Script file	/users/pangwei/bds_atac/atac.bds
Program ID	atac.bds.20160515_230834_571
Start time	2016-05-15 23:08:34
Run time	20:01:27.204
Tasks executed	12
Tasks failed	0
Tasks failed names
Arguments*	[-out_dir, /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22, -num_rep, 2, -fastq1_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC21/ATAC21-trimmed-pair1.fastq.gz, -fastq1_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC21/ATAC21-trimmed-pair2.fastq.gz, -fastq2_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC22/ATAC22-trimmed-pair1.fastq.gz, -fastq2_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC22/ATAC22-trimmed-pair2.fastq.gz, -subsample, 17500000, -true_rep, -species, hg19]
System*	local
Cpus*	1
Exit value	0

Thread ID	Parent	Tasks
thread_Root	None
thread_20	thread_Root	atac.bds.20160515_230834_571_parallel_20/task.align_bowtie2.bowtie2_PE_rep1.line_133.id_6
thread_21	thread_Root	atac.bds.20160515_230834_571_parallel_21/task.align_bowtie2.bowtie2_PE_rep2.line_133.id_7 atac.bds.20160515_230834_571_parallel_21/task.postalign_bam.dedup_bam_PE_rep2.line_215.id_8 atac.bds.20160515_230834_571_parallel_21/task.postalign_bam.nmsrt_bam_rep2.line_321.id_9 atac.bds.20160515_230834_571_parallel_21/task.postalign_bam.bam_to_bedpe_rep2.line_425.id_10 atac.bds.20160515_230834_571_parallel_21/task.postalign_bed.subsample_bedpe_rep2.line_116.id_11 atac.bds.20160515_230834_571_parallel_21/task.postalign_bam.bedpe_to_tag_rep2.line_465.id_12 atac.bds.20160515_230834_571_parallel_21/task.postalign_bed.shift_tag_rep2.line_140.id_13 atac.bds.20160515_230834_571_parallel_21/task.postalign_bed.subsample_bedpe2tagrep2.line_89.id_14 atac.bds.20160515_230834_571_parallel_21/task.postalign_bed.xcor_rep2.line_165.id_15 atac.bds.20160515_230834_571_parallel_21/task.callpeak_macs2.macs2_atac_rep2.pval0.1.line_192.id_16 atac.bds.20160515_230834_571_parallel_21/task.callpeak_macs2.macs2_atac_rep2.line_192.id_17

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.align_bowtie2.bowtie2_PE_rep2.line_133.id_7
Name	bowtie2_PE rep2
Thread	thread_21
PID	88394

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

Start	2016-05-15 23:08:36
End	2016-05-16 11:09:36
Elapsed	12:01:00
Timeout	00:00:-1
Wall Timeout	100 days

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

 
# SYS command. line 135

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

# SYS command. line 139

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

# SYS command. line 142

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

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

Num	2
ID	task.align_bowtie2.bowtie2_PE_rep1.line_133.id_6
Name	bowtie2_PE rep1
Thread	thread_20
PID	88399

OK	false
Exit Code	0
Retries
State	RUNNING
Dep.	WAIT
Cpus	2
Mem

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

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

 
# SYS command. line 135

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

# SYS command. line 139

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

# SYS command. line 142

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

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

Num	3
ID	task.postalign_bam.dedup_bam_PE_rep2.line_215.id_8
Name	dedup_bam_PE rep2
Thread	thread_21
PID	106017

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

Start	2016-05-16 11:09:37
End	2016-05-16 15:38:47
Elapsed	04:29:10
Timeout	00:00:-1
Wall Timeout	100 days

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

 
# SYS command. line 217

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

# SYS command. line 228

 echo

# SYS command. line 229

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

# SYS command. line 230

 echo

# SYS command. line 237

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

# SYS command. line 238

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

# SYS command. line 239

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

# SYS command. line 243

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

# SYS command. line 244

 export MAX_JAVA_MEM="12G"

# SYS command. line 247

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

# SYS command. line 265

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

# SYS command. line 267

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

# SYS command. line 269

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

# SYS command. line 271

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

# SYS command. line 275

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

# SYS command. line 286

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

# SYS command. line 287

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

# SYS command. line 291

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

# SYS command. line 293

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

# SYS command. line 294

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

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



 
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 90 files...
[bam_sort_core] merging from 92 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Mon May 16 13:21:21 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep2/ATAC22-trimmed-pair1.trim.PE2SE.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Mon May 16 13:21:21 PDT 2016] Executing as pangwei@mitra on Linux 3.16.0-70-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_45-b14; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-05-16 13:21:21	MarkDuplicates	Start of doWork freeMemory: 254889800; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-16 13:21:21	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-05-16 13:21:21	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-05-16 13:21:28	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:06s.  Time for last 1,000,000:    6s.  Last read position: chr10:33,624,337
INFO	2016-05-16 13:21:28	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 13:21:33	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:11s.  Time for last 1,000,000:    5s.  Last read position: chr10:73,781,092
INFO	2016-05-16 13:21:33	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 13:21:39	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:17s.  Time for last 1,000,000:    6s.  Last read position: chr10:103,520,526
INFO	2016-05-16 13:21:39	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 13:21:45	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:24s.  Time for last 1,000,000:    6s.  Last read position: chr10:132,286,472
INFO	2016-05-16 13:21:45	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 13:21:50	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:28s.  Time for last 1,000,000:    4s.  Last read position: chr11:23,657,230
INFO	2016-05-16 13:21:50	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 13:21:56	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:34s.  Time for last 1,000,000:    5s.  Last read position: chr11:62,243,844
INFO	2016-05-16 13:21:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:22:01	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:39s.  Time for last 1,000,000:    5s.  Last read position: chr11:86,047,256
INFO	2016-05-16 13:22:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:22:05	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:43s.  Time for last 1,000,000:    3s.  Last read position: chr11:119,842,215
INFO	2016-05-16 13:22:05	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 13:22:09	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:47s.  Time for last 1,000,000:    4s.  Last read position: chr12:12,421,411
INFO	2016-05-16 13:22:09	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 13:22:15	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:54s.  Time for last 1,000,000:    6s.  Last read position: chr12:51,927,525
INFO	2016-05-16 13:22:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:22:20	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:58s.  Time for last 1,000,000:    4s.  Last read position: chr12:85,306,440
INFO	2016-05-16 13:22:20	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-05-16 13:22:24	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:02s.  Time for last 1,000,000:    4s.  Last read position: chr12:116,554,569
INFO	2016-05-16 13:22:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:22:31	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:09s.  Time for last 1,000,000:    6s.  Last read position: chr13:29,825,729
INFO	2016-05-16 13:22:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:22:35	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:13s.  Time for last 1,000,000:    4s.  Last read position: chr13:68,131,684
INFO	2016-05-16 13:22:35	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 13:22:52	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:30s.  Time for last 1,000,000:   17s.  Last read position: chr13:107,603,388
INFO	2016-05-16 13:22:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:22:57	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:35s.  Time for last 1,000,000:    4s.  Last read position: chr14:46,959,987
INFO	2016-05-16 13:22:57	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 13:23:01	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:01:39s.  Time for last 1,000,000:    4s.  Last read position: chr14:77,591,121
INFO	2016-05-16 13:23:01	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 13:23:07	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:01:45s.  Time for last 1,000,000:    5s.  Last read position: chr14:105,437,132
INFO	2016-05-16 13:23:07	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 13:23:11	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:01:49s.  Time for last 1,000,000:    4s.  Last read position: chr15:56,036,257
INFO	2016-05-16 13:23:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:23:15	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:01:53s.  Time for last 1,000,000:    4s.  Last read position: chr15:82,458,858
INFO	2016-05-16 13:23:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:23:19	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:01:57s.  Time for last 1,000,000:    4s.  Last read position: chr16:6,232,634
INFO	2016-05-16 13:23:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:23:23	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:02:01s.  Time for last 1,000,000:    3s.  Last read position: chr16:49,716,586
INFO	2016-05-16 13:23:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:23:29	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:02:07s.  Time for last 1,000,000:    6s.  Last read position: chr16:79,146,911
INFO	2016-05-16 13:23:29	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 13:23:34	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:02:12s.  Time for last 1,000,000:    4s.  Last read position: chr17:11,113,374
INFO	2016-05-16 13:23:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:23:39	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:02:17s.  Time for last 1,000,000:    4s.  Last read position: chr17:40,953,390
INFO	2016-05-16 13:23:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:23:43	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:02:21s.  Time for last 1,000,000:    3s.  Last read position: chr17:68,161,964
INFO	2016-05-16 13:23:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:23:46	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:02:25s.  Time for last 1,000,000:    3s.  Last read position: chr18:11,127,890
INFO	2016-05-16 13:23:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:23:53	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:02:32s.  Time for last 1,000,000:    6s.  Last read position: chr18:48,129,878
INFO	2016-05-16 13:23:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:23:57	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:02:35s.  Time for last 1,000,000:    3s.  Last read position: chr19:2,253,308
INFO	2016-05-16 13:23:57	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 13:24:10	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:02:49s.  Time for last 1,000,000:   13s.  Last read position: chr19:28,242,566
INFO	2016-05-16 13:24:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:24:15	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:02:53s.  Time for last 1,000,000:    4s.  Last read position: chr19:50,939,735
INFO	2016-05-16 13:24:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:24:19	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:02:57s.  Time for last 1,000,000:    3s.  Last read position: chr1:9,818,015
INFO	2016-05-16 13:24:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:24:23	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:03:01s.  Time for last 1,000,000:    4s.  Last read position: chr1:31,932,771
INFO	2016-05-16 13:24:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:24:29	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:03:07s.  Time for last 1,000,000:    5s.  Last read position: chr1:56,894,247
INFO	2016-05-16 13:24:29	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 13:24:33	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:03:11s.  Time for last 1,000,000:    4s.  Last read position: chr1:92,363,900
INFO	2016-05-16 13:24:33	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 13:24:37	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:03:15s.  Time for last 1,000,000:    3s.  Last read position: chr1:151,139,210
INFO	2016-05-16 13:24:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:24:40	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:03:19s.  Time for last 1,000,000:    3s.  Last read position: chr1:180,195,283
INFO	2016-05-16 13:24:40	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 13:24:44	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:03:22s.  Time for last 1,000,000:    3s.  Last read position: chr1:212,379,133
INFO	2016-05-16 13:24:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:24:48	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:03:26s.  Time for last 1,000,000:    3s.  Last read position: chr1:244,201,576
INFO	2016-05-16 13:24:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:24:54	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:03:32s.  Time for last 1,000,000:    5s.  Last read position: chr20:26,249,330
INFO	2016-05-16 13:24:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:24:57	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:03:35s.  Time for last 1,000,000:    3s.  Last read position: chr20:52,884,757
INFO	2016-05-16 13:24:57	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:25:01	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:03:39s.  Time for last 1,000,000:    3s.  Last read position: chr21:34,125,852
INFO	2016-05-16 13:25:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:25:05	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:03:43s.  Time for last 1,000,000:    3s.  Last read position: chr22:28,212,378
INFO	2016-05-16 13:25:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:25:09	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:03:47s.  Time for last 1,000,000:    3s.  Last read position: chr22:50,343,696
INFO	2016-05-16 13:25:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:25:17	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:03:55s.  Time for last 1,000,000:    8s.  Last read position: chr2:27,891,412
INFO	2016-05-16 13:25:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:25:21	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:03:59s.  Time for last 1,000,000:    3s.  Last read position: chr2:61,765,808
INFO	2016-05-16 13:25:21	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 13:25:26	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:04:04s.  Time for last 1,000,000:    5s.  Last read position: chr2:100,217,354
INFO	2016-05-16 13:25:26	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 13:25:30	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:04:08s.  Time for last 1,000,000:    3s.  Last read position: chr2:134,733,820
INFO	2016-05-16 13:25:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:25:35	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:04:13s.  Time for last 1,000,000:    4s.  Last read position: chr2:173,524,446
INFO	2016-05-16 13:25:35	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 13:25:39	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:04:17s.  Time for last 1,000,000:    3s.  Last read position: chr2:210,634,207
INFO	2016-05-16 13:25:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:25:43	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:04:21s.  Time for last 1,000,000:    3s.  Last read position: chr2:240,687,697
INFO	2016-05-16 13:25:43	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 13:25:47	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:04:25s.  Time for last 1,000,000:    4s.  Last read position: chr3:28,307,660
INFO	2016-05-16 13:25:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:25:51	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:04:29s.  Time for last 1,000,000:    4s.  Last read position: chr3:55,954,780
INFO	2016-05-16 13:25:51	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 13:25:58	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:04:36s.  Time for last 1,000,000:    7s.  Last read position: chr3:98,060,441
INFO	2016-05-16 13:25:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:26:02	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:04:40s.  Time for last 1,000,000:    4s.  Last read position: chr3:132,003,853
INFO	2016-05-16 13:26:02	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 13:26:07	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:04:45s.  Time for last 1,000,000:    4s.  Last read position: chr3:167,994,379
INFO	2016-05-16 13:26:07	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 13:26:11	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:04:49s.  Time for last 1,000,000:    4s.  Last read position: chr4:1,834,834
INFO	2016-05-16 13:26:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:26:16	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:04:54s.  Time for last 1,000,000:    4s.  Last read position: chr4:35,404,631
INFO	2016-05-16 13:26:16	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 13:26:28	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:05:06s.  Time for last 1,000,000:   11s.  Last read position: chr4:79,145,978
INFO	2016-05-16 13:26:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:26:32	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:05:10s.  Time for last 1,000,000:    4s.  Last read position: chr4:118,544,853
INFO	2016-05-16 13:26:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:26:36	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:05:14s.  Time for last 1,000,000:    3s.  Last read position: chr4:158,488,082
INFO	2016-05-16 13:26:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:26:39	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:05:17s.  Time for last 1,000,000:    3s.  Last read position: chr5:4,411,919
INFO	2016-05-16 13:26:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:26:44	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:05:22s.  Time for last 1,000,000:    4s.  Last read position: chr5:43,312,679
INFO	2016-05-16 13:26:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:26:48	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:05:26s.  Time for last 1,000,000:    3s.  Last read position: chr5:85,713,177
INFO	2016-05-16 13:26:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:26:52	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:05:30s.  Time for last 1,000,000:    3s.  Last read position: chr5:125,343,613
INFO	2016-05-16 13:26:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:26:55	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:05:33s.  Time for last 1,000,000:    3s.  Last read position: chr5:148,378,014
INFO	2016-05-16 13:26:55	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 13:26:59	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:05:37s.  Time for last 1,000,000:    3s.  Last read position: chr5:177,993,958
INFO	2016-05-16 13:26:59	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 13:27:03	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:05:41s.  Time for last 1,000,000:    3s.  Last read position: chr6:27,045,581
INFO	2016-05-16 13:27:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:27:06	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:05:45s.  Time for last 1,000,000:    3s.  Last read position: chr6:52,908,953
INFO	2016-05-16 13:27:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:27:10	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:05:49s.  Time for last 1,000,000:    4s.  Last read position: chr6:96,333,869
INFO	2016-05-16 13:27:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:27:17	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:05:55s.  Time for last 1,000,000:    6s.  Last read position: chr6:133,055,769
INFO	2016-05-16 13:27:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:27:21	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:06:00s.  Time for last 1,000,000:    4s.  Last read position: chr6:165,968,735
INFO	2016-05-16 13:27:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:27:25	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:06:03s.  Time for last 1,000,000:    3s.  Last read position: chr7:25,730,443
INFO	2016-05-16 13:27:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:27:33	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:06:11s.  Time for last 1,000,000:    7s.  Last read position: chr7:64,190,167
INFO	2016-05-16 13:27:33	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 13:27:37	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:06:15s.  Time for last 1,000,000:    3s.  Last read position: chr7:100,289,402
INFO	2016-05-16 13:27:37	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 13:27:41	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:06:19s.  Time for last 1,000,000:    3s.  Last read position: chr7:134,224,285
INFO	2016-05-16 13:27:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:27:45	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:06:23s.  Time for last 1,000,000:    3s.  Last read position: chr8:6,722,926
INFO	2016-05-16 13:27:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:27:49	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:06:27s.  Time for last 1,000,000:    4s.  Last read position: chr8:38,853,694
INFO	2016-05-16 13:27:49	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-16 13:27:53	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:06:31s.  Time for last 1,000,000:    3s.  Last read position: chr8:77,912,991
INFO	2016-05-16 13:27:53	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-16 13:27:59	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:06:37s.  Time for last 1,000,000:    6s.  Last read position: chr8:114,566,376
INFO	2016-05-16 13:27:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:28:03	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:06:41s.  Time for last 1,000,000:    3s.  Last read position: chr8:144,592,782
INFO	2016-05-16 13:28:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:28:07	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:06:45s.  Time for last 1,000,000:    3s.  Last read position: chr9:34,043,638
INFO	2016-05-16 13:28:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:28:11	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:06:49s.  Time for last 1,000,000:    4s.  Last read position: chr9:96,993,696
INFO	2016-05-16 13:28:11	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 13:28:15	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:06:53s.  Time for last 1,000,000:    3s.  Last read position: chr9:127,483,632
INFO	2016-05-16 13:28:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:28:19	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:06:57s.  Time for last 1,000,000:    4s.  Last read position: chrM:80
INFO	2016-05-16 13:28:19	MarkDuplicates	Tracking 15336 as yet unmatched pairs. 15336 records in RAM.
INFO	2016-05-16 13:28:22	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:07:00s.  Time for last 1,000,000:    3s.  Last read position: chrM:490
INFO	2016-05-16 13:28:22	MarkDuplicates	Tracking 13016 as yet unmatched pairs. 13016 records in RAM.
INFO	2016-05-16 13:28:25	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:07:03s.  Time for last 1,000,000:    3s.  Last read position: chrM:759
INFO	2016-05-16 13:28:25	MarkDuplicates	Tracking 5556 as yet unmatched pairs. 5556 records in RAM.
INFO	2016-05-16 13:28:28	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:07:06s.  Time for last 1,000,000:    3s.  Last read position: chrM:1,315
INFO	2016-05-16 13:28:28	MarkDuplicates	Tracking 5162 as yet unmatched pairs. 5162 records in RAM.
INFO	2016-05-16 13:28:40	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:07:18s.  Time for last 1,000,000:   11s.  Last read position: chrM:1,716
INFO	2016-05-16 13:28:40	MarkDuplicates	Tracking 8410 as yet unmatched pairs. 8410 records in RAM.
INFO	2016-05-16 13:28:44	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:07:22s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,243
INFO	2016-05-16 13:28:44	MarkDuplicates	Tracking 3776 as yet unmatched pairs. 3776 records in RAM.
INFO	2016-05-16 13:28:47	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:07:25s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,688
INFO	2016-05-16 13:28:47	MarkDuplicates	Tracking 18694 as yet unmatched pairs. 18694 records in RAM.
INFO	2016-05-16 13:28:50	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:07:28s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,973
INFO	2016-05-16 13:28:50	MarkDuplicates	Tracking 13166 as yet unmatched pairs. 13166 records in RAM.
INFO	2016-05-16 13:28:53	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:07:31s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,272
INFO	2016-05-16 13:28:53	MarkDuplicates	Tracking 9632 as yet unmatched pairs. 9632 records in RAM.
INFO	2016-05-16 13:28:56	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:07:35s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,486
INFO	2016-05-16 13:28:56	MarkDuplicates	Tracking 21606 as yet unmatched pairs. 21606 records in RAM.
INFO	2016-05-16 13:28:59	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:07:38s.  Time for last 1,000,000:    2s.  Last read position: chrM:3,690
INFO	2016-05-16 13:28:59	MarkDuplicates	Tracking 14078 as yet unmatched pairs. 14078 records in RAM.
INFO	2016-05-16 13:29:03	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:07:41s.  Time for last 1,000,000:    3s.  Last read position: chrM:4,060
INFO	2016-05-16 13:29:03	MarkDuplicates	Tracking 4558 as yet unmatched pairs. 4558 records in RAM.
INFO	2016-05-16 13:29:06	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:07:44s.  Time for last 1,000,000:    3s.  Last read position: chrM:4,918
INFO	2016-05-16 13:29:06	MarkDuplicates	Tracking 4500 as yet unmatched pairs. 4500 records in RAM.
INFO	2016-05-16 13:29:09	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:07:47s.  Time for last 1,000,000:    3s.  Last read position: chrM:5,393
INFO	2016-05-16 13:29:09	MarkDuplicates	Tracking 1714 as yet unmatched pairs. 1714 records in RAM.
INFO	2016-05-16 13:29:12	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:07:50s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,230
INFO	2016-05-16 13:29:12	MarkDuplicates	Tracking 13772 as yet unmatched pairs. 13772 records in RAM.
INFO	2016-05-16 13:29:18	MarkDuplicates	Read   100,000,000 records.  Elapsed time: 00:07:56s.  Time for last 1,000,000:    6s.  Last read position: chrM:6,472
INFO	2016-05-16 13:29:18	MarkDuplicates	Tracking 6486 as yet unmatched pairs. 6486 records in RAM.
INFO	2016-05-16 13:29:23	MarkDuplicates	Read   101,000,000 records.  Elapsed time: 00:08:01s.  Time for last 1,000,000:    5s.  Last read position: chrM:6,977
INFO	2016-05-16 13:29:23	MarkDuplicates	Tracking 1694 as yet unmatched pairs. 1694 records in RAM.
INFO	2016-05-16 13:29:27	MarkDuplicates	Read   102,000,000 records.  Elapsed time: 00:08:05s.  Time for last 1,000,000:    3s.  Last read position: chrM:7,699
INFO	2016-05-16 13:29:27	MarkDuplicates	Tracking 5360 as yet unmatched pairs. 5360 records in RAM.
INFO	2016-05-16 13:29:34	MarkDuplicates	Read   103,000,000 records.  Elapsed time: 00:08:12s.  Time for last 1,000,000:    7s.  Last read position: chrM:8,093
INFO	2016-05-16 13:29:34	MarkDuplicates	Tracking 8088 as yet unmatched pairs. 8088 records in RAM.
INFO	2016-05-16 13:29:38	MarkDuplicates	Read   104,000,000 records.  Elapsed time: 00:08:16s.  Time for last 1,000,000:    3s.  Last read position: chrM:8,649
INFO	2016-05-16 13:29:38	MarkDuplicates	Tracking 3646 as yet unmatched pairs. 3646 records in RAM.
INFO	2016-05-16 13:29:41	MarkDuplicates	Read   105,000,000 records.  Elapsed time: 00:08:19s.  Time for last 1,000,000:    3s.  Last read position: chrM:9,382
INFO	2016-05-16 13:29:41	MarkDuplicates	Tracking 542 as yet unmatched pairs. 542 records in RAM.
INFO	2016-05-16 13:29:44	MarkDuplicates	Read   106,000,000 records.  Elapsed time: 00:08:22s.  Time for last 1,000,000:    3s.  Last read position: chrM:9,850
INFO	2016-05-16 13:29:44	MarkDuplicates	Tracking 13360 as yet unmatched pairs. 13360 records in RAM.
INFO	2016-05-16 13:29:47	MarkDuplicates	Read   107,000,000 records.  Elapsed time: 00:08:25s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,218
INFO	2016-05-16 13:29:47	MarkDuplicates	Tracking 6238 as yet unmatched pairs. 6238 records in RAM.
INFO	2016-05-16 13:29:50	MarkDuplicates	Read   108,000,000 records.  Elapsed time: 00:08:29s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,627
INFO	2016-05-16 13:29:50	MarkDuplicates	Tracking 1032 as yet unmatched pairs. 1032 records in RAM.
INFO	2016-05-16 13:29:54	MarkDuplicates	Read   109,000,000 records.  Elapsed time: 00:08:32s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,154
INFO	2016-05-16 13:29:54	MarkDuplicates	Tracking 6374 as yet unmatched pairs. 6374 records in RAM.
INFO	2016-05-16 13:29:59	MarkDuplicates	Read   110,000,000 records.  Elapsed time: 00:08:37s.  Time for last 1,000,000:    4s.  Last read position: chrM:11,534
INFO	2016-05-16 13:29:59	MarkDuplicates	Tracking 1274 as yet unmatched pairs. 1274 records in RAM.
INFO	2016-05-16 13:30:05	MarkDuplicates	Read   111,000,000 records.  Elapsed time: 00:08:43s.  Time for last 1,000,000:    6s.  Last read position: chrM:11,972
INFO	2016-05-16 13:30:05	MarkDuplicates	Tracking 8100 as yet unmatched pairs. 8100 records in RAM.
INFO	2016-05-16 13:30:09	MarkDuplicates	Read   112,000,000 records.  Elapsed time: 00:08:47s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,369
INFO	2016-05-16 13:30:09	MarkDuplicates	Tracking 8560 as yet unmatched pairs. 8560 records in RAM.
INFO	2016-05-16 13:30:12	MarkDuplicates	Read   113,000,000 records.  Elapsed time: 00:08:50s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,657
INFO	2016-05-16 13:30:12	MarkDuplicates	Tracking 13978 as yet unmatched pairs. 13978 records in RAM.
INFO	2016-05-16 13:30:15	MarkDuplicates	Read   114,000,000 records.  Elapsed time: 00:08:54s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,043
INFO	2016-05-16 13:30:15	MarkDuplicates	Tracking 12994 as yet unmatched pairs. 12994 records in RAM.
INFO	2016-05-16 13:30:19	MarkDuplicates	Read   115,000,000 records.  Elapsed time: 00:08:57s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,323
INFO	2016-05-16 13:30:19	MarkDuplicates	Tracking 11798 as yet unmatched pairs. 11798 records in RAM.
INFO	2016-05-16 13:30:22	MarkDuplicates	Read   116,000,000 records.  Elapsed time: 00:09:00s.  Time for last 1,000,000:    2s.  Last read position: chrM:13,625
INFO	2016-05-16 13:30:22	MarkDuplicates	Tracking 12128 as yet unmatched pairs. 12128 records in RAM.
INFO	2016-05-16 13:30:25	MarkDuplicates	Read   117,000,000 records.  Elapsed time: 00:09:03s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,946
INFO	2016-05-16 13:30:25	MarkDuplicates	Tracking 7982 as yet unmatched pairs. 7982 records in RAM.
INFO	2016-05-16 13:30:39	MarkDuplicates	Read   118,000,000 records.  Elapsed time: 00:09:17s.  Time for last 1,000,000:   14s.  Last read position: chrM:14,344
INFO	2016-05-16 13:30:39	MarkDuplicates	Tracking 3894 as yet unmatched pairs. 3894 records in RAM.
INFO	2016-05-16 13:30:42	MarkDuplicates	Read   119,000,000 records.  Elapsed time: 00:09:20s.  Time for last 1,000,000:    3s.  Last read position: chrM:14,811
INFO	2016-05-16 13:30:42	MarkDuplicates	Tracking 5514 as yet unmatched pairs. 5514 records in RAM.
INFO	2016-05-16 13:30:45	MarkDuplicates	Read   120,000,000 records.  Elapsed time: 00:09:23s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,129
INFO	2016-05-16 13:30:45	MarkDuplicates	Tracking 18212 as yet unmatched pairs. 18212 records in RAM.
INFO	2016-05-16 13:30:49	MarkDuplicates	Read   121,000,000 records.  Elapsed time: 00:09:27s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,375
INFO	2016-05-16 13:30:49	MarkDuplicates	Tracking 11676 as yet unmatched pairs. 11676 records in RAM.
INFO	2016-05-16 13:30:55	MarkDuplicates	Read   122,000,000 records.  Elapsed time: 00:09:33s.  Time for last 1,000,000:    5s.  Last read position: chrM:15,628
INFO	2016-05-16 13:30:55	MarkDuplicates	Tracking 14400 as yet unmatched pairs. 14400 records in RAM.
INFO	2016-05-16 13:30:58	MarkDuplicates	Read   123,000,000 records.  Elapsed time: 00:09:36s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,866
INFO	2016-05-16 13:30:58	MarkDuplicates	Tracking 14046 as yet unmatched pairs. 14046 records in RAM.
INFO	2016-05-16 13:31:01	MarkDuplicates	Read   124,000,000 records.  Elapsed time: 00:09:39s.  Time for last 1,000,000:    3s.  Last read position: chrM:16,333
INFO	2016-05-16 13:31:01	MarkDuplicates	Tracking 10426 as yet unmatched pairs. 10426 records in RAM.
INFO	2016-05-16 13:31:05	MarkDuplicates	Read   125,000,000 records.  Elapsed time: 00:09:43s.  Time for last 1,000,000:    3s.  Last read position: chrX:9,675,700
INFO	2016-05-16 13:31:05	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 13:31:08	MarkDuplicates	Read   126,000,000 records.  Elapsed time: 00:09:46s.  Time for last 1,000,000:    3s.  Last read position: chrX:45,575,309
INFO	2016-05-16 13:31:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:31:12	MarkDuplicates	Read   127,000,000 records.  Elapsed time: 00:09:50s.  Time for last 1,000,000:    3s.  Last read position: chrX:95,577,986
INFO	2016-05-16 13:31:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:31:16	MarkDuplicates	Read   128,000,000 records.  Elapsed time: 00:09:54s.  Time for last 1,000,000:    4s.  Last read position: chrX:133,405,457
INFO	2016-05-16 13:31:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 13:31:18	MarkDuplicates	Read 128586984 records. 0 pairs never matched.
INFO	2016-05-16 13:31:24	MarkDuplicates	After buildSortedReadEndLists freeMemory: 2893082448; totalMemory: 2921332736; maxMemory: 3817865216
INFO	2016-05-16 13:31:24	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-05-16 13:31:24	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-05-16 13:31:55	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-05-16 13:32:27	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-05-16 13:32:29	MarkDuplicates	After generateDuplicateIndexes freeMemory: 1989391752; totalMemory: 2971664384; maxMemory: 3817865216
INFO	2016-05-16 13:32:29	MarkDuplicates	Marking 50097086 records as duplicates.
INFO	2016-05-16 13:32:29	MarkDuplicates	Found 21552384 optical duplicate clusters.
INFO	2016-05-16 13:34:10	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:38s.  Time for last 10,000,000:   98s.  Last read position: chr12:51,927,525
INFO	2016-05-16 13:35:54	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:03:22s.  Time for last 10,000,000:  104s.  Last read position: chr15:82,458,858
INFO	2016-05-16 13:37:39	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:05:07s.  Time for last 10,000,000:  104s.  Last read position: chr19:28,242,566
INFO	2016-05-16 13:39:19	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:06:48s.  Time for last 10,000,000:  100s.  Last read position: chr20:26,249,330
INFO	2016-05-16 13:41:17	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:08:45s.  Time for last 10,000,000:  117s.  Last read position: chr2:210,634,207
INFO	2016-05-16 13:43:05	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:10:33s.  Time for last 10,000,000:  107s.  Last read position: chr4:118,544,853
INFO	2016-05-16 13:44:51	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:12:19s.  Time for last 10,000,000:  105s.  Last read position: chr6:96,333,869
INFO	2016-05-16 13:46:34	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:14:02s.  Time for last 10,000,000:  102s.  Last read position: chr8:114,566,376
INFO	2016-05-16 13:48:03	MarkDuplicates	Written    90,000,000 records.  Elapsed time: 00:15:32s.  Time for last 10,000,000:   89s.  Last read position: chrM:2,243
INFO	2016-05-16 13:49:22	MarkDuplicates	Written   100,000,000 records.  Elapsed time: 00:16:50s.  Time for last 10,000,000:   78s.  Last read position: chrM:6,472
INFO	2016-05-16 13:50:38	MarkDuplicates	Written   110,000,000 records.  Elapsed time: 00:18:06s.  Time for last 10,000,000:   76s.  Last read position: chrM:11,534
INFO	2016-05-16 13:51:53	MarkDuplicates	Written   120,000,000 records.  Elapsed time: 00:19:21s.  Time for last 10,000,000:   74s.  Last read position: chrM:15,129
INFO	2016-05-16 13:53:10	MarkDuplicates	Before output close freeMemory: 3001152896; totalMemory: 3031433216; maxMemory: 3817865216
INFO	2016-05-16 13:53:10	MarkDuplicates	After output close freeMemory: 3001151840; totalMemory: 3031433216; maxMemory: 3817865216
[Mon May 16 13:53:10 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 31.82 minutes.
Runtime.totalMemory()=3031433216
[bam_sort_core] merging from 93 files...

Num	4
ID	task.postalign_bam.nmsrt_bam_rep2.line_321.id_9
Name	nmsrt_bam rep2
Thread	thread_21
PID	120176

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

Start	2016-05-16 15:38:48
End	2016-05-16 16:19:29
Elapsed	00:40:40
Timeout	00:00:-1
Wall Timeout	100 days

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

 
# SYS command. line 323

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

# SYS command. line 325

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

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

Num	5
ID	task.postalign_bam.bam_to_bedpe_rep2.line_425.id_10
Name	bam_to_bedpe rep2
Thread	thread_21
PID	121428

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

Start	2016-05-16 16:19:29
End	2016-05-16 16:26:13
Elapsed	00:06:44
Timeout	00:00:-1
Wall Timeout	100 days

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

 
# SYS command. line 427

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

# SYS command. line 430

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

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

Num	6
ID	task.postalign_bed.subsample_bedpe_rep2.line_116.id_11
Name	subsample_bedpe rep2
Thread	thread_21
PID	121658

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

Start	2016-05-16 16:26:16
End	2016-05-16 16:29:25
Elapsed	00:03:08
Timeout	00:00:-1
Wall Timeout	100 days

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

 
# SYS command. line 118

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

# SYS command. line 120

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

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

Num	7
ID	task.postalign_bam.bedpe_to_tag_rep2.line_465.id_12
Name	bedpe_to_tag rep2
Thread	thread_21
PID	121799

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

Start	2016-05-16 16:29:26
End	2016-05-16 16:31:14
Elapsed	00:01:48
Timeout	00:00:-1
Wall Timeout	100 days

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

 
# SYS command. line 467

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

# SYS command. line 469

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

# SYS command. line 472

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

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

Num	8
ID	task.postalign_bed.shift_tag_rep2.line_140.id_13
Name	shift_tag rep2
Thread	thread_21
PID	121871

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

Start	2016-05-16 16:31:15
End	2016-05-16 16:32:19
Elapsed	00:01:04
Timeout	00:00:-1
Wall Timeout	100 days

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

 
# SYS command. line 142

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

# SYS command. line 144

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

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

Num	9
ID	task.postalign_bed.subsample_bedpe2tagrep2.line_89.id_14
Name	subsample_bedpe2tagrep2
Thread	thread_21
PID	121935

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

Start	2016-05-16 16:32:20
End	2016-05-16 16:34:53
Elapsed	00:02:33
Timeout	00:00:-1
Wall Timeout	100 days

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

 
# SYS command. line 91

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

# SYS command. line 95

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

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

Num	10
ID	task.postalign_bed.xcor_rep2.line_165.id_15
Name	xcor rep2
Thread	thread_21
PID	122012

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

Start	2016-05-16 16:34:53
End	2016-05-16 17:23:19
Elapsed	00:48:26
Timeout	00:00:-1
Wall Timeout	100 days

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

 
# SYS command. line 167

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

# SYS command. line 171

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

# SYS command. line 174

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

# SYS command. line 175

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

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

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz 
opened /tmp/RtmpwGXncr/ATAC22-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign1dd3f1969d3fa
done. read 25000000 fragments
ChIP data read length 64 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.2481371 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.265230395730548 
Top 3 estimates for fragment length 0 
Window half size 475 
Phantom peak location 55 
Phantom peak Correlation 0.2671327 
Normalized Strand cross-correlation coefficient (NSC) 1.068886 
Relative Strand Cross correlation Coefficient (RSC) 0.8998537 
Phantom Peak Quality Tag 0 
null device 
          1 

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

Num	11
ID	task.callpeak_macs2.macs2_atac_rep2.pval0.1.line_192.id_16
Name	macs2_atac rep2.pval0.1
Thread	thread_21
PID	122015

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

Start	2016-05-16 16:34:53
End	2016-05-16 16:54:49
Elapsed	00:19:56
Timeout	00:00:-1
Wall Timeout	100 days

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

 
# SYS command. line 194

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

# SYS command. line 195

 LC_COLLATE=C

# SYS command. line 197

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

# SYS command. line 202

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

# SYS command. line 203

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

# SYS command. line 204

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

# SYS command. line 205

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

# SYS command. line 207

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

# SYS command. line 212

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

# SYS command. line 213

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

# SYS command. line 214

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

# SYS command. line 215

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

# SYS command. line 217

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

# SYS command. line 243

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

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
INFO  @ Mon, 16 May 2016 16:34:56: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 --broad --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-01
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is on
 
INFO  @ Mon, 16 May 2016 16:34:56: #1 read tag files... 
INFO  @ Mon, 16 May 2016 16:34:56: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 16:34:58:  1000000 
INFO  @ Mon, 16 May 2016 16:35:00:  2000000 
INFO  @ Mon, 16 May 2016 16:35:03:  3000000 
INFO  @ Mon, 16 May 2016 16:35:05:  4000000 
INFO  @ Mon, 16 May 2016 16:35:07:  5000000 
INFO  @ Mon, 16 May 2016 16:35:09:  6000000 
INFO  @ Mon, 16 May 2016 16:35:11:  7000000 
INFO  @ Mon, 16 May 2016 16:35:12:  8000000 
INFO  @ Mon, 16 May 2016 16:35:14:  9000000 
INFO  @ Mon, 16 May 2016 16:35:16:  10000000 
INFO  @ Mon, 16 May 2016 16:35:18:  11000000 
INFO  @ Mon, 16 May 2016 16:35:20:  12000000 
INFO  @ Mon, 16 May 2016 16:35:21:  13000000 
INFO  @ Mon, 16 May 2016 16:35:23:  14000000 
INFO  @ Mon, 16 May 2016 16:35:25:  15000000 
INFO  @ Mon, 16 May 2016 16:35:27:  16000000 
INFO  @ Mon, 16 May 2016 16:35:29:  17000000 
INFO  @ Mon, 16 May 2016 16:35:30:  18000000 
INFO  @ Mon, 16 May 2016 16:35:32:  19000000 
INFO  @ Mon, 16 May 2016 16:35:34:  20000000 
INFO  @ Mon, 16 May 2016 16:35:36:  21000000 
INFO  @ Mon, 16 May 2016 16:35:38:  22000000 
INFO  @ Mon, 16 May 2016 16:35:40:  23000000 
INFO  @ Mon, 16 May 2016 16:35:41:  24000000 
INFO  @ Mon, 16 May 2016 16:35:43:  25000000 
INFO  @ Mon, 16 May 2016 16:35:45:  26000000 
INFO  @ Mon, 16 May 2016 16:35:47:  27000000 
INFO  @ Mon, 16 May 2016 16:35:49:  28000000 
INFO  @ Mon, 16 May 2016 16:35:51:  29000000 
INFO  @ Mon, 16 May 2016 16:35:53:  30000000 
INFO  @ Mon, 16 May 2016 16:35:55:  31000000 
INFO  @ Mon, 16 May 2016 16:35:57:  32000000 
INFO  @ Mon, 16 May 2016 16:35:59:  33000000 
INFO  @ Mon, 16 May 2016 16:36:01:  34000000 
INFO  @ Mon, 16 May 2016 16:36:03:  35000000 
INFO  @ Mon, 16 May 2016 16:36:05: #1 tag size is determined as 108 bps 
INFO  @ Mon, 16 May 2016 16:36:05: #1 tag size = 108 
INFO  @ Mon, 16 May 2016 16:36:05: #1  total tags in treatment: 35000000 
INFO  @ Mon, 16 May 2016 16:36:05: #1 finished! 
INFO  @ Mon, 16 May 2016 16:36:05: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 16:36:05: #2 Skipped... 
INFO  @ Mon, 16 May 2016 16:36:05: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 16:36:05: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 16:36:05: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 16:36:05: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Mon, 16 May 2016 16:36:05: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 16:37:43: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 16:40:46: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls 
INFO  @ Mon, 16 May 2016 16:40:50: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Mon, 16 May 2016 16:40:53: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Mon, 16 May 2016 16:40:55: Done! 
INFO  @ Mon, 16 May 2016 16:41:10: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# ARGUMENTS LIST:
# name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Mon, 16 May 2016 16:41:10: #1 read tag files... 
INFO  @ Mon, 16 May 2016 16:41:10: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 16:41:12:  1000000 
INFO  @ Mon, 16 May 2016 16:41:14:  2000000 
INFO  @ Mon, 16 May 2016 16:41:15:  3000000 
INFO  @ Mon, 16 May 2016 16:41:17:  4000000 
INFO  @ Mon, 16 May 2016 16:41:19:  5000000 
INFO  @ Mon, 16 May 2016 16:41:22:  6000000 
INFO  @ Mon, 16 May 2016 16:41:24:  7000000 
INFO  @ Mon, 16 May 2016 16:41:26:  8000000 
INFO  @ Mon, 16 May 2016 16:41:28:  9000000 
INFO  @ Mon, 16 May 2016 16:41:29:  10000000 
INFO  @ Mon, 16 May 2016 16:41:31:  11000000 
INFO  @ Mon, 16 May 2016 16:41:33:  12000000 
INFO  @ Mon, 16 May 2016 16:41:34:  13000000 
INFO  @ Mon, 16 May 2016 16:41:36:  14000000 
INFO  @ Mon, 16 May 2016 16:41:38:  15000000 
INFO  @ Mon, 16 May 2016 16:41:39:  16000000 
INFO  @ Mon, 16 May 2016 16:41:41:  17000000 
INFO  @ Mon, 16 May 2016 16:41:43:  18000000 
INFO  @ Mon, 16 May 2016 16:41:44:  19000000 
INFO  @ Mon, 16 May 2016 16:41:46:  20000000 
INFO  @ Mon, 16 May 2016 16:41:48:  21000000 
INFO  @ Mon, 16 May 2016 16:41:49:  22000000 
INFO  @ Mon, 16 May 2016 16:41:51:  23000000 
INFO  @ Mon, 16 May 2016 16:41:53:  24000000 
INFO  @ Mon, 16 May 2016 16:41:54:  25000000 
INFO  @ Mon, 16 May 2016 16:41:56:  26000000 
INFO  @ Mon, 16 May 2016 16:41:58:  27000000 
INFO  @ Mon, 16 May 2016 16:41:59:  28000000 
INFO  @ Mon, 16 May 2016 16:42:01:  29000000 
INFO  @ Mon, 16 May 2016 16:42:04:  30000000 
INFO  @ Mon, 16 May 2016 16:42:05:  31000000 
INFO  @ Mon, 16 May 2016 16:42:07:  32000000 
INFO  @ Mon, 16 May 2016 16:42:09:  33000000 
INFO  @ Mon, 16 May 2016 16:42:10:  34000000 
INFO  @ Mon, 16 May 2016 16:42:12:  35000000 
INFO  @ Mon, 16 May 2016 16:42:14: #1 tag size is determined as 108 bps 
INFO  @ Mon, 16 May 2016 16:42:14: #1 tag size = 108 
INFO  @ Mon, 16 May 2016 16:42:14: #1  total tags in treatment: 35000000 
INFO  @ Mon, 16 May 2016 16:42:14: #1 finished! 
INFO  @ Mon, 16 May 2016 16:42:14: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 16:42:14: #2 Skipped... 
INFO  @ Mon, 16 May 2016 16:42:14: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 16:42:14: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 16:42:14: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 16:42:14: #3 Going to call summits inside each peak ... 
INFO  @ Mon, 16 May 2016 16:42:14: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Mon, 16 May 2016 16:42:14: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 16:43:43: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Mon, 16 May 2016 16:43:43: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Mon, 16 May 2016 16:43:43: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Mon, 16 May 2016 16:43:43: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Mon, 16 May 2016 16:43:43: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 16:54:20: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls 
INFO  @ Mon, 16 May 2016 16:54:29: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Mon, 16 May 2016 16:54:37: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_summits.bed 
INFO  @ Mon, 16 May 2016 16:54:40: Done!

Num	12
ID	task.callpeak_macs2.macs2_atac_rep2.line_192.id_17
Name	macs2_atac rep2
Thread	thread_21
PID	122029

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

Start	2016-05-16 16:34:54
End	2016-05-16 17:22:07
Elapsed	00:47:13
Timeout	00:00:-1
Wall Timeout	100 days

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

 
# SYS command. line 194

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

# SYS command. line 195

 LC_COLLATE=C

# SYS command. line 197

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

# SYS command. line 202

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

# SYS command. line 203

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

# SYS command. line 204

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

# SYS command. line 205

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

# SYS command. line 207

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

# SYS command. line 212

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

# SYS command. line 213

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

# SYS command. line 214

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

# SYS command. line 215

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

# SYS command. line 217

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

# SYS command. line 243

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

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
INFO  @ Mon, 16 May 2016 16:34:56: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf -g hs -p 0.01 --nomodel --shift -75 --extsize 150 --broad --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is on
 
INFO  @ Mon, 16 May 2016 16:34:56: #1 read tag files... 
INFO  @ Mon, 16 May 2016 16:34:56: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 16:34:58:  1000000 
INFO  @ Mon, 16 May 2016 16:35:00:  2000000 
INFO  @ Mon, 16 May 2016 16:35:01:  3000000 
INFO  @ Mon, 16 May 2016 16:35:03:  4000000 
INFO  @ Mon, 16 May 2016 16:35:05:  5000000 
INFO  @ Mon, 16 May 2016 16:35:07:  6000000 
INFO  @ Mon, 16 May 2016 16:35:08:  7000000 
INFO  @ Mon, 16 May 2016 16:35:10:  8000000 
INFO  @ Mon, 16 May 2016 16:35:12:  9000000 
INFO  @ Mon, 16 May 2016 16:35:14:  10000000 
INFO  @ Mon, 16 May 2016 16:35:16:  11000000 
INFO  @ Mon, 16 May 2016 16:35:19:  12000000 
INFO  @ Mon, 16 May 2016 16:35:22:  13000000 
INFO  @ Mon, 16 May 2016 16:35:25:  14000000 
INFO  @ Mon, 16 May 2016 16:35:27:  15000000 
INFO  @ Mon, 16 May 2016 16:35:29:  16000000 
INFO  @ Mon, 16 May 2016 16:35:31:  17000000 
INFO  @ Mon, 16 May 2016 16:35:33:  18000000 
INFO  @ Mon, 16 May 2016 16:35:35:  19000000 
INFO  @ Mon, 16 May 2016 16:35:37:  20000000 
INFO  @ Mon, 16 May 2016 16:35:38:  21000000 
INFO  @ Mon, 16 May 2016 16:35:40:  22000000 
INFO  @ Mon, 16 May 2016 16:35:42:  23000000 
INFO  @ Mon, 16 May 2016 16:35:44:  24000000 
INFO  @ Mon, 16 May 2016 16:35:46:  25000000 
INFO  @ Mon, 16 May 2016 16:35:48:  26000000 
INFO  @ Mon, 16 May 2016 16:35:50:  27000000 
INFO  @ Mon, 16 May 2016 16:35:52:  28000000 
INFO  @ Mon, 16 May 2016 16:35:53:  29000000 
INFO  @ Mon, 16 May 2016 16:35:55:  30000000 
INFO  @ Mon, 16 May 2016 16:35:57:  31000000 
INFO  @ Mon, 16 May 2016 16:35:59:  32000000 
INFO  @ Mon, 16 May 2016 16:36:01:  33000000 
INFO  @ Mon, 16 May 2016 16:36:02:  34000000 
INFO  @ Mon, 16 May 2016 16:36:04:  35000000 
INFO  @ Mon, 16 May 2016 16:36:07: #1 tag size is determined as 108 bps 
INFO  @ Mon, 16 May 2016 16:36:07: #1 tag size = 108 
INFO  @ Mon, 16 May 2016 16:36:07: #1  total tags in treatment: 35000000 
INFO  @ Mon, 16 May 2016 16:36:07: #1 finished! 
INFO  @ Mon, 16 May 2016 16:36:07: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 16:36:07: #2 Skipped... 
INFO  @ Mon, 16 May 2016 16:36:07: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 16:36:07: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 16:36:07: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 16:36:07: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Mon, 16 May 2016 16:36:07: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 16:37:39: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 16:40:17: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls 
INFO  @ Mon, 16 May 2016 16:40:21: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.broadPeak 
INFO  @ Mon, 16 May 2016 16:40:24: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.gappedPeak 
INFO  @ Mon, 16 May 2016 16:40:27: Done! 
INFO  @ Mon, 16 May 2016 16:40:42: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf -g hs -p 0.01 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# ARGUMENTS LIST:
# name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Mon, 16 May 2016 16:40:42: #1 read tag files... 
INFO  @ Mon, 16 May 2016 16:40:42: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 16:40:45:  1000000 
INFO  @ Mon, 16 May 2016 16:40:48:  2000000 
INFO  @ Mon, 16 May 2016 16:40:50:  3000000 
INFO  @ Mon, 16 May 2016 16:40:51:  4000000 
INFO  @ Mon, 16 May 2016 16:40:53:  5000000 
INFO  @ Mon, 16 May 2016 16:40:55:  6000000 
INFO  @ Mon, 16 May 2016 16:40:56:  7000000 
INFO  @ Mon, 16 May 2016 16:40:58:  8000000 
INFO  @ Mon, 16 May 2016 16:40:59:  9000000 
INFO  @ Mon, 16 May 2016 16:41:01:  10000000 
INFO  @ Mon, 16 May 2016 16:41:03:  11000000 
INFO  @ Mon, 16 May 2016 16:41:05:  12000000 
INFO  @ Mon, 16 May 2016 16:41:06:  13000000 
INFO  @ Mon, 16 May 2016 16:41:08:  14000000 
INFO  @ Mon, 16 May 2016 16:41:09:  15000000 
INFO  @ Mon, 16 May 2016 16:41:11:  16000000 
INFO  @ Mon, 16 May 2016 16:41:13:  17000000 
INFO  @ Mon, 16 May 2016 16:41:14:  18000000 
INFO  @ Mon, 16 May 2016 16:41:16:  19000000 
INFO  @ Mon, 16 May 2016 16:41:18:  20000000 
INFO  @ Mon, 16 May 2016 16:41:19:  21000000 
INFO  @ Mon, 16 May 2016 16:41:21:  22000000 
INFO  @ Mon, 16 May 2016 16:41:22:  23000000 
INFO  @ Mon, 16 May 2016 16:41:24:  24000000 
INFO  @ Mon, 16 May 2016 16:41:26:  25000000 
INFO  @ Mon, 16 May 2016 16:41:27:  26000000 
INFO  @ Mon, 16 May 2016 16:41:29:  27000000 
INFO  @ Mon, 16 May 2016 16:41:31:  28000000 
INFO  @ Mon, 16 May 2016 16:41:32:  29000000 
INFO  @ Mon, 16 May 2016 16:41:34:  30000000 
INFO  @ Mon, 16 May 2016 16:41:35:  31000000 
INFO  @ Mon, 16 May 2016 16:41:37:  32000000 
INFO  @ Mon, 16 May 2016 16:41:39:  33000000 
INFO  @ Mon, 16 May 2016 16:41:40:  34000000 
INFO  @ Mon, 16 May 2016 16:41:42:  35000000 
INFO  @ Mon, 16 May 2016 16:41:44: #1 tag size is determined as 108 bps 
INFO  @ Mon, 16 May 2016 16:41:44: #1 tag size = 108 
INFO  @ Mon, 16 May 2016 16:41:44: #1  total tags in treatment: 35000000 
INFO  @ Mon, 16 May 2016 16:41:44: #1 finished! 
INFO  @ Mon, 16 May 2016 16:41:44: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 16:41:44: #2 Skipped... 
INFO  @ Mon, 16 May 2016 16:41:44: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 16:41:44: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 16:41:44: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 16:41:44: #3 Going to call summits inside each peak ... 
INFO  @ Mon, 16 May 2016 16:41:44: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Mon, 16 May 2016 16:41:44: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 16:43:19: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Mon, 16 May 2016 16:43:19: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_treat_pileup.bdg 
INFO  @ Mon, 16 May 2016 16:43:19: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_control_lambda.bdg 
INFO  @ Mon, 16 May 2016 16:43:19: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Mon, 16 May 2016 16:43:19: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 16:48:18: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls 
INFO  @ Mon, 16 May 2016 16:48:20: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.narrowPeak 
INFO  @ Mon, 16 May 2016 16:48:22: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_summits.bed 
INFO  @ Mon, 16 May 2016 16:48:23: Done! 
INFO  @ Mon, 16 May 2016 16:48:26: Read and build treatment bedGraph... 
INFO  @ Mon, 16 May 2016 16:49:41: Read and build control bedGraph... 
INFO  @ Mon, 16 May 2016 16:50:14: Build scoreTrackII... 
INFO  @ Mon, 16 May 2016 16:50:50: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Mon, 16 May 2016 16:54:59: Write bedGraph of scores... 
INFO  @ Mon, 16 May 2016 16:57:26: Finished 'FE'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_FE.bdg'! 
INFO  @ Mon, 16 May 2016 17:05:33: Read and build treatment bedGraph... 
INFO  @ Mon, 16 May 2016 17:06:49: Read and build control bedGraph... 
INFO  @ Mon, 16 May 2016 17:07:23: Build scoreTrackII... 
INFO  @ Mon, 16 May 2016 17:08:04: Values in your input bedGraph files will be multiplied by 35.000000 ... 
INFO  @ Mon, 16 May 2016 17:12:05: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Mon, 16 May 2016 17:12:39: Write bedGraph of scores... 
INFO  @ Mon, 16 May 2016 17:14:58: Finished 'ppois'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_ppois.bdg'!

BigDataScript report: atac.bds

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