Script file	/users/pangwei/bds_atac/atac.bds
Program ID	atac.bds.20160516_201635_088
Start time	2016-05-16 20:16:35
Run time	18:58:49.520
Tasks executed	47
Tasks failed	0
Tasks failed names
Arguments*	[-out_dir, /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6, -num_rep, 2, -fastq1_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC5/ATAC5-trimmed-pair1.fastq.gz, -fastq1_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC5/ATAC5-trimmed-pair2.fastq.gz, -fastq2_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC6/ATAC6-trimmed-pair1.fastq.gz, -fastq2_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC6/ATAC6-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_088/task.postalign_bed.pool_tag_reps.line_405.id_28 atac.bds.20160516_201635_088/task.callpeak_macs2.macs2_atac_pooled.pval0.1.line_192.id_29 atac.bds.20160516_201635_088/task.callpeak_macs2.macs2_atac_pooled.line_192.id_30 atac.bds.20160516_201635_088/task.callpeak_etc.filt_top_peaks_rep1.line_25.id_31 atac.bds.20160516_201635_088/task.callpeak_etc.filt_top_peaks_rep1.line_25.id_32 atac.bds.20160516_201635_088/task.callpeak_etc.filt_top_peaks_rep2.line_25.id_33 atac.bds.20160516_201635_088/task.callpeak_etc.filt_top_peaks_rep2.line_25.id_34 atac.bds.20160516_201635_088/task.callpeak_etc.filt_top_peaks_pooled.line_25.id_35 atac.bds.20160516_201635_088/task.callpeak_etc.filt_top_peaks_pooled.line_25.id_36 atac.bds.20160516_201635_088/task.idr.idr2_rep1_rep2.line_61.id_37 atac.bds.20160516_201635_088/task.base.line_414.id_40 atac.bds.20160516_201635_088/task.base.line_414.id_41 atac.bds.20160516_201635_088/task.base.line_414.id_42 atac.bds.20160516_201635_088/task.base.line_414.id_43 atac.bds.20160516_201635_088/task.idr.idr_final_qc.line_196.id_44 atac.bds.20160516_201635_088/task.report.line_418.id_49 atac.bds.20160516_201635_088/task.report.line_418.id_50 atac.bds.20160516_201635_088/task.report.line_418.id_51 atac.bds.20160516_201635_088/task.report_graphviz.line_93.id_52 atac.bds.20160516_201635_088/task.report.line_383.id_57 atac.bds.20160516_201635_088/task.report.line_383.id_58
thread_20	thread_Root	atac.bds.20160516_201635_088_parallel_20/task.align_bowtie2.bowtie2_PE_rep1.line_133.id_6 atac.bds.20160516_201635_088_parallel_20/task.postalign_bam.dedup_bam_PE_rep1.line_215.id_8 atac.bds.20160516_201635_088_parallel_20/task.postalign_bam.nmsrt_bam_rep1.line_321.id_10 atac.bds.20160516_201635_088_parallel_20/task.postalign_bam.bam_to_bedpe_rep1.line_425.id_11 atac.bds.20160516_201635_088_parallel_20/task.postalign_bed.subsample_bedpe_rep1.line_116.id_12 atac.bds.20160516_201635_088_parallel_20/task.postalign_bam.bedpe_to_tag_rep1.line_465.id_13 atac.bds.20160516_201635_088_parallel_20/task.postalign_bed.shift_tag_rep1.line_140.id_14 atac.bds.20160516_201635_088_parallel_20/task.postalign_bed.subsample_bedpe2tagrep1.line_89.id_15 atac.bds.20160516_201635_088_parallel_20/task.postalign_bed.xcor_rep1.line_165.id_16 atac.bds.20160516_201635_088_parallel_20/task.callpeak_macs2.macs2_atac_rep1.pval0.1.line_192.id_17 atac.bds.20160516_201635_088_parallel_20/task.callpeak_macs2.macs2_atac_rep1.line_192.id_18
thread_21	thread_Root	atac.bds.20160516_201635_088_parallel_21/task.align_bowtie2.bowtie2_PE_rep2.line_133.id_7 atac.bds.20160516_201635_088_parallel_21/task.postalign_bam.dedup_bam_PE_rep2.line_215.id_9 atac.bds.20160516_201635_088_parallel_21/task.postalign_bam.nmsrt_bam_rep2.line_321.id_19 atac.bds.20160516_201635_088_parallel_21/task.postalign_bam.bam_to_bedpe_rep2.line_425.id_20 atac.bds.20160516_201635_088_parallel_21/task.postalign_bed.subsample_bedpe_rep2.line_116.id_21 atac.bds.20160516_201635_088_parallel_21/task.postalign_bam.bedpe_to_tag_rep2.line_465.id_22 atac.bds.20160516_201635_088_parallel_21/task.postalign_bed.shift_tag_rep2.line_140.id_23 atac.bds.20160516_201635_088_parallel_21/task.postalign_bed.subsample_bedpe2tagrep2.line_89.id_24 atac.bds.20160516_201635_088_parallel_21/task.postalign_bed.xcor_rep2.line_165.id_25 atac.bds.20160516_201635_088_parallel_21/task.callpeak_macs2.macs2_atac_rep2.pval0.1.line_192.id_26 atac.bds.20160516_201635_088_parallel_21/task.callpeak_macs2.macs2_atac_rep2.line_192.id_27
thread_78	thread_Root	atac.bds.20160516_201635_088_parallel_78/task.postalign_bam.srt_bam_rep1.line_345.id_45 atac.bds.20160516_201635_088_parallel_78/task.atac.ataqc_rep1.line_815.id_47
thread_79	thread_Root	atac.bds.20160516_201635_088_parallel_79/task.postalign_bam.srt_bam_rep2.line_345.id_46 atac.bds.20160516_201635_088_parallel_79/task.atac.ataqc_rep2.line_815.id_48

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	129923

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

Start	2016-05-16 20:16:36
End	2016-05-17 04:53:53
Elapsed	08:37:16
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.fastq.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair2.trim.fastq.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep1/ATAC5-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/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.fastq.gz -2 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair2.trim.fastq.gz 2>/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep1/ATAC5-trimmed-pair1.trim.PE2SE.align.log | samtools view -bS - | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE

# SYS command. line 142

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-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 53 files...

Num	2
ID	task.align_bowtie2.bowtie2_PE_rep2.line_133.id_7
Name	bowtie2_PE rep2
Thread	thread_21
PID	129928

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

Start	2016-05-16 20:16:36
End	2016-05-17 05:18:49
Elapsed	09:02:12
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.fastq.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair2.trim.fastq.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep2/ATAC6-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/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.fastq.gz -2 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair2.trim.fastq.gz 2>/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep2/ATAC6-trimmed-pair1.trim.PE2SE.align.log | samtools view -bS - | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE

# SYS command. line 142

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-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 53 files...

Num	3
ID	task.postalign_bam.dedup_bam_PE_rep1.line_215.id_8
Name	dedup_bam_PE rep1
Thread	thread_20
PID	7426

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

Start	2016-05-17 04:53:54
End	2016-05-17 07:27:51
Elapsed	02:33:56
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep1/ATAC5-trimmed-pair1.trim.PE2SE.dup.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep1/ATAC5-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/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-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/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-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/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.filt

# SYS command. line 239

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-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/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep1/ATAC5-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/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep1/ATAC5-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/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-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/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.filt.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 269

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 271

 if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.bai" ]; then \
			cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.bai; \
			fi

# SYS command. line 275

 samtools flagstat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc

# SYS command. line 286

 samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.filt.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.filt.bam.tmp

# SYS command. line 287

 bedtools bamtobed -bedpe -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-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/ATAC5+6/qc/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.pbc.qc

# SYS command. line 291

 rm /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam

# SYS command. line 293

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.filt.bam

# SYS command. line 294

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-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 36 files...
[bam_sort_core] merging from 36 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Tue May 17 06:15:08 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep1/ATAC5-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 06:15:08 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 06:15:08	MarkDuplicates	Start of doWork freeMemory: 254889872; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-17 06:15:08	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-05-17 06:15:08	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-05-17 06:15:15	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:06s.  Time for last 1,000,000:    6s.  Last read position: chr10:75,280,154
INFO	2016-05-17 06:15:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:15:19	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:10s.  Time for last 1,000,000:    4s.  Last read position: chr10:134,584,427
INFO	2016-05-17 06:15:19	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:15:23	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:13s.  Time for last 1,000,000:    3s.  Last read position: chr11:64,545,410
INFO	2016-05-17 06:15:23	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:15:33	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:23s.  Time for last 1,000,000:    9s.  Last read position: chr11:125,597,714
INFO	2016-05-17 06:15:33	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:15:44	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:34s.  Time for last 1,000,000:   11s.  Last read position: chr12:56,465,025
INFO	2016-05-17 06:15:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:15:51	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:41s.  Time for last 1,000,000:    6s.  Last read position: chr12:122,193,943
INFO	2016-05-17 06:15:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:16:00	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:50s.  Time for last 1,000,000:    8s.  Last read position: chr13:80,006,534
INFO	2016-05-17 06:16:00	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-17 06:16:07	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:57s.  Time for last 1,000,000:    7s.  Last read position: chr14:58,309,166
INFO	2016-05-17 06:16:07	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:16:16	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:01:07s.  Time for last 1,000,000:    9s.  Last read position: chr15:37,812,150
INFO	2016-05-17 06:16:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:16:21	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:01:11s.  Time for last 1,000,000:    4s.  Last read position: chr15:95,471,418
INFO	2016-05-17 06:16:21	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:16:26	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:17s.  Time for last 1,000,000:    5s.  Last read position: chr16:65,898,391
INFO	2016-05-17 06:16:26	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:16:35	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:26s.  Time for last 1,000,000:    8s.  Last read position: chr17:33,162,766
INFO	2016-05-17 06:16:35	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:16:40	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:30s.  Time for last 1,000,000:    4s.  Last read position: chr18:5,937,816
INFO	2016-05-17 06:16:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:16:46	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:37s.  Time for last 1,000,000:    6s.  Last read position: chr19:1,656,507
INFO	2016-05-17 06:16:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:17:03	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:54s.  Time for last 1,000,000:   17s.  Last read position: chr19:55,769,606
INFO	2016-05-17 06:17:03	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 06:17:09	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:59s.  Time for last 1,000,000:    5s.  Last read position: chr1:34,573,416
INFO	2016-05-17 06:17:09	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:17:12	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:02:03s.  Time for last 1,000,000:    3s.  Last read position: chr1:95,942,598
INFO	2016-05-17 06:17:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:17:16	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:02:07s.  Time for last 1,000,000:    3s.  Last read position: chr1:185,207,489
INFO	2016-05-17 06:17:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:17:22	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:02:13s.  Time for last 1,000,000:    6s.  Last read position: chr20:299,067
INFO	2016-05-17 06:17:22	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:17:27	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:02:18s.  Time for last 1,000,000:    5s.  Last read position: chr20:60,168,237
INFO	2016-05-17 06:17:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:17:32	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:02:23s.  Time for last 1,000,000:    5s.  Last read position: chr22:39,246,241
INFO	2016-05-17 06:17:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:17:40	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:02:31s.  Time for last 1,000,000:    7s.  Last read position: chr2:45,881,039
INFO	2016-05-17 06:17:40	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 06:17:53	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:02:44s.  Time for last 1,000,000:   12s.  Last read position: chr2:121,029,838
INFO	2016-05-17 06:17:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:17:59	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:02:49s.  Time for last 1,000,000:    5s.  Last read position: chr2:192,767,398
INFO	2016-05-17 06:17:59	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:18:06	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:02:56s.  Time for last 1,000,000:    6s.  Last read position: chr3:11,133,878
INFO	2016-05-17 06:18:06	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:18:12	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:03:03s.  Time for last 1,000,000:    6s.  Last read position: chr3:70,753,346
INFO	2016-05-17 06:18:12	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:18:22	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:03:12s.  Time for last 1,000,000:    9s.  Last read position: chr3:147,884,861
INFO	2016-05-17 06:18:22	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:18:28	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:03:19s.  Time for last 1,000,000:    6s.  Last read position: chr4:12,624,895
INFO	2016-05-17 06:18:28	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:18:34	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:03:25s.  Time for last 1,000,000:    6s.  Last read position: chr4:94,382,739
INFO	2016-05-17 06:18:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:18:51	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:03:42s.  Time for last 1,000,000:   16s.  Last read position: chr4:171,762,742
INFO	2016-05-17 06:18:51	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:18:57	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:03:48s.  Time for last 1,000,000:    6s.  Last read position: chr5:60,620,080
INFO	2016-05-17 06:18:57	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:19:03	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:03:53s.  Time for last 1,000,000:    5s.  Last read position: chr5:134,260,229
INFO	2016-05-17 06:19:03	MarkDuplicates	Tracking 1824 as yet unmatched pairs. 1824 records in RAM.
INFO	2016-05-17 06:19:06	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:03:57s.  Time for last 1,000,000:    3s.  Last read position: chr6:3,833,593
INFO	2016-05-17 06:19:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:19:09	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:04:00s.  Time for last 1,000,000:    3s.  Last read position: chr6:71,666,862
INFO	2016-05-17 06:19:09	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-05-17 06:19:13	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:04:04s.  Time for last 1,000,000:    3s.  Last read position: chr6:147,311,123
INFO	2016-05-17 06:19:13	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:19:18	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:04:09s.  Time for last 1,000,000:    5s.  Last read position: chr7:42,333,218
INFO	2016-05-17 06:19:18	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:19:22	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:04:13s.  Time for last 1,000,000:    3s.  Last read position: chr7:119,480,897
INFO	2016-05-17 06:19:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:19:29	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:04:20s.  Time for last 1,000,000:    6s.  Last read position: chr8:25,364,799
INFO	2016-05-17 06:19:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:19:35	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:04:26s.  Time for last 1,000,000:    6s.  Last read position: chr8:101,839,469
INFO	2016-05-17 06:19:35	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-05-17 06:19:41	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:04:31s.  Time for last 1,000,000:    5s.  Last read position: chr9:21,409,151
INFO	2016-05-17 06:19:41	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 06:19:49	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:04:40s.  Time for last 1,000,000:    8s.  Last read position: chr9:120,157,375
INFO	2016-05-17 06:19:49	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:19:55	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:04:46s.  Time for last 1,000,000:    5s.  Last read position: chrM:304
INFO	2016-05-17 06:19:55	MarkDuplicates	Tracking 7286 as yet unmatched pairs. 7286 records in RAM.
INFO	2016-05-17 06:20:02	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:04:52s.  Time for last 1,000,000:    6s.  Last read position: chrM:673
INFO	2016-05-17 06:20:02	MarkDuplicates	Tracking 62330 as yet unmatched pairs. 62330 records in RAM.
INFO	2016-05-17 06:20:08	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:04:59s.  Time for last 1,000,000:    6s.  Last read position: chrM:981
INFO	2016-05-17 06:20:08	MarkDuplicates	Tracking 88338 as yet unmatched pairs. 88338 records in RAM.
INFO	2016-05-17 06:20:17	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:05:08s.  Time for last 1,000,000:    9s.  Last read position: chrM:1,437
INFO	2016-05-17 06:20:17	MarkDuplicates	Tracking 51444 as yet unmatched pairs. 51444 records in RAM.
INFO	2016-05-17 06:20:23	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:05:14s.  Time for last 1,000,000:    6s.  Last read position: chrM:1,839
INFO	2016-05-17 06:20:23	MarkDuplicates	Tracking 76140 as yet unmatched pairs. 76140 records in RAM.
INFO	2016-05-17 06:20:27	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:05:18s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,284
INFO	2016-05-17 06:20:27	MarkDuplicates	Tracking 27180 as yet unmatched pairs. 27180 records in RAM.
INFO	2016-05-17 06:20:32	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:05:23s.  Time for last 1,000,000:    4s.  Last read position: chrM:2,694
INFO	2016-05-17 06:20:32	MarkDuplicates	Tracking 116392 as yet unmatched pairs. 116392 records in RAM.
INFO	2016-05-17 06:20:37	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:05:28s.  Time for last 1,000,000:    5s.  Last read position: chrM:2,933
INFO	2016-05-17 06:20:37	MarkDuplicates	Tracking 100804 as yet unmatched pairs. 100804 records in RAM.
INFO	2016-05-17 06:20:45	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:05:35s.  Time for last 1,000,000:    7s.  Last read position: chrM:3,208
INFO	2016-05-17 06:20:45	MarkDuplicates	Tracking 132932 as yet unmatched pairs. 132932 records in RAM.
INFO	2016-05-17 06:20:50	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:05:41s.  Time for last 1,000,000:    5s.  Last read position: chrM:3,413
INFO	2016-05-17 06:20:50	MarkDuplicates	Tracking 104194 as yet unmatched pairs. 104194 records in RAM.
INFO	2016-05-17 06:20:56	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:05:47s.  Time for last 1,000,000:    6s.  Last read position: chrM:3,603
INFO	2016-05-17 06:20:56	MarkDuplicates	Tracking 74522 as yet unmatched pairs. 74522 records in RAM.
INFO	2016-05-17 06:21:04	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:05:54s.  Time for last 1,000,000:    7s.  Last read position: chrM:3,810
INFO	2016-05-17 06:21:04	MarkDuplicates	Tracking 119100 as yet unmatched pairs. 119100 records in RAM.
INFO	2016-05-17 06:21:11	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:06:02s.  Time for last 1,000,000:    7s.  Last read position: chrM:4,260
INFO	2016-05-17 06:21:11	MarkDuplicates	Tracking 42858 as yet unmatched pairs. 42858 records in RAM.
INFO	2016-05-17 06:21:22	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:06:12s.  Time for last 1,000,000:   10s.  Last read position: chrM:4,965
INFO	2016-05-17 06:21:22	MarkDuplicates	Tracking 69214 as yet unmatched pairs. 69214 records in RAM.
INFO	2016-05-17 06:21:28	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:06:19s.  Time for last 1,000,000:    6s.  Last read position: chrM:5,456
INFO	2016-05-17 06:21:28	MarkDuplicates	Tracking 31958 as yet unmatched pairs. 31958 records in RAM.
INFO	2016-05-17 06:21:35	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:06:26s.  Time for last 1,000,000:    7s.  Last read position: chrM:6,229
INFO	2016-05-17 06:21:35	MarkDuplicates	Tracking 99108 as yet unmatched pairs. 99108 records in RAM.
INFO	2016-05-17 06:21:43	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:06:34s.  Time for last 1,000,000:    7s.  Last read position: chrM:6,423
INFO	2016-05-17 06:21:43	MarkDuplicates	Tracking 70770 as yet unmatched pairs. 70770 records in RAM.
INFO	2016-05-17 06:22:08	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:06:58s.  Time for last 1,000,000:   24s.  Last read position: chrM:6,633
INFO	2016-05-17 06:22:08	MarkDuplicates	Tracking 102198 as yet unmatched pairs. 102198 records in RAM.
INFO	2016-05-17 06:22:15	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:07:06s.  Time for last 1,000,000:    7s.  Last read position: chrM:7,127
INFO	2016-05-17 06:22:15	MarkDuplicates	Tracking 75380 as yet unmatched pairs. 75380 records in RAM.
INFO	2016-05-17 06:22:21	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:07:12s.  Time for last 1,000,000:    6s.  Last read position: chrM:7,791
INFO	2016-05-17 06:22:21	MarkDuplicates	Tracking 49060 as yet unmatched pairs. 49060 records in RAM.
INFO	2016-05-17 06:22:26	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:07:17s.  Time for last 1,000,000:    5s.  Last read position: chrM:8,087
INFO	2016-05-17 06:22:26	MarkDuplicates	Tracking 81482 as yet unmatched pairs. 81482 records in RAM.
INFO	2016-05-17 06:22:30	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:07:21s.  Time for last 1,000,000:    3s.  Last read position: chrM:8,613
INFO	2016-05-17 06:22:30	MarkDuplicates	Tracking 13030 as yet unmatched pairs. 13030 records in RAM.
INFO	2016-05-17 06:22:33	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:07:24s.  Time for last 1,000,000:    2s.  Last read position: chrM:9,281
INFO	2016-05-17 06:22:33	MarkDuplicates	Tracking 42340 as yet unmatched pairs. 42340 records in RAM.
INFO	2016-05-17 06:22:38	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:07:28s.  Time for last 1,000,000:    4s.  Last read position: chrM:9,812
INFO	2016-05-17 06:22:38	MarkDuplicates	Tracking 87082 as yet unmatched pairs. 87082 records in RAM.
INFO	2016-05-17 06:22:43	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:07:34s.  Time for last 1,000,000:    5s.  Last read position: chrM:10,230
INFO	2016-05-17 06:22:43	MarkDuplicates	Tracking 41660 as yet unmatched pairs. 41660 records in RAM.
INFO	2016-05-17 06:22:51	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:07:42s.  Time for last 1,000,000:    8s.  Last read position: chrM:10,659
INFO	2016-05-17 06:22:51	MarkDuplicates	Tracking 45316 as yet unmatched pairs. 45316 records in RAM.
INFO	2016-05-17 06:22:57	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:07:48s.  Time for last 1,000,000:    5s.  Last read position: chrM:11,218
INFO	2016-05-17 06:22:57	MarkDuplicates	Tracking 57906 as yet unmatched pairs. 57906 records in RAM.
INFO	2016-05-17 06:23:05	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:07:56s.  Time for last 1,000,000:    7s.  Last read position: chrM:11,568
INFO	2016-05-17 06:23:05	MarkDuplicates	Tracking 67428 as yet unmatched pairs. 67428 records in RAM.
INFO	2016-05-17 06:23:12	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:08:03s.  Time for last 1,000,000:    7s.  Last read position: chrM:11,989
INFO	2016-05-17 06:23:12	MarkDuplicates	Tracking 70090 as yet unmatched pairs. 70090 records in RAM.
INFO	2016-05-17 06:23:19	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:08:10s.  Time for last 1,000,000:    6s.  Last read position: chrM:12,353
INFO	2016-05-17 06:23:19	MarkDuplicates	Tracking 44936 as yet unmatched pairs. 44936 records in RAM.
INFO	2016-05-17 06:23:25	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:08:16s.  Time for last 1,000,000:    5s.  Last read position: chrM:12,636
INFO	2016-05-17 06:23:25	MarkDuplicates	Tracking 96710 as yet unmatched pairs. 96710 records in RAM.
INFO	2016-05-17 06:23:34	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:08:25s.  Time for last 1,000,000:    9s.  Last read position: chrM:13,070
INFO	2016-05-17 06:23:34	MarkDuplicates	Tracking 50994 as yet unmatched pairs. 50994 records in RAM.
INFO	2016-05-17 06:23:42	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:08:32s.  Time for last 1,000,000:    7s.  Last read position: chrM:13,316
INFO	2016-05-17 06:23:42	MarkDuplicates	Tracking 64450 as yet unmatched pairs. 64450 records in RAM.
INFO	2016-05-17 06:23:47	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:08:37s.  Time for last 1,000,000:    4s.  Last read position: chrM:13,566
INFO	2016-05-17 06:23:47	MarkDuplicates	Tracking 56536 as yet unmatched pairs. 56536 records in RAM.
INFO	2016-05-17 06:23:52	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:08:42s.  Time for last 1,000,000:    5s.  Last read position: chrM:13,929
INFO	2016-05-17 06:23:52	MarkDuplicates	Tracking 32194 as yet unmatched pairs. 32194 records in RAM.
INFO	2016-05-17 06:23:57	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:08:47s.  Time for last 1,000,000:    5s.  Last read position: chrM:14,344
INFO	2016-05-17 06:23:57	MarkDuplicates	Tracking 36538 as yet unmatched pairs. 36538 records in RAM.
INFO	2016-05-17 06:24:02	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:08:53s.  Time for last 1,000,000:    5s.  Last read position: chrM:14,910
INFO	2016-05-17 06:24:02	MarkDuplicates	Tracking 46590 as yet unmatched pairs. 46590 records in RAM.
INFO	2016-05-17 06:24:08	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:08:59s.  Time for last 1,000,000:    5s.  Last read position: chrM:15,146
INFO	2016-05-17 06:24:08	MarkDuplicates	Tracking 110908 as yet unmatched pairs. 110908 records in RAM.
INFO	2016-05-17 06:24:15	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:09:05s.  Time for last 1,000,000:    6s.  Last read position: chrM:15,376
INFO	2016-05-17 06:24:15	MarkDuplicates	Tracking 105594 as yet unmatched pairs. 105594 records in RAM.
INFO	2016-05-17 06:24:18	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:09:09s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,597
INFO	2016-05-17 06:24:18	MarkDuplicates	Tracking 76392 as yet unmatched pairs. 76392 records in RAM.
INFO	2016-05-17 06:24:21	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:09:12s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,805
INFO	2016-05-17 06:24:21	MarkDuplicates	Tracking 101378 as yet unmatched pairs. 101378 records in RAM.
INFO	2016-05-17 06:24:24	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:09:15s.  Time for last 1,000,000:    3s.  Last read position: chrM:16,223
INFO	2016-05-17 06:24:24	MarkDuplicates	Tracking 30594 as yet unmatched pairs. 30594 records in RAM.
INFO	2016-05-17 06:24:28	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:09:18s.  Time for last 1,000,000:    3s.  Last read position: chrM:16,436
INFO	2016-05-17 06:24:28	MarkDuplicates	Tracking 46948 as yet unmatched pairs. 46948 records in RAM.
INFO	2016-05-17 06:24:31	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:09:22s.  Time for last 1,000,000:    3s.  Last read position: chrX:50,613,018
INFO	2016-05-17 06:24:31	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:24:37	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:09:28s.  Time for last 1,000,000:    6s.  Last read position: chrX:138,796,461
INFO	2016-05-17 06:24:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:24:38	MarkDuplicates	Read 86211478 records. 0 pairs never matched.
INFO	2016-05-17 06:24:48	MarkDuplicates	After buildSortedReadEndLists freeMemory: 3667055944; totalMemory: 3694657536; maxMemory: 3817865216
INFO	2016-05-17 06:24:48	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-05-17 06:24:48	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-05-17 06:25:10	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-05-17 06:25:31	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-05-17 06:25:34	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2694590992; totalMemory: 3675783168; maxMemory: 3817865216
INFO	2016-05-17 06:25:34	MarkDuplicates	Marking 51842328 records as duplicates.
INFO	2016-05-17 06:25:34	MarkDuplicates	Found 13799051 optical duplicate clusters.
INFO	2016-05-17 06:27:08	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:33s.  Time for last 10,000,000:   93s.  Last read position: chr15:95,471,418
INFO	2016-05-17 06:29:02	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:03:27s.  Time for last 10,000,000:  114s.  Last read position: chr20:60,168,237
INFO	2016-05-17 06:31:25	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:05:49s.  Time for last 10,000,000:  142s.  Last read position: chr4:171,762,742
INFO	2016-05-17 06:33:04	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:07:29s.  Time for last 10,000,000:   99s.  Last read position: chr9:21,409,151
INFO	2016-05-17 06:34:26	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:08:51s.  Time for last 10,000,000:   82s.  Last read position: chrM:3,208
INFO	2016-05-17 06:35:42	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:10:07s.  Time for last 10,000,000:   76s.  Last read position: chrM:7,127
INFO	2016-05-17 06:37:15	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:11:40s.  Time for last 10,000,000:   92s.  Last read position: chrM:11,989
INFO	2016-05-17 06:38:34	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:12:59s.  Time for last 10,000,000:   78s.  Last read position: chrM:15,376
INFO	2016-05-17 06:39:36	MarkDuplicates	Before output close freeMemory: 3807027296; totalMemory: 3837263872; maxMemory: 3837263872
INFO	2016-05-17 06:39:36	MarkDuplicates	After output close freeMemory: 3807026240; totalMemory: 3837263872; maxMemory: 3837263872
[Tue May 17 06:39:36 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 24.47 minutes.
Runtime.totalMemory()=3837263872
[bam_sort_core] merging from 36 files...

Num	4
ID	task.postalign_bam.dedup_bam_PE_rep2.line_215.id_9
Name	dedup_bam_PE rep2
Thread	thread_21
PID	9090

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

Start	2016-05-17 05:18:50
End	2016-05-17 08:19:14
Elapsed	03:00:24
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep2/ATAC6-trimmed-pair1.trim.PE2SE.dup.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep2/ATAC6-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/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-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/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-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/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.filt

# SYS command. line 239

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-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/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep2/ATAC6-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/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep2/ATAC6-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/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-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/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.filt.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 269

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 271

 if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.bai" ]; then \
			cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.bai; \
			fi

# SYS command. line 275

 samtools flagstat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc

# SYS command. line 286

 samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.filt.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.filt.bam.tmp

# SYS command. line 287

 bedtools bamtobed -bedpe -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-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/ATAC5+6/qc/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.pbc.qc

# SYS command. line 291

 rm /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam

# SYS command. line 293

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.filt.bam

# SYS command. line 294

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-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 40 files...
[bam_sort_core] merging from 40 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Tue May 17 06:50:22 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep2/ATAC6-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 06:50:22 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 06:50:22	MarkDuplicates	Start of doWork freeMemory: 254889728; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-17 06:50:22	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-05-17 06:50:22	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-05-17 06:50:43	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:20s.  Time for last 1,000,000:   20s.  Last read position: chr10:37,888,044
INFO	2016-05-17 06:50:43	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 06:50:59	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:35s.  Time for last 1,000,000:   15s.  Last read position: chr10:80,502,978
INFO	2016-05-17 06:50:59	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:51:18	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:54s.  Time for last 1,000,000:   18s.  Last read position: chr10:112,908,817
INFO	2016-05-17 06:51:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:51:22	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:58s.  Time for last 1,000,000:    3s.  Last read position: chr11:7,534,496
INFO	2016-05-17 06:51:22	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-17 06:51:31	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:01:07s.  Time for last 1,000,000:    8s.  Last read position: chr11:45,718,393
INFO	2016-05-17 06:51:31	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 06:51:36	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:01:12s.  Time for last 1,000,000:    5s.  Last read position: chr11:76,794,949
INFO	2016-05-17 06:51:36	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:51:46	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:01:22s.  Time for last 1,000,000:    9s.  Last read position: chr11:117,195,703
INFO	2016-05-17 06:51:46	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:51:51	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:01:27s.  Time for last 1,000,000:    5s.  Last read position: chr12:12,422,650
INFO	2016-05-17 06:51:51	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 06:51:59	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:01:35s.  Time for last 1,000,000:    7s.  Last read position: chr12:53,816,610
INFO	2016-05-17 06:51:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:52:04	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:01:40s.  Time for last 1,000,000:    5s.  Last read position: chr12:93,931,394
INFO	2016-05-17 06:52:04	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:52:14	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:50s.  Time for last 1,000,000:   10s.  Last read position: chr12:124,478,451
INFO	2016-05-17 06:52:14	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 06:52:20	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:57s.  Time for last 1,000,000:    6s.  Last read position: chr13:45,997,224
INFO	2016-05-17 06:52:20	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:52:27	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:02:03s.  Time for last 1,000,000:    6s.  Last read position: chr13:93,978,023
INFO	2016-05-17 06:52:27	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:52:34	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:02:11s.  Time for last 1,000,000:    7s.  Last read position: chr14:35,985,231
INFO	2016-05-17 06:52:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:52:51	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:02:27s.  Time for last 1,000,000:   16s.  Last read position: chr14:74,551,152
INFO	2016-05-17 06:52:51	MarkDuplicates	Tracking 24 as yet unmatched pairs. 24 records in RAM.
INFO	2016-05-17 06:52:56	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:02:32s.  Time for last 1,000,000:    5s.  Last read position: chr14:105,584,986
INFO	2016-05-17 06:52:56	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:53:03	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:02:40s.  Time for last 1,000,000:    7s.  Last read position: chr15:59,118,068
INFO	2016-05-17 06:53:03	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:53:07	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:02:43s.  Time for last 1,000,000:    3s.  Last read position: chr15:89,306,304
INFO	2016-05-17 06:53:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:53:12	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:02:48s.  Time for last 1,000,000:    4s.  Last read position: chr16:16,189,080
INFO	2016-05-17 06:53:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:53:16	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:02:52s.  Time for last 1,000,000:    3s.  Last read position: chr16:62,422,675
INFO	2016-05-17 06:53:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:53:22	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:02:58s.  Time for last 1,000,000:    5s.  Last read position: chr17:519,438
INFO	2016-05-17 06:53:22	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:53:31	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:03:07s.  Time for last 1,000,000:    8s.  Last read position: chr17:32,902,800
INFO	2016-05-17 06:53:31	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:53:36	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:03:12s.  Time for last 1,000,000:    4s.  Last read position: chr17:60,931,769
INFO	2016-05-17 06:53:36	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:53:41	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:03:17s.  Time for last 1,000,000:    5s.  Last read position: chr18:8,430,345
INFO	2016-05-17 06:53:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:53:45	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:03:22s.  Time for last 1,000,000:    4s.  Last read position: chr18:48,945,780
INFO	2016-05-17 06:53:45	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:53:53	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:03:30s.  Time for last 1,000,000:    8s.  Last read position: chr19:5,411,426
INFO	2016-05-17 06:53:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:54:00	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:03:36s.  Time for last 1,000,000:    6s.  Last read position: chr19:36,199,116
INFO	2016-05-17 06:54:00	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:54:06	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:03:42s.  Time for last 1,000,000:    5s.  Last read position: chr1:569,917
INFO	2016-05-17 06:54:06	MarkDuplicates	Tracking 1744 as yet unmatched pairs. 1744 records in RAM.
INFO	2016-05-17 06:54:15	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:03:51s.  Time for last 1,000,000:    8s.  Last read position: chr1:24,673,198
INFO	2016-05-17 06:54:15	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:54:28	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:04:04s.  Time for last 1,000,000:   13s.  Last read position: chr1:49,085,283
INFO	2016-05-17 06:54:28	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-05-17 06:54:33	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:04:10s.  Time for last 1,000,000:    5s.  Last read position: chr1:86,866,472
INFO	2016-05-17 06:54:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:54:40	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:04:16s.  Time for last 1,000,000:    6s.  Last read position: chr1:150,290,618
INFO	2016-05-17 06:54:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:54:46	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:04:22s.  Time for last 1,000,000:    5s.  Last read position: chr1:181,680,978
INFO	2016-05-17 06:54:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:54:50	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:04:26s.  Time for last 1,000,000:    3s.  Last read position: chr1:218,040,934
INFO	2016-05-17 06:54:50	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:54:53	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:04:29s.  Time for last 1,000,000:    3s.  Last read position: chr20:3,628,236
INFO	2016-05-17 06:54:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:54:57	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:04:33s.  Time for last 1,000,000:    3s.  Last read position: chr20:37,307,843
INFO	2016-05-17 06:54:57	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:55:01	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:04:38s.  Time for last 1,000,000:    4s.  Last read position: chr21:11,134,994
INFO	2016-05-17 06:55:01	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:55:07	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:04:44s.  Time for last 1,000,000:    6s.  Last read position: chr22:20,125,612
INFO	2016-05-17 06:55:07	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-17 06:55:13	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:04:50s.  Time for last 1,000,000:    6s.  Last read position: chr22:46,010,306
INFO	2016-05-17 06:55:13	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:55:22	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:04:58s.  Time for last 1,000,000:    8s.  Last read position: chr2:26,573,808
INFO	2016-05-17 06:55:22	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:55:27	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:05:04s.  Time for last 1,000,000:    5s.  Last read position: chr2:62,813,327
INFO	2016-05-17 06:55:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:55:32	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:05:08s.  Time for last 1,000,000:    4s.  Last read position: chr2:105,780,277
INFO	2016-05-17 06:55:32	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 06:55:37	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:05:13s.  Time for last 1,000,000:    4s.  Last read position: chr2:145,662,508
INFO	2016-05-17 06:55:37	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:55:44	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:05:20s.  Time for last 1,000,000:    6s.  Last read position: chr2:187,255,152
INFO	2016-05-17 06:55:44	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:55:53	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:05:29s.  Time for last 1,000,000:    9s.  Last read position: chr2:226,638,022
INFO	2016-05-17 06:55:53	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:55:58	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:05:34s.  Time for last 1,000,000:    4s.  Last read position: chr3:14,573,229
INFO	2016-05-17 06:55:58	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:56:05	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:05:41s.  Time for last 1,000,000:    6s.  Last read position: chr3:49,197,188
INFO	2016-05-17 06:56:05	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 06:56:11	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:05:47s.  Time for last 1,000,000:    6s.  Last read position: chr3:85,499,606
INFO	2016-05-17 06:56:11	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:56:18	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:05:54s.  Time for last 1,000,000:    6s.  Last read position: chr3:129,115,298
INFO	2016-05-17 06:56:18	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-17 06:56:22	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:05:58s.  Time for last 1,000,000:    3s.  Last read position: chr3:168,852,200
INFO	2016-05-17 06:56:22	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:56:26	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:06:02s.  Time for last 1,000,000:    3s.  Last read position: chr4:4,409,839
INFO	2016-05-17 06:56:26	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:56:29	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:06:06s.  Time for last 1,000,000:    3s.  Last read position: chr4:44,683,362
INFO	2016-05-17 06:56:29	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:56:35	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:06:12s.  Time for last 1,000,000:    5s.  Last read position: chr4:93,012,870
INFO	2016-05-17 06:56:35	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:56:42	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:06:18s.  Time for last 1,000,000:    6s.  Last read position: chr4:139,678,754
INFO	2016-05-17 06:56:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:56:48	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:06:24s.  Time for last 1,000,000:    6s.  Last read position: chr4:184,160,708
INFO	2016-05-17 06:56:48	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:56:52	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:06:28s.  Time for last 1,000,000:    3s.  Last read position: chr5:33,419,771
INFO	2016-05-17 06:56:52	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:56:56	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:06:32s.  Time for last 1,000,000:    4s.  Last read position: chr5:79,187,047
INFO	2016-05-17 06:56:56	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:57:03	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:06:39s.  Time for last 1,000,000:    6s.  Last read position: chr5:123,404,026
INFO	2016-05-17 06:57:03	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 06:57:15	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:06:52s.  Time for last 1,000,000:   12s.  Last read position: chr5:152,288,393
INFO	2016-05-17 06:57:15	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:57:20	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:06:57s.  Time for last 1,000,000:    5s.  Last read position: chr6:4,503,717
INFO	2016-05-17 06:57:20	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:57:27	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:07:03s.  Time for last 1,000,000:    6s.  Last read position: chr6:36,702,473
INFO	2016-05-17 06:57:27	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:57:33	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:07:10s.  Time for last 1,000,000:    6s.  Last read position: chr6:79,516,581
INFO	2016-05-17 06:57:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:57:40	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:07:16s.  Time for last 1,000,000:    6s.  Last read position: chr6:122,161,808
INFO	2016-05-17 06:57:40	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:57:44	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:07:20s.  Time for last 1,000,000:    4s.  Last read position: chr6:161,573,395
INFO	2016-05-17 06:57:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:57:47	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:07:24s.  Time for last 1,000,000:    3s.  Last read position: chr7:26,474,453
INFO	2016-05-17 06:57:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:57:51	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:07:27s.  Time for last 1,000,000:    3s.  Last read position: chr7:69,988,327
INFO	2016-05-17 06:57:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:57:54	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:07:31s.  Time for last 1,000,000:    3s.  Last read position: chr7:107,384,087
INFO	2016-05-17 06:57:54	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-05-17 06:58:00	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:07:37s.  Time for last 1,000,000:    5s.  Last read position: chr7:146,204,795
INFO	2016-05-17 06:58:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:58:06	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:07:42s.  Time for last 1,000,000:    5s.  Last read position: chr8:22,530,750
INFO	2016-05-17 06:58:06	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-05-17 06:58:12	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:07:48s.  Time for last 1,000,000:    5s.  Last read position: chr8:64,021,072
INFO	2016-05-17 06:58:12	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:58:18	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:07:54s.  Time for last 1,000,000:    6s.  Last read position: chr8:104,974,913
INFO	2016-05-17 06:58:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:58:24	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:08:01s.  Time for last 1,000,000:    6s.  Last read position: chr8:143,575,684
INFO	2016-05-17 06:58:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 06:58:32	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:08:08s.  Time for last 1,000,000:    7s.  Last read position: chr9:36,111,113
INFO	2016-05-17 06:58:32	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:58:40	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:08:16s.  Time for last 1,000,000:    7s.  Last read position: chr9:103,107,714
INFO	2016-05-17 06:58:40	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:58:44	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:08:20s.  Time for last 1,000,000:    3s.  Last read position: chr9:133,886,678
INFO	2016-05-17 06:58:44	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 06:58:49	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:08:26s.  Time for last 1,000,000:    5s.  Last read position: chrM:682
INFO	2016-05-17 06:58:49	MarkDuplicates	Tracking 17034 as yet unmatched pairs. 17034 records in RAM.
INFO	2016-05-17 06:58:55	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:08:31s.  Time for last 1,000,000:    5s.  Last read position: chrM:1,693
INFO	2016-05-17 06:58:55	MarkDuplicates	Tracking 10222 as yet unmatched pairs. 10222 records in RAM.
INFO	2016-05-17 06:58:59	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:08:35s.  Time for last 1,000,000:    4s.  Last read position: chrM:2,728
INFO	2016-05-17 06:58:59	MarkDuplicates	Tracking 46266 as yet unmatched pairs. 46266 records in RAM.
INFO	2016-05-17 06:59:06	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:08:42s.  Time for last 1,000,000:    6s.  Last read position: chrM:3,346
INFO	2016-05-17 06:59:06	MarkDuplicates	Tracking 29956 as yet unmatched pairs. 29956 records in RAM.
INFO	2016-05-17 06:59:10	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:08:46s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,906
INFO	2016-05-17 06:59:10	MarkDuplicates	Tracking 31200 as yet unmatched pairs. 31200 records in RAM.
INFO	2016-05-17 06:59:14	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:08:50s.  Time for last 1,000,000:    3s.  Last read position: chrM:5,413
INFO	2016-05-17 06:59:14	MarkDuplicates	Tracking 3462 as yet unmatched pairs. 3462 records in RAM.
INFO	2016-05-17 06:59:18	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:08:54s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,551
INFO	2016-05-17 06:59:18	MarkDuplicates	Tracking 18274 as yet unmatched pairs. 18274 records in RAM.
INFO	2016-05-17 06:59:21	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:08:58s.  Time for last 1,000,000:    3s.  Last read position: chrM:7,841
INFO	2016-05-17 06:59:21	MarkDuplicates	Tracking 19588 as yet unmatched pairs. 19588 records in RAM.
INFO	2016-05-17 06:59:28	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:09:04s.  Time for last 1,000,000:    6s.  Last read position: chrM:9,216
INFO	2016-05-17 06:59:28	MarkDuplicates	Tracking 11438 as yet unmatched pairs. 11438 records in RAM.
INFO	2016-05-17 06:59:32	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:09:09s.  Time for last 1,000,000:    4s.  Last read position: chrM:10,184
INFO	2016-05-17 06:59:32	MarkDuplicates	Tracking 21318 as yet unmatched pairs. 21318 records in RAM.
INFO	2016-05-17 06:59:38	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:09:14s.  Time for last 1,000,000:    5s.  Last read position: chrM:11,201
INFO	2016-05-17 06:59:38	MarkDuplicates	Tracking 7262 as yet unmatched pairs. 7262 records in RAM.
INFO	2016-05-17 06:59:43	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:09:20s.  Time for last 1,000,000:    5s.  Last read position: chrM:12,098
INFO	2016-05-17 06:59:43	MarkDuplicates	Tracking 26696 as yet unmatched pairs. 26696 records in RAM.
INFO	2016-05-17 06:59:49	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:09:25s.  Time for last 1,000,000:    5s.  Last read position: chrM:12,990
INFO	2016-05-17 06:59:49	MarkDuplicates	Tracking 5706 as yet unmatched pairs. 5706 records in RAM.
INFO	2016-05-17 07:00:03	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:09:39s.  Time for last 1,000,000:   14s.  Last read position: chrM:13,685
INFO	2016-05-17 07:00:03	MarkDuplicates	Tracking 14714 as yet unmatched pairs. 14714 records in RAM.
INFO	2016-05-17 07:00:09	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:09:45s.  Time for last 1,000,000:    5s.  Last read position: chrM:14,681
INFO	2016-05-17 07:00:09	MarkDuplicates	Tracking 2460 as yet unmatched pairs. 2460 records in RAM.
INFO	2016-05-17 07:00:14	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:09:50s.  Time for last 1,000,000:    5s.  Last read position: chrM:15,421
INFO	2016-05-17 07:00:14	MarkDuplicates	Tracking 28378 as yet unmatched pairs. 28378 records in RAM.
INFO	2016-05-17 07:00:17	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:09:53s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,989
INFO	2016-05-17 07:00:17	MarkDuplicates	Tracking 28842 as yet unmatched pairs. 28842 records in RAM.
INFO	2016-05-17 07:00:20	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:09:57s.  Time for last 1,000,000:    3s.  Last read position: chrX:13,405,754
INFO	2016-05-17 07:00:20	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:00:24	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:10:00s.  Time for last 1,000,000:    3s.  Last read position: chrX:55,017,452
INFO	2016-05-17 07:00:24	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:00:27	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:10:03s.  Time for last 1,000,000:    3s.  Last read position: chrX:110,524,399
INFO	2016-05-17 07:00:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 07:00:31	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:10:07s.  Time for last 1,000,000:    3s.  Last read position: chrX:154,503,909
INFO	2016-05-17 07:00:31	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:00:31	MarkDuplicates	Read 96022082 records. 0 pairs never matched.
INFO	2016-05-17 07:00:35	MarkDuplicates	After buildSortedReadEndLists freeMemory: 2275076976; totalMemory: 2302672896; maxMemory: 3817865216
INFO	2016-05-17 07:00:35	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-05-17 07:00:35	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-05-17 07:00:52	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-05-17 07:01:15	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-05-17 07:01:17	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2210789160; totalMemory: 3192389632; maxMemory: 3817865216
INFO	2016-05-17 07:01:17	MarkDuplicates	Marking 29766566 records as duplicates.
INFO	2016-05-17 07:01:17	MarkDuplicates	Found 5213050 optical duplicate clusters.
INFO	2016-05-17 07:02:52	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:34s.  Time for last 10,000,000:   94s.  Last read position: chr12:93,931,394
INFO	2016-05-17 07:04:26	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:03:08s.  Time for last 10,000,000:   93s.  Last read position: chr16:62,422,675
INFO	2016-05-17 07:05:58	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:04:40s.  Time for last 10,000,000:   92s.  Last read position: chr1:49,085,283
INFO	2016-05-17 07:07:31	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:06:13s.  Time for last 10,000,000:   93s.  Last read position: chr2:26,573,808
INFO	2016-05-17 07:09:06	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:07:48s.  Time for last 10,000,000:   95s.  Last read position: chr3:168,852,200
INFO	2016-05-17 07:10:40	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:09:22s.  Time for last 10,000,000:   93s.  Last read position: chr6:4,503,717
INFO	2016-05-17 07:12:15	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:10:57s.  Time for last 10,000,000:   95s.  Last read position: chr8:64,021,072
INFO	2016-05-17 07:13:39	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:12:21s.  Time for last 10,000,000:   84s.  Last read position: chrM:3,906
INFO	2016-05-17 07:14:57	MarkDuplicates	Written    90,000,000 records.  Elapsed time: 00:13:39s.  Time for last 10,000,000:   77s.  Last read position: chrM:14,681
INFO	2016-05-17 07:15:49	MarkDuplicates	Before output close freeMemory: 3301222408; totalMemory: 3331325952; maxMemory: 3817865216
INFO	2016-05-17 07:15:49	MarkDuplicates	After output close freeMemory: 3301221352; totalMemory: 3331325952; maxMemory: 3817865216
[Tue May 17 07:15:49 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 25.45 minutes.
Runtime.totalMemory()=3331325952
[bam_sort_core] merging from 40 files...

Num	5
ID	task.postalign_bam.nmsrt_bam_rep1.line_321.id_10
Name	nmsrt_bam rep1
Thread	thread_20
PID	38742

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

Start	2016-05-17 07:27:51
End	2016-05-17 07:41:13
Elapsed	00:13:22
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-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/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-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 14 files...

Num	6
ID	task.postalign_bam.bam_to_bedpe_rep1.line_425.id_11
Name	bam_to_bedpe rep1
Thread	thread_20
PID	39265

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

Start	2016-05-17 07:41:14
End	2016-05-17 07:42:47
Elapsed	00:01:33
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-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/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz

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

Num	7
ID	task.postalign_bed.subsample_bedpe_rep1.line_116.id_12
Name	subsample_bedpe rep1
Thread	thread_20
PID	39459

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

Start	2016-05-17 07:42:48
End	2016-05-17 07:44:09
Elapsed	00:01:21
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-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/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | grep -v "chrM" | shuf -n 17500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz

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

Num	8
ID	task.postalign_bam.bedpe_to_tag_rep1.line_465.id_13
Name	bedpe_to_tag rep1
Thread	thread_20
PID	39552

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

Start	2016-05-17 07:44:11
End	2016-05-17 07:45:38
Elapsed	00:01:27
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-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/ATAC5+6/align/rep1/ATAC5-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/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz

# SYS command. line 472

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz | grep -P -v 'chrM' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz; mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz

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

Num	9
ID	task.postalign_bed.shift_tag_rep1.line_140.id_14
Name	shift_tag rep1
Thread	thread_20
PID	39626

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

Start	2016-05-17 07:45:39
End	2016-05-17 07:46:34
Elapsed	00:00:55
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-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/ATAC5+6/align/rep1/ATAC5-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/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz

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

Num	10
ID	task.postalign_bed.subsample_bedpe2tagrep1.line_89.id_15
Name	subsample_bedpe2tagrep1
Thread	thread_20
PID	39690

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

Start	2016-05-17 07:46:35
End	2016-05-17 07:47:49
Elapsed	00:01:13
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-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/ATAC5+6/align/rep1/ATAC5-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/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz

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

Num	11
ID	task.postalign_bed.xcor_rep1.line_165.id_16
Name	xcor rep1
Thread	thread_20
PID	39755

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

Start	2016-05-17 07:47:49
End	2016-05-17 08:10:50
Elapsed	00:23:01
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep1/ATAC5-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/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz -p=1 \
			-filtchr=chrM -savp=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf -out=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep1/ATAC5-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/ATAC5+6/qc/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp

# SYS command. line 175

 mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc

   
--------------------Stdout--------------------
################
ChIP data: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-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/ATAC5+6/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/ATAC5+6/qc/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf 
result filename: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep1/ATAC5-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/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz 
opened /tmp/RtmpyBmyLs/ATAC5-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign9bf46433b966
done. read 15993598 fragments
ChIP data read length 76 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1755677 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.188741860252882 
Top 3 estimates for fragment length 0 
Window half size 525 
Phantom peak location 70 
Phantom peak Correlation 0.190159 
Normalized Strand cross-correlation coefficient (NSC) 1.075038 
Relative Strand Cross correlation Coefficient (RSC) 0.9028795 
Phantom Peak Quality Tag 0 
null device 
          1 

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

Num	12
ID	task.callpeak_macs2.macs2_atac_rep1.pval0.1.line_192.id_17
Name	macs2_atac rep1.pval0.1
Thread	thread_20
PID	39757

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

Start	2016-05-17 07:47:50
End	2016-05-17 08:04:23
Elapsed	00:16:33
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/signal/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/signal/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-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 07:47:52: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-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 07:47:52: #1 read tag files... 
INFO  @ Tue, 17 May 2016 07:47:52: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 07:47:53:  1000000 
INFO  @ Tue, 17 May 2016 07:47:55:  2000000 
INFO  @ Tue, 17 May 2016 07:47:57:  3000000 
INFO  @ Tue, 17 May 2016 07:47:58:  4000000 
INFO  @ Tue, 17 May 2016 07:48:00:  5000000 
INFO  @ Tue, 17 May 2016 07:48:01:  6000000 
INFO  @ Tue, 17 May 2016 07:48:03:  7000000 
INFO  @ Tue, 17 May 2016 07:48:04:  8000000 
INFO  @ Tue, 17 May 2016 07:48:06:  9000000 
INFO  @ Tue, 17 May 2016 07:48:08:  10000000 
INFO  @ Tue, 17 May 2016 07:48:09:  11000000 
INFO  @ Tue, 17 May 2016 07:48:11:  12000000 
INFO  @ Tue, 17 May 2016 07:48:12:  13000000 
INFO  @ Tue, 17 May 2016 07:48:14:  14000000 
INFO  @ Tue, 17 May 2016 07:48:16:  15000000 
INFO  @ Tue, 17 May 2016 07:48:17:  16000000 
INFO  @ Tue, 17 May 2016 07:48:19:  17000000 
INFO  @ Tue, 17 May 2016 07:48:20:  18000000 
INFO  @ Tue, 17 May 2016 07:48:22:  19000000 
INFO  @ Tue, 17 May 2016 07:48:24:  20000000 
INFO  @ Tue, 17 May 2016 07:48:25:  21000000 
INFO  @ Tue, 17 May 2016 07:48:27:  22000000 
INFO  @ Tue, 17 May 2016 07:48:29:  23000000 
INFO  @ Tue, 17 May 2016 07:48:30:  24000000 
INFO  @ Tue, 17 May 2016 07:48:32:  25000000 
INFO  @ Tue, 17 May 2016 07:48:33:  26000000 
INFO  @ Tue, 17 May 2016 07:48:35:  27000000 
INFO  @ Tue, 17 May 2016 07:48:37:  28000000 
INFO  @ Tue, 17 May 2016 07:48:38:  29000000 
INFO  @ Tue, 17 May 2016 07:48:40:  30000000 
INFO  @ Tue, 17 May 2016 07:48:41:  31000000 
INFO  @ Tue, 17 May 2016 07:48:45: #1 tag size is determined as 50 bps 
INFO  @ Tue, 17 May 2016 07:48:45: #1 tag size = 50 
INFO  @ Tue, 17 May 2016 07:48:45: #1  total tags in treatment: 31987196 
INFO  @ Tue, 17 May 2016 07:48:45: #1 finished! 
INFO  @ Tue, 17 May 2016 07:48:45: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 07:48:45: #2 Skipped... 
INFO  @ Tue, 17 May 2016 07:48:45: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 07:48:45: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 07:48:45: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 07:48:45: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 07:48:45: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 07:50:15: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 07:52:44: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 07:52:48: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 07:52:50: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 07:52:53: Done! 
INFO  @ Tue, 17 May 2016 07:53:07: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-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 07:53:07: #1 read tag files... 
INFO  @ Tue, 17 May 2016 07:53:07: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 07:53:08:  1000000 
INFO  @ Tue, 17 May 2016 07:53:10:  2000000 
INFO  @ Tue, 17 May 2016 07:53:12:  3000000 
INFO  @ Tue, 17 May 2016 07:53:13:  4000000 
INFO  @ Tue, 17 May 2016 07:53:15:  5000000 
INFO  @ Tue, 17 May 2016 07:53:16:  6000000 
INFO  @ Tue, 17 May 2016 07:53:18:  7000000 
INFO  @ Tue, 17 May 2016 07:53:20:  8000000 
INFO  @ Tue, 17 May 2016 07:53:21:  9000000 
INFO  @ Tue, 17 May 2016 07:53:23:  10000000 
INFO  @ Tue, 17 May 2016 07:53:24:  11000000 
INFO  @ Tue, 17 May 2016 07:53:26:  12000000 
INFO  @ Tue, 17 May 2016 07:53:28:  13000000 
INFO  @ Tue, 17 May 2016 07:53:29:  14000000 
INFO  @ Tue, 17 May 2016 07:53:31:  15000000 
INFO  @ Tue, 17 May 2016 07:53:32:  16000000 
INFO  @ Tue, 17 May 2016 07:53:34:  17000000 
INFO  @ Tue, 17 May 2016 07:53:36:  18000000 
INFO  @ Tue, 17 May 2016 07:53:37:  19000000 
INFO  @ Tue, 17 May 2016 07:53:39:  20000000 
INFO  @ Tue, 17 May 2016 07:53:40:  21000000 
INFO  @ Tue, 17 May 2016 07:53:42:  22000000 
INFO  @ Tue, 17 May 2016 07:53:44:  23000000 
INFO  @ Tue, 17 May 2016 07:53:45:  24000000 
INFO  @ Tue, 17 May 2016 07:53:47:  25000000 
INFO  @ Tue, 17 May 2016 07:53:49:  26000000 
INFO  @ Tue, 17 May 2016 07:53:50:  27000000 
INFO  @ Tue, 17 May 2016 07:53:52:  28000000 
INFO  @ Tue, 17 May 2016 07:53:53:  29000000 
INFO  @ Tue, 17 May 2016 07:53:55:  30000000 
INFO  @ Tue, 17 May 2016 07:53:57:  31000000 
INFO  @ Tue, 17 May 2016 07:54:00: #1 tag size is determined as 50 bps 
INFO  @ Tue, 17 May 2016 07:54:00: #1 tag size = 50 
INFO  @ Tue, 17 May 2016 07:54:00: #1  total tags in treatment: 31987196 
INFO  @ Tue, 17 May 2016 07:54:00: #1 finished! 
INFO  @ Tue, 17 May 2016 07:54:00: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 07:54:00: #2 Skipped... 
INFO  @ Tue, 17 May 2016 07:54:00: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 07:54:00: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 07:54:00: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 07:54:00: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 07:54:00: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Tue, 17 May 2016 07:54:00: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 07:55:27: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 07:55:27: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 07:55:27: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 07:55:27: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 07:55:27: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 08:03:59: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 08:04:06: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 08:04:10: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_summits.bed 
INFO  @ Tue, 17 May 2016 08:04:13: Done!

Num	13
ID	task.callpeak_macs2.macs2_atac_rep1.line_192.id_18
Name	macs2_atac rep1
Thread	thread_20
PID	39767

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

Start	2016-05-17 07:47:50
End	2016-05-17 08:29:30
Elapsed	00:41:40
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.gappedPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/signal/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/signal/macs2/rep1/ATAC5-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/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/signal/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/signal/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-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 07:47:52: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-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 07:47:52: #1 read tag files... 
INFO  @ Tue, 17 May 2016 07:47:52: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 07:47:53:  1000000 
INFO  @ Tue, 17 May 2016 07:47:55:  2000000 
INFO  @ Tue, 17 May 2016 07:47:57:  3000000 
INFO  @ Tue, 17 May 2016 07:47:58:  4000000 
INFO  @ Tue, 17 May 2016 07:48:00:  5000000 
INFO  @ Tue, 17 May 2016 07:48:01:  6000000 
INFO  @ Tue, 17 May 2016 07:48:03:  7000000 
INFO  @ Tue, 17 May 2016 07:48:05:  8000000 
INFO  @ Tue, 17 May 2016 07:48:06:  9000000 
INFO  @ Tue, 17 May 2016 07:48:08:  10000000 
INFO  @ Tue, 17 May 2016 07:48:09:  11000000 
INFO  @ Tue, 17 May 2016 07:48:11:  12000000 
INFO  @ Tue, 17 May 2016 07:48:13:  13000000 
INFO  @ Tue, 17 May 2016 07:48:14:  14000000 
INFO  @ Tue, 17 May 2016 07:48:16:  15000000 
INFO  @ Tue, 17 May 2016 07:48:18:  16000000 
INFO  @ Tue, 17 May 2016 07:48:19:  17000000 
INFO  @ Tue, 17 May 2016 07:48:21:  18000000 
INFO  @ Tue, 17 May 2016 07:48:22:  19000000 
INFO  @ Tue, 17 May 2016 07:48:24:  20000000 
INFO  @ Tue, 17 May 2016 07:48:26:  21000000 
INFO  @ Tue, 17 May 2016 07:48:27:  22000000 
INFO  @ Tue, 17 May 2016 07:48:29:  23000000 
INFO  @ Tue, 17 May 2016 07:48:30:  24000000 
INFO  @ Tue, 17 May 2016 07:48:32:  25000000 
INFO  @ Tue, 17 May 2016 07:48:34:  26000000 
INFO  @ Tue, 17 May 2016 07:48:35:  27000000 
INFO  @ Tue, 17 May 2016 07:48:37:  28000000 
INFO  @ Tue, 17 May 2016 07:48:38:  29000000 
INFO  @ Tue, 17 May 2016 07:48:40:  30000000 
INFO  @ Tue, 17 May 2016 07:48:42:  31000000 
INFO  @ Tue, 17 May 2016 07:48:45: #1 tag size is determined as 50 bps 
INFO  @ Tue, 17 May 2016 07:48:45: #1 tag size = 50 
INFO  @ Tue, 17 May 2016 07:48:45: #1  total tags in treatment: 31987196 
INFO  @ Tue, 17 May 2016 07:48:45: #1 finished! 
INFO  @ Tue, 17 May 2016 07:48:45: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 07:48:45: #2 Skipped... 
INFO  @ Tue, 17 May 2016 07:48:45: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 07:48:45: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 07:48:45: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 07:48:45: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 07:48:45: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 07:50:14: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 07:52:13: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls 
INFO  @ Tue, 17 May 2016 07:52:17: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 07:52:20: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 07:52:24: Done! 
INFO  @ Tue, 17 May 2016 07:52:40: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-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 07:52:40: #1 read tag files... 
INFO  @ Tue, 17 May 2016 07:52:40: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 07:52:42:  1000000 
INFO  @ Tue, 17 May 2016 07:52:44:  2000000 
INFO  @ Tue, 17 May 2016 07:52:45:  3000000 
INFO  @ Tue, 17 May 2016 07:52:47:  4000000 
INFO  @ Tue, 17 May 2016 07:52:49:  5000000 
INFO  @ Tue, 17 May 2016 07:52:51:  6000000 
INFO  @ Tue, 17 May 2016 07:52:52:  7000000 
INFO  @ Tue, 17 May 2016 07:52:54:  8000000 
INFO  @ Tue, 17 May 2016 07:52:56:  9000000 
INFO  @ Tue, 17 May 2016 07:52:58:  10000000 
INFO  @ Tue, 17 May 2016 07:52:59:  11000000 
INFO  @ Tue, 17 May 2016 07:53:01:  12000000 
INFO  @ Tue, 17 May 2016 07:53:03:  13000000 
INFO  @ Tue, 17 May 2016 07:53:04:  14000000 
INFO  @ Tue, 17 May 2016 07:53:06:  15000000 
INFO  @ Tue, 17 May 2016 07:53:08:  16000000 
INFO  @ Tue, 17 May 2016 07:53:10:  17000000 
INFO  @ Tue, 17 May 2016 07:53:11:  18000000 
INFO  @ Tue, 17 May 2016 07:53:13:  19000000 
INFO  @ Tue, 17 May 2016 07:53:15:  20000000 
INFO  @ Tue, 17 May 2016 07:53:17:  21000000 
INFO  @ Tue, 17 May 2016 07:53:18:  22000000 
INFO  @ Tue, 17 May 2016 07:53:20:  23000000 
INFO  @ Tue, 17 May 2016 07:53:22:  24000000 
INFO  @ Tue, 17 May 2016 07:53:23:  25000000 
INFO  @ Tue, 17 May 2016 07:53:25:  26000000 
INFO  @ Tue, 17 May 2016 07:53:27:  27000000 
INFO  @ Tue, 17 May 2016 07:53:29:  28000000 
INFO  @ Tue, 17 May 2016 07:53:30:  29000000 
INFO  @ Tue, 17 May 2016 07:53:32:  30000000 
INFO  @ Tue, 17 May 2016 07:53:34:  31000000 
INFO  @ Tue, 17 May 2016 07:53:38: #1 tag size is determined as 50 bps 
INFO  @ Tue, 17 May 2016 07:53:38: #1 tag size = 50 
INFO  @ Tue, 17 May 2016 07:53:38: #1  total tags in treatment: 31987196 
INFO  @ Tue, 17 May 2016 07:53:38: #1 finished! 
INFO  @ Tue, 17 May 2016 07:53:38: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 07:53:38: #2 Skipped... 
INFO  @ Tue, 17 May 2016 07:53:38: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 07:53:38: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 07:53:38: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 07:53:38: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 07:53:38: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Tue, 17 May 2016 07:53:38: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 07:55:00: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 07:55:00: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 07:55:00: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 07:55:00: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 07:55:00: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 08:00:31: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls 
INFO  @ Tue, 17 May 2016 08:00:34: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 08:00:35: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_summits.bed 
INFO  @ Tue, 17 May 2016 08:00:36: Done! 
INFO  @ Tue, 17 May 2016 08:00:40: Read and build treatment bedGraph... 
INFO  @ Tue, 17 May 2016 08:01:44: Read and build control bedGraph... 
INFO  @ Tue, 17 May 2016 08:02:15: Build scoreTrackII... 
INFO  @ Tue, 17 May 2016 08:02:55: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Tue, 17 May 2016 08:06:23: Write bedGraph of scores... 
INFO  @ Tue, 17 May 2016 08:08:40: Finished 'FE'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_FE.bdg'! 
INFO  @ Tue, 17 May 2016 08:15:06: Read and build treatment bedGraph... 
INFO  @ Tue, 17 May 2016 08:16:09: Read and build control bedGraph... 
INFO  @ Tue, 17 May 2016 08:16:40: Build scoreTrackII... 
INFO  @ Tue, 17 May 2016 08:17:25: Values in your input bedGraph files will be multiplied by 31.987196 ... 
INFO  @ Tue, 17 May 2016 08:21:11: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Tue, 17 May 2016 08:21:44: Write bedGraph of scores... 
INFO  @ Tue, 17 May 2016 08:23:33: Finished 'ppois'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_ppois.bdg'!

Num	14
ID	task.postalign_bam.nmsrt_bam_rep2.line_321.id_19
Name	nmsrt_bam rep2
Thread	thread_21
PID	41099

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

Start	2016-05-17 08:19:14
End	2016-05-17 08:44:33
Elapsed	00:25:18
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-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/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.nmsrt

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

Num	15
ID	task.postalign_bam.bam_to_bedpe_rep2.line_425.id_20
Name	bam_to_bedpe rep2
Thread	thread_21
PID	41890

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

Start	2016-05-17 08:44:33
End	2016-05-17 08:47:58
Elapsed	00:03:24
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-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/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz

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

Num	16
ID	task.postalign_bed.subsample_bedpe_rep2.line_116.id_21
Name	subsample_bedpe rep2
Thread	thread_21
PID	42044

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

Start	2016-05-17 08:47:59
End	2016-05-17 08:51:00
Elapsed	00:03:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-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/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | grep -v "chrM" | shuf -n 17500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz

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

Num	17
ID	task.postalign_bam.bedpe_to_tag_rep2.line_465.id_22
Name	bedpe_to_tag rep2
Thread	thread_21
PID	42144

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

Start	2016-05-17 08:51:01
End	2016-05-17 08:52:36
Elapsed	00:01:35
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-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/ATAC5+6/align/rep2/ATAC6-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/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz

# SYS command. line 472

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz | grep -P -v 'chrM' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz; mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz

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

Num	18
ID	task.postalign_bed.shift_tag_rep2.line_140.id_23
Name	shift_tag rep2
Thread	thread_21
PID	42218

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

Start	2016-05-17 08:52:37
End	2016-05-17 08:53:33
Elapsed	00:00:56
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-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/ATAC5+6/align/rep2/ATAC6-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/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz

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

Num	19
ID	task.postalign_bed.subsample_bedpe2tagrep2.line_89.id_24
Name	subsample_bedpe2tagrep2
Thread	thread_21
PID	42284

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

Start	2016-05-17 08:53:34
End	2016-05-17 08:56:00
Elapsed	00:02:26
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-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/ATAC5+6/align/rep2/ATAC6-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/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz

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

Num	20
ID	task.postalign_bed.xcor_rep2.line_165.id_25
Name	xcor rep2
Thread	thread_21
PID	42355

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

Start	2016-05-17 08:56:01
End	2016-05-17 09:34:40
Elapsed	00:38:39
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep2/ATAC6-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/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz -p=1 \
			-filtchr=chrM -savp=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf -out=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep2/ATAC6-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/ATAC5+6/qc/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp

# SYS command. line 175

 mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc

   
--------------------Stdout--------------------
################
ChIP data: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-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/ATAC5+6/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/ATAC5+6/qc/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf 
result filename: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep2/ATAC6-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/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz 
opened /tmp/Rtmp31U0d2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.25.tagAligna60c2b80f03e
done. read 25000000 fragments
ChIP data read length 75 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.2507344 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.25854675177943 
Top 3 estimates for fragment length 0 
Window half size 530 
Phantom peak location 65 
Phantom peak Correlation 0.2588778 
Normalized Strand cross-correlation coefficient (NSC) 1.031158 
Relative Strand Cross correlation Coefficient (RSC) 0.9593494 
Phantom Peak Quality Tag 0 
null device 
          1 

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

Num	21
ID	task.callpeak_macs2.macs2_atac_rep2.pval0.1.line_192.id_26
Name	macs2_atac rep2.pval0.1
Thread	thread_21
PID	42357

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

Start	2016-05-17 08:56:01
End	2016-05-17 09:14:40
Elapsed	00:18:39
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/signal/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/signal/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-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 08:56:04: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-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 08:56:04: #1 read tag files... 
INFO  @ Tue, 17 May 2016 08:56:04: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 08:56:05:  1000000 
INFO  @ Tue, 17 May 2016 08:56:07:  2000000 
INFO  @ Tue, 17 May 2016 08:56:09:  3000000 
INFO  @ Tue, 17 May 2016 08:56:10:  4000000 
INFO  @ Tue, 17 May 2016 08:56:12:  5000000 
INFO  @ Tue, 17 May 2016 08:56:13:  6000000 
INFO  @ Tue, 17 May 2016 08:56:15:  7000000 
INFO  @ Tue, 17 May 2016 08:56:17:  8000000 
INFO  @ Tue, 17 May 2016 08:56:18:  9000000 
INFO  @ Tue, 17 May 2016 08:56:20:  10000000 
INFO  @ Tue, 17 May 2016 08:56:21:  11000000 
INFO  @ Tue, 17 May 2016 08:56:23:  12000000 
INFO  @ Tue, 17 May 2016 08:56:25:  13000000 
INFO  @ Tue, 17 May 2016 08:56:26:  14000000 
INFO  @ Tue, 17 May 2016 08:56:28:  15000000 
INFO  @ Tue, 17 May 2016 08:56:29:  16000000 
INFO  @ Tue, 17 May 2016 08:56:31:  17000000 
INFO  @ Tue, 17 May 2016 08:56:32:  18000000 
INFO  @ Tue, 17 May 2016 08:56:34:  19000000 
INFO  @ Tue, 17 May 2016 08:56:36:  20000000 
INFO  @ Tue, 17 May 2016 08:56:37:  21000000 
INFO  @ Tue, 17 May 2016 08:56:39:  22000000 
INFO  @ Tue, 17 May 2016 08:56:40:  23000000 
INFO  @ Tue, 17 May 2016 08:56:42:  24000000 
INFO  @ Tue, 17 May 2016 08:56:44:  25000000 
INFO  @ Tue, 17 May 2016 08:56:45:  26000000 
INFO  @ Tue, 17 May 2016 08:56:47:  27000000 
INFO  @ Tue, 17 May 2016 08:56:48:  28000000 
INFO  @ Tue, 17 May 2016 08:56:50:  29000000 
INFO  @ Tue, 17 May 2016 08:56:52:  30000000 
INFO  @ Tue, 17 May 2016 08:56:53:  31000000 
INFO  @ Tue, 17 May 2016 08:56:55:  32000000 
INFO  @ Tue, 17 May 2016 08:56:56:  33000000 
INFO  @ Tue, 17 May 2016 08:56:58:  34000000 
INFO  @ Tue, 17 May 2016 08:57:00:  35000000 
INFO  @ Tue, 17 May 2016 08:57:02: #1 tag size is determined as 63 bps 
INFO  @ Tue, 17 May 2016 08:57:02: #1 tag size = 63 
INFO  @ Tue, 17 May 2016 08:57:02: #1  total tags in treatment: 35000000 
INFO  @ Tue, 17 May 2016 08:57:02: #1 finished! 
INFO  @ Tue, 17 May 2016 08:57:02: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 08:57:02: #2 Skipped... 
INFO  @ Tue, 17 May 2016 08:57:02: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 08:57:02: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 08:57:02: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 08:57:02: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 08:57:02: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 08:58:29: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 09:00:52: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 09:00:56: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 09:00:59: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 09:01:02: Done! 
INFO  @ Tue, 17 May 2016 09:01:15: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-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 09:01:15: #1 read tag files... 
INFO  @ Tue, 17 May 2016 09:01:15: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 09:01:16:  1000000 
INFO  @ Tue, 17 May 2016 09:01:18:  2000000 
INFO  @ Tue, 17 May 2016 09:01:20:  3000000 
INFO  @ Tue, 17 May 2016 09:01:22:  4000000 
INFO  @ Tue, 17 May 2016 09:01:23:  5000000 
INFO  @ Tue, 17 May 2016 09:01:25:  6000000 
INFO  @ Tue, 17 May 2016 09:01:27:  7000000 
INFO  @ Tue, 17 May 2016 09:01:29:  8000000 
INFO  @ Tue, 17 May 2016 09:01:30:  9000000 
INFO  @ Tue, 17 May 2016 09:01:32:  10000000 
INFO  @ Tue, 17 May 2016 09:01:34:  11000000 
INFO  @ Tue, 17 May 2016 09:01:36:  12000000 
INFO  @ Tue, 17 May 2016 09:01:37:  13000000 
INFO  @ Tue, 17 May 2016 09:01:39:  14000000 
INFO  @ Tue, 17 May 2016 09:01:41:  15000000 
INFO  @ Tue, 17 May 2016 09:01:43:  16000000 
INFO  @ Tue, 17 May 2016 09:01:44:  17000000 
INFO  @ Tue, 17 May 2016 09:01:46:  18000000 
INFO  @ Tue, 17 May 2016 09:01:48:  19000000 
INFO  @ Tue, 17 May 2016 09:01:50:  20000000 
INFO  @ Tue, 17 May 2016 09:01:51:  21000000 
INFO  @ Tue, 17 May 2016 09:01:53:  22000000 
INFO  @ Tue, 17 May 2016 09:01:55:  23000000 
INFO  @ Tue, 17 May 2016 09:01:57:  24000000 
INFO  @ Tue, 17 May 2016 09:01:58:  25000000 
INFO  @ Tue, 17 May 2016 09:02:00:  26000000 
INFO  @ Tue, 17 May 2016 09:02:02:  27000000 
INFO  @ Tue, 17 May 2016 09:02:04:  28000000 
INFO  @ Tue, 17 May 2016 09:02:05:  29000000 
INFO  @ Tue, 17 May 2016 09:02:07:  30000000 
INFO  @ Tue, 17 May 2016 09:02:09:  31000000 
INFO  @ Tue, 17 May 2016 09:02:11:  32000000 
INFO  @ Tue, 17 May 2016 09:02:12:  33000000 
INFO  @ Tue, 17 May 2016 09:02:14:  34000000 
INFO  @ Tue, 17 May 2016 09:02:16:  35000000 
INFO  @ Tue, 17 May 2016 09:02:18: #1 tag size is determined as 63 bps 
INFO  @ Tue, 17 May 2016 09:02:18: #1 tag size = 63 
INFO  @ Tue, 17 May 2016 09:02:18: #1  total tags in treatment: 35000000 
INFO  @ Tue, 17 May 2016 09:02:18: #1 finished! 
INFO  @ Tue, 17 May 2016 09:02:18: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 09:02:18: #2 Skipped... 
INFO  @ Tue, 17 May 2016 09:02:18: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 09:02:18: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 09:02:18: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 09:02:18: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 09:02:18: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Tue, 17 May 2016 09:02:18: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 09:04:00: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 09:04:00: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 09:04:00: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 09:04:00: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 09:04:00: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 09:14:08: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 09:14:17: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 09:14:24: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_summits.bed 
INFO  @ Tue, 17 May 2016 09:14:27: Done!

Num	22
ID	task.callpeak_macs2.macs2_atac_rep2.line_192.id_27
Name	macs2_atac rep2
Thread	thread_21
PID	42370

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

Start	2016-05-17 08:56:01
End	2016-05-17 09:43:33
Elapsed	00:47:31
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.gappedPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/signal/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/signal/macs2/rep2/ATAC6-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/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/signal/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/signal/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-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 08:56:03: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-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 08:56:03: #1 read tag files... 
INFO  @ Tue, 17 May 2016 08:56:03: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 08:56:05:  1000000 
INFO  @ Tue, 17 May 2016 08:56:07:  2000000 
INFO  @ Tue, 17 May 2016 08:56:09:  3000000 
INFO  @ Tue, 17 May 2016 08:56:10:  4000000 
INFO  @ Tue, 17 May 2016 08:56:12:  5000000 
INFO  @ Tue, 17 May 2016 08:56:13:  6000000 
INFO  @ Tue, 17 May 2016 08:56:15:  7000000 
INFO  @ Tue, 17 May 2016 08:56:17:  8000000 
INFO  @ Tue, 17 May 2016 08:56:18:  9000000 
INFO  @ Tue, 17 May 2016 08:56:20:  10000000 
INFO  @ Tue, 17 May 2016 08:56:21:  11000000 
INFO  @ Tue, 17 May 2016 08:56:23:  12000000 
INFO  @ Tue, 17 May 2016 08:56:25:  13000000 
INFO  @ Tue, 17 May 2016 08:56:26:  14000000 
INFO  @ Tue, 17 May 2016 08:56:28:  15000000 
INFO  @ Tue, 17 May 2016 08:56:29:  16000000 
INFO  @ Tue, 17 May 2016 08:56:31:  17000000 
INFO  @ Tue, 17 May 2016 08:56:33:  18000000 
INFO  @ Tue, 17 May 2016 08:56:34:  19000000 
INFO  @ Tue, 17 May 2016 08:56:36:  20000000 
INFO  @ Tue, 17 May 2016 08:56:37:  21000000 
INFO  @ Tue, 17 May 2016 08:56:39:  22000000 
INFO  @ Tue, 17 May 2016 08:56:41:  23000000 
INFO  @ Tue, 17 May 2016 08:56:42:  24000000 
INFO  @ Tue, 17 May 2016 08:56:44:  25000000 
INFO  @ Tue, 17 May 2016 08:56:45:  26000000 
INFO  @ Tue, 17 May 2016 08:56:47:  27000000 
INFO  @ Tue, 17 May 2016 08:56:49:  28000000 
INFO  @ Tue, 17 May 2016 08:56:50:  29000000 
INFO  @ Tue, 17 May 2016 08:56:52:  30000000 
INFO  @ Tue, 17 May 2016 08:56:53:  31000000 
INFO  @ Tue, 17 May 2016 08:56:55:  32000000 
INFO  @ Tue, 17 May 2016 08:56:57:  33000000 
INFO  @ Tue, 17 May 2016 08:56:58:  34000000 
INFO  @ Tue, 17 May 2016 08:57:00:  35000000 
INFO  @ Tue, 17 May 2016 08:57:02: #1 tag size is determined as 63 bps 
INFO  @ Tue, 17 May 2016 08:57:02: #1 tag size = 63 
INFO  @ Tue, 17 May 2016 08:57:02: #1  total tags in treatment: 35000000 
INFO  @ Tue, 17 May 2016 08:57:02: #1 finished! 
INFO  @ Tue, 17 May 2016 08:57:02: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 08:57:02: #2 Skipped... 
INFO  @ Tue, 17 May 2016 08:57:02: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 08:57:02: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 08:57:02: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 08:57:02: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 08:57:02: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 08:58:31: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 09:00:28: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls 
INFO  @ Tue, 17 May 2016 09:00:32: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 09:00:35: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 09:00:38: Done! 
INFO  @ Tue, 17 May 2016 09:00:51: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-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 09:00:51: #1 read tag files... 
INFO  @ Tue, 17 May 2016 09:00:51: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 09:00:53:  1000000 
INFO  @ Tue, 17 May 2016 09:00:55:  2000000 
INFO  @ Tue, 17 May 2016 09:00:56:  3000000 
INFO  @ Tue, 17 May 2016 09:00:58:  4000000 
INFO  @ Tue, 17 May 2016 09:00:59:  5000000 
INFO  @ Tue, 17 May 2016 09:01:01:  6000000 
INFO  @ Tue, 17 May 2016 09:01:03:  7000000 
INFO  @ Tue, 17 May 2016 09:01:04:  8000000 
INFO  @ Tue, 17 May 2016 09:01:06:  9000000 
INFO  @ Tue, 17 May 2016 09:01:08:  10000000 
INFO  @ Tue, 17 May 2016 09:01:09:  11000000 
INFO  @ Tue, 17 May 2016 09:01:11:  12000000 
INFO  @ Tue, 17 May 2016 09:01:12:  13000000 
INFO  @ Tue, 17 May 2016 09:01:14:  14000000 
INFO  @ Tue, 17 May 2016 09:01:16:  15000000 
INFO  @ Tue, 17 May 2016 09:01:17:  16000000 
INFO  @ Tue, 17 May 2016 09:01:19:  17000000 
INFO  @ Tue, 17 May 2016 09:01:20:  18000000 
INFO  @ Tue, 17 May 2016 09:01:22:  19000000 
INFO  @ Tue, 17 May 2016 09:01:23:  20000000 
INFO  @ Tue, 17 May 2016 09:01:25:  21000000 
INFO  @ Tue, 17 May 2016 09:01:27:  22000000 
INFO  @ Tue, 17 May 2016 09:01:28:  23000000 
INFO  @ Tue, 17 May 2016 09:01:30:  24000000 
INFO  @ Tue, 17 May 2016 09:01:31:  25000000 
INFO  @ Tue, 17 May 2016 09:01:33:  26000000 
INFO  @ Tue, 17 May 2016 09:01:35:  27000000 
INFO  @ Tue, 17 May 2016 09:01:36:  28000000 
INFO  @ Tue, 17 May 2016 09:01:38:  29000000 
INFO  @ Tue, 17 May 2016 09:01:39:  30000000 
INFO  @ Tue, 17 May 2016 09:01:41:  31000000 
INFO  @ Tue, 17 May 2016 09:01:43:  32000000 
INFO  @ Tue, 17 May 2016 09:01:44:  33000000 
INFO  @ Tue, 17 May 2016 09:01:46:  34000000 
INFO  @ Tue, 17 May 2016 09:01:47:  35000000 
INFO  @ Tue, 17 May 2016 09:01:50: #1 tag size is determined as 63 bps 
INFO  @ Tue, 17 May 2016 09:01:50: #1 tag size = 63 
INFO  @ Tue, 17 May 2016 09:01:50: #1  total tags in treatment: 35000000 
INFO  @ Tue, 17 May 2016 09:01:50: #1 finished! 
INFO  @ Tue, 17 May 2016 09:01:50: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 09:01:50: #2 Skipped... 
INFO  @ Tue, 17 May 2016 09:01:50: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 09:01:50: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 09:01:50: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 09:01:50: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 09:01:50: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Tue, 17 May 2016 09:01:50: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 09:03:18: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 09:03:18: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 09:03:18: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 09:03:18: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 09:03:18: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 09:08:29: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls 
INFO  @ Tue, 17 May 2016 09:08:31: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 09:08:32: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_summits.bed 
INFO  @ Tue, 17 May 2016 09:08:33: Done! 
INFO  @ Tue, 17 May 2016 09:08:36: Read and build treatment bedGraph... 
INFO  @ Tue, 17 May 2016 09:10:22: Read and build control bedGraph... 
INFO  @ Tue, 17 May 2016 09:11:05: Build scoreTrackII... 
INFO  @ Tue, 17 May 2016 09:11:53: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Tue, 17 May 2016 09:16:25: Write bedGraph of scores... 
INFO  @ Tue, 17 May 2016 09:19:06: Finished 'FE'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_FE.bdg'! 
INFO  @ Tue, 17 May 2016 09:27:11: Read and build treatment bedGraph... 
INFO  @ Tue, 17 May 2016 09:28:23: Read and build control bedGraph... 
INFO  @ Tue, 17 May 2016 09:29:00: Build scoreTrackII... 
INFO  @ Tue, 17 May 2016 09:29:37: Values in your input bedGraph files will be multiplied by 35.000000 ... 
INFO  @ Tue, 17 May 2016 09:33:41: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Tue, 17 May 2016 09:34:16: Write bedGraph of scores... 
INFO  @ Tue, 17 May 2016 09:36:47: Finished 'ppois'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_ppois.bdg'!

Num	23
ID	task.postalign_bed.pool_tag_reps.line_405.id_28
Name	pool_tag reps
Thread	thread_Root
PID	45285

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

Start	2016-05-17 09:43:34
End	2016-05-17 09:45:07
Elapsed	00:01:33
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/pooled_rep/ATAC5-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/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz  | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz

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

Num	24
ID	task.callpeak_macs2.macs2_atac_pooled.pval0.1.line_192.id_29
Name	macs2_atac pooled.pval0.1
Thread	thread_Root
PID	45479

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

Start	2016-05-17 09:45:08
End	2016-05-17 10:35:11
Elapsed	00:50:03
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/align/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/align/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/signal/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/align/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/signal/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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 09:45:11: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/align/pooled_rep/ATAC5-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 09:45:11: #1 read tag files... 
INFO  @ Tue, 17 May 2016 09:45:11: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 09:45:13:  1000000 
INFO  @ Tue, 17 May 2016 09:45:15:  2000000 
INFO  @ Tue, 17 May 2016 09:45:16:  3000000 
INFO  @ Tue, 17 May 2016 09:45:18:  4000000 
INFO  @ Tue, 17 May 2016 09:45:19:  5000000 
INFO  @ Tue, 17 May 2016 09:45:21:  6000000 
INFO  @ Tue, 17 May 2016 09:45:23:  7000000 
INFO  @ Tue, 17 May 2016 09:45:24:  8000000 
INFO  @ Tue, 17 May 2016 09:45:26:  9000000 
INFO  @ Tue, 17 May 2016 09:45:28:  10000000 
INFO  @ Tue, 17 May 2016 09:45:29:  11000000 
INFO  @ Tue, 17 May 2016 09:45:31:  12000000 
INFO  @ Tue, 17 May 2016 09:45:33:  13000000 
INFO  @ Tue, 17 May 2016 09:45:34:  14000000 
INFO  @ Tue, 17 May 2016 09:45:36:  15000000 
INFO  @ Tue, 17 May 2016 09:45:38:  16000000 
INFO  @ Tue, 17 May 2016 09:45:39:  17000000 
INFO  @ Tue, 17 May 2016 09:45:41:  18000000 
INFO  @ Tue, 17 May 2016 09:45:43:  19000000 
INFO  @ Tue, 17 May 2016 09:45:44:  20000000 
INFO  @ Tue, 17 May 2016 09:45:46:  21000000 
INFO  @ Tue, 17 May 2016 09:45:48:  22000000 
INFO  @ Tue, 17 May 2016 09:45:50:  23000000 
INFO  @ Tue, 17 May 2016 09:45:53:  24000000 
INFO  @ Tue, 17 May 2016 09:45:57:  25000000 
INFO  @ Tue, 17 May 2016 09:46:01:  26000000 
INFO  @ Tue, 17 May 2016 09:46:05:  27000000 
INFO  @ Tue, 17 May 2016 09:46:09:  28000000 
INFO  @ Tue, 17 May 2016 09:46:12:  29000000 
INFO  @ Tue, 17 May 2016 09:46:16:  30000000 
INFO  @ Tue, 17 May 2016 09:46:21:  31000000 
INFO  @ Tue, 17 May 2016 09:46:25:  32000000 
INFO  @ Tue, 17 May 2016 09:46:28:  33000000 
INFO  @ Tue, 17 May 2016 09:46:31:  34000000 
INFO  @ Tue, 17 May 2016 09:46:35:  35000000 
INFO  @ Tue, 17 May 2016 09:46:37:  36000000 
INFO  @ Tue, 17 May 2016 09:46:38:  37000000 
INFO  @ Tue, 17 May 2016 09:46:40:  38000000 
INFO  @ Tue, 17 May 2016 09:46:42:  39000000 
INFO  @ Tue, 17 May 2016 09:46:45:  40000000 
INFO  @ Tue, 17 May 2016 09:46:47:  41000000 
INFO  @ Tue, 17 May 2016 09:46:49:  42000000 
INFO  @ Tue, 17 May 2016 09:46:52:  43000000 
INFO  @ Tue, 17 May 2016 09:46:55:  44000000 
INFO  @ Tue, 17 May 2016 09:46:58:  45000000 
INFO  @ Tue, 17 May 2016 09:47:01:  46000000 
INFO  @ Tue, 17 May 2016 09:47:02:  47000000 
INFO  @ Tue, 17 May 2016 09:47:04:  48000000 
INFO  @ Tue, 17 May 2016 09:47:06:  49000000 
INFO  @ Tue, 17 May 2016 09:47:07:  50000000 
INFO  @ Tue, 17 May 2016 09:47:09:  51000000 
INFO  @ Tue, 17 May 2016 09:47:11:  52000000 
INFO  @ Tue, 17 May 2016 09:47:12:  53000000 
INFO  @ Tue, 17 May 2016 09:47:14:  54000000 
INFO  @ Tue, 17 May 2016 09:47:16:  55000000 
INFO  @ Tue, 17 May 2016 09:47:17:  56000000 
INFO  @ Tue, 17 May 2016 09:47:19:  57000000 
INFO  @ Tue, 17 May 2016 09:47:21:  58000000 
INFO  @ Tue, 17 May 2016 09:47:22:  59000000 
INFO  @ Tue, 17 May 2016 09:47:24:  60000000 
INFO  @ Tue, 17 May 2016 09:47:25:  61000000 
INFO  @ Tue, 17 May 2016 09:47:27:  62000000 
INFO  @ Tue, 17 May 2016 09:47:29:  63000000 
INFO  @ Tue, 17 May 2016 09:47:30:  64000000 
INFO  @ Tue, 17 May 2016 09:47:32:  65000000 
INFO  @ Tue, 17 May 2016 09:47:34:  66000000 
INFO  @ Tue, 17 May 2016 09:47:41: #1 tag size is determined as 50 bps 
INFO  @ Tue, 17 May 2016 09:47:41: #1 tag size = 50 
INFO  @ Tue, 17 May 2016 09:47:41: #1  total tags in treatment: 66987196 
INFO  @ Tue, 17 May 2016 09:47:41: #1 finished! 
INFO  @ Tue, 17 May 2016 09:47:41: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 09:47:41: #2 Skipped... 
INFO  @ Tue, 17 May 2016 09:47:41: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 09:47:41: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 09:47:41: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 09:47:41: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 09:47:41: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 09:52:22: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 10:01:29: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 10:01:33: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 10:01:36: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 10:01:37: Done! 
INFO  @ Tue, 17 May 2016 10:01:49: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/align/pooled_rep/ATAC5-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 10:01:49: #1 read tag files... 
INFO  @ Tue, 17 May 2016 10:01:49: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 10:01:51:  1000000 
INFO  @ Tue, 17 May 2016 10:01:52:  2000000 
INFO  @ Tue, 17 May 2016 10:01:54:  3000000 
INFO  @ Tue, 17 May 2016 10:01:56:  4000000 
INFO  @ Tue, 17 May 2016 10:01:58:  5000000 
INFO  @ Tue, 17 May 2016 10:02:01:  6000000 
INFO  @ Tue, 17 May 2016 10:02:03:  7000000 
INFO  @ Tue, 17 May 2016 10:02:05:  8000000 
INFO  @ Tue, 17 May 2016 10:02:08:  9000000 
INFO  @ Tue, 17 May 2016 10:02:11:  10000000 
INFO  @ Tue, 17 May 2016 10:02:14:  11000000 
INFO  @ Tue, 17 May 2016 10:02:16:  12000000 
INFO  @ Tue, 17 May 2016 10:02:17:  13000000 
INFO  @ Tue, 17 May 2016 10:02:19:  14000000 
INFO  @ Tue, 17 May 2016 10:02:21:  15000000 
INFO  @ Tue, 17 May 2016 10:02:24:  16000000 
INFO  @ Tue, 17 May 2016 10:02:27:  17000000 
INFO  @ Tue, 17 May 2016 10:02:29:  18000000 
INFO  @ Tue, 17 May 2016 10:02:31:  19000000 
INFO  @ Tue, 17 May 2016 10:02:33:  20000000 
INFO  @ Tue, 17 May 2016 10:02:34:  21000000 
INFO  @ Tue, 17 May 2016 10:02:36:  22000000 
INFO  @ Tue, 17 May 2016 10:02:38:  23000000 
INFO  @ Tue, 17 May 2016 10:02:41:  24000000 
INFO  @ Tue, 17 May 2016 10:02:43:  25000000 
INFO  @ Tue, 17 May 2016 10:02:46:  26000000 
INFO  @ Tue, 17 May 2016 10:02:49:  27000000 
INFO  @ Tue, 17 May 2016 10:02:53:  28000000 
INFO  @ Tue, 17 May 2016 10:02:56:  29000000 
INFO  @ Tue, 17 May 2016 10:02:59:  30000000 
INFO  @ Tue, 17 May 2016 10:03:00:  31000000 
INFO  @ Tue, 17 May 2016 10:03:02:  32000000 
INFO  @ Tue, 17 May 2016 10:03:03:  33000000 
INFO  @ Tue, 17 May 2016 10:03:05:  34000000 
INFO  @ Tue, 17 May 2016 10:03:07:  35000000 
INFO  @ Tue, 17 May 2016 10:03:08:  36000000 
INFO  @ Tue, 17 May 2016 10:03:10:  37000000 
INFO  @ Tue, 17 May 2016 10:03:12:  38000000 
INFO  @ Tue, 17 May 2016 10:03:13:  39000000 
INFO  @ Tue, 17 May 2016 10:03:16:  40000000 
INFO  @ Tue, 17 May 2016 10:03:19:  41000000 
INFO  @ Tue, 17 May 2016 10:03:22:  42000000 
INFO  @ Tue, 17 May 2016 10:03:26:  43000000 
INFO  @ Tue, 17 May 2016 10:03:29:  44000000 
INFO  @ Tue, 17 May 2016 10:03:32:  45000000 
INFO  @ Tue, 17 May 2016 10:03:35:  46000000 
INFO  @ Tue, 17 May 2016 10:03:39:  47000000 
INFO  @ Tue, 17 May 2016 10:03:42:  48000000 
INFO  @ Tue, 17 May 2016 10:03:45:  49000000 
INFO  @ Tue, 17 May 2016 10:03:48:  50000000 
INFO  @ Tue, 17 May 2016 10:03:52:  51000000 
INFO  @ Tue, 17 May 2016 10:03:55:  52000000 
INFO  @ Tue, 17 May 2016 10:03:59:  53000000 
INFO  @ Tue, 17 May 2016 10:04:02:  54000000 
INFO  @ Tue, 17 May 2016 10:04:05:  55000000 
INFO  @ Tue, 17 May 2016 10:04:08:  56000000 
INFO  @ Tue, 17 May 2016 10:04:12:  57000000 
INFO  @ Tue, 17 May 2016 10:04:15:  58000000 
INFO  @ Tue, 17 May 2016 10:04:18:  59000000 
INFO  @ Tue, 17 May 2016 10:04:22:  60000000 
INFO  @ Tue, 17 May 2016 10:04:25:  61000000 
INFO  @ Tue, 17 May 2016 10:04:28:  62000000 
INFO  @ Tue, 17 May 2016 10:04:32:  63000000 
INFO  @ Tue, 17 May 2016 10:04:35:  64000000 
INFO  @ Tue, 17 May 2016 10:04:38:  65000000 
INFO  @ Tue, 17 May 2016 10:04:41:  66000000 
INFO  @ Tue, 17 May 2016 10:04:51: #1 tag size is determined as 50 bps 
INFO  @ Tue, 17 May 2016 10:04:51: #1 tag size = 50 
INFO  @ Tue, 17 May 2016 10:04:51: #1  total tags in treatment: 66987196 
INFO  @ Tue, 17 May 2016 10:04:51: #1 finished! 
INFO  @ Tue, 17 May 2016 10:04:51: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 10:04:51: #2 Skipped... 
INFO  @ Tue, 17 May 2016 10:04:51: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 10:04:51: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 10:04:51: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 10:04:51: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 10:04:51: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Tue, 17 May 2016 10:04:51: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 10:10:06: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 10:10:06: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 10:10:06: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 10:10:06: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 10:10:06: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 10:34:21: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 10:34:38: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 10:34:50: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_summits.bed 
INFO  @ Tue, 17 May 2016 10:34:54: Done!

Num	25
ID	task.callpeak_macs2.macs2_atac_pooled.line_192.id_30
Name	macs2_atac pooled
Thread	thread_Root
PID	45481

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

Start	2016-05-17 09:45:08
End	2016-05-17 11:41:06
Elapsed	01:55:58
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.gappedPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/signal/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/signal/macs2/pooled_rep/ATAC5-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/ATAC5+6/align/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/align/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/signal/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/align/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/signal/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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 09:45:11: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/pooled_rep/ATAC5-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 09:45:11: #1 read tag files... 
INFO  @ Tue, 17 May 2016 09:45:11: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 09:45:13:  1000000 
INFO  @ Tue, 17 May 2016 09:45:15:  2000000 
INFO  @ Tue, 17 May 2016 09:45:16:  3000000 
INFO  @ Tue, 17 May 2016 09:45:18:  4000000 
INFO  @ Tue, 17 May 2016 09:45:20:  5000000 
INFO  @ Tue, 17 May 2016 09:45:22:  6000000 
INFO  @ Tue, 17 May 2016 09:45:24:  7000000 
INFO  @ Tue, 17 May 2016 09:45:25:  8000000 
INFO  @ Tue, 17 May 2016 09:45:27:  9000000 
INFO  @ Tue, 17 May 2016 09:45:29:  10000000 
INFO  @ Tue, 17 May 2016 09:45:31:  11000000 
INFO  @ Tue, 17 May 2016 09:45:32:  12000000 
INFO  @ Tue, 17 May 2016 09:45:34:  13000000 
INFO  @ Tue, 17 May 2016 09:45:36:  14000000 
INFO  @ Tue, 17 May 2016 09:45:38:  15000000 
INFO  @ Tue, 17 May 2016 09:45:39:  16000000 
INFO  @ Tue, 17 May 2016 09:45:41:  17000000 
INFO  @ Tue, 17 May 2016 09:45:43:  18000000 
INFO  @ Tue, 17 May 2016 09:45:45:  19000000 
INFO  @ Tue, 17 May 2016 09:45:47:  20000000 
INFO  @ Tue, 17 May 2016 09:45:48:  21000000 
INFO  @ Tue, 17 May 2016 09:45:51:  22000000 
INFO  @ Tue, 17 May 2016 09:45:55:  23000000 
INFO  @ Tue, 17 May 2016 09:45:58:  24000000 
INFO  @ Tue, 17 May 2016 09:46:03:  25000000 
INFO  @ Tue, 17 May 2016 09:46:07:  26000000 
INFO  @ Tue, 17 May 2016 09:46:10:  27000000 
INFO  @ Tue, 17 May 2016 09:46:14:  28000000 
INFO  @ Tue, 17 May 2016 09:46:18:  29000000 
INFO  @ Tue, 17 May 2016 09:46:22:  30000000 
INFO  @ Tue, 17 May 2016 09:46:25:  31000000 
INFO  @ Tue, 17 May 2016 09:46:29:  32000000 
INFO  @ Tue, 17 May 2016 09:46:32:  33000000 
INFO  @ Tue, 17 May 2016 09:46:34:  34000000 
INFO  @ Tue, 17 May 2016 09:46:36:  35000000 
INFO  @ Tue, 17 May 2016 09:46:38:  36000000 
INFO  @ Tue, 17 May 2016 09:46:40:  37000000 
INFO  @ Tue, 17 May 2016 09:46:42:  38000000 
INFO  @ Tue, 17 May 2016 09:46:45:  39000000 
INFO  @ Tue, 17 May 2016 09:46:47:  40000000 
INFO  @ Tue, 17 May 2016 09:46:49:  41000000 
INFO  @ Tue, 17 May 2016 09:46:51:  42000000 
INFO  @ Tue, 17 May 2016 09:46:52:  43000000 
INFO  @ Tue, 17 May 2016 09:46:54:  44000000 
INFO  @ Tue, 17 May 2016 09:46:56:  45000000 
INFO  @ Tue, 17 May 2016 09:46:58:  46000000 
INFO  @ Tue, 17 May 2016 09:47:01:  47000000 
INFO  @ Tue, 17 May 2016 09:47:02:  48000000 
INFO  @ Tue, 17 May 2016 09:47:04:  49000000 
INFO  @ Tue, 17 May 2016 09:47:06:  50000000 
INFO  @ Tue, 17 May 2016 09:47:08:  51000000 
INFO  @ Tue, 17 May 2016 09:47:10:  52000000 
INFO  @ Tue, 17 May 2016 09:47:11:  53000000 
INFO  @ Tue, 17 May 2016 09:47:13:  54000000 
INFO  @ Tue, 17 May 2016 09:47:15:  55000000 
INFO  @ Tue, 17 May 2016 09:47:17:  56000000 
INFO  @ Tue, 17 May 2016 09:47:19:  57000000 
INFO  @ Tue, 17 May 2016 09:47:20:  58000000 
INFO  @ Tue, 17 May 2016 09:47:22:  59000000 
INFO  @ Tue, 17 May 2016 09:47:24:  60000000 
INFO  @ Tue, 17 May 2016 09:47:26:  61000000 
INFO  @ Tue, 17 May 2016 09:47:27:  62000000 
INFO  @ Tue, 17 May 2016 09:47:29:  63000000 
INFO  @ Tue, 17 May 2016 09:47:31:  64000000 
INFO  @ Tue, 17 May 2016 09:47:33:  65000000 
INFO  @ Tue, 17 May 2016 09:47:35:  66000000 
INFO  @ Tue, 17 May 2016 09:47:43: #1 tag size is determined as 50 bps 
INFO  @ Tue, 17 May 2016 09:47:43: #1 tag size = 50 
INFO  @ Tue, 17 May 2016 09:47:43: #1  total tags in treatment: 66987196 
INFO  @ Tue, 17 May 2016 09:47:43: #1 finished! 
INFO  @ Tue, 17 May 2016 09:47:43: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 09:47:43: #2 Skipped... 
INFO  @ Tue, 17 May 2016 09:47:43: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 09:47:43: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 09:47:43: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 09:47:43: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 09:47:43: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 09:52:49: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 10:00:06: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.xls 
INFO  @ Tue, 17 May 2016 10:00:12: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 10:00:16: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 10:00:19: Done! 
INFO  @ Tue, 17 May 2016 10:00:37: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/pooled_rep/ATAC5-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 10:00:37: #1 read tag files... 
INFO  @ Tue, 17 May 2016 10:00:37: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 10:00:40:  1000000 
INFO  @ Tue, 17 May 2016 10:00:43:  2000000 
INFO  @ Tue, 17 May 2016 10:00:45:  3000000 
INFO  @ Tue, 17 May 2016 10:00:48:  4000000 
INFO  @ Tue, 17 May 2016 10:00:52:  5000000 
INFO  @ Tue, 17 May 2016 10:00:56:  6000000 
INFO  @ Tue, 17 May 2016 10:00:58:  7000000 
INFO  @ Tue, 17 May 2016 10:01:00:  8000000 
INFO  @ Tue, 17 May 2016 10:01:02:  9000000 
INFO  @ Tue, 17 May 2016 10:01:05:  10000000 
INFO  @ Tue, 17 May 2016 10:01:08:  11000000 
INFO  @ Tue, 17 May 2016 10:01:11:  12000000 
INFO  @ Tue, 17 May 2016 10:01:14:  13000000 
INFO  @ Tue, 17 May 2016 10:01:18:  14000000 
INFO  @ Tue, 17 May 2016 10:01:21:  15000000 
INFO  @ Tue, 17 May 2016 10:01:24:  16000000 
INFO  @ Tue, 17 May 2016 10:01:27:  17000000 
INFO  @ Tue, 17 May 2016 10:01:30:  18000000 
INFO  @ Tue, 17 May 2016 10:01:33:  19000000 
INFO  @ Tue, 17 May 2016 10:01:36:  20000000 
INFO  @ Tue, 17 May 2016 10:01:38:  21000000 
INFO  @ Tue, 17 May 2016 10:01:40:  22000000 
INFO  @ Tue, 17 May 2016 10:01:41:  23000000 
INFO  @ Tue, 17 May 2016 10:01:44:  24000000 
INFO  @ Tue, 17 May 2016 10:01:45:  25000000 
INFO  @ Tue, 17 May 2016 10:01:47:  26000000 
INFO  @ Tue, 17 May 2016 10:01:49:  27000000 
INFO  @ Tue, 17 May 2016 10:01:50:  28000000 
INFO  @ Tue, 17 May 2016 10:01:52:  29000000 
INFO  @ Tue, 17 May 2016 10:01:54:  30000000 
INFO  @ Tue, 17 May 2016 10:01:57:  31000000 
INFO  @ Tue, 17 May 2016 10:01:59:  32000000 
INFO  @ Tue, 17 May 2016 10:02:02:  33000000 
INFO  @ Tue, 17 May 2016 10:02:04:  34000000 
INFO  @ Tue, 17 May 2016 10:02:06:  35000000 
INFO  @ Tue, 17 May 2016 10:02:09:  36000000 
INFO  @ Tue, 17 May 2016 10:02:12:  37000000 
INFO  @ Tue, 17 May 2016 10:02:15:  38000000 
INFO  @ Tue, 17 May 2016 10:02:18:  39000000 
INFO  @ Tue, 17 May 2016 10:02:21:  40000000 
INFO  @ Tue, 17 May 2016 10:02:23:  41000000 
INFO  @ Tue, 17 May 2016 10:02:25:  42000000 
INFO  @ Tue, 17 May 2016 10:02:29:  43000000 
INFO  @ Tue, 17 May 2016 10:02:32:  44000000 
INFO  @ Tue, 17 May 2016 10:02:35:  45000000 
INFO  @ Tue, 17 May 2016 10:02:38:  46000000 
INFO  @ Tue, 17 May 2016 10:02:41:  47000000 
INFO  @ Tue, 17 May 2016 10:02:44:  48000000 
INFO  @ Tue, 17 May 2016 10:02:47:  49000000 
INFO  @ Tue, 17 May 2016 10:02:50:  50000000 
INFO  @ Tue, 17 May 2016 10:02:53:  51000000 
INFO  @ Tue, 17 May 2016 10:02:56:  52000000 
INFO  @ Tue, 17 May 2016 10:02:59:  53000000 
INFO  @ Tue, 17 May 2016 10:03:02:  54000000 
INFO  @ Tue, 17 May 2016 10:03:05:  55000000 
INFO  @ Tue, 17 May 2016 10:03:08:  56000000 
INFO  @ Tue, 17 May 2016 10:03:11:  57000000 
INFO  @ Tue, 17 May 2016 10:03:14:  58000000 
INFO  @ Tue, 17 May 2016 10:03:17:  59000000 
INFO  @ Tue, 17 May 2016 10:03:21:  60000000 
INFO  @ Tue, 17 May 2016 10:03:24:  61000000 
INFO  @ Tue, 17 May 2016 10:03:27:  62000000 
INFO  @ Tue, 17 May 2016 10:03:31:  63000000 
INFO  @ Tue, 17 May 2016 10:03:34:  64000000 
INFO  @ Tue, 17 May 2016 10:03:37:  65000000 
INFO  @ Tue, 17 May 2016 10:03:40:  66000000 
INFO  @ Tue, 17 May 2016 10:03:49: #1 tag size is determined as 50 bps 
INFO  @ Tue, 17 May 2016 10:03:49: #1 tag size = 50 
INFO  @ Tue, 17 May 2016 10:03:49: #1  total tags in treatment: 66987196 
INFO  @ Tue, 17 May 2016 10:03:49: #1 finished! 
INFO  @ Tue, 17 May 2016 10:03:49: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 10:03:49: #2 Skipped... 
INFO  @ Tue, 17 May 2016 10:03:49: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 10:03:49: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 10:03:49: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 10:03:49: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 10:03:49: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Tue, 17 May 2016 10:03:49: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 10:08:49: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 10:08:49: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 10:08:49: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 10:08:49: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 10:08:49: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 10:24:54: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.xls 
INFO  @ Tue, 17 May 2016 10:24:58: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 10:25:02: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_summits.bed 
INFO  @ Tue, 17 May 2016 10:25:04: Done! 
INFO  @ Tue, 17 May 2016 10:25:11: Read and build treatment bedGraph... 
INFO  @ Tue, 17 May 2016 10:29:18: Read and build control bedGraph... 
INFO  @ Tue, 17 May 2016 10:31:11: Build scoreTrackII... 
INFO  @ Tue, 17 May 2016 10:33:16: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Tue, 17 May 2016 10:44:42: Write bedGraph of scores... 
INFO  @ Tue, 17 May 2016 10:54:29: Finished 'FE'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_FE.bdg'! 
INFO  @ Tue, 17 May 2016 11:10:09: Read and build treatment bedGraph... 
INFO  @ Tue, 17 May 2016 11:12:48: Read and build control bedGraph... 
INFO  @ Tue, 17 May 2016 11:14:03: Build scoreTrackII... 
INFO  @ Tue, 17 May 2016 11:15:07: Values in your input bedGraph files will be multiplied by 66.987196 ... 
INFO  @ Tue, 17 May 2016 11:22:30: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Tue, 17 May 2016 11:23:35: Write bedGraph of scores... 
INFO  @ Tue, 17 May 2016 11:27:50: Finished 'ppois'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_ppois.bdg'!

Num	26
ID	task.callpeak_etc.filt_top_peaks_rep1.line_25.id_31
Name	filt_top_peaks rep1
Thread	thread_Root
PID	51022

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

Start	2016-05-17 11:41:07
End	2016-05-17 11:41:18
Elapsed	00:00:10
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz

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

Num	27
ID	task.callpeak_etc.filt_top_peaks_rep1.line_25.id_32
Name	filt_top_peaks rep1
Thread	thread_Root
PID	51024

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

Start	2016-05-17 11:41:07
End	2016-05-17 11:41:17
Elapsed	00:00:10
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-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/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.gappedPeak.gz

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

Num	28
ID	task.callpeak_etc.filt_top_peaks_rep2.line_25.id_33
Name	filt_top_peaks rep2
Thread	thread_Root
PID	51026

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

Start	2016-05-17 11:41:07
End	2016-05-17 11:41:20
Elapsed	00:00:13
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz

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

Num	29
ID	task.callpeak_etc.filt_top_peaks_rep2.line_25.id_34
Name	filt_top_peaks rep2
Thread	thread_Root
PID	51028

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

Start	2016-05-17 11:41:07
End	2016-05-17 11:41:18
Elapsed	00:00:10
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-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/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.gappedPeak.gz

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

Num	30
ID	task.callpeak_etc.filt_top_peaks_pooled.line_25.id_35
Name	filt_top_peaks pooled
Thread	thread_Root
PID	51031

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

Start	2016-05-17 11:41:07
End	2016-05-17 11:41:18
Elapsed	00:00:11
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz

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

Num	31
ID	task.callpeak_etc.filt_top_peaks_pooled.line_25.id_36
Name	filt_top_peaks pooled
Thread	thread_Root
PID	51049

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

Start	2016-05-17 11:41:07
End	2016-05-17 11:41:17
Elapsed	00:00:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.gappedPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/macs2/pooled_rep/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.gappedPeak.gz

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

Num	32
ID	task.idr.idr2_rep1_rep2.line_61.id_37
Name	idr2 rep1-rep2
Thread	thread_Root
PID	51620

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

Start	2016-05-17 11:41:21
End	2016-05-17 11:45:07
Elapsed	00:03:46
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt.png /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/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/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz --peak-list /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/pooled_rep/ATAC5-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/ATAC5+6/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/ATAC5+6/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/ATAC5+6/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/ATAC5+6/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/ATAC5+6/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/ATAC5+6/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/ATAC5+6/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/ATAC5+6/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/ATAC5+6/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/ATAC5+6/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: [1.50 0.88 0.62 0.29]
Number of reported peaks - 191677/191677 (100.0%)

Number of peaks passing IDR cutoff of 0.1 - 57909/191677 (30.2%)

Num	33
ID	task.base.line_414.id_40
Name	task.base.line_414.id_40
Thread	thread_Root
PID	51975

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

Start	2016-05-17 11:45:08
End	2016-05-17 11:45:08
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/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/ATAC5+6/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/idr/optimal_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	51970

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

Start	2016-05-17 11:45:08
End	2016-05-17 11:45:08
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/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/ATAC5+6/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz

Num	35
ID	task.base.line_414.id_42
Name	task.base.line_414.id_42
Thread	thread_Root
PID	51972

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

Start	2016-05-17 11:45:08
End	2016-05-17 11:45:08
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/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/ATAC5+6/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/ATAC5+6/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.gz

Num	36
ID	task.base.line_414.id_43
Name	task.base.line_414.id_43
Thread	thread_Root
PID	51974

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

Start	2016-05-17 11:45:08
End	2016-05-17 11:45:08
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/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/ATAC5+6/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/ATAC5+6/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.13-col.bed.gz

Num	37
ID	task.idr.idr_final_qc.line_196.id_44
Name	idr final qc
Thread	thread_Root
PID	52013

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

Start	2016-05-17 11:45:09
End	2016-05-17 11:45:10
Elapsed	00:00:01
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/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/ATAC5+6/qc/IDR_final.qc

# SYS command. line 201

 echo -e "57945\t""0\trep1-rep2\trep1-rep2\tInfinity\tNaN\t0" >> /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/IDR_final.qc

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

Num	38
ID	task.postalign_bam.srt_bam_rep1.line_345.id_45
Name	srt_bam rep1
Thread	thread_78
PID	52016

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

Start	2016-05-17 11:45:09
End	2016-05-17 12:24:33
Elapsed	00:39:23
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-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/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.srt

# SYS command. line 354

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.srt.bam

# SYS command. line 356

 if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.srt.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.srt.bai" ]; then \
			cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.srt.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-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 53 files...

Num	39
ID	task.postalign_bam.srt_bam_rep2.line_345.id_46
Name	srt_bam rep2
Thread	thread_79
PID	52020

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

Start	2016-05-17 11:45:09
End	2016-05-17 12:27:42
Elapsed	00:42:33
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-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/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.srt

# SYS command. line 354

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.srt.bam

# SYS command. line 356

 if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.srt.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.srt.bai" ]; then \
			cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.srt.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-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 53 files...

Num	40
ID	task.atac.ataqc_rep1.line_815.id_47
Name	ataqc rep1
Thread	thread_78
PID	52716

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

Start	2016-05-17 12:24:34
End	2016-05-17 15:08:34
Elapsed	02:43:59
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC5/ATAC5-trimmed-pair1.fastq.gz /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC5/ATAC5-trimmed-pair2.fastq.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep1/ATAC5-trimmed-pair1.trim.PE2SE.align.log /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.pbc.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep1/ATAC5-trimmed-pair1.trim.PE2SE.dup.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/signal/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep1/ATAC5-trimmed-pair1.PE2SE_qc.html /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep1/ATAC5-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/ATAC5+6/qc/rep1

# SYS command. line 825

 /users/pangwei/bds_atac/ataqc/run_ataqc.py \
			    --workdir /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep1 \
			    --outdir /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep1 \
			    --outprefix ATAC5-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/ATAC5+6/qc/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.pbc.qc\
			    --fastq1 /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC5/ATAC5-trimmed-pair1.fastq.gz --fastq2 /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC5/ATAC5-trimmed-pair2.fastq.gz \
			    --alignedbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.bam \
			    --alignmentlog /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep1/ATAC5-trimmed-pair1.trim.PE2SE.align.log \
			    --coordsortbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.srt.bam \
			    --duplog /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep1/ATAC5-trimmed-pair1.trim.PE2SE.dup.qc \
			    --finalbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.bam \
			    --finalbed /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz \
			    --bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/signal/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig \
			    --peaks /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz \
			     \
			    --idr_peaks /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz

   
--------------------Stdout--------------------
Run time: 2:43:51

 
--------------------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 12:29:35	ProcessExecutor	Warning messages:
ERROR	2016-05-17 12:29:35	ProcessExecutor	1: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
ERROR	2016-05-17 12:29:35	ProcessExecutor	  zero-length arrow is of indeterminate angle and so skipped
ERROR	2016-05-17 12:29:35	ProcessExecutor	2: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
ERROR	2016-05-17 12:29:35	ProcessExecutor	  zero-length arrow is of indeterminate angle and so skipped
ERROR	2016-05-17 12:29:35	ProcessExecutor	3: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
ERROR	2016-05-17 12:29:35	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 54 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
processing chromosomes
/users/pangwei/bds_atac/ataqc/run_ataqc.py:851: FutureWarning: sort(columns=....) is deprecated, use sort_values(by=.....)
  sorted_results = merged.sort('corr', ascending=True)

Num	41
ID	task.atac.ataqc_rep2.line_815.id_48
Name	ataqc rep2
Thread	thread_79
PID	52867

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

Start	2016-05-17 12:27:43
End	2016-05-17 15:15:06
Elapsed	02:47:22
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC6/ATAC6-trimmed-pair1.fastq.gz /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC6/ATAC6-trimmed-pair2.fastq.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep2/ATAC6-trimmed-pair1.trim.PE2SE.align.log /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.pbc.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep2/ATAC6-trimmed-pair1.trim.PE2SE.dup.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/signal/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep2/ATAC6-trimmed-pair1.PE2SE_qc.html /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep2/ATAC6-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/ATAC5+6/qc/rep2

# SYS command. line 825

 /users/pangwei/bds_atac/ataqc/run_ataqc.py \
			    --workdir /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep2 \
			    --outdir /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep2 \
			    --outprefix ATAC6-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/ATAC5+6/qc/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.pbc.qc\
			    --fastq1 /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC6/ATAC6-trimmed-pair1.fastq.gz --fastq2 /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC6/ATAC6-trimmed-pair2.fastq.gz \
			    --alignedbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.bam \
			    --alignmentlog /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep2/ATAC6-trimmed-pair1.trim.PE2SE.align.log \
			    --coordsortbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.srt.bam \
			    --duplog /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep2/ATAC6-trimmed-pair1.trim.PE2SE.dup.qc \
			    --finalbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.bam \
			    --finalbed /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/align/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz \
			    --bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/signal/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig \
			    --peaks /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz \
			     \
			    --idr_peaks /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz

   
--------------------Stdout--------------------
Run time: 2:47:14

 
--------------------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 12:33:39	ProcessExecutor	Warning messages:
ERROR	2016-05-17 12:33:39	ProcessExecutor	1: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
ERROR	2016-05-17 12:33:39	ProcessExecutor	  zero-length arrow is of indeterminate angle and so skipped
ERROR	2016-05-17 12:33:39	ProcessExecutor	2: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
ERROR	2016-05-17 12:33:39	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 54 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
processing chromosomes
/users/pangwei/bds_atac/ataqc/run_ataqc.py:851: FutureWarning: sort(columns=....) is deprecated, use sort_values(by=.....)
  sorted_results = merged.sort('corr', ascending=True)

Num	42
ID	task.report.line_418.id_49
Name	task.report.line_418.id_49
Thread	thread_Root
PID	61260

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

Start	2016-05-17 15:15:07
End	2016-05-17 15:15:09
Elapsed	00:00:02
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.hammock.gz
Dependencies

 
# SYS command. line 420

 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 421

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.tmp

# SYS command. line 423

 /users/pangwei/bds_atac/utils/narrowpeak_idr.py /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.hammock

# SYS command. line 424

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.tmp

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

Num	43
ID	task.report.line_418.id_50
Name	task.report.line_418.id_50
Thread	thread_Root
PID	61329

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

Start	2016-05-17 15:15:10
End	2016-05-17 15:15:16
Elapsed	00:00:05
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.hammock.gz
Dependencies

 
# SYS command. line 420

 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 421

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.tmp

# SYS command. line 423

 /users/pangwei/bds_atac/utils/narrowpeak.py /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.hammock

# SYS command. line 424

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.tmp

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

Num	44
ID	task.report.line_418.id_51
Name	task.report.line_418.id_51
Thread	thread_Root
PID	61401

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

Start	2016-05-17 15:15:17
End	2016-05-17 15:15:21
Elapsed	00:00:04
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.hammock.gz
Dependencies

 
# SYS command. line 420

 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 421

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.tmp

# SYS command. line 423

 /users/pangwei/bds_atac/utils/narrowpeak.py /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.hammock

# SYS command. line 424

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/peak/macs2/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.tmp

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

Num	45
ID	task.report_graphviz.line_93.id_52
Name	task.report_graphviz.line_93.id_52
Thread	thread_Root
PID	61490

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

Start	2016-05-17 15:15:22
End	2016-05-17 15:15:24
Elapsed	00:00:02
Timeout	00:00:-1
Wall Timeout	100 days

Input files
Output files
Dependencies

 
# SYS command. line 94

 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

 dot -Tsvg /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/report/workflow.dot > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/report/workflow.svg

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

Num	46
ID	task.report.line_383.id_57
Name	task.report.line_383.id_57
Thread	thread_Root
PID	61495

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

Start	2016-05-17 15:15:22
End	2016-05-17 15:15:23
Elapsed	00:00:01
Timeout	00:00:-1
Wall Timeout	100 days

Input files
Output files
Dependencies

 
# SYS command. line 384

 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 385

 gs -dFirstPage=1 -dLastPage=1 -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -r110x110 \
			-dUseCropBox -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -sDEVICE=png16m \
			-sOutputFile=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.png \
			-r144 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep1/ATAC5-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf

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

Num	47
ID	task.report.line_383.id_58
Name	task.report.line_383.id_58
Thread	thread_Root
PID	61504

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

Start	2016-05-17 15:15:22
End	2016-05-17 15:15:23
Elapsed	00:00:01
Timeout	00:00:-1
Wall Timeout	100 days

Input files
Output files
Dependencies

 
# SYS command. line 384

 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 385

 gs -dFirstPage=1 -dLastPage=1 -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -r110x110 \
			-dUseCropBox -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -sDEVICE=png16m \
			-sOutputFile=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.png \
			-r144 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6/qc/rep2/ATAC6-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf

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

Type	Name	Value
string	_	/usr/bin/bds
string	_LMFILES_	/software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/samtools/1.2:/software/modulefiles/bedtools/2.23.0:/software/modulefiles/rsem/1.2.21
string	_ZSH_TMUX_FIXED_CONFIG	/users/pangwei/.oh-my-zsh/plugins/tmux/tmux.extra.conf
bool	allowEmpty	false
string[]	args	[-out_dir, /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC5+6, -num_rep, 2, -fastq1_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC5/ATAC5-trimmed-pair1.fastq.gz, -fastq1_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC5/ATAC5-trimmed-pair2.fastq.gz, -fastq2_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC6/ATAC6-trimmed-pair1.fastq.gz, -fastq2_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC6/ATAC6-trimmed-pair2.fastq.gz, -subsample, 17500000, -true_rep, -species, hg19]
string	C_INCLUDE_PATH	/software/samtools/samtools-1.2/include/htslib
bool	canFail	false
int	cpus	1
int	cpusLocal	48
int	day	86400
real	E	2.718281828459045
int	G	1073741824
string	HOME	/users/pangwei/
int	hour	3600
int	K	1024
string	LANG	en_US.UTF-8
string	LC_CTYPE	en_US.UTF-8
string	LD_LIBRARY_PATH	/software/samtools/samtools-1.2/lib:/usr/local/cudnn-3/lib64/:/usr/local/cudnn-3/lib64/
string	LESS	-R
string	LOADEDMODULES	modsappsdir/modsappsdir:samtools/1.2:bedtools/2.23.0:rsem/1.2.21
string	LOGNAME	pangwei
string	LSCOLORS	Gxfxcxdxbxegedabagacad
int	M	1048576
string	MAIL	/var/mail/pangwei
string	MANPATH	/software/samtools/samtools-1.2/share/man:/usr/share/man
int	mem	-1
int	minute	60
string	MODULE_VERSION	3.2.10
string	MODULE_VERSION_STACK	3.2.10
string	MODULEPATH	/usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles
string	MODULESAPPSDIR	/software
string	MODULESHOME	/software/env_module/3.2.10
string	node
int	P	1125899906842624
string	PAGER	less
string	PATH	/software/RSEM/rsem-1.2.21/:/software/bedtools/2.23.0/bin:/software/samtools/samtools-1.2/bin:/users/pangwei/anaconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
real	PI	3.141592653589793
string	ppwd	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata
string	programName	atac.bds
string	programPath	/users/pangwei/bds_atac/atac.bds
string	PWD	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata
string	PYTHONPATH	/home/jisraeli/src/caffe_atac/python/:/users/pangwei/stemcells:/home/jisraeli/src/caffe_atac/python/:/users/pangwei/stemcells:
string	queue
int	retry	0
string	SAMTOOLS_HOME	/software/samtools/samtools-1.2/bin
string	SHELL	/usr/bin/zsh
string	SHLVL	3
string	SSH_AUTH_SOCK	/tmp/ssh-5gr8qSU2WF/agent.74700
string	SSH_CLIENT	171.65.76.244 36245 22
string	SSH_CONNECTION	171.65.76.244 49273 171.65.76.236 22
string	SSH_TTY	/dev/pts/0
string	system	local
int	T	1099511627776
string	TERM	screen
string	THEANO_FLAGS	device=gpu6,floatX=float32,warn_float64=warn,optimizer_excluding=cudnn
int	timeout	-1
string	TMUX	/tmp/tmux-1077/default,106699,3
string	TMUX_PANE	%3
string	USER	pangwei
string	UTIL_SCRIPTS_DIR	/users/pangwei/av_scripts
int	walltimeout	8640000
int	week	604800
string	WWW	/srv/www/kundaje/pangwei
string	XDG_RUNTIME_DIR	/run/user/1077
string	XDG_SESSION_ID	1907
string	ZSH	/users/pangwei//.oh-my-zsh
string	ZSH_TMUX_TERM	screen

BigDataScript report: atac.bds

Timeline

Task Graph

Parallel (threads) details

Task details

Global scope