Script file	/users/pangwei/bds_atac/atac.bds
Program ID	atac.bds.20160513_182614_674
Start time	2016-05-13 18:26:14
Run time	17:44:21.087
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/ATAC7+8, -num_rep, 2, -fastq1_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC7/ATAC7-trimmed-pair1.fastq.gz, -fastq1_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC7/ATAC7-trimmed-pair2.fastq.gz, -fastq2_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC8/ATAC8-trimmed-pair1.fastq.gz, -fastq2_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC8/ATAC8-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_20	thread_Root	atac.bds.20160513_182614_674_parallel_20/task.align_bowtie2.bowtie2_PE_rep1.line_133.id_6 atac.bds.20160513_182614_674_parallel_20/task.postalign_bam.dedup_bam_PE_rep1.line_215.id_9 atac.bds.20160513_182614_674_parallel_20/task.postalign_bam.nmsrt_bam_rep1.line_321.id_19 atac.bds.20160513_182614_674_parallel_20/task.postalign_bam.bam_to_bedpe_rep1.line_425.id_20 atac.bds.20160513_182614_674_parallel_20/task.postalign_bed.subsample_bedpe_rep1.line_116.id_21 atac.bds.20160513_182614_674_parallel_20/task.postalign_bam.bedpe_to_tag_rep1.line_465.id_22 atac.bds.20160513_182614_674_parallel_20/task.postalign_bed.shift_tag_rep1.line_140.id_23 atac.bds.20160513_182614_674_parallel_20/task.postalign_bed.subsample_bedpe2tagrep1.line_89.id_24 atac.bds.20160513_182614_674_parallel_20/task.postalign_bed.xcor_rep1.line_165.id_25
thread_21	thread_Root	atac.bds.20160513_182614_674_parallel_21/task.align_bowtie2.bowtie2_PE_rep2.line_133.id_7 atac.bds.20160513_182614_674_parallel_21/task.postalign_bam.dedup_bam_PE_rep2.line_215.id_8 atac.bds.20160513_182614_674_parallel_21/task.postalign_bam.nmsrt_bam_rep2.line_321.id_10 atac.bds.20160513_182614_674_parallel_21/task.postalign_bam.bam_to_bedpe_rep2.line_425.id_11 atac.bds.20160513_182614_674_parallel_21/task.postalign_bed.subsample_bedpe_rep2.line_116.id_12 atac.bds.20160513_182614_674_parallel_21/task.postalign_bam.bedpe_to_tag_rep2.line_465.id_13 atac.bds.20160513_182614_674_parallel_21/task.postalign_bed.shift_tag_rep2.line_140.id_14 atac.bds.20160513_182614_674_parallel_21/task.postalign_bed.subsample_bedpe2tagrep2.line_89.id_15 atac.bds.20160513_182614_674_parallel_21/task.postalign_bed.xcor_rep2.line_165.id_16 atac.bds.20160513_182614_674_parallel_21/task.callpeak_macs2.macs2_atac_rep2.pval0.1.line_192.id_17 atac.bds.20160513_182614_674_parallel_21/task.callpeak_macs2.macs2_atac_rep2.line_192.id_18

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.align_bowtie2.bowtie2_PE_rep1.line_133.id_6
Name	bowtie2_PE rep1
Thread	thread_20
PID	103943

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

Start	2016-05-13 18:26:15
End	2016-05-14 07:57:20
Elapsed	13:31:05
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.fastq.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair2.trim.fastq.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-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/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.fastq.gz -2 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair2.trim.fastq.gz 2>/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.align.log | samtools view -bS - | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE

# SYS command. line 142

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-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 79 files...

Num	2
ID	task.align_bowtie2.bowtie2_PE_rep2.line_133.id_7
Name	bowtie2_PE rep2
Thread	thread_21
PID	103950

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

Start	2016-05-13 18:26:15
End	2016-05-14 05:27:44
Elapsed	11:01:28
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.fastq.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair2.trim.fastq.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-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/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.fastq.gz -2 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair2.trim.fastq.gz 2>/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.align.log | samtools view -bS - | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE

# SYS command. line 142

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-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 60 files...

Num	3
ID	task.postalign_bam.dedup_bam_PE_rep2.line_215.id_8
Name	dedup_bam_PE rep2
Thread	thread_21
PID	16768

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

Start	2016-05-14 05:27:45
End	2016-05-14 08:13:38
Elapsed	02:45:53
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.dup.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-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/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-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/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-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/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.filt

# SYS command. line 239

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-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/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-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/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-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/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-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/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.filt.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 269

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 271

 if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.bai" ]; then \
			cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.bai; \
			fi

# SYS command. line 275

 samtools flagstat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc

# SYS command. line 286

 samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.filt.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.filt.bam.tmp

# SYS command. line 287

 bedtools bamtobed -bedpe -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-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/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.pbc.qc

# SYS command. line 291

 rm /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam

# SYS command. line 293

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.filt.bam

# SYS command. line 294

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-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 41 files...
[bam_sort_core] merging from 41 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Sat May 14 06:53:32 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-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 06:53:32 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 06:53:32	MarkDuplicates	Start of doWork freeMemory: 254889728; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-14 06:53:32	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-05-14 06:53:32	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-05-14 06:53:40	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:07s.  Time for last 1,000,000:    7s.  Last read position: chr10:66,873,921
INFO	2016-05-14 06:53:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 06:53:46	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:13s.  Time for last 1,000,000:    6s.  Last read position: chr10:115,628,215
INFO	2016-05-14 06:53:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 06:53:50	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:18s.  Time for last 1,000,000:    4s.  Last read position: chr11:27,486,088
INFO	2016-05-14 06:53:50	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 06:53:56	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:23s.  Time for last 1,000,000:    5s.  Last read position: chr11:76,637,610
INFO	2016-05-14 06:53:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 06:53:59	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:26s.  Time for last 1,000,000:    3s.  Last read position: chr11:131,365,519
INFO	2016-05-14 06:53:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 06:54:04	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:31s.  Time for last 1,000,000:    4s.  Last read position: chr12:53,782,518
INFO	2016-05-14 06:54:04	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 06:54:08	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:35s.  Time for last 1,000,000:    3s.  Last read position: chr12:109,925,902
INFO	2016-05-14 06:54:08	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-14 06:54:12	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:39s.  Time for last 1,000,000:    4s.  Last read position: chr13:47,660,661
INFO	2016-05-14 06:54:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 06:54:16	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:43s.  Time for last 1,000,000:    3s.  Last read position: chr13:112,110,943
INFO	2016-05-14 06:54:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 06:54:21	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:49s.  Time for last 1,000,000:    5s.  Last read position: chr14:75,019,195
INFO	2016-05-14 06:54:21	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 06:54:25	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:52s.  Time for last 1,000,000:    3s.  Last read position: chr15:42,705,390
INFO	2016-05-14 06:54:25	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-14 06:54:29	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:00:56s.  Time for last 1,000,000:    3s.  Last read position: chr15:93,809,340
INFO	2016-05-14 06:54:29	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 06:54:35	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:02s.  Time for last 1,000,000:    5s.  Last read position: chr16:53,468,387
INFO	2016-05-14 06:54:35	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-05-14 06:54:38	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:06s.  Time for last 1,000,000:    3s.  Last read position: chr17:6,485,989
INFO	2016-05-14 06:54:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 06:54:53	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:20s.  Time for last 1,000,000:   14s.  Last read position: chr17:54,671,685
INFO	2016-05-14 06:54:53	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-14 06:54:57	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:24s.  Time for last 1,000,000:    4s.  Last read position: chr18:22,901,727
INFO	2016-05-14 06:54:57	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 06:55:01	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:01:28s.  Time for last 1,000,000:    3s.  Last read position: chr19:1,146,450
INFO	2016-05-14 06:55:01	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 06:55:06	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:01:33s.  Time for last 1,000,000:    5s.  Last read position: chr19:44,031,431
INFO	2016-05-14 06:55:06	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-14 06:55:09	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:01:37s.  Time for last 1,000,000:    3s.  Last read position: chr1:14,580,295
INFO	2016-05-14 06:55:09	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 06:55:14	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:01:41s.  Time for last 1,000,000:    4s.  Last read position: chr1:54,712,429
INFO	2016-05-14 06:55:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 06:55:19	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:01:47s.  Time for last 1,000,000:    5s.  Last read position: chr1:113,971,495
INFO	2016-05-14 06:55:19	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 06:55:23	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:01:50s.  Time for last 1,000,000:    3s.  Last read position: chr1:191,762,010
INFO	2016-05-14 06:55:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 06:55:27	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:01:54s.  Time for last 1,000,000:    3s.  Last read position: chr1:243,582,818
INFO	2016-05-14 06:55:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 06:55:30	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:01:57s.  Time for last 1,000,000:    3s.  Last read position: chr20:44,957,998
INFO	2016-05-14 06:55:30	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 06:55:36	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:02:04s.  Time for last 1,000,000:    6s.  Last read position: chr21:46,823,760
INFO	2016-05-14 06:55:36	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-14 06:55:40	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:02:07s.  Time for last 1,000,000:    3s.  Last read position: chr2:5,831,591
INFO	2016-05-14 06:55:40	MarkDuplicates	Tracking 12 as yet unmatched pairs. 12 records in RAM.
INFO	2016-05-14 06:55:45	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:02:12s.  Time for last 1,000,000:    4s.  Last read position: chr2:57,779,939
INFO	2016-05-14 06:55:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 06:55:49	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:02:16s.  Time for last 1,000,000:    4s.  Last read position: chr2:121,732,014
INFO	2016-05-14 06:55:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 06:55:55	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:02:23s.  Time for last 1,000,000:    6s.  Last read position: chr2:182,548,706
INFO	2016-05-14 06:55:55	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-05-14 06:56:08	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:02:35s.  Time for last 1,000,000:   12s.  Last read position: chr2:239,144,937
INFO	2016-05-14 06:56:08	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-14 06:56:12	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:02:39s.  Time for last 1,000,000:    3s.  Last read position: chr3:46,466,280
INFO	2016-05-14 06:56:12	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 06:56:17	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:02:44s.  Time for last 1,000,000:    4s.  Last read position: chr3:109,563,611
INFO	2016-05-14 06:56:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 06:56:21	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:02:48s.  Time for last 1,000,000:    3s.  Last read position: chr3:167,434,229
INFO	2016-05-14 06:56:21	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 06:56:26	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:02:53s.  Time for last 1,000,000:    5s.  Last read position: chr4:20,758,886
INFO	2016-05-14 06:56:26	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 06:56:30	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:02:57s.  Time for last 1,000,000:    3s.  Last read position: chr4:90,190,660
INFO	2016-05-14 06:56:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 06:56:33	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:03:01s.  Time for last 1,000,000:    3s.  Last read position: chr4:155,686,735
INFO	2016-05-14 06:56:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 06:56:37	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:03:05s.  Time for last 1,000,000:    3s.  Last read position: chr5:28,450,549
INFO	2016-05-14 06:56:37	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 06:56:41	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:03:08s.  Time for last 1,000,000:    3s.  Last read position: chr5:96,682,690
INFO	2016-05-14 06:56:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 06:56:47	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:03:14s.  Time for last 1,000,000:    6s.  Last read position: chr5:139,717,380
INFO	2016-05-14 06:56:47	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 06:56:51	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:03:18s.  Time for last 1,000,000:    3s.  Last read position: chr6:9,841,124
INFO	2016-05-14 06:56:51	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 06:56:54	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:03:21s.  Time for last 1,000,000:    3s.  Last read position: chr6:65,428,861
INFO	2016-05-14 06:56:54	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 06:56:58	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:03:25s.  Time for last 1,000,000:    3s.  Last read position: chr6:130,321,827
INFO	2016-05-14 06:56:58	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 06:57:01	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:03:29s.  Time for last 1,000,000:    3s.  Last read position: chr7:11,462,415
INFO	2016-05-14 06:57:01	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 06:57:08	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:03:35s.  Time for last 1,000,000:    6s.  Last read position: chr7:77,146,657
INFO	2016-05-14 06:57:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 06:57:15	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:03:43s.  Time for last 1,000,000:    7s.  Last read position: chr7:133,812,224
INFO	2016-05-14 06:57:15	MarkDuplicates	Tracking 20 as yet unmatched pairs. 20 records in RAM.
INFO	2016-05-14 06:57:19	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:03:46s.  Time for last 1,000,000:    3s.  Last read position: chr8:29,274,695
INFO	2016-05-14 06:57:19	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 06:57:23	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:03:50s.  Time for last 1,000,000:    3s.  Last read position: chr8:92,720,317
INFO	2016-05-14 06:57:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 06:57:26	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:03:54s.  Time for last 1,000,000:    3s.  Last read position: chr8:145,021,372
INFO	2016-05-14 06:57:26	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-14 06:57:30	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:03:57s.  Time for last 1,000,000:    3s.  Last read position: chr9:89,553,899
INFO	2016-05-14 06:57:30	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 06:57:35	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:04:03s.  Time for last 1,000,000:    5s.  Last read position: chr9:136,603,402
INFO	2016-05-14 06:57:35	MarkDuplicates	Tracking 14 as yet unmatched pairs. 14 records in RAM.
INFO	2016-05-14 06:57:39	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:04:06s.  Time for last 1,000,000:    3s.  Last read position: chrM:347
INFO	2016-05-14 06:57:39	MarkDuplicates	Tracking 27616 as yet unmatched pairs. 27616 records in RAM.
INFO	2016-05-14 06:57:42	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:04:09s.  Time for last 1,000,000:    3s.  Last read position: chrM:684
INFO	2016-05-14 06:57:42	MarkDuplicates	Tracking 42136 as yet unmatched pairs. 42136 records in RAM.
INFO	2016-05-14 06:57:45	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:04:13s.  Time for last 1,000,000:    3s.  Last read position: chrM:964
INFO	2016-05-14 06:57:45	MarkDuplicates	Tracking 73702 as yet unmatched pairs. 73702 records in RAM.
INFO	2016-05-14 06:57:49	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:04:16s.  Time for last 1,000,000:    3s.  Last read position: chrM:1,454
INFO	2016-05-14 06:57:49	MarkDuplicates	Tracking 25298 as yet unmatched pairs. 25298 records in RAM.
INFO	2016-05-14 06:57:52	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:04:19s.  Time for last 1,000,000:    3s.  Last read position: chrM:1,840
INFO	2016-05-14 06:57:52	MarkDuplicates	Tracking 52750 as yet unmatched pairs. 52750 records in RAM.
INFO	2016-05-14 06:57:59	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:04:26s.  Time for last 1,000,000:    6s.  Last read position: chrM:2,256
INFO	2016-05-14 06:57:59	MarkDuplicates	Tracking 27828 as yet unmatched pairs. 27828 records in RAM.
INFO	2016-05-14 06:58:02	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:04:29s.  Time for last 1,000,000:    2s.  Last read position: chrM:2,660
INFO	2016-05-14 06:58:02	MarkDuplicates	Tracking 62426 as yet unmatched pairs. 62426 records in RAM.
INFO	2016-05-14 06:58:05	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:04:32s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,888
INFO	2016-05-14 06:58:05	MarkDuplicates	Tracking 59160 as yet unmatched pairs. 59160 records in RAM.
INFO	2016-05-14 06:58:18	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:04:45s.  Time for last 1,000,000:   12s.  Last read position: chrM:3,153
INFO	2016-05-14 06:58:18	MarkDuplicates	Tracking 47620 as yet unmatched pairs. 47620 records in RAM.
INFO	2016-05-14 06:58:21	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:04:49s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,370
INFO	2016-05-14 06:58:21	MarkDuplicates	Tracking 58078 as yet unmatched pairs. 58078 records in RAM.
INFO	2016-05-14 06:58:26	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:04:53s.  Time for last 1,000,000:    4s.  Last read position: chrM:3,577
INFO	2016-05-14 06:58:26	MarkDuplicates	Tracking 20456 as yet unmatched pairs. 20456 records in RAM.
INFO	2016-05-14 06:58:30	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:04:58s.  Time for last 1,000,000:    4s.  Last read position: chrM:3,769
INFO	2016-05-14 06:58:30	MarkDuplicates	Tracking 49876 as yet unmatched pairs. 49876 records in RAM.
INFO	2016-05-14 06:58:36	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:05:03s.  Time for last 1,000,000:    5s.  Last read position: chrM:4,092
INFO	2016-05-14 06:58:36	MarkDuplicates	Tracking 20782 as yet unmatched pairs. 20782 records in RAM.
INFO	2016-05-14 06:58:39	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:05:06s.  Time for last 1,000,000:    2s.  Last read position: chrM:4,889
INFO	2016-05-14 06:58:39	MarkDuplicates	Tracking 28790 as yet unmatched pairs. 28790 records in RAM.
INFO	2016-05-14 06:58:42	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:05:09s.  Time for last 1,000,000:    2s.  Last read position: chrM:5,331
INFO	2016-05-14 06:58:42	MarkDuplicates	Tracking 28592 as yet unmatched pairs. 28592 records in RAM.
INFO	2016-05-14 06:58:45	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:05:12s.  Time for last 1,000,000:    2s.  Last read position: chrM:5,999
INFO	2016-05-14 06:58:45	MarkDuplicates	Tracking 43716 as yet unmatched pairs. 43716 records in RAM.
INFO	2016-05-14 06:58:48	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:05:15s.  Time for last 1,000,000:    2s.  Last read position: chrM:6,338
INFO	2016-05-14 06:58:48	MarkDuplicates	Tracking 45416 as yet unmatched pairs. 45416 records in RAM.
INFO	2016-05-14 06:58:51	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:05:18s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,528
INFO	2016-05-14 06:58:51	MarkDuplicates	Tracking 55880 as yet unmatched pairs. 55880 records in RAM.
INFO	2016-05-14 06:58:54	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:05:21s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,947
INFO	2016-05-14 06:58:54	MarkDuplicates	Tracking 34012 as yet unmatched pairs. 34012 records in RAM.
INFO	2016-05-14 06:58:59	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:05:26s.  Time for last 1,000,000:    5s.  Last read position: chrM:7,501
INFO	2016-05-14 06:58:59	MarkDuplicates	Tracking 31718 as yet unmatched pairs. 31718 records in RAM.
INFO	2016-05-14 06:59:02	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:05:29s.  Time for last 1,000,000:    3s.  Last read position: chrM:7,870
INFO	2016-05-14 06:59:02	MarkDuplicates	Tracking 42444 as yet unmatched pairs. 42444 records in RAM.
INFO	2016-05-14 06:59:05	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:05:32s.  Time for last 1,000,000:    3s.  Last read position: chrM:8,200
INFO	2016-05-14 06:59:05	MarkDuplicates	Tracking 42028 as yet unmatched pairs. 42028 records in RAM.
INFO	2016-05-14 06:59:08	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:05:36s.  Time for last 1,000,000:    3s.  Last read position: chrM:8,915
INFO	2016-05-14 06:59:08	MarkDuplicates	Tracking 9626 as yet unmatched pairs. 9626 records in RAM.
INFO	2016-05-14 06:59:15	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:05:42s.  Time for last 1,000,000:    6s.  Last read position: chrM:9,310
INFO	2016-05-14 06:59:15	MarkDuplicates	Tracking 4438 as yet unmatched pairs. 4438 records in RAM.
INFO	2016-05-14 06:59:18	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:05:45s.  Time for last 1,000,000:    2s.  Last read position: chrM:9,811
INFO	2016-05-14 06:59:18	MarkDuplicates	Tracking 61974 as yet unmatched pairs. 61974 records in RAM.
INFO	2016-05-14 06:59:21	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:05:48s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,127
INFO	2016-05-14 06:59:21	MarkDuplicates	Tracking 22360 as yet unmatched pairs. 22360 records in RAM.
INFO	2016-05-14 06:59:24	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:05:51s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,407
INFO	2016-05-14 06:59:24	MarkDuplicates	Tracking 60142 as yet unmatched pairs. 60142 records in RAM.
INFO	2016-05-14 06:59:27	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:05:54s.  Time for last 1,000,000:    2s.  Last read position: chrM:10,738
INFO	2016-05-14 06:59:27	MarkDuplicates	Tracking 5214 as yet unmatched pairs. 5214 records in RAM.
INFO	2016-05-14 06:59:32	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:05:59s.  Time for last 1,000,000:    4s.  Last read position: chrM:11,231
INFO	2016-05-14 06:59:32	MarkDuplicates	Tracking 27076 as yet unmatched pairs. 27076 records in RAM.
INFO	2016-05-14 06:59:35	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:06:02s.  Time for last 1,000,000:    2s.  Last read position: chrM:11,552
INFO	2016-05-14 06:59:35	MarkDuplicates	Tracking 50466 as yet unmatched pairs. 50466 records in RAM.
INFO	2016-05-14 06:59:38	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:06:05s.  Time for last 1,000,000:    2s.  Last read position: chrM:11,949
INFO	2016-05-14 06:59:38	MarkDuplicates	Tracking 12810 as yet unmatched pairs. 12810 records in RAM.
INFO	2016-05-14 06:59:41	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:06:08s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,186
INFO	2016-05-14 06:59:41	MarkDuplicates	Tracking 25078 as yet unmatched pairs. 25078 records in RAM.
INFO	2016-05-14 06:59:44	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:06:11s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,519
INFO	2016-05-14 06:59:44	MarkDuplicates	Tracking 42182 as yet unmatched pairs. 42182 records in RAM.
INFO	2016-05-14 06:59:47	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:06:14s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,742
INFO	2016-05-14 06:59:47	MarkDuplicates	Tracking 28676 as yet unmatched pairs. 28676 records in RAM.
INFO	2016-05-14 06:59:50	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:06:17s.  Time for last 1,000,000:    2s.  Last read position: chrM:13,099
INFO	2016-05-14 06:59:50	MarkDuplicates	Tracking 47836 as yet unmatched pairs. 47836 records in RAM.
INFO	2016-05-14 06:59:56	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:06:23s.  Time for last 1,000,000:    6s.  Last read position: chrM:13,345
INFO	2016-05-14 06:59:56	MarkDuplicates	Tracking 51718 as yet unmatched pairs. 51718 records in RAM.
INFO	2016-05-14 06:59:59	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:06:26s.  Time for last 1,000,000:    2s.  Last read position: chrM:13,574
INFO	2016-05-14 06:59:59	MarkDuplicates	Tracking 35522 as yet unmatched pairs. 35522 records in RAM.
INFO	2016-05-14 07:00:02	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:06:29s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,886
INFO	2016-05-14 07:00:02	MarkDuplicates	Tracking 54928 as yet unmatched pairs. 54928 records in RAM.
INFO	2016-05-14 07:00:17	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:06:44s.  Time for last 1,000,000:   15s.  Last read position: chrM:14,258
INFO	2016-05-14 07:00:17	MarkDuplicates	Tracking 19900 as yet unmatched pairs. 19900 records in RAM.
INFO	2016-05-14 07:00:20	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:06:48s.  Time for last 1,000,000:    3s.  Last read position: chrM:14,535
INFO	2016-05-14 07:00:20	MarkDuplicates	Tracking 6088 as yet unmatched pairs. 6088 records in RAM.
INFO	2016-05-14 07:00:23	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:06:51s.  Time for last 1,000,000:    2s.  Last read position: chrM:15,015
INFO	2016-05-14 07:00:23	MarkDuplicates	Tracking 52984 as yet unmatched pairs. 52984 records in RAM.
INFO	2016-05-14 07:00:28	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:06:55s.  Time for last 1,000,000:    4s.  Last read position: chrM:15,206
INFO	2016-05-14 07:00:28	MarkDuplicates	Tracking 26206 as yet unmatched pairs. 26206 records in RAM.
INFO	2016-05-14 07:00:32	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:07:00s.  Time for last 1,000,000:    4s.  Last read position: chrM:15,421
INFO	2016-05-14 07:00:32	MarkDuplicates	Tracking 66808 as yet unmatched pairs. 66808 records in RAM.
INFO	2016-05-14 07:00:37	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:07:04s.  Time for last 1,000,000:    4s.  Last read position: chrM:15,626
INFO	2016-05-14 07:00:37	MarkDuplicates	Tracking 49896 as yet unmatched pairs. 49896 records in RAM.
INFO	2016-05-14 07:00:41	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:07:08s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,813
INFO	2016-05-14 07:00:41	MarkDuplicates	Tracking 76192 as yet unmatched pairs. 76192 records in RAM.
INFO	2016-05-14 07:00:46	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:07:13s.  Time for last 1,000,000:    5s.  Last read position: chrM:16,110
INFO	2016-05-14 07:00:46	MarkDuplicates	Tracking 27428 as yet unmatched pairs. 27428 records in RAM.
INFO	2016-05-14 07:00:49	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:07:16s.  Time for last 1,000,000:    3s.  Last read position: chrM:16,420
INFO	2016-05-14 07:00:49	MarkDuplicates	Tracking 31140 as yet unmatched pairs. 31140 records in RAM.
INFO	2016-05-14 07:00:53	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:07:20s.  Time for last 1,000,000:    3s.  Last read position: chrX:36,869,809
INFO	2016-05-14 07:00:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 07:00:56	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:07:24s.  Time for last 1,000,000:    3s.  Last read position: chrX:110,946,315
INFO	2016-05-14 07:00:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 07:00:59	MarkDuplicates	Read 99719144 records. 0 pairs never matched.
INFO	2016-05-14 07:01:05	MarkDuplicates	After buildSortedReadEndLists freeMemory: 2939969496; totalMemory: 2967470080; maxMemory: 3817865216
INFO	2016-05-14 07:01:05	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-05-14 07:01:05	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-05-14 07:01:33	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-05-14 07:01:56	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-05-14 07:01:59	MarkDuplicates	After generateDuplicateIndexes freeMemory: 1979258624; totalMemory: 2960654336; maxMemory: 3817865216
INFO	2016-05-14 07:01:59	MarkDuplicates	Marking 51580156 records as duplicates.
INFO	2016-05-14 07:01:59	MarkDuplicates	Found 16577536 optical duplicate clusters.
INFO	2016-05-14 07:03:29	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:29s.  Time for last 10,000,000:   89s.  Last read position: chr14:75,019,195
INFO	2016-05-14 07:05:01	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:03:01s.  Time for last 10,000,000:   92s.  Last read position: chr1:54,712,429
INFO	2016-05-14 07:06:35	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:04:34s.  Time for last 10,000,000:   93s.  Last read position: chr2:239,144,937
INFO	2016-05-14 07:08:08	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:06:07s.  Time for last 10,000,000:   93s.  Last read position: chr6:9,841,124
INFO	2016-05-14 07:09:40	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:07:40s.  Time for last 10,000,000:   92s.  Last read position: chr9:136,603,402
INFO	2016-05-14 07:10:54	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:08:54s.  Time for last 10,000,000:   73s.  Last read position: chrM:3,370
INFO	2016-05-14 07:12:06	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:10:05s.  Time for last 10,000,000:   71s.  Last read position: chrM:7,501
INFO	2016-05-14 07:13:18	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:11:17s.  Time for last 10,000,000:   71s.  Last read position: chrM:11,552
INFO	2016-05-14 07:14:30	MarkDuplicates	Written    90,000,000 records.  Elapsed time: 00:12:29s.  Time for last 10,000,000:   72s.  Last read position: chrM:14,535
INFO	2016-05-14 07:15:47	MarkDuplicates	Before output close freeMemory: 3075394040; totalMemory: 3105882112; maxMemory: 3817865216
INFO	2016-05-14 07:15:47	MarkDuplicates	After output close freeMemory: 3075392984; totalMemory: 3105882112; maxMemory: 3817865216
[Sat May 14 07:15:47 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 22.25 minutes.
Runtime.totalMemory()=3105882112
[bam_sort_core] merging from 41 files...

Num	4
ID	task.postalign_bam.dedup_bam_PE_rep1.line_215.id_9
Name	dedup_bam_PE rep1
Thread	thread_20
PID	18734

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

Start	2016-05-14 07:57:21
End	2016-05-14 11:38:19
Elapsed	03:40:57
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.dup.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-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/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-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/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-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/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.filt

# SYS command. line 239

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-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/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-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/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-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/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-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/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.filt.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 269

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 271

 if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.bai" ]; then \
			cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.bai; \
			fi

# SYS command. line 275

 samtools flagstat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc

# SYS command. line 286

 samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.filt.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.filt.bam.tmp

# SYS command. line 287

 bedtools bamtobed -bedpe -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-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/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.pbc.qc

# SYS command. line 291

 rm /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam

# SYS command. line 293

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.filt.bam

# SYS command. line 294

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-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 54 files...
[bam_sort_core] merging from 54 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Sat May 14 09:48:04 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-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 09:48:04 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 09:48:04	MarkDuplicates	Start of doWork freeMemory: 254889728; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-14 09:48:04	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-05-14 09:48:04	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-05-14 09:48:23	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:17s.  Time for last 1,000,000:   17s.  Last read position: chr10:47,682,104
INFO	2016-05-14 09:48:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:48:36	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:30s.  Time for last 1,000,000:   12s.  Last read position: chr10:87,979,282
INFO	2016-05-14 09:48:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:48:50	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:43s.  Time for last 1,000,000:   13s.  Last read position: chr10:122,973,590
INFO	2016-05-14 09:48:50	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:48:54	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:48s.  Time for last 1,000,000:    4s.  Last read position: chr11:17,874,423
INFO	2016-05-14 09:48:54	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:49:00	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:54s.  Time for last 1,000,000:    5s.  Last read position: chr11:61,531,946
INFO	2016-05-14 09:49:00	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-14 09:49:03	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:57s.  Time for last 1,000,000:    3s.  Last read position: chr11:90,730,603
INFO	2016-05-14 09:49:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:49:10	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:01:03s.  Time for last 1,000,000:    6s.  Last read position: chr11:128,646,378
INFO	2016-05-14 09:49:10	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:49:14	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:01:08s.  Time for last 1,000,000:    4s.  Last read position: chr12:32,639,398
INFO	2016-05-14 09:49:14	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:49:21	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:01:15s.  Time for last 1,000,000:    7s.  Last read position: chr12:74,414,485
INFO	2016-05-14 09:49:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:49:25	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:01:19s.  Time for last 1,000,000:    4s.  Last read position: chr12:114,576,505
INFO	2016-05-14 09:49:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:49:33	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:27s.  Time for last 1,000,000:    7s.  Last read position: chr13:36,060,965
INFO	2016-05-14 09:49:33	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-14 09:49:37	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:31s.  Time for last 1,000,000:    4s.  Last read position: chr13:86,694,120
INFO	2016-05-14 09:49:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:49:42	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:35s.  Time for last 1,000,000:    4s.  Last read position: chr14:33,048,057
INFO	2016-05-14 09:49:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:49:47	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:41s.  Time for last 1,000,000:    5s.  Last read position: chr14:75,748,120
INFO	2016-05-14 09:49:47	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-05-14 09:50:03	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:57s.  Time for last 1,000,000:   16s.  Last read position: chr15:25,461,777
INFO	2016-05-14 09:50:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:50:08	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:02:02s.  Time for last 1,000,000:    4s.  Last read position: chr15:67,223,343
INFO	2016-05-14 09:50:08	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:50:14	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:02:08s.  Time for last 1,000,000:    5s.  Last read position: chr15:100,016,840
INFO	2016-05-14 09:50:14	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-14 09:50:17	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:02:11s.  Time for last 1,000,000:    3s.  Last read position: chr16:30,871,981
INFO	2016-05-14 09:50:17	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-14 09:50:22	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:02:16s.  Time for last 1,000,000:    4s.  Last read position: chr16:77,429,151
INFO	2016-05-14 09:50:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:50:25	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:02:19s.  Time for last 1,000,000:    3s.  Last read position: chr17:15,465,278
INFO	2016-05-14 09:50:25	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:50:29	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:02:23s.  Time for last 1,000,000:    3s.  Last read position: chr17:47,379,883
INFO	2016-05-14 09:50:29	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:50:36	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:02:30s.  Time for last 1,000,000:    7s.  Last read position: chr17:77,289,969
INFO	2016-05-14 09:50:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:50:41	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:02:34s.  Time for last 1,000,000:    4s.  Last read position: chr18:36,574,182
INFO	2016-05-14 09:50:41	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:50:45	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:02:39s.  Time for last 1,000,000:    4s.  Last read position: chr18:78,005,138
INFO	2016-05-14 09:50:45	MarkDuplicates	Tracking 14 as yet unmatched pairs. 14 records in RAM.
INFO	2016-05-14 09:50:54	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:02:47s.  Time for last 1,000,000:    8s.  Last read position: chr19:24,555,243
INFO	2016-05-14 09:50:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:50:58	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:02:52s.  Time for last 1,000,000:    4s.  Last read position: chr19:56,056,093
INFO	2016-05-14 09:50:58	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:51:03	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:02:57s.  Time for last 1,000,000:    5s.  Last read position: chr1:16,381,361
INFO	2016-05-14 09:51:03	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-14 09:51:07	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:03:01s.  Time for last 1,000,000:    4s.  Last read position: chr1:41,908,588
INFO	2016-05-14 09:51:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:51:14	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:03:07s.  Time for last 1,000,000:    6s.  Last read position: chr1:78,257,892
INFO	2016-05-14 09:51:14	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:51:26	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:03:20s.  Time for last 1,000,000:   12s.  Last read position: chr1:145,062,021
INFO	2016-05-14 09:51:26	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-14 09:51:31	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:03:24s.  Time for last 1,000,000:    4s.  Last read position: chr1:182,021,994
INFO	2016-05-14 09:51:31	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:51:38	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:03:32s.  Time for last 1,000,000:    7s.  Last read position: chr1:220,683,136
INFO	2016-05-14 09:51:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:51:45	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:03:38s.  Time for last 1,000,000:    6s.  Last read position: chr20:7,808,358
INFO	2016-05-14 09:51:45	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-14 09:51:50	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:03:44s.  Time for last 1,000,000:    5s.  Last read position: chr20:44,518,883
INFO	2016-05-14 09:51:50	MarkDuplicates	Tracking 16 as yet unmatched pairs. 16 records in RAM.
INFO	2016-05-14 09:51:54	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:03:48s.  Time for last 1,000,000:    3s.  Last read position: chr21:32,622,640
INFO	2016-05-14 09:51:54	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:51:57	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:03:51s.  Time for last 1,000,000:    3s.  Last read position: chr22:31,873,140
INFO	2016-05-14 09:51:57	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:52:02	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:03:56s.  Time for last 1,000,000:    4s.  Last read position: chr2:9,716,914
INFO	2016-05-14 09:52:02	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:52:05	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:03:59s.  Time for last 1,000,000:    3s.  Last read position: chr2:45,155,838
INFO	2016-05-14 09:52:05	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:52:09	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:04:03s.  Time for last 1,000,000:    3s.  Last read position: chr2:85,977,990
INFO	2016-05-14 09:52:09	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-14 09:52:12	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:04:06s.  Time for last 1,000,000:    3s.  Last read position: chr2:133,493,474
INFO	2016-05-14 09:52:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:52:19	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:04:13s.  Time for last 1,000,000:    6s.  Last read position: chr2:179,469,154
INFO	2016-05-14 09:52:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:52:23	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:04:17s.  Time for last 1,000,000:    4s.  Last read position: chr2:222,666,314
INFO	2016-05-14 09:52:23	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:52:28	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:04:22s.  Time for last 1,000,000:    5s.  Last read position: chr3:13,216,647
INFO	2016-05-14 09:52:28	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:52:33	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:04:27s.  Time for last 1,000,000:    5s.  Last read position: chr3:49,943,050
INFO	2016-05-14 09:52:33	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-14 09:52:42	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:04:36s.  Time for last 1,000,000:    8s.  Last read position: chr3:98,299,908
INFO	2016-05-14 09:52:42	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:52:47	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:04:41s.  Time for last 1,000,000:    5s.  Last read position: chr3:139,817,067
INFO	2016-05-14 09:52:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:52:51	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:04:45s.  Time for last 1,000,000:    3s.  Last read position: chr3:185,519,389
INFO	2016-05-14 09:52:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:52:54	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:04:48s.  Time for last 1,000,000:    3s.  Last read position: chr4:21,843,017
INFO	2016-05-14 09:52:54	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:52:58	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:04:52s.  Time for last 1,000,000:    3s.  Last read position: chr4:75,272,597
INFO	2016-05-14 09:52:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:53:01	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:04:55s.  Time for last 1,000,000:    3s.  Last read position: chr4:122,632,863
INFO	2016-05-14 09:53:01	MarkDuplicates	Tracking 32 as yet unmatched pairs. 32 records in RAM.
INFO	2016-05-14 09:53:07	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:05:01s.  Time for last 1,000,000:    5s.  Last read position: chr4:171,486,263
INFO	2016-05-14 09:53:07	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:53:11	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:05:05s.  Time for last 1,000,000:    3s.  Last read position: chr5:25,599,507
INFO	2016-05-14 09:53:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:53:16	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:05:10s.  Time for last 1,000,000:    5s.  Last read position: chr5:77,930,708
INFO	2016-05-14 09:53:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:53:21	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:05:15s.  Time for last 1,000,000:    5s.  Last read position: chr5:126,231,620
INFO	2016-05-14 09:53:21	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-14 09:53:29	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:05:23s.  Time for last 1,000,000:    8s.  Last read position: chr5:149,815,720
INFO	2016-05-14 09:53:29	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-14 09:53:34	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:05:27s.  Time for last 1,000,000:    4s.  Last read position: chr6:5,084,300
INFO	2016-05-14 09:53:34	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-14 09:53:39	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:05:33s.  Time for last 1,000,000:    5s.  Last read position: chr6:40,874,972
INFO	2016-05-14 09:53:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:53:44	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:05:38s.  Time for last 1,000,000:    5s.  Last read position: chr6:88,443,215
INFO	2016-05-14 09:53:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:53:57	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:05:51s.  Time for last 1,000,000:   13s.  Last read position: chr6:134,545,417
INFO	2016-05-14 09:53:57	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:54:01	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:05:54s.  Time for last 1,000,000:    3s.  Last read position: chr7:1,499,783
INFO	2016-05-14 09:54:01	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-05-14 09:54:07	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:06:00s.  Time for last 1,000,000:    6s.  Last read position: chr7:40,642,804
INFO	2016-05-14 09:54:07	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:54:10	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:06:04s.  Time for last 1,000,000:    3s.  Last read position: chr7:91,043,101
INFO	2016-05-14 09:54:10	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:54:15	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:06:09s.  Time for last 1,000,000:    4s.  Last read position: chr7:130,537,009
INFO	2016-05-14 09:54:15	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:54:18	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:06:12s.  Time for last 1,000,000:    3s.  Last read position: chr8:11,030,925
INFO	2016-05-14 09:54:18	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:54:22	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:06:16s.  Time for last 1,000,000:    3s.  Last read position: chr8:55,163,663
INFO	2016-05-14 09:54:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:54:27	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:06:20s.  Time for last 1,000,000:    4s.  Last read position: chr8:100,508,110
INFO	2016-05-14 09:54:27	MarkDuplicates	Tracking 598 as yet unmatched pairs. 598 records in RAM.
INFO	2016-05-14 09:54:30	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:06:24s.  Time for last 1,000,000:    3s.  Last read position: chr8:141,943,274
INFO	2016-05-14 09:54:30	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:54:34	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:06:28s.  Time for last 1,000,000:    3s.  Last read position: chr9:34,675,256
INFO	2016-05-14 09:54:34	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:54:38	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:06:32s.  Time for last 1,000,000:    3s.  Last read position: chr9:105,432,834
INFO	2016-05-14 09:54:38	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-14 09:54:41	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:06:35s.  Time for last 1,000,000:    3s.  Last read position: chr9:136,019,607
INFO	2016-05-14 09:54:41	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-05-14 09:54:44	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:06:38s.  Time for last 1,000,000:    3s.  Last read position: chrM:196
INFO	2016-05-14 09:54:44	MarkDuplicates	Tracking 60162 as yet unmatched pairs. 60162 records in RAM.
INFO	2016-05-14 09:54:52	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:06:46s.  Time for last 1,000,000:    8s.  Last read position: chrM:550
INFO	2016-05-14 09:54:52	MarkDuplicates	Tracking 6832 as yet unmatched pairs. 6832 records in RAM.
INFO	2016-05-14 09:54:56	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:06:50s.  Time for last 1,000,000:    4s.  Last read position: chrM:790
INFO	2016-05-14 09:54:56	MarkDuplicates	Tracking 66822 as yet unmatched pairs. 66822 records in RAM.
INFO	2016-05-14 09:55:05	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:06:59s.  Time for last 1,000,000:    9s.  Last read position: chrM:1,233
INFO	2016-05-14 09:55:05	MarkDuplicates	Tracking 30934 as yet unmatched pairs. 30934 records in RAM.
INFO	2016-05-14 09:55:11	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:07:05s.  Time for last 1,000,000:    5s.  Last read position: chrM:1,476
INFO	2016-05-14 09:55:11	MarkDuplicates	Tracking 51128 as yet unmatched pairs. 51128 records in RAM.
INFO	2016-05-14 09:55:16	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:07:10s.  Time for last 1,000,000:    4s.  Last read position: chrM:1,745
INFO	2016-05-14 09:55:16	MarkDuplicates	Tracking 15262 as yet unmatched pairs. 15262 records in RAM.
INFO	2016-05-14 09:55:21	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:07:15s.  Time for last 1,000,000:    4s.  Last read position: chrM:2,116
INFO	2016-05-14 09:55:21	MarkDuplicates	Tracking 38316 as yet unmatched pairs. 38316 records in RAM.
INFO	2016-05-14 09:55:25	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:07:18s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,531
INFO	2016-05-14 09:55:25	MarkDuplicates	Tracking 48308 as yet unmatched pairs. 48308 records in RAM.
INFO	2016-05-14 09:55:31	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:07:25s.  Time for last 1,000,000:    6s.  Last read position: chrM:2,712
INFO	2016-05-14 09:55:31	MarkDuplicates	Tracking 93758 as yet unmatched pairs. 93758 records in RAM.
INFO	2016-05-14 09:55:34	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:07:28s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,884
INFO	2016-05-14 09:55:34	MarkDuplicates	Tracking 81858 as yet unmatched pairs. 81858 records in RAM.
INFO	2016-05-14 09:55:37	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:07:31s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,088
INFO	2016-05-14 09:55:37	MarkDuplicates	Tracking 85476 as yet unmatched pairs. 85476 records in RAM.
INFO	2016-05-14 09:55:41	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:07:35s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,307
INFO	2016-05-14 09:55:41	MarkDuplicates	Tracking 57724 as yet unmatched pairs. 57724 records in RAM.
INFO	2016-05-14 09:55:44	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:07:38s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,438
INFO	2016-05-14 09:55:44	MarkDuplicates	Tracking 76512 as yet unmatched pairs. 76512 records in RAM.
INFO	2016-05-14 09:55:50	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:07:43s.  Time for last 1,000,000:    5s.  Last read position: chrM:3,604
INFO	2016-05-14 09:55:50	MarkDuplicates	Tracking 54834 as yet unmatched pairs. 54834 records in RAM.
INFO	2016-05-14 09:55:53	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:07:47s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,758
INFO	2016-05-14 09:55:53	MarkDuplicates	Tracking 58322 as yet unmatched pairs. 58322 records in RAM.
INFO	2016-05-14 09:55:56	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:07:50s.  Time for last 1,000,000:    3s.  Last read position: chrM:4,013
INFO	2016-05-14 09:55:56	MarkDuplicates	Tracking 26124 as yet unmatched pairs. 26124 records in RAM.
INFO	2016-05-14 09:55:59	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:07:53s.  Time for last 1,000,000:    3s.  Last read position: chrM:4,684
INFO	2016-05-14 09:55:59	MarkDuplicates	Tracking 7362 as yet unmatched pairs. 7362 records in RAM.
INFO	2016-05-14 09:56:02	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:07:56s.  Time for last 1,000,000:    3s.  Last read position: chrM:4,977
INFO	2016-05-14 09:56:02	MarkDuplicates	Tracking 57718 as yet unmatched pairs. 57718 records in RAM.
INFO	2016-05-14 09:56:18	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:08:12s.  Time for last 1,000,000:   15s.  Last read position: chrM:5,385
INFO	2016-05-14 09:56:18	MarkDuplicates	Tracking 30782 as yet unmatched pairs. 30782 records in RAM.
INFO	2016-05-14 09:56:22	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:08:15s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,000
INFO	2016-05-14 09:56:22	MarkDuplicates	Tracking 39282 as yet unmatched pairs. 39282 records in RAM.
INFO	2016-05-14 09:56:26	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:08:20s.  Time for last 1,000,000:    4s.  Last read position: chrM:6,286
INFO	2016-05-14 09:56:26	MarkDuplicates	Tracking 63596 as yet unmatched pairs. 63596 records in RAM.
INFO	2016-05-14 09:56:30	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:08:24s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,456
INFO	2016-05-14 09:56:30	MarkDuplicates	Tracking 51216 as yet unmatched pairs. 51216 records in RAM.
INFO	2016-05-14 09:56:34	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:08:28s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,625
INFO	2016-05-14 09:56:34	MarkDuplicates	Tracking 73486 as yet unmatched pairs. 73486 records in RAM.
INFO	2016-05-14 09:56:37	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:08:31s.  Time for last 1,000,000:    3s.  Last read position: chrM:7,009
INFO	2016-05-14 09:56:37	MarkDuplicates	Tracking 27776 as yet unmatched pairs. 27776 records in RAM.
INFO	2016-05-14 09:56:40	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:08:34s.  Time for last 1,000,000:    3s.  Last read position: chrM:7,492
INFO	2016-05-14 09:56:40	MarkDuplicates	Tracking 36418 as yet unmatched pairs. 36418 records in RAM.
INFO	2016-05-14 09:56:44	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:08:38s.  Time for last 1,000,000:    3s.  Last read position: chrM:7,838
INFO	2016-05-14 09:56:44	MarkDuplicates	Tracking 59306 as yet unmatched pairs. 59306 records in RAM.
INFO	2016-05-14 09:56:48	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:08:42s.  Time for last 1,000,000:    4s.  Last read position: chrM:8,087
INFO	2016-05-14 09:56:48	MarkDuplicates	Tracking 60686 as yet unmatched pairs. 60686 records in RAM.
INFO	2016-05-14 09:56:54	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:08:48s.  Time for last 1,000,000:    5s.  Last read position: chrM:8,456
INFO	2016-05-14 09:56:54	MarkDuplicates	Tracking 43424 as yet unmatched pairs. 43424 records in RAM.
INFO	2016-05-14 09:56:58	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:08:52s.  Time for last 1,000,000:    3s.  Last read position: chrM:9,065
INFO	2016-05-14 09:56:58	MarkDuplicates	Tracking 18646 as yet unmatched pairs. 18646 records in RAM.
INFO	2016-05-14 09:57:01	MarkDuplicates	Read   100,000,000 records.  Elapsed time: 00:08:55s.  Time for last 1,000,000:    3s.  Last read position: chrM:9,386
INFO	2016-05-14 09:57:01	MarkDuplicates	Tracking 8162 as yet unmatched pairs. 8162 records in RAM.
INFO	2016-05-14 09:57:05	MarkDuplicates	Read   101,000,000 records.  Elapsed time: 00:08:59s.  Time for last 1,000,000:    3s.  Last read position: chrM:9,778
INFO	2016-05-14 09:57:05	MarkDuplicates	Tracking 77358 as yet unmatched pairs. 77358 records in RAM.
INFO	2016-05-14 09:57:08	MarkDuplicates	Read   102,000,000 records.  Elapsed time: 00:09:02s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,005
INFO	2016-05-14 09:57:08	MarkDuplicates	Tracking 106210 as yet unmatched pairs. 106210 records in RAM.
INFO	2016-05-14 09:57:16	MarkDuplicates	Read   103,000,000 records.  Elapsed time: 00:09:10s.  Time for last 1,000,000:    7s.  Last read position: chrM:10,279
INFO	2016-05-14 09:57:16	MarkDuplicates	Tracking 42924 as yet unmatched pairs. 42924 records in RAM.
INFO	2016-05-14 09:57:20	MarkDuplicates	Read   104,000,000 records.  Elapsed time: 00:09:14s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,589
INFO	2016-05-14 09:57:20	MarkDuplicates	Tracking 28818 as yet unmatched pairs. 28818 records in RAM.
INFO	2016-05-14 09:57:23	MarkDuplicates	Read   105,000,000 records.  Elapsed time: 00:09:17s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,905
INFO	2016-05-14 09:57:23	MarkDuplicates	Tracking 2686 as yet unmatched pairs. 2686 records in RAM.
INFO	2016-05-14 09:57:29	MarkDuplicates	Read   106,000,000 records.  Elapsed time: 00:09:23s.  Time for last 1,000,000:    5s.  Last read position: chrM:11,219
INFO	2016-05-14 09:57:29	MarkDuplicates	Tracking 47816 as yet unmatched pairs. 47816 records in RAM.
INFO	2016-05-14 09:57:32	MarkDuplicates	Read   107,000,000 records.  Elapsed time: 00:09:26s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,495
INFO	2016-05-14 09:57:32	MarkDuplicates	Tracking 26502 as yet unmatched pairs. 26502 records in RAM.
INFO	2016-05-14 09:57:35	MarkDuplicates	Read   108,000,000 records.  Elapsed time: 00:09:29s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,771
INFO	2016-05-14 09:57:35	MarkDuplicates	Tracking 39276 as yet unmatched pairs. 39276 records in RAM.
INFO	2016-05-14 09:57:38	MarkDuplicates	Read   109,000,000 records.  Elapsed time: 00:09:32s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,008
INFO	2016-05-14 09:57:38	MarkDuplicates	Tracking 39198 as yet unmatched pairs. 39198 records in RAM.
INFO	2016-05-14 09:57:42	MarkDuplicates	Read   110,000,000 records.  Elapsed time: 00:09:35s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,219
INFO	2016-05-14 09:57:42	MarkDuplicates	Tracking 29282 as yet unmatched pairs. 29282 records in RAM.
INFO	2016-05-14 09:57:45	MarkDuplicates	Read   111,000,000 records.  Elapsed time: 00:09:39s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,509
INFO	2016-05-14 09:57:45	MarkDuplicates	Tracking 53382 as yet unmatched pairs. 53382 records in RAM.
INFO	2016-05-14 09:57:48	MarkDuplicates	Read   112,000,000 records.  Elapsed time: 00:09:42s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,675
INFO	2016-05-14 09:57:48	MarkDuplicates	Tracking 94382 as yet unmatched pairs. 94382 records in RAM.
INFO	2016-05-14 09:57:51	MarkDuplicates	Read   113,000,000 records.  Elapsed time: 00:09:45s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,988
INFO	2016-05-14 09:57:51	MarkDuplicates	Tracking 21120 as yet unmatched pairs. 21120 records in RAM.
INFO	2016-05-14 09:57:57	MarkDuplicates	Read   114,000,000 records.  Elapsed time: 00:09:51s.  Time for last 1,000,000:    5s.  Last read position: chrM:13,185
INFO	2016-05-14 09:57:57	MarkDuplicates	Tracking 77274 as yet unmatched pairs. 77274 records in RAM.
INFO	2016-05-14 09:58:00	MarkDuplicates	Read   115,000,000 records.  Elapsed time: 00:09:54s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,383
INFO	2016-05-14 09:58:00	MarkDuplicates	Tracking 63470 as yet unmatched pairs. 63470 records in RAM.
INFO	2016-05-14 09:58:03	MarkDuplicates	Read   116,000,000 records.  Elapsed time: 00:09:57s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,580
INFO	2016-05-14 09:58:03	MarkDuplicates	Tracking 41142 as yet unmatched pairs. 41142 records in RAM.
INFO	2016-05-14 09:58:07	MarkDuplicates	Read   117,000,000 records.  Elapsed time: 00:10:00s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,844
INFO	2016-05-14 09:58:07	MarkDuplicates	Tracking 87536 as yet unmatched pairs. 87536 records in RAM.
INFO	2016-05-14 09:58:21	MarkDuplicates	Read   118,000,000 records.  Elapsed time: 00:10:15s.  Time for last 1,000,000:   14s.  Last read position: chrM:14,055
INFO	2016-05-14 09:58:21	MarkDuplicates	Tracking 62288 as yet unmatched pairs. 62288 records in RAM.
INFO	2016-05-14 09:58:25	MarkDuplicates	Read   119,000,000 records.  Elapsed time: 00:10:18s.  Time for last 1,000,000:    3s.  Last read position: chrM:14,372
INFO	2016-05-14 09:58:25	MarkDuplicates	Tracking 23790 as yet unmatched pairs. 23790 records in RAM.
INFO	2016-05-14 09:58:28	MarkDuplicates	Read   120,000,000 records.  Elapsed time: 00:10:21s.  Time for last 1,000,000:    3s.  Last read position: chrM:14,805
INFO	2016-05-14 09:58:28	MarkDuplicates	Tracking 8666 as yet unmatched pairs. 8666 records in RAM.
INFO	2016-05-14 09:58:31	MarkDuplicates	Read   121,000,000 records.  Elapsed time: 00:10:25s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,043
INFO	2016-05-14 09:58:31	MarkDuplicates	Tracking 98206 as yet unmatched pairs. 98206 records in RAM.
INFO	2016-05-14 09:58:36	MarkDuplicates	Read   122,000,000 records.  Elapsed time: 00:10:30s.  Time for last 1,000,000:    5s.  Last read position: chrM:15,190
INFO	2016-05-14 09:58:36	MarkDuplicates	Tracking 33004 as yet unmatched pairs. 33004 records in RAM.
INFO	2016-05-14 09:58:39	MarkDuplicates	Read   123,000,000 records.  Elapsed time: 00:10:33s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,371
INFO	2016-05-14 09:58:39	MarkDuplicates	Tracking 89050 as yet unmatched pairs. 89050 records in RAM.
INFO	2016-05-14 09:58:42	MarkDuplicates	Read   124,000,000 records.  Elapsed time: 00:10:36s.  Time for last 1,000,000:    2s.  Last read position: chrM:15,538
INFO	2016-05-14 09:58:42	MarkDuplicates	Tracking 76128 as yet unmatched pairs. 76128 records in RAM.
INFO	2016-05-14 09:58:45	MarkDuplicates	Read   125,000,000 records.  Elapsed time: 00:10:39s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,703
INFO	2016-05-14 09:58:45	MarkDuplicates	Tracking 79862 as yet unmatched pairs. 79862 records in RAM.
INFO	2016-05-14 09:58:49	MarkDuplicates	Read   126,000,000 records.  Elapsed time: 00:10:42s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,843
INFO	2016-05-14 09:58:49	MarkDuplicates	Tracking 78330 as yet unmatched pairs. 78330 records in RAM.
INFO	2016-05-14 09:58:52	MarkDuplicates	Read   127,000,000 records.  Elapsed time: 00:10:46s.  Time for last 1,000,000:    3s.  Last read position: chrM:16,105
INFO	2016-05-14 09:58:52	MarkDuplicates	Tracking 33850 as yet unmatched pairs. 33850 records in RAM.
INFO	2016-05-14 09:58:55	MarkDuplicates	Read   128,000,000 records.  Elapsed time: 00:10:49s.  Time for last 1,000,000:    3s.  Last read position: chrM:16,384
INFO	2016-05-14 09:58:55	MarkDuplicates	Tracking 47272 as yet unmatched pairs. 47272 records in RAM.
INFO	2016-05-14 09:58:58	MarkDuplicates	Read   129,000,000 records.  Elapsed time: 00:10:52s.  Time for last 1,000,000:    3s.  Last read position: chrX:10,575,286
INFO	2016-05-14 09:58:58	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-14 09:59:02	MarkDuplicates	Read   130,000,000 records.  Elapsed time: 00:10:56s.  Time for last 1,000,000:    3s.  Last read position: chrX:57,337,012
INFO	2016-05-14 09:59:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:59:08	MarkDuplicates	Read   131,000,000 records.  Elapsed time: 00:11:02s.  Time for last 1,000,000:    6s.  Last read position: chrX:116,383,097
INFO	2016-05-14 09:59:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:59:11	MarkDuplicates	Read 131866052 records. 0 pairs never matched.
INFO	2016-05-14 09:59:20	MarkDuplicates	After buildSortedReadEndLists freeMemory: 3628843600; totalMemory: 3656384512; maxMemory: 3817865216
INFO	2016-05-14 09:59:20	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-05-14 09:59:20	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-05-14 09:59:59	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-05-14 10:00:28	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-05-14 10:00:32	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2689072192; totalMemory: 3671064576; maxMemory: 3817865216
INFO	2016-05-14 10:00:32	MarkDuplicates	Marking 65805438 records as duplicates.
INFO	2016-05-14 10:00:32	MarkDuplicates	Found 21775038 optical duplicate clusters.
INFO	2016-05-14 10:02:07	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:33s.  Time for last 10,000,000:   93s.  Last read position: chr12:114,576,505
INFO	2016-05-14 10:03:40	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:03:05s.  Time for last 10,000,000:   92s.  Last read position: chr17:15,465,278
INFO	2016-05-14 10:05:16	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:04:41s.  Time for last 10,000,000:   96s.  Last read position: chr1:145,062,021
INFO	2016-05-14 10:06:51	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:06:17s.  Time for last 10,000,000:   95s.  Last read position: chr2:133,493,474
INFO	2016-05-14 10:08:26	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:07:52s.  Time for last 10,000,000:   94s.  Last read position: chr4:122,632,863
INFO	2016-05-14 10:10:01	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:09:27s.  Time for last 10,000,000:   95s.  Last read position: chr7:1,499,783
INFO	2016-05-14 10:11:42	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:11:08s.  Time for last 10,000,000:  101s.  Last read position: chr9:136,019,607
INFO	2016-05-14 10:13:07	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:12:33s.  Time for last 10,000,000:   85s.  Last read position: chrM:2,884
INFO	2016-05-14 10:14:27	MarkDuplicates	Written    90,000,000 records.  Elapsed time: 00:13:53s.  Time for last 10,000,000:   80s.  Last read position: chrM:6,000
INFO	2016-05-14 10:15:45	MarkDuplicates	Written   100,000,000 records.  Elapsed time: 00:15:11s.  Time for last 10,000,000:   77s.  Last read position: chrM:9,386
INFO	2016-05-14 10:17:06	MarkDuplicates	Written   110,000,000 records.  Elapsed time: 00:16:32s.  Time for last 10,000,000:   80s.  Last read position: chrM:12,219
INFO	2016-05-14 10:18:25	MarkDuplicates	Written   120,000,000 records.  Elapsed time: 00:17:51s.  Time for last 10,000,000:   79s.  Last read position: chrM:14,805
INFO	2016-05-14 10:19:48	MarkDuplicates	Written   130,000,000 records.  Elapsed time: 00:19:13s.  Time for last 10,000,000:   82s.  Last read position: chrX:57,337,012
INFO	2016-05-14 10:20:06	MarkDuplicates	Before output close freeMemory: 3706637696; totalMemory: 3737124864; maxMemory: 3817865216
INFO	2016-05-14 10:20:06	MarkDuplicates	After output close freeMemory: 3706636640; totalMemory: 3737124864; maxMemory: 3817865216
[Sat May 14 10:20:06 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 32.03 minutes.
Runtime.totalMemory()=3737124864
[bam_sort_core] merging from 54 files...

Num	5
ID	task.postalign_bam.nmsrt_bam_rep2.line_321.id_10
Name	nmsrt_bam rep2
Thread	thread_21
PID	18933

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

Start	2016-05-14 08:13:39
End	2016-05-14 08:32:26
Elapsed	00:18:47
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-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/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-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 20 files...

Num	6
ID	task.postalign_bam.bam_to_bedpe_rep2.line_425.id_11
Name	bam_to_bedpe rep2
Thread	thread_21
PID	19120

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

Start	2016-05-14 08:32:26
End	2016-05-14 08:35:04
Elapsed	00:02:37
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-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/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-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	7
ID	task.postalign_bed.subsample_bedpe_rep2.line_116.id_12
Name	subsample_bedpe rep2
Thread	thread_21
PID	19189

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

Start	2016-05-14 08:35:05
End	2016-05-14 08:37:15
Elapsed	00:02:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-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/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | grep -v "chrM" | shuf -n 17500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-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	8
ID	task.postalign_bam.bedpe_to_tag_rep2.line_465.id_13
Name	bedpe_to_tag rep2
Thread	thread_21
PID	19259

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

Start	2016-05-14 08:37:16
End	2016-05-14 08:38:57
Elapsed	00:01:41
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-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/ATAC7+8/align/rep2/ATAC8-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/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz

# SYS command. line 472

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz | grep -P -v 'chrM' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz; mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-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	9
ID	task.postalign_bed.shift_tag_rep2.line_140.id_14
Name	shift_tag rep2
Thread	thread_21
PID	19329

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

Start	2016-05-14 08:38:58
End	2016-05-14 08:40:02
Elapsed	00:01:04
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-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/ATAC7+8/align/rep2/ATAC8-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/ATAC7+8/align/rep2/ATAC8-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	10
ID	task.postalign_bed.subsample_bedpe2tagrep2.line_89.id_15
Name	subsample_bedpe2tagrep2
Thread	thread_21
PID	19391

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

Start	2016-05-14 08:40:03
End	2016-05-14 08:41:50
Elapsed	00:01:47
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-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/ATAC7+8/align/rep2/ATAC8-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/ATAC7+8/align/rep2/ATAC8-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	11
ID	task.postalign_bed.xcor_rep2.line_165.id_16
Name	xcor rep2
Thread	thread_21
PID	19459

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

Start	2016-05-14 08:41:50
End	2016-05-14 09:19:03
Elapsed	00:37:12
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-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/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz -p=1 \
			-filtchr=chrM -savp=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf -out=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-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/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp

# SYS command. line 175

 mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc

   
--------------------Stdout--------------------
################
ChIP data: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-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/ATAC7+8/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/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf 
result filename: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-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/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz 
opened /tmp/RtmpijqwUp/ATAC8-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign4cac271dd801
done. read 22997955 fragments
ChIP data read length 73 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.2315254 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.251607847757416 
Top 3 estimates for fragment length 0 
Window half size 480 
Phantom peak location 65 
Phantom peak Correlation 0.2533923 
Normalized Strand cross-correlation coefficient (NSC) 1.08674 
Relative Strand Cross correlation Coefficient (RSC) 0.9183944 
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	12
ID	task.callpeak_macs2.macs2_atac_rep2.pval0.1.line_192.id_17
Name	macs2_atac rep2.pval0.1
Thread	thread_21
PID	19461

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

Start	2016-05-14 08:41:50
End	2016-05-14 08:41:50
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/signal/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/signal/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-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	13
ID	task.callpeak_macs2.macs2_atac_rep2.line_192.id_18
Name	macs2_atac rep2
Thread	thread_21
PID	19473

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

Start	2016-05-14 08:41:51
End	2016-05-14 08:41:51
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.gappedPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/signal/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/signal/macs2/rep2/ATAC8-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/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/signal/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/signal/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-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/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-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	14
ID	task.postalign_bam.nmsrt_bam_rep1.line_321.id_19
Name	nmsrt_bam rep1
Thread	thread_20
PID	21421

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

Start	2016-05-14 11:38:19
End	2016-05-14 12:02:31
Elapsed	00:24:11
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-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/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-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 27 files...

Num	15
ID	task.postalign_bam.bam_to_bedpe_rep1.line_425.id_20
Name	bam_to_bedpe rep1
Thread	thread_20
PID	23075

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

Start	2016-05-14 12:02:31
End	2016-05-14 12:05:19
Elapsed	00:02:47
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-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/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-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	23328

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

Start	2016-05-14 12:05:20
End	2016-05-14 12:06:57
Elapsed	00:01:36
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-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/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | grep -v "chrM" | shuf -n 17500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-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	23426

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

Start	2016-05-14 12:06:58
End	2016-05-14 12:08:32
Elapsed	00:01:34
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-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/ATAC7+8/align/rep1/ATAC7-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/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz

# SYS command. line 472

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz | grep -P -v 'chrM' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz; mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-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	23562

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

Start	2016-05-14 12:08:33
End	2016-05-14 12:09:26
Elapsed	00:00:52
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-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/ATAC7+8/align/rep1/ATAC7-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/ATAC7+8/align/rep1/ATAC7-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	23631

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

Start	2016-05-14 12:09:27
End	2016-05-14 12:10:35
Elapsed	00:01:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-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/ATAC7+8/align/rep1/ATAC7-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/ATAC7+8/align/rep1/ATAC7-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/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-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/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz -p=1 \
			-filtchr=chrM -savp=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf -out=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-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/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp

# SYS command. line 175

 mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-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/ATAC7+8, -num_rep, 2, -fastq1_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC7/ATAC7-trimmed-pair1.fastq.gz, -fastq1_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC7/ATAC7-trimmed-pair2.fastq.gz, -fastq2_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC8/ATAC8-trimmed-pair1.fastq.gz, -fastq2_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC8/ATAC8-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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Parallel (threads) details

Task details

Global scope