Script file	/users/pangwei/bds_atac/atac.bds
Program ID	atac.bds.20160516_201635_209
Start time	2016-05-16 20:16:35
Run time	20:34:28.237
Tasks executed	40
Tasks failed	0
Tasks failed names
Arguments*	[-out_dir, /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20, -num_rep, 2, -fastq1_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC19/ATAC19-trimmed-pair1.fastq.gz, -fastq1_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC19/ATAC19-trimmed-pair2.fastq.gz, -fastq2_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC20/ATAC20-trimmed-pair1.fastq.gz, -fastq2_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC20/ATAC20-trimmed-pair2.fastq.gz, -subsample, 17500000, -true_rep, -species, hg19]
System*	local
Cpus*	1
Exit value	0

Thread ID	Parent	Tasks
thread_Root	None	atac.bds.20160516_201635_209/task.postalign_bed.pool_tag_reps.line_405.id_27 atac.bds.20160516_201635_209/task.callpeak_macs2.macs2_atac_pooled.pval0.1.line_192.id_28 atac.bds.20160516_201635_209/task.callpeak_macs2.macs2_atac_pooled.line_192.id_29 atac.bds.20160516_201635_209/task.callpeak_etc.filt_top_peaks_rep1.line_25.id_30 atac.bds.20160516_201635_209/task.callpeak_etc.filt_top_peaks_rep1.line_25.id_31 atac.bds.20160516_201635_209/task.callpeak_etc.filt_top_peaks_rep2.line_25.id_32 atac.bds.20160516_201635_209/task.callpeak_etc.filt_top_peaks_rep2.line_25.id_33 atac.bds.20160516_201635_209/task.callpeak_etc.filt_top_peaks_pooled.line_25.id_34 atac.bds.20160516_201635_209/task.callpeak_etc.filt_top_peaks_pooled.line_25.id_35 atac.bds.20160516_201635_209/task.idr.idr2_rep1_rep2.line_61.id_36 atac.bds.20160516_201635_209/task.base.line_414.id_39 atac.bds.20160516_201635_209/task.base.line_414.id_40 atac.bds.20160516_201635_209/task.base.line_414.id_41 atac.bds.20160516_201635_209/task.base.line_414.id_42 atac.bds.20160516_201635_209/task.idr.idr_final_qc.line_196.id_43
thread_77	thread_Root	atac.bds.20160516_201635_209_parallel_77/task.postalign_bam.srt_bam_rep1.line_345.id_45 atac.bds.20160516_201635_209_parallel_77/task.atac.ataqc_rep1.line_815.id_47
thread_78	thread_Root	atac.bds.20160516_201635_209_parallel_78/task.postalign_bam.srt_bam_rep2.line_345.id_44 atac.bds.20160516_201635_209_parallel_78/task.atac.ataqc_rep2.line_815.id_46
thread_21	thread_Root	atac.bds.20160516_201635_209_parallel_21/task.postalign_bam.dedup_bam_PE_rep2.line_215.id_7 atac.bds.20160516_201635_209_parallel_21/task.postalign_bam.nmsrt_bam_rep2.line_321.id_8 atac.bds.20160516_201635_209_parallel_21/task.postalign_bam.bam_to_bedpe_rep2.line_425.id_9 atac.bds.20160516_201635_209_parallel_21/task.postalign_bed.subsample_bedpe_rep2.line_116.id_10 atac.bds.20160516_201635_209_parallel_21/task.postalign_bam.bedpe_to_tag_rep2.line_465.id_11 atac.bds.20160516_201635_209_parallel_21/task.postalign_bed.shift_tag_rep2.line_140.id_12 atac.bds.20160516_201635_209_parallel_21/task.postalign_bed.subsample_bedpe2tagrep2.line_89.id_13 atac.bds.20160516_201635_209_parallel_21/task.postalign_bed.xcor_rep2.line_165.id_14 atac.bds.20160516_201635_209_parallel_21/task.callpeak_macs2.macs2_atac_rep2.pval0.1.line_192.id_15 atac.bds.20160516_201635_209_parallel_21/task.callpeak_macs2.macs2_atac_rep2.line_192.id_16
thread_20	thread_Root	atac.bds.20160516_201635_209_parallel_20/task.align_bowtie2.bowtie2_PE_rep1.line_133.id_6 atac.bds.20160516_201635_209_parallel_20/task.postalign_bam.dedup_bam_PE_rep1.line_215.id_17 atac.bds.20160516_201635_209_parallel_20/task.postalign_bam.nmsrt_bam_rep1.line_321.id_18 atac.bds.20160516_201635_209_parallel_20/task.postalign_bam.bam_to_bedpe_rep1.line_425.id_19 atac.bds.20160516_201635_209_parallel_20/task.postalign_bed.subsample_bedpe_rep1.line_116.id_20 atac.bds.20160516_201635_209_parallel_20/task.postalign_bam.bedpe_to_tag_rep1.line_465.id_21 atac.bds.20160516_201635_209_parallel_20/task.postalign_bed.shift_tag_rep1.line_140.id_22 atac.bds.20160516_201635_209_parallel_20/task.postalign_bed.subsample_bedpe2tagrep1.line_89.id_23 atac.bds.20160516_201635_209_parallel_20/task.postalign_bed.xcor_rep1.line_165.id_24 atac.bds.20160516_201635_209_parallel_20/task.callpeak_macs2.macs2_atac_rep1.pval0.1.line_192.id_25 atac.bds.20160516_201635_209_parallel_20/task.callpeak_macs2.macs2_atac_rep1.line_192.id_26

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.align_bowtie2.bowtie2_PE_rep1.line_133.id_6
Name	bowtie2_PE rep1
Thread	thread_20
PID	130096

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

Start	2016-05-16 20:16:36
End	2016-05-17 08:03:07
Elapsed	11:46:31
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.fastq.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair2.trim.fastq.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep1/ATAC19-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/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.fastq.gz -2 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair2.trim.fastq.gz 2>/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep1/ATAC19-trimmed-pair1.trim.PE2SE.align.log | samtools view -bS - | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE

# SYS command. line 142

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-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 107 files...

Num	2
ID	task.postalign_bam.dedup_bam_PE_rep2.line_215.id_7
Name	dedup_bam_PE rep2
Thread	thread_21
PID	130103

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

Start	2016-05-16 20:16:36
End	2016-05-16 22:08:29
Elapsed	01:51:53
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep2/ATAC20-trimmed-pair1.trim.PE2SE.dup.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep2/ATAC20-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/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-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/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-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/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.filt

# SYS command. line 239

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-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/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep2/ATAC20-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/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep2/ATAC20-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/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-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/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.filt.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 269

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 271

 if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.bai" ]; then \
			cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.bai; \
			fi

# SYS command. line 275

 samtools flagstat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc

# SYS command. line 286

 samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.filt.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.filt.bam.tmp

# SYS command. line 287

 bedtools bamtobed -bedpe -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-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/ATAC19+20/qc/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.pbc.qc

# SYS command. line 291

 rm /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam

# SYS command. line 293

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.filt.bam

# SYS command. line 294

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-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 35 files...
[bam_sort_core] merging from 35 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Mon May 16 21:12:19 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep2/ATAC20-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 21:12:19 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 21:12:20	MarkDuplicates	Start of doWork freeMemory: 254889800; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-16 21:12:20	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-05-16 21:12:20	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-05-16 21:12:34	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:14s.  Time for last 1,000,000:   14s.  Last read position: chr10:96,305,314
INFO	2016-05-16 21:12:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:12:45	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:24s.  Time for last 1,000,000:   10s.  Last read position: chr11:40,894,941
INFO	2016-05-16 21:12:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:12:54	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:34s.  Time for last 1,000,000:    9s.  Last read position: chr11:124,695,923
INFO	2016-05-16 21:12:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:13:03	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:43s.  Time for last 1,000,000:    8s.  Last read position: chr12:80,479,601
INFO	2016-05-16 21:13:03	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 21:13:11	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:50s.  Time for last 1,000,000:    7s.  Last read position: chr13:52,251,234
INFO	2016-05-16 21:13:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:13:16	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:56s.  Time for last 1,000,000:    5s.  Last read position: chr14:58,927,793
INFO	2016-05-16 21:13:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:13:24	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:01:04s.  Time for last 1,000,000:    8s.  Last read position: chr15:59,273,692
INFO	2016-05-16 21:13:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:13:31	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:01:10s.  Time for last 1,000,000:    6s.  Last read position: chr16:33,964,002
INFO	2016-05-16 21:13:31	MarkDuplicates	Tracking 24 as yet unmatched pairs. 24 records in RAM.
INFO	2016-05-16 21:13:39	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:01:19s.  Time for last 1,000,000:    8s.  Last read position: chr17:30,640,012
INFO	2016-05-16 21:13:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:13:45	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:01:25s.  Time for last 1,000,000:    6s.  Last read position: chr18:27,345,815
INFO	2016-05-16 21:13:45	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 21:13:52	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:31s.  Time for last 1,000,000:    6s.  Last read position: chr19:30,086,975
INFO	2016-05-16 21:13:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:14:00	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:40s.  Time for last 1,000,000:    8s.  Last read position: chr1:27,019,750
INFO	2016-05-16 21:14:00	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 21:14:07	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:46s.  Time for last 1,000,000:    6s.  Last read position: chr1:112,123,846
INFO	2016-05-16 21:14:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:14:17	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:56s.  Time for last 1,000,000:    9s.  Last read position: chr1:222,014,533
INFO	2016-05-16 21:14:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:14:34	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:02:13s.  Time for last 1,000,000:   17s.  Last read position: chr20:54,005,834
INFO	2016-05-16 21:14:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:14:40	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:02:19s.  Time for last 1,000,000:    6s.  Last read position: chr22:43,630,817
INFO	2016-05-16 21:14:40	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 21:14:48	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:02:28s.  Time for last 1,000,000:    8s.  Last read position: chr2:72,745,139
INFO	2016-05-16 21:14:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:14:53	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:02:33s.  Time for last 1,000,000:    4s.  Last read position: chr2:173,367,608
INFO	2016-05-16 21:14:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:14:58	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:02:38s.  Time for last 1,000,000:    5s.  Last read position: chr3:16,801,546
INFO	2016-05-16 21:14:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:15:06	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:02:46s.  Time for last 1,000,000:    7s.  Last read position: chr3:112,985,447
INFO	2016-05-16 21:15:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:15:12	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:02:51s.  Time for last 1,000,000:    5s.  Last read position: chr4:3,254,961
INFO	2016-05-16 21:15:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:15:18	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:02:57s.  Time for last 1,000,000:    6s.  Last read position: chr4:106,901,003
INFO	2016-05-16 21:15:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:15:28	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:03:07s.  Time for last 1,000,000:    9s.  Last read position: chr5:16,936,282
INFO	2016-05-16 21:15:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:15:34	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:03:13s.  Time for last 1,000,000:    6s.  Last read position: chr5:126,324,483
INFO	2016-05-16 21:15:34	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 21:15:40	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:03:20s.  Time for last 1,000,000:    6s.  Last read position: chr6:19,518,937
INFO	2016-05-16 21:15:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:15:46	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:03:26s.  Time for last 1,000,000:    6s.  Last read position: chr6:115,911,036
INFO	2016-05-16 21:15:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:15:55	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:03:35s.  Time for last 1,000,000:    8s.  Last read position: chr7:35,436,031
INFO	2016-05-16 21:15:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:16:01	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:03:41s.  Time for last 1,000,000:    5s.  Last read position: chr7:134,080,705
INFO	2016-05-16 21:16:01	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 21:16:07	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:03:47s.  Time for last 1,000,000:    5s.  Last read position: chr8:67,579,198
INFO	2016-05-16 21:16:07	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 21:16:24	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:04:03s.  Time for last 1,000,000:   16s.  Last read position: chr9:13,002,156
INFO	2016-05-16 21:16:24	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 21:16:30	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:04:09s.  Time for last 1,000,000:    6s.  Last read position: chr9:131,419,129
INFO	2016-05-16 21:16:30	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-16 21:16:34	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:04:14s.  Time for last 1,000,000:    4s.  Last read position: chrM:639
INFO	2016-05-16 21:16:34	MarkDuplicates	Tracking 4132 as yet unmatched pairs. 4132 records in RAM.
INFO	2016-05-16 21:16:39	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:04:18s.  Time for last 1,000,000:    4s.  Last read position: chrM:1,671
INFO	2016-05-16 21:16:39	MarkDuplicates	Tracking 3906 as yet unmatched pairs. 3906 records in RAM.
INFO	2016-05-16 21:16:43	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:04:22s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,727
INFO	2016-05-16 21:16:43	MarkDuplicates	Tracking 6682 as yet unmatched pairs. 6682 records in RAM.
INFO	2016-05-16 21:16:48	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:04:27s.  Time for last 1,000,000:    5s.  Last read position: chrM:3,364
INFO	2016-05-16 21:16:48	MarkDuplicates	Tracking 16840 as yet unmatched pairs. 16840 records in RAM.
INFO	2016-05-16 21:16:53	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:04:32s.  Time for last 1,000,000:    5s.  Last read position: chrM:3,863
INFO	2016-05-16 21:16:53	MarkDuplicates	Tracking 6310 as yet unmatched pairs. 6310 records in RAM.
INFO	2016-05-16 21:16:58	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:04:37s.  Time for last 1,000,000:    4s.  Last read position: chrM:5,372
INFO	2016-05-16 21:16:58	MarkDuplicates	Tracking 1190 as yet unmatched pairs. 1190 records in RAM.
INFO	2016-05-16 21:17:03	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:04:43s.  Time for last 1,000,000:    5s.  Last read position: chrM:6,506
INFO	2016-05-16 21:17:03	MarkDuplicates	Tracking 2532 as yet unmatched pairs. 2532 records in RAM.
INFO	2016-05-16 21:17:11	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:04:51s.  Time for last 1,000,000:    7s.  Last read position: chrM:7,868
INFO	2016-05-16 21:17:11	MarkDuplicates	Tracking 4368 as yet unmatched pairs. 4368 records in RAM.
INFO	2016-05-16 21:17:17	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:04:56s.  Time for last 1,000,000:    5s.  Last read position: chrM:9,271
INFO	2016-05-16 21:17:17	MarkDuplicates	Tracking 2564 as yet unmatched pairs. 2564 records in RAM.
INFO	2016-05-16 21:17:23	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:05:03s.  Time for last 1,000,000:    6s.  Last read position: chrM:10,292
INFO	2016-05-16 21:17:23	MarkDuplicates	Tracking 5814 as yet unmatched pairs. 5814 records in RAM.
INFO	2016-05-16 21:17:28	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:05:08s.  Time for last 1,000,000:    5s.  Last read position: chrM:11,352
INFO	2016-05-16 21:17:28	MarkDuplicates	Tracking 6350 as yet unmatched pairs. 6350 records in RAM.
INFO	2016-05-16 21:17:37	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:05:16s.  Time for last 1,000,000:    8s.  Last read position: chrM:12,352
INFO	2016-05-16 21:17:37	MarkDuplicates	Tracking 6216 as yet unmatched pairs. 6216 records in RAM.
INFO	2016-05-16 21:17:43	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:05:22s.  Time for last 1,000,000:    6s.  Last read position: chrM:13,093
INFO	2016-05-16 21:17:43	MarkDuplicates	Tracking 3066 as yet unmatched pairs. 3066 records in RAM.
INFO	2016-05-16 21:17:55	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:05:34s.  Time for last 1,000,000:   11s.  Last read position: chrM:13,821
INFO	2016-05-16 21:17:55	MarkDuplicates	Tracking 5510 as yet unmatched pairs. 5510 records in RAM.
INFO	2016-05-16 21:17:59	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:05:38s.  Time for last 1,000,000:    4s.  Last read position: chrM:14,820
INFO	2016-05-16 21:17:59	MarkDuplicates	Tracking 2284 as yet unmatched pairs. 2284 records in RAM.
INFO	2016-05-16 21:18:04	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:05:44s.  Time for last 1,000,000:    5s.  Last read position: chrM:15,479
INFO	2016-05-16 21:18:04	MarkDuplicates	Tracking 9314 as yet unmatched pairs. 9314 records in RAM.
INFO	2016-05-16 21:18:11	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:05:50s.  Time for last 1,000,000:    6s.  Last read position: chrM:16,230
INFO	2016-05-16 21:18:11	MarkDuplicates	Tracking 4802 as yet unmatched pairs. 4802 records in RAM.
INFO	2016-05-16 21:18:16	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:05:55s.  Time for last 1,000,000:    4s.  Last read position: chrX:48,681,779
INFO	2016-05-16 21:18:16	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 21:18:21	MarkDuplicates	Read 49968188 records. 0 pairs never matched.
INFO	2016-05-16 21:18:28	MarkDuplicates	After buildSortedReadEndLists freeMemory: 2668702632; totalMemory: 2696413184; maxMemory: 3817865216
INFO	2016-05-16 21:18:28	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-05-16 21:18:29	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-05-16 21:18:41	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-05-16 21:18:58	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-05-16 21:19:00	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2154195552; totalMemory: 3135766528; maxMemory: 3817865216
INFO	2016-05-16 21:19:00	MarkDuplicates	Marking 20312274 records as duplicates.
INFO	2016-05-16 21:19:00	MarkDuplicates	Found 8328134 optical duplicate clusters.
INFO	2016-05-16 21:21:13	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:02:11s.  Time for last 10,000,000:  131s.  Last read position: chr18:27,345,815
INFO	2016-05-16 21:23:29	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:04:27s.  Time for last 10,000,000:  136s.  Last read position: chr3:112,985,447
INFO	2016-05-16 21:25:43	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:06:42s.  Time for last 10,000,000:  134s.  Last read position: chr9:13,002,156
INFO	2016-05-16 21:27:27	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:08:26s.  Time for last 10,000,000:  104s.  Last read position: chrM:9,271
INFO	2016-05-16 21:29:14	MarkDuplicates	Before output close freeMemory: 3184447528; totalMemory: 3214934016; maxMemory: 3817865216
INFO	2016-05-16 21:29:14	MarkDuplicates	After output close freeMemory: 3184446472; totalMemory: 3214934016; maxMemory: 3817865216
[Mon May 16 21:29:14 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 16.91 minutes.
Runtime.totalMemory()=3214934016
[bam_sort_core] merging from 36 files...

Num	3
ID	task.postalign_bam.nmsrt_bam_rep2.line_321.id_8
Name	nmsrt_bam rep2
Thread	thread_21
PID	134614

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

Start	2016-05-16 22:08:30
End	2016-05-16 22:24:09
Elapsed	00:15:38
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-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/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-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 21 files...

Num	4
ID	task.postalign_bam.bam_to_bedpe_rep2.line_425.id_9
Name	bam_to_bedpe rep2
Thread	thread_21
PID	135027

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

Start	2016-05-16 22:24:09
End	2016-05-16 22:26:18
Elapsed	00:02:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-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/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-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	5
ID	task.postalign_bed.subsample_bedpe_rep2.line_116.id_10
Name	subsample_bedpe rep2
Thread	thread_21
PID	135149

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

Start	2016-05-16 22:26:19
End	2016-05-16 22:27:37
Elapsed	00:01:17
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-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/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | grep -v "chrM" | shuf -n 17500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-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	6
ID	task.postalign_bam.bedpe_to_tag_rep2.line_465.id_11
Name	bedpe_to_tag rep2
Thread	thread_21
PID	135244

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

Start	2016-05-16 22:27:38
End	2016-05-16 22:29:07
Elapsed	00:01:29
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-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/ATAC19+20/align/rep2/ATAC20-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/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz

# SYS command. line 472

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz | grep -P -v 'chrM' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz; mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-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	7
ID	task.postalign_bed.shift_tag_rep2.line_140.id_12
Name	shift_tag rep2
Thread	thread_21
PID	135324

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

Start	2016-05-16 22:29:08
End	2016-05-16 22:30:11
Elapsed	00:01:02
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-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/ATAC19+20/align/rep2/ATAC20-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/ATAC19+20/align/rep2/ATAC20-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	8
ID	task.postalign_bed.subsample_bedpe2tagrep2.line_89.id_13
Name	subsample_bedpe2tagrep2
Thread	thread_21
PID	135386

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

Start	2016-05-16 22:30:12
End	2016-05-16 22:31:25
Elapsed	00:01:13
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-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/ATAC19+20/align/rep2/ATAC20-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/ATAC19+20/align/rep2/ATAC20-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	9
ID	task.postalign_bed.xcor_rep2.line_165.id_14
Name	xcor rep2
Thread	thread_21
PID	135461

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

Start	2016-05-16 22:31:25
End	2016-05-16 23:00:55
Elapsed	00:29:29
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep2/ATAC20-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/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz -p=1 \
			-filtchr=chrM -savp=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf -out=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep2/ATAC20-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/ATAC19+20/qc/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp

# SYS command. line 175

 mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc

   
--------------------Stdout--------------------
################
ChIP data: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-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/ATAC19+20/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/ATAC19+20/qc/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf 
result filename: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep2/ATAC20-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/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz 
opened /tmp/RtmpYI9aQk/ATAC20-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign211be1337ed3a
done. read 14137793 fragments
ChIP data read length 64 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1602002 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.169155598672431 
Top 3 estimates for fragment length 0 
Window half size 490 
Phantom peak location 55 
Phantom peak Correlation 0.1702842 
Normalized Strand cross-correlation coefficient (NSC) 1.055901 
Relative Strand Cross correlation Coefficient (RSC) 0.8880825 
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	10
ID	task.callpeak_macs2.macs2_atac_rep2.pval0.1.line_192.id_15
Name	macs2_atac rep2.pval0.1
Thread	thread_21
PID	135463

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

Start	2016-05-16 22:31:25
End	2016-05-16 22:53:27
Elapsed	00:22:01
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/signal/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/signal/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-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 22:31:29: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-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 22:31:29: #1 read tag files... 
INFO  @ Mon, 16 May 2016 22:31:29: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 22:31:31:  1000000 
INFO  @ Mon, 16 May 2016 22:31:34:  2000000 
INFO  @ Mon, 16 May 2016 22:31:36:  3000000 
INFO  @ Mon, 16 May 2016 22:31:38:  4000000 
INFO  @ Mon, 16 May 2016 22:31:40:  5000000 
INFO  @ Mon, 16 May 2016 22:31:43:  6000000 
INFO  @ Mon, 16 May 2016 22:31:45:  7000000 
INFO  @ Mon, 16 May 2016 22:31:47:  8000000 
INFO  @ Mon, 16 May 2016 22:31:50:  9000000 
INFO  @ Mon, 16 May 2016 22:31:52:  10000000 
INFO  @ Mon, 16 May 2016 22:31:54:  11000000 
INFO  @ Mon, 16 May 2016 22:31:56:  12000000 
INFO  @ Mon, 16 May 2016 22:31:58:  13000000 
INFO  @ Mon, 16 May 2016 22:32:01:  14000000 
INFO  @ Mon, 16 May 2016 22:32:03:  15000000 
INFO  @ Mon, 16 May 2016 22:32:05:  16000000 
INFO  @ Mon, 16 May 2016 22:32:07:  17000000 
INFO  @ Mon, 16 May 2016 22:32:09:  18000000 
INFO  @ Mon, 16 May 2016 22:32:12:  19000000 
INFO  @ Mon, 16 May 2016 22:32:14:  20000000 
INFO  @ Mon, 16 May 2016 22:32:16:  21000000 
INFO  @ Mon, 16 May 2016 22:32:18:  22000000 
INFO  @ Mon, 16 May 2016 22:32:19:  23000000 
INFO  @ Mon, 16 May 2016 22:32:21:  24000000 
INFO  @ Mon, 16 May 2016 22:32:24:  25000000 
INFO  @ Mon, 16 May 2016 22:32:26:  26000000 
INFO  @ Mon, 16 May 2016 22:32:28:  27000000 
INFO  @ Mon, 16 May 2016 22:32:30:  28000000 
INFO  @ Mon, 16 May 2016 22:32:33: #1 tag size is determined as 43 bps 
INFO  @ Mon, 16 May 2016 22:32:33: #1 tag size = 43 
INFO  @ Mon, 16 May 2016 22:32:33: #1  total tags in treatment: 28275586 
INFO  @ Mon, 16 May 2016 22:32:33: #1 finished! 
INFO  @ Mon, 16 May 2016 22:32:33: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 22:32:33: #2 Skipped... 
INFO  @ Mon, 16 May 2016 22:32:33: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 22:32:33: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 22:32:33: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 22:32:33: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Mon, 16 May 2016 22:32:33: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 22:33:49: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 22:37:04: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls 
INFO  @ Mon, 16 May 2016 22:37:09: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Mon, 16 May 2016 22:37:13: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Mon, 16 May 2016 22:37:16: Done! 
INFO  @ Mon, 16 May 2016 22:37:38: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-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 22:37:38: #1 read tag files... 
INFO  @ Mon, 16 May 2016 22:37:38: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 22:37:40:  1000000 
INFO  @ Mon, 16 May 2016 22:37:42:  2000000 
INFO  @ Mon, 16 May 2016 22:37:44:  3000000 
INFO  @ Mon, 16 May 2016 22:37:46:  4000000 
INFO  @ Mon, 16 May 2016 22:37:48:  5000000 
INFO  @ Mon, 16 May 2016 22:37:50:  6000000 
INFO  @ Mon, 16 May 2016 22:37:52:  7000000 
INFO  @ Mon, 16 May 2016 22:37:54:  8000000 
INFO  @ Mon, 16 May 2016 22:37:56:  9000000 
INFO  @ Mon, 16 May 2016 22:37:57:  10000000 
INFO  @ Mon, 16 May 2016 22:37:59:  11000000 
INFO  @ Mon, 16 May 2016 22:38:01:  12000000 
INFO  @ Mon, 16 May 2016 22:38:03:  13000000 
INFO  @ Mon, 16 May 2016 22:38:05:  14000000 
INFO  @ Mon, 16 May 2016 22:38:07:  15000000 
INFO  @ Mon, 16 May 2016 22:38:09:  16000000 
INFO  @ Mon, 16 May 2016 22:38:10:  17000000 
INFO  @ Mon, 16 May 2016 22:38:13:  18000000 
INFO  @ Mon, 16 May 2016 22:38:15:  19000000 
INFO  @ Mon, 16 May 2016 22:38:16:  20000000 
INFO  @ Mon, 16 May 2016 22:38:18:  21000000 
INFO  @ Mon, 16 May 2016 22:38:20:  22000000 
INFO  @ Mon, 16 May 2016 22:38:22:  23000000 
INFO  @ Mon, 16 May 2016 22:38:24:  24000000 
INFO  @ Mon, 16 May 2016 22:38:26:  25000000 
INFO  @ Mon, 16 May 2016 22:38:28:  26000000 
INFO  @ Mon, 16 May 2016 22:38:30:  27000000 
INFO  @ Mon, 16 May 2016 22:38:32:  28000000 
INFO  @ Mon, 16 May 2016 22:38:35: #1 tag size is determined as 43 bps 
INFO  @ Mon, 16 May 2016 22:38:35: #1 tag size = 43 
INFO  @ Mon, 16 May 2016 22:38:35: #1  total tags in treatment: 28275586 
INFO  @ Mon, 16 May 2016 22:38:35: #1 finished! 
INFO  @ Mon, 16 May 2016 22:38:35: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 22:38:35: #2 Skipped... 
INFO  @ Mon, 16 May 2016 22:38:35: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 22:38:35: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 22:38:35: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 22:38:35: #3 Going to call summits inside each peak ... 
INFO  @ Mon, 16 May 2016 22:38:35: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Mon, 16 May 2016 22:38:35: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 22:39:52: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Mon, 16 May 2016 22:39:52: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Mon, 16 May 2016 22:39:52: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Mon, 16 May 2016 22:39:52: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Mon, 16 May 2016 22:39:52: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 22:52:51: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls 
INFO  @ Mon, 16 May 2016 22:53:03: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Mon, 16 May 2016 22:53:11: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_summits.bed 
INFO  @ Mon, 16 May 2016 22:53:16: Done!

Num	11
ID	task.callpeak_macs2.macs2_atac_rep2.line_192.id_16
Name	macs2_atac rep2
Thread	thread_21
PID	135476

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

Start	2016-05-16 22:31:26
End	2016-05-16 23:13:41
Elapsed	00:42:15
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.gappedPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/signal/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/signal/macs2/rep2/ATAC20-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/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/signal/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/signal/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-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 22:31:29: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-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 22:31:29: #1 read tag files... 
INFO  @ Mon, 16 May 2016 22:31:29: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 22:31:31:  1000000 
INFO  @ Mon, 16 May 2016 22:31:33:  2000000 
INFO  @ Mon, 16 May 2016 22:31:36:  3000000 
INFO  @ Mon, 16 May 2016 22:31:38:  4000000 
INFO  @ Mon, 16 May 2016 22:31:40:  5000000 
INFO  @ Mon, 16 May 2016 22:31:42:  6000000 
INFO  @ Mon, 16 May 2016 22:31:45:  7000000 
INFO  @ Mon, 16 May 2016 22:31:47:  8000000 
INFO  @ Mon, 16 May 2016 22:31:49:  9000000 
INFO  @ Mon, 16 May 2016 22:31:51:  10000000 
INFO  @ Mon, 16 May 2016 22:31:53:  11000000 
INFO  @ Mon, 16 May 2016 22:31:55:  12000000 
INFO  @ Mon, 16 May 2016 22:31:58:  13000000 
INFO  @ Mon, 16 May 2016 22:32:00:  14000000 
INFO  @ Mon, 16 May 2016 22:32:03:  15000000 
INFO  @ Mon, 16 May 2016 22:32:04:  16000000 
INFO  @ Mon, 16 May 2016 22:32:07:  17000000 
INFO  @ Mon, 16 May 2016 22:32:09:  18000000 
INFO  @ Mon, 16 May 2016 22:32:11:  19000000 
INFO  @ Mon, 16 May 2016 22:32:13:  20000000 
INFO  @ Mon, 16 May 2016 22:32:15:  21000000 
INFO  @ Mon, 16 May 2016 22:32:17:  22000000 
INFO  @ Mon, 16 May 2016 22:32:20:  23000000 
INFO  @ Mon, 16 May 2016 22:32:22:  24000000 
INFO  @ Mon, 16 May 2016 22:32:24:  25000000 
INFO  @ Mon, 16 May 2016 22:32:26:  26000000 
INFO  @ Mon, 16 May 2016 22:32:28:  27000000 
INFO  @ Mon, 16 May 2016 22:32:30:  28000000 
INFO  @ Mon, 16 May 2016 22:32:32: #1 tag size is determined as 43 bps 
INFO  @ Mon, 16 May 2016 22:32:32: #1 tag size = 43 
INFO  @ Mon, 16 May 2016 22:32:32: #1  total tags in treatment: 28275586 
INFO  @ Mon, 16 May 2016 22:32:32: #1 finished! 
INFO  @ Mon, 16 May 2016 22:32:32: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 22:32:32: #2 Skipped... 
INFO  @ Mon, 16 May 2016 22:32:32: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 22:32:32: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 22:32:32: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 22:32:32: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Mon, 16 May 2016 22:32:32: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 22:33:51: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 22:35:57: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls 
INFO  @ Mon, 16 May 2016 22:36:01: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.broadPeak 
INFO  @ Mon, 16 May 2016 22:36:04: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.gappedPeak 
INFO  @ Mon, 16 May 2016 22:36:07: Done! 
INFO  @ Mon, 16 May 2016 22:36:25: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-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 22:36:25: #1 read tag files... 
INFO  @ Mon, 16 May 2016 22:36:25: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 22:36:27:  1000000 
INFO  @ Mon, 16 May 2016 22:36:28:  2000000 
INFO  @ Mon, 16 May 2016 22:36:30:  3000000 
INFO  @ Mon, 16 May 2016 22:36:31:  4000000 
INFO  @ Mon, 16 May 2016 22:36:33:  5000000 
INFO  @ Mon, 16 May 2016 22:36:35:  6000000 
INFO  @ Mon, 16 May 2016 22:36:36:  7000000 
INFO  @ Mon, 16 May 2016 22:36:38:  8000000 
INFO  @ Mon, 16 May 2016 22:36:40:  9000000 
INFO  @ Mon, 16 May 2016 22:36:42:  10000000 
INFO  @ Mon, 16 May 2016 22:36:43:  11000000 
INFO  @ Mon, 16 May 2016 22:36:45:  12000000 
INFO  @ Mon, 16 May 2016 22:36:47:  13000000 
INFO  @ Mon, 16 May 2016 22:36:49:  14000000 
INFO  @ Mon, 16 May 2016 22:36:50:  15000000 
INFO  @ Mon, 16 May 2016 22:36:52:  16000000 
INFO  @ Mon, 16 May 2016 22:36:54:  17000000 
INFO  @ Mon, 16 May 2016 22:36:55:  18000000 
INFO  @ Mon, 16 May 2016 22:36:57:  19000000 
INFO  @ Mon, 16 May 2016 22:36:59:  20000000 
INFO  @ Mon, 16 May 2016 22:37:01:  21000000 
INFO  @ Mon, 16 May 2016 22:37:03:  22000000 
INFO  @ Mon, 16 May 2016 22:37:05:  23000000 
INFO  @ Mon, 16 May 2016 22:37:08:  24000000 
INFO  @ Mon, 16 May 2016 22:37:10:  25000000 
INFO  @ Mon, 16 May 2016 22:37:11:  26000000 
INFO  @ Mon, 16 May 2016 22:37:13:  27000000 
INFO  @ Mon, 16 May 2016 22:37:15:  28000000 
INFO  @ Mon, 16 May 2016 22:37:17: #1 tag size is determined as 43 bps 
INFO  @ Mon, 16 May 2016 22:37:17: #1 tag size = 43 
INFO  @ Mon, 16 May 2016 22:37:17: #1  total tags in treatment: 28275586 
INFO  @ Mon, 16 May 2016 22:37:17: #1 finished! 
INFO  @ Mon, 16 May 2016 22:37:17: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 22:37:17: #2 Skipped... 
INFO  @ Mon, 16 May 2016 22:37:17: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 22:37:17: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 22:37:17: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 22:37:17: #3 Going to call summits inside each peak ... 
INFO  @ Mon, 16 May 2016 22:37:17: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Mon, 16 May 2016 22:37:17: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 22:38:46: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Mon, 16 May 2016 22:38:46: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_treat_pileup.bdg 
INFO  @ Mon, 16 May 2016 22:38:46: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_control_lambda.bdg 
INFO  @ Mon, 16 May 2016 22:38:46: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Mon, 16 May 2016 22:38:46: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 22:44:11: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls 
INFO  @ Mon, 16 May 2016 22:44:13: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.narrowPeak 
INFO  @ Mon, 16 May 2016 22:44:14: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_summits.bed 
INFO  @ Mon, 16 May 2016 22:44:15: Done! 
INFO  @ Mon, 16 May 2016 22:44:18: Read and build treatment bedGraph... 
INFO  @ Mon, 16 May 2016 22:45:24: Read and build control bedGraph... 
INFO  @ Mon, 16 May 2016 22:45:57: Build scoreTrackII... 
INFO  @ Mon, 16 May 2016 22:46:33: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Mon, 16 May 2016 22:50:36: Write bedGraph of scores... 
INFO  @ Mon, 16 May 2016 22:52:47: Finished 'FE'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_FE.bdg'! 
INFO  @ Mon, 16 May 2016 22:59:35: Read and build treatment bedGraph... 
INFO  @ Mon, 16 May 2016 23:00:52: Read and build control bedGraph... 
INFO  @ Mon, 16 May 2016 23:01:28: Build scoreTrackII... 
INFO  @ Mon, 16 May 2016 23:02:04: Values in your input bedGraph files will be multiplied by 28.275586 ... 
INFO  @ Mon, 16 May 2016 23:06:09: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Mon, 16 May 2016 23:06:48: Write bedGraph of scores... 
INFO  @ Mon, 16 May 2016 23:08:41: Finished 'ppois'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_ppois.bdg'!

Num	12
ID	task.postalign_bam.dedup_bam_PE_rep1.line_215.id_17
Name	dedup_bam_PE rep1
Thread	thread_20
PID	40461

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

Start	2016-05-17 08:03:08
End	2016-05-17 11:55:54
Elapsed	03:52:46
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep1/ATAC19-trimmed-pair1.trim.PE2SE.dup.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep1/ATAC19-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/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-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/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-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/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.filt

# SYS command. line 239

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-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/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep1/ATAC19-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/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep1/ATAC19-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/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-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/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.filt.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 269

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 271

 if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.bai" ]; then \
			cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.bai; \
			fi

# SYS command. line 275

 samtools flagstat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc

# SYS command. line 286

 samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.filt.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.filt.bam.tmp

# SYS command. line 287

 bedtools bamtobed -bedpe -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-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/ATAC19+20/qc/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.pbc.qc

# SYS command. line 291

 rm /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam

# SYS command. line 293

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.filt.bam

# SYS command. line 294

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-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 76 files...
[bam_sort_core] merging from 77 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Tue May 17 09:46:41 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep1/ATAC19-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
[Tue May 17 09:46:41 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	2016-05-17 09:46:41	MarkDuplicates	Start of doWork freeMemory: 254889656; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-17 09:46:41	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-05-17 09:46:41	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-05-17 09:47:00	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:16s.  Time for last 1,000,000:   16s.  Last read position: chr10:44,738,053
INFO	2016-05-17 09:47:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:47:14	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:31s.  Time for last 1,000,000:   14s.  Last read position: chr10:86,929,986
INFO	2016-05-17 09:47:14	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:47:32	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:48s.  Time for last 1,000,000:   17s.  Last read position: chr10:123,779,267
INFO	2016-05-17 09:47:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:47:43	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:01:00s.  Time for last 1,000,000:   11s.  Last read position: chr11:19,462,800
INFO	2016-05-17 09:47:43	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:47:49	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:01:05s.  Time for last 1,000,000:    5s.  Last read position: chr11:63,643,457
INFO	2016-05-17 09:47:49	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:47:58	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:01:14s.  Time for last 1,000,000:    8s.  Last read position: chr11:97,206,385
INFO	2016-05-17 09:47:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:48:03	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:01:19s.  Time for last 1,000,000:    4s.  Last read position: chr11:133,936,397
INFO	2016-05-17 09:48:03	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:48:10	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:01:27s.  Time for last 1,000,000:    7s.  Last read position: chr12:43,723,751
INFO	2016-05-17 09:48:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:48:17	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:01:34s.  Time for last 1,000,000:    6s.  Last read position: chr12:83,399,975
INFO	2016-05-17 09:48:17	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:48:26	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:01:43s.  Time for last 1,000,000:    9s.  Last read position: chr12:121,721,031
INFO	2016-05-17 09:48:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:48:33	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:50s.  Time for last 1,000,000:    6s.  Last read position: chr13:44,960,239
INFO	2016-05-17 09:48:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:48:41	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:58s.  Time for last 1,000,000:    7s.  Last read position: chr13:94,981,380
INFO	2016-05-17 09:48:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:48:50	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:02:07s.  Time for last 1,000,000:    9s.  Last read position: chr14:39,879,696
INFO	2016-05-17 09:48:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:48:56	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:02:13s.  Time for last 1,000,000:    6s.  Last read position: chr14:80,195,182
INFO	2016-05-17 09:48:56	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:49:17	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:02:33s.  Time for last 1,000,000:   20s.  Last read position: chr15:31,467,945
INFO	2016-05-17 09:49:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:49:25	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:02:42s.  Time for last 1,000,000:    8s.  Last read position: chr15:70,288,036
INFO	2016-05-17 09:49:25	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:49:31	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:02:48s.  Time for last 1,000,000:    5s.  Last read position: chr16:1,551,116
INFO	2016-05-17 09:49:31	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:49:35	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:02:51s.  Time for last 1,000,000:    3s.  Last read position: chr16:48,537,887
INFO	2016-05-17 09:49:35	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:49:41	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:02:58s.  Time for last 1,000,000:    6s.  Last read position: chr16:83,692,006
INFO	2016-05-17 09:49:41	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:49:46	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:03:03s.  Time for last 1,000,000:    5s.  Last read position: chr17:25,667,348
INFO	2016-05-17 09:49:46	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:49:52	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:03:08s.  Time for last 1,000,000:    5s.  Last read position: chr17:56,641,596
INFO	2016-05-17 09:49:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:49:57	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:03:14s.  Time for last 1,000,000:    5s.  Last read position: chr18:6,790,446
INFO	2016-05-17 09:49:57	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:50:05	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:03:22s.  Time for last 1,000,000:    7s.  Last read position: chr18:51,336,560
INFO	2016-05-17 09:50:05	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:50:12	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:03:29s.  Time for last 1,000,000:    7s.  Last read position: chr19:7,977,839
INFO	2016-05-17 09:50:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:50:20	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:03:37s.  Time for last 1,000,000:    7s.  Last read position: chr19:40,612,038
INFO	2016-05-17 09:50:20	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:50:32	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:03:49s.  Time for last 1,000,000:   12s.  Last read position: chr1:2,624,693
INFO	2016-05-17 09:50:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:50:39	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:03:56s.  Time for last 1,000,000:    6s.  Last read position: chr1:29,832,075
INFO	2016-05-17 09:50:39	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:50:47	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:04:03s.  Time for last 1,000,000:    7s.  Last read position: chr1:61,388,439
INFO	2016-05-17 09:50:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:50:54	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:04:11s.  Time for last 1,000,000:    7s.  Last read position: chr1:106,241,076
INFO	2016-05-17 09:50:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:51:23	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:04:40s.  Time for last 1,000,000:   28s.  Last read position: chr1:165,816,340
INFO	2016-05-17 09:51:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:51:35	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:04:51s.  Time for last 1,000,000:   11s.  Last read position: chr1:206,239,717
INFO	2016-05-17 09:51:35	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:51:45	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:05:01s.  Time for last 1,000,000:    9s.  Last read position: chr1:244,718,836
INFO	2016-05-17 09:51:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:51:53	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:05:10s.  Time for last 1,000,000:    8s.  Last read position: chr20:33,264,915
INFO	2016-05-17 09:51:53	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 09:52:03	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:05:19s.  Time for last 1,000,000:    9s.  Last read position: chr21:9,825,591
INFO	2016-05-17 09:52:03	MarkDuplicates	Tracking 624 as yet unmatched pairs. 624 records in RAM.
INFO	2016-05-17 09:52:09	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:05:26s.  Time for last 1,000,000:    6s.  Last read position: chr22:17,680,141
INFO	2016-05-17 09:52:09	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:52:15	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:05:32s.  Time for last 1,000,000:    5s.  Last read position: chr22:46,470,926
INFO	2016-05-17 09:52:15	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:52:19	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:05:36s.  Time for last 1,000,000:    4s.  Last read position: chr2:28,033,924
INFO	2016-05-17 09:52:19	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:52:24	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:05:41s.  Time for last 1,000,000:    5s.  Last read position: chr2:68,051,011
INFO	2016-05-17 09:52:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:52:30	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:05:47s.  Time for last 1,000,000:    5s.  Last read position: chr2:113,999,845
INFO	2016-05-17 09:52:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:52:36	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:05:52s.  Time for last 1,000,000:    5s.  Last read position: chr2:157,194,681
INFO	2016-05-17 09:52:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:52:43	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:05:59s.  Time for last 1,000,000:    6s.  Last read position: chr2:202,399,028
INFO	2016-05-17 09:52:43	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:52:52	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:06:09s.  Time for last 1,000,000:    9s.  Last read position: chr2:239,747,607
INFO	2016-05-17 09:52:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:53:00	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:06:17s.  Time for last 1,000,000:    7s.  Last read position: chr3:34,253,544
INFO	2016-05-17 09:53:00	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:53:07	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:06:24s.  Time for last 1,000,000:    6s.  Last read position: chr3:69,490,364
INFO	2016-05-17 09:53:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:53:17	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:06:33s.  Time for last 1,000,000:    9s.  Last read position: chr3:120,597,397
INFO	2016-05-17 09:53:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:53:24	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:06:41s.  Time for last 1,000,000:    7s.  Last read position: chr3:159,531,892
INFO	2016-05-17 09:53:24	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 09:53:31	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:06:48s.  Time for last 1,000,000:    7s.  Last read position: chr4:2,010,801
INFO	2016-05-17 09:53:31	MarkDuplicates	Tracking 26 as yet unmatched pairs. 26 records in RAM.
INFO	2016-05-17 09:53:40	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:06:57s.  Time for last 1,000,000:    8s.  Last read position: chr4:41,805,270
INFO	2016-05-17 09:53:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:53:46	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:07:03s.  Time for last 1,000,000:    6s.  Last read position: chr4:92,028,027
INFO	2016-05-17 09:53:46	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:53:52	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:07:09s.  Time for last 1,000,000:    6s.  Last read position: chr4:140,998,771
INFO	2016-05-17 09:53:52	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 09:53:59	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:07:15s.  Time for last 1,000,000:    6s.  Last read position: chr4:187,591,965
INFO	2016-05-17 09:53:59	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:54:05	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:07:21s.  Time for last 1,000,000:    6s.  Last read position: chr5:40,022,871
INFO	2016-05-17 09:54:05	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:54:15	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:07:32s.  Time for last 1,000,000:   10s.  Last read position: chr5:90,175,393
INFO	2016-05-17 09:54:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:54:24	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:07:40s.  Time for last 1,000,000:    8s.  Last read position: chr5:134,260,229
INFO	2016-05-17 09:54:24	MarkDuplicates	Tracking 1072 as yet unmatched pairs. 1072 records in RAM.
INFO	2016-05-17 09:54:31	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:07:48s.  Time for last 1,000,000:    7s.  Last read position: chr5:165,879,714
INFO	2016-05-17 09:54:31	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:54:38	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:07:54s.  Time for last 1,000,000:    6s.  Last read position: chr6:20,034,736
INFO	2016-05-17 09:54:38	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:54:46	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:08:03s.  Time for last 1,000,000:    8s.  Last read position: chr6:55,543,946
INFO	2016-05-17 09:54:46	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:55:00	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:08:16s.  Time for last 1,000,000:   13s.  Last read position: chr6:107,610,150
INFO	2016-05-17 09:55:00	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:55:22	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:08:38s.  Time for last 1,000,000:   22s.  Last read position: chr6:151,506,977
INFO	2016-05-17 09:55:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:55:29	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:08:46s.  Time for last 1,000,000:    7s.  Last read position: chr7:18,414,247
INFO	2016-05-17 09:55:29	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:55:37	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:08:54s.  Time for last 1,000,000:    8s.  Last read position: chr7:64,421,768
INFO	2016-05-17 09:55:37	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:55:46	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:09:02s.  Time for last 1,000,000:    8s.  Last read position: chr7:107,122,054
INFO	2016-05-17 09:55:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:55:54	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:09:11s.  Time for last 1,000,000:    8s.  Last read position: chr7:150,516,505
INFO	2016-05-17 09:55:54	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:56:05	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:09:21s.  Time for last 1,000,000:   10s.  Last read position: chr8:29,039,274
INFO	2016-05-17 09:56:05	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:56:11	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:09:28s.  Time for last 1,000,000:    6s.  Last read position: chr8:74,218,314
INFO	2016-05-17 09:56:11	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:56:18	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:09:35s.  Time for last 1,000,000:    6s.  Last read position: chr8:119,911,878
INFO	2016-05-17 09:56:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:56:26	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:09:42s.  Time for last 1,000,000:    7s.  Last read position: chr9:9,283,192
INFO	2016-05-17 09:56:26	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:56:33	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:09:49s.  Time for last 1,000,000:    7s.  Last read position: chr9:84,079,179
INFO	2016-05-17 09:56:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 09:56:39	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:09:56s.  Time for last 1,000,000:    6s.  Last read position: chr9:123,287,764
INFO	2016-05-17 09:56:39	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 09:56:48	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:10:05s.  Time for last 1,000,000:    9s.  Last read position: chrM:97
INFO	2016-05-17 09:56:48	MarkDuplicates	Tracking 13520 as yet unmatched pairs. 13520 records in RAM.
INFO	2016-05-17 09:56:55	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:10:12s.  Time for last 1,000,000:    6s.  Last read position: chrM:521
INFO	2016-05-17 09:56:55	MarkDuplicates	Tracking 8444 as yet unmatched pairs. 8444 records in RAM.
INFO	2016-05-17 09:57:03	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:10:19s.  Time for last 1,000,000:    7s.  Last read position: chrM:857
INFO	2016-05-17 09:57:03	MarkDuplicates	Tracking 15732 as yet unmatched pairs. 15732 records in RAM.
INFO	2016-05-17 09:57:10	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:10:27s.  Time for last 1,000,000:    7s.  Last read position: chrM:1,476
INFO	2016-05-17 09:57:10	MarkDuplicates	Tracking 7488 as yet unmatched pairs. 7488 records in RAM.
INFO	2016-05-17 09:57:24	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:10:40s.  Time for last 1,000,000:   13s.  Last read position: chrM:2,018
INFO	2016-05-17 09:57:24	MarkDuplicates	Tracking 13392 as yet unmatched pairs. 13392 records in RAM.
INFO	2016-05-17 09:57:31	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:10:48s.  Time for last 1,000,000:    7s.  Last read position: chrM:2,619
INFO	2016-05-17 09:57:31	MarkDuplicates	Tracking 10402 as yet unmatched pairs. 10402 records in RAM.
INFO	2016-05-17 09:57:38	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:10:55s.  Time for last 1,000,000:    7s.  Last read position: chrM:2,933
INFO	2016-05-17 09:57:38	MarkDuplicates	Tracking 17242 as yet unmatched pairs. 17242 records in RAM.
INFO	2016-05-17 09:57:47	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:11:04s.  Time for last 1,000,000:    8s.  Last read position: chrM:3,271
INFO	2016-05-17 09:57:47	MarkDuplicates	Tracking 13294 as yet unmatched pairs. 13294 records in RAM.
INFO	2016-05-17 09:57:53	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:11:09s.  Time for last 1,000,000:    5s.  Last read position: chrM:3,510
INFO	2016-05-17 09:57:53	MarkDuplicates	Tracking 7966 as yet unmatched pairs. 7966 records in RAM.
INFO	2016-05-17 09:57:58	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:11:15s.  Time for last 1,000,000:    5s.  Last read position: chrM:3,735
INFO	2016-05-17 09:57:58	MarkDuplicates	Tracking 13308 as yet unmatched pairs. 13308 records in RAM.
INFO	2016-05-17 09:58:04	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:11:21s.  Time for last 1,000,000:    5s.  Last read position: chrM:4,300
INFO	2016-05-17 09:58:04	MarkDuplicates	Tracking 5352 as yet unmatched pairs. 5352 records in RAM.
INFO	2016-05-17 09:58:10	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:11:27s.  Time for last 1,000,000:    5s.  Last read position: chrM:5,104
INFO	2016-05-17 09:58:10	MarkDuplicates	Tracking 2676 as yet unmatched pairs. 2676 records in RAM.
INFO	2016-05-17 09:58:14	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:11:31s.  Time for last 1,000,000:    4s.  Last read position: chrM:5,998
INFO	2016-05-17 09:58:14	MarkDuplicates	Tracking 10204 as yet unmatched pairs. 10204 records in RAM.
INFO	2016-05-17 09:58:18	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:11:35s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,388
INFO	2016-05-17 09:58:18	MarkDuplicates	Tracking 6566 as yet unmatched pairs. 6566 records in RAM.
INFO	2016-05-17 09:58:24	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:11:40s.  Time for last 1,000,000:    5s.  Last read position: chrM:6,897
INFO	2016-05-17 09:58:24	MarkDuplicates	Tracking 4606 as yet unmatched pairs. 4606 records in RAM.
INFO	2016-05-17 09:58:28	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:11:45s.  Time for last 1,000,000:    4s.  Last read position: chrM:7,743
INFO	2016-05-17 09:58:28	MarkDuplicates	Tracking 4430 as yet unmatched pairs. 4430 records in RAM.
INFO	2016-05-17 09:58:34	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:11:51s.  Time for last 1,000,000:    5s.  Last read position: chrM:8,143
INFO	2016-05-17 09:58:34	MarkDuplicates	Tracking 9862 as yet unmatched pairs. 9862 records in RAM.
INFO	2016-05-17 09:58:41	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:11:58s.  Time for last 1,000,000:    7s.  Last read position: chrM:9,059
INFO	2016-05-17 09:58:41	MarkDuplicates	Tracking 2918 as yet unmatched pairs. 2918 records in RAM.
INFO	2016-05-17 09:58:49	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:12:05s.  Time for last 1,000,000:    7s.  Last read position: chrM:9,664
INFO	2016-05-17 09:58:49	MarkDuplicates	Tracking 19268 as yet unmatched pairs. 19268 records in RAM.
INFO	2016-05-17 09:59:12	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:12:29s.  Time for last 1,000,000:   23s.  Last read position: chrM:10,132
INFO	2016-05-17 09:59:12	MarkDuplicates	Tracking 19128 as yet unmatched pairs. 19128 records in RAM.
INFO	2016-05-17 09:59:19	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:12:36s.  Time for last 1,000,000:    6s.  Last read position: chrM:10,594
INFO	2016-05-17 09:59:19	MarkDuplicates	Tracking 4806 as yet unmatched pairs. 4806 records in RAM.
INFO	2016-05-17 09:59:25	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:12:42s.  Time for last 1,000,000:    6s.  Last read position: chrM:11,176
INFO	2016-05-17 09:59:25	MarkDuplicates	Tracking 8644 as yet unmatched pairs. 8644 records in RAM.
INFO	2016-05-17 09:59:32	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:12:49s.  Time for last 1,000,000:    7s.  Last read position: chrM:11,607
INFO	2016-05-17 09:59:32	MarkDuplicates	Tracking 528 as yet unmatched pairs. 528 records in RAM.
INFO	2016-05-17 09:59:38	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:12:55s.  Time for last 1,000,000:    5s.  Last read position: chrM:12,081
INFO	2016-05-17 09:59:38	MarkDuplicates	Tracking 6098 as yet unmatched pairs. 6098 records in RAM.
INFO	2016-05-17 09:59:44	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:13:00s.  Time for last 1,000,000:    5s.  Last read position: chrM:12,549
INFO	2016-05-17 09:59:44	MarkDuplicates	Tracking 13980 as yet unmatched pairs. 13980 records in RAM.
INFO	2016-05-17 09:59:50	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:13:06s.  Time for last 1,000,000:    5s.  Last read position: chrM:12,986
INFO	2016-05-17 09:59:50	MarkDuplicates	Tracking 10334 as yet unmatched pairs. 10334 records in RAM.
INFO	2016-05-17 09:59:55	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:13:11s.  Time for last 1,000,000:    5s.  Last read position: chrM:13,273
INFO	2016-05-17 09:59:55	MarkDuplicates	Tracking 10238 as yet unmatched pairs. 10238 records in RAM.
INFO	2016-05-17 10:00:00	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:13:17s.  Time for last 1,000,000:    5s.  Last read position: chrM:13,627
INFO	2016-05-17 10:00:00	MarkDuplicates	Tracking 14246 as yet unmatched pairs. 14246 records in RAM.
INFO	2016-05-17 10:00:06	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:13:23s.  Time for last 1,000,000:    5s.  Last read position: chrM:13,993
INFO	2016-05-17 10:00:06	MarkDuplicates	Tracking 23248 as yet unmatched pairs. 23248 records in RAM.
INFO	2016-05-17 10:00:16	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:13:32s.  Time for last 1,000,000:    9s.  Last read position: chrM:14,437
INFO	2016-05-17 10:00:16	MarkDuplicates	Tracking 1910 as yet unmatched pairs. 1910 records in RAM.
INFO	2016-05-17 10:00:22	MarkDuplicates	Read   100,000,000 records.  Elapsed time: 00:13:38s.  Time for last 1,000,000:    5s.  Last read position: chrM:15,031
INFO	2016-05-17 10:00:22	MarkDuplicates	Tracking 20924 as yet unmatched pairs. 20924 records in RAM.
INFO	2016-05-17 10:00:28	MarkDuplicates	Read   101,000,000 records.  Elapsed time: 00:13:45s.  Time for last 1,000,000:    6s.  Last read position: chrM:15,320
INFO	2016-05-17 10:00:28	MarkDuplicates	Tracking 16520 as yet unmatched pairs. 16520 records in RAM.
INFO	2016-05-17 10:00:36	MarkDuplicates	Read   102,000,000 records.  Elapsed time: 00:13:53s.  Time for last 1,000,000:    8s.  Last read position: chrM:15,597
INFO	2016-05-17 10:00:36	MarkDuplicates	Tracking 14796 as yet unmatched pairs. 14796 records in RAM.
INFO	2016-05-17 10:00:51	MarkDuplicates	Read   103,000,000 records.  Elapsed time: 00:14:08s.  Time for last 1,000,000:   15s.  Last read position: chrM:15,851
INFO	2016-05-17 10:00:51	MarkDuplicates	Tracking 22374 as yet unmatched pairs. 22374 records in RAM.
INFO	2016-05-17 10:00:58	MarkDuplicates	Read   104,000,000 records.  Elapsed time: 00:14:15s.  Time for last 1,000,000:    7s.  Last read position: chrM:16,359
INFO	2016-05-17 10:00:58	MarkDuplicates	Tracking 5764 as yet unmatched pairs. 5764 records in RAM.
INFO	2016-05-17 10:01:05	MarkDuplicates	Read   105,000,000 records.  Elapsed time: 00:14:21s.  Time for last 1,000,000:    6s.  Last read position: chrX:18,959,871
INFO	2016-05-17 10:01:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 10:01:12	MarkDuplicates	Read   106,000,000 records.  Elapsed time: 00:14:29s.  Time for last 1,000,000:    7s.  Last read position: chrX:67,876,146
INFO	2016-05-17 10:01:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 10:01:20	MarkDuplicates	Read   107,000,000 records.  Elapsed time: 00:14:36s.  Time for last 1,000,000:    7s.  Last read position: chrX:118,592,267
INFO	2016-05-17 10:01:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 10:01:27	MarkDuplicates	Read 107844960 records. 0 pairs never matched.
INFO	2016-05-17 10:01:32	MarkDuplicates	After buildSortedReadEndLists freeMemory: 3092267304; totalMemory: 3120562176; maxMemory: 3817865216
INFO	2016-05-17 10:01:32	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-05-17 10:01:32	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-05-17 10:01:55	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-05-17 10:02:20	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-05-17 10:02:22	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2176130992; totalMemory: 3158310912; maxMemory: 3817865216
INFO	2016-05-17 10:02:22	MarkDuplicates	Marking 47767166 records as duplicates.
INFO	2016-05-17 10:02:22	MarkDuplicates	Found 19774167 optical duplicate clusters.
INFO	2016-05-17 10:04:40	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:02:16s.  Time for last 10,000,000:  136s.  Last read position: chr12:121,721,031
INFO	2016-05-17 10:07:14	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:04:50s.  Time for last 10,000,000:  153s.  Last read position: chr17:25,667,348
INFO	2016-05-17 10:09:24	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:07:00s.  Time for last 10,000,000:  129s.  Last read position: chr1:165,816,340
INFO	2016-05-17 10:11:19	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:08:54s.  Time for last 10,000,000:  114s.  Last read position: chr2:157,194,681
INFO	2016-05-17 10:13:38	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:11:14s.  Time for last 10,000,000:  139s.  Last read position: chr4:140,998,771
INFO	2016-05-17 10:16:13	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:13:48s.  Time for last 10,000,000:  154s.  Last read position: chr7:18,414,247
INFO	2016-05-17 10:18:55	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:16:30s.  Time for last 10,000,000:  162s.  Last read position: chrM:97
INFO	2016-05-17 10:21:06	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:18:41s.  Time for last 10,000,000:  130s.  Last read position: chrM:4,300
INFO	2016-05-17 10:23:12	MarkDuplicates	Written    90,000,000 records.  Elapsed time: 00:20:47s.  Time for last 10,000,000:  125s.  Last read position: chrM:10,594
INFO	2016-05-17 10:25:16	MarkDuplicates	Written   100,000,000 records.  Elapsed time: 00:22:51s.  Time for last 10,000,000:  123s.  Last read position: chrM:15,031
INFO	2016-05-17 10:27:09	MarkDuplicates	Before output close freeMemory: 3198077632; totalMemory: 3228565504; maxMemory: 3817865216
INFO	2016-05-17 10:27:09	MarkDuplicates	After output close freeMemory: 3198076576; totalMemory: 3228565504; maxMemory: 3817865216
[Tue May 17 10:27:09 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 40.47 minutes.
Runtime.totalMemory()=3228565504
[bam_sort_core] merging from 78 files...

Num	13
ID	task.postalign_bam.nmsrt_bam_rep1.line_321.id_18
Name	nmsrt_bam rep1
Thread	thread_20
PID	52364

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

Start	2016-05-17 11:55:55
End	2016-05-17 12:30:05
Elapsed	00:34:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-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/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-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 43 files...

Num	14
ID	task.postalign_bam.bam_to_bedpe_rep1.line_425.id_19
Name	bam_to_bedpe rep1
Thread	thread_20
PID	53111

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

Start	2016-05-17 12:30:05
End	2016-05-17 12:33:53
Elapsed	00:03:47
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-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/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-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	15
ID	task.postalign_bed.subsample_bedpe_rep1.line_116.id_20
Name	subsample_bedpe rep1
Thread	thread_20
PID	53640

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

Start	2016-05-17 12:33:54
End	2016-05-17 12:36:02
Elapsed	00:02:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-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/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | grep -v "chrM" | shuf -n 17500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-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	16
ID	task.postalign_bam.bedpe_to_tag_rep1.line_465.id_21
Name	bedpe_to_tag rep1
Thread	thread_20
PID	53776

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

Start	2016-05-17 12:36:03
End	2016-05-17 12:37:45
Elapsed	00:01:42
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-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/ATAC19+20/align/rep1/ATAC19-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/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz

# SYS command. line 472

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz | grep -P -v 'chrM' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz; mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-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	17
ID	task.postalign_bed.shift_tag_rep1.line_140.id_22
Name	shift_tag rep1
Thread	thread_20
PID	54103

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

Start	2016-05-17 12:37:46
End	2016-05-17 12:38:54
Elapsed	00:01:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-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/ATAC19+20/align/rep1/ATAC19-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/ATAC19+20/align/rep1/ATAC19-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	18
ID	task.postalign_bed.subsample_bedpe2tagrep1.line_89.id_23
Name	subsample_bedpe2tagrep1
Thread	thread_20
PID	54185

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

Start	2016-05-17 12:38:55
End	2016-05-17 12:40:43
Elapsed	00:01:48
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-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/ATAC19+20/align/rep1/ATAC19-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/ATAC19+20/align/rep1/ATAC19-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	19
ID	task.postalign_bed.xcor_rep1.line_165.id_24
Name	xcor rep1
Thread	thread_20
PID	54280

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

Start	2016-05-17 12:40:44
End	2016-05-17 13:20:56
Elapsed	00:40:12
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep1/ATAC19-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/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz -p=1 \
			-filtchr=chrM -savp=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf -out=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep1/ATAC19-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/ATAC19+20/qc/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp

# SYS command. line 175

 mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc

   
--------------------Stdout--------------------
################
ChIP data: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-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/ATAC19+20/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/ATAC19+20/qc/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf 
result filename: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep1/ATAC19-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/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz 
opened /tmp/RtmpMc8LX2/ATAC19-trimmed-pair1.trim.PE2SE.nodup.25.tagAlignd4b34145af06
done. read 25000000 fragments
ChIP data read length 70 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.2487734 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.261558288052601 
Top 3 estimates for fragment length 0 
Window half size 520 
Phantom peak location 60 
Phantom peak Correlation 0.262241 
Normalized Strand cross-correlation coefficient (NSC) 1.051392 
Relative Strand Cross correlation Coefficient (RSC) 0.9493101 
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	20
ID	task.callpeak_macs2.macs2_atac_rep1.pval0.1.line_192.id_25
Name	macs2_atac rep1.pval0.1
Thread	thread_20
PID	54282

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

Start	2016-05-17 12:40:44
End	2016-05-17 13:00:04
Elapsed	00:19:20
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/signal/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/signal/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-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  @ Tue, 17 May 2016 12:40:50: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-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  @ Tue, 17 May 2016 12:40:50: #1 read tag files... 
INFO  @ Tue, 17 May 2016 12:40:50: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 12:40:53:  1000000 
INFO  @ Tue, 17 May 2016 12:40:55:  2000000 
INFO  @ Tue, 17 May 2016 12:40:57:  3000000 
INFO  @ Tue, 17 May 2016 12:40:58:  4000000 
INFO  @ Tue, 17 May 2016 12:41:00:  5000000 
INFO  @ Tue, 17 May 2016 12:41:02:  6000000 
INFO  @ Tue, 17 May 2016 12:41:04:  7000000 
INFO  @ Tue, 17 May 2016 12:41:06:  8000000 
INFO  @ Tue, 17 May 2016 12:41:07:  9000000 
INFO  @ Tue, 17 May 2016 12:41:09:  10000000 
INFO  @ Tue, 17 May 2016 12:41:11:  11000000 
INFO  @ Tue, 17 May 2016 12:41:14:  12000000 
INFO  @ Tue, 17 May 2016 12:41:17:  13000000 
INFO  @ Tue, 17 May 2016 12:41:18:  14000000 
INFO  @ Tue, 17 May 2016 12:41:20:  15000000 
INFO  @ Tue, 17 May 2016 12:41:22:  16000000 
INFO  @ Tue, 17 May 2016 12:41:23:  17000000 
INFO  @ Tue, 17 May 2016 12:41:25:  18000000 
INFO  @ Tue, 17 May 2016 12:41:27:  19000000 
INFO  @ Tue, 17 May 2016 12:41:28:  20000000 
INFO  @ Tue, 17 May 2016 12:41:30:  21000000 
INFO  @ Tue, 17 May 2016 12:41:32:  22000000 
INFO  @ Tue, 17 May 2016 12:41:33:  23000000 
INFO  @ Tue, 17 May 2016 12:41:35:  24000000 
INFO  @ Tue, 17 May 2016 12:41:37:  25000000 
INFO  @ Tue, 17 May 2016 12:41:39:  26000000 
INFO  @ Tue, 17 May 2016 12:41:41:  27000000 
INFO  @ Tue, 17 May 2016 12:41:43:  28000000 
INFO  @ Tue, 17 May 2016 12:41:44:  29000000 
INFO  @ Tue, 17 May 2016 12:41:46:  30000000 
INFO  @ Tue, 17 May 2016 12:41:48:  31000000 
INFO  @ Tue, 17 May 2016 12:41:50:  32000000 
INFO  @ Tue, 17 May 2016 12:41:51:  33000000 
INFO  @ Tue, 17 May 2016 12:41:53:  34000000 
INFO  @ Tue, 17 May 2016 12:41:55:  35000000 
INFO  @ Tue, 17 May 2016 12:41:58: #1 tag size is determined as 59 bps 
INFO  @ Tue, 17 May 2016 12:41:58: #1 tag size = 59 
INFO  @ Tue, 17 May 2016 12:41:58: #1  total tags in treatment: 35000000 
INFO  @ Tue, 17 May 2016 12:41:58: #1 finished! 
INFO  @ Tue, 17 May 2016 12:41:58: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 12:41:58: #2 Skipped... 
INFO  @ Tue, 17 May 2016 12:41:58: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 12:41:58: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 12:41:58: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 12:41:58: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 12:41:58: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 12:43:17: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 12:46:05: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 12:46:10: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 12:46:12: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 12:46:15: Done! 
INFO  @ Tue, 17 May 2016 12:46:33: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-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  @ Tue, 17 May 2016 12:46:33: #1 read tag files... 
INFO  @ Tue, 17 May 2016 12:46:33: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 12:46:35:  1000000 
INFO  @ Tue, 17 May 2016 12:46:37:  2000000 
INFO  @ Tue, 17 May 2016 12:46:39:  3000000 
INFO  @ Tue, 17 May 2016 12:46:41:  4000000 
INFO  @ Tue, 17 May 2016 12:46:42:  5000000 
INFO  @ Tue, 17 May 2016 12:46:45:  6000000 
INFO  @ Tue, 17 May 2016 12:46:47:  7000000 
INFO  @ Tue, 17 May 2016 12:46:48:  8000000 
INFO  @ Tue, 17 May 2016 12:46:50:  9000000 
INFO  @ Tue, 17 May 2016 12:46:52:  10000000 
INFO  @ Tue, 17 May 2016 12:46:53:  11000000 
INFO  @ Tue, 17 May 2016 12:46:55:  12000000 
INFO  @ Tue, 17 May 2016 12:46:57:  13000000 
INFO  @ Tue, 17 May 2016 12:46:59:  14000000 
INFO  @ Tue, 17 May 2016 12:47:00:  15000000 
INFO  @ Tue, 17 May 2016 12:47:02:  16000000 
INFO  @ Tue, 17 May 2016 12:47:04:  17000000 
INFO  @ Tue, 17 May 2016 12:47:06:  18000000 
INFO  @ Tue, 17 May 2016 12:47:08:  19000000 
INFO  @ Tue, 17 May 2016 12:47:10:  20000000 
INFO  @ Tue, 17 May 2016 12:47:11:  21000000 
INFO  @ Tue, 17 May 2016 12:47:14:  22000000 
INFO  @ Tue, 17 May 2016 12:47:15:  23000000 
INFO  @ Tue, 17 May 2016 12:47:17:  24000000 
INFO  @ Tue, 17 May 2016 12:47:19:  25000000 
INFO  @ Tue, 17 May 2016 12:47:21:  26000000 
INFO  @ Tue, 17 May 2016 12:47:23:  27000000 
INFO  @ Tue, 17 May 2016 12:47:24:  28000000 
INFO  @ Tue, 17 May 2016 12:47:26:  29000000 
INFO  @ Tue, 17 May 2016 12:47:28:  30000000 
INFO  @ Tue, 17 May 2016 12:47:30:  31000000 
INFO  @ Tue, 17 May 2016 12:47:31:  32000000 
INFO  @ Tue, 17 May 2016 12:47:33:  33000000 
INFO  @ Tue, 17 May 2016 12:47:37:  34000000 
INFO  @ Tue, 17 May 2016 12:47:39:  35000000 
INFO  @ Tue, 17 May 2016 12:47:41: #1 tag size is determined as 59 bps 
INFO  @ Tue, 17 May 2016 12:47:41: #1 tag size = 59 
INFO  @ Tue, 17 May 2016 12:47:41: #1  total tags in treatment: 35000000 
INFO  @ Tue, 17 May 2016 12:47:41: #1 finished! 
INFO  @ Tue, 17 May 2016 12:47:41: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 12:47:41: #2 Skipped... 
INFO  @ Tue, 17 May 2016 12:47:41: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 12:47:41: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 12:47:41: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 12:47:41: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 12:47:41: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Tue, 17 May 2016 12:47:41: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 12:49:04: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 12:49:04: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 12:49:04: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 12:49:04: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 12:49:04: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 12:59:36: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 12:59:45: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 12:59:51: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_summits.bed 
INFO  @ Tue, 17 May 2016 12:59:54: Done!

Num	21
ID	task.callpeak_macs2.macs2_atac_rep1.line_192.id_26
Name	macs2_atac rep1
Thread	thread_20
PID	54293

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

Start	2016-05-17 12:40:44
End	2016-05-17 13:25:28
Elapsed	00:44:43
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.gappedPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/signal/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/signal/macs2/rep1/ATAC19-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/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/signal/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/signal/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-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  @ Tue, 17 May 2016 12:40:50: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-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  @ Tue, 17 May 2016 12:40:50: #1 read tag files... 
INFO  @ Tue, 17 May 2016 12:40:50: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 12:40:53:  1000000 
INFO  @ Tue, 17 May 2016 12:40:55:  2000000 
INFO  @ Tue, 17 May 2016 12:40:57:  3000000 
INFO  @ Tue, 17 May 2016 12:40:59:  4000000 
INFO  @ Tue, 17 May 2016 12:41:00:  5000000 
INFO  @ Tue, 17 May 2016 12:41:02:  6000000 
INFO  @ Tue, 17 May 2016 12:41:04:  7000000 
INFO  @ Tue, 17 May 2016 12:41:06:  8000000 
INFO  @ Tue, 17 May 2016 12:41:07:  9000000 
INFO  @ Tue, 17 May 2016 12:41:09:  10000000 
INFO  @ Tue, 17 May 2016 12:41:11:  11000000 
INFO  @ Tue, 17 May 2016 12:41:14:  12000000 
INFO  @ Tue, 17 May 2016 12:41:17:  13000000 
INFO  @ Tue, 17 May 2016 12:41:19:  14000000 
INFO  @ Tue, 17 May 2016 12:41:20:  15000000 
INFO  @ Tue, 17 May 2016 12:41:22:  16000000 
INFO  @ Tue, 17 May 2016 12:41:23:  17000000 
INFO  @ Tue, 17 May 2016 12:41:25:  18000000 
INFO  @ Tue, 17 May 2016 12:41:27:  19000000 
INFO  @ Tue, 17 May 2016 12:41:28:  20000000 
INFO  @ Tue, 17 May 2016 12:41:30:  21000000 
INFO  @ Tue, 17 May 2016 12:41:32:  22000000 
INFO  @ Tue, 17 May 2016 12:41:33:  23000000 
INFO  @ Tue, 17 May 2016 12:41:35:  24000000 
INFO  @ Tue, 17 May 2016 12:41:37:  25000000 
INFO  @ Tue, 17 May 2016 12:41:39:  26000000 
INFO  @ Tue, 17 May 2016 12:41:41:  27000000 
INFO  @ Tue, 17 May 2016 12:41:43:  28000000 
INFO  @ Tue, 17 May 2016 12:41:44:  29000000 
INFO  @ Tue, 17 May 2016 12:41:46:  30000000 
INFO  @ Tue, 17 May 2016 12:41:48:  31000000 
INFO  @ Tue, 17 May 2016 12:41:50:  32000000 
INFO  @ Tue, 17 May 2016 12:41:51:  33000000 
INFO  @ Tue, 17 May 2016 12:41:53:  34000000 
INFO  @ Tue, 17 May 2016 12:41:55:  35000000 
INFO  @ Tue, 17 May 2016 12:41:58: #1 tag size is determined as 59 bps 
INFO  @ Tue, 17 May 2016 12:41:58: #1 tag size = 59 
INFO  @ Tue, 17 May 2016 12:41:58: #1  total tags in treatment: 35000000 
INFO  @ Tue, 17 May 2016 12:41:58: #1 finished! 
INFO  @ Tue, 17 May 2016 12:41:58: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 12:41:58: #2 Skipped... 
INFO  @ Tue, 17 May 2016 12:41:58: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 12:41:58: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 12:41:58: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 12:41:58: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 12:41:58: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 12:43:15: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 12:45:31: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls 
INFO  @ Tue, 17 May 2016 12:45:35: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 12:45:38: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 12:45:41: Done! 
INFO  @ Tue, 17 May 2016 12:46:03: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-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  @ Tue, 17 May 2016 12:46:03: #1 read tag files... 
INFO  @ Tue, 17 May 2016 12:46:03: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 12:46:05:  1000000 
INFO  @ Tue, 17 May 2016 12:46:08:  2000000 
INFO  @ Tue, 17 May 2016 12:46:10:  3000000 
INFO  @ Tue, 17 May 2016 12:46:12:  4000000 
INFO  @ Tue, 17 May 2016 12:46:14:  5000000 
INFO  @ Tue, 17 May 2016 12:46:17:  6000000 
INFO  @ Tue, 17 May 2016 12:46:19:  7000000 
INFO  @ Tue, 17 May 2016 12:46:22:  8000000 
INFO  @ Tue, 17 May 2016 12:46:24:  9000000 
INFO  @ Tue, 17 May 2016 12:46:26:  10000000 
INFO  @ Tue, 17 May 2016 12:46:29:  11000000 
INFO  @ Tue, 17 May 2016 12:46:31:  12000000 
INFO  @ Tue, 17 May 2016 12:46:33:  13000000 
INFO  @ Tue, 17 May 2016 12:46:35:  14000000 
INFO  @ Tue, 17 May 2016 12:46:37:  15000000 
INFO  @ Tue, 17 May 2016 12:46:39:  16000000 
INFO  @ Tue, 17 May 2016 12:46:41:  17000000 
INFO  @ Tue, 17 May 2016 12:46:43:  18000000 
INFO  @ Tue, 17 May 2016 12:46:46:  19000000 
INFO  @ Tue, 17 May 2016 12:46:48:  20000000 
INFO  @ Tue, 17 May 2016 12:46:50:  21000000 
INFO  @ Tue, 17 May 2016 12:46:52:  22000000 
INFO  @ Tue, 17 May 2016 12:46:54:  23000000 
INFO  @ Tue, 17 May 2016 12:46:57:  24000000 
INFO  @ Tue, 17 May 2016 12:46:59:  25000000 
INFO  @ Tue, 17 May 2016 12:47:01:  26000000 
INFO  @ Tue, 17 May 2016 12:47:03:  27000000 
INFO  @ Tue, 17 May 2016 12:47:04:  28000000 
INFO  @ Tue, 17 May 2016 12:47:07:  29000000 
INFO  @ Tue, 17 May 2016 12:47:09:  30000000 
INFO  @ Tue, 17 May 2016 12:47:11:  31000000 
INFO  @ Tue, 17 May 2016 12:47:13:  32000000 
INFO  @ Tue, 17 May 2016 12:47:15:  33000000 
INFO  @ Tue, 17 May 2016 12:47:17:  34000000 
INFO  @ Tue, 17 May 2016 12:47:19:  35000000 
INFO  @ Tue, 17 May 2016 12:47:22: #1 tag size is determined as 59 bps 
INFO  @ Tue, 17 May 2016 12:47:22: #1 tag size = 59 
INFO  @ Tue, 17 May 2016 12:47:22: #1  total tags in treatment: 35000000 
INFO  @ Tue, 17 May 2016 12:47:22: #1 finished! 
INFO  @ Tue, 17 May 2016 12:47:22: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 12:47:22: #2 Skipped... 
INFO  @ Tue, 17 May 2016 12:47:22: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 12:47:22: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 12:47:22: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 12:47:22: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 12:47:22: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Tue, 17 May 2016 12:47:22: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 12:48:43: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 12:48:43: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 12:48:43: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 12:48:43: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 12:48:43: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 12:54:15: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls 
INFO  @ Tue, 17 May 2016 12:54:17: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 12:54:18: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_summits.bed 
INFO  @ Tue, 17 May 2016 12:54:19: Done! 
INFO  @ Tue, 17 May 2016 12:54:25: Read and build treatment bedGraph... 
INFO  @ Tue, 17 May 2016 12:56:00: Read and build control bedGraph... 
INFO  @ Tue, 17 May 2016 12:56:37: Build scoreTrackII... 
INFO  @ Tue, 17 May 2016 12:57:10: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Tue, 17 May 2016 13:01:17: Write bedGraph of scores... 
INFO  @ Tue, 17 May 2016 13:03:45: Finished 'FE'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_FE.bdg'! 
INFO  @ Tue, 17 May 2016 13:09:38: Read and build treatment bedGraph... 
INFO  @ Tue, 17 May 2016 13:10:58: Read and build control bedGraph... 
INFO  @ Tue, 17 May 2016 13:11:37: Build scoreTrackII... 
INFO  @ Tue, 17 May 2016 13:12:04: Values in your input bedGraph files will be multiplied by 35.000000 ... 
INFO  @ Tue, 17 May 2016 13:16:23: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Tue, 17 May 2016 13:16:54: Write bedGraph of scores... 
INFO  @ Tue, 17 May 2016 13:19:15: Finished 'ppois'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_ppois.bdg'!

Num	22
ID	task.postalign_bed.pool_tag_reps.line_405.id_27
Name	pool_tag reps
Thread	thread_Root
PID	56993

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

Start	2016-05-17 13:25:29
End	2016-05-17 13:27:30
Elapsed	00:02:01
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/pooled_rep/ATAC19-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/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz  | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/pooled_rep/ATAC19-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	23
ID	task.callpeak_macs2.macs2_atac_pooled.pval0.1.line_192.id_28
Name	macs2_atac pooled.pval0.1
Thread	thread_Root
PID	57138

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

Start	2016-05-17 13:27:31
End	2016-05-17 14:04:37
Elapsed	00:37:05
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/align/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/align/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/signal/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/align/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/signal/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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  @ Tue, 17 May 2016 13:27:37: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/align/pooled_rep/ATAC19-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  @ Tue, 17 May 2016 13:27:37: #1 read tag files... 
INFO  @ Tue, 17 May 2016 13:27:37: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 13:27:40:  1000000 
INFO  @ Tue, 17 May 2016 13:27:44:  2000000 
INFO  @ Tue, 17 May 2016 13:27:48:  3000000 
INFO  @ Tue, 17 May 2016 13:27:51:  4000000 
INFO  @ Tue, 17 May 2016 13:27:55:  5000000 
INFO  @ Tue, 17 May 2016 13:27:58:  6000000 
INFO  @ Tue, 17 May 2016 13:28:02:  7000000 
INFO  @ Tue, 17 May 2016 13:28:05:  8000000 
INFO  @ Tue, 17 May 2016 13:28:09:  9000000 
INFO  @ Tue, 17 May 2016 13:28:12:  10000000 
INFO  @ Tue, 17 May 2016 13:28:16:  11000000 
INFO  @ Tue, 17 May 2016 13:28:19:  12000000 
INFO  @ Tue, 17 May 2016 13:28:22:  13000000 
INFO  @ Tue, 17 May 2016 13:28:25:  14000000 
INFO  @ Tue, 17 May 2016 13:28:27:  15000000 
INFO  @ Tue, 17 May 2016 13:28:29:  16000000 
INFO  @ Tue, 17 May 2016 13:28:31:  17000000 
INFO  @ Tue, 17 May 2016 13:28:33:  18000000 
INFO  @ Tue, 17 May 2016 13:28:36:  19000000 
INFO  @ Tue, 17 May 2016 13:28:38:  20000000 
INFO  @ Tue, 17 May 2016 13:28:40:  21000000 
INFO  @ Tue, 17 May 2016 13:28:41:  22000000 
INFO  @ Tue, 17 May 2016 13:28:43:  23000000 
INFO  @ Tue, 17 May 2016 13:28:45:  24000000 
INFO  @ Tue, 17 May 2016 13:28:46:  25000000 
INFO  @ Tue, 17 May 2016 13:28:48:  26000000 
INFO  @ Tue, 17 May 2016 13:28:50:  27000000 
INFO  @ Tue, 17 May 2016 13:28:51:  28000000 
INFO  @ Tue, 17 May 2016 13:28:53:  29000000 
INFO  @ Tue, 17 May 2016 13:28:54:  30000000 
INFO  @ Tue, 17 May 2016 13:28:56:  31000000 
INFO  @ Tue, 17 May 2016 13:28:58:  32000000 
INFO  @ Tue, 17 May 2016 13:28:59:  33000000 
INFO  @ Tue, 17 May 2016 13:29:01:  34000000 
INFO  @ Tue, 17 May 2016 13:29:03:  35000000 
INFO  @ Tue, 17 May 2016 13:29:04:  36000000 
INFO  @ Tue, 17 May 2016 13:29:06:  37000000 
INFO  @ Tue, 17 May 2016 13:29:07:  38000000 
INFO  @ Tue, 17 May 2016 13:29:09:  39000000 
INFO  @ Tue, 17 May 2016 13:29:11:  40000000 
INFO  @ Tue, 17 May 2016 13:29:12:  41000000 
INFO  @ Tue, 17 May 2016 13:29:14:  42000000 
INFO  @ Tue, 17 May 2016 13:29:16:  43000000 
INFO  @ Tue, 17 May 2016 13:29:17:  44000000 
INFO  @ Tue, 17 May 2016 13:29:19:  45000000 
INFO  @ Tue, 17 May 2016 13:29:20:  46000000 
INFO  @ Tue, 17 May 2016 13:29:22:  47000000 
INFO  @ Tue, 17 May 2016 13:29:24:  48000000 
INFO  @ Tue, 17 May 2016 13:29:25:  49000000 
INFO  @ Tue, 17 May 2016 13:29:27:  50000000 
INFO  @ Tue, 17 May 2016 13:29:28:  51000000 
INFO  @ Tue, 17 May 2016 13:29:30:  52000000 
INFO  @ Tue, 17 May 2016 13:29:32:  53000000 
INFO  @ Tue, 17 May 2016 13:29:33:  54000000 
INFO  @ Tue, 17 May 2016 13:29:35:  55000000 
INFO  @ Tue, 17 May 2016 13:29:37:  56000000 
INFO  @ Tue, 17 May 2016 13:29:38:  57000000 
INFO  @ Tue, 17 May 2016 13:29:40:  58000000 
INFO  @ Tue, 17 May 2016 13:29:41:  59000000 
INFO  @ Tue, 17 May 2016 13:29:43:  60000000 
INFO  @ Tue, 17 May 2016 13:29:45:  61000000 
INFO  @ Tue, 17 May 2016 13:29:46:  62000000 
INFO  @ Tue, 17 May 2016 13:29:48:  63000000 
INFO  @ Tue, 17 May 2016 13:29:53: #1 tag size is determined as 59 bps 
INFO  @ Tue, 17 May 2016 13:29:53: #1 tag size = 59 
INFO  @ Tue, 17 May 2016 13:29:53: #1  total tags in treatment: 63275586 
INFO  @ Tue, 17 May 2016 13:29:53: #1 finished! 
INFO  @ Tue, 17 May 2016 13:29:53: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 13:29:53: #2 Skipped... 
INFO  @ Tue, 17 May 2016 13:29:53: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 13:29:53: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 13:29:53: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 13:29:53: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 13:29:53: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 13:31:52: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 13:35:32: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 13:35:35: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 13:35:37: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 13:35:39: Done! 
INFO  @ Tue, 17 May 2016 13:35:49: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/align/pooled_rep/ATAC19-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  @ Tue, 17 May 2016 13:35:49: #1 read tag files... 
INFO  @ Tue, 17 May 2016 13:35:49: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 13:35:50:  1000000 
INFO  @ Tue, 17 May 2016 13:35:52:  2000000 
INFO  @ Tue, 17 May 2016 13:35:54:  3000000 
INFO  @ Tue, 17 May 2016 13:35:55:  4000000 
INFO  @ Tue, 17 May 2016 13:35:57:  5000000 
INFO  @ Tue, 17 May 2016 13:35:58:  6000000 
INFO  @ Tue, 17 May 2016 13:36:00:  7000000 
INFO  @ Tue, 17 May 2016 13:36:02:  8000000 
INFO  @ Tue, 17 May 2016 13:36:03:  9000000 
INFO  @ Tue, 17 May 2016 13:36:05:  10000000 
INFO  @ Tue, 17 May 2016 13:36:06:  11000000 
INFO  @ Tue, 17 May 2016 13:36:08:  12000000 
INFO  @ Tue, 17 May 2016 13:36:09:  13000000 
INFO  @ Tue, 17 May 2016 13:36:11:  14000000 
INFO  @ Tue, 17 May 2016 13:36:13:  15000000 
INFO  @ Tue, 17 May 2016 13:36:14:  16000000 
INFO  @ Tue, 17 May 2016 13:36:16:  17000000 
INFO  @ Tue, 17 May 2016 13:36:17:  18000000 
INFO  @ Tue, 17 May 2016 13:36:19:  19000000 
INFO  @ Tue, 17 May 2016 13:36:21:  20000000 
INFO  @ Tue, 17 May 2016 13:36:22:  21000000 
INFO  @ Tue, 17 May 2016 13:36:24:  22000000 
INFO  @ Tue, 17 May 2016 13:36:25:  23000000 
INFO  @ Tue, 17 May 2016 13:36:27:  24000000 
INFO  @ Tue, 17 May 2016 13:36:28:  25000000 
INFO  @ Tue, 17 May 2016 13:36:30:  26000000 
INFO  @ Tue, 17 May 2016 13:36:32:  27000000 
INFO  @ Tue, 17 May 2016 13:36:33:  28000000 
INFO  @ Tue, 17 May 2016 13:36:35:  29000000 
INFO  @ Tue, 17 May 2016 13:36:36:  30000000 
INFO  @ Tue, 17 May 2016 13:36:38:  31000000 
INFO  @ Tue, 17 May 2016 13:36:40:  32000000 
INFO  @ Tue, 17 May 2016 13:36:41:  33000000 
INFO  @ Tue, 17 May 2016 13:36:43:  34000000 
INFO  @ Tue, 17 May 2016 13:36:44:  35000000 
INFO  @ Tue, 17 May 2016 13:36:46:  36000000 
INFO  @ Tue, 17 May 2016 13:36:47:  37000000 
INFO  @ Tue, 17 May 2016 13:36:49:  38000000 
INFO  @ Tue, 17 May 2016 13:36:51:  39000000 
INFO  @ Tue, 17 May 2016 13:36:52:  40000000 
INFO  @ Tue, 17 May 2016 13:36:54:  41000000 
INFO  @ Tue, 17 May 2016 13:36:55:  42000000 
INFO  @ Tue, 17 May 2016 13:36:57:  43000000 
INFO  @ Tue, 17 May 2016 13:36:59:  44000000 
INFO  @ Tue, 17 May 2016 13:37:00:  45000000 
INFO  @ Tue, 17 May 2016 13:37:02:  46000000 
INFO  @ Tue, 17 May 2016 13:37:03:  47000000 
INFO  @ Tue, 17 May 2016 13:37:05:  48000000 
INFO  @ Tue, 17 May 2016 13:37:06:  49000000 
INFO  @ Tue, 17 May 2016 13:37:08:  50000000 
INFO  @ Tue, 17 May 2016 13:37:10:  51000000 
INFO  @ Tue, 17 May 2016 13:37:11:  52000000 
INFO  @ Tue, 17 May 2016 13:37:13:  53000000 
INFO  @ Tue, 17 May 2016 13:37:15:  54000000 
INFO  @ Tue, 17 May 2016 13:37:16:  55000000 
INFO  @ Tue, 17 May 2016 13:37:18:  56000000 
INFO  @ Tue, 17 May 2016 13:37:19:  57000000 
INFO  @ Tue, 17 May 2016 13:37:21:  58000000 
INFO  @ Tue, 17 May 2016 13:37:23:  59000000 
INFO  @ Tue, 17 May 2016 13:37:24:  60000000 
INFO  @ Tue, 17 May 2016 13:37:26:  61000000 
INFO  @ Tue, 17 May 2016 13:37:27:  62000000 
INFO  @ Tue, 17 May 2016 13:37:29:  63000000 
INFO  @ Tue, 17 May 2016 13:37:34: #1 tag size is determined as 59 bps 
INFO  @ Tue, 17 May 2016 13:37:34: #1 tag size = 59 
INFO  @ Tue, 17 May 2016 13:37:34: #1  total tags in treatment: 63275586 
INFO  @ Tue, 17 May 2016 13:37:34: #1 finished! 
INFO  @ Tue, 17 May 2016 13:37:34: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 13:37:34: #2 Skipped... 
INFO  @ Tue, 17 May 2016 13:37:34: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 13:37:34: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 13:37:34: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 13:37:34: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 13:37:34: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Tue, 17 May 2016 13:37:34: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 13:40:34: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 13:40:34: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 13:40:34: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 13:40:34: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 13:40:34: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 14:04:01: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 14:04:12: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 14:04:22: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_summits.bed 
INFO  @ Tue, 17 May 2016 14:04:28: Done!

Num	24
ID	task.callpeak_macs2.macs2_atac_pooled.line_192.id_29
Name	macs2_atac pooled
Thread	thread_Root
PID	57144

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

Start	2016-05-17 13:27:31
End	2016-05-17 15:00:06
Elapsed	01:32:35
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.gappedPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/signal/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/signal/macs2/pooled_rep/ATAC19-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/ATAC19+20/align/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/align/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/signal/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/align/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/signal/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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  @ Tue, 17 May 2016 13:27:37: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/pooled_rep/ATAC19-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  @ Tue, 17 May 2016 13:27:37: #1 read tag files... 
INFO  @ Tue, 17 May 2016 13:27:37: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 13:27:41:  1000000 
INFO  @ Tue, 17 May 2016 13:27:44:  2000000 
INFO  @ Tue, 17 May 2016 13:27:48:  3000000 
INFO  @ Tue, 17 May 2016 13:27:52:  4000000 
INFO  @ Tue, 17 May 2016 13:27:55:  5000000 
INFO  @ Tue, 17 May 2016 13:27:59:  6000000 
INFO  @ Tue, 17 May 2016 13:28:02:  7000000 
INFO  @ Tue, 17 May 2016 13:28:06:  8000000 
INFO  @ Tue, 17 May 2016 13:28:10:  9000000 
INFO  @ Tue, 17 May 2016 13:28:13:  10000000 
INFO  @ Tue, 17 May 2016 13:28:17:  11000000 
INFO  @ Tue, 17 May 2016 13:28:20:  12000000 
INFO  @ Tue, 17 May 2016 13:28:23:  13000000 
INFO  @ Tue, 17 May 2016 13:28:26:  14000000 
INFO  @ Tue, 17 May 2016 13:28:28:  15000000 
INFO  @ Tue, 17 May 2016 13:28:30:  16000000 
INFO  @ Tue, 17 May 2016 13:28:32:  17000000 
INFO  @ Tue, 17 May 2016 13:28:35:  18000000 
INFO  @ Tue, 17 May 2016 13:28:38:  19000000 
INFO  @ Tue, 17 May 2016 13:28:40:  20000000 
INFO  @ Tue, 17 May 2016 13:28:42:  21000000 
INFO  @ Tue, 17 May 2016 13:28:44:  22000000 
INFO  @ Tue, 17 May 2016 13:28:45:  23000000 
INFO  @ Tue, 17 May 2016 13:28:47:  24000000 
INFO  @ Tue, 17 May 2016 13:28:48:  25000000 
INFO  @ Tue, 17 May 2016 13:28:50:  26000000 
INFO  @ Tue, 17 May 2016 13:28:52:  27000000 
INFO  @ Tue, 17 May 2016 13:28:53:  28000000 
INFO  @ Tue, 17 May 2016 13:28:55:  29000000 
INFO  @ Tue, 17 May 2016 13:28:56:  30000000 
INFO  @ Tue, 17 May 2016 13:28:58:  31000000 
INFO  @ Tue, 17 May 2016 13:29:00:  32000000 
INFO  @ Tue, 17 May 2016 13:29:01:  33000000 
INFO  @ Tue, 17 May 2016 13:29:03:  34000000 
INFO  @ Tue, 17 May 2016 13:29:05:  35000000 
INFO  @ Tue, 17 May 2016 13:29:06:  36000000 
INFO  @ Tue, 17 May 2016 13:29:08:  37000000 
INFO  @ Tue, 17 May 2016 13:29:09:  38000000 
INFO  @ Tue, 17 May 2016 13:29:11:  39000000 
INFO  @ Tue, 17 May 2016 13:29:13:  40000000 
INFO  @ Tue, 17 May 2016 13:29:14:  41000000 
INFO  @ Tue, 17 May 2016 13:29:16:  42000000 
INFO  @ Tue, 17 May 2016 13:29:17:  43000000 
INFO  @ Tue, 17 May 2016 13:29:20:  44000000 
INFO  @ Tue, 17 May 2016 13:29:23:  45000000 
INFO  @ Tue, 17 May 2016 13:29:26:  46000000 
INFO  @ Tue, 17 May 2016 13:29:29:  47000000 
INFO  @ Tue, 17 May 2016 13:29:32:  48000000 
INFO  @ Tue, 17 May 2016 13:29:35:  49000000 
INFO  @ Tue, 17 May 2016 13:29:38:  50000000 
INFO  @ Tue, 17 May 2016 13:29:41:  51000000 
INFO  @ Tue, 17 May 2016 13:29:44:  52000000 
INFO  @ Tue, 17 May 2016 13:29:47:  53000000 
INFO  @ Tue, 17 May 2016 13:29:50:  54000000 
INFO  @ Tue, 17 May 2016 13:29:53:  55000000 
INFO  @ Tue, 17 May 2016 13:29:56:  56000000 
INFO  @ Tue, 17 May 2016 13:29:59:  57000000 
INFO  @ Tue, 17 May 2016 13:30:02:  58000000 
INFO  @ Tue, 17 May 2016 13:30:04:  59000000 
INFO  @ Tue, 17 May 2016 13:30:05:  60000000 
INFO  @ Tue, 17 May 2016 13:30:07:  61000000 
INFO  @ Tue, 17 May 2016 13:30:09:  62000000 
INFO  @ Tue, 17 May 2016 13:30:10:  63000000 
INFO  @ Tue, 17 May 2016 13:30:15: #1 tag size is determined as 59 bps 
INFO  @ Tue, 17 May 2016 13:30:15: #1 tag size = 59 
INFO  @ Tue, 17 May 2016 13:30:15: #1  total tags in treatment: 63275586 
INFO  @ Tue, 17 May 2016 13:30:15: #1 finished! 
INFO  @ Tue, 17 May 2016 13:30:15: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 13:30:15: #2 Skipped... 
INFO  @ Tue, 17 May 2016 13:30:15: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 13:30:15: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 13:30:15: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 13:30:15: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 13:30:15: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 13:32:17: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 13:34:48: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.xls 
INFO  @ Tue, 17 May 2016 13:34:51: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 13:34:53: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 13:34:55: Done! 
INFO  @ Tue, 17 May 2016 13:35:05: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/pooled_rep/ATAC19-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  @ Tue, 17 May 2016 13:35:05: #1 read tag files... 
INFO  @ Tue, 17 May 2016 13:35:05: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 13:35:06:  1000000 
INFO  @ Tue, 17 May 2016 13:35:08:  2000000 
INFO  @ Tue, 17 May 2016 13:35:09:  3000000 
INFO  @ Tue, 17 May 2016 13:35:11:  4000000 
INFO  @ Tue, 17 May 2016 13:35:13:  5000000 
INFO  @ Tue, 17 May 2016 13:35:14:  6000000 
INFO  @ Tue, 17 May 2016 13:35:16:  7000000 
INFO  @ Tue, 17 May 2016 13:35:17:  8000000 
INFO  @ Tue, 17 May 2016 13:35:19:  9000000 
INFO  @ Tue, 17 May 2016 13:35:20:  10000000 
INFO  @ Tue, 17 May 2016 13:35:22:  11000000 
INFO  @ Tue, 17 May 2016 13:35:24:  12000000 
INFO  @ Tue, 17 May 2016 13:35:25:  13000000 
INFO  @ Tue, 17 May 2016 13:35:27:  14000000 
INFO  @ Tue, 17 May 2016 13:35:28:  15000000 
INFO  @ Tue, 17 May 2016 13:35:30:  16000000 
INFO  @ Tue, 17 May 2016 13:35:32:  17000000 
INFO  @ Tue, 17 May 2016 13:35:33:  18000000 
INFO  @ Tue, 17 May 2016 13:35:35:  19000000 
INFO  @ Tue, 17 May 2016 13:35:36:  20000000 
INFO  @ Tue, 17 May 2016 13:35:38:  21000000 
INFO  @ Tue, 17 May 2016 13:35:39:  22000000 
INFO  @ Tue, 17 May 2016 13:35:41:  23000000 
INFO  @ Tue, 17 May 2016 13:35:43:  24000000 
INFO  @ Tue, 17 May 2016 13:35:44:  25000000 
INFO  @ Tue, 17 May 2016 13:35:46:  26000000 
INFO  @ Tue, 17 May 2016 13:35:47:  27000000 
INFO  @ Tue, 17 May 2016 13:35:49:  28000000 
INFO  @ Tue, 17 May 2016 13:35:51:  29000000 
INFO  @ Tue, 17 May 2016 13:35:52:  30000000 
INFO  @ Tue, 17 May 2016 13:35:54:  31000000 
INFO  @ Tue, 17 May 2016 13:35:55:  32000000 
INFO  @ Tue, 17 May 2016 13:35:57:  33000000 
INFO  @ Tue, 17 May 2016 13:35:58:  34000000 
INFO  @ Tue, 17 May 2016 13:36:00:  35000000 
INFO  @ Tue, 17 May 2016 13:36:02:  36000000 
INFO  @ Tue, 17 May 2016 13:36:03:  37000000 
INFO  @ Tue, 17 May 2016 13:36:05:  38000000 
INFO  @ Tue, 17 May 2016 13:36:06:  39000000 
INFO  @ Tue, 17 May 2016 13:36:08:  40000000 
INFO  @ Tue, 17 May 2016 13:36:10:  41000000 
INFO  @ Tue, 17 May 2016 13:36:11:  42000000 
INFO  @ Tue, 17 May 2016 13:36:13:  43000000 
INFO  @ Tue, 17 May 2016 13:36:14:  44000000 
INFO  @ Tue, 17 May 2016 13:36:16:  45000000 
INFO  @ Tue, 17 May 2016 13:36:17:  46000000 
INFO  @ Tue, 17 May 2016 13:36:19:  47000000 
INFO  @ Tue, 17 May 2016 13:36:21:  48000000 
INFO  @ Tue, 17 May 2016 13:36:22:  49000000 
INFO  @ Tue, 17 May 2016 13:36:24:  50000000 
INFO  @ Tue, 17 May 2016 13:36:25:  51000000 
INFO  @ Tue, 17 May 2016 13:36:27:  52000000 
INFO  @ Tue, 17 May 2016 13:36:29:  53000000 
INFO  @ Tue, 17 May 2016 13:36:30:  54000000 
INFO  @ Tue, 17 May 2016 13:36:32:  55000000 
INFO  @ Tue, 17 May 2016 13:36:33:  56000000 
INFO  @ Tue, 17 May 2016 13:36:35:  57000000 
INFO  @ Tue, 17 May 2016 13:36:36:  58000000 
INFO  @ Tue, 17 May 2016 13:36:38:  59000000 
INFO  @ Tue, 17 May 2016 13:36:40:  60000000 
INFO  @ Tue, 17 May 2016 13:36:41:  61000000 
INFO  @ Tue, 17 May 2016 13:36:43:  62000000 
INFO  @ Tue, 17 May 2016 13:36:44:  63000000 
INFO  @ Tue, 17 May 2016 13:36:49: #1 tag size is determined as 59 bps 
INFO  @ Tue, 17 May 2016 13:36:49: #1 tag size = 59 
INFO  @ Tue, 17 May 2016 13:36:49: #1  total tags in treatment: 63275586 
INFO  @ Tue, 17 May 2016 13:36:49: #1 finished! 
INFO  @ Tue, 17 May 2016 13:36:49: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 13:36:49: #2 Skipped... 
INFO  @ Tue, 17 May 2016 13:36:49: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 13:36:49: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 13:36:49: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 13:36:49: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 13:36:49: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Tue, 17 May 2016 13:36:49: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 13:39:05: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 13:39:05: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 13:39:05: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 13:39:05: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 13:39:05: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 13:53:36: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.xls 
INFO  @ Tue, 17 May 2016 13:53:40: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 13:53:43: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_summits.bed 
INFO  @ Tue, 17 May 2016 13:53:44: Done! 
INFO  @ Tue, 17 May 2016 13:53:52: Read and build treatment bedGraph... 
INFO  @ Tue, 17 May 2016 13:58:00: Read and build control bedGraph... 
INFO  @ Tue, 17 May 2016 13:59:45: Build scoreTrackII... 
INFO  @ Tue, 17 May 2016 14:01:27: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Tue, 17 May 2016 14:10:17: Write bedGraph of scores... 
INFO  @ Tue, 17 May 2016 14:17:51: Finished 'FE'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_FE.bdg'! 
INFO  @ Tue, 17 May 2016 14:34:10: Read and build treatment bedGraph... 
INFO  @ Tue, 17 May 2016 14:36:32: Read and build control bedGraph... 
INFO  @ Tue, 17 May 2016 14:37:33: Build scoreTrackII... 
INFO  @ Tue, 17 May 2016 14:38:44: Values in your input bedGraph files will be multiplied by 63.275586 ... 
INFO  @ Tue, 17 May 2016 14:46:57: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Tue, 17 May 2016 14:47:48: Write bedGraph of scores... 
INFO  @ Tue, 17 May 2016 14:50:52: Finished 'ppois'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_ppois.bdg'!

Num	25
ID	task.callpeak_etc.filt_top_peaks_rep1.line_25.id_30
Name	filt_top_peaks rep1
Thread	thread_Root
PID	59664

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

Start	2016-05-17 15:00:07
End	2016-05-17 15:00:18
Elapsed	00:00:11
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-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	26
ID	task.callpeak_etc.filt_top_peaks_rep1.line_25.id_31
Name	filt_top_peaks rep1
Thread	thread_Root
PID	59666

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

Start	2016-05-17 15:00:07
End	2016-05-17 15:00:15
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-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/ATAC19+20/peak/macs2/rep1/ATAC19-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	27
ID	task.callpeak_etc.filt_top_peaks_rep2.line_25.id_32
Name	filt_top_peaks rep2
Thread	thread_Root
PID	59678

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

Start	2016-05-17 15:00:07
End	2016-05-17 15:00:23
Elapsed	00:00:16
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-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	28
ID	task.callpeak_etc.filt_top_peaks_rep2.line_25.id_33
Name	filt_top_peaks rep2
Thread	thread_Root
PID	59693

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

Start	2016-05-17 15:00:07
End	2016-05-17 15:00:16
Elapsed	00:00:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-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/ATAC19+20/peak/macs2/rep2/ATAC20-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	29
ID	task.callpeak_etc.filt_top_peaks_pooled.line_25.id_34
Name	filt_top_peaks pooled
Thread	thread_Root
PID	59710

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

Start	2016-05-17 15:00:07
End	2016-05-17 15:00:17
Elapsed	00:00:10
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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	30
ID	task.callpeak_etc.filt_top_peaks_pooled.line_25.id_35
Name	filt_top_peaks pooled
Thread	thread_Root
PID	59732

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

Start	2016-05-17 15:00:07
End	2016-05-17 15:00:14
Elapsed	00:00:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.gappedPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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	31
ID	task.idr.idr2_rep1_rep2.line_61.id_36
Name	idr2 rep1-rep2
Thread	thread_Root
PID	60023

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

Start	2016-05-17 15:00:24
End	2016-05-17 15:03:14
Elapsed	00:02:50
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt.png /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/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/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz --peak-list /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/pooled_rep/ATAC19-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/ATAC19+20/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/ATAC19+20/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/ATAC19+20/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/ATAC19+20/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/ATAC19+20/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/ATAC19+20/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/ATAC19+20/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/ATAC19+20/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/ATAC19+20/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/ATAC19+20/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac_py3/bin to PATH
Initial parameter values: [0.10 1.00 0.20 0.50]
Final parameter values: [1.87 0.77 0.77 0.22]
Number of reported peaks - 172959/172959 (100.0%)

Number of peaks passing IDR cutoff of 0.1 - 49092/172959 (28.4%)

Num	32
ID	task.base.line_414.id_39
Name	task.base.line_414.id_39
Thread	thread_Root
PID	60113

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

Start	2016-05-17 15:03:15
End	2016-05-17 15:03:15
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 416

 cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz

Num	33
ID	task.base.line_414.id_40
Name	task.base.line_414.id_40
Thread	thread_Root
PID	60118

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

Start	2016-05-17 15:03:15
End	2016-05-17 15:03:15
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 416

 cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz

Num	34
ID	task.base.line_414.id_41
Name	task.base.line_414.id_41
Thread	thread_Root
PID	60127

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

Start	2016-05-17 15:03:15
End	2016-05-17 15:03:15
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.gz
Dependencies

 
# SYS command. line 416

 cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.gz

Num	35
ID	task.base.line_414.id_42
Name	task.base.line_414.id_42
Thread	thread_Root
PID	60138

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

Start	2016-05-17 15:03:15
End	2016-05-17 15:03:15
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.13-col.bed.gz
Dependencies

 
# SYS command. line 416

 cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.13-col.bed.gz

Num	36
ID	task.idr.idr_final_qc.line_196.id_43
Name	idr final qc
Thread	thread_Root
PID	60162

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

Start	2016-05-17 15:03:16
End	2016-05-17 15:03:17
Elapsed	00:00:01
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/IDR_final.qc
Dependencies

 
# SYS command. line 198

 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 200

 echo -e "Nt\t""Np\tconservative_set\toptimal_set\trescue_ratio\tself_consistency_ratio\treproducibility" > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/IDR_final.qc

# SYS command. line 201

 echo -e "48916\t""0\trep1-rep2\trep1-rep2\tInfinity\tNaN\t0" >> /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/IDR_final.qc

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

Num	37
ID	task.postalign_bam.srt_bam_rep2.line_345.id_44
Name	srt_bam rep2
Thread	thread_78
PID	60167

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

Start	2016-05-17 15:03:16
End	2016-05-17 15:24:34
Elapsed	00:21:17
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.srt.bam
Dependencies

 
# SYS command. line 347

 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 353

 samtools sort /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.srt

# SYS command. line 354

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.srt.bam

# SYS command. line 356

 if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.srt.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.srt.bai" ]; then \
			cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.srt.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.srt.bai; \
			fi

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 50 files...

Num	38
ID	task.postalign_bam.srt_bam_rep1.line_345.id_45
Name	srt_bam rep1
Thread	thread_77
PID	60177

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

Start	2016-05-17 15:03:16
End	2016-05-17 15:47:25
Elapsed	00:44:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.srt.bam
Dependencies

 
# SYS command. line 347

 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 353

 samtools sort /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.srt

# SYS command. line 354

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.srt.bam

# SYS command. line 356

 if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.srt.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.srt.bai" ]; then \
			cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.srt.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.srt.bai; \
			fi

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 108 files...

Num	39
ID	task.atac.ataqc_rep2.line_815.id_46
Name	ataqc rep2
Thread	thread_78
PID	61969

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

Start	2016-05-17 15:24:35
End	2016-05-17 15:24:35
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC20/ATAC20-trimmed-pair1.fastq.gz /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC20/ATAC20-trimmed-pair2.fastq.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep2/ATAC20-trimmed-pair1.trim.PE2SE.align.log /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.pbc.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep2/ATAC20-trimmed-pair1.trim.PE2SE.dup.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/signal/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep2/ATAC20-trimmed-pair1.PE2SE_qc.html /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep2/ATAC20-trimmed-pair1.PE2SE_qc.txt
Dependencies

 
# SYS command. line 817

 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 821

 export _JAVA_OPTIONS="-Xms256M -Xmx4096M -XX:ParallelGCThreads=1"

# SYS command. line 823

 cd /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep2

# SYS command. line 825

 /users/pangwei/bds_atac/ataqc/run_ataqc.py \
			    --workdir /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep2 \
			    --outdir /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep2 \
			    --outprefix ATAC20-trimmed-pair1.PE2SE \
			    --genome hg19 \
			    --ref /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/encodeHg19Male.fa \
			    --tss /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/hg19_RefSeq_stranded.bed.gz \
			    --dnase /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_all_p10_ucsc.bed.gz \
			    --blacklist /mnt/data/ENCODE/blacklists/wgEncodeDacMapabilityConsensusExcludable.bed.gz \
			    --prom /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_prom_p2.bed.gz \
			    --enh /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_enh_p2.bed.gz \
			    --reg2map /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/dnase_avgs_reg2map_p10_merged_named.pvals.gz \
			    --meta /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/eid_to_mnemonic.txt \
			    --pbc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.pbc.qc\
			    --fastq1 /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC20/ATAC20-trimmed-pair1.fastq.gz --fastq2 /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC20/ATAC20-trimmed-pair2.fastq.gz \
			    --alignedbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.bam \
			    --alignmentlog /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep2/ATAC20-trimmed-pair1.trim.PE2SE.align.log \
			    --coordsortbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.srt.bam \
			    --duplog /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep2/ATAC20-trimmed-pair1.trim.PE2SE.dup.qc \
			    --finalbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.bam \
			    --finalbed /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz \
			    --bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/signal/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig \
			    --peaks /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep2/ATAC20-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz \
			     \
			    --idr_peaks /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
ERROR	2016-05-17 15:27:50	ProcessExecutor	Warning messages:
ERROR	2016-05-17 15:27:50	ProcessExecutor	1: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
ERROR	2016-05-17 15:27:50	ProcessExecutor	  zero-length arrow is of indeterminate angle and so skipped
ERROR	2016-05-17 15:27:50	ProcessExecutor	2: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
ERROR	2016-05-17 15:27:50	ProcessExecutor	  zero-length arrow is of indeterminate angle and so skipped
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
[bam_sort_core] merging from 50 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1

Num	40
ID	task.atac.ataqc_rep1.line_815.id_47
Name	ataqc rep1
Thread	thread_77
PID	62998

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

Start	2016-05-17 15:47:26
End	2016-05-17 15:47:26
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC19/ATAC19-trimmed-pair1.fastq.gz /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC19/ATAC19-trimmed-pair2.fastq.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep1/ATAC19-trimmed-pair1.trim.PE2SE.align.log /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.pbc.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep1/ATAC19-trimmed-pair1.trim.PE2SE.dup.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/signal/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep1/ATAC19-trimmed-pair1.PE2SE_qc.html /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep1/ATAC19-trimmed-pair1.PE2SE_qc.txt
Dependencies

 
# SYS command. line 817

 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 821

 export _JAVA_OPTIONS="-Xms256M -Xmx4096M -XX:ParallelGCThreads=1"

# SYS command. line 823

 cd /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep1

# SYS command. line 825

 /users/pangwei/bds_atac/ataqc/run_ataqc.py \
			    --workdir /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep1 \
			    --outdir /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep1 \
			    --outprefix ATAC19-trimmed-pair1.PE2SE \
			    --genome hg19 \
			    --ref /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/encodeHg19Male.fa \
			    --tss /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/hg19_RefSeq_stranded.bed.gz \
			    --dnase /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_all_p10_ucsc.bed.gz \
			    --blacklist /mnt/data/ENCODE/blacklists/wgEncodeDacMapabilityConsensusExcludable.bed.gz \
			    --prom /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_prom_p2.bed.gz \
			    --enh /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_enh_p2.bed.gz \
			    --reg2map /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/dnase_avgs_reg2map_p10_merged_named.pvals.gz \
			    --meta /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/eid_to_mnemonic.txt \
			    --pbc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.pbc.qc\
			    --fastq1 /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC19/ATAC19-trimmed-pair1.fastq.gz --fastq2 /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC19/ATAC19-trimmed-pair2.fastq.gz \
			    --alignedbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.bam \
			    --alignmentlog /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep1/ATAC19-trimmed-pair1.trim.PE2SE.align.log \
			    --coordsortbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.srt.bam \
			    --duplog /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/qc/rep1/ATAC19-trimmed-pair1.trim.PE2SE.dup.qc \
			    --finalbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.bam \
			    --finalbed /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/align/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz \
			    --bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/signal/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig \
			    --peaks /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/macs2/rep1/ATAC19-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz \
			     \
			    --idr_peaks /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC19+20/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
ERROR	2016-05-17 15:53:26	ProcessExecutor	Warning messages:
ERROR	2016-05-17 15:53:26	ProcessExecutor	1: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
ERROR	2016-05-17 15:53:26	ProcessExecutor	  zero-length arrow is of indeterminate angle and so skipped
ERROR	2016-05-17 15:53:26	ProcessExecutor	2: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
ERROR	2016-05-17 15:53:26	ProcessExecutor	  zero-length arrow is of indeterminate angle and so skipped
ERROR	2016-05-17 15:53:26	ProcessExecutor	3: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
ERROR	2016-05-17 15:53:26	ProcessExecutor	  zero-length arrow is of indeterminate angle and so skipped
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
[bam_sort_core] merging from 106 files...

BigDataScript report: atac.bds

Timeline

Task Graph

Parallel (threads) details

Task details

Global scope