Script file	/users/pangwei/bds_atac/atac.bds
Program ID	atac.bds.20160516_201635_161
Start time	2016-05-16 20:16:35
Run time	20:10:46.213
Tasks executed	47
Tasks failed	0
Tasks failed names
Arguments*	[-out_dir, /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2, -num_rep, 2, -fastq1_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC1/ATAC1-trimmed-pair1.fastq.gz, -fastq1_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC1/ATAC1-trimmed-pair2.fastq.gz, -fastq2_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC2/ATAC2-trimmed-pair1.fastq.gz, -fastq2_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC2/ATAC2-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_161/task.postalign_bed.pool_tag_reps.line_405.id_28 atac.bds.20160516_201635_161/task.callpeak_macs2.macs2_atac_pooled.pval0.1.line_192.id_29 atac.bds.20160516_201635_161/task.callpeak_macs2.macs2_atac_pooled.line_192.id_30 atac.bds.20160516_201635_161/task.callpeak_etc.filt_top_peaks_rep1.line_25.id_31 atac.bds.20160516_201635_161/task.callpeak_etc.filt_top_peaks_rep1.line_25.id_32 atac.bds.20160516_201635_161/task.callpeak_etc.filt_top_peaks_rep2.line_25.id_33 atac.bds.20160516_201635_161/task.callpeak_etc.filt_top_peaks_rep2.line_25.id_34 atac.bds.20160516_201635_161/task.callpeak_etc.filt_top_peaks_pooled.line_25.id_35 atac.bds.20160516_201635_161/task.callpeak_etc.filt_top_peaks_pooled.line_25.id_36 atac.bds.20160516_201635_161/task.idr.idr2_rep1_rep2.line_61.id_37 atac.bds.20160516_201635_161/task.base.line_414.id_40 atac.bds.20160516_201635_161/task.base.line_414.id_41 atac.bds.20160516_201635_161/task.base.line_414.id_42 atac.bds.20160516_201635_161/task.base.line_414.id_43 atac.bds.20160516_201635_161/task.idr.idr_final_qc.line_196.id_44 atac.bds.20160516_201635_161/task.report.line_418.id_49 atac.bds.20160516_201635_161/task.report.line_418.id_50 atac.bds.20160516_201635_161/task.report.line_418.id_51 atac.bds.20160516_201635_161/task.report_graphviz.line_93.id_52 atac.bds.20160516_201635_161/task.report.line_383.id_57 atac.bds.20160516_201635_161/task.report.line_383.id_58
thread_78	thread_Root	atac.bds.20160516_201635_161_parallel_78/task.postalign_bam.srt_bam_rep1.line_345.id_46 atac.bds.20160516_201635_161_parallel_78/task.atac.ataqc_rep1.line_815.id_47
thread_79	thread_Root	atac.bds.20160516_201635_161_parallel_79/task.postalign_bam.srt_bam_rep2.line_345.id_45 atac.bds.20160516_201635_161_parallel_79/task.atac.ataqc_rep2.line_815.id_48
thread_20	thread_Root	atac.bds.20160516_201635_161_parallel_20/task.align_bowtie2.bowtie2_PE_rep1.line_133.id_7 atac.bds.20160516_201635_161_parallel_20/task.postalign_bam.dedup_bam_PE_rep1.line_215.id_8 atac.bds.20160516_201635_161_parallel_20/task.postalign_bam.nmsrt_bam_rep1.line_321.id_9 atac.bds.20160516_201635_161_parallel_20/task.postalign_bam.bam_to_bedpe_rep1.line_425.id_10 atac.bds.20160516_201635_161_parallel_20/task.postalign_bed.subsample_bedpe_rep1.line_116.id_11 atac.bds.20160516_201635_161_parallel_20/task.postalign_bam.bedpe_to_tag_rep1.line_465.id_12 atac.bds.20160516_201635_161_parallel_20/task.postalign_bed.shift_tag_rep1.line_140.id_13 atac.bds.20160516_201635_161_parallel_20/task.postalign_bed.subsample_bedpe2tagrep1.line_89.id_14 atac.bds.20160516_201635_161_parallel_20/task.postalign_bed.xcor_rep1.line_165.id_15 atac.bds.20160516_201635_161_parallel_20/task.callpeak_macs2.macs2_atac_rep1.pval0.1.line_192.id_16 atac.bds.20160516_201635_161_parallel_20/task.callpeak_macs2.macs2_atac_rep1.line_192.id_17
thread_21	thread_Root	atac.bds.20160516_201635_161_parallel_21/task.align_bowtie2.bowtie2_PE_rep2.line_133.id_6 atac.bds.20160516_201635_161_parallel_21/task.postalign_bam.dedup_bam_PE_rep2.line_215.id_18 atac.bds.20160516_201635_161_parallel_21/task.postalign_bam.nmsrt_bam_rep2.line_321.id_19 atac.bds.20160516_201635_161_parallel_21/task.postalign_bam.bam_to_bedpe_rep2.line_425.id_20 atac.bds.20160516_201635_161_parallel_21/task.postalign_bed.subsample_bedpe_rep2.line_116.id_21 atac.bds.20160516_201635_161_parallel_21/task.postalign_bam.bedpe_to_tag_rep2.line_465.id_22 atac.bds.20160516_201635_161_parallel_21/task.postalign_bed.shift_tag_rep2.line_140.id_23 atac.bds.20160516_201635_161_parallel_21/task.postalign_bed.subsample_bedpe2tagrep2.line_89.id_24 atac.bds.20160516_201635_161_parallel_21/task.postalign_bed.xcor_rep2.line_165.id_25 atac.bds.20160516_201635_161_parallel_21/task.callpeak_macs2.macs2_atac_rep2.pval0.1.line_192.id_26 atac.bds.20160516_201635_161_parallel_21/task.callpeak_macs2.macs2_atac_rep2.line_192.id_27

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.align_bowtie2.bowtie2_PE_rep1.line_133.id_7
Name	bowtie2_PE rep1
Thread	thread_20
PID	129994

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

Start	2016-05-16 20:16:35
End	2016-05-17 02:29:27
Elapsed	06:12:51
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.fastq.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair2.trim.fastq.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep1/ATAC1-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/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.fastq.gz -2 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair2.trim.fastq.gz 2>/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep1/ATAC1-trimmed-pair1.trim.PE2SE.align.log | samtools view -bS - | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE

# SYS command. line 142

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-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 38 files...

Num	2
ID	task.align_bowtie2.bowtie2_PE_rep2.line_133.id_6
Name	bowtie2_PE rep2
Thread	thread_21
PID	130006

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

Start	2016-05-16 20:16:36
End	2016-05-17 06:15:36
Elapsed	09:59:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.fastq.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair2.trim.fastq.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep2/ATAC2-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/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.fastq.gz -2 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair2.trim.fastq.gz 2>/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep2/ATAC2-trimmed-pair1.trim.PE2SE.align.log | samtools view -bS - | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE

# SYS command. line 142

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-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 62 files...

Num	3
ID	task.postalign_bam.dedup_bam_PE_rep1.line_215.id_8
Name	dedup_bam_PE rep1
Thread	thread_20
PID	1245

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

Start	2016-05-17 02:29:28
End	2016-05-17 04:35:47
Elapsed	02:06:19
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep1/ATAC1-trimmed-pair1.trim.PE2SE.dup.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep1/ATAC1-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/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-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/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-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/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.filt

# SYS command. line 239

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-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/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep1/ATAC1-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/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep1/ATAC1-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/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-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/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.filt.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 269

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 271

 if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.bai" ]; then \
			cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.bai; \
			fi

# SYS command. line 275

 samtools flagstat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc

# SYS command. line 286

 samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.filt.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.filt.bam.tmp

# SYS command. line 287

 bedtools bamtobed -bedpe -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-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/ATAC1+2/qc/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.pbc.qc

# SYS command. line 291

 rm /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam

# SYS command. line 293

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.filt.bam

# SYS command. line 294

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-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 26 files...
[bam_sort_core] merging from 26 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Tue May 17 03:34:35 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep1/ATAC1-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 03:34:35 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 03:34:35	MarkDuplicates	Start of doWork freeMemory: 254889728; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-17 03:34:35	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-05-17 03:34:35	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-05-17 03:34:55	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:17s.  Time for last 1,000,000:   17s.  Last read position: chr10:90,536,749
INFO	2016-05-17 03:34:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:35:07	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:29s.  Time for last 1,000,000:   12s.  Last read position: chr11:23,812,648
INFO	2016-05-17 03:35:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:35:22	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:44s.  Time for last 1,000,000:   15s.  Last read position: chr11:105,311,592
INFO	2016-05-17 03:35:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:35:27	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:49s.  Time for last 1,000,000:    4s.  Last read position: chr12:51,612,062
INFO	2016-05-17 03:35:27	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-05-17 03:35:32	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:54s.  Time for last 1,000,000:    5s.  Last read position: chr12:129,432,882
INFO	2016-05-17 03:35:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:35:37	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:01:00s.  Time for last 1,000,000:    5s.  Last read position: chr13:107,234,814
INFO	2016-05-17 03:35:37	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 03:35:43	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:01:05s.  Time for last 1,000,000:    5s.  Last read position: chr14:93,169,383
INFO	2016-05-17 03:35:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:35:51	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:01:13s.  Time for last 1,000,000:    7s.  Last read position: chr15:80,693,464
INFO	2016-05-17 03:35:51	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 03:35:56	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:01:19s.  Time for last 1,000,000:    5s.  Last read position: chr16:63,260,925
INFO	2016-05-17 03:35:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:36:05	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:01:27s.  Time for last 1,000,000:    8s.  Last read position: chr17:38,874,885
INFO	2016-05-17 03:36:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:36:10	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:32s.  Time for last 1,000,000:    4s.  Last read position: chr18:30,249,694
INFO	2016-05-17 03:36:10	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 03:36:19	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:42s.  Time for last 1,000,000:    9s.  Last read position: chr19:21,404,269
INFO	2016-05-17 03:36:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:36:23	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:46s.  Time for last 1,000,000:    3s.  Last read position: chr1:16,339,627
INFO	2016-05-17 03:36:23	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-17 03:36:29	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:52s.  Time for last 1,000,000:    6s.  Last read position: chr1:81,464,024
INFO	2016-05-17 03:36:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:36:51	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:02:13s.  Time for last 1,000,000:   21s.  Last read position: chr1:187,392,517
INFO	2016-05-17 03:36:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:36:56	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:02:18s.  Time for last 1,000,000:    5s.  Last read position: chr20:17,832,819
INFO	2016-05-17 03:36:56	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 03:37:01	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:02:24s.  Time for last 1,000,000:    5s.  Last read position: chr21:43,161,556
INFO	2016-05-17 03:37:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:37:07	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:02:29s.  Time for last 1,000,000:    5s.  Last read position: chr2:22,496,328
INFO	2016-05-17 03:37:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:37:11	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:02:34s.  Time for last 1,000,000:    4s.  Last read position: chr2:109,641,708
INFO	2016-05-17 03:37:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:37:17	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:02:39s.  Time for last 1,000,000:    5s.  Last read position: chr2:201,451,445
INFO	2016-05-17 03:37:17	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 03:37:21	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:02:43s.  Time for last 1,000,000:    3s.  Last read position: chr3:35,302,547
INFO	2016-05-17 03:37:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:37:27	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:02:50s.  Time for last 1,000,000:    6s.  Last read position: chr3:122,375,492
INFO	2016-05-17 03:37:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:37:37	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:02:59s.  Time for last 1,000,000:    9s.  Last read position: chr4:3,742,818
INFO	2016-05-17 03:37:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:37:42	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:03:04s.  Time for last 1,000,000:    4s.  Last read position: chr4:102,090,472
INFO	2016-05-17 03:37:42	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 03:37:47	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:03:09s.  Time for last 1,000,000:    5s.  Last read position: chr5:8,351,800
INFO	2016-05-17 03:37:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:37:56	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:03:18s.  Time for last 1,000,000:    9s.  Last read position: chr5:110,269,097
INFO	2016-05-17 03:37:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:38:02	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:03:24s.  Time for last 1,000,000:    6s.  Last read position: chr5:178,449,932
INFO	2016-05-17 03:38:02	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 03:38:09	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:03:31s.  Time for last 1,000,000:    7s.  Last read position: chr6:76,833,809
INFO	2016-05-17 03:38:09	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 03:38:21	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:03:43s.  Time for last 1,000,000:   11s.  Last read position: chr6:166,884,662
INFO	2016-05-17 03:38:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:38:37	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:03:59s.  Time for last 1,000,000:   16s.  Last read position: chr7:82,647,565
INFO	2016-05-17 03:38:37	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 03:38:43	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:04:06s.  Time for last 1,000,000:    6s.  Last read position: chr8:3,206,976
INFO	2016-05-17 03:38:43	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 03:38:49	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:04:12s.  Time for last 1,000,000:    6s.  Last read position: chr8:95,820,565
INFO	2016-05-17 03:38:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:38:56	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:04:18s.  Time for last 1,000,000:    6s.  Last read position: chr9:32,703,754
INFO	2016-05-17 03:38:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:39:00	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:04:22s.  Time for last 1,000,000:    3s.  Last read position: chr9:136,489,904
INFO	2016-05-17 03:39:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:39:04	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:04:26s.  Time for last 1,000,000:    3s.  Last read position: chrM:601
INFO	2016-05-17 03:39:04	MarkDuplicates	Tracking 30604 as yet unmatched pairs. 30604 records in RAM.
INFO	2016-05-17 03:39:07	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:04:30s.  Time for last 1,000,000:    3s.  Last read position: chrM:1,306
INFO	2016-05-17 03:39:07	MarkDuplicates	Tracking 40598 as yet unmatched pairs. 40598 records in RAM.
INFO	2016-05-17 03:39:12	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:04:35s.  Time for last 1,000,000:    4s.  Last read position: chrM:1,898
INFO	2016-05-17 03:39:12	MarkDuplicates	Tracking 22364 as yet unmatched pairs. 22364 records in RAM.
INFO	2016-05-17 03:39:18	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:04:40s.  Time for last 1,000,000:    5s.  Last read position: chrM:2,641
INFO	2016-05-17 03:39:18	MarkDuplicates	Tracking 65994 as yet unmatched pairs. 65994 records in RAM.
INFO	2016-05-17 03:39:24	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:04:46s.  Time for last 1,000,000:    6s.  Last read position: chrM:3,016
INFO	2016-05-17 03:39:24	MarkDuplicates	Tracking 55588 as yet unmatched pairs. 55588 records in RAM.
INFO	2016-05-17 03:39:31	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:04:54s.  Time for last 1,000,000:    7s.  Last read position: chrM:3,396
INFO	2016-05-17 03:39:31	MarkDuplicates	Tracking 72446 as yet unmatched pairs. 72446 records in RAM.
INFO	2016-05-17 03:39:36	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:04:58s.  Time for last 1,000,000:    4s.  Last read position: chrM:3,715
INFO	2016-05-17 03:39:36	MarkDuplicates	Tracking 83630 as yet unmatched pairs. 83630 records in RAM.
INFO	2016-05-17 03:39:40	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:05:03s.  Time for last 1,000,000:    4s.  Last read position: chrM:4,312
INFO	2016-05-17 03:39:40	MarkDuplicates	Tracking 21454 as yet unmatched pairs. 21454 records in RAM.
INFO	2016-05-17 03:39:46	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:05:08s.  Time for last 1,000,000:    5s.  Last read position: chrM:5,342
INFO	2016-05-17 03:39:46	MarkDuplicates	Tracking 25716 as yet unmatched pairs. 25716 records in RAM.
INFO	2016-05-17 03:39:54	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:05:17s.  Time for last 1,000,000:    8s.  Last read position: chrM:6,262
INFO	2016-05-17 03:39:54	MarkDuplicates	Tracking 33744 as yet unmatched pairs. 33744 records in RAM.
INFO	2016-05-17 03:40:04	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:05:27s.  Time for last 1,000,000:    9s.  Last read position: chrM:6,572
INFO	2016-05-17 03:40:04	MarkDuplicates	Tracking 39550 as yet unmatched pairs. 39550 records in RAM.
INFO	2016-05-17 03:40:10	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:05:32s.  Time for last 1,000,000:    5s.  Last read position: chrM:7,459
INFO	2016-05-17 03:40:10	MarkDuplicates	Tracking 2924 as yet unmatched pairs. 2924 records in RAM.
INFO	2016-05-17 03:40:15	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:05:37s.  Time for last 1,000,000:    5s.  Last read position: chrM:8,118
INFO	2016-05-17 03:40:15	MarkDuplicates	Tracking 24990 as yet unmatched pairs. 24990 records in RAM.
INFO	2016-05-17 03:40:22	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:05:44s.  Time for last 1,000,000:    7s.  Last read position: chrM:9,183
INFO	2016-05-17 03:40:22	MarkDuplicates	Tracking 27296 as yet unmatched pairs. 27296 records in RAM.
INFO	2016-05-17 03:40:28	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:05:50s.  Time for last 1,000,000:    5s.  Last read position: chrM:9,854
INFO	2016-05-17 03:40:28	MarkDuplicates	Tracking 76158 as yet unmatched pairs. 76158 records in RAM.
INFO	2016-05-17 03:40:32	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:05:54s.  Time for last 1,000,000:    4s.  Last read position: chrM:10,424
INFO	2016-05-17 03:40:32	MarkDuplicates	Tracking 41708 as yet unmatched pairs. 41708 records in RAM.
INFO	2016-05-17 03:40:37	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:05:59s.  Time for last 1,000,000:    5s.  Last read position: chrM:11,185
INFO	2016-05-17 03:40:37	MarkDuplicates	Tracking 21948 as yet unmatched pairs. 21948 records in RAM.
INFO	2016-05-17 03:40:41	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:06:03s.  Time for last 1,000,000:    4s.  Last read position: chrM:11,778
INFO	2016-05-17 03:40:41	MarkDuplicates	Tracking 19092 as yet unmatched pairs. 19092 records in RAM.
INFO	2016-05-17 03:40:49	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:06:11s.  Time for last 1,000,000:    7s.  Last read position: chrM:12,354
INFO	2016-05-17 03:40:49	MarkDuplicates	Tracking 18812 as yet unmatched pairs. 18812 records in RAM.
INFO	2016-05-17 03:40:53	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:06:16s.  Time for last 1,000,000:    4s.  Last read position: chrM:12,879
INFO	2016-05-17 03:40:53	MarkDuplicates	Tracking 7208 as yet unmatched pairs. 7208 records in RAM.
INFO	2016-05-17 03:40:59	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:06:22s.  Time for last 1,000,000:    5s.  Last read position: chrM:13,324
INFO	2016-05-17 03:40:59	MarkDuplicates	Tracking 45768 as yet unmatched pairs. 45768 records in RAM.
INFO	2016-05-17 03:41:06	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:06:28s.  Time for last 1,000,000:    6s.  Last read position: chrM:13,830
INFO	2016-05-17 03:41:06	MarkDuplicates	Tracking 31420 as yet unmatched pairs. 31420 records in RAM.
INFO	2016-05-17 03:41:16	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:06:38s.  Time for last 1,000,000:    9s.  Last read position: chrM:14,420
INFO	2016-05-17 03:41:16	MarkDuplicates	Tracking 10718 as yet unmatched pairs. 10718 records in RAM.
INFO	2016-05-17 03:41:21	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:06:43s.  Time for last 1,000,000:    5s.  Last read position: chrM:15,094
INFO	2016-05-17 03:41:21	MarkDuplicates	Tracking 54926 as yet unmatched pairs. 54926 records in RAM.
INFO	2016-05-17 03:41:39	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:07:01s.  Time for last 1,000,000:   17s.  Last read position: chrM:15,439
INFO	2016-05-17 03:41:39	MarkDuplicates	Tracking 50560 as yet unmatched pairs. 50560 records in RAM.
INFO	2016-05-17 03:41:44	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:07:07s.  Time for last 1,000,000:    5s.  Last read position: chrM:15,771
INFO	2016-05-17 03:41:44	MarkDuplicates	Tracking 49962 as yet unmatched pairs. 49962 records in RAM.
INFO	2016-05-17 03:41:51	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:07:13s.  Time for last 1,000,000:    6s.  Last read position: chrM:16,326
INFO	2016-05-17 03:41:51	MarkDuplicates	Tracking 44876 as yet unmatched pairs. 44876 records in RAM.
INFO	2016-05-17 03:42:00	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:07:22s.  Time for last 1,000,000:    9s.  Last read position: chrX:39,462,350
INFO	2016-05-17 03:42:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:42:06	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:07:28s.  Time for last 1,000,000:    5s.  Last read position: chrX:145,262,026
INFO	2016-05-17 03:42:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:42:07	MarkDuplicates	Read 63108976 records. 0 pairs never matched.
INFO	2016-05-17 03:42:10	MarkDuplicates	After buildSortedReadEndLists freeMemory: 2226858648; totalMemory: 2254438400; maxMemory: 3817865216
INFO	2016-05-17 03:42:10	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-05-17 03:42:10	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-05-17 03:42:32	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-05-17 03:42:48	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-05-17 03:42:50	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2144174984; totalMemory: 3125280768; maxMemory: 3817865216
INFO	2016-05-17 03:42:50	MarkDuplicates	Marking 30051736 records as duplicates.
INFO	2016-05-17 03:42:50	MarkDuplicates	Found 8159780 optical duplicate clusters.
INFO	2016-05-17 03:44:39	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:47s.  Time for last 10,000,000:  107s.  Last read position: chr17:38,874,885
INFO	2016-05-17 03:46:32	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:03:40s.  Time for last 10,000,000:  112s.  Last read position: chr2:201,451,445
INFO	2016-05-17 03:48:16	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:05:25s.  Time for last 10,000,000:  104s.  Last read position: chr7:82,647,565
INFO	2016-05-17 03:49:45	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:06:53s.  Time for last 10,000,000:   88s.  Last read position: chrM:3,396
INFO	2016-05-17 03:51:07	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:08:16s.  Time for last 10,000,000:   82s.  Last read position: chrM:10,424
INFO	2016-05-17 03:52:49	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:09:57s.  Time for last 10,000,000:  101s.  Last read position: chrM:15,771
INFO	2016-05-17 03:53:18	MarkDuplicates	Before output close freeMemory: 3258372936; totalMemory: 3288858624; maxMemory: 3817865216
INFO	2016-05-17 03:53:18	MarkDuplicates	After output close freeMemory: 3258371880; totalMemory: 3288858624; maxMemory: 3817865216
[Tue May 17 03:53:18 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 18.72 minutes.
Runtime.totalMemory()=3288858624
[bam_sort_core] merging from 26 files...

Num	4
ID	task.postalign_bam.nmsrt_bam_rep1.line_321.id_9
Name	nmsrt_bam rep1
Thread	thread_20
PID	6927

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

Start	2016-05-17 04:35:48
End	2016-05-17 04:49:42
Elapsed	00:13:54
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-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/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-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	5
ID	task.postalign_bam.bam_to_bedpe_rep1.line_425.id_10
Name	bam_to_bedpe rep1
Thread	thread_20
PID	7229

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

Start	2016-05-17 04:49:42
End	2016-05-17 04:51:26
Elapsed	00:01:43
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-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/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz

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

Num	6
ID	task.postalign_bed.subsample_bedpe_rep1.line_116.id_11
Name	subsample_bedpe rep1
Thread	thread_20
PID	7296

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

Start	2016-05-17 04:51:27
End	2016-05-17 04:53:32
Elapsed	00:02:04
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-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/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | grep -v "chrM" | shuf -n 17500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz

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

Num	7
ID	task.postalign_bam.bedpe_to_tag_rep1.line_465.id_12
Name	bedpe_to_tag rep1
Thread	thread_20
PID	7366

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

Start	2016-05-17 04:53:33
End	2016-05-17 04:55:07
Elapsed	00:01:34
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-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/ATAC1+2/align/rep1/ATAC1-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/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz

# SYS command. line 472

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz | grep -P -v 'chrM' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz; mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz

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

Num	8
ID	task.postalign_bed.shift_tag_rep1.line_140.id_13
Name	shift_tag rep1
Thread	thread_20
PID	7496

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

Start	2016-05-17 04:55:08
End	2016-05-17 04:56:16
Elapsed	00:01:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-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/ATAC1+2/align/rep1/ATAC1-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/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz

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

Num	9
ID	task.postalign_bed.subsample_bedpe2tagrep1.line_89.id_14
Name	subsample_bedpe2tagrep1
Thread	thread_20
PID	7561

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

Start	2016-05-17 04:56:17
End	2016-05-17 04:57:34
Elapsed	00:01:17
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-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/ATAC1+2/align/rep1/ATAC1-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/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz

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

Num	10
ID	task.postalign_bed.xcor_rep1.line_165.id_15
Name	xcor rep1
Thread	thread_20
PID	7633

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

Start	2016-05-17 04:57:34
End	2016-05-17 05:28:49
Elapsed	00:31:15
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep1/ATAC1-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/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz -p=1 \
			-filtchr=chrM -savp=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf -out=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep1/ATAC1-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/ATAC1+2/qc/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp

# SYS command. line 175

 mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc

   
--------------------Stdout--------------------
################
ChIP data: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-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/ATAC1+2/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/ATAC1+2/qc/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf 
result filename: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep1/ATAC1-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/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz 
opened /tmp/Rtmp4PLLOP/ATAC1-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign1e711dd67099
done. read 15587992 fragments
ChIP data read length 74 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1740045 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.183482442061438 
Top 3 estimates for fragment length 0 
Window half size 480 
Phantom peak location 65 
Phantom peak Correlation 0.1844801 
Normalized Strand cross-correlation coefficient (NSC) 1.05447 
Relative Strand Cross correlation Coefficient (RSC) 0.9047655 
Phantom Peak Quality Tag 0 
null device 
          1 

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

Num	11
ID	task.callpeak_macs2.macs2_atac_rep1.pval0.1.line_192.id_16
Name	macs2_atac rep1.pval0.1
Thread	thread_20
PID	7638

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

Start	2016-05-17 04:57:35
End	2016-05-17 05:22:28
Elapsed	00:24:53
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/signal/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/signal/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-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 04:57:39: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-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 04:57:39: #1 read tag files... 
INFO  @ Tue, 17 May 2016 04:57:39: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 04:57:41:  1000000 
INFO  @ Tue, 17 May 2016 04:57:43:  2000000 
INFO  @ Tue, 17 May 2016 04:57:45:  3000000 
INFO  @ Tue, 17 May 2016 04:57:46:  4000000 
INFO  @ Tue, 17 May 2016 04:57:48:  5000000 
INFO  @ Tue, 17 May 2016 04:57:50:  6000000 
INFO  @ Tue, 17 May 2016 04:57:53:  7000000 
INFO  @ Tue, 17 May 2016 04:57:56:  8000000 
INFO  @ Tue, 17 May 2016 04:57:59:  9000000 
INFO  @ Tue, 17 May 2016 04:58:02:  10000000 
INFO  @ Tue, 17 May 2016 04:58:06:  11000000 
INFO  @ Tue, 17 May 2016 04:58:09:  12000000 
INFO  @ Tue, 17 May 2016 04:58:11:  13000000 
INFO  @ Tue, 17 May 2016 04:58:12:  14000000 
INFO  @ Tue, 17 May 2016 04:58:14:  15000000 
INFO  @ Tue, 17 May 2016 04:58:16:  16000000 
INFO  @ Tue, 17 May 2016 04:58:17:  17000000 
INFO  @ Tue, 17 May 2016 04:58:19:  18000000 
INFO  @ Tue, 17 May 2016 04:58:20:  19000000 
INFO  @ Tue, 17 May 2016 04:58:22:  20000000 
INFO  @ Tue, 17 May 2016 04:58:24:  21000000 
INFO  @ Tue, 17 May 2016 04:58:25:  22000000 
INFO  @ Tue, 17 May 2016 04:58:27:  23000000 
INFO  @ Tue, 17 May 2016 04:58:28:  24000000 
INFO  @ Tue, 17 May 2016 04:58:30:  25000000 
INFO  @ Tue, 17 May 2016 04:58:32:  26000000 
INFO  @ Tue, 17 May 2016 04:58:33:  27000000 
INFO  @ Tue, 17 May 2016 04:58:35:  28000000 
INFO  @ Tue, 17 May 2016 04:58:36:  29000000 
INFO  @ Tue, 17 May 2016 04:58:38:  30000000 
INFO  @ Tue, 17 May 2016 04:58:40:  31000000 
INFO  @ Tue, 17 May 2016 04:58:42: #1 tag size is determined as 60 bps 
INFO  @ Tue, 17 May 2016 04:58:42: #1 tag size = 60 
INFO  @ Tue, 17 May 2016 04:58:42: #1  total tags in treatment: 31175984 
INFO  @ Tue, 17 May 2016 04:58:42: #1 finished! 
INFO  @ Tue, 17 May 2016 04:58:42: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 04:58:42: #2 Skipped... 
INFO  @ Tue, 17 May 2016 04:58:42: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 04:58:42: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 04:58:42: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 04:58:42: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 04:58:42: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 05:00:24: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 05:03:28: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 05:03:32: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 05:03:35: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 05:03:38: Done! 
INFO  @ Tue, 17 May 2016 05:04:01: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-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 05:04:01: #1 read tag files... 
INFO  @ Tue, 17 May 2016 05:04:01: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 05:04:03:  1000000 
INFO  @ Tue, 17 May 2016 05:04:05:  2000000 
INFO  @ Tue, 17 May 2016 05:04:06:  3000000 
INFO  @ Tue, 17 May 2016 05:04:08:  4000000 
INFO  @ Tue, 17 May 2016 05:04:10:  5000000 
INFO  @ Tue, 17 May 2016 05:04:12:  6000000 
INFO  @ Tue, 17 May 2016 05:04:13:  7000000 
INFO  @ Tue, 17 May 2016 05:04:15:  8000000 
INFO  @ Tue, 17 May 2016 05:04:17:  9000000 
INFO  @ Tue, 17 May 2016 05:04:19:  10000000 
INFO  @ Tue, 17 May 2016 05:04:20:  11000000 
INFO  @ Tue, 17 May 2016 05:04:22:  12000000 
INFO  @ Tue, 17 May 2016 05:04:24:  13000000 
INFO  @ Tue, 17 May 2016 05:04:26:  14000000 
INFO  @ Tue, 17 May 2016 05:04:27:  15000000 
INFO  @ Tue, 17 May 2016 05:04:29:  16000000 
INFO  @ Tue, 17 May 2016 05:04:31:  17000000 
INFO  @ Tue, 17 May 2016 05:04:33:  18000000 
INFO  @ Tue, 17 May 2016 05:04:34:  19000000 
INFO  @ Tue, 17 May 2016 05:04:36:  20000000 
INFO  @ Tue, 17 May 2016 05:04:38:  21000000 
INFO  @ Tue, 17 May 2016 05:04:40:  22000000 
INFO  @ Tue, 17 May 2016 05:04:41:  23000000 
INFO  @ Tue, 17 May 2016 05:04:43:  24000000 
INFO  @ Tue, 17 May 2016 05:04:45:  25000000 
INFO  @ Tue, 17 May 2016 05:04:47:  26000000 
INFO  @ Tue, 17 May 2016 05:04:48:  27000000 
INFO  @ Tue, 17 May 2016 05:04:50:  28000000 
INFO  @ Tue, 17 May 2016 05:04:52:  29000000 
INFO  @ Tue, 17 May 2016 05:04:54:  30000000 
INFO  @ Tue, 17 May 2016 05:04:55:  31000000 
INFO  @ Tue, 17 May 2016 05:04:58: #1 tag size is determined as 60 bps 
INFO  @ Tue, 17 May 2016 05:04:58: #1 tag size = 60 
INFO  @ Tue, 17 May 2016 05:04:58: #1  total tags in treatment: 31175984 
INFO  @ Tue, 17 May 2016 05:04:58: #1 finished! 
INFO  @ Tue, 17 May 2016 05:04:58: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 05:04:58: #2 Skipped... 
INFO  @ Tue, 17 May 2016 05:04:58: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 05:04:58: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 05:04:58: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 05:04:58: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 05:04:58: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Tue, 17 May 2016 05:04:58: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 05:06:12: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 05:06:12: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 05:06:12: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 05:06:12: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 05:06:12: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 05:21:31: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 05:21:50: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 05:22:01: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_summits.bed 
INFO  @ Tue, 17 May 2016 05:22:08: Done!

Num	12
ID	task.callpeak_macs2.macs2_atac_rep1.line_192.id_17
Name	macs2_atac rep1
Thread	thread_20
PID	7649

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

Start	2016-05-17 04:57:35
End	2016-05-17 05:48:27
Elapsed	00:50:52
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.gappedPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/signal/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/signal/macs2/rep1/ATAC1-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/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/signal/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/signal/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-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 04:57:39: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-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 04:57:39: #1 read tag files... 
INFO  @ Tue, 17 May 2016 04:57:39: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 04:57:42:  1000000 
INFO  @ Tue, 17 May 2016 04:57:45:  2000000 
INFO  @ Tue, 17 May 2016 04:57:47:  3000000 
INFO  @ Tue, 17 May 2016 04:57:48:  4000000 
INFO  @ Tue, 17 May 2016 04:57:50:  5000000 
INFO  @ Tue, 17 May 2016 04:57:52:  6000000 
INFO  @ Tue, 17 May 2016 04:57:53:  7000000 
INFO  @ Tue, 17 May 2016 04:57:55:  8000000 
INFO  @ Tue, 17 May 2016 04:57:56:  9000000 
INFO  @ Tue, 17 May 2016 04:57:58:  10000000 
INFO  @ Tue, 17 May 2016 04:58:00:  11000000 
INFO  @ Tue, 17 May 2016 04:58:01:  12000000 
INFO  @ Tue, 17 May 2016 04:58:03:  13000000 
INFO  @ Tue, 17 May 2016 04:58:05:  14000000 
INFO  @ Tue, 17 May 2016 04:58:06:  15000000 
INFO  @ Tue, 17 May 2016 04:58:08:  16000000 
INFO  @ Tue, 17 May 2016 04:58:10:  17000000 
INFO  @ Tue, 17 May 2016 04:58:12:  18000000 
INFO  @ Tue, 17 May 2016 04:58:14:  19000000 
INFO  @ Tue, 17 May 2016 04:58:17:  20000000 
INFO  @ Tue, 17 May 2016 04:58:20:  21000000 
INFO  @ Tue, 17 May 2016 04:58:23:  22000000 
INFO  @ Tue, 17 May 2016 04:58:25:  23000000 
INFO  @ Tue, 17 May 2016 04:58:28:  24000000 
INFO  @ Tue, 17 May 2016 04:58:31:  25000000 
INFO  @ Tue, 17 May 2016 04:58:34:  26000000 
INFO  @ Tue, 17 May 2016 04:58:36:  27000000 
INFO  @ Tue, 17 May 2016 04:58:39:  28000000 
INFO  @ Tue, 17 May 2016 04:58:42:  29000000 
INFO  @ Tue, 17 May 2016 04:58:44:  30000000 
INFO  @ Tue, 17 May 2016 04:58:47:  31000000 
INFO  @ Tue, 17 May 2016 04:58:50: #1 tag size is determined as 60 bps 
INFO  @ Tue, 17 May 2016 04:58:50: #1 tag size = 60 
INFO  @ Tue, 17 May 2016 04:58:50: #1  total tags in treatment: 31175984 
INFO  @ Tue, 17 May 2016 04:58:50: #1 finished! 
INFO  @ Tue, 17 May 2016 04:58:50: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 04:58:50: #2 Skipped... 
INFO  @ Tue, 17 May 2016 04:58:50: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 04:58:50: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 04:58:50: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 04:58:50: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 04:58:50: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 05:00:32: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 05:02:31: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls 
INFO  @ Tue, 17 May 2016 05:02:39: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 05:02:43: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 05:02:47: Done! 
INFO  @ Tue, 17 May 2016 05:03:06: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-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 05:03:06: #1 read tag files... 
INFO  @ Tue, 17 May 2016 05:03:06: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 05:03:08:  1000000 
INFO  @ Tue, 17 May 2016 05:03:10:  2000000 
INFO  @ Tue, 17 May 2016 05:03:12:  3000000 
INFO  @ Tue, 17 May 2016 05:03:13:  4000000 
INFO  @ Tue, 17 May 2016 05:03:15:  5000000 
INFO  @ Tue, 17 May 2016 05:03:17:  6000000 
INFO  @ Tue, 17 May 2016 05:03:18:  7000000 
INFO  @ Tue, 17 May 2016 05:03:20:  8000000 
INFO  @ Tue, 17 May 2016 05:03:22:  9000000 
INFO  @ Tue, 17 May 2016 05:03:25:  10000000 
INFO  @ Tue, 17 May 2016 05:03:28:  11000000 
INFO  @ Tue, 17 May 2016 05:03:31:  12000000 
INFO  @ Tue, 17 May 2016 05:03:34:  13000000 
INFO  @ Tue, 17 May 2016 05:03:37:  14000000 
INFO  @ Tue, 17 May 2016 05:03:40:  15000000 
INFO  @ Tue, 17 May 2016 05:03:43:  16000000 
INFO  @ Tue, 17 May 2016 05:03:46:  17000000 
INFO  @ Tue, 17 May 2016 05:03:47:  18000000 
INFO  @ Tue, 17 May 2016 05:03:49:  19000000 
INFO  @ Tue, 17 May 2016 05:03:51:  20000000 
INFO  @ Tue, 17 May 2016 05:03:54:  21000000 
INFO  @ Tue, 17 May 2016 05:03:57:  22000000 
INFO  @ Tue, 17 May 2016 05:04:00:  23000000 
INFO  @ Tue, 17 May 2016 05:04:02:  24000000 
INFO  @ Tue, 17 May 2016 05:04:03:  25000000 
INFO  @ Tue, 17 May 2016 05:04:05:  26000000 
INFO  @ Tue, 17 May 2016 05:04:07:  27000000 
INFO  @ Tue, 17 May 2016 05:04:09:  28000000 
INFO  @ Tue, 17 May 2016 05:04:10:  29000000 
INFO  @ Tue, 17 May 2016 05:04:12:  30000000 
INFO  @ Tue, 17 May 2016 05:04:14:  31000000 
INFO  @ Tue, 17 May 2016 05:04:16: #1 tag size is determined as 60 bps 
INFO  @ Tue, 17 May 2016 05:04:16: #1 tag size = 60 
INFO  @ Tue, 17 May 2016 05:04:16: #1  total tags in treatment: 31175984 
INFO  @ Tue, 17 May 2016 05:04:16: #1 finished! 
INFO  @ Tue, 17 May 2016 05:04:16: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 05:04:16: #2 Skipped... 
INFO  @ Tue, 17 May 2016 05:04:16: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 05:04:16: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 05:04:16: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 05:04:16: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 05:04:16: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Tue, 17 May 2016 05:04:16: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 05:05:37: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 05:05:37: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 05:05:37: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 05:05:37: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 05:05:37: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 05:11:24: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls 
INFO  @ Tue, 17 May 2016 05:11:27: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 05:11:29: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_summits.bed 
INFO  @ Tue, 17 May 2016 05:11:30: Done! 
INFO  @ Tue, 17 May 2016 05:11:38: Read and build treatment bedGraph... 
INFO  @ Tue, 17 May 2016 05:12:51: Read and build control bedGraph... 
INFO  @ Tue, 17 May 2016 05:13:28: Build scoreTrackII... 
INFO  @ Tue, 17 May 2016 05:14:06: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Tue, 17 May 2016 05:18:34: Write bedGraph of scores... 
INFO  @ Tue, 17 May 2016 05:21:40: Finished 'FE'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_FE.bdg'! 
INFO  @ Tue, 17 May 2016 05:30:43: Read and build treatment bedGraph... 
INFO  @ Tue, 17 May 2016 05:32:24: Read and build control bedGraph... 
INFO  @ Tue, 17 May 2016 05:33:10: Build scoreTrackII... 
INFO  @ Tue, 17 May 2016 05:34:08: Values in your input bedGraph files will be multiplied by 31.175984 ... 
INFO  @ Tue, 17 May 2016 05:39:46: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Tue, 17 May 2016 05:40:24: Write bedGraph of scores... 
INFO  @ Tue, 17 May 2016 05:42:24: Finished 'ppois'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_ppois.bdg'!

Num	13
ID	task.postalign_bam.dedup_bam_PE_rep2.line_215.id_18
Name	dedup_bam_PE rep2
Thread	thread_21
PID	12474

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

Start	2016-05-17 06:15:37
End	2016-05-17 09:07:01
Elapsed	02:51:23
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep2/ATAC2-trimmed-pair1.trim.PE2SE.dup.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep2/ATAC2-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/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-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/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-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/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.filt

# SYS command. line 239

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-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/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep2/ATAC2-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/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep2/ATAC2-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/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-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/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.filt.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 269

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 271

 if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.bai" ]; then \
			cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.bai; \
			fi

# SYS command. line 275

 samtools flagstat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc

# SYS command. line 286

 samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.filt.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.filt.bam.tmp

# SYS command. line 287

 bedtools bamtobed -bedpe -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-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/ATAC1+2/qc/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.pbc.qc

# SYS command. line 291

 rm /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam

# SYS command. line 293

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.filt.bam

# SYS command. line 294

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-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 42 files...
[bam_sort_core] merging from 42 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Tue May 17 07:44:01 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep2/ATAC2-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 07:44:01 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 07:44:01	MarkDuplicates	Start of doWork freeMemory: 254889872; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-17 07:44:01	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-05-17 07:44:01	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-05-17 07:44:10	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:08s.  Time for last 1,000,000:    8s.  Last read position: chr10:62,609,207
INFO	2016-05-17 07:44:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 07:44:14	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:13s.  Time for last 1,000,000:    4s.  Last read position: chr10:109,879,925
INFO	2016-05-17 07:44:14	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 07:44:19	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:18s.  Time for last 1,000,000:    4s.  Last read position: chr11:18,785,881
INFO	2016-05-17 07:44:19	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 07:44:23	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:22s.  Time for last 1,000,000:    4s.  Last read position: chr11:71,621,986
INFO	2016-05-17 07:44:23	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:44:28	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:26s.  Time for last 1,000,000:    4s.  Last read position: chr11:121,840,865
INFO	2016-05-17 07:44:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 07:44:34	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:33s.  Time for last 1,000,000:    6s.  Last read position: chr12:40,740,366
INFO	2016-05-17 07:44:34	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:44:42	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:40s.  Time for last 1,000,000:    7s.  Last read position: chr12:93,250,354
INFO	2016-05-17 07:44:42	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:44:47	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:46s.  Time for last 1,000,000:    5s.  Last read position: chr13:24,607,045
INFO	2016-05-17 07:44:47	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:44:53	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:51s.  Time for last 1,000,000:    5s.  Last read position: chr13:82,520,490
INFO	2016-05-17 07:44:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 07:44:58	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:56s.  Time for last 1,000,000:    4s.  Last read position: chr14:43,331,015
INFO	2016-05-17 07:44:58	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:45:05	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:04s.  Time for last 1,000,000:    7s.  Last read position: chr14:93,225,507
INFO	2016-05-17 07:45:05	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:45:11	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:09s.  Time for last 1,000,000:    5s.  Last read position: chr15:59,867,707
INFO	2016-05-17 07:45:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 07:45:16	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:15s.  Time for last 1,000,000:    5s.  Last read position: chr16:1,244,974
INFO	2016-05-17 07:45:16	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:45:24	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:23s.  Time for last 1,000,000:    8s.  Last read position: chr16:63,039,688
INFO	2016-05-17 07:45:24	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:45:43	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:41s.  Time for last 1,000,000:   18s.  Last read position: chr17:15,637,182
INFO	2016-05-17 07:45:43	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:45:48	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:46s.  Time for last 1,000,000:    4s.  Last read position: chr17:62,828,915
INFO	2016-05-17 07:45:48	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:45:52	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:01:51s.  Time for last 1,000,000:    4s.  Last read position: chr18:32,758,556
INFO	2016-05-17 07:45:52	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:46:00	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:01:58s.  Time for last 1,000,000:    7s.  Last read position: chr19:5,039,387
INFO	2016-05-17 07:46:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 07:46:04	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:02:03s.  Time for last 1,000,000:    4s.  Last read position: chr19:48,264,419
INFO	2016-05-17 07:46:04	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 07:46:08	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:02:06s.  Time for last 1,000,000:    3s.  Last read position: chr1:18,916,020
INFO	2016-05-17 07:46:08	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:46:12	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:02:10s.  Time for last 1,000,000:    3s.  Last read position: chr1:57,000,361
INFO	2016-05-17 07:46:12	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:46:18	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:02:17s.  Time for last 1,000,000:    6s.  Last read position: chr1:111,979,908
INFO	2016-05-17 07:46:18	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:46:23	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:02:21s.  Time for last 1,000,000:    4s.  Last read position: chr1:184,396,268
INFO	2016-05-17 07:46:23	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:46:28	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:02:26s.  Time for last 1,000,000:    5s.  Last read position: chr1:234,681,068
INFO	2016-05-17 07:46:28	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:46:34	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:02:33s.  Time for last 1,000,000:    6s.  Last read position: chr20:36,767,516
INFO	2016-05-17 07:46:34	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:46:41	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:02:40s.  Time for last 1,000,000:    6s.  Last read position: chr21:38,857,717
INFO	2016-05-17 07:46:41	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:46:50	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:02:48s.  Time for last 1,000,000:    8s.  Last read position: chr22:47,801,985
INFO	2016-05-17 07:46:50	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:46:56	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:02:54s.  Time for last 1,000,000:    5s.  Last read position: chr2:45,115,201
INFO	2016-05-17 07:46:56	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:47:02	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:03:00s.  Time for last 1,000,000:    6s.  Last read position: chr2:103,101,374
INFO	2016-05-17 07:47:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 07:47:16	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:03:14s.  Time for last 1,000,000:   14s.  Last read position: chr2:160,919,444
INFO	2016-05-17 07:47:16	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 07:47:21	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:03:20s.  Time for last 1,000,000:    5s.  Last read position: chr2:215,782,826
INFO	2016-05-17 07:47:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 07:47:28	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:03:27s.  Time for last 1,000,000:    7s.  Last read position: chr3:18,631,081
INFO	2016-05-17 07:47:28	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:47:34	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:03:32s.  Time for last 1,000,000:    5s.  Last read position: chr3:65,358,044
INFO	2016-05-17 07:47:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 07:47:37	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:03:35s.  Time for last 1,000,000:    3s.  Last read position: chr3:127,432,582
INFO	2016-05-17 07:47:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 07:47:40	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:03:39s.  Time for last 1,000,000:    3s.  Last read position: chr3:182,082,144
INFO	2016-05-17 07:47:40	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:47:44	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:03:42s.  Time for last 1,000,000:    3s.  Last read position: chr4:34,742,018
INFO	2016-05-17 07:47:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 07:47:48	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:03:46s.  Time for last 1,000,000:    3s.  Last read position: chr4:97,418,809
INFO	2016-05-17 07:47:48	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:47:54	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:03:52s.  Time for last 1,000,000:    6s.  Last read position: chr4:155,899,108
INFO	2016-05-17 07:47:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 07:47:58	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:03:56s.  Time for last 1,000,000:    4s.  Last read position: chr5:21,912,134
INFO	2016-05-17 07:47:58	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:48:03	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:04:01s.  Time for last 1,000,000:    4s.  Last read position: chr5:84,722,884
INFO	2016-05-17 07:48:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 07:48:08	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:04:06s.  Time for last 1,000,000:    5s.  Last read position: chr5:134,262,553
INFO	2016-05-17 07:48:08	MarkDuplicates	Tracking 586 as yet unmatched pairs. 586 records in RAM.
INFO	2016-05-17 07:48:13	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:04:11s.  Time for last 1,000,000:    5s.  Last read position: chr5:177,554,232
INFO	2016-05-17 07:48:13	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:48:21	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:04:20s.  Time for last 1,000,000:    8s.  Last read position: chr6:40,941,824
INFO	2016-05-17 07:48:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 07:48:26	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:04:25s.  Time for last 1,000,000:    5s.  Last read position: chr6:102,611,635
INFO	2016-05-17 07:48:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 07:48:35	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:04:33s.  Time for last 1,000,000:    8s.  Last read position: chr6:157,055,159
INFO	2016-05-17 07:48:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 07:48:40	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:04:38s.  Time for last 1,000,000:    5s.  Last read position: chr7:36,397,640
INFO	2016-05-17 07:48:40	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:48:44	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:04:42s.  Time for last 1,000,000:    4s.  Last read position: chr7:98,407,959
INFO	2016-05-17 07:48:44	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:48:50	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:04:49s.  Time for last 1,000,000:    6s.  Last read position: chr7:149,204,649
INFO	2016-05-17 07:48:50	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:48:57	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:04:55s.  Time for last 1,000,000:    6s.  Last read position: chr8:41,400,371
INFO	2016-05-17 07:48:57	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-17 07:49:03	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:05:02s.  Time for last 1,000,000:    6s.  Last read position: chr8:100,508,103
INFO	2016-05-17 07:49:03	MarkDuplicates	Tracking 906 as yet unmatched pairs. 906 records in RAM.
INFO	2016-05-17 07:49:07	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:05:05s.  Time for last 1,000,000:    3s.  Last read position: chr9:4,298,519
INFO	2016-05-17 07:49:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 07:49:10	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:05:09s.  Time for last 1,000,000:    3s.  Last read position: chr9:90,340,963
INFO	2016-05-17 07:49:10	MarkDuplicates	Tracking 14 as yet unmatched pairs. 14 records in RAM.
INFO	2016-05-17 07:49:15	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:05:13s.  Time for last 1,000,000:    4s.  Last read position: chr9:134,701,923
INFO	2016-05-17 07:49:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 07:49:19	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:05:17s.  Time for last 1,000,000:    3s.  Last read position: chrM:372
INFO	2016-05-17 07:49:19	MarkDuplicates	Tracking 77326 as yet unmatched pairs. 77326 records in RAM.
INFO	2016-05-17 07:49:25	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:05:24s.  Time for last 1,000,000:    6s.  Last read position: chrM:697
INFO	2016-05-17 07:49:25	MarkDuplicates	Tracking 70970 as yet unmatched pairs. 70970 records in RAM.
INFO	2016-05-17 07:49:29	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:05:28s.  Time for last 1,000,000:    4s.  Last read position: chrM:983
INFO	2016-05-17 07:49:29	MarkDuplicates	Tracking 98446 as yet unmatched pairs. 98446 records in RAM.
INFO	2016-05-17 07:49:35	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:05:33s.  Time for last 1,000,000:    5s.  Last read position: chrM:1,431
INFO	2016-05-17 07:49:35	MarkDuplicates	Tracking 52984 as yet unmatched pairs. 52984 records in RAM.
INFO	2016-05-17 07:49:40	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:05:38s.  Time for last 1,000,000:    5s.  Last read position: chrM:1,823
INFO	2016-05-17 07:49:40	MarkDuplicates	Tracking 41926 as yet unmatched pairs. 41926 records in RAM.
INFO	2016-05-17 07:49:56	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:05:54s.  Time for last 1,000,000:   15s.  Last read position: chrM:2,211
INFO	2016-05-17 07:49:56	MarkDuplicates	Tracking 65664 as yet unmatched pairs. 65664 records in RAM.
INFO	2016-05-17 07:50:01	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:05:59s.  Time for last 1,000,000:    4s.  Last read position: chrM:2,647
INFO	2016-05-17 07:50:01	MarkDuplicates	Tracking 117446 as yet unmatched pairs. 117446 records in RAM.
INFO	2016-05-17 07:50:06	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:06:05s.  Time for last 1,000,000:    5s.  Last read position: chrM:2,866
INFO	2016-05-17 07:50:06	MarkDuplicates	Tracking 123870 as yet unmatched pairs. 123870 records in RAM.
INFO	2016-05-17 07:50:14	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:06:13s.  Time for last 1,000,000:    8s.  Last read position: chrM:3,125
INFO	2016-05-17 07:50:14	MarkDuplicates	Tracking 113290 as yet unmatched pairs. 113290 records in RAM.
INFO	2016-05-17 07:50:19	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:06:17s.  Time for last 1,000,000:    4s.  Last read position: chrM:3,351
INFO	2016-05-17 07:50:19	MarkDuplicates	Tracking 119318 as yet unmatched pairs. 119318 records in RAM.
INFO	2016-05-17 07:50:24	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:06:22s.  Time for last 1,000,000:    5s.  Last read position: chrM:3,515
INFO	2016-05-17 07:50:24	MarkDuplicates	Tracking 53366 as yet unmatched pairs. 53366 records in RAM.
INFO	2016-05-17 07:50:29	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:06:27s.  Time for last 1,000,000:    4s.  Last read position: chrM:3,725
INFO	2016-05-17 07:50:29	MarkDuplicates	Tracking 116320 as yet unmatched pairs. 116320 records in RAM.
INFO	2016-05-17 07:50:33	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:06:31s.  Time for last 1,000,000:    4s.  Last read position: chrM:3,987
INFO	2016-05-17 07:50:33	MarkDuplicates	Tracking 60100 as yet unmatched pairs. 60100 records in RAM.
INFO	2016-05-17 07:50:37	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:06:35s.  Time for last 1,000,000:    3s.  Last read position: chrM:4,790
INFO	2016-05-17 07:50:37	MarkDuplicates	Tracking 29388 as yet unmatched pairs. 29388 records in RAM.
INFO	2016-05-17 07:50:42	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:06:40s.  Time for last 1,000,000:    5s.  Last read position: chrM:5,114
INFO	2016-05-17 07:50:42	MarkDuplicates	Tracking 29588 as yet unmatched pairs. 29588 records in RAM.
INFO	2016-05-17 07:50:45	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:06:43s.  Time for last 1,000,000:    3s.  Last read position: chrM:5,772
INFO	2016-05-17 07:50:45	MarkDuplicates	Tracking 40374 as yet unmatched pairs. 40374 records in RAM.
INFO	2016-05-17 07:50:50	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:06:48s.  Time for last 1,000,000:    4s.  Last read position: chrM:6,261
INFO	2016-05-17 07:50:50	MarkDuplicates	Tracking 72014 as yet unmatched pairs. 72014 records in RAM.
INFO	2016-05-17 07:50:55	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:06:53s.  Time for last 1,000,000:    5s.  Last read position: chrM:6,454
INFO	2016-05-17 07:50:55	MarkDuplicates	Tracking 68894 as yet unmatched pairs. 68894 records in RAM.
INFO	2016-05-17 07:51:00	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:06:59s.  Time for last 1,000,000:    5s.  Last read position: chrM:6,659
INFO	2016-05-17 07:51:00	MarkDuplicates	Tracking 56188 as yet unmatched pairs. 56188 records in RAM.
INFO	2016-05-17 07:51:05	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:07:04s.  Time for last 1,000,000:    4s.  Last read position: chrM:7,165
INFO	2016-05-17 07:51:05	MarkDuplicates	Tracking 55932 as yet unmatched pairs. 55932 records in RAM.
INFO	2016-05-17 07:51:13	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:07:12s.  Time for last 1,000,000:    8s.  Last read position: chrM:7,775
INFO	2016-05-17 07:51:13	MarkDuplicates	Tracking 49342 as yet unmatched pairs. 49342 records in RAM.
INFO	2016-05-17 07:51:20	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:07:18s.  Time for last 1,000,000:    6s.  Last read position: chrM:8,039
INFO	2016-05-17 07:51:20	MarkDuplicates	Tracking 68734 as yet unmatched pairs. 68734 records in RAM.
INFO	2016-05-17 07:51:23	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:07:22s.  Time for last 1,000,000:    3s.  Last read position: chrM:8,467
INFO	2016-05-17 07:51:23	MarkDuplicates	Tracking 93524 as yet unmatched pairs. 93524 records in RAM.
INFO	2016-05-17 07:51:27	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:07:25s.  Time for last 1,000,000:    3s.  Last read position: chrM:9,183
INFO	2016-05-17 07:51:27	MarkDuplicates	Tracking 51044 as yet unmatched pairs. 51044 records in RAM.
INFO	2016-05-17 07:51:30	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:07:29s.  Time for last 1,000,000:    3s.  Last read position: chrM:9,618
INFO	2016-05-17 07:51:30	MarkDuplicates	Tracking 44304 as yet unmatched pairs. 44304 records in RAM.
INFO	2016-05-17 07:51:35	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:07:34s.  Time for last 1,000,000:    4s.  Last read position: chrM:9,958
INFO	2016-05-17 07:51:35	MarkDuplicates	Tracking 73730 as yet unmatched pairs. 73730 records in RAM.
INFO	2016-05-17 07:51:39	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:07:37s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,281
INFO	2016-05-17 07:51:39	MarkDuplicates	Tracking 62734 as yet unmatched pairs. 62734 records in RAM.
INFO	2016-05-17 07:51:42	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:07:40s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,631
INFO	2016-05-17 07:51:42	MarkDuplicates	Tracking 66480 as yet unmatched pairs. 66480 records in RAM.
INFO	2016-05-17 07:51:48	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:07:46s.  Time for last 1,000,000:    6s.  Last read position: chrM:11,161
INFO	2016-05-17 07:51:48	MarkDuplicates	Tracking 50296 as yet unmatched pairs. 50296 records in RAM.
INFO	2016-05-17 07:51:52	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:07:51s.  Time for last 1,000,000:    4s.  Last read position: chrM:11,500
INFO	2016-05-17 07:51:52	MarkDuplicates	Tracking 25874 as yet unmatched pairs. 25874 records in RAM.
INFO	2016-05-17 07:51:58	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:07:56s.  Time for last 1,000,000:    5s.  Last read position: chrM:11,838
INFO	2016-05-17 07:51:58	MarkDuplicates	Tracking 36780 as yet unmatched pairs. 36780 records in RAM.
INFO	2016-05-17 07:52:04	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:08:02s.  Time for last 1,000,000:    6s.  Last read position: chrM:12,141
INFO	2016-05-17 07:52:04	MarkDuplicates	Tracking 74808 as yet unmatched pairs. 74808 records in RAM.
INFO	2016-05-17 07:52:12	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:08:10s.  Time for last 1,000,000:    7s.  Last read position: chrM:12,505
INFO	2016-05-17 07:52:12	MarkDuplicates	Tracking 75648 as yet unmatched pairs. 75648 records in RAM.
INFO	2016-05-17 07:52:19	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:08:17s.  Time for last 1,000,000:    7s.  Last read position: chrM:12,743
INFO	2016-05-17 07:52:19	MarkDuplicates	Tracking 39958 as yet unmatched pairs. 39958 records in RAM.
INFO	2016-05-17 07:52:25	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:08:23s.  Time for last 1,000,000:    6s.  Last read position: chrM:13,123
INFO	2016-05-17 07:52:25	MarkDuplicates	Tracking 71904 as yet unmatched pairs. 71904 records in RAM.
INFO	2016-05-17 07:52:41	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:08:40s.  Time for last 1,000,000:   16s.  Last read position: chrM:13,362
INFO	2016-05-17 07:52:41	MarkDuplicates	Tracking 89754 as yet unmatched pairs. 89754 records in RAM.
INFO	2016-05-17 07:52:47	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:08:46s.  Time for last 1,000,000:    5s.  Last read position: chrM:13,601
INFO	2016-05-17 07:52:47	MarkDuplicates	Tracking 52696 as yet unmatched pairs. 52696 records in RAM.
INFO	2016-05-17 07:52:50	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:08:49s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,939
INFO	2016-05-17 07:52:50	MarkDuplicates	Tracking 32536 as yet unmatched pairs. 32536 records in RAM.
INFO	2016-05-17 07:52:53	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:08:52s.  Time for last 1,000,000:    3s.  Last read position: chrM:14,316
INFO	2016-05-17 07:52:53	MarkDuplicates	Tracking 32900 as yet unmatched pairs. 32900 records in RAM.
INFO	2016-05-17 07:52:56	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:08:55s.  Time for last 1,000,000:    2s.  Last read position: chrM:14,746
INFO	2016-05-17 07:52:56	MarkDuplicates	Tracking 17458 as yet unmatched pairs. 17458 records in RAM.
INFO	2016-05-17 07:53:00	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:08:58s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,073
INFO	2016-05-17 07:53:00	MarkDuplicates	Tracking 118140 as yet unmatched pairs. 118140 records in RAM.
INFO	2016-05-17 07:53:03	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:09:01s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,278
INFO	2016-05-17 07:53:03	MarkDuplicates	Tracking 68224 as yet unmatched pairs. 68224 records in RAM.
INFO	2016-05-17 07:53:06	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:09:05s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,484
INFO	2016-05-17 07:53:06	MarkDuplicates	Tracking 57444 as yet unmatched pairs. 57444 records in RAM.
INFO	2016-05-17 07:53:10	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:09:09s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,678
INFO	2016-05-17 07:53:10	MarkDuplicates	Tracking 115678 as yet unmatched pairs. 115678 records in RAM.
INFO	2016-05-17 07:53:16	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:09:14s.  Time for last 1,000,000:    5s.  Last read position: chrM:15,885
INFO	2016-05-17 07:53:16	MarkDuplicates	Tracking 86028 as yet unmatched pairs. 86028 records in RAM.
INFO	2016-05-17 07:53:20	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:09:18s.  Time for last 1,000,000:    3s.  Last read position: chrM:16,281
INFO	2016-05-17 07:53:20	MarkDuplicates	Tracking 60678 as yet unmatched pairs. 60678 records in RAM.
INFO	2016-05-17 07:53:25	MarkDuplicates	Read   100,000,000 records.  Elapsed time: 00:09:23s.  Time for last 1,000,000:    4s.  Last read position: chrM:16,495
INFO	2016-05-17 07:53:25	MarkDuplicates	Tracking 8038 as yet unmatched pairs. 8038 records in RAM.
INFO	2016-05-17 07:53:30	MarkDuplicates	Read   101,000,000 records.  Elapsed time: 00:09:28s.  Time for last 1,000,000:    4s.  Last read position: chrX:53,101,080
INFO	2016-05-17 07:53:30	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:53:35	MarkDuplicates	Read   102,000,000 records.  Elapsed time: 00:09:33s.  Time for last 1,000,000:    5s.  Last read position: chrX:124,080,680
INFO	2016-05-17 07:53:35	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 07:53:37	MarkDuplicates	Read 102534716 records. 0 pairs never matched.
INFO	2016-05-17 07:53:46	MarkDuplicates	After buildSortedReadEndLists freeMemory: 3160122696; totalMemory: 3187146752; maxMemory: 3817865216
INFO	2016-05-17 07:53:46	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-05-17 07:53:46	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-05-17 07:54:11	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-05-17 07:54:35	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-05-17 07:54:38	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2151385896; totalMemory: 3133145088; maxMemory: 3817865216
INFO	2016-05-17 07:54:38	MarkDuplicates	Marking 56454370 records as duplicates.
INFO	2016-05-17 07:54:38	MarkDuplicates	Found 15609427 optical duplicate clusters.
INFO	2016-05-17 07:56:19	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:39s.  Time for last 10,000,000:   99s.  Last read position: chr14:43,331,015
INFO	2016-05-17 07:57:51	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:03:11s.  Time for last 10,000,000:   92s.  Last read position: chr1:18,916,020
INFO	2016-05-17 07:59:24	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:04:45s.  Time for last 10,000,000:   93s.  Last read position: chr2:160,919,444
INFO	2016-05-17 08:01:00	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:06:20s.  Time for last 10,000,000:   95s.  Last read position: chr5:84,722,884
INFO	2016-05-17 08:02:35	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:07:56s.  Time for last 10,000,000:   95s.  Last read position: chr8:100,508,103
INFO	2016-05-17 08:03:57	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:09:17s.  Time for last 10,000,000:   81s.  Last read position: chrM:2,647
INFO	2016-05-17 08:05:11	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:10:31s.  Time for last 10,000,000:   74s.  Last read position: chrM:6,261
INFO	2016-05-17 08:06:25	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:11:45s.  Time for last 10,000,000:   73s.  Last read position: chrM:10,281
INFO	2016-05-17 08:07:43	MarkDuplicates	Written    90,000,000 records.  Elapsed time: 00:13:03s.  Time for last 10,000,000:   77s.  Last read position: chrM:13,601
INFO	2016-05-17 08:09:02	MarkDuplicates	Written   100,000,000 records.  Elapsed time: 00:14:22s.  Time for last 10,000,000:   79s.  Last read position: chrM:16,495
INFO	2016-05-17 08:09:26	MarkDuplicates	Before output close freeMemory: 3243947000; totalMemory: 3274178560; maxMemory: 3817865216
INFO	2016-05-17 08:09:26	MarkDuplicates	After output close freeMemory: 3243945944; totalMemory: 3274178560; maxMemory: 3817865216
[Tue May 17 08:09:26 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 25.42 minutes.
Runtime.totalMemory()=3274178560
[bam_sort_core] merging from 42 files...

Num	14
ID	task.postalign_bam.nmsrt_bam_rep2.line_321.id_19
Name	nmsrt_bam rep2
Thread	thread_21
PID	43137

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

Start	2016-05-17 09:07:01
End	2016-05-17 09:24:59
Elapsed	00:17:57
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-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/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-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 19 files...

Num	15
ID	task.postalign_bam.bam_to_bedpe_rep2.line_425.id_20
Name	bam_to_bedpe rep2
Thread	thread_21
PID	44033

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

Start	2016-05-17 09:24:59
End	2016-05-17 09:27:10
Elapsed	00:02:10
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-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/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-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	44143

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

Start	2016-05-17 09:27:11
End	2016-05-17 09:29:23
Elapsed	00:02:11
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-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/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | grep -v "chrM" | shuf -n 17500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-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	44215

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

Start	2016-05-17 09:29:24
End	2016-05-17 09:31:04
Elapsed	00:01:40
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-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/ATAC1+2/align/rep2/ATAC2-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/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz

# SYS command. line 472

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz | grep -P -v 'chrM' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz; mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-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	44315

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

Start	2016-05-17 09:31:05
End	2016-05-17 09:32:15
Elapsed	00:01:10
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-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/ATAC1+2/align/rep2/ATAC2-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/ATAC1+2/align/rep2/ATAC2-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	44397

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

Start	2016-05-17 09:32:16
End	2016-05-17 09:33:40
Elapsed	00:01:23
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-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/ATAC1+2/align/rep2/ATAC2-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/ATAC1+2/align/rep2/ATAC2-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	44464

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

Start	2016-05-17 09:33:40
End	2016-05-17 10:17:06
Elapsed	00:43:25
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep2/ATAC2-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/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz -p=1 \
			-filtchr=chrM -savp=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf -out=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep2/ATAC2-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/ATAC1+2/qc/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp

# SYS command. line 175

 mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc

   
--------------------Stdout--------------------
################
ChIP data: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-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/ATAC1+2/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/ATAC1+2/qc/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf 
result filename: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep2/ATAC2-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/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz 
opened /tmp/Rtmp4aEK30/ATAC2-trimmed-pair1.trim.PE2SE.nodup.25.tagAlignae4f588e9336
done. read 21839082 fragments
ChIP data read length 76 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.2246924 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.235009198328317 
Top 3 estimates for fragment length 0 
Window half size 505 
Phantom peak location 70 
Phantom peak Correlation 0.2353667 
Normalized Strand cross-correlation coefficient (NSC) 1.045915 
Relative Strand Cross correlation Coefficient (RSC) 0.9665075 
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	44466

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

Start	2016-05-17 09:33:41
End	2016-05-17 09:56:44
Elapsed	00:23:02
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/signal/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/signal/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-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 09:33:45: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-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 09:33:45: #1 read tag files... 
INFO  @ Tue, 17 May 2016 09:33:45: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 09:33:47:  1000000 
INFO  @ Tue, 17 May 2016 09:33:48:  2000000 
INFO  @ Tue, 17 May 2016 09:33:50:  3000000 
INFO  @ Tue, 17 May 2016 09:33:52:  4000000 
INFO  @ Tue, 17 May 2016 09:33:53:  5000000 
INFO  @ Tue, 17 May 2016 09:33:55:  6000000 
INFO  @ Tue, 17 May 2016 09:33:57:  7000000 
INFO  @ Tue, 17 May 2016 09:33:59:  8000000 
INFO  @ Tue, 17 May 2016 09:34:00:  9000000 
INFO  @ Tue, 17 May 2016 09:34:02:  10000000 
INFO  @ Tue, 17 May 2016 09:34:04:  11000000 
INFO  @ Tue, 17 May 2016 09:34:06:  12000000 
INFO  @ Tue, 17 May 2016 09:34:07:  13000000 
INFO  @ Tue, 17 May 2016 09:34:09:  14000000 
INFO  @ Tue, 17 May 2016 09:34:11:  15000000 
INFO  @ Tue, 17 May 2016 09:34:12:  16000000 
INFO  @ Tue, 17 May 2016 09:34:14:  17000000 
INFO  @ Tue, 17 May 2016 09:34:16:  18000000 
INFO  @ Tue, 17 May 2016 09:34:18:  19000000 
INFO  @ Tue, 17 May 2016 09:34:19:  20000000 
INFO  @ Tue, 17 May 2016 09:34:21:  21000000 
INFO  @ Tue, 17 May 2016 09:34:23:  22000000 
INFO  @ Tue, 17 May 2016 09:34:25:  23000000 
INFO  @ Tue, 17 May 2016 09:34:27:  24000000 
INFO  @ Tue, 17 May 2016 09:34:30:  25000000 
INFO  @ Tue, 17 May 2016 09:34:33:  26000000 
INFO  @ Tue, 17 May 2016 09:34:37:  27000000 
INFO  @ Tue, 17 May 2016 09:34:39:  28000000 
INFO  @ Tue, 17 May 2016 09:34:41:  29000000 
INFO  @ Tue, 17 May 2016 09:34:43:  30000000 
INFO  @ Tue, 17 May 2016 09:34:45:  31000000 
INFO  @ Tue, 17 May 2016 09:34:46:  32000000 
INFO  @ Tue, 17 May 2016 09:34:48:  33000000 
INFO  @ Tue, 17 May 2016 09:34:50:  34000000 
INFO  @ Tue, 17 May 2016 09:34:52:  35000000 
INFO  @ Tue, 17 May 2016 09:34:54: #1 tag size is determined as 47 bps 
INFO  @ Tue, 17 May 2016 09:34:54: #1 tag size = 47 
INFO  @ Tue, 17 May 2016 09:34:54: #1  total tags in treatment: 35000000 
INFO  @ Tue, 17 May 2016 09:34:54: #1 finished! 
INFO  @ Tue, 17 May 2016 09:34:54: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 09:34:54: #2 Skipped... 
INFO  @ Tue, 17 May 2016 09:34:54: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 09:34:54: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 09:34:54: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 09:34:54: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 09:34:54: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 09:36:25: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 09:38:49: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 09:38:53: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 09:38:56: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 09:38:59: Done! 
INFO  @ Tue, 17 May 2016 09:39:22: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-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 09:39:22: #1 read tag files... 
INFO  @ Tue, 17 May 2016 09:39:22: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 09:39:24:  1000000 
INFO  @ Tue, 17 May 2016 09:39:25:  2000000 
INFO  @ Tue, 17 May 2016 09:39:27:  3000000 
INFO  @ Tue, 17 May 2016 09:39:29:  4000000 
INFO  @ Tue, 17 May 2016 09:39:30:  5000000 
INFO  @ Tue, 17 May 2016 09:39:32:  6000000 
INFO  @ Tue, 17 May 2016 09:39:33:  7000000 
INFO  @ Tue, 17 May 2016 09:39:35:  8000000 
INFO  @ Tue, 17 May 2016 09:39:37:  9000000 
INFO  @ Tue, 17 May 2016 09:39:38:  10000000 
INFO  @ Tue, 17 May 2016 09:39:40:  11000000 
INFO  @ Tue, 17 May 2016 09:39:41:  12000000 
INFO  @ Tue, 17 May 2016 09:39:43:  13000000 
INFO  @ Tue, 17 May 2016 09:39:45:  14000000 
INFO  @ Tue, 17 May 2016 09:39:46:  15000000 
INFO  @ Tue, 17 May 2016 09:39:48:  16000000 
INFO  @ Tue, 17 May 2016 09:39:49:  17000000 
INFO  @ Tue, 17 May 2016 09:39:51:  18000000 
INFO  @ Tue, 17 May 2016 09:39:53:  19000000 
INFO  @ Tue, 17 May 2016 09:39:54:  20000000 
INFO  @ Tue, 17 May 2016 09:39:56:  21000000 
INFO  @ Tue, 17 May 2016 09:39:57:  22000000 
INFO  @ Tue, 17 May 2016 09:39:59:  23000000 
INFO  @ Tue, 17 May 2016 09:40:01:  24000000 
INFO  @ Tue, 17 May 2016 09:40:02:  25000000 
INFO  @ Tue, 17 May 2016 09:40:04:  26000000 
INFO  @ Tue, 17 May 2016 09:40:05:  27000000 
INFO  @ Tue, 17 May 2016 09:40:07:  28000000 
INFO  @ Tue, 17 May 2016 09:40:09:  29000000 
INFO  @ Tue, 17 May 2016 09:40:10:  30000000 
INFO  @ Tue, 17 May 2016 09:40:12:  31000000 
INFO  @ Tue, 17 May 2016 09:40:13:  32000000 
INFO  @ Tue, 17 May 2016 09:40:15:  33000000 
INFO  @ Tue, 17 May 2016 09:40:17:  34000000 
INFO  @ Tue, 17 May 2016 09:40:18:  35000000 
INFO  @ Tue, 17 May 2016 09:40:21: #1 tag size is determined as 47 bps 
INFO  @ Tue, 17 May 2016 09:40:21: #1 tag size = 47 
INFO  @ Tue, 17 May 2016 09:40:21: #1  total tags in treatment: 35000000 
INFO  @ Tue, 17 May 2016 09:40:21: #1 finished! 
INFO  @ Tue, 17 May 2016 09:40:21: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 09:40:21: #2 Skipped... 
INFO  @ Tue, 17 May 2016 09:40:21: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 09:40:21: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 09:40:21: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 09:40:21: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 09:40:21: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Tue, 17 May 2016 09:40:21: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 09:42:00: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 09:42:00: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 09:42:00: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 09:42:00: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 09:42:00: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 09:55:41: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 09:56:03: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 09:56:19: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_summits.bed 
INFO  @ Tue, 17 May 2016 09:56:27: Done!

Num	22
ID	task.callpeak_macs2.macs2_atac_rep2.line_192.id_27
Name	macs2_atac rep2
Thread	thread_21
PID	44476

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

Start	2016-05-17 09:33:41
End	2016-05-17 10:46:27
Elapsed	01:12:45
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.gappedPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/signal/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/signal/macs2/rep2/ATAC2-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/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/signal/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/signal/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-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 09:33:45: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-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 09:33:45: #1 read tag files... 
INFO  @ Tue, 17 May 2016 09:33:45: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 09:33:46:  1000000 
INFO  @ Tue, 17 May 2016 09:33:48:  2000000 
INFO  @ Tue, 17 May 2016 09:33:49:  3000000 
INFO  @ Tue, 17 May 2016 09:33:51:  4000000 
INFO  @ Tue, 17 May 2016 09:33:53:  5000000 
INFO  @ Tue, 17 May 2016 09:33:54:  6000000 
INFO  @ Tue, 17 May 2016 09:33:56:  7000000 
INFO  @ Tue, 17 May 2016 09:33:57:  8000000 
INFO  @ Tue, 17 May 2016 09:33:59:  9000000 
INFO  @ Tue, 17 May 2016 09:34:01:  10000000 
INFO  @ Tue, 17 May 2016 09:34:02:  11000000 
INFO  @ Tue, 17 May 2016 09:34:04:  12000000 
INFO  @ Tue, 17 May 2016 09:34:05:  13000000 
INFO  @ Tue, 17 May 2016 09:34:07:  14000000 
INFO  @ Tue, 17 May 2016 09:34:09:  15000000 
INFO  @ Tue, 17 May 2016 09:34:10:  16000000 
INFO  @ Tue, 17 May 2016 09:34:12:  17000000 
INFO  @ Tue, 17 May 2016 09:34:14:  18000000 
INFO  @ Tue, 17 May 2016 09:34:15:  19000000 
INFO  @ Tue, 17 May 2016 09:34:17:  20000000 
INFO  @ Tue, 17 May 2016 09:34:18:  21000000 
INFO  @ Tue, 17 May 2016 09:34:21:  22000000 
INFO  @ Tue, 17 May 2016 09:34:24:  23000000 
INFO  @ Tue, 17 May 2016 09:34:27:  24000000 
INFO  @ Tue, 17 May 2016 09:34:30:  25000000 
INFO  @ Tue, 17 May 2016 09:34:34:  26000000 
INFO  @ Tue, 17 May 2016 09:34:37:  27000000 
INFO  @ Tue, 17 May 2016 09:34:40:  28000000 
INFO  @ Tue, 17 May 2016 09:34:41:  29000000 
INFO  @ Tue, 17 May 2016 09:34:43:  30000000 
INFO  @ Tue, 17 May 2016 09:34:45:  31000000 
INFO  @ Tue, 17 May 2016 09:34:46:  32000000 
INFO  @ Tue, 17 May 2016 09:34:48:  33000000 
INFO  @ Tue, 17 May 2016 09:34:49:  34000000 
INFO  @ Tue, 17 May 2016 09:34:51:  35000000 
INFO  @ Tue, 17 May 2016 09:34:53: #1 tag size is determined as 47 bps 
INFO  @ Tue, 17 May 2016 09:34:53: #1 tag size = 47 
INFO  @ Tue, 17 May 2016 09:34:53: #1  total tags in treatment: 35000000 
INFO  @ Tue, 17 May 2016 09:34:53: #1 finished! 
INFO  @ Tue, 17 May 2016 09:34:53: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 09:34:53: #2 Skipped... 
INFO  @ Tue, 17 May 2016 09:34:53: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 09:34:53: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 09:34:53: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 09:34:53: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 09:34:53: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 09:36:26: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 09:38:35: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls 
INFO  @ Tue, 17 May 2016 09:38:39: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 09:38:41: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 09:38:44: Done! 
INFO  @ Tue, 17 May 2016 09:39:00: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-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 09:39:00: #1 read tag files... 
INFO  @ Tue, 17 May 2016 09:39:00: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 09:39:02:  1000000 
INFO  @ Tue, 17 May 2016 09:39:04:  2000000 
INFO  @ Tue, 17 May 2016 09:39:05:  3000000 
INFO  @ Tue, 17 May 2016 09:39:07:  4000000 
INFO  @ Tue, 17 May 2016 09:39:09:  5000000 
INFO  @ Tue, 17 May 2016 09:39:10:  6000000 
INFO  @ Tue, 17 May 2016 09:39:12:  7000000 
INFO  @ Tue, 17 May 2016 09:39:13:  8000000 
INFO  @ Tue, 17 May 2016 09:39:15:  9000000 
INFO  @ Tue, 17 May 2016 09:39:17:  10000000 
INFO  @ Tue, 17 May 2016 09:39:18:  11000000 
INFO  @ Tue, 17 May 2016 09:39:20:  12000000 
INFO  @ Tue, 17 May 2016 09:39:21:  13000000 
INFO  @ Tue, 17 May 2016 09:39:23:  14000000 
INFO  @ Tue, 17 May 2016 09:39:25:  15000000 
INFO  @ Tue, 17 May 2016 09:39:26:  16000000 
INFO  @ Tue, 17 May 2016 09:39:28:  17000000 
INFO  @ Tue, 17 May 2016 09:39:30:  18000000 
INFO  @ Tue, 17 May 2016 09:39:31:  19000000 
INFO  @ Tue, 17 May 2016 09:39:33:  20000000 
INFO  @ Tue, 17 May 2016 09:39:34:  21000000 
INFO  @ Tue, 17 May 2016 09:39:36:  22000000 
INFO  @ Tue, 17 May 2016 09:39:38:  23000000 
INFO  @ Tue, 17 May 2016 09:39:39:  24000000 
INFO  @ Tue, 17 May 2016 09:39:41:  25000000 
INFO  @ Tue, 17 May 2016 09:39:43:  26000000 
INFO  @ Tue, 17 May 2016 09:39:44:  27000000 
INFO  @ Tue, 17 May 2016 09:39:46:  28000000 
INFO  @ Tue, 17 May 2016 09:39:47:  29000000 
INFO  @ Tue, 17 May 2016 09:39:49:  30000000 
INFO  @ Tue, 17 May 2016 09:39:51:  31000000 
INFO  @ Tue, 17 May 2016 09:39:52:  32000000 
INFO  @ Tue, 17 May 2016 09:39:54:  33000000 
INFO  @ Tue, 17 May 2016 09:39:55:  34000000 
INFO  @ Tue, 17 May 2016 09:39:57:  35000000 
INFO  @ Tue, 17 May 2016 09:39:59: #1 tag size is determined as 47 bps 
INFO  @ Tue, 17 May 2016 09:39:59: #1 tag size = 47 
INFO  @ Tue, 17 May 2016 09:39:59: #1  total tags in treatment: 35000000 
INFO  @ Tue, 17 May 2016 09:39:59: #1 finished! 
INFO  @ Tue, 17 May 2016 09:39:59: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 09:39:59: #2 Skipped... 
INFO  @ Tue, 17 May 2016 09:39:59: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 09:39:59: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 09:39:59: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 09:39:59: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 09:39:59: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Tue, 17 May 2016 09:39:59: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 09:41:41: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 09:41:41: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 09:41:41: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 09:41:41: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 09:41:41: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 09:47:30: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls 
INFO  @ Tue, 17 May 2016 09:47:32: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 09:47:33: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_summits.bed 
INFO  @ Tue, 17 May 2016 09:47:34: Done! 
INFO  @ Tue, 17 May 2016 09:47:40: Read and build treatment bedGraph... 
INFO  @ Tue, 17 May 2016 09:49:29: Read and build control bedGraph... 
INFO  @ Tue, 17 May 2016 09:50:07: Build scoreTrackII... 
INFO  @ Tue, 17 May 2016 09:51:24: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Tue, 17 May 2016 09:59:59: Write bedGraph of scores... 
INFO  @ Tue, 17 May 2016 10:03:49: Finished 'FE'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_FE.bdg'! 
INFO  @ Tue, 17 May 2016 10:15:45: Read and build treatment bedGraph... 
INFO  @ Tue, 17 May 2016 10:18:08: Read and build control bedGraph... 
INFO  @ Tue, 17 May 2016 10:19:15: Build scoreTrackII... 
INFO  @ Tue, 17 May 2016 10:20:30: Values in your input bedGraph files will be multiplied by 35.000000 ... 
INFO  @ Tue, 17 May 2016 10:29:28: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Tue, 17 May 2016 10:30:31: Write bedGraph of scores... 
INFO  @ Tue, 17 May 2016 10:35:02: Finished 'ppois'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-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	49456

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

Start	2016-05-17 10:46:28
End	2016-05-17 10:49:12
Elapsed	00:02:44
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/pooled_rep/ATAC1-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/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz  | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/pooled_rep/ATAC1-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	49532

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

Start	2016-05-17 10:49:13
End	2016-05-17 11:26:28
Elapsed	00:37:14
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/align/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/align/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/signal/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/align/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/signal/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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 10:49:22: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/align/pooled_rep/ATAC1-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 10:49:22: #1 read tag files... 
INFO  @ Tue, 17 May 2016 10:49:22: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 10:49:26:  1000000 
INFO  @ Tue, 17 May 2016 10:49:29:  2000000 
INFO  @ Tue, 17 May 2016 10:49:33:  3000000 
INFO  @ Tue, 17 May 2016 10:49:36:  4000000 
INFO  @ Tue, 17 May 2016 10:49:40:  5000000 
INFO  @ Tue, 17 May 2016 10:49:43:  6000000 
INFO  @ Tue, 17 May 2016 10:49:46:  7000000 
INFO  @ Tue, 17 May 2016 10:49:50:  8000000 
INFO  @ Tue, 17 May 2016 10:49:53:  9000000 
INFO  @ Tue, 17 May 2016 10:49:57:  10000000 
INFO  @ Tue, 17 May 2016 10:50:00:  11000000 
INFO  @ Tue, 17 May 2016 10:50:04:  12000000 
INFO  @ Tue, 17 May 2016 10:50:07:  13000000 
INFO  @ Tue, 17 May 2016 10:50:11:  14000000 
INFO  @ Tue, 17 May 2016 10:50:14:  15000000 
INFO  @ Tue, 17 May 2016 10:50:18:  16000000 
INFO  @ Tue, 17 May 2016 10:50:21:  17000000 
INFO  @ Tue, 17 May 2016 10:50:25:  18000000 
INFO  @ Tue, 17 May 2016 10:50:28:  19000000 
INFO  @ Tue, 17 May 2016 10:50:32:  20000000 
INFO  @ Tue, 17 May 2016 10:50:35:  21000000 
INFO  @ Tue, 17 May 2016 10:50:38:  22000000 
INFO  @ Tue, 17 May 2016 10:50:42:  23000000 
INFO  @ Tue, 17 May 2016 10:50:45:  24000000 
INFO  @ Tue, 17 May 2016 10:50:49:  25000000 
INFO  @ Tue, 17 May 2016 10:50:53:  26000000 
INFO  @ Tue, 17 May 2016 10:50:56:  27000000 
INFO  @ Tue, 17 May 2016 10:51:00:  28000000 
INFO  @ Tue, 17 May 2016 10:51:03:  29000000 
INFO  @ Tue, 17 May 2016 10:51:07:  30000000 
INFO  @ Tue, 17 May 2016 10:51:10:  31000000 
INFO  @ Tue, 17 May 2016 10:51:14:  32000000 
INFO  @ Tue, 17 May 2016 10:51:17:  33000000 
INFO  @ Tue, 17 May 2016 10:51:21:  34000000 
INFO  @ Tue, 17 May 2016 10:51:24:  35000000 
INFO  @ Tue, 17 May 2016 10:51:28:  36000000 
INFO  @ Tue, 17 May 2016 10:51:31:  37000000 
INFO  @ Tue, 17 May 2016 10:51:35:  38000000 
INFO  @ Tue, 17 May 2016 10:51:39:  39000000 
INFO  @ Tue, 17 May 2016 10:51:42:  40000000 
INFO  @ Tue, 17 May 2016 10:51:46:  41000000 
INFO  @ Tue, 17 May 2016 10:51:49:  42000000 
INFO  @ Tue, 17 May 2016 10:51:53:  43000000 
INFO  @ Tue, 17 May 2016 10:51:56:  44000000 
INFO  @ Tue, 17 May 2016 10:52:00:  45000000 
INFO  @ Tue, 17 May 2016 10:52:03:  46000000 
INFO  @ Tue, 17 May 2016 10:52:07:  47000000 
INFO  @ Tue, 17 May 2016 10:52:11:  48000000 
INFO  @ Tue, 17 May 2016 10:52:14:  49000000 
INFO  @ Tue, 17 May 2016 10:52:18:  50000000 
INFO  @ Tue, 17 May 2016 10:52:21:  51000000 
INFO  @ Tue, 17 May 2016 10:52:25:  52000000 
INFO  @ Tue, 17 May 2016 10:52:28:  53000000 
INFO  @ Tue, 17 May 2016 10:52:32:  54000000 
INFO  @ Tue, 17 May 2016 10:52:35:  55000000 
INFO  @ Tue, 17 May 2016 10:52:38:  56000000 
INFO  @ Tue, 17 May 2016 10:52:42:  57000000 
INFO  @ Tue, 17 May 2016 10:52:45:  58000000 
INFO  @ Tue, 17 May 2016 10:52:49:  59000000 
INFO  @ Tue, 17 May 2016 10:52:52:  60000000 
INFO  @ Tue, 17 May 2016 10:52:56:  61000000 
INFO  @ Tue, 17 May 2016 10:52:59:  62000000 
INFO  @ Tue, 17 May 2016 10:53:03:  63000000 
INFO  @ Tue, 17 May 2016 10:53:06:  64000000 
INFO  @ Tue, 17 May 2016 10:53:10:  65000000 
INFO  @ Tue, 17 May 2016 10:53:13:  66000000 
INFO  @ Tue, 17 May 2016 10:53:20: #1 tag size is determined as 60 bps 
INFO  @ Tue, 17 May 2016 10:53:20: #1 tag size = 60 
INFO  @ Tue, 17 May 2016 10:53:20: #1  total tags in treatment: 66175984 
INFO  @ Tue, 17 May 2016 10:53:20: #1 finished! 
INFO  @ Tue, 17 May 2016 10:53:20: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 10:53:20: #2 Skipped... 
INFO  @ Tue, 17 May 2016 10:53:20: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 10:53:20: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 10:53:20: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 10:53:20: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 10:53:20: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 10:58:49: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 11:05:59: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 11:06:02: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 11:06:04: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 11:06:06: Done! 
INFO  @ Tue, 17 May 2016 11:06:18: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/align/pooled_rep/ATAC1-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 11:06:18: #1 read tag files... 
INFO  @ Tue, 17 May 2016 11:06:18: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 11:06:20:  1000000 
INFO  @ Tue, 17 May 2016 11:06:21:  2000000 
INFO  @ Tue, 17 May 2016 11:06:23:  3000000 
INFO  @ Tue, 17 May 2016 11:06:26:  4000000 
INFO  @ Tue, 17 May 2016 11:06:30:  5000000 
INFO  @ Tue, 17 May 2016 11:06:34:  6000000 
INFO  @ Tue, 17 May 2016 11:06:37:  7000000 
INFO  @ Tue, 17 May 2016 11:06:39:  8000000 
INFO  @ Tue, 17 May 2016 11:06:41:  9000000 
INFO  @ Tue, 17 May 2016 11:06:42:  10000000 
INFO  @ Tue, 17 May 2016 11:06:44:  11000000 
INFO  @ Tue, 17 May 2016 11:06:45:  12000000 
INFO  @ Tue, 17 May 2016 11:06:47:  13000000 
INFO  @ Tue, 17 May 2016 11:06:50:  14000000 
INFO  @ Tue, 17 May 2016 11:06:53:  15000000 
INFO  @ Tue, 17 May 2016 11:06:55:  16000000 
INFO  @ Tue, 17 May 2016 11:06:57:  17000000 
INFO  @ Tue, 17 May 2016 11:06:59:  18000000 
INFO  @ Tue, 17 May 2016 11:07:01:  19000000 
INFO  @ Tue, 17 May 2016 11:07:02:  20000000 
INFO  @ Tue, 17 May 2016 11:07:04:  21000000 
INFO  @ Tue, 17 May 2016 11:07:06:  22000000 
INFO  @ Tue, 17 May 2016 11:07:07:  23000000 
INFO  @ Tue, 17 May 2016 11:07:09:  24000000 
INFO  @ Tue, 17 May 2016 11:07:11:  25000000 
INFO  @ Tue, 17 May 2016 11:07:12:  26000000 
INFO  @ Tue, 17 May 2016 11:07:14:  27000000 
INFO  @ Tue, 17 May 2016 11:07:15:  28000000 
INFO  @ Tue, 17 May 2016 11:07:17:  29000000 
INFO  @ Tue, 17 May 2016 11:07:19:  30000000 
INFO  @ Tue, 17 May 2016 11:07:20:  31000000 
INFO  @ Tue, 17 May 2016 11:07:22:  32000000 
INFO  @ Tue, 17 May 2016 11:07:23:  33000000 
INFO  @ Tue, 17 May 2016 11:07:25:  34000000 
INFO  @ Tue, 17 May 2016 11:07:26:  35000000 
INFO  @ Tue, 17 May 2016 11:07:28:  36000000 
INFO  @ Tue, 17 May 2016 11:07:30:  37000000 
INFO  @ Tue, 17 May 2016 11:07:31:  38000000 
INFO  @ Tue, 17 May 2016 11:07:33:  39000000 
INFO  @ Tue, 17 May 2016 11:07:35:  40000000 
INFO  @ Tue, 17 May 2016 11:07:36:  41000000 
INFO  @ Tue, 17 May 2016 11:07:38:  42000000 
INFO  @ Tue, 17 May 2016 11:07:39:  43000000 
INFO  @ Tue, 17 May 2016 11:07:41:  44000000 
INFO  @ Tue, 17 May 2016 11:07:43:  45000000 
INFO  @ Tue, 17 May 2016 11:07:44:  46000000 
INFO  @ Tue, 17 May 2016 11:07:46:  47000000 
INFO  @ Tue, 17 May 2016 11:07:47:  48000000 
INFO  @ Tue, 17 May 2016 11:07:49:  49000000 
INFO  @ Tue, 17 May 2016 11:07:51:  50000000 
INFO  @ Tue, 17 May 2016 11:07:52:  51000000 
INFO  @ Tue, 17 May 2016 11:07:54:  52000000 
INFO  @ Tue, 17 May 2016 11:07:55:  53000000 
INFO  @ Tue, 17 May 2016 11:07:57:  54000000 
INFO  @ Tue, 17 May 2016 11:07:59:  55000000 
INFO  @ Tue, 17 May 2016 11:08:00:  56000000 
INFO  @ Tue, 17 May 2016 11:08:02:  57000000 
INFO  @ Tue, 17 May 2016 11:08:03:  58000000 
INFO  @ Tue, 17 May 2016 11:08:05:  59000000 
INFO  @ Tue, 17 May 2016 11:08:07:  60000000 
INFO  @ Tue, 17 May 2016 11:08:08:  61000000 
INFO  @ Tue, 17 May 2016 11:08:10:  62000000 
INFO  @ Tue, 17 May 2016 11:08:11:  63000000 
INFO  @ Tue, 17 May 2016 11:08:13:  64000000 
INFO  @ Tue, 17 May 2016 11:08:15:  65000000 
INFO  @ Tue, 17 May 2016 11:08:16:  66000000 
INFO  @ Tue, 17 May 2016 11:08:21: #1 tag size is determined as 60 bps 
INFO  @ Tue, 17 May 2016 11:08:21: #1 tag size = 60 
INFO  @ Tue, 17 May 2016 11:08:21: #1  total tags in treatment: 66175984 
INFO  @ Tue, 17 May 2016 11:08:21: #1 finished! 
INFO  @ Tue, 17 May 2016 11:08:21: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 11:08:21: #2 Skipped... 
INFO  @ Tue, 17 May 2016 11:08:21: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 11:08:21: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 11:08:21: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 11:08:21: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 11:08:21: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Tue, 17 May 2016 11:08:21: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 11:11:30: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 11:11:30: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 11:11:30: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 11:11:30: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 11:11:30: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 11:26:00: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 11:26:08: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 11:26:14: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_summits.bed 
INFO  @ Tue, 17 May 2016 11:26:17: Done!

Num	25
ID	task.callpeak_macs2.macs2_atac_pooled.line_192.id_30
Name	macs2_atac pooled
Thread	thread_Root
PID	49533

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

Start	2016-05-17 10:49:13
End	2016-05-17 12:33:07
Elapsed	01:43:53
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.gappedPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/signal/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/signal/macs2/pooled_rep/ATAC1-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/ATAC1+2/align/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/align/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/signal/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/align/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/signal/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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 10:49:22: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/pooled_rep/ATAC1-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 10:49:22: #1 read tag files... 
INFO  @ Tue, 17 May 2016 10:49:22: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 10:49:25:  1000000 
INFO  @ Tue, 17 May 2016 10:49:29:  2000000 
INFO  @ Tue, 17 May 2016 10:49:32:  3000000 
INFO  @ Tue, 17 May 2016 10:49:35:  4000000 
INFO  @ Tue, 17 May 2016 10:49:39:  5000000 
INFO  @ Tue, 17 May 2016 10:49:42:  6000000 
INFO  @ Tue, 17 May 2016 10:49:45:  7000000 
INFO  @ Tue, 17 May 2016 10:49:49:  8000000 
INFO  @ Tue, 17 May 2016 10:49:52:  9000000 
INFO  @ Tue, 17 May 2016 10:49:55:  10000000 
INFO  @ Tue, 17 May 2016 10:49:58:  11000000 
INFO  @ Tue, 17 May 2016 10:50:02:  12000000 
INFO  @ Tue, 17 May 2016 10:50:05:  13000000 
INFO  @ Tue, 17 May 2016 10:50:08:  14000000 
INFO  @ Tue, 17 May 2016 10:50:12:  15000000 
INFO  @ Tue, 17 May 2016 10:50:15:  16000000 
INFO  @ Tue, 17 May 2016 10:50:18:  17000000 
INFO  @ Tue, 17 May 2016 10:50:22:  18000000 
INFO  @ Tue, 17 May 2016 10:50:25:  19000000 
INFO  @ Tue, 17 May 2016 10:50:28:  20000000 
INFO  @ Tue, 17 May 2016 10:50:32:  21000000 
INFO  @ Tue, 17 May 2016 10:50:35:  22000000 
INFO  @ Tue, 17 May 2016 10:50:38:  23000000 
INFO  @ Tue, 17 May 2016 10:50:42:  24000000 
INFO  @ Tue, 17 May 2016 10:50:45:  25000000 
INFO  @ Tue, 17 May 2016 10:50:48:  26000000 
INFO  @ Tue, 17 May 2016 10:50:52:  27000000 
INFO  @ Tue, 17 May 2016 10:50:55:  28000000 
INFO  @ Tue, 17 May 2016 10:50:58:  29000000 
INFO  @ Tue, 17 May 2016 10:51:01:  30000000 
INFO  @ Tue, 17 May 2016 10:51:05:  31000000 
INFO  @ Tue, 17 May 2016 10:51:08:  32000000 
INFO  @ Tue, 17 May 2016 10:51:11:  33000000 
INFO  @ Tue, 17 May 2016 10:51:15:  34000000 
INFO  @ Tue, 17 May 2016 10:51:18:  35000000 
INFO  @ Tue, 17 May 2016 10:51:21:  36000000 
INFO  @ Tue, 17 May 2016 10:51:24:  37000000 
INFO  @ Tue, 17 May 2016 10:51:28:  38000000 
INFO  @ Tue, 17 May 2016 10:51:31:  39000000 
INFO  @ Tue, 17 May 2016 10:51:34:  40000000 
INFO  @ Tue, 17 May 2016 10:51:38:  41000000 
INFO  @ Tue, 17 May 2016 10:51:41:  42000000 
INFO  @ Tue, 17 May 2016 10:51:44:  43000000 
INFO  @ Tue, 17 May 2016 10:51:48:  44000000 
INFO  @ Tue, 17 May 2016 10:51:50:  45000000 
INFO  @ Tue, 17 May 2016 10:51:53:  46000000 
INFO  @ Tue, 17 May 2016 10:51:57:  47000000 
INFO  @ Tue, 17 May 2016 10:52:00:  48000000 
INFO  @ Tue, 17 May 2016 10:52:04:  49000000 
INFO  @ Tue, 17 May 2016 10:52:07:  50000000 
INFO  @ Tue, 17 May 2016 10:52:11:  51000000 
INFO  @ Tue, 17 May 2016 10:52:14:  52000000 
INFO  @ Tue, 17 May 2016 10:52:18:  53000000 
INFO  @ Tue, 17 May 2016 10:52:21:  54000000 
INFO  @ Tue, 17 May 2016 10:52:24:  55000000 
INFO  @ Tue, 17 May 2016 10:52:28:  56000000 
INFO  @ Tue, 17 May 2016 10:52:31:  57000000 
INFO  @ Tue, 17 May 2016 10:52:34:  58000000 
INFO  @ Tue, 17 May 2016 10:52:38:  59000000 
INFO  @ Tue, 17 May 2016 10:52:42:  60000000 
INFO  @ Tue, 17 May 2016 10:52:45:  61000000 
INFO  @ Tue, 17 May 2016 10:52:48:  62000000 
INFO  @ Tue, 17 May 2016 10:52:52:  63000000 
INFO  @ Tue, 17 May 2016 10:52:55:  64000000 
INFO  @ Tue, 17 May 2016 10:52:59:  65000000 
INFO  @ Tue, 17 May 2016 10:53:02:  66000000 
INFO  @ Tue, 17 May 2016 10:53:10: #1 tag size is determined as 60 bps 
INFO  @ Tue, 17 May 2016 10:53:10: #1 tag size = 60 
INFO  @ Tue, 17 May 2016 10:53:10: #1  total tags in treatment: 66175984 
INFO  @ Tue, 17 May 2016 10:53:10: #1 finished! 
INFO  @ Tue, 17 May 2016 10:53:10: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 10:53:10: #2 Skipped... 
INFO  @ Tue, 17 May 2016 10:53:10: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 10:53:10: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 10:53:10: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 10:53:10: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 10:53:10: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 10:58:37: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 11:04:45: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.xls 
INFO  @ Tue, 17 May 2016 11:04:51: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 11:04:55: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 11:04:59: Done! 
INFO  @ Tue, 17 May 2016 11:05:16: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/pooled_rep/ATAC1-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 11:05:16: #1 read tag files... 
INFO  @ Tue, 17 May 2016 11:05:16: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 11:05:19:  1000000 
INFO  @ Tue, 17 May 2016 11:05:20:  2000000 
INFO  @ Tue, 17 May 2016 11:05:22:  3000000 
INFO  @ Tue, 17 May 2016 11:05:24:  4000000 
INFO  @ Tue, 17 May 2016 11:05:26:  5000000 
INFO  @ Tue, 17 May 2016 11:05:28:  6000000 
INFO  @ Tue, 17 May 2016 11:05:31:  7000000 
INFO  @ Tue, 17 May 2016 11:05:33:  8000000 
INFO  @ Tue, 17 May 2016 11:05:35:  9000000 
INFO  @ Tue, 17 May 2016 11:05:37:  10000000 
INFO  @ Tue, 17 May 2016 11:05:39:  11000000 
INFO  @ Tue, 17 May 2016 11:05:41:  12000000 
INFO  @ Tue, 17 May 2016 11:05:43:  13000000 
INFO  @ Tue, 17 May 2016 11:05:46:  14000000 
INFO  @ Tue, 17 May 2016 11:05:48:  15000000 
INFO  @ Tue, 17 May 2016 11:05:50:  16000000 
INFO  @ Tue, 17 May 2016 11:05:51:  17000000 
INFO  @ Tue, 17 May 2016 11:05:53:  18000000 
INFO  @ Tue, 17 May 2016 11:05:55:  19000000 
INFO  @ Tue, 17 May 2016 11:05:56:  20000000 
INFO  @ Tue, 17 May 2016 11:05:58:  21000000 
INFO  @ Tue, 17 May 2016 11:05:59:  22000000 
INFO  @ Tue, 17 May 2016 11:06:01:  23000000 
INFO  @ Tue, 17 May 2016 11:06:03:  24000000 
INFO  @ Tue, 17 May 2016 11:06:04:  25000000 
INFO  @ Tue, 17 May 2016 11:06:06:  26000000 
INFO  @ Tue, 17 May 2016 11:06:08:  27000000 
INFO  @ Tue, 17 May 2016 11:06:09:  28000000 
INFO  @ Tue, 17 May 2016 11:06:11:  29000000 
INFO  @ Tue, 17 May 2016 11:06:13:  30000000 
INFO  @ Tue, 17 May 2016 11:06:14:  31000000 
INFO  @ Tue, 17 May 2016 11:06:16:  32000000 
INFO  @ Tue, 17 May 2016 11:06:18:  33000000 
INFO  @ Tue, 17 May 2016 11:06:19:  34000000 
INFO  @ Tue, 17 May 2016 11:06:21:  35000000 
INFO  @ Tue, 17 May 2016 11:06:23:  36000000 
INFO  @ Tue, 17 May 2016 11:06:24:  37000000 
INFO  @ Tue, 17 May 2016 11:06:26:  38000000 
INFO  @ Tue, 17 May 2016 11:06:28:  39000000 
INFO  @ Tue, 17 May 2016 11:06:29:  40000000 
INFO  @ Tue, 17 May 2016 11:06:32:  41000000 
INFO  @ Tue, 17 May 2016 11:06:34:  42000000 
INFO  @ Tue, 17 May 2016 11:06:36:  43000000 
INFO  @ Tue, 17 May 2016 11:06:38:  44000000 
INFO  @ Tue, 17 May 2016 11:06:40:  45000000 
INFO  @ Tue, 17 May 2016 11:06:42:  46000000 
INFO  @ Tue, 17 May 2016 11:06:44:  47000000 
INFO  @ Tue, 17 May 2016 11:06:45:  48000000 
INFO  @ Tue, 17 May 2016 11:06:47:  49000000 
INFO  @ Tue, 17 May 2016 11:06:49:  50000000 
INFO  @ Tue, 17 May 2016 11:06:51:  51000000 
INFO  @ Tue, 17 May 2016 11:06:53:  52000000 
INFO  @ Tue, 17 May 2016 11:06:55:  53000000 
INFO  @ Tue, 17 May 2016 11:06:57:  54000000 
INFO  @ Tue, 17 May 2016 11:06:58:  55000000 
INFO  @ Tue, 17 May 2016 11:07:00:  56000000 
INFO  @ Tue, 17 May 2016 11:07:02:  57000000 
INFO  @ Tue, 17 May 2016 11:07:04:  58000000 
INFO  @ Tue, 17 May 2016 11:07:06:  59000000 
INFO  @ Tue, 17 May 2016 11:07:08:  60000000 
INFO  @ Tue, 17 May 2016 11:07:10:  61000000 
INFO  @ Tue, 17 May 2016 11:07:11:  62000000 
INFO  @ Tue, 17 May 2016 11:07:13:  63000000 
INFO  @ Tue, 17 May 2016 11:07:15:  64000000 
INFO  @ Tue, 17 May 2016 11:07:16:  65000000 
INFO  @ Tue, 17 May 2016 11:07:18:  66000000 
INFO  @ Tue, 17 May 2016 11:07:23: #1 tag size is determined as 60 bps 
INFO  @ Tue, 17 May 2016 11:07:23: #1 tag size = 60 
INFO  @ Tue, 17 May 2016 11:07:23: #1  total tags in treatment: 66175984 
INFO  @ Tue, 17 May 2016 11:07:23: #1 finished! 
INFO  @ Tue, 17 May 2016 11:07:23: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 11:07:23: #2 Skipped... 
INFO  @ Tue, 17 May 2016 11:07:23: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 11:07:23: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 11:07:23: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 11:07:23: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 11:07:23: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Tue, 17 May 2016 11:07:23: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 11:10:08: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 11:10:08: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 11:10:08: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 11:10:08: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 11:10:08: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 11:19:12: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.xls 
INFO  @ Tue, 17 May 2016 11:19:14: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 11:19:15: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_summits.bed 
INFO  @ Tue, 17 May 2016 11:19:16: Done! 
INFO  @ Tue, 17 May 2016 11:19:23: Read and build treatment bedGraph... 
INFO  @ Tue, 17 May 2016 11:21:40: Read and build control bedGraph... 
INFO  @ Tue, 17 May 2016 11:22:43: Build scoreTrackII... 
INFO  @ Tue, 17 May 2016 11:23:52: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Tue, 17 May 2016 11:35:07: Write bedGraph of scores... 
INFO  @ Tue, 17 May 2016 11:41:11: Finished 'FE'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_FE.bdg'! 
INFO  @ Tue, 17 May 2016 11:54:14: Read and build treatment bedGraph... 
INFO  @ Tue, 17 May 2016 11:56:43: Read and build control bedGraph... 
INFO  @ Tue, 17 May 2016 11:58:35: Build scoreTrackII... 
INFO  @ Tue, 17 May 2016 12:00:11: Values in your input bedGraph files will be multiplied by 66.175984 ... 
INFO  @ Tue, 17 May 2016 12:11:17: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Tue, 17 May 2016 12:12:22: Write bedGraph of scores... 
INFO  @ Tue, 17 May 2016 12:18:39: Finished 'ppois'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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	53189

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

Start	2016-05-17 12:33:07
End	2016-05-17 12:33:23
Elapsed	00:00:16
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-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	53194

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

Start	2016-05-17 12:33:07
End	2016-05-17 12:33:17
Elapsed	00:00:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-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	53208

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

Start	2016-05-17 12:33:07
End	2016-05-17 12:33:18
Elapsed	00:00:11
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-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	53221

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

Start	2016-05-17 12:33:07
End	2016-05-17 12:33:17
Elapsed	00:00:10
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-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	53230

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

Start	2016-05-17 12:33:08
End	2016-05-17 12:33:20
Elapsed	00:00:12
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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	53241

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

Start	2016-05-17 12:33:08
End	2016-05-17 12:33:16
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.gappedPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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	53550

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

Start	2016-05-17 12:33:24
End	2016-05-17 12:36:57
Elapsed	00:03:32
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt.png /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/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/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz --peak-list /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/pooled_rep/ATAC1-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/ATAC1+2/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/ATAC1+2/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/ATAC1+2/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/ATAC1+2/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/ATAC1+2/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/ATAC1+2/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/ATAC1+2/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/ATAC1+2/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/ATAC1+2/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/ATAC1+2/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: [1.56 0.82 0.69 0.31]
Number of reported peaks - 198958/198958 (100.0%)

Number of peaks passing IDR cutoff of 0.1 - 72034/198958 (36.2%)

Num	33
ID	task.base.line_414.id_40
Name	task.base.line_414.id_40
Thread	thread_Root
PID	53869

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

Start	2016-05-17 12:36:58
End	2016-05-17 12:36:58
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/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/ATAC1+2/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/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	53871

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

Start	2016-05-17 12:36:58
End	2016-05-17 12:36:58
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/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/ATAC1+2/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/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	53874

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

Start	2016-05-17 12:36:58
End	2016-05-17 12:36:58
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/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/ATAC1+2/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/ATAC1+2/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/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	53877

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

Start	2016-05-17 12:36:58
End	2016-05-17 12:36:58
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/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/ATAC1+2/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/ATAC1+2/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/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	53919

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

Start	2016-05-17 12:36:59
End	2016-05-17 12:37:00
Elapsed	00:00:01
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/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/ATAC1+2/qc/IDR_final.qc

# SYS command. line 201

 echo -e "72107\t""0\trep1-rep2\trep1-rep2\tInfinity\tNaN\t0" >> /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/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_rep2.line_345.id_45
Name	srt_bam rep2
Thread	thread_79
PID	53921

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

Start	2016-05-17 12:36:59
End	2016-05-17 13:17:15
Elapsed	00:40:15
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-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/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.srt

# SYS command. line 354

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.srt.bam

# SYS command. line 356

 if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.srt.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.srt.bai" ]; then \
			cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.srt.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-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 62 files...

Num	39
ID	task.postalign_bam.srt_bam_rep1.line_345.id_46
Name	srt_bam rep1
Thread	thread_78
PID	53923

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

Start	2016-05-17 12:36:59
End	2016-05-17 13:03:16
Elapsed	00:26:17
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-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/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.srt

# SYS command. line 354

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.srt.bam

# SYS command. line 356

 if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.srt.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.srt.bai" ]; then \
			cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.srt.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-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 38 files...

Num	40
ID	task.atac.ataqc_rep1.line_815.id_47
Name	ataqc rep1
Thread	thread_78
PID	55327

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

Start	2016-05-17 13:03:17
End	2016-05-17 15:12:33
Elapsed	02:09:16
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC1/ATAC1-trimmed-pair1.fastq.gz /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC1/ATAC1-trimmed-pair2.fastq.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep1/ATAC1-trimmed-pair1.trim.PE2SE.align.log /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.pbc.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep1/ATAC1-trimmed-pair1.trim.PE2SE.dup.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/signal/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep1/ATAC1-trimmed-pair1.PE2SE_qc.html /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep1/ATAC1-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/ATAC1+2/qc/rep1

# SYS command. line 825

 /users/pangwei/bds_atac/ataqc/run_ataqc.py \
			    --workdir /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep1 \
			    --outdir /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep1 \
			    --outprefix ATAC1-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/ATAC1+2/qc/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.pbc.qc\
			    --fastq1 /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC1/ATAC1-trimmed-pair1.fastq.gz --fastq2 /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC1/ATAC1-trimmed-pair2.fastq.gz \
			    --alignedbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.bam \
			    --alignmentlog /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep1/ATAC1-trimmed-pair1.trim.PE2SE.align.log \
			    --coordsortbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.srt.bam \
			    --duplog /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep1/ATAC1-trimmed-pair1.trim.PE2SE.dup.qc \
			    --finalbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.bam \
			    --finalbed /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz \
			    --bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/signal/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig \
			    --peaks /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz \
			     \
			    --idr_peaks /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz

   
--------------------Stdout--------------------
Run time: 2:09:10

 
--------------------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 13:06:31	ProcessExecutor	Warning messages:
ERROR	2016-05-17 13:06:31	ProcessExecutor	1: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
ERROR	2016-05-17 13:06:31	ProcessExecutor	  zero-length arrow is of indeterminate angle and so skipped
ERROR	2016-05-17 13:06:31	ProcessExecutor	2: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
ERROR	2016-05-17 13:06:31	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 38 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	56399

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

Start	2016-05-17 13:17:16
End	2016-05-17 16:26:51
Elapsed	03:09:35
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC2/ATAC2-trimmed-pair1.fastq.gz /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC2/ATAC2-trimmed-pair2.fastq.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep2/ATAC2-trimmed-pair1.trim.PE2SE.align.log /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.pbc.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep2/ATAC2-trimmed-pair1.trim.PE2SE.dup.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/signal/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep2/ATAC2-trimmed-pair1.PE2SE_qc.html /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep2/ATAC2-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/ATAC1+2/qc/rep2

# SYS command. line 825

 /users/pangwei/bds_atac/ataqc/run_ataqc.py \
			    --workdir /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep2 \
			    --outdir /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep2 \
			    --outprefix ATAC2-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/ATAC1+2/qc/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.pbc.qc\
			    --fastq1 /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC2/ATAC2-trimmed-pair1.fastq.gz --fastq2 /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC2/ATAC2-trimmed-pair2.fastq.gz \
			    --alignedbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.bam \
			    --alignmentlog /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep2/ATAC2-trimmed-pair1.trim.PE2SE.align.log \
			    --coordsortbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.srt.bam \
			    --duplog /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep2/ATAC2-trimmed-pair1.trim.PE2SE.dup.qc \
			    --finalbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.bam \
			    --finalbed /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz \
			    --bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/signal/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig \
			    --peaks /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz \
			     \
			    --idr_peaks /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz

   
--------------------Stdout--------------------
Run time: 3:09:33

 
--------------------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 13:21:26	ProcessExecutor	Warning messages:
ERROR	2016-05-17 13:21:26	ProcessExecutor	1: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
ERROR	2016-05-17 13:21:26	ProcessExecutor	  zero-length arrow is of indeterminate angle and so skipped
ERROR	2016-05-17 13:21:26	ProcessExecutor	2: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
ERROR	2016-05-17 13:21:26	ProcessExecutor	  zero-length arrow is of indeterminate angle and so skipped
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
[bam_sort_core] merging from 62 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	65719

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

Start	2016-05-17 16:26:53
End	2016-05-17 16:26:58
Elapsed	00:00:04
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/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/ATAC1+2/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/ATAC1+2/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/ATAC1+2/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/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/ATAC1+2/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	65788

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

Start	2016-05-17 16:26:59
End	2016-05-17 16:27:07
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep1/ATAC1-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/ATAC1+2/peak/macs2/rep1/ATAC1-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	65861

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

Start	2016-05-17 16:27:08
End	2016-05-17 16:27:15
Elapsed	00:00:06
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/peak/macs2/rep2/ATAC2-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/ATAC1+2/peak/macs2/rep2/ATAC2-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	65953

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

Start	2016-05-17 16:27:16
End	2016-05-17 16:27:21
Elapsed	00:00:04
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/ATAC1+2/report/workflow.dot > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/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	65978

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

Start	2016-05-17 16:27:17
End	2016-05-17 16:27:20
Elapsed	00:00:03
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/ATAC1+2/qc/rep1/ATAC1-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.png \
			-r144 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep1/ATAC1-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	65977

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

Start	2016-05-17 16:27:17
End	2016-05-17 16:27:20
Elapsed	00:00:03
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/ATAC1+2/qc/rep2/ATAC2-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.png \
			-r144 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep2/ATAC2-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/ATAC1+2, -num_rep, 2, -fastq1_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC1/ATAC1-trimmed-pair1.fastq.gz, -fastq1_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC1/ATAC1-trimmed-pair2.fastq.gz, -fastq2_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC2/ATAC2-trimmed-pair1.fastq.gz, -fastq2_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC2/ATAC2-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

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