Script file	/users/pangwei/bds_atac/atac.bds
Program ID	atac.bds.20160515_230834_730
Start time	2016-05-15 23:08:34
Run time	17:34:57.859
Tasks executed	32
Tasks failed	1
Tasks failed names	idr2 rep1-rep2
Arguments*	[-out_dir, /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8, -num_rep, 2, -fastq1_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC7/ATAC7-trimmed-pair1.fastq.gz, -fastq1_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC7/ATAC7-trimmed-pair2.fastq.gz, -fastq2_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC8/ATAC8-trimmed-pair1.fastq.gz, -fastq2_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC8/ATAC8-trimmed-pair2.fastq.gz, -subsample, 17500000, -true_rep, -species, hg19]
System*	local
Cpus*	1
Exit value	1

Thread ID	Parent	Tasks
thread_Root	None	atac.bds.20160515_230834_730/task.postalign_bed.pool_tag_reps.line_405.id_28 atac.bds.20160515_230834_730/task.callpeak_macs2.macs2_atac_pooled.pval0.1.line_192.id_29 atac.bds.20160515_230834_730/task.callpeak_macs2.macs2_atac_pooled.line_192.id_30 atac.bds.20160515_230834_730/task.callpeak_etc.filt_top_peaks_rep1.line_25.id_31 atac.bds.20160515_230834_730/task.callpeak_etc.filt_top_peaks_rep1.line_25.id_32 atac.bds.20160515_230834_730/task.callpeak_etc.filt_top_peaks_rep2.line_25.id_33 atac.bds.20160515_230834_730/task.callpeak_etc.filt_top_peaks_rep2.line_25.id_34 atac.bds.20160515_230834_730/task.callpeak_etc.filt_top_peaks_pooled.line_25.id_35 atac.bds.20160515_230834_730/task.callpeak_etc.filt_top_peaks_pooled.line_25.id_36 atac.bds.20160515_230834_730/task.idr.idr2_rep1_rep2.line_61.id_37
thread_21	thread_Root	atac.bds.20160515_230834_730_parallel_21/task.align_bowtie2.bowtie2_PE_rep2.line_133.id_6 atac.bds.20160515_230834_730_parallel_21/task.postalign_bam.dedup_bam_PE_rep2.line_215.id_8 atac.bds.20160515_230834_730_parallel_21/task.postalign_bam.nmsrt_bam_rep2.line_321.id_10 atac.bds.20160515_230834_730_parallel_21/task.postalign_bam.bam_to_bedpe_rep2.line_425.id_11 atac.bds.20160515_230834_730_parallel_21/task.postalign_bed.subsample_bedpe_rep2.line_116.id_12 atac.bds.20160515_230834_730_parallel_21/task.postalign_bam.bedpe_to_tag_rep2.line_465.id_13 atac.bds.20160515_230834_730_parallel_21/task.postalign_bed.shift_tag_rep2.line_140.id_14 atac.bds.20160515_230834_730_parallel_21/task.postalign_bed.subsample_bedpe2tagrep2.line_89.id_15 atac.bds.20160515_230834_730_parallel_21/task.postalign_bed.xcor_rep2.line_165.id_16 atac.bds.20160515_230834_730_parallel_21/task.callpeak_macs2.macs2_atac_rep2.pval0.1.line_192.id_17 atac.bds.20160515_230834_730_parallel_21/task.callpeak_macs2.macs2_atac_rep2.line_192.id_18
thread_20	thread_Root	atac.bds.20160515_230834_730_parallel_20/task.align_bowtie2.bowtie2_PE_rep1.line_133.id_7 atac.bds.20160515_230834_730_parallel_20/task.postalign_bam.dedup_bam_PE_rep1.line_215.id_9 atac.bds.20160515_230834_730_parallel_20/task.postalign_bam.nmsrt_bam_rep1.line_321.id_19 atac.bds.20160515_230834_730_parallel_20/task.postalign_bam.bam_to_bedpe_rep1.line_425.id_20 atac.bds.20160515_230834_730_parallel_20/task.postalign_bed.subsample_bedpe_rep1.line_116.id_21 atac.bds.20160515_230834_730_parallel_20/task.postalign_bam.bedpe_to_tag_rep1.line_465.id_22 atac.bds.20160515_230834_730_parallel_20/task.postalign_bed.shift_tag_rep1.line_140.id_23 atac.bds.20160515_230834_730_parallel_20/task.postalign_bed.subsample_bedpe2tagrep1.line_89.id_24 atac.bds.20160515_230834_730_parallel_20/task.postalign_bed.xcor_rep1.line_165.id_25 atac.bds.20160515_230834_730_parallel_20/task.callpeak_macs2.macs2_atac_rep1.pval0.1.line_192.id_26 atac.bds.20160515_230834_730_parallel_20/task.callpeak_macs2.macs2_atac_rep1.line_192.id_27

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.align_bowtie2.bowtie2_PE_rep2.line_133.id_6
Name	bowtie2_PE rep2
Thread	thread_21
PID	88316

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

Start	2016-05-15 23:08:35
End	2016-05-16 07:37:06
Elapsed	08:28:30
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.fastq.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair2.trim.fastq.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.align.log
Dependencies

 
# SYS command. line 135

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

# SYS command. line 139

 bowtie2  -X2000 --mm --threads 2 -x /mnt/data/annotations/indexes/bowtie2_indexes/bowtie2/ENCODEHg19_male \
			-1 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.fastq.gz -2 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair2.trim.fastq.gz 2>/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.align.log | samtools view -bS - | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE

# SYS command. line 142

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

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 60 files...

Num	2
ID	task.align_bowtie2.bowtie2_PE_rep1.line_133.id_7
Name	bowtie2_PE rep1
Thread	thread_20
PID	88325

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

Start	2016-05-15 23:08:36
End	2016-05-16 10:05:26
Elapsed	10:56:50
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.fastq.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair2.trim.fastq.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.align.log
Dependencies

 
# SYS command. line 135

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

# SYS command. line 139

 bowtie2  -X2000 --mm --threads 2 -x /mnt/data/annotations/indexes/bowtie2_indexes/bowtie2/ENCODEHg19_male \
			-1 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.fastq.gz -2 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair2.trim.fastq.gz 2>/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.align.log | samtools view -bS - | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE

# SYS command. line 142

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

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 79 files...

Num	3
ID	task.postalign_bam.dedup_bam_PE_rep2.line_215.id_8
Name	dedup_bam_PE rep2
Thread	thread_21
PID	101206

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

Start	2016-05-16 07:37:07
End	2016-05-16 10:16:49
Elapsed	02:39:41
Timeout	00:00:-1
Wall Timeout	100 days

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

 
# SYS command. line 217

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

# SYS command. line 228

 echo

# SYS command. line 229

 samtools view -F 1804 -f 2 -q 30 -u /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.dupmark

# SYS command. line 230

 echo

# SYS command. line 237

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

# SYS command. line 238

 samtools view -F 1804 -f 2 -u /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.filt

# SYS command. line 239

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

# SYS command. line 243

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

# SYS command. line 244

 export MAX_JAVA_MEM="12G"

# SYS command. line 247

 if [ -f ${PICARDROOT}/MarkDuplicates.jar ]; then \
			java -Xmx4G -jar ${PICARDROOT}/MarkDuplicates.jar \
				INPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
			else \
			java -Xmx4G -jar ${PICARDROOT}/picard.jar MarkDuplicates \
				INPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
			fi

# SYS command. line 265

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

# SYS command. line 267

 samtools view -F 1804 -f 2 -b /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.filt.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 269

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

# SYS command. line 271

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

# SYS command. line 275

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

# SYS command. line 286

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

# SYS command. line 287

 bedtools bamtobed -bedpe -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam | \
			awk 'BEGIN{OFS="\t"}{print $1,$2,$4,$6,$9,$10}' | \
			grep -v 'chrM' | sort | uniq -c | \
			awk 'BEGIN{mt=0;m0=0;m1=0;m2=0} ($1==1){m1=m1+1} ($1==2){m2=m2+1} {m0=m0+1} {mt=mt+$1} END{printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1/m2}' > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.pbc.qc

# SYS command. line 291

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

# SYS command. line 293

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

# SYS command. line 294

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

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



 
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 41 files...
[bam_sort_core] merging from 41 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Mon May 16 08:59:00 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Mon May 16 08:59:00 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 08:59:00	MarkDuplicates	Start of doWork freeMemory: 254889728; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-16 08:59:00	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-05-16 08:59:00	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-05-16 08:59:06	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:05s.  Time for last 1,000,000:    5s.  Last read position: chr10:66,873,921
INFO	2016-05-16 08:59:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 08:59:11	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:10s.  Time for last 1,000,000:    4s.  Last read position: chr10:115,628,215
INFO	2016-05-16 08:59:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 08:59:15	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:15s.  Time for last 1,000,000:    4s.  Last read position: chr11:27,486,088
INFO	2016-05-16 08:59:15	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 08:59:21	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:20s.  Time for last 1,000,000:    5s.  Last read position: chr11:76,637,610
INFO	2016-05-16 08:59:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 08:59:28	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:27s.  Time for last 1,000,000:    7s.  Last read position: chr11:131,365,519
INFO	2016-05-16 08:59:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 08:59:35	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:34s.  Time for last 1,000,000:    6s.  Last read position: chr12:53,782,518
INFO	2016-05-16 08:59:35	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 08:59:40	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:39s.  Time for last 1,000,000:    4s.  Last read position: chr12:109,925,902
INFO	2016-05-16 08:59:40	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 08:59:45	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:44s.  Time for last 1,000,000:    4s.  Last read position: chr13:47,660,661
INFO	2016-05-16 08:59:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 08:59:51	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:50s.  Time for last 1,000,000:    6s.  Last read position: chr13:112,110,943
INFO	2016-05-16 08:59:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 08:59:55	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:54s.  Time for last 1,000,000:    4s.  Last read position: chr14:75,019,195
INFO	2016-05-16 08:59:55	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 08:59:59	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:59s.  Time for last 1,000,000:    4s.  Last read position: chr15:42,705,390
INFO	2016-05-16 08:59:59	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-16 09:00:06	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:06s.  Time for last 1,000,000:    7s.  Last read position: chr15:93,809,340
INFO	2016-05-16 09:00:06	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 09:00:12	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:11s.  Time for last 1,000,000:    5s.  Last read position: chr16:53,468,387
INFO	2016-05-16 09:00:12	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-05-16 09:00:18	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:17s.  Time for last 1,000,000:    6s.  Last read position: chr17:6,485,989
INFO	2016-05-16 09:00:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 09:00:36	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:35s.  Time for last 1,000,000:   17s.  Last read position: chr17:54,671,685
INFO	2016-05-16 09:00:36	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-16 09:00:40	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:39s.  Time for last 1,000,000:    4s.  Last read position: chr18:22,901,727
INFO	2016-05-16 09:00:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 09:00:45	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:01:45s.  Time for last 1,000,000:    5s.  Last read position: chr19:1,146,450
INFO	2016-05-16 09:00:45	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 09:00:50	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:01:50s.  Time for last 1,000,000:    4s.  Last read position: chr19:44,031,431
INFO	2016-05-16 09:00:50	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 09:00:57	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:01:56s.  Time for last 1,000,000:    6s.  Last read position: chr1:14,580,295
INFO	2016-05-16 09:00:57	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 09:01:02	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:02:01s.  Time for last 1,000,000:    4s.  Last read position: chr1:54,712,429
INFO	2016-05-16 09:01:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 09:01:06	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:02:06s.  Time for last 1,000,000:    4s.  Last read position: chr1:113,971,495
INFO	2016-05-16 09:01:06	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 09:01:12	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:02:11s.  Time for last 1,000,000:    5s.  Last read position: chr1:191,762,010
INFO	2016-05-16 09:01:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 09:01:16	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:02:15s.  Time for last 1,000,000:    3s.  Last read position: chr1:243,582,818
INFO	2016-05-16 09:01:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 09:01:20	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:02:19s.  Time for last 1,000,000:    4s.  Last read position: chr20:44,957,998
INFO	2016-05-16 09:01:20	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 09:01:24	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:02:24s.  Time for last 1,000,000:    4s.  Last read position: chr21:46,823,760
INFO	2016-05-16 09:01:24	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 09:01:32	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:02:32s.  Time for last 1,000,000:    8s.  Last read position: chr2:5,831,591
INFO	2016-05-16 09:01:32	MarkDuplicates	Tracking 12 as yet unmatched pairs. 12 records in RAM.
INFO	2016-05-16 09:01:36	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:02:36s.  Time for last 1,000,000:    4s.  Last read position: chr2:57,779,939
INFO	2016-05-16 09:01:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 09:01:40	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:02:39s.  Time for last 1,000,000:    3s.  Last read position: chr2:121,732,014
INFO	2016-05-16 09:01:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 09:01:44	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:02:44s.  Time for last 1,000,000:    4s.  Last read position: chr2:182,548,706
INFO	2016-05-16 09:01:44	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-05-16 09:01:59	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:02:59s.  Time for last 1,000,000:   14s.  Last read position: chr2:239,144,937
INFO	2016-05-16 09:01:59	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 09:02:03	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:03:02s.  Time for last 1,000,000:    3s.  Last read position: chr3:46,466,280
INFO	2016-05-16 09:02:03	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 09:02:07	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:03:06s.  Time for last 1,000,000:    3s.  Last read position: chr3:109,563,611
INFO	2016-05-16 09:02:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 09:02:10	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:03:10s.  Time for last 1,000,000:    3s.  Last read position: chr3:167,434,229
INFO	2016-05-16 09:02:10	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 09:02:17	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:03:16s.  Time for last 1,000,000:    6s.  Last read position: chr4:20,758,886
INFO	2016-05-16 09:02:17	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 09:02:21	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:03:20s.  Time for last 1,000,000:    4s.  Last read position: chr4:90,190,660
INFO	2016-05-16 09:02:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 09:02:25	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:03:24s.  Time for last 1,000,000:    3s.  Last read position: chr4:155,686,735
INFO	2016-05-16 09:02:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 09:02:28	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:03:28s.  Time for last 1,000,000:    3s.  Last read position: chr5:28,450,549
INFO	2016-05-16 09:02:28	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 09:02:32	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:03:32s.  Time for last 1,000,000:    3s.  Last read position: chr5:96,682,690
INFO	2016-05-16 09:02:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 09:02:36	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:03:35s.  Time for last 1,000,000:    3s.  Last read position: chr5:139,717,380
INFO	2016-05-16 09:02:36	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 09:02:41	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:03:41s.  Time for last 1,000,000:    5s.  Last read position: chr6:9,841,124
INFO	2016-05-16 09:02:41	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 09:02:45	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:03:45s.  Time for last 1,000,000:    3s.  Last read position: chr6:65,428,861
INFO	2016-05-16 09:02:45	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 09:02:49	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:03:48s.  Time for last 1,000,000:    3s.  Last read position: chr6:130,321,827
INFO	2016-05-16 09:02:49	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 09:02:53	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:03:52s.  Time for last 1,000,000:    3s.  Last read position: chr7:11,462,415
INFO	2016-05-16 09:02:53	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 09:02:56	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:03:56s.  Time for last 1,000,000:    3s.  Last read position: chr7:77,146,657
INFO	2016-05-16 09:02:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 09:03:04	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:04:03s.  Time for last 1,000,000:    7s.  Last read position: chr7:133,812,224
INFO	2016-05-16 09:03:04	MarkDuplicates	Tracking 20 as yet unmatched pairs. 20 records in RAM.
INFO	2016-05-16 09:03:07	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:04:07s.  Time for last 1,000,000:    3s.  Last read position: chr8:29,274,695
INFO	2016-05-16 09:03:07	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 09:03:12	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:04:11s.  Time for last 1,000,000:    4s.  Last read position: chr8:92,720,317
INFO	2016-05-16 09:03:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 09:03:16	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:04:15s.  Time for last 1,000,000:    3s.  Last read position: chr8:145,021,372
INFO	2016-05-16 09:03:16	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 09:03:19	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:04:18s.  Time for last 1,000,000:    3s.  Last read position: chr9:89,553,899
INFO	2016-05-16 09:03:19	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 09:03:22	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:04:22s.  Time for last 1,000,000:    3s.  Last read position: chr9:136,603,402
INFO	2016-05-16 09:03:22	MarkDuplicates	Tracking 14 as yet unmatched pairs. 14 records in RAM.
INFO	2016-05-16 09:03:25	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:04:25s.  Time for last 1,000,000:    3s.  Last read position: chrM:347
INFO	2016-05-16 09:03:25	MarkDuplicates	Tracking 27616 as yet unmatched pairs. 27616 records in RAM.
INFO	2016-05-16 09:03:28	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:04:28s.  Time for last 1,000,000:    2s.  Last read position: chrM:684
INFO	2016-05-16 09:03:28	MarkDuplicates	Tracking 42136 as yet unmatched pairs. 42136 records in RAM.
INFO	2016-05-16 09:03:34	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:04:33s.  Time for last 1,000,000:    5s.  Last read position: chrM:964
INFO	2016-05-16 09:03:34	MarkDuplicates	Tracking 73702 as yet unmatched pairs. 73702 records in RAM.
INFO	2016-05-16 09:03:37	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:04:36s.  Time for last 1,000,000:    3s.  Last read position: chrM:1,454
INFO	2016-05-16 09:03:37	MarkDuplicates	Tracking 25298 as yet unmatched pairs. 25298 records in RAM.
INFO	2016-05-16 09:03:40	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:04:39s.  Time for last 1,000,000:    2s.  Last read position: chrM:1,840
INFO	2016-05-16 09:03:40	MarkDuplicates	Tracking 52750 as yet unmatched pairs. 52750 records in RAM.
INFO	2016-05-16 09:03:43	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:04:42s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,256
INFO	2016-05-16 09:03:43	MarkDuplicates	Tracking 27828 as yet unmatched pairs. 27828 records in RAM.
INFO	2016-05-16 09:03:46	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:04:45s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,660
INFO	2016-05-16 09:03:46	MarkDuplicates	Tracking 62426 as yet unmatched pairs. 62426 records in RAM.
INFO	2016-05-16 09:03:49	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:04:49s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,888
INFO	2016-05-16 09:03:49	MarkDuplicates	Tracking 59160 as yet unmatched pairs. 59160 records in RAM.
INFO	2016-05-16 09:04:01	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:05:00s.  Time for last 1,000,000:   11s.  Last read position: chrM:3,153
INFO	2016-05-16 09:04:01	MarkDuplicates	Tracking 47620 as yet unmatched pairs. 47620 records in RAM.
INFO	2016-05-16 09:04:04	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:05:03s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,370
INFO	2016-05-16 09:04:04	MarkDuplicates	Tracking 58078 as yet unmatched pairs. 58078 records in RAM.
INFO	2016-05-16 09:04:08	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:05:08s.  Time for last 1,000,000:    4s.  Last read position: chrM:3,577
INFO	2016-05-16 09:04:08	MarkDuplicates	Tracking 20456 as yet unmatched pairs. 20456 records in RAM.
INFO	2016-05-16 09:04:12	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:05:11s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,769
INFO	2016-05-16 09:04:12	MarkDuplicates	Tracking 49876 as yet unmatched pairs. 49876 records in RAM.
INFO	2016-05-16 09:04:15	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:05:14s.  Time for last 1,000,000:    3s.  Last read position: chrM:4,092
INFO	2016-05-16 09:04:15	MarkDuplicates	Tracking 20782 as yet unmatched pairs. 20782 records in RAM.
INFO	2016-05-16 09:04:18	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:05:17s.  Time for last 1,000,000:    2s.  Last read position: chrM:4,889
INFO	2016-05-16 09:04:18	MarkDuplicates	Tracking 28790 as yet unmatched pairs. 28790 records in RAM.
INFO	2016-05-16 09:04:21	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:05:20s.  Time for last 1,000,000:    2s.  Last read position: chrM:5,331
INFO	2016-05-16 09:04:21	MarkDuplicates	Tracking 28592 as yet unmatched pairs. 28592 records in RAM.
INFO	2016-05-16 09:04:23	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:05:23s.  Time for last 1,000,000:    2s.  Last read position: chrM:5,999
INFO	2016-05-16 09:04:23	MarkDuplicates	Tracking 43716 as yet unmatched pairs. 43716 records in RAM.
INFO	2016-05-16 09:04:26	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:05:26s.  Time for last 1,000,000:    2s.  Last read position: chrM:6,338
INFO	2016-05-16 09:04:26	MarkDuplicates	Tracking 45416 as yet unmatched pairs. 45416 records in RAM.
INFO	2016-05-16 09:04:29	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:05:29s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,528
INFO	2016-05-16 09:04:29	MarkDuplicates	Tracking 55880 as yet unmatched pairs. 55880 records in RAM.
INFO	2016-05-16 09:04:34	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:05:34s.  Time for last 1,000,000:    4s.  Last read position: chrM:6,947
INFO	2016-05-16 09:04:34	MarkDuplicates	Tracking 34012 as yet unmatched pairs. 34012 records in RAM.
INFO	2016-05-16 09:04:37	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:05:37s.  Time for last 1,000,000:    2s.  Last read position: chrM:7,501
INFO	2016-05-16 09:04:37	MarkDuplicates	Tracking 31718 as yet unmatched pairs. 31718 records in RAM.
INFO	2016-05-16 09:04:40	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:05:40s.  Time for last 1,000,000:    2s.  Last read position: chrM:7,870
INFO	2016-05-16 09:04:40	MarkDuplicates	Tracking 42444 as yet unmatched pairs. 42444 records in RAM.
INFO	2016-05-16 09:04:43	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:05:43s.  Time for last 1,000,000:    3s.  Last read position: chrM:8,200
INFO	2016-05-16 09:04:43	MarkDuplicates	Tracking 42028 as yet unmatched pairs. 42028 records in RAM.
INFO	2016-05-16 09:04:46	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:05:46s.  Time for last 1,000,000:    2s.  Last read position: chrM:8,915
INFO	2016-05-16 09:04:46	MarkDuplicates	Tracking 9626 as yet unmatched pairs. 9626 records in RAM.
INFO	2016-05-16 09:04:53	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:05:53s.  Time for last 1,000,000:    6s.  Last read position: chrM:9,310
INFO	2016-05-16 09:04:53	MarkDuplicates	Tracking 4438 as yet unmatched pairs. 4438 records in RAM.
INFO	2016-05-16 09:04:56	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:05:56s.  Time for last 1,000,000:    3s.  Last read position: chrM:9,811
INFO	2016-05-16 09:04:56	MarkDuplicates	Tracking 61974 as yet unmatched pairs. 61974 records in RAM.
INFO	2016-05-16 09:04:59	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:05:59s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,127
INFO	2016-05-16 09:04:59	MarkDuplicates	Tracking 22360 as yet unmatched pairs. 22360 records in RAM.
INFO	2016-05-16 09:05:04	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:06:03s.  Time for last 1,000,000:    4s.  Last read position: chrM:10,407
INFO	2016-05-16 09:05:04	MarkDuplicates	Tracking 60142 as yet unmatched pairs. 60142 records in RAM.
INFO	2016-05-16 09:05:08	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:06:07s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,738
INFO	2016-05-16 09:05:08	MarkDuplicates	Tracking 5214 as yet unmatched pairs. 5214 records in RAM.
INFO	2016-05-16 09:05:11	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:06:10s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,231
INFO	2016-05-16 09:05:11	MarkDuplicates	Tracking 27076 as yet unmatched pairs. 27076 records in RAM.
INFO	2016-05-16 09:05:14	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:06:13s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,552
INFO	2016-05-16 09:05:14	MarkDuplicates	Tracking 50466 as yet unmatched pairs. 50466 records in RAM.
INFO	2016-05-16 09:05:17	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:06:17s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,949
INFO	2016-05-16 09:05:17	MarkDuplicates	Tracking 12810 as yet unmatched pairs. 12810 records in RAM.
INFO	2016-05-16 09:05:20	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:06:20s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,186
INFO	2016-05-16 09:05:20	MarkDuplicates	Tracking 25078 as yet unmatched pairs. 25078 records in RAM.
INFO	2016-05-16 09:05:23	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:06:23s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,519
INFO	2016-05-16 09:05:23	MarkDuplicates	Tracking 42182 as yet unmatched pairs. 42182 records in RAM.
INFO	2016-05-16 09:05:26	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:06:26s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,742
INFO	2016-05-16 09:05:26	MarkDuplicates	Tracking 28676 as yet unmatched pairs. 28676 records in RAM.
INFO	2016-05-16 09:05:29	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:06:29s.  Time for last 1,000,000:    2s.  Last read position: chrM:13,099
INFO	2016-05-16 09:05:29	MarkDuplicates	Tracking 47836 as yet unmatched pairs. 47836 records in RAM.
INFO	2016-05-16 09:05:32	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:06:32s.  Time for last 1,000,000:    2s.  Last read position: chrM:13,345
INFO	2016-05-16 09:05:32	MarkDuplicates	Tracking 51718 as yet unmatched pairs. 51718 records in RAM.
INFO	2016-05-16 09:05:39	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:06:38s.  Time for last 1,000,000:    6s.  Last read position: chrM:13,574
INFO	2016-05-16 09:05:39	MarkDuplicates	Tracking 35522 as yet unmatched pairs. 35522 records in RAM.
INFO	2016-05-16 09:05:42	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:06:41s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,886
INFO	2016-05-16 09:05:42	MarkDuplicates	Tracking 54928 as yet unmatched pairs. 54928 records in RAM.
INFO	2016-05-16 09:05:56	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:06:55s.  Time for last 1,000,000:   13s.  Last read position: chrM:14,258
INFO	2016-05-16 09:05:56	MarkDuplicates	Tracking 19900 as yet unmatched pairs. 19900 records in RAM.
INFO	2016-05-16 09:05:59	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:06:58s.  Time for last 1,000,000:    3s.  Last read position: chrM:14,535
INFO	2016-05-16 09:05:59	MarkDuplicates	Tracking 6088 as yet unmatched pairs. 6088 records in RAM.
INFO	2016-05-16 09:06:02	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:07:01s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,015
INFO	2016-05-16 09:06:02	MarkDuplicates	Tracking 52984 as yet unmatched pairs. 52984 records in RAM.
INFO	2016-05-16 09:06:06	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:07:05s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,206
INFO	2016-05-16 09:06:06	MarkDuplicates	Tracking 26206 as yet unmatched pairs. 26206 records in RAM.
INFO	2016-05-16 09:06:09	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:07:08s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,421
INFO	2016-05-16 09:06:09	MarkDuplicates	Tracking 66808 as yet unmatched pairs. 66808 records in RAM.
INFO	2016-05-16 09:06:13	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:07:12s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,626
INFO	2016-05-16 09:06:13	MarkDuplicates	Tracking 49896 as yet unmatched pairs. 49896 records in RAM.
INFO	2016-05-16 09:06:16	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:07:16s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,813
INFO	2016-05-16 09:06:16	MarkDuplicates	Tracking 76192 as yet unmatched pairs. 76192 records in RAM.
INFO	2016-05-16 09:06:20	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:07:19s.  Time for last 1,000,000:    3s.  Last read position: chrM:16,110
INFO	2016-05-16 09:06:20	MarkDuplicates	Tracking 27428 as yet unmatched pairs. 27428 records in RAM.
INFO	2016-05-16 09:06:25	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:07:24s.  Time for last 1,000,000:    5s.  Last read position: chrM:16,420
INFO	2016-05-16 09:06:25	MarkDuplicates	Tracking 31140 as yet unmatched pairs. 31140 records in RAM.
INFO	2016-05-16 09:06:28	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:07:27s.  Time for last 1,000,000:    3s.  Last read position: chrX:36,869,809
INFO	2016-05-16 09:06:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 09:06:31	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:07:31s.  Time for last 1,000,000:    3s.  Last read position: chrX:110,946,315
INFO	2016-05-16 09:06:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 09:06:34	MarkDuplicates	Read 99719144 records. 0 pairs never matched.
INFO	2016-05-16 09:06:43	MarkDuplicates	After buildSortedReadEndLists freeMemory: 3204433656; totalMemory: 3232235520; maxMemory: 3817865216
INFO	2016-05-16 09:06:43	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-05-16 09:06:43	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-05-16 09:07:11	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-05-16 09:07:33	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-05-16 09:07:36	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2241373360; totalMemory: 3222798336; maxMemory: 3817865216
INFO	2016-05-16 09:07:36	MarkDuplicates	Marking 51580156 records as duplicates.
INFO	2016-05-16 09:07:36	MarkDuplicates	Found 16577536 optical duplicate clusters.
INFO	2016-05-16 09:09:05	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:28s.  Time for last 10,000,000:   88s.  Last read position: chr14:75,019,195
INFO	2016-05-16 09:10:36	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:02:58s.  Time for last 10,000,000:   90s.  Last read position: chr1:54,712,429
INFO	2016-05-16 09:12:07	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:04:30s.  Time for last 10,000,000:   91s.  Last read position: chr2:239,144,937
INFO	2016-05-16 09:13:51	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:06:14s.  Time for last 10,000,000:  103s.  Last read position: chr6:9,841,124
INFO	2016-05-16 09:15:37	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:07:59s.  Time for last 10,000,000:  105s.  Last read position: chr9:136,603,402
INFO	2016-05-16 09:16:50	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:09:13s.  Time for last 10,000,000:   73s.  Last read position: chrM:3,370
INFO	2016-05-16 09:18:01	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:10:24s.  Time for last 10,000,000:   71s.  Last read position: chrM:7,501
INFO	2016-05-16 09:19:14	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:11:37s.  Time for last 10,000,000:   73s.  Last read position: chrM:11,552
INFO	2016-05-16 09:20:29	MarkDuplicates	Written    90,000,000 records.  Elapsed time: 00:12:52s.  Time for last 10,000,000:   74s.  Last read position: chrM:14,535
INFO	2016-05-16 09:21:47	MarkDuplicates	Before output close freeMemory: 3334718104; totalMemory: 3364880384; maxMemory: 3817865216
INFO	2016-05-16 09:21:47	MarkDuplicates	After output close freeMemory: 3334717048; totalMemory: 3364880384; maxMemory: 3817865216
[Mon May 16 09:21:47 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 22.78 minutes.
Runtime.totalMemory()=3364880384
[bam_sort_core] merging from 41 files...

Num	4
ID	task.postalign_bam.dedup_bam_PE_rep1.line_215.id_9
Name	dedup_bam_PE rep1
Thread	thread_20
PID	103769

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

Start	2016-05-16 10:05:27
End	2016-05-16 13:50:49
Elapsed	03:45:22
Timeout	00:00:-1
Wall Timeout	100 days

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

 
# SYS command. line 217

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

# SYS command. line 228

 echo

# SYS command. line 229

 samtools view -F 1804 -f 2 -q 30 -u /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.dupmark

# SYS command. line 230

 echo

# SYS command. line 237

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

# SYS command. line 238

 samtools view -F 1804 -f 2 -u /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.filt

# SYS command. line 239

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

# SYS command. line 243

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

# SYS command. line 244

 export MAX_JAVA_MEM="12G"

# SYS command. line 247

 if [ -f ${PICARDROOT}/MarkDuplicates.jar ]; then \
			java -Xmx4G -jar ${PICARDROOT}/MarkDuplicates.jar \
				INPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
			else \
			java -Xmx4G -jar ${PICARDROOT}/picard.jar MarkDuplicates \
				INPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
			fi

# SYS command. line 265

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

# SYS command. line 267

 samtools view -F 1804 -f 2 -b /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.filt.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 269

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

# SYS command. line 271

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

# SYS command. line 275

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

# SYS command. line 286

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

# SYS command. line 287

 bedtools bamtobed -bedpe -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam | \
			awk 'BEGIN{OFS="\t"}{print $1,$2,$4,$6,$9,$10}' | \
			grep -v 'chrM' | sort | uniq -c | \
			awk 'BEGIN{mt=0;m0=0;m1=0;m2=0} ($1==1){m1=m1+1} ($1==2){m2=m2+1} {m0=m0+1} {mt=mt+$1} END{printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1/m2}' > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.pbc.qc

# SYS command. line 291

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

# SYS command. line 293

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

# SYS command. line 294

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

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



 
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 54 files...
[bam_sort_core] merging from 54 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Mon May 16 11:56:29 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Mon May 16 11:56:29 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 11:56:29	MarkDuplicates	Start of doWork freeMemory: 254889872; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-16 11:56:29	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-05-16 11:56:29	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-05-16 11:56:33	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:04s.  Time for last 1,000,000:    4s.  Last read position: chr10:47,682,104
INFO	2016-05-16 11:56:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 11:56:37	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:07s.  Time for last 1,000,000:    3s.  Last read position: chr10:87,979,282
INFO	2016-05-16 11:56:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 11:56:40	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:11s.  Time for last 1,000,000:    3s.  Last read position: chr10:122,973,590
INFO	2016-05-16 11:56:40	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:56:44	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:15s.  Time for last 1,000,000:    3s.  Last read position: chr11:17,874,423
INFO	2016-05-16 11:56:44	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:56:49	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:20s.  Time for last 1,000,000:    5s.  Last read position: chr11:61,531,946
INFO	2016-05-16 11:56:49	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 11:56:54	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:25s.  Time for last 1,000,000:    4s.  Last read position: chr11:90,730,603
INFO	2016-05-16 11:56:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 11:56:58	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:29s.  Time for last 1,000,000:    3s.  Last read position: chr11:128,646,378
INFO	2016-05-16 11:56:58	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:57:04	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:35s.  Time for last 1,000,000:    6s.  Last read position: chr12:32,639,398
INFO	2016-05-16 11:57:04	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:57:08	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:38s.  Time for last 1,000,000:    3s.  Last read position: chr12:74,414,485
INFO	2016-05-16 11:57:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 11:57:11	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:42s.  Time for last 1,000,000:    3s.  Last read position: chr12:114,576,505
INFO	2016-05-16 11:57:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 11:57:14	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:45s.  Time for last 1,000,000:    3s.  Last read position: chr13:36,060,965
INFO	2016-05-16 11:57:14	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 11:57:20	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:00:51s.  Time for last 1,000,000:    5s.  Last read position: chr13:86,694,120
INFO	2016-05-16 11:57:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 11:57:24	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:00:54s.  Time for last 1,000,000:    3s.  Last read position: chr14:33,048,057
INFO	2016-05-16 11:57:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 11:57:31	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:01s.  Time for last 1,000,000:    6s.  Last read position: chr14:75,748,120
INFO	2016-05-16 11:57:31	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-05-16 11:57:45	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:16s.  Time for last 1,000,000:   14s.  Last read position: chr15:25,461,777
INFO	2016-05-16 11:57:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 11:57:49	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:19s.  Time for last 1,000,000:    3s.  Last read position: chr15:67,223,343
INFO	2016-05-16 11:57:49	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:57:52	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:01:23s.  Time for last 1,000,000:    3s.  Last read position: chr15:100,016,840
INFO	2016-05-16 11:57:52	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 11:57:56	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:01:27s.  Time for last 1,000,000:    4s.  Last read position: chr16:30,871,981
INFO	2016-05-16 11:57:56	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 11:58:02	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:01:32s.  Time for last 1,000,000:    5s.  Last read position: chr16:77,429,151
INFO	2016-05-16 11:58:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 11:58:05	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:01:36s.  Time for last 1,000,000:    3s.  Last read position: chr17:15,465,278
INFO	2016-05-16 11:58:05	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:58:08	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:01:39s.  Time for last 1,000,000:    3s.  Last read position: chr17:47,379,883
INFO	2016-05-16 11:58:08	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:58:11	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:01:42s.  Time for last 1,000,000:    3s.  Last read position: chr17:77,289,969
INFO	2016-05-16 11:58:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 11:58:15	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:01:46s.  Time for last 1,000,000:    4s.  Last read position: chr18:36,574,182
INFO	2016-05-16 11:58:15	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:58:19	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:01:49s.  Time for last 1,000,000:    3s.  Last read position: chr18:78,005,138
INFO	2016-05-16 11:58:19	MarkDuplicates	Tracking 14 as yet unmatched pairs. 14 records in RAM.
INFO	2016-05-16 11:58:25	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:01:55s.  Time for last 1,000,000:    5s.  Last read position: chr19:24,555,243
INFO	2016-05-16 11:58:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 11:58:28	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:01:58s.  Time for last 1,000,000:    3s.  Last read position: chr19:56,056,093
INFO	2016-05-16 11:58:28	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:58:31	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:02:02s.  Time for last 1,000,000:    3s.  Last read position: chr1:16,381,361
INFO	2016-05-16 11:58:31	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 11:58:34	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:02:05s.  Time for last 1,000,000:    3s.  Last read position: chr1:41,908,588
INFO	2016-05-16 11:58:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 11:58:40	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:02:11s.  Time for last 1,000,000:    6s.  Last read position: chr1:78,257,892
INFO	2016-05-16 11:58:40	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:58:51	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:02:22s.  Time for last 1,000,000:   10s.  Last read position: chr1:145,062,021
INFO	2016-05-16 11:58:51	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-16 11:58:54	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:02:25s.  Time for last 1,000,000:    3s.  Last read position: chr1:182,021,994
INFO	2016-05-16 11:58:54	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:58:58	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:02:29s.  Time for last 1,000,000:    3s.  Last read position: chr1:220,683,136
INFO	2016-05-16 11:58:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 11:59:02	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:02:32s.  Time for last 1,000,000:    3s.  Last read position: chr20:7,808,358
INFO	2016-05-16 11:59:02	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 11:59:05	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:02:36s.  Time for last 1,000,000:    3s.  Last read position: chr20:44,518,883
INFO	2016-05-16 11:59:05	MarkDuplicates	Tracking 16 as yet unmatched pairs. 16 records in RAM.
INFO	2016-05-16 11:59:10	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:02:40s.  Time for last 1,000,000:    4s.  Last read position: chr21:32,622,640
INFO	2016-05-16 11:59:10	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:59:13	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:02:43s.  Time for last 1,000,000:    3s.  Last read position: chr22:31,873,140
INFO	2016-05-16 11:59:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 11:59:16	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:02:46s.  Time for last 1,000,000:    3s.  Last read position: chr2:9,716,914
INFO	2016-05-16 11:59:16	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:59:19	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:02:50s.  Time for last 1,000,000:    3s.  Last read position: chr2:45,155,838
INFO	2016-05-16 11:59:19	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:59:22	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:02:53s.  Time for last 1,000,000:    3s.  Last read position: chr2:85,977,990
INFO	2016-05-16 11:59:22	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-16 11:59:25	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:02:56s.  Time for last 1,000,000:    3s.  Last read position: chr2:133,493,474
INFO	2016-05-16 11:59:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 11:59:28	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:02:59s.  Time for last 1,000,000:    3s.  Last read position: chr2:179,469,154
INFO	2016-05-16 11:59:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 11:59:34	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:03:05s.  Time for last 1,000,000:    5s.  Last read position: chr2:222,666,314
INFO	2016-05-16 11:59:34	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:59:37	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:03:08s.  Time for last 1,000,000:    3s.  Last read position: chr3:13,216,647
INFO	2016-05-16 11:59:37	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:59:40	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:03:11s.  Time for last 1,000,000:    3s.  Last read position: chr3:49,943,050
INFO	2016-05-16 11:59:40	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 11:59:48	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:03:18s.  Time for last 1,000,000:    7s.  Last read position: chr3:98,299,908
INFO	2016-05-16 11:59:48	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 11:59:51	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:03:22s.  Time for last 1,000,000:    3s.  Last read position: chr3:139,817,067
INFO	2016-05-16 11:59:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 11:59:54	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:03:25s.  Time for last 1,000,000:    3s.  Last read position: chr3:185,519,389
INFO	2016-05-16 11:59:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 11:59:59	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:03:30s.  Time for last 1,000,000:    4s.  Last read position: chr4:21,843,017
INFO	2016-05-16 11:59:59	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 12:00:02	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:03:33s.  Time for last 1,000,000:    3s.  Last read position: chr4:75,272,597
INFO	2016-05-16 12:00:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 12:00:06	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:03:37s.  Time for last 1,000,000:    3s.  Last read position: chr4:122,632,863
INFO	2016-05-16 12:00:06	MarkDuplicates	Tracking 32 as yet unmatched pairs. 32 records in RAM.
INFO	2016-05-16 12:00:10	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:03:40s.  Time for last 1,000,000:    3s.  Last read position: chr4:171,486,263
INFO	2016-05-16 12:00:10	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 12:00:13	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:03:43s.  Time for last 1,000,000:    3s.  Last read position: chr5:25,599,507
INFO	2016-05-16 12:00:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 12:00:16	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:03:47s.  Time for last 1,000,000:    3s.  Last read position: chr5:77,930,708
INFO	2016-05-16 12:00:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 12:00:19	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:03:50s.  Time for last 1,000,000:    3s.  Last read position: chr5:126,231,620
INFO	2016-05-16 12:00:19	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 12:00:24	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:03:55s.  Time for last 1,000,000:    5s.  Last read position: chr5:149,815,720
INFO	2016-05-16 12:00:24	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 12:00:28	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:03:58s.  Time for last 1,000,000:    3s.  Last read position: chr6:5,084,300
INFO	2016-05-16 12:00:28	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 12:00:31	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:04:02s.  Time for last 1,000,000:    3s.  Last read position: chr6:40,874,972
INFO	2016-05-16 12:00:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 12:00:34	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:04:05s.  Time for last 1,000,000:    3s.  Last read position: chr6:88,443,215
INFO	2016-05-16 12:00:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 12:00:45	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:04:16s.  Time for last 1,000,000:   11s.  Last read position: chr6:134,545,417
INFO	2016-05-16 12:00:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 12:00:49	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:04:20s.  Time for last 1,000,000:    3s.  Last read position: chr7:1,499,783
INFO	2016-05-16 12:00:49	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-05-16 12:00:53	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:04:23s.  Time for last 1,000,000:    3s.  Last read position: chr7:40,642,804
INFO	2016-05-16 12:00:53	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 12:00:56	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:04:27s.  Time for last 1,000,000:    3s.  Last read position: chr7:91,043,101
INFO	2016-05-16 12:00:56	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 12:01:00	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:04:31s.  Time for last 1,000,000:    3s.  Last read position: chr7:130,537,009
INFO	2016-05-16 12:01:00	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 12:01:05	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:04:36s.  Time for last 1,000,000:    4s.  Last read position: chr8:11,030,925
INFO	2016-05-16 12:01:05	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 12:01:09	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:04:39s.  Time for last 1,000,000:    3s.  Last read position: chr8:55,163,663
INFO	2016-05-16 12:01:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 12:01:12	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:04:43s.  Time for last 1,000,000:    3s.  Last read position: chr8:100,508,110
INFO	2016-05-16 12:01:12	MarkDuplicates	Tracking 598 as yet unmatched pairs. 598 records in RAM.
INFO	2016-05-16 12:01:17	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:04:48s.  Time for last 1,000,000:    4s.  Last read position: chr8:141,943,274
INFO	2016-05-16 12:01:17	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 12:01:22	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:04:53s.  Time for last 1,000,000:    5s.  Last read position: chr9:34,675,256
INFO	2016-05-16 12:01:22	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 12:01:27	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:04:57s.  Time for last 1,000,000:    4s.  Last read position: chr9:105,432,834
INFO	2016-05-16 12:01:27	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 12:01:31	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:05:02s.  Time for last 1,000,000:    4s.  Last read position: chr9:136,019,607
INFO	2016-05-16 12:01:31	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-05-16 12:01:35	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:05:06s.  Time for last 1,000,000:    3s.  Last read position: chrM:196
INFO	2016-05-16 12:01:35	MarkDuplicates	Tracking 60162 as yet unmatched pairs. 60162 records in RAM.
INFO	2016-05-16 12:01:42	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:05:12s.  Time for last 1,000,000:    6s.  Last read position: chrM:550
INFO	2016-05-16 12:01:42	MarkDuplicates	Tracking 6832 as yet unmatched pairs. 6832 records in RAM.
INFO	2016-05-16 12:01:46	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:05:16s.  Time for last 1,000,000:    4s.  Last read position: chrM:790
INFO	2016-05-16 12:01:46	MarkDuplicates	Tracking 66822 as yet unmatched pairs. 66822 records in RAM.
INFO	2016-05-16 12:01:54	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:05:24s.  Time for last 1,000,000:    7s.  Last read position: chrM:1,233
INFO	2016-05-16 12:01:54	MarkDuplicates	Tracking 30934 as yet unmatched pairs. 30934 records in RAM.
INFO	2016-05-16 12:01:58	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:05:28s.  Time for last 1,000,000:    4s.  Last read position: chrM:1,476
INFO	2016-05-16 12:01:58	MarkDuplicates	Tracking 51128 as yet unmatched pairs. 51128 records in RAM.
INFO	2016-05-16 12:02:02	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:05:32s.  Time for last 1,000,000:    3s.  Last read position: chrM:1,745
INFO	2016-05-16 12:02:02	MarkDuplicates	Tracking 15262 as yet unmatched pairs. 15262 records in RAM.
INFO	2016-05-16 12:02:06	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:05:37s.  Time for last 1,000,000:    4s.  Last read position: chrM:2,116
INFO	2016-05-16 12:02:06	MarkDuplicates	Tracking 38316 as yet unmatched pairs. 38316 records in RAM.
INFO	2016-05-16 12:02:09	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:05:40s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,531
INFO	2016-05-16 12:02:09	MarkDuplicates	Tracking 48308 as yet unmatched pairs. 48308 records in RAM.
INFO	2016-05-16 12:02:13	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:05:44s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,712
INFO	2016-05-16 12:02:13	MarkDuplicates	Tracking 93758 as yet unmatched pairs. 93758 records in RAM.
INFO	2016-05-16 12:02:18	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:05:48s.  Time for last 1,000,000:    4s.  Last read position: chrM:2,884
INFO	2016-05-16 12:02:18	MarkDuplicates	Tracking 81858 as yet unmatched pairs. 81858 records in RAM.
INFO	2016-05-16 12:02:25	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:05:56s.  Time for last 1,000,000:    7s.  Last read position: chrM:3,088
INFO	2016-05-16 12:02:25	MarkDuplicates	Tracking 85476 as yet unmatched pairs. 85476 records in RAM.
INFO	2016-05-16 12:02:29	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:06:00s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,307
INFO	2016-05-16 12:02:29	MarkDuplicates	Tracking 57724 as yet unmatched pairs. 57724 records in RAM.
INFO	2016-05-16 12:02:33	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:06:04s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,438
INFO	2016-05-16 12:02:33	MarkDuplicates	Tracking 76512 as yet unmatched pairs. 76512 records in RAM.
INFO	2016-05-16 12:02:37	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:06:08s.  Time for last 1,000,000:    4s.  Last read position: chrM:3,604
INFO	2016-05-16 12:02:37	MarkDuplicates	Tracking 54834 as yet unmatched pairs. 54834 records in RAM.
INFO	2016-05-16 12:02:42	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:06:12s.  Time for last 1,000,000:    4s.  Last read position: chrM:3,758
INFO	2016-05-16 12:02:42	MarkDuplicates	Tracking 58322 as yet unmatched pairs. 58322 records in RAM.
INFO	2016-05-16 12:02:46	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:06:16s.  Time for last 1,000,000:    4s.  Last read position: chrM:4,013
INFO	2016-05-16 12:02:46	MarkDuplicates	Tracking 26124 as yet unmatched pairs. 26124 records in RAM.
INFO	2016-05-16 12:02:49	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:06:20s.  Time for last 1,000,000:    3s.  Last read position: chrM:4,684
INFO	2016-05-16 12:02:49	MarkDuplicates	Tracking 7362 as yet unmatched pairs. 7362 records in RAM.
INFO	2016-05-16 12:02:53	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:06:24s.  Time for last 1,000,000:    3s.  Last read position: chrM:4,977
INFO	2016-05-16 12:02:53	MarkDuplicates	Tracking 57718 as yet unmatched pairs. 57718 records in RAM.
INFO	2016-05-16 12:03:09	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:06:40s.  Time for last 1,000,000:   15s.  Last read position: chrM:5,385
INFO	2016-05-16 12:03:09	MarkDuplicates	Tracking 30782 as yet unmatched pairs. 30782 records in RAM.
INFO	2016-05-16 12:03:14	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:06:44s.  Time for last 1,000,000:    4s.  Last read position: chrM:6,000
INFO	2016-05-16 12:03:14	MarkDuplicates	Tracking 39282 as yet unmatched pairs. 39282 records in RAM.
INFO	2016-05-16 12:03:18	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:06:49s.  Time for last 1,000,000:    4s.  Last read position: chrM:6,286
INFO	2016-05-16 12:03:18	MarkDuplicates	Tracking 63596 as yet unmatched pairs. 63596 records in RAM.
INFO	2016-05-16 12:03:21	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:06:52s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,456
INFO	2016-05-16 12:03:21	MarkDuplicates	Tracking 51216 as yet unmatched pairs. 51216 records in RAM.
INFO	2016-05-16 12:03:25	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:06:56s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,625
INFO	2016-05-16 12:03:25	MarkDuplicates	Tracking 73486 as yet unmatched pairs. 73486 records in RAM.
INFO	2016-05-16 12:03:30	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:07:00s.  Time for last 1,000,000:    4s.  Last read position: chrM:7,009
INFO	2016-05-16 12:03:30	MarkDuplicates	Tracking 27776 as yet unmatched pairs. 27776 records in RAM.
INFO	2016-05-16 12:03:33	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:07:04s.  Time for last 1,000,000:    3s.  Last read position: chrM:7,492
INFO	2016-05-16 12:03:33	MarkDuplicates	Tracking 36418 as yet unmatched pairs. 36418 records in RAM.
INFO	2016-05-16 12:03:37	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:07:08s.  Time for last 1,000,000:    3s.  Last read position: chrM:7,838
INFO	2016-05-16 12:03:37	MarkDuplicates	Tracking 59306 as yet unmatched pairs. 59306 records in RAM.
INFO	2016-05-16 12:03:41	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:07:11s.  Time for last 1,000,000:    3s.  Last read position: chrM:8,087
INFO	2016-05-16 12:03:41	MarkDuplicates	Tracking 60686 as yet unmatched pairs. 60686 records in RAM.
INFO	2016-05-16 12:03:44	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:07:15s.  Time for last 1,000,000:    3s.  Last read position: chrM:8,456
INFO	2016-05-16 12:03:44	MarkDuplicates	Tracking 43424 as yet unmatched pairs. 43424 records in RAM.
INFO	2016-05-16 12:03:47	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:07:18s.  Time for last 1,000,000:    3s.  Last read position: chrM:9,065
INFO	2016-05-16 12:03:47	MarkDuplicates	Tracking 18646 as yet unmatched pairs. 18646 records in RAM.
INFO	2016-05-16 12:03:51	MarkDuplicates	Read   100,000,000 records.  Elapsed time: 00:07:22s.  Time for last 1,000,000:    3s.  Last read position: chrM:9,386
INFO	2016-05-16 12:03:51	MarkDuplicates	Tracking 8162 as yet unmatched pairs. 8162 records in RAM.
INFO	2016-05-16 12:03:59	MarkDuplicates	Read   101,000,000 records.  Elapsed time: 00:07:29s.  Time for last 1,000,000:    7s.  Last read position: chrM:9,778
INFO	2016-05-16 12:03:59	MarkDuplicates	Tracking 77358 as yet unmatched pairs. 77358 records in RAM.
INFO	2016-05-16 12:04:02	MarkDuplicates	Read   102,000,000 records.  Elapsed time: 00:07:33s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,005
INFO	2016-05-16 12:04:02	MarkDuplicates	Tracking 106210 as yet unmatched pairs. 106210 records in RAM.
INFO	2016-05-16 12:04:10	MarkDuplicates	Read   103,000,000 records.  Elapsed time: 00:07:41s.  Time for last 1,000,000:    8s.  Last read position: chrM:10,279
INFO	2016-05-16 12:04:10	MarkDuplicates	Tracking 42924 as yet unmatched pairs. 42924 records in RAM.
INFO	2016-05-16 12:04:15	MarkDuplicates	Read   104,000,000 records.  Elapsed time: 00:07:45s.  Time for last 1,000,000:    4s.  Last read position: chrM:10,589
INFO	2016-05-16 12:04:15	MarkDuplicates	Tracking 28818 as yet unmatched pairs. 28818 records in RAM.
INFO	2016-05-16 12:04:19	MarkDuplicates	Read   105,000,000 records.  Elapsed time: 00:07:49s.  Time for last 1,000,000:    4s.  Last read position: chrM:10,905
INFO	2016-05-16 12:04:19	MarkDuplicates	Tracking 2686 as yet unmatched pairs. 2686 records in RAM.
INFO	2016-05-16 12:04:23	MarkDuplicates	Read   106,000,000 records.  Elapsed time: 00:07:53s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,219
INFO	2016-05-16 12:04:23	MarkDuplicates	Tracking 47816 as yet unmatched pairs. 47816 records in RAM.
INFO	2016-05-16 12:04:27	MarkDuplicates	Read   107,000,000 records.  Elapsed time: 00:07:58s.  Time for last 1,000,000:    4s.  Last read position: chrM:11,495
INFO	2016-05-16 12:04:27	MarkDuplicates	Tracking 26502 as yet unmatched pairs. 26502 records in RAM.
INFO	2016-05-16 12:04:31	MarkDuplicates	Read   108,000,000 records.  Elapsed time: 00:08:02s.  Time for last 1,000,000:    4s.  Last read position: chrM:11,771
INFO	2016-05-16 12:04:31	MarkDuplicates	Tracking 39276 as yet unmatched pairs. 39276 records in RAM.
INFO	2016-05-16 12:04:35	MarkDuplicates	Read   109,000,000 records.  Elapsed time: 00:08:06s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,008
INFO	2016-05-16 12:04:35	MarkDuplicates	Tracking 39198 as yet unmatched pairs. 39198 records in RAM.
INFO	2016-05-16 12:04:39	MarkDuplicates	Read   110,000,000 records.  Elapsed time: 00:08:09s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,219
INFO	2016-05-16 12:04:39	MarkDuplicates	Tracking 29282 as yet unmatched pairs. 29282 records in RAM.
INFO	2016-05-16 12:04:43	MarkDuplicates	Read   111,000,000 records.  Elapsed time: 00:08:13s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,509
INFO	2016-05-16 12:04:43	MarkDuplicates	Tracking 53382 as yet unmatched pairs. 53382 records in RAM.
INFO	2016-05-16 12:04:47	MarkDuplicates	Read   112,000,000 records.  Elapsed time: 00:08:17s.  Time for last 1,000,000:    4s.  Last read position: chrM:12,675
INFO	2016-05-16 12:04:47	MarkDuplicates	Tracking 94382 as yet unmatched pairs. 94382 records in RAM.
INFO	2016-05-16 12:04:54	MarkDuplicates	Read   113,000,000 records.  Elapsed time: 00:08:25s.  Time for last 1,000,000:    7s.  Last read position: chrM:12,988
INFO	2016-05-16 12:04:54	MarkDuplicates	Tracking 21120 as yet unmatched pairs. 21120 records in RAM.
INFO	2016-05-16 12:04:58	MarkDuplicates	Read   114,000,000 records.  Elapsed time: 00:08:28s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,185
INFO	2016-05-16 12:04:58	MarkDuplicates	Tracking 77274 as yet unmatched pairs. 77274 records in RAM.
INFO	2016-05-16 12:05:02	MarkDuplicates	Read   115,000,000 records.  Elapsed time: 00:08:32s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,383
INFO	2016-05-16 12:05:02	MarkDuplicates	Tracking 63470 as yet unmatched pairs. 63470 records in RAM.
INFO	2016-05-16 12:05:05	MarkDuplicates	Read   116,000,000 records.  Elapsed time: 00:08:36s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,580
INFO	2016-05-16 12:05:05	MarkDuplicates	Tracking 41142 as yet unmatched pairs. 41142 records in RAM.
INFO	2016-05-16 12:05:09	MarkDuplicates	Read   117,000,000 records.  Elapsed time: 00:08:40s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,844
INFO	2016-05-16 12:05:09	MarkDuplicates	Tracking 87536 as yet unmatched pairs. 87536 records in RAM.
INFO	2016-05-16 12:05:26	MarkDuplicates	Read   118,000,000 records.  Elapsed time: 00:08:57s.  Time for last 1,000,000:   16s.  Last read position: chrM:14,055
INFO	2016-05-16 12:05:26	MarkDuplicates	Tracking 62288 as yet unmatched pairs. 62288 records in RAM.
INFO	2016-05-16 12:05:30	MarkDuplicates	Read   119,000,000 records.  Elapsed time: 00:09:00s.  Time for last 1,000,000:    3s.  Last read position: chrM:14,372
INFO	2016-05-16 12:05:30	MarkDuplicates	Tracking 23790 as yet unmatched pairs. 23790 records in RAM.
INFO	2016-05-16 12:05:34	MarkDuplicates	Read   120,000,000 records.  Elapsed time: 00:09:05s.  Time for last 1,000,000:    4s.  Last read position: chrM:14,805
INFO	2016-05-16 12:05:34	MarkDuplicates	Tracking 8666 as yet unmatched pairs. 8666 records in RAM.
INFO	2016-05-16 12:05:38	MarkDuplicates	Read   121,000,000 records.  Elapsed time: 00:09:08s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,043
INFO	2016-05-16 12:05:38	MarkDuplicates	Tracking 98206 as yet unmatched pairs. 98206 records in RAM.
INFO	2016-05-16 12:05:42	MarkDuplicates	Read   122,000,000 records.  Elapsed time: 00:09:12s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,190
INFO	2016-05-16 12:05:42	MarkDuplicates	Tracking 33004 as yet unmatched pairs. 33004 records in RAM.
INFO	2016-05-16 12:05:45	MarkDuplicates	Read   123,000,000 records.  Elapsed time: 00:09:16s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,371
INFO	2016-05-16 12:05:45	MarkDuplicates	Tracking 89050 as yet unmatched pairs. 89050 records in RAM.
INFO	2016-05-16 12:05:49	MarkDuplicates	Read   124,000,000 records.  Elapsed time: 00:09:20s.  Time for last 1,000,000:    4s.  Last read position: chrM:15,538
INFO	2016-05-16 12:05:49	MarkDuplicates	Tracking 76128 as yet unmatched pairs. 76128 records in RAM.
INFO	2016-05-16 12:05:55	MarkDuplicates	Read   125,000,000 records.  Elapsed time: 00:09:26s.  Time for last 1,000,000:    5s.  Last read position: chrM:15,703
INFO	2016-05-16 12:05:55	MarkDuplicates	Tracking 79862 as yet unmatched pairs. 79862 records in RAM.
INFO	2016-05-16 12:05:58	MarkDuplicates	Read   126,000,000 records.  Elapsed time: 00:09:29s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,843
INFO	2016-05-16 12:05:58	MarkDuplicates	Tracking 78330 as yet unmatched pairs. 78330 records in RAM.
INFO	2016-05-16 12:06:01	MarkDuplicates	Read   127,000,000 records.  Elapsed time: 00:09:32s.  Time for last 1,000,000:    3s.  Last read position: chrM:16,105
INFO	2016-05-16 12:06:01	MarkDuplicates	Tracking 33850 as yet unmatched pairs. 33850 records in RAM.
INFO	2016-05-16 12:06:05	MarkDuplicates	Read   128,000,000 records.  Elapsed time: 00:09:35s.  Time for last 1,000,000:    3s.  Last read position: chrM:16,384
INFO	2016-05-16 12:06:05	MarkDuplicates	Tracking 47272 as yet unmatched pairs. 47272 records in RAM.
INFO	2016-05-16 12:06:08	MarkDuplicates	Read   129,000,000 records.  Elapsed time: 00:09:39s.  Time for last 1,000,000:    3s.  Last read position: chrX:10,575,286
INFO	2016-05-16 12:06:08	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 12:06:13	MarkDuplicates	Read   130,000,000 records.  Elapsed time: 00:09:43s.  Time for last 1,000,000:    4s.  Last read position: chrX:57,337,012
INFO	2016-05-16 12:06:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 12:06:18	MarkDuplicates	Read   131,000,000 records.  Elapsed time: 00:09:48s.  Time for last 1,000,000:    4s.  Last read position: chrX:116,383,097
INFO	2016-05-16 12:06:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 12:06:21	MarkDuplicates	Read 131866052 records. 0 pairs never matched.
INFO	2016-05-16 12:06:30	MarkDuplicates	After buildSortedReadEndLists freeMemory: 3263395544; totalMemory: 3290955776; maxMemory: 3817865216
INFO	2016-05-16 12:06:30	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-05-16 12:06:30	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-05-16 12:07:19	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-05-16 12:07:54	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-05-16 12:07:58	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2329455264; totalMemory: 3311927296; maxMemory: 3817865216
INFO	2016-05-16 12:07:58	MarkDuplicates	Marking 65805438 records as duplicates.
INFO	2016-05-16 12:07:58	MarkDuplicates	Found 21775038 optical duplicate clusters.
INFO	2016-05-16 12:09:46	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:46s.  Time for last 10,000,000:  106s.  Last read position: chr12:114,576,505
INFO	2016-05-16 12:11:26	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:03:26s.  Time for last 10,000,000:   99s.  Last read position: chr17:15,465,278
INFO	2016-05-16 12:12:59	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:04:59s.  Time for last 10,000,000:   93s.  Last read position: chr1:145,062,021
INFO	2016-05-16 12:14:38	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:06:38s.  Time for last 10,000,000:   98s.  Last read position: chr2:133,493,474
INFO	2016-05-16 12:16:20	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:08:20s.  Time for last 10,000,000:  102s.  Last read position: chr4:122,632,863
INFO	2016-05-16 12:18:09	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:10:09s.  Time for last 10,000,000:  108s.  Last read position: chr7:1,499,783
INFO	2016-05-16 12:19:57	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:11:56s.  Time for last 10,000,000:  107s.  Last read position: chr9:136,019,607
INFO	2016-05-16 12:21:20	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:13:20s.  Time for last 10,000,000:   83s.  Last read position: chrM:2,884
INFO	2016-05-16 12:22:48	MarkDuplicates	Written    90,000,000 records.  Elapsed time: 00:14:48s.  Time for last 10,000,000:   87s.  Last read position: chrM:6,000
INFO	2016-05-16 12:24:10	MarkDuplicates	Written   100,000,000 records.  Elapsed time: 00:16:10s.  Time for last 10,000,000:   82s.  Last read position: chrM:9,386
INFO	2016-05-16 12:25:35	MarkDuplicates	Written   110,000,000 records.  Elapsed time: 00:17:35s.  Time for last 10,000,000:   85s.  Last read position: chrM:12,219
INFO	2016-05-16 12:27:04	MarkDuplicates	Written   120,000,000 records.  Elapsed time: 00:19:04s.  Time for last 10,000,000:   88s.  Last read position: chrM:14,805
INFO	2016-05-16 12:28:37	MarkDuplicates	Written   130,000,000 records.  Elapsed time: 00:20:36s.  Time for last 10,000,000:   92s.  Last read position: chrX:57,337,012
INFO	2016-05-16 12:28:59	MarkDuplicates	Before output close freeMemory: 3341209408; totalMemory: 3371696128; maxMemory: 3817865216
INFO	2016-05-16 12:28:59	MarkDuplicates	After output close freeMemory: 3341208352; totalMemory: 3371696128; maxMemory: 3817865216
[Mon May 16 12:28:59 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 32.50 minutes.
Runtime.totalMemory()=3371696128
[bam_sort_core] merging from 54 files...

Num	5
ID	task.postalign_bam.nmsrt_bam_rep2.line_321.id_10
Name	nmsrt_bam rep2
Thread	thread_21
PID	103935

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

Start	2016-05-16 10:16:49
End	2016-05-16 10:35:04
Elapsed	00:18:14
Timeout	00:00:-1
Wall Timeout	100 days

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

 
# SYS command. line 323

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

# SYS command. line 325

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

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 20 files...

Num	6
ID	task.postalign_bam.bam_to_bedpe_rep2.line_425.id_11
Name	bam_to_bedpe rep2
Thread	thread_21
PID	104134

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

Start	2016-05-16 10:35:04
End	2016-05-16 10:37:12
Elapsed	00:02:07
Timeout	00:00:-1
Wall Timeout	100 days

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

 
# SYS command. line 427

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

# SYS command. line 430

 bedtools bamtobed -bedpe -mate1 -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz

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

Num	7
ID	task.postalign_bed.subsample_bedpe_rep2.line_116.id_12
Name	subsample_bedpe rep2
Thread	thread_21
PID	104202

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

Start	2016-05-16 10:37:13
End	2016-05-16 10:39:22
Elapsed	00:02:09
Timeout	00:00:-1
Wall Timeout	100 days

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

 
# SYS command. line 118

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

# SYS command. line 120

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | grep -v "chrM" | shuf -n 17500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz

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

Num	8
ID	task.postalign_bam.bedpe_to_tag_rep2.line_465.id_13
Name	bedpe_to_tag rep2
Thread	thread_21
PID	104275

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

Start	2016-05-16 10:39:23
End	2016-05-16 10:40:58
Elapsed	00:01:35
Timeout	00:00:-1
Wall Timeout	100 days

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

 
# SYS command. line 467

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

# SYS command. line 469

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz | awk 'BEGIN{OFS="\t"}{printf "%s\t%s\t%s\tN\t1000\t%s\n%s\t%s\t%s\tN\t1000\t%s\n",$1,$2,$3,$9,$4,$5,$6,$10}' | \
			gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz

# SYS command. line 472

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz | grep -P -v 'chrM' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz; mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz

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

Num	9
ID	task.postalign_bed.shift_tag_rep2.line_140.id_14
Name	shift_tag rep2
Thread	thread_21
PID	104344

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

Start	2016-05-16 10:40:59
End	2016-05-16 10:41:51
Elapsed	00:00:51
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Dependencies

 
# SYS command. line 142

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

# SYS command. line 144

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz | awk -F $'\t' 'BEGIN {OFS = FS}{ if ($6 == "+") {$2 = $2 + 4} else if ($6 == "-") {$3 = $3 - 5} print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz

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

Num	10
ID	task.postalign_bed.subsample_bedpe2tagrep2.line_89.id_15
Name	subsample_bedpe2tagrep2
Thread	thread_21
PID	104407

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

Start	2016-05-16 10:41:52
End	2016-05-16 10:43:04
Elapsed	00:01:12
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
Dependencies

 
# SYS command. line 91

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

# SYS command. line 95

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | \
			grep -v "chrM" | shuf -n 25000000 | \
			awk 'BEGIN{OFS="\t"}{print $1,$2,$3,"N","1000",$9}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz

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

Num	11
ID	task.postalign_bed.xcor_rep2.line_165.id_16
Name	xcor rep2
Thread	thread_21
PID	104472

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

Start	2016-05-16 10:43:05
End	2016-05-16 11:18:11
Elapsed	00:35:06
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf
Dependencies

 
# SYS command. line 167

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

# SYS command. line 171

 Rscript $(which run_spp_nodups.R) -rf \
			-c=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz -p=1 \
			-filtchr=chrM -savp=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf -out=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc -speak=0

# SYS command. line 174

 sed -r 's/,[^\t]+//g' /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp

# SYS command. line 175

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

   
--------------------Stdout--------------------
################
ChIP data: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz 
Control data: NA 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 0 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: NA 
Output Directory: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2 
narrowPeak output file name: NA 
regionPeak output file name: NA 
Rdata filename: NA 
plot pdf filename: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf 
result filename: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz 
opened /tmp/RtmpNRk9zn/ATAC8-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign198c263e50ce6
done. read 22997955 fragments
ChIP data read length 74 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.2315254 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.251607847757416 
Top 3 estimates for fragment length 0 
Window half size 480 
Phantom peak location 65 
Phantom peak Correlation 0.2533923 
Normalized Strand cross-correlation coefficient (NSC) 1.08674 
Relative Strand Cross correlation Coefficient (RSC) 0.9183944 
Phantom Peak Quality Tag 0 
null device 
          1 

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

Num	12
ID	task.callpeak_macs2.macs2_atac_rep2.pval0.1.line_192.id_17
Name	macs2_atac rep2.pval0.1
Thread	thread_21
PID	104474

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

Start	2016-05-16 10:43:05
End	2016-05-16 10:59:56
Elapsed	00:16:50
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz
Dependencies

 
# SYS command. line 194

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

# SYS command. line 195

 LC_COLLATE=C

# SYS command. line 197

 macs2 callpeak \
			-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 --broad --keep-dup all

# SYS command. line 202

 sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.broadPeak.gz

# SYS command. line 203

 sort -k 14gr,14gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz

# SYS command. line 204

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.broadPeak

# SYS command. line 205

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.gappedPeak

# SYS command. line 207

 macs2 callpeak \
			-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits

# SYS command. line 212

 sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz

# SYS command. line 213

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.narrowPeak

# SYS command. line 214

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.xls

# SYS command. line 215

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_summits.bed

# SYS command. line 217

 if [[ false == "true" ]]; then \
			\
			macs2 bdgcmp -t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_FE.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/signal/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			\
			# sval counts the number of tags per million in the (compressed) BED file; \
			sval=$(wc -l <(zcat -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_ppois.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/signal/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			\
			fi

# SYS command. line 243

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
INFO  @ Mon, 16 May 2016 10:43:08: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 --broad --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-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 10:43:08: #1 read tag files... 
INFO  @ Mon, 16 May 2016 10:43:08: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 10:43:09:  1000000 
INFO  @ Mon, 16 May 2016 10:43:11:  2000000 
INFO  @ Mon, 16 May 2016 10:43:12:  3000000 
INFO  @ Mon, 16 May 2016 10:43:14:  4000000 
INFO  @ Mon, 16 May 2016 10:43:16:  5000000 
INFO  @ Mon, 16 May 2016 10:43:17:  6000000 
INFO  @ Mon, 16 May 2016 10:43:19:  7000000 
INFO  @ Mon, 16 May 2016 10:43:20:  8000000 
INFO  @ Mon, 16 May 2016 10:43:22:  9000000 
INFO  @ Mon, 16 May 2016 10:43:24:  10000000 
INFO  @ Mon, 16 May 2016 10:43:25:  11000000 
INFO  @ Mon, 16 May 2016 10:43:27:  12000000 
INFO  @ Mon, 16 May 2016 10:43:28:  13000000 
INFO  @ Mon, 16 May 2016 10:43:30:  14000000 
INFO  @ Mon, 16 May 2016 10:43:32:  15000000 
INFO  @ Mon, 16 May 2016 10:43:33:  16000000 
INFO  @ Mon, 16 May 2016 10:43:35:  17000000 
INFO  @ Mon, 16 May 2016 10:43:36:  18000000 
INFO  @ Mon, 16 May 2016 10:43:38:  19000000 
INFO  @ Mon, 16 May 2016 10:43:39:  20000000 
INFO  @ Mon, 16 May 2016 10:43:41:  21000000 
INFO  @ Mon, 16 May 2016 10:43:43:  22000000 
INFO  @ Mon, 16 May 2016 10:43:44:  23000000 
INFO  @ Mon, 16 May 2016 10:43:46:  24000000 
INFO  @ Mon, 16 May 2016 10:43:47:  25000000 
INFO  @ Mon, 16 May 2016 10:43:49:  26000000 
INFO  @ Mon, 16 May 2016 10:43:51:  27000000 
INFO  @ Mon, 16 May 2016 10:43:52:  28000000 
INFO  @ Mon, 16 May 2016 10:43:54:  29000000 
INFO  @ Mon, 16 May 2016 10:43:55:  30000000 
INFO  @ Mon, 16 May 2016 10:43:57:  31000000 
INFO  @ Mon, 16 May 2016 10:43:58:  32000000 
INFO  @ Mon, 16 May 2016 10:44:00:  33000000 
INFO  @ Mon, 16 May 2016 10:44:02:  34000000 
INFO  @ Mon, 16 May 2016 10:44:03:  35000000 
INFO  @ Mon, 16 May 2016 10:44:06: #1 tag size is determined as 60 bps 
INFO  @ Mon, 16 May 2016 10:44:06: #1 tag size = 60 
INFO  @ Mon, 16 May 2016 10:44:06: #1  total tags in treatment: 35000000 
INFO  @ Mon, 16 May 2016 10:44:06: #1 finished! 
INFO  @ Mon, 16 May 2016 10:44:06: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 10:44:06: #2 Skipped... 
INFO  @ Mon, 16 May 2016 10:44:06: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 10:44:06: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 10:44:06: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 10:44:06: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Mon, 16 May 2016 10:44:06: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 10:45:19: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 10:47:35: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls 
INFO  @ Mon, 16 May 2016 10:47:38: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Mon, 16 May 2016 10:47:41: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Mon, 16 May 2016 10:47:43: Done! 
INFO  @ Mon, 16 May 2016 10:47:56: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# ARGUMENTS LIST:
# name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-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 10:47:56: #1 read tag files... 
INFO  @ Mon, 16 May 2016 10:47:56: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 10:47:57:  1000000 
INFO  @ Mon, 16 May 2016 10:47:59:  2000000 
INFO  @ Mon, 16 May 2016 10:48:00:  3000000 
INFO  @ Mon, 16 May 2016 10:48:02:  4000000 
INFO  @ Mon, 16 May 2016 10:48:04:  5000000 
INFO  @ Mon, 16 May 2016 10:48:05:  6000000 
INFO  @ Mon, 16 May 2016 10:48:07:  7000000 
INFO  @ Mon, 16 May 2016 10:48:08:  8000000 
INFO  @ Mon, 16 May 2016 10:48:10:  9000000 
INFO  @ Mon, 16 May 2016 10:48:12:  10000000 
INFO  @ Mon, 16 May 2016 10:48:13:  11000000 
INFO  @ Mon, 16 May 2016 10:48:15:  12000000 
INFO  @ Mon, 16 May 2016 10:48:16:  13000000 
INFO  @ Mon, 16 May 2016 10:48:18:  14000000 
INFO  @ Mon, 16 May 2016 10:48:20:  15000000 
INFO  @ Mon, 16 May 2016 10:48:21:  16000000 
INFO  @ Mon, 16 May 2016 10:48:23:  17000000 
INFO  @ Mon, 16 May 2016 10:48:24:  18000000 
INFO  @ Mon, 16 May 2016 10:48:26:  19000000 
INFO  @ Mon, 16 May 2016 10:48:28:  20000000 
INFO  @ Mon, 16 May 2016 10:48:29:  21000000 
INFO  @ Mon, 16 May 2016 10:48:31:  22000000 
INFO  @ Mon, 16 May 2016 10:48:32:  23000000 
INFO  @ Mon, 16 May 2016 10:48:34:  24000000 
INFO  @ Mon, 16 May 2016 10:48:36:  25000000 
INFO  @ Mon, 16 May 2016 10:48:37:  26000000 
INFO  @ Mon, 16 May 2016 10:48:39:  27000000 
INFO  @ Mon, 16 May 2016 10:48:40:  28000000 
INFO  @ Mon, 16 May 2016 10:48:42:  29000000 
INFO  @ Mon, 16 May 2016 10:48:43:  30000000 
INFO  @ Mon, 16 May 2016 10:48:45:  31000000 
INFO  @ Mon, 16 May 2016 10:48:47:  32000000 
INFO  @ Mon, 16 May 2016 10:48:48:  33000000 
INFO  @ Mon, 16 May 2016 10:48:50:  34000000 
INFO  @ Mon, 16 May 2016 10:48:51:  35000000 
INFO  @ Mon, 16 May 2016 10:48:54: #1 tag size is determined as 60 bps 
INFO  @ Mon, 16 May 2016 10:48:54: #1 tag size = 60 
INFO  @ Mon, 16 May 2016 10:48:54: #1  total tags in treatment: 35000000 
INFO  @ Mon, 16 May 2016 10:48:54: #1 finished! 
INFO  @ Mon, 16 May 2016 10:48:54: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 10:48:54: #2 Skipped... 
INFO  @ Mon, 16 May 2016 10:48:54: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 10:48:54: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 10:48:54: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 10:48:54: #3 Going to call summits inside each peak ... 
INFO  @ Mon, 16 May 2016 10:48:54: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Mon, 16 May 2016 10:48:54: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 10:50:28: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Mon, 16 May 2016 10:50:28: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Mon, 16 May 2016 10:50:28: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Mon, 16 May 2016 10:50:28: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Mon, 16 May 2016 10:50:28: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 10:59:34: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls 
INFO  @ Mon, 16 May 2016 10:59:40: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Mon, 16 May 2016 10:59:45: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_summits.bed 
INFO  @ Mon, 16 May 2016 10:59:48: Done!

Num	13
ID	task.callpeak_macs2.macs2_atac_rep2.line_192.id_18
Name	macs2_atac rep2
Thread	thread_21
PID	104484

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

Start	2016-05-16 10:43:05
End	2016-05-16 11:25:07
Elapsed	00:42:01
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.gappedPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/signal/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/signal/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig
Dependencies

 
# SYS command. line 194

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

# SYS command. line 195

 LC_COLLATE=C

# SYS command. line 197

 macs2 callpeak \
			-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -g "hs" -p 0.01 \
			--nomodel --shift -75 --extsize 150 --broad --keep-dup all

# SYS command. line 202

 sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.broadPeak.gz

# SYS command. line 203

 sort -k 14gr,14gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.gappedPeak.gz

# SYS command. line 204

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.broadPeak

# SYS command. line 205

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.gappedPeak

# SYS command. line 207

 macs2 callpeak \
			-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -g "hs" -p 0.01 \
			--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits

# SYS command. line 212

 sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz

# SYS command. line 213

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.narrowPeak

# SYS command. line 214

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.xls

# SYS command. line 215

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_summits.bed

# SYS command. line 217

 if [[ true == "true" ]]; then \
			\
			macs2 bdgcmp -t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_FE.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/signal/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph; \
			\
			# sval counts the number of tags per million in the (compressed) BED file; \
			sval=$(wc -l <(zcat -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_ppois.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/signal/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph; \
			\
			fi

# SYS command. line 243

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
INFO  @ Mon, 16 May 2016 10:43:08: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf -g hs -p 0.01 --nomodel --shift -75 --extsize 150 --broad --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-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 10:43:08: #1 read tag files... 
INFO  @ Mon, 16 May 2016 10:43:08: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 10:43:09:  1000000 
INFO  @ Mon, 16 May 2016 10:43:11:  2000000 
INFO  @ Mon, 16 May 2016 10:43:12:  3000000 
INFO  @ Mon, 16 May 2016 10:43:14:  4000000 
INFO  @ Mon, 16 May 2016 10:43:16:  5000000 
INFO  @ Mon, 16 May 2016 10:43:17:  6000000 
INFO  @ Mon, 16 May 2016 10:43:19:  7000000 
INFO  @ Mon, 16 May 2016 10:43:20:  8000000 
INFO  @ Mon, 16 May 2016 10:43:22:  9000000 
INFO  @ Mon, 16 May 2016 10:43:23:  10000000 
INFO  @ Mon, 16 May 2016 10:43:25:  11000000 
INFO  @ Mon, 16 May 2016 10:43:27:  12000000 
INFO  @ Mon, 16 May 2016 10:43:28:  13000000 
INFO  @ Mon, 16 May 2016 10:43:30:  14000000 
INFO  @ Mon, 16 May 2016 10:43:31:  15000000 
INFO  @ Mon, 16 May 2016 10:43:33:  16000000 
INFO  @ Mon, 16 May 2016 10:43:35:  17000000 
INFO  @ Mon, 16 May 2016 10:43:36:  18000000 
INFO  @ Mon, 16 May 2016 10:43:38:  19000000 
INFO  @ Mon, 16 May 2016 10:43:39:  20000000 
INFO  @ Mon, 16 May 2016 10:43:41:  21000000 
INFO  @ Mon, 16 May 2016 10:43:42:  22000000 
INFO  @ Mon, 16 May 2016 10:43:44:  23000000 
INFO  @ Mon, 16 May 2016 10:43:46:  24000000 
INFO  @ Mon, 16 May 2016 10:43:47:  25000000 
INFO  @ Mon, 16 May 2016 10:43:49:  26000000 
INFO  @ Mon, 16 May 2016 10:43:50:  27000000 
INFO  @ Mon, 16 May 2016 10:43:52:  28000000 
INFO  @ Mon, 16 May 2016 10:43:53:  29000000 
INFO  @ Mon, 16 May 2016 10:43:55:  30000000 
INFO  @ Mon, 16 May 2016 10:43:57:  31000000 
INFO  @ Mon, 16 May 2016 10:43:58:  32000000 
INFO  @ Mon, 16 May 2016 10:44:00:  33000000 
INFO  @ Mon, 16 May 2016 10:44:01:  34000000 
INFO  @ Mon, 16 May 2016 10:44:03:  35000000 
INFO  @ Mon, 16 May 2016 10:44:05: #1 tag size is determined as 60 bps 
INFO  @ Mon, 16 May 2016 10:44:05: #1 tag size = 60 
INFO  @ Mon, 16 May 2016 10:44:05: #1  total tags in treatment: 35000000 
INFO  @ Mon, 16 May 2016 10:44:05: #1 finished! 
INFO  @ Mon, 16 May 2016 10:44:05: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 10:44:05: #2 Skipped... 
INFO  @ Mon, 16 May 2016 10:44:05: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 10:44:05: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 10:44:05: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 10:44:05: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Mon, 16 May 2016 10:44:05: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 10:45:41: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 10:47:32: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls 
INFO  @ Mon, 16 May 2016 10:47:36: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.broadPeak 
INFO  @ Mon, 16 May 2016 10:47:38: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.gappedPeak 
INFO  @ Mon, 16 May 2016 10:47:41: Done! 
INFO  @ Mon, 16 May 2016 10:47:53: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf -g hs -p 0.01 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# ARGUMENTS LIST:
# name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-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 10:47:53: #1 read tag files... 
INFO  @ Mon, 16 May 2016 10:47:53: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 10:47:55:  1000000 
INFO  @ Mon, 16 May 2016 10:47:57:  2000000 
INFO  @ Mon, 16 May 2016 10:47:58:  3000000 
INFO  @ Mon, 16 May 2016 10:48:00:  4000000 
INFO  @ Mon, 16 May 2016 10:48:02:  5000000 
INFO  @ Mon, 16 May 2016 10:48:03:  6000000 
INFO  @ Mon, 16 May 2016 10:48:05:  7000000 
INFO  @ Mon, 16 May 2016 10:48:07:  8000000 
INFO  @ Mon, 16 May 2016 10:48:08:  9000000 
INFO  @ Mon, 16 May 2016 10:48:10:  10000000 
INFO  @ Mon, 16 May 2016 10:48:12:  11000000 
INFO  @ Mon, 16 May 2016 10:48:13:  12000000 
INFO  @ Mon, 16 May 2016 10:48:15:  13000000 
INFO  @ Mon, 16 May 2016 10:48:17:  14000000 
INFO  @ Mon, 16 May 2016 10:48:18:  15000000 
INFO  @ Mon, 16 May 2016 10:48:20:  16000000 
INFO  @ Mon, 16 May 2016 10:48:22:  17000000 
INFO  @ Mon, 16 May 2016 10:48:23:  18000000 
INFO  @ Mon, 16 May 2016 10:48:25:  19000000 
INFO  @ Mon, 16 May 2016 10:48:27:  20000000 
INFO  @ Mon, 16 May 2016 10:48:28:  21000000 
INFO  @ Mon, 16 May 2016 10:48:30:  22000000 
INFO  @ Mon, 16 May 2016 10:48:32:  23000000 
INFO  @ Mon, 16 May 2016 10:48:33:  24000000 
INFO  @ Mon, 16 May 2016 10:48:35:  25000000 
INFO  @ Mon, 16 May 2016 10:48:37:  26000000 
INFO  @ Mon, 16 May 2016 10:48:38:  27000000 
INFO  @ Mon, 16 May 2016 10:48:40:  28000000 
INFO  @ Mon, 16 May 2016 10:48:42:  29000000 
INFO  @ Mon, 16 May 2016 10:48:43:  30000000 
INFO  @ Mon, 16 May 2016 10:48:45:  31000000 
INFO  @ Mon, 16 May 2016 10:48:47:  32000000 
INFO  @ Mon, 16 May 2016 10:48:48:  33000000 
INFO  @ Mon, 16 May 2016 10:48:50:  34000000 
INFO  @ Mon, 16 May 2016 10:48:52:  35000000 
INFO  @ Mon, 16 May 2016 10:48:54: #1 tag size is determined as 60 bps 
INFO  @ Mon, 16 May 2016 10:48:54: #1 tag size = 60 
INFO  @ Mon, 16 May 2016 10:48:54: #1  total tags in treatment: 35000000 
INFO  @ Mon, 16 May 2016 10:48:54: #1 finished! 
INFO  @ Mon, 16 May 2016 10:48:54: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 10:48:54: #2 Skipped... 
INFO  @ Mon, 16 May 2016 10:48:54: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 10:48:54: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 10:48:54: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 10:48:54: #3 Going to call summits inside each peak ... 
INFO  @ Mon, 16 May 2016 10:48:54: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Mon, 16 May 2016 10:48:54: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 10:50:16: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Mon, 16 May 2016 10:50:16: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_treat_pileup.bdg 
INFO  @ Mon, 16 May 2016 10:50:16: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_control_lambda.bdg 
INFO  @ Mon, 16 May 2016 10:50:16: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Mon, 16 May 2016 10:50:16: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 10:55:09: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls 
INFO  @ Mon, 16 May 2016 10:55:11: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.narrowPeak 
INFO  @ Mon, 16 May 2016 10:55:12: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_summits.bed 
INFO  @ Mon, 16 May 2016 10:55:13: Done! 
INFO  @ Mon, 16 May 2016 10:55:16: Read and build treatment bedGraph... 
INFO  @ Mon, 16 May 2016 10:56:24: Read and build control bedGraph... 
INFO  @ Mon, 16 May 2016 10:56:55: Build scoreTrackII... 
INFO  @ Mon, 16 May 2016 10:57:26: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Mon, 16 May 2016 11:01:06: Write bedGraph of scores... 
INFO  @ Mon, 16 May 2016 11:03:30: Finished 'FE'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_FE.bdg'! 
INFO  @ Mon, 16 May 2016 11:09:57: Read and build treatment bedGraph... 
INFO  @ Mon, 16 May 2016 11:11:06: Read and build control bedGraph... 
INFO  @ Mon, 16 May 2016 11:11:37: Build scoreTrackII... 
INFO  @ Mon, 16 May 2016 11:12:03: Values in your input bedGraph files will be multiplied by 35.000000 ... 
INFO  @ Mon, 16 May 2016 11:16:07: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Mon, 16 May 2016 11:16:44: Write bedGraph of scores... 
INFO  @ Mon, 16 May 2016 11:19:15: Finished 'ppois'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_ppois.bdg'!

Num	14
ID	task.postalign_bam.nmsrt_bam_rep1.line_321.id_19
Name	nmsrt_bam rep1
Thread	thread_20
PID	113817

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

Start	2016-05-16 13:50:50
End	2016-05-16 14:18:14
Elapsed	00:27:24
Timeout	00:00:-1
Wall Timeout	100 days

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

 
# SYS command. line 323

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

# SYS command. line 325

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

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 27 files...

Num	15
ID	task.postalign_bam.bam_to_bedpe_rep1.line_425.id_20
Name	bam_to_bedpe rep1
Thread	thread_20
PID	115984

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

Start	2016-05-16 14:18:15
End	2016-05-16 14:21:22
Elapsed	00:03:07
Timeout	00:00:-1
Wall Timeout	100 days

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

 
# SYS command. line 427

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

# SYS command. line 430

 bedtools bamtobed -bedpe -mate1 -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz

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

Num	16
ID	task.postalign_bed.subsample_bedpe_rep1.line_116.id_21
Name	subsample_bedpe rep1
Thread	thread_20
PID	116194

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

Start	2016-05-16 14:21:24
End	2016-05-16 14:23:47
Elapsed	00:02:23
Timeout	00:00:-1
Wall Timeout	100 days

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

 
# SYS command. line 118

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

# SYS command. line 120

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | grep -v "chrM" | shuf -n 17500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz

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

Num	17
ID	task.postalign_bam.bedpe_to_tag_rep1.line_465.id_22
Name	bedpe_to_tag rep1
Thread	thread_20
PID	116458

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

Start	2016-05-16 14:23:48
End	2016-05-16 14:25:31
Elapsed	00:01:43
Timeout	00:00:-1
Wall Timeout	100 days

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

 
# SYS command. line 467

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

# SYS command. line 469

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz | awk 'BEGIN{OFS="\t"}{printf "%s\t%s\t%s\tN\t1000\t%s\n%s\t%s\t%s\tN\t1000\t%s\n",$1,$2,$3,$9,$4,$5,$6,$10}' | \
			gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz

# SYS command. line 472

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

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

Num	18
ID	task.postalign_bed.shift_tag_rep1.line_140.id_23
Name	shift_tag rep1
Thread	thread_20
PID	116536

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

Start	2016-05-16 14:25:32
End	2016-05-16 14:26:32
Elapsed	00:01:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Dependencies

 
# SYS command. line 142

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

# SYS command. line 144

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz | awk -F $'\t' 'BEGIN {OFS = FS}{ if ($6 == "+") {$2 = $2 + 4} else if ($6 == "-") {$3 = $3 - 5} print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz

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

Num	19
ID	task.postalign_bed.subsample_bedpe2tagrep1.line_89.id_24
Name	subsample_bedpe2tagrep1
Thread	thread_20
PID	116606

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

Start	2016-05-16 14:26:33
End	2016-05-16 14:27:53
Elapsed	00:01:19
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
Dependencies

 
# SYS command. line 91

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

# SYS command. line 95

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | \
			grep -v "chrM" | shuf -n 25000000 | \
			awk 'BEGIN{OFS="\t"}{print $1,$2,$3,"N","1000",$9}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz

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

Num	20
ID	task.postalign_bed.xcor_rep1.line_165.id_25
Name	xcor rep1
Thread	thread_20
PID	116808

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

Start	2016-05-16 14:27:54
End	2016-05-16 15:15:08
Elapsed	00:47:14
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf
Dependencies

 
# SYS command. line 167

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

# SYS command. line 171

 Rscript $(which run_spp_nodups.R) -rf \
			-c=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz -p=1 \
			-filtchr=chrM -savp=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf -out=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc -speak=0

# SYS command. line 174

 sed -r 's/,[^\t]+//g' /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp

# SYS command. line 175

 mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc

   
--------------------Stdout--------------------
################
ChIP data: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz 
Control data: NA 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 0 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: NA 
Output Directory: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1 
narrowPeak output file name: NA 
regionPeak output file name: NA 
Rdata filename: NA 
plot pdf filename: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf 
result filename: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz 
opened /tmp/Rtmp6CdXaA/ATAC7-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign1c8e26b5640a1
done. read 25000000 fragments
ChIP data read length 72 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.242828 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.272281553000674 
Top 3 estimates for fragment length 0 
Window half size 455 
Phantom peak location 65 
Phantom peak Correlation 0.2751338 
Normalized Strand cross-correlation coefficient (NSC) 1.121294 
Relative Strand Cross correlation Coefficient (RSC) 0.9117121 
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	21
ID	task.callpeak_macs2.macs2_atac_rep1.pval0.1.line_192.id_26
Name	macs2_atac rep1.pval0.1
Thread	thread_20
PID	116810

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

Start	2016-05-16 14:27:54
End	2016-05-16 14:45:01
Elapsed	00:17:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz
Dependencies

 
# SYS command. line 194

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

# SYS command. line 195

 LC_COLLATE=C

# SYS command. line 197

 macs2 callpeak \
			-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 --broad --keep-dup all

# SYS command. line 202

 sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.broadPeak.gz

# SYS command. line 203

 sort -k 14gr,14gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz

# SYS command. line 204

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.broadPeak

# SYS command. line 205

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.gappedPeak

# SYS command. line 207

 macs2 callpeak \
			-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits

# SYS command. line 212

 sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz

# SYS command. line 213

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.narrowPeak

# SYS command. line 214

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.xls

# SYS command. line 215

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_summits.bed

# SYS command. line 217

 if [[ false == "true" ]]; then \
			\
			macs2 bdgcmp -t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_FE.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/signal/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			\
			# sval counts the number of tags per million in the (compressed) BED file; \
			sval=$(wc -l <(zcat -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_ppois.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/signal/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			\
			fi

# SYS command. line 243

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-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 14:27:57: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-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/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-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 14:27:57: #1 read tag files... 
INFO  @ Mon, 16 May 2016 14:27:57: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 14:27:59:  1000000 
INFO  @ Mon, 16 May 2016 14:28:00:  2000000 
INFO  @ Mon, 16 May 2016 14:28:02:  3000000 
INFO  @ Mon, 16 May 2016 14:28:04:  4000000 
INFO  @ Mon, 16 May 2016 14:28:06:  5000000 
INFO  @ Mon, 16 May 2016 14:28:08:  6000000 
INFO  @ Mon, 16 May 2016 14:28:10:  7000000 
INFO  @ Mon, 16 May 2016 14:28:11:  8000000 
INFO  @ Mon, 16 May 2016 14:28:13:  9000000 
INFO  @ Mon, 16 May 2016 14:28:15:  10000000 
INFO  @ Mon, 16 May 2016 14:28:17:  11000000 
INFO  @ Mon, 16 May 2016 14:28:18:  12000000 
INFO  @ Mon, 16 May 2016 14:28:20:  13000000 
INFO  @ Mon, 16 May 2016 14:28:22:  14000000 
INFO  @ Mon, 16 May 2016 14:28:24:  15000000 
INFO  @ Mon, 16 May 2016 14:28:26:  16000000 
INFO  @ Mon, 16 May 2016 14:28:27:  17000000 
INFO  @ Mon, 16 May 2016 14:28:29:  18000000 
INFO  @ Mon, 16 May 2016 14:28:31:  19000000 
INFO  @ Mon, 16 May 2016 14:28:33:  20000000 
INFO  @ Mon, 16 May 2016 14:28:34:  21000000 
INFO  @ Mon, 16 May 2016 14:28:36:  22000000 
INFO  @ Mon, 16 May 2016 14:28:38:  23000000 
INFO  @ Mon, 16 May 2016 14:28:40:  24000000 
INFO  @ Mon, 16 May 2016 14:28:42:  25000000 
INFO  @ Mon, 16 May 2016 14:28:43:  26000000 
INFO  @ Mon, 16 May 2016 14:28:45:  27000000 
INFO  @ Mon, 16 May 2016 14:28:47:  28000000 
INFO  @ Mon, 16 May 2016 14:28:49:  29000000 
INFO  @ Mon, 16 May 2016 14:28:52:  30000000 
INFO  @ Mon, 16 May 2016 14:28:54:  31000000 
INFO  @ Mon, 16 May 2016 14:28:55:  32000000 
INFO  @ Mon, 16 May 2016 14:28:57:  33000000 
INFO  @ Mon, 16 May 2016 14:28:59:  34000000 
INFO  @ Mon, 16 May 2016 14:29:01:  35000000 
INFO  @ Mon, 16 May 2016 14:29:03: #1 tag size is determined as 66 bps 
INFO  @ Mon, 16 May 2016 14:29:03: #1 tag size = 66 
INFO  @ Mon, 16 May 2016 14:29:03: #1  total tags in treatment: 35000000 
INFO  @ Mon, 16 May 2016 14:29:03: #1 finished! 
INFO  @ Mon, 16 May 2016 14:29:03: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 14:29:03: #2 Skipped... 
INFO  @ Mon, 16 May 2016 14:29:03: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 14:29:03: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 14:29:03: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 14:29:03: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Mon, 16 May 2016 14:29:03: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 14:30:21: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 14:32:43: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls 
INFO  @ Mon, 16 May 2016 14:32:47: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Mon, 16 May 2016 14:32:49: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Mon, 16 May 2016 14:32:52: Done! 
INFO  @ Mon, 16 May 2016 14:33:04: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-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/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-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 14:33:04: #1 read tag files... 
INFO  @ Mon, 16 May 2016 14:33:04: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 14:33:05:  1000000 
INFO  @ Mon, 16 May 2016 14:33:07:  2000000 
INFO  @ Mon, 16 May 2016 14:33:09:  3000000 
INFO  @ Mon, 16 May 2016 14:33:10:  4000000 
INFO  @ Mon, 16 May 2016 14:33:12:  5000000 
INFO  @ Mon, 16 May 2016 14:33:14:  6000000 
INFO  @ Mon, 16 May 2016 14:33:15:  7000000 
INFO  @ Mon, 16 May 2016 14:33:17:  8000000 
INFO  @ Mon, 16 May 2016 14:33:18:  9000000 
INFO  @ Mon, 16 May 2016 14:33:20:  10000000 
INFO  @ Mon, 16 May 2016 14:33:22:  11000000 
INFO  @ Mon, 16 May 2016 14:33:24:  12000000 
INFO  @ Mon, 16 May 2016 14:33:25:  13000000 
INFO  @ Mon, 16 May 2016 14:33:27:  14000000 
INFO  @ Mon, 16 May 2016 14:33:28:  15000000 
INFO  @ Mon, 16 May 2016 14:33:30:  16000000 
INFO  @ Mon, 16 May 2016 14:33:32:  17000000 
INFO  @ Mon, 16 May 2016 14:33:33:  18000000 
INFO  @ Mon, 16 May 2016 14:33:35:  19000000 
INFO  @ Mon, 16 May 2016 14:33:37:  20000000 
INFO  @ Mon, 16 May 2016 14:33:38:  21000000 
INFO  @ Mon, 16 May 2016 14:33:40:  22000000 
INFO  @ Mon, 16 May 2016 14:33:41:  23000000 
INFO  @ Mon, 16 May 2016 14:33:43:  24000000 
INFO  @ Mon, 16 May 2016 14:33:45:  25000000 
INFO  @ Mon, 16 May 2016 14:33:46:  26000000 
INFO  @ Mon, 16 May 2016 14:33:48:  27000000 
INFO  @ Mon, 16 May 2016 14:33:50:  28000000 
INFO  @ Mon, 16 May 2016 14:33:51:  29000000 
INFO  @ Mon, 16 May 2016 14:33:53:  30000000 
INFO  @ Mon, 16 May 2016 14:33:54:  31000000 
INFO  @ Mon, 16 May 2016 14:33:56:  32000000 
INFO  @ Mon, 16 May 2016 14:33:58:  33000000 
INFO  @ Mon, 16 May 2016 14:34:00:  34000000 
INFO  @ Mon, 16 May 2016 14:34:01:  35000000 
INFO  @ Mon, 16 May 2016 14:34:04: #1 tag size is determined as 66 bps 
INFO  @ Mon, 16 May 2016 14:34:04: #1 tag size = 66 
INFO  @ Mon, 16 May 2016 14:34:04: #1  total tags in treatment: 35000000 
INFO  @ Mon, 16 May 2016 14:34:04: #1 finished! 
INFO  @ Mon, 16 May 2016 14:34:04: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 14:34:04: #2 Skipped... 
INFO  @ Mon, 16 May 2016 14:34:04: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 14:34:04: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 14:34:04: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 14:34:04: #3 Going to call summits inside each peak ... 
INFO  @ Mon, 16 May 2016 14:34:04: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Mon, 16 May 2016 14:34:04: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 14:35:26: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Mon, 16 May 2016 14:35:26: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Mon, 16 May 2016 14:35:26: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Mon, 16 May 2016 14:35:26: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Mon, 16 May 2016 14:35:26: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 14:44:38: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls 
INFO  @ Mon, 16 May 2016 14:44:45: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Mon, 16 May 2016 14:44:50: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_summits.bed 
INFO  @ Mon, 16 May 2016 14:44:53: Done!

Num	22
ID	task.callpeak_macs2.macs2_atac_rep1.line_192.id_27
Name	macs2_atac rep1
Thread	thread_20
PID	116819

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

Start	2016-05-16 14:27:54
End	2016-05-16 15:13:19
Elapsed	00:45:25
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.gappedPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/signal/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/signal/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig
Dependencies

 
# SYS command. line 194

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

# SYS command. line 195

 LC_COLLATE=C

# SYS command. line 197

 macs2 callpeak \
			-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -g "hs" -p 0.01 \
			--nomodel --shift -75 --extsize 150 --broad --keep-dup all

# SYS command. line 202

 sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.broadPeak.gz

# SYS command. line 203

 sort -k 14gr,14gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.gappedPeak.gz

# SYS command. line 204

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.broadPeak

# SYS command. line 205

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.gappedPeak

# SYS command. line 207

 macs2 callpeak \
			-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -g "hs" -p 0.01 \
			--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits

# SYS command. line 212

 sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz

# SYS command. line 213

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.narrowPeak

# SYS command. line 214

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.xls

# SYS command. line 215

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_summits.bed

# SYS command. line 217

 if [[ true == "true" ]]; then \
			\
			macs2 bdgcmp -t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_FE.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/signal/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph; \
			\
			# sval counts the number of tags per million in the (compressed) BED file; \
			sval=$(wc -l <(zcat -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_ppois.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/signal/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph; \
			\
			fi

# SYS command. line 243

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-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 14:27:57: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-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/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-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 14:27:57: #1 read tag files... 
INFO  @ Mon, 16 May 2016 14:27:57: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 14:27:58:  1000000 
INFO  @ Mon, 16 May 2016 14:28:00:  2000000 
INFO  @ Mon, 16 May 2016 14:28:02:  3000000 
INFO  @ Mon, 16 May 2016 14:28:04:  4000000 
INFO  @ Mon, 16 May 2016 14:28:05:  5000000 
INFO  @ Mon, 16 May 2016 14:28:07:  6000000 
INFO  @ Mon, 16 May 2016 14:28:09:  7000000 
INFO  @ Mon, 16 May 2016 14:28:10:  8000000 
INFO  @ Mon, 16 May 2016 14:28:12:  9000000 
INFO  @ Mon, 16 May 2016 14:28:14:  10000000 
INFO  @ Mon, 16 May 2016 14:28:15:  11000000 
INFO  @ Mon, 16 May 2016 14:28:17:  12000000 
INFO  @ Mon, 16 May 2016 14:28:19:  13000000 
INFO  @ Mon, 16 May 2016 14:28:20:  14000000 
INFO  @ Mon, 16 May 2016 14:28:22:  15000000 
INFO  @ Mon, 16 May 2016 14:28:24:  16000000 
INFO  @ Mon, 16 May 2016 14:28:25:  17000000 
INFO  @ Mon, 16 May 2016 14:28:27:  18000000 
INFO  @ Mon, 16 May 2016 14:28:29:  19000000 
INFO  @ Mon, 16 May 2016 14:28:30:  20000000 
INFO  @ Mon, 16 May 2016 14:28:32:  21000000 
INFO  @ Mon, 16 May 2016 14:28:33:  22000000 
INFO  @ Mon, 16 May 2016 14:28:35:  23000000 
INFO  @ Mon, 16 May 2016 14:28:37:  24000000 
INFO  @ Mon, 16 May 2016 14:28:38:  25000000 
INFO  @ Mon, 16 May 2016 14:28:40:  26000000 
INFO  @ Mon, 16 May 2016 14:28:42:  27000000 
INFO  @ Mon, 16 May 2016 14:28:43:  28000000 
INFO  @ Mon, 16 May 2016 14:28:45:  29000000 
INFO  @ Mon, 16 May 2016 14:28:46:  30000000 
INFO  @ Mon, 16 May 2016 14:28:48:  31000000 
INFO  @ Mon, 16 May 2016 14:28:50:  32000000 
INFO  @ Mon, 16 May 2016 14:28:51:  33000000 
INFO  @ Mon, 16 May 2016 14:28:53:  34000000 
INFO  @ Mon, 16 May 2016 14:28:55:  35000000 
INFO  @ Mon, 16 May 2016 14:28:57: #1 tag size is determined as 66 bps 
INFO  @ Mon, 16 May 2016 14:28:57: #1 tag size = 66 
INFO  @ Mon, 16 May 2016 14:28:57: #1  total tags in treatment: 35000000 
INFO  @ Mon, 16 May 2016 14:28:57: #1 finished! 
INFO  @ Mon, 16 May 2016 14:28:57: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 14:28:57: #2 Skipped... 
INFO  @ Mon, 16 May 2016 14:28:57: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 14:28:57: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 14:28:57: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 14:28:57: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Mon, 16 May 2016 14:28:57: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 14:30:13: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 14:32:00: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls 
INFO  @ Mon, 16 May 2016 14:32:04: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.broadPeak 
INFO  @ Mon, 16 May 2016 14:32:07: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.gappedPeak 
INFO  @ Mon, 16 May 2016 14:32:09: Done! 
INFO  @ Mon, 16 May 2016 14:32:21: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-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/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-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 14:32:21: #1 read tag files... 
INFO  @ Mon, 16 May 2016 14:32:21: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 14:32:23:  1000000 
INFO  @ Mon, 16 May 2016 14:32:25:  2000000 
INFO  @ Mon, 16 May 2016 14:32:27:  3000000 
INFO  @ Mon, 16 May 2016 14:32:28:  4000000 
INFO  @ Mon, 16 May 2016 14:32:30:  5000000 
INFO  @ Mon, 16 May 2016 14:32:32:  6000000 
INFO  @ Mon, 16 May 2016 14:32:33:  7000000 
INFO  @ Mon, 16 May 2016 14:32:35:  8000000 
INFO  @ Mon, 16 May 2016 14:32:36:  9000000 
INFO  @ Mon, 16 May 2016 14:32:38:  10000000 
INFO  @ Mon, 16 May 2016 14:32:40:  11000000 
INFO  @ Mon, 16 May 2016 14:32:42:  12000000 
INFO  @ Mon, 16 May 2016 14:32:43:  13000000 
INFO  @ Mon, 16 May 2016 14:32:45:  14000000 
INFO  @ Mon, 16 May 2016 14:32:47:  15000000 
INFO  @ Mon, 16 May 2016 14:32:48:  16000000 
INFO  @ Mon, 16 May 2016 14:32:50:  17000000 
INFO  @ Mon, 16 May 2016 14:32:52:  18000000 
INFO  @ Mon, 16 May 2016 14:32:53:  19000000 
INFO  @ Mon, 16 May 2016 14:32:55:  20000000 
INFO  @ Mon, 16 May 2016 14:32:57:  21000000 
INFO  @ Mon, 16 May 2016 14:32:59:  22000000 
INFO  @ Mon, 16 May 2016 14:33:01:  23000000 
INFO  @ Mon, 16 May 2016 14:33:03:  24000000 
INFO  @ Mon, 16 May 2016 14:33:04:  25000000 
INFO  @ Mon, 16 May 2016 14:33:06:  26000000 
INFO  @ Mon, 16 May 2016 14:33:08:  27000000 
INFO  @ Mon, 16 May 2016 14:33:10:  28000000 
INFO  @ Mon, 16 May 2016 14:33:11:  29000000 
INFO  @ Mon, 16 May 2016 14:33:13:  30000000 
INFO  @ Mon, 16 May 2016 14:33:15:  31000000 
INFO  @ Mon, 16 May 2016 14:33:16:  32000000 
INFO  @ Mon, 16 May 2016 14:33:18:  33000000 
INFO  @ Mon, 16 May 2016 14:33:20:  34000000 
INFO  @ Mon, 16 May 2016 14:33:21:  35000000 
INFO  @ Mon, 16 May 2016 14:33:24: #1 tag size is determined as 66 bps 
INFO  @ Mon, 16 May 2016 14:33:24: #1 tag size = 66 
INFO  @ Mon, 16 May 2016 14:33:24: #1  total tags in treatment: 35000000 
INFO  @ Mon, 16 May 2016 14:33:24: #1 finished! 
INFO  @ Mon, 16 May 2016 14:33:24: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 14:33:24: #2 Skipped... 
INFO  @ Mon, 16 May 2016 14:33:24: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 14:33:24: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 14:33:24: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 14:33:24: #3 Going to call summits inside each peak ... 
INFO  @ Mon, 16 May 2016 14:33:24: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Mon, 16 May 2016 14:33:24: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 14:34:50: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Mon, 16 May 2016 14:34:50: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_treat_pileup.bdg 
INFO  @ Mon, 16 May 2016 14:34:50: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_control_lambda.bdg 
INFO  @ Mon, 16 May 2016 14:34:50: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Mon, 16 May 2016 14:34:50: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 14:40:03: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls 
INFO  @ Mon, 16 May 2016 14:40:05: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.narrowPeak 
INFO  @ Mon, 16 May 2016 14:40:06: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_summits.bed 
INFO  @ Mon, 16 May 2016 14:40:07: Done! 
INFO  @ Mon, 16 May 2016 14:40:11: Read and build treatment bedGraph... 
INFO  @ Mon, 16 May 2016 14:41:31: Read and build control bedGraph... 
INFO  @ Mon, 16 May 2016 14:42:08: Build scoreTrackII... 
INFO  @ Mon, 16 May 2016 14:42:43: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Mon, 16 May 2016 14:46:38: Write bedGraph of scores... 
INFO  @ Mon, 16 May 2016 14:49:02: Finished 'FE'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_FE.bdg'! 
INFO  @ Mon, 16 May 2016 14:56:34: Read and build treatment bedGraph... 
INFO  @ Mon, 16 May 2016 14:57:48: Read and build control bedGraph... 
INFO  @ Mon, 16 May 2016 14:58:21: Build scoreTrackII... 
INFO  @ Mon, 16 May 2016 14:58:58: Values in your input bedGraph files will be multiplied by 35.000000 ... 
INFO  @ Mon, 16 May 2016 15:03:41: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Mon, 16 May 2016 15:04:18: Write bedGraph of scores... 
INFO  @ Mon, 16 May 2016 15:06:42: Finished 'ppois'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_ppois.bdg'!

Num	23
ID	task.postalign_bed.pool_tag_reps.line_405.id_28
Name	pool_tag reps
Thread	thread_Root
PID	119037

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

Start	2016-05-16 15:15:09
End	2016-05-16 15:16:49
Elapsed	00:01:40
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz
Dependencies

 
# SYS command. line 407

 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 408

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz  | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz

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

Num	24
ID	task.callpeak_macs2.macs2_atac_pooled.pval0.1.line_192.id_29
Name	macs2_atac pooled.pval0.1
Thread	thread_Root
PID	119106

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

Start	2016-05-16 15:16:50
End	2016-05-16 15:47:04
Elapsed	00:30:14
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.gappedPeak.gz
Dependencies

 
# SYS command. line 194

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

# SYS command. line 195

 LC_COLLATE=C

# SYS command. line 197

 macs2 callpeak \
			-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 --broad --keep-dup all

# SYS command. line 202

 sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.broadPeak.gz

# SYS command. line 203

 sort -k 14gr,14gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.gappedPeak.gz

# SYS command. line 204

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_peaks.broadPeak

# SYS command. line 205

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_peaks.gappedPeak

# SYS command. line 207

 macs2 callpeak \
			-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits

# SYS command. line 212

 sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.narrowPeak.gz

# SYS command. line 213

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_peaks.narrowPeak

# SYS command. line 214

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_peaks.xls

# SYS command. line 215

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_summits.bed

# SYS command. line 217

 if [[ false == "true" ]]; then \
			\
			macs2 bdgcmp -t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_FE.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/signal/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.srt.bedgraph; \
			\
			# sval counts the number of tags per million in the (compressed) BED file; \
			sval=$(wc -l <(zcat -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_ppois.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/signal/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.srt.bedgraph; \
			\
			fi

# SYS command. line 243

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.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 15:16:52: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.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/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.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 15:16:52: #1 read tag files... 
INFO  @ Mon, 16 May 2016 15:16:52: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 15:16:54:  1000000 
INFO  @ Mon, 16 May 2016 15:16:55:  2000000 
INFO  @ Mon, 16 May 2016 15:16:57:  3000000 
INFO  @ Mon, 16 May 2016 15:16:59:  4000000 
INFO  @ Mon, 16 May 2016 15:17:01:  5000000 
INFO  @ Mon, 16 May 2016 15:17:03:  6000000 
INFO  @ Mon, 16 May 2016 15:17:04:  7000000 
INFO  @ Mon, 16 May 2016 15:17:06:  8000000 
INFO  @ Mon, 16 May 2016 15:17:08:  9000000 
INFO  @ Mon, 16 May 2016 15:17:09:  10000000 
INFO  @ Mon, 16 May 2016 15:17:11:  11000000 
INFO  @ Mon, 16 May 2016 15:17:13:  12000000 
INFO  @ Mon, 16 May 2016 15:17:14:  13000000 
INFO  @ Mon, 16 May 2016 15:17:16:  14000000 
INFO  @ Mon, 16 May 2016 15:17:18:  15000000 
INFO  @ Mon, 16 May 2016 15:17:19:  16000000 
INFO  @ Mon, 16 May 2016 15:17:21:  17000000 
INFO  @ Mon, 16 May 2016 15:17:22:  18000000 
INFO  @ Mon, 16 May 2016 15:17:24:  19000000 
INFO  @ Mon, 16 May 2016 15:17:26:  20000000 
INFO  @ Mon, 16 May 2016 15:17:27:  21000000 
INFO  @ Mon, 16 May 2016 15:17:29:  22000000 
INFO  @ Mon, 16 May 2016 15:17:31:  23000000 
INFO  @ Mon, 16 May 2016 15:17:32:  24000000 
INFO  @ Mon, 16 May 2016 15:17:34:  25000000 
INFO  @ Mon, 16 May 2016 15:17:35:  26000000 
INFO  @ Mon, 16 May 2016 15:17:37:  27000000 
INFO  @ Mon, 16 May 2016 15:17:39:  28000000 
INFO  @ Mon, 16 May 2016 15:17:40:  29000000 
INFO  @ Mon, 16 May 2016 15:17:42:  30000000 
INFO  @ Mon, 16 May 2016 15:17:44:  31000000 
INFO  @ Mon, 16 May 2016 15:17:45:  32000000 
INFO  @ Mon, 16 May 2016 15:17:47:  33000000 
INFO  @ Mon, 16 May 2016 15:17:48:  34000000 
INFO  @ Mon, 16 May 2016 15:17:50:  35000000 
INFO  @ Mon, 16 May 2016 15:17:52:  36000000 
INFO  @ Mon, 16 May 2016 15:17:53:  37000000 
INFO  @ Mon, 16 May 2016 15:17:55:  38000000 
INFO  @ Mon, 16 May 2016 15:17:57:  39000000 
INFO  @ Mon, 16 May 2016 15:17:58:  40000000 
INFO  @ Mon, 16 May 2016 15:18:00:  41000000 
INFO  @ Mon, 16 May 2016 15:18:03:  42000000 
INFO  @ Mon, 16 May 2016 15:18:05:  43000000 
INFO  @ Mon, 16 May 2016 15:18:07:  44000000 
INFO  @ Mon, 16 May 2016 15:18:09:  45000000 
INFO  @ Mon, 16 May 2016 15:18:10:  46000000 
INFO  @ Mon, 16 May 2016 15:18:12:  47000000 
INFO  @ Mon, 16 May 2016 15:18:13:  48000000 
INFO  @ Mon, 16 May 2016 15:18:15:  49000000 
INFO  @ Mon, 16 May 2016 15:18:17:  50000000 
INFO  @ Mon, 16 May 2016 15:18:18:  51000000 
INFO  @ Mon, 16 May 2016 15:18:20:  52000000 
INFO  @ Mon, 16 May 2016 15:18:22:  53000000 
INFO  @ Mon, 16 May 2016 15:18:23:  54000000 
INFO  @ Mon, 16 May 2016 15:18:25:  55000000 
INFO  @ Mon, 16 May 2016 15:18:27:  56000000 
INFO  @ Mon, 16 May 2016 15:18:28:  57000000 
INFO  @ Mon, 16 May 2016 15:18:30:  58000000 
INFO  @ Mon, 16 May 2016 15:18:32:  59000000 
INFO  @ Mon, 16 May 2016 15:18:33:  60000000 
INFO  @ Mon, 16 May 2016 15:18:35:  61000000 
INFO  @ Mon, 16 May 2016 15:18:36:  62000000 
INFO  @ Mon, 16 May 2016 15:18:39:  63000000 
INFO  @ Mon, 16 May 2016 15:18:41:  64000000 
INFO  @ Mon, 16 May 2016 15:18:43:  65000000 
INFO  @ Mon, 16 May 2016 15:18:45:  66000000 
INFO  @ Mon, 16 May 2016 15:18:46:  67000000 
INFO  @ Mon, 16 May 2016 15:18:48:  68000000 
INFO  @ Mon, 16 May 2016 15:18:50:  69000000 
INFO  @ Mon, 16 May 2016 15:18:51:  70000000 
INFO  @ Mon, 16 May 2016 15:18:56: #1 tag size is determined as 66 bps 
INFO  @ Mon, 16 May 2016 15:18:56: #1 tag size = 66 
INFO  @ Mon, 16 May 2016 15:18:56: #1  total tags in treatment: 70000000 
INFO  @ Mon, 16 May 2016 15:18:56: #1 finished! 
INFO  @ Mon, 16 May 2016 15:18:56: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 15:18:56: #2 Skipped... 
INFO  @ Mon, 16 May 2016 15:18:56: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 15:18:56: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 15:18:56: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 15:18:56: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Mon, 16 May 2016 15:18:56: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 15:22:07: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 15:26:59: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.xls 
INFO  @ Mon, 16 May 2016 15:27:02: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.broadPeak 
INFO  @ Mon, 16 May 2016 15:27:04: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.gappedPeak 
INFO  @ Mon, 16 May 2016 15:27:06: Done! 
INFO  @ Mon, 16 May 2016 15:27:15: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.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/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.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 15:27:15: #1 read tag files... 
INFO  @ Mon, 16 May 2016 15:27:15: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 15:27:17:  1000000 
INFO  @ Mon, 16 May 2016 15:27:18:  2000000 
INFO  @ Mon, 16 May 2016 15:27:20:  3000000 
INFO  @ Mon, 16 May 2016 15:27:22:  4000000 
INFO  @ Mon, 16 May 2016 15:27:23:  5000000 
INFO  @ Mon, 16 May 2016 15:27:25:  6000000 
INFO  @ Mon, 16 May 2016 15:27:27:  7000000 
INFO  @ Mon, 16 May 2016 15:27:28:  8000000 
INFO  @ Mon, 16 May 2016 15:27:30:  9000000 
INFO  @ Mon, 16 May 2016 15:27:32:  10000000 
INFO  @ Mon, 16 May 2016 15:27:33:  11000000 
INFO  @ Mon, 16 May 2016 15:27:35:  12000000 
INFO  @ Mon, 16 May 2016 15:27:36:  13000000 
INFO  @ Mon, 16 May 2016 15:27:38:  14000000 
INFO  @ Mon, 16 May 2016 15:27:40:  15000000 
INFO  @ Mon, 16 May 2016 15:27:41:  16000000 
INFO  @ Mon, 16 May 2016 15:27:43:  17000000 
INFO  @ Mon, 16 May 2016 15:27:44:  18000000 
INFO  @ Mon, 16 May 2016 15:27:46:  19000000 
INFO  @ Mon, 16 May 2016 15:27:48:  20000000 
INFO  @ Mon, 16 May 2016 15:27:49:  21000000 
INFO  @ Mon, 16 May 2016 15:27:51:  22000000 
INFO  @ Mon, 16 May 2016 15:27:53:  23000000 
INFO  @ Mon, 16 May 2016 15:27:54:  24000000 
INFO  @ Mon, 16 May 2016 15:27:56:  25000000 
INFO  @ Mon, 16 May 2016 15:27:57:  26000000 
INFO  @ Mon, 16 May 2016 15:27:59:  27000000 
INFO  @ Mon, 16 May 2016 15:28:01:  28000000 
INFO  @ Mon, 16 May 2016 15:28:02:  29000000 
INFO  @ Mon, 16 May 2016 15:28:04:  30000000 
INFO  @ Mon, 16 May 2016 15:28:05:  31000000 
INFO  @ Mon, 16 May 2016 15:28:07:  32000000 
INFO  @ Mon, 16 May 2016 15:28:09:  33000000 
INFO  @ Mon, 16 May 2016 15:28:11:  34000000 
INFO  @ Mon, 16 May 2016 15:28:12:  35000000 
INFO  @ Mon, 16 May 2016 15:28:14:  36000000 
INFO  @ Mon, 16 May 2016 15:28:16:  37000000 
INFO  @ Mon, 16 May 2016 15:28:18:  38000000 
INFO  @ Mon, 16 May 2016 15:28:20:  39000000 
INFO  @ Mon, 16 May 2016 15:28:21:  40000000 
INFO  @ Mon, 16 May 2016 15:28:23:  41000000 
INFO  @ Mon, 16 May 2016 15:28:25:  42000000 
INFO  @ Mon, 16 May 2016 15:28:26:  43000000 
INFO  @ Mon, 16 May 2016 15:28:28:  44000000 
INFO  @ Mon, 16 May 2016 15:28:30:  45000000 
INFO  @ Mon, 16 May 2016 15:28:31:  46000000 
INFO  @ Mon, 16 May 2016 15:28:33:  47000000 
INFO  @ Mon, 16 May 2016 15:28:35:  48000000 
INFO  @ Mon, 16 May 2016 15:28:36:  49000000 
INFO  @ Mon, 16 May 2016 15:28:38:  50000000 
INFO  @ Mon, 16 May 2016 15:28:40:  51000000 
INFO  @ Mon, 16 May 2016 15:28:41:  52000000 
INFO  @ Mon, 16 May 2016 15:28:43:  53000000 
INFO  @ Mon, 16 May 2016 15:28:44:  54000000 
INFO  @ Mon, 16 May 2016 15:28:46:  55000000 
INFO  @ Mon, 16 May 2016 15:28:48:  56000000 
INFO  @ Mon, 16 May 2016 15:28:50:  57000000 
INFO  @ Mon, 16 May 2016 15:28:51:  58000000 
INFO  @ Mon, 16 May 2016 15:28:53:  59000000 
INFO  @ Mon, 16 May 2016 15:28:55:  60000000 
INFO  @ Mon, 16 May 2016 15:28:57:  61000000 
INFO  @ Mon, 16 May 2016 15:28:58:  62000000 
INFO  @ Mon, 16 May 2016 15:29:00:  63000000 
INFO  @ Mon, 16 May 2016 15:29:01:  64000000 
INFO  @ Mon, 16 May 2016 15:29:03:  65000000 
INFO  @ Mon, 16 May 2016 15:29:06:  66000000 
INFO  @ Mon, 16 May 2016 15:29:08:  67000000 
INFO  @ Mon, 16 May 2016 15:29:10:  68000000 
INFO  @ Mon, 16 May 2016 15:29:11:  69000000 
INFO  @ Mon, 16 May 2016 15:29:13:  70000000 
INFO  @ Mon, 16 May 2016 15:29:18: #1 tag size is determined as 66 bps 
INFO  @ Mon, 16 May 2016 15:29:18: #1 tag size = 66 
INFO  @ Mon, 16 May 2016 15:29:18: #1  total tags in treatment: 70000000 
INFO  @ Mon, 16 May 2016 15:29:18: #1 finished! 
INFO  @ Mon, 16 May 2016 15:29:18: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 15:29:18: #2 Skipped... 
INFO  @ Mon, 16 May 2016 15:29:18: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 15:29:18: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 15:29:18: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 15:29:18: #3 Going to call summits inside each peak ... 
INFO  @ Mon, 16 May 2016 15:29:18: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Mon, 16 May 2016 15:29:18: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 15:32:51: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Mon, 16 May 2016 15:32:51: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_treat_pileup.bdg 
INFO  @ Mon, 16 May 2016 15:32:51: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_control_lambda.bdg 
INFO  @ Mon, 16 May 2016 15:32:51: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Mon, 16 May 2016 15:32:51: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 15:46:37: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.xls 
INFO  @ Mon, 16 May 2016 15:46:46: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.narrowPeak 
INFO  @ Mon, 16 May 2016 15:46:52: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_summits.bed 
INFO  @ Mon, 16 May 2016 15:46:55: Done!

Num	25
ID	task.callpeak_macs2.macs2_atac_pooled.line_192.id_30
Name	macs2_atac pooled
Thread	thread_Root
PID	119108

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

Start	2016-05-16 15:16:50
End	2016-05-16 16:43:20
Elapsed	01:26:30
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.gappedPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/signal/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/signal/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bigwig
Dependencies

 
# SYS command. line 194

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

# SYS command. line 195

 LC_COLLATE=C

# SYS command. line 197

 macs2 callpeak \
			-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf" -g "hs" -p 0.01 \
			--nomodel --shift -75 --extsize 150 --broad --keep-dup all

# SYS command. line 202

 sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.broadPeak.gz

# SYS command. line 203

 sort -k 14gr,14gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.gappedPeak.gz

# SYS command. line 204

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_peaks.broadPeak

# SYS command. line 205

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_peaks.gappedPeak

# SYS command. line 207

 macs2 callpeak \
			-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf" -g "hs" -p 0.01 \
			--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits

# SYS command. line 212

 sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.narrowPeak.gz

# SYS command. line 213

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_peaks.narrowPeak

# SYS command. line 214

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_peaks.xls

# SYS command. line 215

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_summits.bed

# SYS command. line 217

 if [[ true == "true" ]]; then \
			\
			macs2 bdgcmp -t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_FE.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/signal/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.srt.bedgraph; \
			\
			# sval counts the number of tags per million in the (compressed) BED file; \
			sval=$(wc -l <(zcat -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_ppois.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/signal/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.srt.bedgraph; \
			\
			fi

# SYS command. line 243

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.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 15:16:52: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.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/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.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 15:16:52: #1 read tag files... 
INFO  @ Mon, 16 May 2016 15:16:52: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 15:16:54:  1000000 
INFO  @ Mon, 16 May 2016 15:16:55:  2000000 
INFO  @ Mon, 16 May 2016 15:16:57:  3000000 
INFO  @ Mon, 16 May 2016 15:16:59:  4000000 
INFO  @ Mon, 16 May 2016 15:17:00:  5000000 
INFO  @ Mon, 16 May 2016 15:17:02:  6000000 
INFO  @ Mon, 16 May 2016 15:17:04:  7000000 
INFO  @ Mon, 16 May 2016 15:17:05:  8000000 
INFO  @ Mon, 16 May 2016 15:17:07:  9000000 
INFO  @ Mon, 16 May 2016 15:17:09:  10000000 
INFO  @ Mon, 16 May 2016 15:17:10:  11000000 
INFO  @ Mon, 16 May 2016 15:17:12:  12000000 
INFO  @ Mon, 16 May 2016 15:17:14:  13000000 
INFO  @ Mon, 16 May 2016 15:17:15:  14000000 
INFO  @ Mon, 16 May 2016 15:17:17:  15000000 
INFO  @ Mon, 16 May 2016 15:17:18:  16000000 
INFO  @ Mon, 16 May 2016 15:17:20:  17000000 
INFO  @ Mon, 16 May 2016 15:17:22:  18000000 
INFO  @ Mon, 16 May 2016 15:17:23:  19000000 
INFO  @ Mon, 16 May 2016 15:17:25:  20000000 
INFO  @ Mon, 16 May 2016 15:17:27:  21000000 
INFO  @ Mon, 16 May 2016 15:17:28:  22000000 
INFO  @ Mon, 16 May 2016 15:17:30:  23000000 
INFO  @ Mon, 16 May 2016 15:17:31:  24000000 
INFO  @ Mon, 16 May 2016 15:17:33:  25000000 
INFO  @ Mon, 16 May 2016 15:17:35:  26000000 
INFO  @ Mon, 16 May 2016 15:17:36:  27000000 
INFO  @ Mon, 16 May 2016 15:17:38:  28000000 
INFO  @ Mon, 16 May 2016 15:17:40:  29000000 
INFO  @ Mon, 16 May 2016 15:17:41:  30000000 
INFO  @ Mon, 16 May 2016 15:17:43:  31000000 
INFO  @ Mon, 16 May 2016 15:17:45:  32000000 
INFO  @ Mon, 16 May 2016 15:17:46:  33000000 
INFO  @ Mon, 16 May 2016 15:17:48:  34000000 
INFO  @ Mon, 16 May 2016 15:17:50:  35000000 
INFO  @ Mon, 16 May 2016 15:17:51:  36000000 
INFO  @ Mon, 16 May 2016 15:17:53:  37000000 
INFO  @ Mon, 16 May 2016 15:17:55:  38000000 
INFO  @ Mon, 16 May 2016 15:17:56:  39000000 
INFO  @ Mon, 16 May 2016 15:17:58:  40000000 
INFO  @ Mon, 16 May 2016 15:18:00:  41000000 
INFO  @ Mon, 16 May 2016 15:18:01:  42000000 
INFO  @ Mon, 16 May 2016 15:18:03:  43000000 
INFO  @ Mon, 16 May 2016 15:18:04:  44000000 
INFO  @ Mon, 16 May 2016 15:18:06:  45000000 
INFO  @ Mon, 16 May 2016 15:18:08:  46000000 
INFO  @ Mon, 16 May 2016 15:18:09:  47000000 
INFO  @ Mon, 16 May 2016 15:18:11:  48000000 
INFO  @ Mon, 16 May 2016 15:18:13:  49000000 
INFO  @ Mon, 16 May 2016 15:18:14:  50000000 
INFO  @ Mon, 16 May 2016 15:18:16:  51000000 
INFO  @ Mon, 16 May 2016 15:18:18:  52000000 
INFO  @ Mon, 16 May 2016 15:18:19:  53000000 
INFO  @ Mon, 16 May 2016 15:18:21:  54000000 
INFO  @ Mon, 16 May 2016 15:18:23:  55000000 
INFO  @ Mon, 16 May 2016 15:18:24:  56000000 
INFO  @ Mon, 16 May 2016 15:18:26:  57000000 
INFO  @ Mon, 16 May 2016 15:18:28:  58000000 
INFO  @ Mon, 16 May 2016 15:18:29:  59000000 
INFO  @ Mon, 16 May 2016 15:18:31:  60000000 
INFO  @ Mon, 16 May 2016 15:18:33:  61000000 
INFO  @ Mon, 16 May 2016 15:18:34:  62000000 
INFO  @ Mon, 16 May 2016 15:18:36:  63000000 
INFO  @ Mon, 16 May 2016 15:18:38:  64000000 
INFO  @ Mon, 16 May 2016 15:18:40:  65000000 
INFO  @ Mon, 16 May 2016 15:18:42:  66000000 
INFO  @ Mon, 16 May 2016 15:18:43:  67000000 
INFO  @ Mon, 16 May 2016 15:18:45:  68000000 
INFO  @ Mon, 16 May 2016 15:18:47:  69000000 
INFO  @ Mon, 16 May 2016 15:18:49:  70000000 
INFO  @ Mon, 16 May 2016 15:18:54: #1 tag size is determined as 66 bps 
INFO  @ Mon, 16 May 2016 15:18:54: #1 tag size = 66 
INFO  @ Mon, 16 May 2016 15:18:54: #1  total tags in treatment: 70000000 
INFO  @ Mon, 16 May 2016 15:18:54: #1 finished! 
INFO  @ Mon, 16 May 2016 15:18:54: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 15:18:54: #2 Skipped... 
INFO  @ Mon, 16 May 2016 15:18:54: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 15:18:54: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 15:18:54: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 15:18:54: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Mon, 16 May 2016 15:18:54: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 15:22:02: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 15:25:49: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.xls 
INFO  @ Mon, 16 May 2016 15:25:52: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.broadPeak 
INFO  @ Mon, 16 May 2016 15:25:54: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.gappedPeak 
INFO  @ Mon, 16 May 2016 15:25:56: Done! 
INFO  @ Mon, 16 May 2016 15:26:07: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.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/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.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 15:26:07: #1 read tag files... 
INFO  @ Mon, 16 May 2016 15:26:07: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 15:26:08:  1000000 
INFO  @ Mon, 16 May 2016 15:26:10:  2000000 
INFO  @ Mon, 16 May 2016 15:26:12:  3000000 
INFO  @ Mon, 16 May 2016 15:26:14:  4000000 
INFO  @ Mon, 16 May 2016 15:26:15:  5000000 
INFO  @ Mon, 16 May 2016 15:26:17:  6000000 
INFO  @ Mon, 16 May 2016 15:26:18:  7000000 
INFO  @ Mon, 16 May 2016 15:26:20:  8000000 
INFO  @ Mon, 16 May 2016 15:26:22:  9000000 
INFO  @ Mon, 16 May 2016 15:26:23:  10000000 
INFO  @ Mon, 16 May 2016 15:26:25:  11000000 
INFO  @ Mon, 16 May 2016 15:26:27:  12000000 
INFO  @ Mon, 16 May 2016 15:26:28:  13000000 
INFO  @ Mon, 16 May 2016 15:26:30:  14000000 
INFO  @ Mon, 16 May 2016 15:26:32:  15000000 
INFO  @ Mon, 16 May 2016 15:26:33:  16000000 
INFO  @ Mon, 16 May 2016 15:26:35:  17000000 
INFO  @ Mon, 16 May 2016 15:26:37:  18000000 
INFO  @ Mon, 16 May 2016 15:26:38:  19000000 
INFO  @ Mon, 16 May 2016 15:26:40:  20000000 
INFO  @ Mon, 16 May 2016 15:26:42:  21000000 
INFO  @ Mon, 16 May 2016 15:26:44:  22000000 
INFO  @ Mon, 16 May 2016 15:26:45:  23000000 
INFO  @ Mon, 16 May 2016 15:26:47:  24000000 
INFO  @ Mon, 16 May 2016 15:26:49:  25000000 
INFO  @ Mon, 16 May 2016 15:26:50:  26000000 
INFO  @ Mon, 16 May 2016 15:26:52:  27000000 
INFO  @ Mon, 16 May 2016 15:26:54:  28000000 
INFO  @ Mon, 16 May 2016 15:26:55:  29000000 
INFO  @ Mon, 16 May 2016 15:26:57:  30000000 
INFO  @ Mon, 16 May 2016 15:26:59:  31000000 
INFO  @ Mon, 16 May 2016 15:27:00:  32000000 
INFO  @ Mon, 16 May 2016 15:27:02:  33000000 
INFO  @ Mon, 16 May 2016 15:27:04:  34000000 
INFO  @ Mon, 16 May 2016 15:27:05:  35000000 
INFO  @ Mon, 16 May 2016 15:27:07:  36000000 
INFO  @ Mon, 16 May 2016 15:27:08:  37000000 
INFO  @ Mon, 16 May 2016 15:27:10:  38000000 
INFO  @ Mon, 16 May 2016 15:27:12:  39000000 
INFO  @ Mon, 16 May 2016 15:27:14:  40000000 
INFO  @ Mon, 16 May 2016 15:27:15:  41000000 
INFO  @ Mon, 16 May 2016 15:27:17:  42000000 
INFO  @ Mon, 16 May 2016 15:27:18:  43000000 
INFO  @ Mon, 16 May 2016 15:27:20:  44000000 
INFO  @ Mon, 16 May 2016 15:27:22:  45000000 
INFO  @ Mon, 16 May 2016 15:27:23:  46000000 
INFO  @ Mon, 16 May 2016 15:27:25:  47000000 
INFO  @ Mon, 16 May 2016 15:27:27:  48000000 
INFO  @ Mon, 16 May 2016 15:27:29:  49000000 
INFO  @ Mon, 16 May 2016 15:27:30:  50000000 
INFO  @ Mon, 16 May 2016 15:27:32:  51000000 
INFO  @ Mon, 16 May 2016 15:27:34:  52000000 
INFO  @ Mon, 16 May 2016 15:27:35:  53000000 
INFO  @ Mon, 16 May 2016 15:27:37:  54000000 
INFO  @ Mon, 16 May 2016 15:27:39:  55000000 
INFO  @ Mon, 16 May 2016 15:27:40:  56000000 
INFO  @ Mon, 16 May 2016 15:27:42:  57000000 
INFO  @ Mon, 16 May 2016 15:27:43:  58000000 
INFO  @ Mon, 16 May 2016 15:27:45:  59000000 
INFO  @ Mon, 16 May 2016 15:27:47:  60000000 
INFO  @ Mon, 16 May 2016 15:27:48:  61000000 
INFO  @ Mon, 16 May 2016 15:27:50:  62000000 
INFO  @ Mon, 16 May 2016 15:27:52:  63000000 
INFO  @ Mon, 16 May 2016 15:27:53:  64000000 
INFO  @ Mon, 16 May 2016 15:27:55:  65000000 
INFO  @ Mon, 16 May 2016 15:27:57:  66000000 
INFO  @ Mon, 16 May 2016 15:27:58:  67000000 
INFO  @ Mon, 16 May 2016 15:28:00:  68000000 
INFO  @ Mon, 16 May 2016 15:28:01:  69000000 
INFO  @ Mon, 16 May 2016 15:28:03:  70000000 
INFO  @ Mon, 16 May 2016 15:28:08: #1 tag size is determined as 66 bps 
INFO  @ Mon, 16 May 2016 15:28:08: #1 tag size = 66 
INFO  @ Mon, 16 May 2016 15:28:08: #1  total tags in treatment: 70000000 
INFO  @ Mon, 16 May 2016 15:28:08: #1 finished! 
INFO  @ Mon, 16 May 2016 15:28:08: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 15:28:08: #2 Skipped... 
INFO  @ Mon, 16 May 2016 15:28:08: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 15:28:08: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 15:28:08: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 15:28:08: #3 Going to call summits inside each peak ... 
INFO  @ Mon, 16 May 2016 15:28:08: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Mon, 16 May 2016 15:28:08: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 15:31:44: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Mon, 16 May 2016 15:31:44: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_treat_pileup.bdg 
INFO  @ Mon, 16 May 2016 15:31:44: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_control_lambda.bdg 
INFO  @ Mon, 16 May 2016 15:31:44: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Mon, 16 May 2016 15:31:44: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 15:40:49: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.xls 
INFO  @ Mon, 16 May 2016 15:40:52: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.narrowPeak 
INFO  @ Mon, 16 May 2016 15:40:54: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_summits.bed 
INFO  @ Mon, 16 May 2016 15:40:55: Done! 
INFO  @ Mon, 16 May 2016 15:40:59: Read and build treatment bedGraph... 
INFO  @ Mon, 16 May 2016 15:43:15: Read and build control bedGraph... 
INFO  @ Mon, 16 May 2016 15:44:15: Build scoreTrackII... 
INFO  @ Mon, 16 May 2016 15:45:36: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Mon, 16 May 2016 15:53:14: Write bedGraph of scores... 
INFO  @ Mon, 16 May 2016 15:58:06: Finished 'FE'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_FE.bdg'! 
INFO  @ Mon, 16 May 2016 16:13:42: Read and build treatment bedGraph... 
INFO  @ Mon, 16 May 2016 16:16:33: Read and build control bedGraph... 
INFO  @ Mon, 16 May 2016 16:17:36: Build scoreTrackII... 
INFO  @ Mon, 16 May 2016 16:19:10: Values in your input bedGraph files will be multiplied by 70.000000 ... 
INFO  @ Mon, 16 May 2016 16:27:43: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Mon, 16 May 2016 16:29:17: Write bedGraph of scores... 
INFO  @ Mon, 16 May 2016 16:32:52: Finished 'ppois'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_ppois.bdg'!

Num	26
ID	task.callpeak_etc.filt_top_peaks_rep1.line_25.id_31
Name	filt_top_peaks rep1
Thread	thread_Root
PID	122304

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

Start	2016-05-16 16:43:21
End	2016-05-16 16:43:30
Elapsed	00:00:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz
Dependencies

 
# SYS command. line 27

 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 30

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz

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

Num	27
ID	task.callpeak_etc.filt_top_peaks_rep1.line_25.id_32
Name	filt_top_peaks rep1
Thread	thread_Root
PID	122306

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

Start	2016-05-16 16:43:21
End	2016-05-16 16:43:29
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.gappedPeak.gz
Dependencies

 
# SYS command. line 27

 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 30

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.gappedPeak.gz

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

Num	28
ID	task.callpeak_etc.filt_top_peaks_rep2.line_25.id_33
Name	filt_top_peaks rep2
Thread	thread_Root
PID	122317

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

Start	2016-05-16 16:43:21
End	2016-05-16 16:43:30
Elapsed	00:00:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz
Dependencies

 
# SYS command. line 27

 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 30

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz

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

Num	29
ID	task.callpeak_etc.filt_top_peaks_rep2.line_25.id_34
Name	filt_top_peaks rep2
Thread	thread_Root
PID	122335

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

Start	2016-05-16 16:43:21
End	2016-05-16 16:43:29
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.gappedPeak.gz
Dependencies

 
# SYS command. line 27

 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 30

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.gappedPeak.gz

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

Num	30
ID	task.callpeak_etc.filt_top_peaks_pooled.line_25.id_35
Name	filt_top_peaks pooled
Thread	thread_Root
PID	122348

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

Start	2016-05-16 16:43:21
End	2016-05-16 16:43:31
Elapsed	00:00:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz
Dependencies

 
# SYS command. line 27

 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 30

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.narrowPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz

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

Num	31
ID	task.callpeak_etc.filt_top_peaks_pooled.line_25.id_36
Name	filt_top_peaks pooled
Thread	thread_Root
PID	122363

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

Start	2016-05-16 16:43:21
End	2016-05-16 16:43:27
Elapsed	00:00:06
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.gappedPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.gappedPeak.gz
Dependencies

 
# SYS command. line 27

 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 30

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.gappedPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.gappedPeak.gz

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

Num	32
ID	task.idr.idr2_rep1_rep2.line_61.id_37
Name	idr2 rep1-rep2
Thread	thread_Root
PID	122663

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

Start	2016-05-16 16:43:32
End	2016-05-16 16:43:32
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt.png /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz
Dependencies

 
# SYS command. line 63

 if [[ -f $(which activate) ]]; then source activate bds_atac_py3; fi;  export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 65

 idr --samples /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz --peak-list /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/macs2/pooled_rep/ATAC7-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt --rank p.value --soft-idr-threshold 0.1 \
			--plot --use-best-multisummit-IDR

# SYS command. line 69

 idr_thresh_transformed=$(awk -v p=0.1 'BEGIN{print -log(p)/log(10)}')

# SYS command. line 72

 awk 'BEGIN{OFS="\t"} $12>='"${idr_thresh_transformed}"' {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.narrowPeak.gz

# SYS command. line 75

 awk 'BEGIN{OFS="\t"} $12>='"${idr_thresh_transformed}"' {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,"0"}' /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.13-col.bed.gz

# SYS command. line 78

 bedtools intersect -v -a /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.narrowPeak.gz -b /mnt/data/ENCODE/blacklists/wgEncodeDacMapabilityConsensusExcludable.bed.gz | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz; bedtools intersect -v -a /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.13-col.bed.gz -b /mnt/data/ENCODE/blacklists/wgEncodeDacMapabilityConsensusExcludable.bed.gz | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz

# SYS command. line 80

 gzip -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt

    
--------------------Stderr--------------------
Error: could not find environment: bds_atac_py3

Type	Name	Value
string	_	/usr/bin/bds
string	_LMFILES_	/software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/samtools/1.2:/software/modulefiles/bedtools/2.23.0:/software/modulefiles/rsem/1.2.21
string	_ZSH_TMUX_FIXED_CONFIG	/users/pangwei/.oh-my-zsh/plugins/tmux/tmux.extra.conf
bool	allowEmpty	false
string[]	args	[-out_dir, /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8, -num_rep, 2, -fastq1_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC7/ATAC7-trimmed-pair1.fastq.gz, -fastq1_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC7/ATAC7-trimmed-pair2.fastq.gz, -fastq2_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC8/ATAC8-trimmed-pair1.fastq.gz, -fastq2_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC8/ATAC8-trimmed-pair2.fastq.gz, -subsample, 17500000, -true_rep, -species, hg19]
string	C_INCLUDE_PATH	/software/samtools/samtools-1.2/include/htslib
bool	canFail	false
int	cpus	1
int	cpusLocal	48
int	day	86400
real	E	2.718281828459045
int	G	1073741824
string	HOME	/users/pangwei/
int	hour	3600
int	K	1024
string	LANG	en_US.UTF-8
string	LC_CTYPE	en_US.UTF-8
string	LD_LIBRARY_PATH	/software/samtools/samtools-1.2/lib:/usr/local/cudnn-3/lib64/:/usr/local/cudnn-3/lib64/
string	LESS	-R
string	LOADEDMODULES	modsappsdir/modsappsdir:samtools/1.2:bedtools/2.23.0:rsem/1.2.21
string	LOGNAME	pangwei
string	LSCOLORS	Gxfxcxdxbxegedabagacad
int	M	1048576
string	MAIL	/var/mail/pangwei
string	MANPATH	/software/samtools/samtools-1.2/share/man:/usr/share/man
int	mem	-1
int	minute	60
string	MODULE_VERSION	3.2.10
string	MODULE_VERSION_STACK	3.2.10
string	MODULEPATH	/usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles
string	MODULESAPPSDIR	/software
string	MODULESHOME	/software/env_module/3.2.10
string	node
string	OLDPWD	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4
int	P	1125899906842624
string	PAGER	less
string	PATH	/software/RSEM/rsem-1.2.21/:/software/bedtools/2.23.0/bin:/software/samtools/samtools-1.2/bin:/users/pangwei/anaconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
real	PI	3.141592653589793
string	ppwd	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata
string	programName	atac.bds
string	programPath	/users/pangwei/bds_atac/atac.bds
string	PWD	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata
string	PYTHONPATH	/home/jisraeli/src/caffe_atac/python/:/users/pangwei/stemcells:/home/jisraeli/src/caffe_atac/python/:/users/pangwei/stemcells:
string	queue
int	retry	0
string	SAMTOOLS_HOME	/software/samtools/samtools-1.2/bin
string	SHELL	/usr/bin/zsh
string	SHLVL	2
string	SSH_AUTH_SOCK	/tmp/ssh-5gr8qSU2WF/agent.74700
string	SSH_CLIENT	171.65.76.244 36245 22
string	SSH_CONNECTION	171.65.76.244 49273 171.65.76.236 22
string	SSH_TTY	/dev/pts/0
string	system	local
int	T	1099511627776
string	TERM	screen
string	THEANO_FLAGS	device=gpu6,floatX=float32,warn_float64=warn,optimizer_excluding=cudnn
int	timeout	-1
string	TMUX	/tmp/tmux-1077/default,106699,3
string	TMUX_PANE	%3
string	USER	pangwei
string	UTIL_SCRIPTS_DIR	/users/pangwei/av_scripts
int	walltimeout	8640000
int	week	604800
string	WWW	/srv/www/kundaje/pangwei
string	XDG_RUNTIME_DIR	/run/user/1077
string	XDG_SESSION_ID	1907
string	ZSH	/users/pangwei//.oh-my-zsh
string	ZSH_TMUX_TERM	screen

BigDataScript report: atac.bds

Timeline

Task Graph

Parallel (threads) details

Task details

Global scope