6:16,333,012
INFO	2016-05-14 16:12:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 16:12:25	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:04:04s.  Time for last 1,000,000:    5s.  Last read position: chr6:77,584,470
INFO	2016-05-14 16:12:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 16:12:30	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:04:10s.  Time for last 1,000,000:    5s.  Last read position: chr6:141,339,636
INFO	2016-05-14 16:12:30	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 16:12:38	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:04:17s.  Time for last 1,000,000:    7s.  Last read position: chr7:25,165,063
INFO	2016-05-14 16:12:38	MarkDuplicates	Tracking 44 as yet unmatched pairs. 44 records in RAM.
INFO	2016-05-14 16:12:44	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:04:23s.  Time for last 1,000,000:    6s.  Last read position: chr7:90,893,507
INFO	2016-05-14 16:12:44	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-05-14 16:12:49	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:04:29s.  Time for last 1,000,000:    5s.  Last read position: chr7:147,418,833
INFO	2016-05-14 16:12:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 16:12:57	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:04:37s.  Time for last 1,000,000:    8s.  Last read position: chr8:49,274,376
INFO	2016-05-14 16:12:57	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 16:13:02	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:04:42s.  Time for last 1,000,000:    5s.  Last read position: chr8:109,818,145
INFO	2016-05-14 16:13:02	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 16:13:08	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:04:47s.  Time for last 1,000,000:    5s.  Last read position: chr9:21,557,327
INFO	2016-05-14 16:13:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 16:13:14	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:04:53s.  Time for last 1,000,000:    5s.  Last read position: chr9:110,744,448
INFO	2016-05-14 16:13:14	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 16:13:17	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:04:57s.  Time for last 1,000,000:    3s.  Last read position: chrM:19
INFO	2016-05-14 16:13:17	MarkDuplicates	Tracking 51818 as yet unmatched pairs. 51818 records in RAM.
INFO	2016-05-14 16:13:22	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:05:01s.  Time for last 1,000,000:    4s.  Last read position: chrM:122
INFO	2016-05-14 16:13:22	MarkDuplicates	Tracking 126448 as yet unmatched pairs. 126448 records in RAM.
INFO	2016-05-14 16:13:26	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:05:05s.  Time for last 1,000,000:    4s.  Last read position: chrM:266
INFO	2016-05-14 16:13:26	MarkDuplicates	Tracking 19932 as yet unmatched pairs. 19932 records in RAM.
INFO	2016-05-14 16:13:30	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:05:09s.  Time for last 1,000,000:    3s.  Last read position: chrM:421
INFO	2016-05-14 16:13:30	MarkDuplicates	Tracking 76558 as yet unmatched pairs. 76558 records in RAM.
INFO	2016-05-14 16:13:35	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:05:15s.  Time for last 1,000,000:    5s.  Last read position: chrM:506
INFO	2016-05-14 16:13:35	MarkDuplicates	Tracking 34786 as yet unmatched pairs. 34786 records in RAM.
INFO	2016-05-14 16:13:39	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:05:19s.  Time for last 1,000,000:    3s.  Last read position: chrM:621
INFO	2016-05-14 16:13:39	MarkDuplicates	Tracking 92732 as yet unmatched pairs. 92732 records in RAM.
INFO	2016-05-14 16:13:45	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:05:24s.  Time for last 1,000,000:    5s.  Last read position: chrM:728
INFO	2016-05-14 16:13:45	MarkDuplicates	Tracking 117038 as yet unmatched pairs. 117038 records in RAM.
INFO	2016-05-14 16:13:51	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:05:30s.  Time for last 1,000,000:    5s.  Last read position: chrM:806
INFO	2016-05-14 16:13:51	MarkDuplicates	Tracking 76800 as yet unmatched pairs. 76800 records in RAM.
INFO	2016-05-14 16:13:57	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:05:36s.  Time for last 1,000,000:    6s.  Last read position: chrM:935
INFO	2016-05-14 16:13:57	MarkDuplicates	Tracking 145056 as yet unmatched pairs. 145056 records in RAM.
INFO	2016-05-14 16:14:07	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:05:46s.  Time for last 1,000,000:    9s.  Last read position: chrM:1,244
INFO	2016-05-14 16:14:07	MarkDuplicates	Tracking 122062 as yet unmatched pairs. 122062 records in RAM.
INFO	2016-05-14 16:14:14	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:05:54s.  Time for last 1,000,000:    7s.  Last read position: chrM:1,342
INFO	2016-05-14 16:14:14	MarkDuplicates	Tracking 278588 as yet unmatched pairs. 278588 records in RAM.
INFO	2016-05-14 16:14:25	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:06:05s.  Time for last 1,000,000:   11s.  Last read position: chrM:1,474
INFO	2016-05-14 16:14:25	MarkDuplicates	Tracking 99380 as yet unmatched pairs. 99380 records in RAM.
INFO	2016-05-14 16:14:31	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:06:11s.  Time for last 1,000,000:    5s.  Last read position: chrM:1,601
INFO	2016-05-14 16:14:31	MarkDuplicates	Tracking 149618 as yet unmatched pairs. 149618 records in RAM.
INFO	2016-05-14 16:14:37	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:06:17s.  Time for last 1,000,000:    6s.  Last read position: chrM:1,728
INFO	2016-05-14 16:14:37	MarkDuplicates	Tracking 35912 as yet unmatched pairs. 35912 records in RAM.
INFO	2016-05-14 16:14:43	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:06:23s.  Time for last 1,000,000:    6s.  Last read position: chrM:1,950
INFO	2016-05-14 16:14:43	MarkDuplicates	Tracking 89994 as yet unmatched pairs. 89994 records in RAM.
INFO	2016-05-14 16:14:49	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:06:29s.  Time for last 1,000,000:    6s.  Last read position: chrM:2,109
INFO	2016-05-14 16:14:49	MarkDuplicates	Tracking 113002 as yet unmatched pairs. 113002 records in RAM.
INFO	2016-05-14 16:14:57	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:06:37s.  Time for last 1,000,000:    7s.  Last read position: chrM:2,253
INFO	2016-05-14 16:14:57	MarkDuplicates	Tracking 85488 as yet unmatched pairs. 85488 records in RAM.
INFO	2016-05-14 16:15:01	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:06:41s.  Time for last 1,000,000:    4s.  Last read position: chrM:2,525
INFO	2016-05-14 16:15:01	MarkDuplicates	Tracking 55432 as yet unmatched pairs. 55432 records in RAM.
INFO	2016-05-14 16:15:05	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:06:45s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,600
INFO	2016-05-14 16:15:05	MarkDuplicates	Tracking 154564 as yet unmatched pairs. 154564 records in RAM.
INFO	2016-05-14 16:15:09	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:06:48s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,684
INFO	2016-05-14 16:15:09	MarkDuplicates	Tracking 251152 as yet unmatched pairs. 251152 records in RAM.
INFO	2016-05-14 16:15:13	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:06:53s.  Time for last 1,000,000:    4s.  Last read position: chrM:2,760
INFO	2016-05-14 16:15:13	MarkDuplicates	Tracking 443520 as yet unmatched pairs. 443520 records in RAM.
INFO	2016-05-14 16:15:20	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:06:59s.  Time for last 1,000,000:    6s.  Last read position: chrM:2,834
INFO	2016-05-14 16:15:20	MarkDuplicates	Tracking 166578 as yet unmatched pairs. 166578 records in RAM.
INFO	2016-05-14 16:15:24	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:07:03s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,884
INFO	2016-05-14 16:15:24	MarkDuplicates	Tracking 277906 as yet unmatched pairs. 277906 records in RAM.
INFO	2016-05-14 16:15:28	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:07:07s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,991
INFO	2016-05-14 16:15:28	MarkDuplicates	Tracking 187966 as yet unmatched pairs. 187966 records in RAM.
INFO	2016-05-14 16:15:34	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:07:13s.  Time for last 1,000,000:    6s.  Last read position: chrM:3,073
INFO	2016-05-14 16:15:34	MarkDuplicates	Tracking 229578 as yet unmatched pairs. 229578 records in RAM.
INFO	2016-05-14 16:15:43	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:07:22s.  Time for last 1,000,000:    8s.  Last read position: chrM:3,149
INFO	2016-05-14 16:15:43	MarkDuplicates	Tracking 126858 as yet unmatched pairs. 126858 records in RAM.
INFO	2016-05-14 16:15:47	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:07:26s.  Time for last 1,000,000:    4s.  Last read position: chrM:3,243
INFO	2016-05-14 16:15:47	MarkDuplicates	Tracking 352520 as yet unmatched pairs. 352520 records in RAM.
INFO	2016-05-14 16:15:53	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:07:33s.  Time for last 1,000,000:    6s.  Last read position: chrM:3,321
INFO	2016-05-14 16:15:53	MarkDuplicates	Tracking 303578 as yet unmatched pairs. 303578 records in RAM.
INFO	2016-05-14 16:15:57	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:07:36s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,363
INFO	2016-05-14 16:15:57	MarkDuplicates	Tracking 350344 as yet unmatched pairs. 350344 records in RAM.
INFO	2016-05-14 16:16:01	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:07:41s.  Time for last 1,000,000:    4s.  Last read position: chrM:3,415
INFO	2016-05-14 16:16:01	MarkDuplicates	Tracking 217312 as yet unmatched pairs. 217312 records in RAM.
INFO	2016-05-14 16:16:05	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:07:44s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,463
INFO	2016-05-14 16:16:05	MarkDuplicates	Tracking 116254 as yet unmatched pairs. 116254 records in RAM.
INFO	2016-05-14 16:16:09	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:07:48s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,574
INFO	2016-05-14 16:16:09	MarkDuplicates	Tracking 51018 as yet unmatched pairs. 51018 records in RAM.
INFO	2016-05-14 16:16:13	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:07:52s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,630
INFO	2016-05-14 16:16:13	MarkDuplicates	Tracking 198432 as yet unmatched pairs. 198432 records in RAM.
INFO	2016-05-14 16:16:20	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:07:59s.  Time for last 1,000,000:    7s.  Last read position: chrM:3,679
INFO	2016-05-14 16:16:20	MarkDuplicates	Tracking 274198 as yet unmatched pairs. 274198 records in RAM.
INFO	2016-05-14 16:16:24	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:08:03s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,732
INFO	2016-05-14 16:16:24	MarkDuplicates	Tracking 247156 as yet unmatched pairs. 247156 records in RAM.
INFO	2016-05-14 16:16:28	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:08:07s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,808
INFO	2016-05-14 16:16:28	MarkDuplicates	Tracking 237654 as yet unmatched pairs. 237654 records in RAM.
INFO	2016-05-14 16:16:32	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:08:11s.  Time for last 1,000,000:    4s.  Last read position: chrM:3,875
INFO	2016-05-14 16:16:32	MarkDuplicates	Tracking 287772 as yet unmatched pairs. 287772 records in RAM.
INFO	2016-05-14 16:16:36	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:08:15s.  Time for last 1,000,000:    4s.  Last read position: chrM:3,997
INFO	2016-05-14 16:16:36	MarkDuplicates	Tracking 79882 as yet unmatched pairs. 79882 records in RAM.
INFO	2016-05-14 16:16:39	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:08:19s.  Time for last 1,000,000:    3s.  Last read position: chrM:4,245
INFO	2016-05-14 16:16:39	MarkDuplicates	Tracking 104094 as yet unmatched pairs. 104094 records in RAM.
INFO	2016-05-14 16:16:43	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:08:23s.  Time for last 1,000,000:    3s.  Last read position: chrM:4,670
INFO	2016-05-14 16:16:43	MarkDuplicates	Tracking 12576 as yet unmatched pairs. 12576 records in RAM.
INFO	2016-05-14 16:16:59	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:08:39s.  Time for last 1,000,000:   16s.  Last read position: chrM:4,885
INFO	2016-05-14 16:16:59	MarkDuplicates	Tracking 96476 as yet unmatched pairs. 96476 records in RAM.
INFO	2016-05-14 16:17:04	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:08:44s.  Time for last 1,000,000:    4s.  Last read position: chrM:4,963
INFO	2016-05-14 16:17:04	MarkDuplicates	Tracking 144888 as yet unmatched pairs. 144888 records in RAM.
INFO	2016-05-14 16:17:08	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:08:48s.  Time for last 1,000,000:    3s.  Last read position: chrM:5,114
INFO	2016-05-14 16:17:08	MarkDuplicates	Tracking 46680 as yet unmatched pairs. 46680 records in RAM.
INFO	2016-05-14 16:17:12	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:08:51s.  Time for last 1,000,000:    3s.  Last read position: chrM:5,353
INFO	2016-05-14 16:17:12	MarkDuplicates	Tracking 95746 as yet unmatched pairs. 95746 records in RAM.
INFO	2016-05-14 16:17:15	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:08:55s.  Time for last 1,000,000:    3s.  Last read position: chrM:5,471
INFO	2016-05-14 16:17:15	MarkDuplicates	Tracking 73850 as yet unmatched pairs. 73850 records in RAM.
INFO	2016-05-14 16:17:19	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:08:59s.  Time for last 1,000,000:    3s.  Last read position: chrM:5,986
INFO	2016-05-14 16:17:19	MarkDuplicates	Tracking 50676 as yet unmatched pairs. 50676 records in RAM.
INFO	2016-05-14 16:17:23	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:09:03s.  Time for last 1,000,000:    4s.  Last read position: chrM:6,200
INFO	2016-05-14 16:17:23	MarkDuplicates	Tracking 131118 as yet unmatched pairs. 131118 records in RAM.
INFO	2016-05-14 16:17:27	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:09:06s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,253
INFO	2016-05-14 16:17:27	MarkDuplicates	Tracking 133516 as yet unmatched pairs. 133516 records in RAM.
INFO	2016-05-14 16:17:33	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:09:13s.  Time for last 1,000,000:    6s.  Last read position: chrM:6,330
INFO	2016-05-14 16:17:33	MarkDuplicates	Tracking 141528 as yet unmatched pairs. 141528 records in RAM.
INFO	2016-05-14 16:17:37	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:09:16s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,427
INFO	2016-05-14 16:17:37	MarkDuplicates	Tracking 107762 as yet unmatched pairs. 107762 records in RAM.
INFO	2016-05-14 16:17:40	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:09:20s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,491
INFO	2016-05-14 16:17:40	MarkDuplicates	Tracking 88388 as yet unmatched pairs. 88388 records in RAM.
INFO	2016-05-14 16:17:44	MarkDuplicates	Read   100,000,000 records.  Elapsed time: 00:09:23s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,589
INFO	2016-05-14 16:17:44	MarkDuplicates	Tracking 128508 as yet unmatched pairs. 128508 records in RAM.
INFO	2016-05-14 16:17:48	MarkDuplicates	Read   101,000,000 records.  Elapsed time: 00:09:27s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,791
INFO	2016-05-14 16:17:48	MarkDuplicates	Tracking 24950 as yet unmatched pairs. 24950 records in RAM.
INFO	2016-05-14 16:17:52	MarkDuplicates	Read   102,000,000 records.  Elapsed time: 00:09:31s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,988
INFO	2016-05-14 16:17:52	MarkDuplicates	Tracking 68352 as yet unmatched pairs. 68352 records in RAM.
INFO	2016-05-14 16:17:59	MarkDuplicates	Read   103,000,000 records.  Elapsed time: 00:09:39s.  Time for last 1,000,000:    7s.  Last read position: chrM:7,191
INFO	2016-05-14 16:17:59	MarkDuplicates	Tracking 41376 as yet unmatched pairs. 41376 records in RAM.
INFO	2016-05-14 16:18:03	MarkDuplicates	Read   104,000,000 records.  Elapsed time: 00:09:43s.  Time for last 1,000,000:    4s.  Last read position: chrM:7,487
INFO	2016-05-14 16:18:03	MarkDuplicates	Tracking 50064 as yet unmatched pairs. 50064 records in RAM.
INFO	2016-05-14 16:18:07	MarkDuplicates	Read   105,000,000 records.  Elapsed time: 00:09:47s.  Time for last 1,000,000:    4s.  Last read position: chrM:7,731
INFO	2016-05-14 16:18:07	MarkDuplicates	Tracking 48094 as yet unmatched pairs. 48094 records in RAM.
INFO	2016-05-14 16:18:13	MarkDuplicates	Read   106,000,000 records.  Elapsed time: 00:09:53s.  Time for last 1,000,000:    5s.  Last read position: chrM:7,853
INFO	2016-05-14 16:18:13	MarkDuplicates	Tracking 103082 as yet unmatched pairs. 103082 records in RAM.
INFO	2016-05-14 16:18:17	MarkDuplicates	Read   107,000,000 records.  Elapsed time: 00:09:56s.  Time for last 1,000,000:    3s.  Last read position: chrM:7,998
INFO	2016-05-14 16:18:17	MarkDuplicates	Tracking 104448 as yet unmatched pairs. 104448 records in RAM.
INFO	2016-05-14 16:18:20	MarkDuplicates	Read   108,000,000 records.  Elapsed time: 00:09:59s.  Time for last 1,000,000:    3s.  Last read position: chrM:8,142
INFO	2016-05-14 16:18:20	MarkDuplicates	Tracking 72264 as yet unmatched pairs. 72264 records in RAM.
INFO	2016-05-14 16:18:23	MarkDuplicates	Read   109,000,000 records.  Elapsed time: 00:10:03s.  Time for last 1,000,000:    3s.  Last read position: chrM:8,402
INFO	2016-05-14 16:18:23	MarkDuplicates	Tracking 54792 as yet unmatched pairs. 54792 records in RAM.
INFO	2016-05-14 16:18:27	MarkDuplicates	Read   110,000,000 records.  Elapsed time: 00:10:06s.  Time for last 1,000,000:    3s.  Last read position: chrM:8,613
INFO	2016-05-14 16:18:27	MarkDuplicates	Tracking 31842 as yet unmatched pairs. 31842 records in RAM.
INFO	2016-05-14 16:18:30	MarkDuplicates	Read   111,000,000 records.  Elapsed time: 00:10:09s.  Time for last 1,000,000:    3s.  Last read position: chrM:9,046
INFO	2016-05-14 16:18:30	MarkDuplicates	Tracking 22186 as yet unmatched pairs. 22186 records in RAM.
INFO	2016-05-14 16:18:33	MarkDuplicates	Read   112,000,000 records.  Elapsed time: 00:10:12s.  Time for last 1,000,000:    3s.  Last read position: chrM:9,214
INFO	2016-05-14 16:18:33	MarkDuplicates	Tracking 89662 as yet unmatched pairs. 89662 records in RAM.
INFO	2016-05-14 16:18:36	MarkDuplicates	Read   113,000,000 records.  Elapsed time: 00:10:16s.  Time for last 1,000,000:    3s.  Last read position: chrM:9,290
INFO	2016-05-14 16:18:36	MarkDuplicates	Tracking 90966 as yet unmatched pairs. 90966 records in RAM.
INFO	2016-05-14 16:18:43	MarkDuplicates	Read   114,000,000 records.  Elapsed time: 00:10:22s.  Time for last 1,000,000:    6s.  Last read position: chrM:9,583
INFO	2016-05-14 16:18:43	MarkDuplicates	Tracking 32944 as yet unmatched pairs. 32944 records in RAM.
INFO	2016-05-14 16:18:46	MarkDuplicates	Read   115,000,000 records.  Elapsed time: 00:10:26s.  Time for last 1,000,000:    3s.  Last read position: chrM:9,732
INFO	2016-05-14 16:18:46	MarkDuplicates	Tracking 239980 as yet unmatched pairs. 239980 records in RAM.
INFO	2016-05-14 16:18:50	MarkDuplicates	Read   116,000,000 records.  Elapsed time: 00:10:30s.  Time for last 1,000,000:    4s.  Last read position: chrM:9,813
INFO	2016-05-14 16:18:50	MarkDuplicates	Tracking 222242 as yet unmatched pairs. 222242 records in RAM.
INFO	2016-05-14 16:18:55	MarkDuplicates	Read   117,000,000 records.  Elapsed time: 00:10:34s.  Time for last 1,000,000:    4s.  Last read position: chrM:9,907
INFO	2016-05-14 16:18:55	MarkDuplicates	Tracking 191448 as yet unmatched pairs. 191448 records in RAM.
INFO	2016-05-14 16:19:12	MarkDuplicates	Read   118,000,000 records.  Elapsed time: 00:10:51s.  Time for last 1,000,000:   16s.  Last read position: chrM:10,026
INFO	2016-05-14 16:19:12	MarkDuplicates	Tracking 316342 as yet unmatched pairs. 316342 records in RAM.
INFO	2016-05-14 16:19:16	MarkDuplicates	Read   119,000,000 records.  Elapsed time: 00:10:55s.  Time for last 1,000,000:    4s.  Last read position: chrM:10,140
INFO	2016-05-14 16:19:16	MarkDuplicates	Tracking 84822 as yet unmatched pairs. 84822 records in RAM.
INFO	2016-05-14 16:19:20	MarkDuplicates	Read   120,000,000 records.  Elapsed time: 00:10:59s.  Time for last 1,000,000:    4s.  Last read position: chrM:10,245
INFO	2016-05-14 16:19:20	MarkDuplicates	Tracking 119318 as yet unmatched pairs. 119318 records in RAM.
INFO	2016-05-14 16:19:24	MarkDuplicates	Read   121,000,000 records.  Elapsed time: 00:11:04s.  Time for last 1,000,000:    4s.  Last read position: chrM:10,341
INFO	2016-05-14 16:19:24	MarkDuplicates	Tracking 77232 as yet unmatched pairs. 77232 records in RAM.
INFO	2016-05-14 16:19:29	MarkDuplicates	Read   122,000,000 records.  Elapsed time: 00:11:08s.  Time for last 1,000,000:    4s.  Last read position: chrM:10,503
INFO	2016-05-14 16:19:29	MarkDuplicates	Tracking 23976 as yet unmatched pairs. 23976 records in RAM.
INFO	2016-05-14 16:19:34	MarkDuplicates	Read   123,000,000 records.  Elapsed time: 00:11:14s.  Time for last 1,000,000:    5s.  Last read position: chrM:10,621
INFO	2016-05-14 16:19:34	MarkDuplicates	Tracking 188276 as yet unmatched pairs. 188276 records in RAM.
INFO	2016-05-14 16:19:37	MarkDuplicates	Read   124,000,000 records.  Elapsed time: 00:11:17s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,673
INFO	2016-05-14 16:19:37	MarkDuplicates	Tracking 63434 as yet unmatched pairs. 63434 records in RAM.
INFO	2016-05-14 16:19:40	MarkDuplicates	Read   125,000,000 records.  Elapsed time: 00:11:20s.  Time for last 1,000,000:    2s.  Last read position: chrM:10,887
INFO	2016-05-14 16:19:40	MarkDuplicates	Tracking 7040 as yet unmatched pairs. 7040 records in RAM.
INFO	2016-05-14 16:19:44	MarkDuplicates	Read   126,000,000 records.  Elapsed time: 00:11:23s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,139
INFO	2016-05-14 16:19:44	MarkDuplicates	Tracking 131732 as yet unmatched pairs. 131732 records in RAM.
INFO	2016-05-14 16:19:47	MarkDuplicates	Read   127,000,000 records.  Elapsed time: 00:11:26s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,218
INFO	2016-05-14 16:19:47	MarkDuplicates	Tracking 104886 as yet unmatched pairs. 104886 records in RAM.
INFO	2016-05-14 16:19:50	MarkDuplicates	Read   128,000,000 records.  Elapsed time: 00:11:29s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,323
INFO	2016-05-14 16:19:50	MarkDuplicates	Tracking 101054 as yet unmatched pairs. 101054 records in RAM.
INFO	2016-05-14 16:19:53	MarkDuplicates	Read   129,000,000 records.  Elapsed time: 00:11:32s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,485
INFO	2016-05-14 16:19:53	MarkDuplicates	Tracking 51764 as yet unmatched pairs. 51764 records in RAM.
INFO	2016-05-14 16:19:56	MarkDuplicates	Read   130,000,000 records.  Elapsed time: 00:11:35s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,571
INFO	2016-05-14 16:19:56	MarkDuplicates	Tracking 93640 as yet unmatched pairs. 93640 records in RAM.
INFO	2016-05-14 16:19:59	MarkDuplicates	Read   131,000,000 records.  Elapsed time: 00:11:38s.  Time for last 1,000,000:    2s.  Last read position: chrM:11,771
INFO	2016-05-14 16:19:59	MarkDuplicates	Tracking 77586 as yet unmatched pairs. 77586 records in RAM.
INFO	2016-05-14 16:20:05	MarkDuplicates	Read   132,000,000 records.  Elapsed time: 00:11:44s.  Time for last 1,000,000:    5s.  Last read position: chrM:11,931
INFO	2016-05-14 16:20:05	MarkDuplicates	Tracking 22452 as yet unmatched pairs. 22452 records in RAM.
INFO	2016-05-14 16:20:12	MarkDuplicates	Read   133,000,000 records.  Elapsed time: 00:11:52s.  Time for last 1,000,000:    7s.  Last read position: chrM:12,021
INFO	2016-05-14 16:20:12	MarkDuplicates	Tracking 74160 as yet unmatched pairs. 74160 records in RAM.
INFO	2016-05-14 16:20:16	MarkDuplicates	Read   134,000,000 records.  Elapsed time: 00:11:55s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,139
INFO	2016-05-14 16:20:16	MarkDuplicates	Tracking 110920 as yet unmatched pairs. 110920 records in RAM.
INFO	2016-05-14 16:20:19	MarkDuplicates	Read   135,000,000 records.  Elapsed time: 00:11:58s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,347
INFO	2016-05-14 16:20:19	MarkDuplicates	Tracking 25060 as yet unmatched pairs. 25060 records in RAM.
INFO	2016-05-14 16:20:22	MarkDuplicates	Read   136,000,000 records.  Elapsed time: 00:12:01s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,465
INFO	2016-05-14 16:20:22	MarkDuplicates	Tracking 116620 as yet unmatched pairs. 116620 records in RAM.
INFO	2016-05-14 16:20:25	MarkDuplicates	Read   137,000,000 records.  Elapsed time: 00:12:04s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,549
INFO	2016-05-14 16:20:25	MarkDuplicates	Tracking 168524 as yet unmatched pairs. 168524 records in RAM.
INFO	2016-05-14 16:20:29	MarkDuplicates	Read   138,000,000 records.  Elapsed time: 00:12:08s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,615
INFO	2016-05-14 16:20:29	MarkDuplicates	Tracking 216066 as yet unmatched pairs. 216066 records in RAM.
INFO	2016-05-14 16:20:32	MarkDuplicates	Read   139,000,000 records.  Elapsed time: 00:12:12s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,705
INFO	2016-05-14 16:20:32	MarkDuplicates	Tracking 149784 as yet unmatched pairs. 149784 records in RAM.
INFO	2016-05-14 16:20:36	MarkDuplicates	Read   140,000,000 records.  Elapsed time: 00:12:15s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,864
INFO	2016-05-14 16:20:36	MarkDuplicates	Tracking 29900 as yet unmatched pairs. 29900 records in RAM.
INFO	2016-05-14 16:20:39	MarkDuplicates	Read   141,000,000 records.  Elapsed time: 00:12:19s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,011
INFO	2016-05-14 16:20:39	MarkDuplicates	Tracking 15068 as yet unmatched pairs. 15068 records in RAM.
INFO	2016-05-14 16:20:46	MarkDuplicates	Read   142,000,000 records.  Elapsed time: 00:12:25s.  Time for last 1,000,000:    6s.  Last read position: chrM:13,099
INFO	2016-05-14 16:20:46	MarkDuplicates	Tracking 138558 as yet unmatched pairs. 138558 records in RAM.
INFO	2016-05-14 16:20:50	MarkDuplicates	Read   143,000,000 records.  Elapsed time: 00:12:29s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,179
INFO	2016-05-14 16:20:50	MarkDuplicates	Tracking 169240 as yet unmatched pairs. 169240 records in RAM.
INFO	2016-05-14 16:20:53	MarkDuplicates	Read   144,000,000 records.  Elapsed time: 00:12:33s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,270
INFO	2016-05-14 16:20:53	MarkDuplicates	Tracking 112190 as yet unmatched pairs. 112190 records in RAM.
INFO	2016-05-14 16:20:57	MarkDuplicates	Read   145,000,000 records.  Elapsed time: 00:12:36s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,368
INFO	2016-05-14 16:20:57	MarkDuplicates	Tracking 148274 as yet unmatched pairs. 148274 records in RAM.
INFO	2016-05-14 16:21:00	MarkDuplicates	Read   146,000,000 records.  Elapsed time: 00:12:39s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,459
INFO	2016-05-14 16:21:00	MarkDuplicates	Tracking 153034 as yet unmatched pairs. 153034 records in RAM.
INFO	2016-05-14 16:21:16	MarkDuplicates	Read   147,000,000 records.  Elapsed time: 00:12:55s.  Time for last 1,000,000:   15s.  Last read position: chrM:13,564
INFO	2016-05-14 16:21:16	MarkDuplicates	Tracking 93660 as yet unmatched pairs. 93660 records in RAM.
INFO	2016-05-14 16:21:19	MarkDuplicates	Read   148,000,000 records.  Elapsed time: 00:12:58s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,676
INFO	2016-05-14 16:21:19	MarkDuplicates	Tracking 88726 as yet unmatched pairs. 88726 records in RAM.
INFO	2016-05-14 16:21:22	MarkDuplicates	Read   149,000,000 records.  Elapsed time: 00:13:02s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,814
INFO	2016-05-14 16:21:22	MarkDuplicates	Tracking 107138 as yet unmatched pairs. 107138 records in RAM.
INFO	2016-05-14 16:21:26	MarkDuplicates	Read   150,000,000 records.  Elapsed time: 00:13:05s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,918
INFO	2016-05-14 16:21:26	MarkDuplicates	Tracking 99686 as yet unmatched pairs. 99686 records in RAM.
INFO	2016-05-14 16:21:29	MarkDuplicates	Read   151,000,000 records.  Elapsed time: 00:13:08s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,988
INFO	2016-05-14 16:21:29	MarkDuplicates	Tracking 101710 as yet unmatched pairs. 101710 records in RAM.
INFO	2016-05-14 16:21:35	MarkDuplicates	Read   152,000,000 records.  Elapsed time: 00:13:14s.  Time for last 1,000,000:    5s.  Last read position: chrM:14,083
INFO	2016-05-14 16:21:35	MarkDuplicates	Tracking 13964 as yet unmatched pairs. 13964 records in RAM.
INFO	2016-05-14 16:21:38	MarkDuplicates	Read   153,000,000 records.  Elapsed time: 00:13:17s.  Time for last 1,000,000:    3s.  Last read position: chrM:14,302
INFO	2016-05-14 16:21:38	MarkDuplicates	Tracking 45550 as yet unmatched pairs. 45550 records in RAM.
INFO	2016-05-14 16:21:41	MarkDuplicates	Read   154,000,000 records.  Elapsed time: 00:13:20s.  Time for last 1,000,000:    3s.  Last read position: chrM:14,414
INFO	2016-05-14 16:21:41	MarkDuplicates	Tracking 28948 as yet unmatched pairs. 28948 records in RAM.
INFO	2016-05-14 16:21:44	MarkDuplicates	Read   155,000,000 records.  Elapsed time: 00:13:24s.  Time for last 1,000,000:    3s.  Last read position: chrM:14,608
INFO	2016-05-14 16:21:44	MarkDuplicates	Tracking 54308 as yet unmatched pairs. 54308 records in RAM.
INFO	2016-05-14 16:21:47	MarkDuplicates	Read   156,000,000 records.  Elapsed time: 00:13:27s.  Time for last 1,000,000:    3s.  Last read position: chrM:14,826
INFO	2016-05-14 16:21:47	MarkDuplicates	Tracking 43954 as yet unmatched pairs. 43954 records in RAM.
INFO	2016-05-14 16:21:51	MarkDuplicates	Read   157,000,000 records.  Elapsed time: 00:13:30s.  Time for last 1,000,000:    3s.  Last read position: chrM:14,977
INFO	2016-05-14 16:21:51	MarkDuplicates	Tracking 162238 as yet unmatched pairs. 162238 records in RAM.
INFO	2016-05-14 16:21:54	MarkDuplicates	Read   158,000,000 records.  Elapsed time: 00:13:33s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,043
INFO	2016-05-14 16:21:54	MarkDuplicates	Tracking 304582 as yet unmatched pairs. 304582 records in RAM.
INFO	2016-05-14 16:21:57	MarkDuplicates	Read   159,000,000 records.  Elapsed time: 00:13:37s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,097
INFO	2016-05-14 16:21:57	MarkDuplicates	Tracking 202550 as yet unmatched pairs. 202550 records in RAM.
INFO	2016-05-14 16:22:01	MarkDuplicates	Read   160,000,000 records.  Elapsed time: 00:13:40s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,160
INFO	2016-05-14 16:22:01	MarkDuplicates	Tracking 222340 as yet unmatched pairs. 222340 records in RAM.
INFO	2016-05-14 16:22:04	MarkDuplicates	Read   161,000,000 records.  Elapsed time: 00:13:44s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,222
INFO	2016-05-14 16:22:04	MarkDuplicates	Tracking 107908 as yet unmatched pairs. 107908 records in RAM.
INFO	2016-05-14 16:22:12	MarkDuplicates	Read   162,000,000 records.  Elapsed time: 00:13:51s.  Time for last 1,000,000:    7s.  Last read position: chrM:15,307
INFO	2016-05-14 16:22:12	MarkDuplicates	Tracking 86756 as yet unmatched pairs. 86756 records in RAM.
INFO	2016-05-14 16:22:17	MarkDuplicates	Read   163,000,000 records.  Elapsed time: 00:13:57s.  Time for last 1,000,000:    5s.  Last read position: chrM:15,392
INFO	2016-05-14 16:22:17	MarkDuplicates	Tracking 197274 as yet unmatched pairs. 197274 records in RAM.
INFO	2016-05-14 16:22:21	MarkDuplicates	Read   164,000,000 records.  Elapsed time: 00:14:00s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,444
INFO	2016-05-14 16:22:21	MarkDuplicates	Tracking 185138 as yet unmatched pairs. 185138 records in RAM.
INFO	2016-05-14 16:22:24	MarkDuplicates	Read   165,000,000 records.  Elapsed time: 00:14:03s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,512
INFO	2016-05-14 16:22:24	MarkDuplicates	Tracking 155996 as yet unmatched pairs. 155996 records in RAM.
INFO	2016-05-14 16:22:28	MarkDuplicates	Read   166,000,000 records.  Elapsed time: 00:14:07s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,588
INFO	2016-05-14 16:22:28	MarkDuplicates	Tracking 152518 as yet unmatched pairs. 152518 records in RAM.
INFO	2016-05-14 16:22:31	MarkDuplicates	Read   167,000,000 records.  Elapsed time: 00:14:10s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,652
INFO	2016-05-14 16:22:31	MarkDuplicates	Tracking 237900 as yet unmatched pairs. 237900 records in RAM.
INFO	2016-05-14 16:22:34	MarkDuplicates	Read   168,000,000 records.  Elapsed time: 00:14:14s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,717
INFO	2016-05-14 16:22:34	MarkDuplicates	Tracking 218604 as yet unmatched pairs. 218604 records in RAM.
INFO	2016-05-14 16:22:38	MarkDuplicates	Read   169,000,000 records.  Elapsed time: 00:14:17s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,771
INFO	2016-05-14 16:22:38	MarkDuplicates	Tracking 209396 as yet unmatched pairs. 209396 records in RAM.
INFO	2016-05-14 16:22:41	MarkDuplicates	Read   170,000,000 records.  Elapsed time: 00:14:21s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,823
INFO	2016-05-14 16:22:41	MarkDuplicates	Tracking 349994 as yet unmatched pairs. 349994 records in RAM.
INFO	2016-05-14 16:22:45	MarkDuplicates	Read   171,000,000 records.  Elapsed time: 00:14:24s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,903
INFO	2016-05-14 16:22:45	MarkDuplicates	Tracking 310018 as yet unmatched pairs. 310018 records in RAM.
INFO	2016-05-14 16:22:48	MarkDuplicates	Read   172,000,000 records.  Elapsed time: 00:14:28s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,989
INFO	2016-05-14 16:22:48	MarkDuplicates	Tracking 222442 as yet unmatched pairs. 222442 records in RAM.
INFO	2016-05-14 16:22:52	MarkDuplicates	Read   173,000,000 records.  Elapsed time: 00:14:31s.  Time for last 1,000,000:    3s.  Last read position: chrM:16,094
INFO	2016-05-14 16:22:52	MarkDuplicates	Tracking 83942 as yet unmatched pairs. 83942 records in RAM.
INFO	2016-05-14 16:22:59	MarkDuplicates	Read   174,000,000 records.  Elapsed time: 00:14:38s.  Time for last 1,000,000:    7s.  Last read position: chrM:16,273
INFO	2016-05-14 16:22:59	MarkDuplicates	Tracking 116406 as yet unmatched pairs. 116406 records in RAM.
INFO	2016-05-14 16:23:02	MarkDuplicates	Read   175,000,000 records.  Elapsed time: 00:14:41s.  Time for last 1,000,000:    3s.  Last read position: chrM:16,337
INFO	2016-05-14 16:23:02	MarkDuplicates	Tracking 180842 as yet unmatched pairs. 180842 records in RAM.
INFO	2016-05-14 16:23:05	MarkDuplicates	Read   176,000,000 records.  Elapsed time: 00:14:45s.  Time for last 1,000,000:    3s.  Last read position: chrM:16,386
INFO	2016-05-14 16:23:05	MarkDuplicates	Tracking 189210 as yet unmatched pairs. 189210 records in RAM.
INFO	2016-05-14 16:23:20	MarkDuplicates	Read   177,000,000 records.  Elapsed time: 00:14:59s.  Time for last 1,000,000:   14s.  Last read position: chrM:16,439
INFO	2016-05-14 16:23:20	MarkDuplicates	Tracking 176236 as yet unmatched pairs. 176236 records in RAM.
INFO	2016-05-14 16:23:24	MarkDuplicates	Read   178,000,000 records.  Elapsed time: 00:15:03s.  Time for last 1,000,000:    3s.  Last read position: chrM:16,509
INFO	2016-05-14 16:23:24	MarkDuplicates	Tracking 2804 as yet unmatched pairs. 2804 records in RAM.
INFO	2016-05-14 16:23:29	MarkDuplicates	Read   179,000,000 records.  Elapsed time: 00:15:08s.  Time for last 1,000,000:    4s.  Last read position: chrX:62,537,485
INFO	2016-05-14 16:23:29	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 16:23:34	MarkDuplicates	Read   180,000,000 records.  Elapsed time: 00:15:13s.  Time for last 1,000,000:    5s.  Last read position: chrX:133,965,902
INFO	2016-05-14 16:23:34	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 16:23:36	MarkDuplicates	Read 180344434 records. 0 pairs never matched.
INFO	2016-05-14 16:23:38	MarkDuplicates	After buildSortedReadEndLists freeMemory: 4105036784; totalMemory: 4131913728; maxMemory: 4131913728
INFO	2016-05-14 16:23:38	MarkDuplicates	Will retain up to 129122304 duplicate indices before spilling to disk.
INFO	2016-05-14 16:23:38	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-05-14 16:25:47	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-05-14 16:26:27	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-05-14 16:26:29	MarkDuplicates	After generateDuplicateIndexes freeMemory: 4224044600; totalMemory: 4253024256; maxMemory: 4253024256
INFO	2016-05-14 16:26:29	MarkDuplicates	Marking 159785066 records as duplicates.
INFO	2016-05-14 16:26:29	MarkDuplicates	Found 55413083 optical duplicate clusters.
INFO	2016-05-14 16:27:54	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:22s.  Time for last 10,000,000:   82s.  Last read position: chr14:101,288,904
INFO	2016-05-14 16:29:20	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:02:48s.  Time for last 10,000,000:   86s.  Last read position: chr1:91,852,955
INFO	2016-05-14 16:30:47	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:04:15s.  Time for last 10,000,000:   86s.  Last read position: chr3:49,843,879
INFO	2016-05-14 16:32:14	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:05:42s.  Time for last 10,000,000:   86s.  Last read position: chr6:77,584,470
INFO	2016-05-14 16:33:38	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:07:06s.  Time for last 10,000,000:   83s.  Last read position: chrM:122
INFO	2016-05-14 16:34:52	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:08:20s.  Time for last 10,000,000:   74s.  Last read position: chrM:1,474
INFO	2016-05-14 16:36:06	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:09:34s.  Time for last 10,000,000:   74s.  Last read position: chrM:2,834
INFO	2016-05-14 16:37:21	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:10:50s.  Time for last 10,000,000:   75s.  Last read position: chrM:3,574
INFO	2016-05-14 16:38:36	MarkDuplicates	Written    90,000,000 records.  Elapsed time: 00:12:04s.  Time for last 10,000,000:   74s.  Last read position: chrM:4,963
INFO	2016-05-14 16:39:45	MarkDuplicates	Written   100,000,000 records.  Elapsed time: 00:13:13s.  Time for last 10,000,000:   69s.  Last read position: chrM:6,589
INFO	2016-05-14 16:40:54	MarkDuplicates	Written   110,000,000 records.  Elapsed time: 00:14:22s.  Time for last 10,000,000:   68s.  Last read position: chrM:8,613
INFO	2016-05-14 16:42:05	MarkDuplicates	Written   120,000,000 records.  Elapsed time: 00:15:33s.  Time for last 10,000,000:   71s.  Last read position: chrM:10,245
INFO	2016-05-14 16:43:16	MarkDuplicates	Written   130,000,000 records.  Elapsed time: 00:16:44s.  Time for last 10,000,000:   70s.  Last read position: chrM:11,571
INFO	2016-05-14 16:44:30	MarkDuplicates	Written   140,000,000 records.  Elapsed time: 00:17:58s.  Time for last 10,000,000:   74s.  Last read position: chrM:12,864
INFO	2016-05-14 16:45:40	MarkDuplicates	Written   150,000,000 records.  Elapsed time: 00:19:08s.  Time for last 10,000,000:   69s.  Last read position: chrM:13,918
INFO	2016-05-14 16:46:53	MarkDuplicates	Written   160,000,000 records.  Elapsed time: 00:20:21s.  Time for last 10,000,000:   73s.  Last read position: chrM:15,160
INFO	2016-05-14 16:48:08	MarkDuplicates	Written   170,000,000 records.  Elapsed time: 00:21:36s.  Time for last 10,000,000:   74s.  Last read position: chrM:15,823
INFO	2016-05-14 16:49:25	MarkDuplicates	Written   180,000,000 records.  Elapsed time: 00:22:53s.  Time for last 10,000,000:   76s.  Last read position: chrX:133,965,902
Could not delete file /tmp/pangwei/sortingcollection.1210233218572055304.tmp
Could not delete file /tmp/pangwei/sortingcollection.5799931692014331028.tmp
INFO	2016-05-14 16:49:28	MarkDuplicates	Before output close freeMemory: 4263950136; totalMemory: 4294443008; maxMemory: 4294443008
INFO	2016-05-14 16:49:28	MarkDuplicates	After output close freeMemory: 4263949320; totalMemory: 4294443008; maxMemory: 4294443008
[Sat May 14 16:49:28 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 41.13 minutes.
Runtime.totalMemory()=4294443008
[bam_sort_core] merging from 74 files...

Num	14
ID	task.postalign_bam.nmsrt_bam_rep1.line_321.id_19
Name	nmsrt_bam rep1
Thread	thread_20
PID	28571

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

Start	2016-05-14 18:13:55
End	2016-05-14 18:21:38
Elapsed	00:07:42
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.nodup.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-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/rep1/ATAC11-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-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 9 files...

Num	15
ID	task.postalign_bam.bam_to_bedpe_rep1.line_425.id_20
Name	bam_to_bedpe rep1
Thread	thread_20
PID	28671

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

Start	2016-05-14 18:21:38
End	2016-05-14 18:22:34
Elapsed	00:00:56
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.nodup.nmsrt.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Dependencies	nmsrt_bam rep1 nmsrt_bam rep1

 
# SYS command. line 427

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

# SYS command. line 430

 bedtools bamtobed -bedpe -mate1 -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz

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

Num	16
ID	task.postalign_bed.subsample_bedpe_rep1.line_116.id_21
Name	subsample_bedpe rep1
Thread	thread_20
PID	28733

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

Start	2016-05-14 18:22:35
End	2016-05-14 18:23:23
Elapsed	00:00:48
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.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-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/rep1/ATAC11-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/rep1/ATAC11-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz

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

Num	17
ID	task.postalign_bam.bedpe_to_tag_rep1.line_465.id_22
Name	bedpe_to_tag rep1
Thread	thread_20
PID	28795

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

Start	2016-05-14 18:23:24
End	2016-05-14 18:24:14
Elapsed	00:00:49
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.nodup.17.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-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/rep1/ATAC11-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/rep1/ATAC11-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/rep1/ATAC11-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/rep1/ATAC11-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz; mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz

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

Num	18
ID	task.postalign_bed.shift_tag_rep1.line_140.id_23
Name	shift_tag rep1
Thread	thread_20
PID	28861

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

Start	2016-05-14 18:24:15
End	2016-05-14 18:24:42
Elapsed	00:00:27
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.nodup.17.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-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/rep1/ATAC11-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/rep1/ATAC11-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz

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

Num	19
ID	task.postalign_bed.subsample_bedpe2tagrep1.line_89.id_24
Name	subsample_bedpe2tagrep1
Thread	thread_20
PID	28920

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

Start	2016-05-14 18:24:43
End	2016-05-14 18:25:04
Elapsed	00:00:20
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.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-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/rep1/ATAC11-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/rep1/ATAC11-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz

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

Num	20
ID	task.postalign_bed.xcor_rep1.line_165.id_25
Name	xcor rep1
Thread	thread_20
PID

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

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

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/align/rep1/ATAC11-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/qc/rep1/ATAC11-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/qc/rep1/ATAC11-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/rep1/ATAC11-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/rep1/ATAC11-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf -out=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/qc/rep1/ATAC11-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/rep1/ATAC11-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/qc/rep1/ATAC11-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/rep1/ATAC11-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC11+12/qc/rep1/ATAC11-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc

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

BigDataScript report: atac.bds

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