idr2 rep1-rep2

 atac.bds.20160515_230834_746/task.postalign_bed.pool_tag_reps.line_405.id_28
atac.bds.20160515_230834_746/task.callpeak_macs2.macs2_atac_pooled.pval0.1.line_192.id_29
atac.bds.20160515_230834_746/task.callpeak_macs2.macs2_atac_pooled.line_192.id_30
atac.bds.20160515_230834_746/task.callpeak_etc.filt_top_peaks_rep1.line_25.id_31
atac.bds.20160515_230834_746/task.callpeak_etc.filt_top_peaks_rep1.line_25.id_32
atac.bds.20160515_230834_746/task.callpeak_etc.filt_top_peaks_rep2.line_25.id_33
atac.bds.20160515_230834_746/task.callpeak_etc.filt_top_peaks_rep2.line_25.id_34
atac.bds.20160515_230834_746/task.callpeak_etc.filt_top_peaks_pooled.line_25.id_35
atac.bds.20160515_230834_746/task.callpeak_etc.filt_top_peaks_pooled.line_25.id_36
atac.bds.20160515_230834_746/task.idr.idr2_rep1_rep2.line_61.id_37
 

 atac.bds.20160515_230834_746_parallel_20/task.align_bowtie2.bowtie2_PE_rep1.line_133.id_6
atac.bds.20160515_230834_746_parallel_20/task.postalign_bam.dedup_bam_PE_rep1.line_215.id_9
atac.bds.20160515_230834_746_parallel_20/task.postalign_bam.nmsrt_bam_rep1.line_321.id_19
atac.bds.20160515_230834_746_parallel_20/task.postalign_bam.bam_to_bedpe_rep1.line_425.id_20
atac.bds.20160515_230834_746_parallel_20/task.postalign_bed.subsample_bedpe_rep1.line_116.id_21
atac.bds.20160515_230834_746_parallel_20/task.postalign_bam.bedpe_to_tag_rep1.line_465.id_22
atac.bds.20160515_230834_746_parallel_20/task.postalign_bed.shift_tag_rep1.line_140.id_23
atac.bds.20160515_230834_746_parallel_20/task.postalign_bed.subsample_bedpe2tagrep1.line_89.id_24
atac.bds.20160515_230834_746_parallel_20/task.postalign_bed.xcor_rep1.line_165.id_25
atac.bds.20160515_230834_746_parallel_20/task.callpeak_macs2.macs2_atac_rep1.pval0.1.line_192.id_26
atac.bds.20160515_230834_746_parallel_20/task.callpeak_macs2.macs2_atac_rep1.line_192.id_27
 

 atac.bds.20160515_230834_746_parallel_21/task.align_bowtie2.bowtie2_PE_rep2.line_133.id_7
atac.bds.20160515_230834_746_parallel_21/task.postalign_bam.dedup_bam_PE_rep2.line_215.id_8
atac.bds.20160515_230834_746_parallel_21/task.postalign_bam.nmsrt_bam_rep2.line_321.id_10
atac.bds.20160515_230834_746_parallel_21/task.postalign_bam.bam_to_bedpe_rep2.line_425.id_11
atac.bds.20160515_230834_746_parallel_21/task.postalign_bed.subsample_bedpe_rep2.line_116.id_12
atac.bds.20160515_230834_746_parallel_21/task.postalign_bam.bedpe_to_tag_rep2.line_465.id_13
atac.bds.20160515_230834_746_parallel_21/task.postalign_bed.shift_tag_rep2.line_140.id_14
atac.bds.20160515_230834_746_parallel_21/task.postalign_bed.subsample_bedpe2tagrep2.line_89.id_15
atac.bds.20160515_230834_746_parallel_21/task.postalign_bed.xcor_rep2.line_165.id_16
atac.bds.20160515_230834_746_parallel_21/task.callpeak_macs2.macs2_atac_rep2.pval0.1.line_192.id_17
atac.bds.20160515_230834_746_parallel_21/task.callpeak_macs2.macs2_atac_rep2.line_192.id_18
 

 
# 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/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.fastq.gz -2 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair2.trim.fastq.gz 2>/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1/ATAC3-trimmed-pair1.trim.PE2SE.align.log | samtools view -bS - | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE

# SYS command. line 142

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-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 37 files...

 

 
# 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/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.fastq.gz -2 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair2.trim.fastq.gz 2>/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2/ATAC4-trimmed-pair1.trim.PE2SE.align.log | samtools view -bS - | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE

# SYS command. line 142

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-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 28 files...

 

 
# 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/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-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/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-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/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.filt

# SYS command. line 239

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-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/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2/ATAC4-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/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2/ATAC4-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/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-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/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.filt.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 269

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 271

 if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.bai" ]; then \
			cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.bai; \
			fi

# SYS command. line 275

 samtools flagstat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc

# SYS command. line 286

 samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.filt.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.filt.bam.tmp

# SYS command. line 287

 bedtools bamtobed -bedpe -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-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/ATAC3+4/qc/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.pbc.qc

# SYS command. line 291

 rm /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam

# SYS command. line 293

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.filt.bam

# SYS command. line 294

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-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 21 files...
[bam_sort_core] merging from 21 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Mon May 16 04:56:26 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2/ATAC4-trimmed-pair1.trim.PE2SE.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Mon May 16 04:56:26 PDT 2016] Executing as pangwei@mitra on Linux 3.16.0-70-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_45-b14; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-05-16 04:56:26	MarkDuplicates	Start of doWork freeMemory: 254889872; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-16 04:56:26	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-05-16 04:56:26	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-05-16 04:56:32	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:05s.  Time for last 1,000,000:    5s.  Last read position: chr10:74,124,139
INFO	2016-05-16 04:56:32	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-16 04:56:36	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:10s.  Time for last 1,000,000:    4s.  Last read position: chr10:132,107,667
INFO	2016-05-16 04:56:36	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 04:56:40	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:14s.  Time for last 1,000,000:    4s.  Last read position: chr11:60,823,574
INFO	2016-05-16 04:56:40	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 04:56:46	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:19s.  Time for last 1,000,000:    5s.  Last read position: chr11:117,293,957
INFO	2016-05-16 04:56:46	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 04:56:51	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:24s.  Time for last 1,000,000:    5s.  Last read position: chr12:47,193,361
INFO	2016-05-16 04:56:51	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 04:57:00	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:33s.  Time for last 1,000,000:    8s.  Last read position: chr12:110,185,504
INFO	2016-05-16 04:57:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 04:57:04	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:38s.  Time for last 1,000,000:    4s.  Last read position: chr13:53,245,407
INFO	2016-05-16 04:57:04	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 04:57:10	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:44s.  Time for last 1,000,000:    5s.  Last read position: chr14:32,548,618
INFO	2016-05-16 04:57:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 04:57:15	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:48s.  Time for last 1,000,000:    4s.  Last read position: chr14:96,525,271
INFO	2016-05-16 04:57:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 04:57:19	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:53s.  Time for last 1,000,000:    4s.  Last read position: chr15:70,478,482
INFO	2016-05-16 04:57:19	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 04:57:24	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:58s.  Time for last 1,000,000:    4s.  Last read position: chr16:21,584,966
INFO	2016-05-16 04:57:24	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 04:57:32	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:05s.  Time for last 1,000,000:    7s.  Last read position: chr16:87,904,667
INFO	2016-05-16 04:57:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 04:57:36	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:10s.  Time for last 1,000,000:    4s.  Last read position: chr17:47,979,114
INFO	2016-05-16 04:57:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 04:57:41	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:15s.  Time for last 1,000,000:    4s.  Last read position: chr18:24,183,934
INFO	2016-05-16 04:57:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 04:58:00	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:34s.  Time for last 1,000,000:   18s.  Last read position: chr19:7,973,961
INFO	2016-05-16 04:58:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 04:58:04	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:37s.  Time for last 1,000,000:    3s.  Last read position: chr19:56,834,594
INFO	2016-05-16 04:58:04	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 04:58:08	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:01:41s.  Time for last 1,000,000:    3s.  Last read position: chr1:39,296,860
INFO	2016-05-16 04:58:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 04:58:11	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:01:45s.  Time for last 1,000,000:    3s.  Last read position: chr1:100,970,703
INFO	2016-05-16 04:58:11	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 04:58:15	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:01:49s.  Time for last 1,000,000:    3s.  Last read position: chr1:185,283,547
INFO	2016-05-16 04:58:15	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 04:58:20	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:01:54s.  Time for last 1,000,000:    5s.  Last read position: chr1:247,443,074
INFO	2016-05-16 04:58:20	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 04:58:24	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:01:57s.  Time for last 1,000,000:    3s.  Last read position: chr20:54,327,904
INFO	2016-05-16 04:58:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 04:58:28	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:02:01s.  Time for last 1,000,000:    3s.  Last read position: chr22:29,402,968
INFO	2016-05-16 04:58:28	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 04:58:32	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:02:06s.  Time for last 1,000,000:    4s.  Last read position: chr2:27,876,314
INFO	2016-05-16 04:58:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 04:58:39	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:02:12s.  Time for last 1,000,000:    6s.  Last read position: chr2:96,976,623
INFO	2016-05-16 04:58:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 04:58:42	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:02:16s.  Time for last 1,000,000:    3s.  Last read position: chr2:166,679,206
INFO	2016-05-16 04:58:42	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 04:58:46	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:02:19s.  Time for last 1,000,000:    3s.  Last read position: chr2:233,323,025
INFO	2016-05-16 04:58:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 04:58:49	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:02:23s.  Time for last 1,000,000:    3s.  Last read position: chr3:47,474,263
INFO	2016-05-16 04:58:49	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 04:58:53	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:02:26s.  Time for last 1,000,000:    3s.  Last read position: chr3:119,087,487
INFO	2016-05-16 04:58:53	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 04:58:57	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:02:30s.  Time for last 1,000,000:    3s.  Last read position: chr3:184,245,820
INFO	2016-05-16 04:58:57	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 04:59:08	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:02:42s.  Time for last 1,000,000:   11s.  Last read position: chr4:53,171,418
INFO	2016-05-16 04:59:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 04:59:12	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:02:45s.  Time for last 1,000,000:    3s.  Last read position: chr4:131,567,992
INFO	2016-05-16 04:59:12	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 04:59:16	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:02:49s.  Time for last 1,000,000:    3s.  Last read position: chr5:14,553,706
INFO	2016-05-16 04:59:16	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 04:59:20	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:02:54s.  Time for last 1,000,000:    4s.  Last read position: chr5:93,791,390
INFO	2016-05-16 04:59:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 04:59:24	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:02:58s.  Time for last 1,000,000:    3s.  Last read position: chr5:156,679,778
INFO	2016-05-16 04:59:24	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 04:59:28	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:03:01s.  Time for last 1,000,000:    3s.  Last read position: chr6:33,247,358
INFO	2016-05-16 04:59:28	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 04:59:31	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:03:05s.  Time for last 1,000,000:    3s.  Last read position: chr6:105,502,535
INFO	2016-05-16 04:59:31	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 04:59:35	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:03:08s.  Time for last 1,000,000:    3s.  Last read position: chr7:598,814
INFO	2016-05-16 04:59:35	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 04:59:41	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:03:14s.  Time for last 1,000,000:    5s.  Last read position: chr7:70,486,662
INFO	2016-05-16 04:59:41	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 04:59:44	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:03:18s.  Time for last 1,000,000:    3s.  Last read position: chr7:137,650,210
INFO	2016-05-16 04:59:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 04:59:48	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:03:22s.  Time for last 1,000,000:    3s.  Last read position: chr8:40,706,520
INFO	2016-05-16 04:59:48	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 04:59:51	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:03:25s.  Time for last 1,000,000:    3s.  Last read position: chr8:117,247,323
INFO	2016-05-16 04:59:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 04:59:55	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:03:29s.  Time for last 1,000,000:    3s.  Last read position: chr9:35,662,360
INFO	2016-05-16 04:59:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 04:59:59	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:03:32s.  Time for last 1,000,000:    3s.  Last read position: chr9:127,962,882
INFO	2016-05-16 04:59:59	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-16 05:00:02	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:03:36s.  Time for last 1,000,000:    3s.  Last read position: chrM:1,857
INFO	2016-05-16 05:00:02	MarkDuplicates	Tracking 6770 as yet unmatched pairs. 6770 records in RAM.
INFO	2016-05-16 05:00:10	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:03:43s.  Time for last 1,000,000:    7s.  Last read position: chrM:4,023
INFO	2016-05-16 05:00:10	MarkDuplicates	Tracking 4528 as yet unmatched pairs. 4528 records in RAM.
INFO	2016-05-16 05:00:13	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:03:46s.  Time for last 1,000,000:    3s.  Last read position: chrM:7,802
INFO	2016-05-16 05:00:13	MarkDuplicates	Tracking 7300 as yet unmatched pairs. 7300 records in RAM.
INFO	2016-05-16 05:00:16	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:03:50s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,063
INFO	2016-05-16 05:00:16	MarkDuplicates	Tracking 9242 as yet unmatched pairs. 9242 records in RAM.
INFO	2016-05-16 05:00:19	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:03:53s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,559
INFO	2016-05-16 05:00:19	MarkDuplicates	Tracking 4852 as yet unmatched pairs. 4852 records in RAM.
INFO	2016-05-16 05:00:22	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:03:56s.  Time for last 1,000,000:    2s.  Last read position: chrM:15,838
INFO	2016-05-16 05:00:22	MarkDuplicates	Tracking 13874 as yet unmatched pairs. 13874 records in RAM.
INFO	2016-05-16 05:00:25	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:03:59s.  Time for last 1,000,000:    3s.  Last read position: chrX:48,553,495
INFO	2016-05-16 05:00:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 05:00:31	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:04:05s.  Time for last 1,000,000:    5s.  Last read position: chrX:133,871,633
INFO	2016-05-16 05:00:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 05:00:32	MarkDuplicates	Read 51292280 records. 0 pairs never matched.
INFO	2016-05-16 05:00:37	MarkDuplicates	After buildSortedReadEndLists freeMemory: 3245486032; totalMemory: 3273129984; maxMemory: 3817865216
INFO	2016-05-16 05:00:37	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-05-16 05:00:37	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-05-16 05:00:46	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-05-16 05:00:58	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-05-16 05:00:59	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2284849080; totalMemory: 3266314240; maxMemory: 3817865216
INFO	2016-05-16 05:00:59	MarkDuplicates	Marking 14581496 records as duplicates.
INFO	2016-05-16 05:00:59	MarkDuplicates	Found 1420693 optical duplicate clusters.
INFO	2016-05-16 05:02:29	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:29s.  Time for last 10,000,000:   89s.  Last read position: chr15:70,478,482
INFO	2016-05-16 05:04:01	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:03:01s.  Time for last 10,000,000:   91s.  Last read position: chr1:247,443,074
INFO	2016-05-16 05:05:33	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:04:33s.  Time for last 10,000,000:   92s.  Last read position: chr4:53,171,418
INFO	2016-05-16 05:07:05	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:06:05s.  Time for last 10,000,000:   92s.  Last read position: chr8:40,706,520
INFO	2016-05-16 05:08:26	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:07:26s.  Time for last 10,000,000:   81s.  Last read position: chrX:48,553,495
INFO	2016-05-16 05:08:38	MarkDuplicates	Before output close freeMemory: 3318359960; totalMemory: 3348627456; maxMemory: 3817865216
INFO	2016-05-16 05:08:38	MarkDuplicates	After output close freeMemory: 3318358904; totalMemory: 3348627456; maxMemory: 3817865216
[Mon May 16 05:08:38 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 12.21 minutes.
Runtime.totalMemory()=3348627456
[bam_sort_core] merging from 21 files...

 

 
# 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/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-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/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-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/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.filt

# SYS command. line 239

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-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/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1/ATAC3-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/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1/ATAC3-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/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-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/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.filt.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 269

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 271

 if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.bai" ]; then \
			cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.bai; \
			fi

# SYS command. line 275

 samtools flagstat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc

# SYS command. line 286

 samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.filt.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.filt.bam.tmp

# SYS command. line 287

 bedtools bamtobed -bedpe -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-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/ATAC3+4/qc/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.pbc.qc

# SYS command. line 291

 rm /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam

# SYS command. line 293

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.filt.bam

# SYS command. line 294

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-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 25 files...
[bam_sort_core] merging from 25 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Mon May 16 06:06:11 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1/ATAC3-trimmed-pair1.trim.PE2SE.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Mon May 16 06:06:11 PDT 2016] Executing as pangwei@mitra on Linux 3.16.0-70-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_45-b14; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-05-16 06:06:11	MarkDuplicates	Start of doWork freeMemory: 254889872; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-16 06:06:11	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-05-16 06:06:11	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-05-16 06:06:16	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:05s.  Time for last 1,000,000:    5s.  Last read position: chr10:86,549,094
INFO	2016-05-16 06:06:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 06:06:20	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:08s.  Time for last 1,000,000:    3s.  Last read position: chr11:17,193,753
INFO	2016-05-16 06:06:20	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 06:06:24	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:12s.  Time for last 1,000,000:    3s.  Last read position: chr11:93,861,804
INFO	2016-05-16 06:06:24	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-05-16 06:06:28	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:16s.  Time for last 1,000,000:    3s.  Last read position: chr12:33,262,622
INFO	2016-05-16 06:06:28	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 06:06:33	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:21s.  Time for last 1,000,000:    5s.  Last read position: chr12:114,193,095
INFO	2016-05-16 06:06:33	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 06:06:38	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:26s.  Time for last 1,000,000:    4s.  Last read position: chr13:81,871,720
INFO	2016-05-16 06:06:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 06:06:42	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:30s.  Time for last 1,000,000:    3s.  Last read position: chr14:71,352,686
INFO	2016-05-16 06:06:42	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 06:06:45	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:33s.  Time for last 1,000,000:    3s.  Last read position: chr15:62,773,208
INFO	2016-05-16 06:06:45	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 06:06:49	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:37s.  Time for last 1,000,000:    3s.  Last read position: chr16:27,298,244
INFO	2016-05-16 06:06:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 06:06:55	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:43s.  Time for last 1,000,000:    5s.  Last read position: chr17:15,135,692
INFO	2016-05-16 06:06:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 06:07:01	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:49s.  Time for last 1,000,000:    5s.  Last read position: chr17:80,281,273
INFO	2016-05-16 06:07:01	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 06:07:04	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:00:52s.  Time for last 1,000,000:    3s.  Last read position: chr19:3,586,853
INFO	2016-05-16 06:07:04	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 06:07:08	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:00:56s.  Time for last 1,000,000:    3s.  Last read position: chr1:1,398,031
INFO	2016-05-16 06:07:08	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 06:07:12	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:00s.  Time for last 1,000,000:    3s.  Last read position: chr1:57,728,395
INFO	2016-05-16 06:07:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 06:07:28	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:16s.  Time for last 1,000,000:   15s.  Last read position: chr1:160,772,328
INFO	2016-05-16 06:07:28	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 06:07:31	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:19s.  Time for last 1,000,000:    3s.  Last read position: chr1:234,436,520
INFO	2016-05-16 06:07:31	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 06:07:35	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:01:23s.  Time for last 1,000,000:    3s.  Last read position: chr20:57,267,687
INFO	2016-05-16 06:07:35	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-16 06:07:41	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:01:29s.  Time for last 1,000,000:    5s.  Last read position: chr22:43,628,911
INFO	2016-05-16 06:07:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 06:07:44	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:01:32s.  Time for last 1,000,000:    3s.  Last read position: chr2:63,277,263
INFO	2016-05-16 06:07:44	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-16 06:07:48	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:01:36s.  Time for last 1,000,000:    3s.  Last read position: chr2:151,761,396
INFO	2016-05-16 06:07:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 06:07:51	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:01:39s.  Time for last 1,000,000:    3s.  Last read position: chr2:232,610,604
INFO	2016-05-16 06:07:51	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 06:07:56	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:01:44s.  Time for last 1,000,000:    4s.  Last read position: chr3:55,670,831
INFO	2016-05-16 06:07:56	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 06:08:02	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:01:50s.  Time for last 1,000,000:    6s.  Last read position: chr3:142,297,945
INFO	2016-05-16 06:08:02	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 06:08:05	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:01:53s.  Time for last 1,000,000:    3s.  Last read position: chr4:20,868,619
INFO	2016-05-16 06:08:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 06:08:08	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:01:57s.  Time for last 1,000,000:    3s.  Last read position: chr4:115,779,520
INFO	2016-05-16 06:08:08	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 06:08:12	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:02:00s.  Time for last 1,000,000:    3s.  Last read position: chr5:13,575,179
INFO	2016-05-16 06:08:12	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 06:08:19	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:02:07s.  Time for last 1,000,000:    7s.  Last read position: chr5:109,374,820
INFO	2016-05-16 06:08:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 06:08:23	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:02:11s.  Time for last 1,000,000:    3s.  Last read position: chr5:176,925,430
INFO	2016-05-16 06:08:23	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 06:08:26	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:02:14s.  Time for last 1,000,000:    3s.  Last read position: chr6:72,198,121
INFO	2016-05-16 06:08:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 06:08:38	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:02:26s.  Time for last 1,000,000:   11s.  Last read position: chr6:157,010,060
INFO	2016-05-16 06:08:38	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 06:08:42	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:02:30s.  Time for last 1,000,000:    4s.  Last read position: chr7:68,837,457
INFO	2016-05-16 06:08:42	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 06:08:47	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:02:35s.  Time for last 1,000,000:    5s.  Last read position: chr7:150,422,796
INFO	2016-05-16 06:08:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 06:08:51	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:02:39s.  Time for last 1,000,000:    4s.  Last read position: chr8:74,842,120
INFO	2016-05-16 06:08:51	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 06:08:56	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:02:44s.  Time for last 1,000,000:    5s.  Last read position: chr9:8,650,915
INFO	2016-05-16 06:08:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 06:09:00	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:02:48s.  Time for last 1,000,000:    3s.  Last read position: chr9:119,134,365
INFO	2016-05-16 06:09:00	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 06:09:03	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:02:51s.  Time for last 1,000,000:    3s.  Last read position: chrM:518
INFO	2016-05-16 06:09:03	MarkDuplicates	Tracking 9690 as yet unmatched pairs. 9690 records in RAM.
INFO	2016-05-16 06:09:06	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:02:54s.  Time for last 1,000,000:    3s.  Last read position: chrM:1,316
INFO	2016-05-16 06:09:06	MarkDuplicates	Tracking 53188 as yet unmatched pairs. 53188 records in RAM.
INFO	2016-05-16 06:09:09	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:02:57s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,010
INFO	2016-05-16 06:09:09	MarkDuplicates	Tracking 40586 as yet unmatched pairs. 40586 records in RAM.
INFO	2016-05-16 06:09:14	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:03:02s.  Time for last 1,000,000:    4s.  Last read position: chrM:2,766
INFO	2016-05-16 06:09:14	MarkDuplicates	Tracking 102666 as yet unmatched pairs. 102666 records in RAM.
INFO	2016-05-16 06:09:17	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:03:05s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,235
INFO	2016-05-16 06:09:17	MarkDuplicates	Tracking 90636 as yet unmatched pairs. 90636 records in RAM.
INFO	2016-05-16 06:09:20	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:03:08s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,582
INFO	2016-05-16 06:09:20	MarkDuplicates	Tracking 31062 as yet unmatched pairs. 31062 records in RAM.
INFO	2016-05-16 06:09:23	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:03:11s.  Time for last 1,000,000:    3s.  Last read position: chrM:4,015
INFO	2016-05-16 06:09:23	MarkDuplicates	Tracking 26592 as yet unmatched pairs. 26592 records in RAM.
INFO	2016-05-16 06:09:26	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:03:15s.  Time for last 1,000,000:    3s.  Last read position: chrM:5,311
INFO	2016-05-16 06:09:26	MarkDuplicates	Tracking 21132 as yet unmatched pairs. 21132 records in RAM.
INFO	2016-05-16 06:09:29	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:03:18s.  Time for last 1,000,000:    2s.  Last read position: chrM:6,286
INFO	2016-05-16 06:09:29	MarkDuplicates	Tracking 51006 as yet unmatched pairs. 51006 records in RAM.
INFO	2016-05-16 06:09:36	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:03:24s.  Time for last 1,000,000:    6s.  Last read position: chrM:6,679
INFO	2016-05-16 06:09:36	MarkDuplicates	Tracking 25158 as yet unmatched pairs. 25158 records in RAM.
INFO	2016-05-16 06:09:41	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:03:29s.  Time for last 1,000,000:    4s.  Last read position: chrM:7,785
INFO	2016-05-16 06:09:41	MarkDuplicates	Tracking 33782 as yet unmatched pairs. 33782 records in RAM.
INFO	2016-05-16 06:09:44	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:03:32s.  Time for last 1,000,000:    3s.  Last read position: chrM:8,479
INFO	2016-05-16 06:09:44	MarkDuplicates	Tracking 54136 as yet unmatched pairs. 54136 records in RAM.
INFO	2016-05-16 06:09:47	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:03:35s.  Time for last 1,000,000:    3s.  Last read position: chrM:9,710
INFO	2016-05-16 06:09:47	MarkDuplicates	Tracking 48660 as yet unmatched pairs. 48660 records in RAM.
INFO	2016-05-16 06:09:51	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:03:39s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,429
INFO	2016-05-16 06:09:51	MarkDuplicates	Tracking 33750 as yet unmatched pairs. 33750 records in RAM.
INFO	2016-05-16 06:09:54	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:03:42s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,316
INFO	2016-05-16 06:09:54	MarkDuplicates	Tracking 29254 as yet unmatched pairs. 29254 records in RAM.
INFO	2016-05-16 06:09:58	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:03:46s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,023
INFO	2016-05-16 06:09:58	MarkDuplicates	Tracking 34896 as yet unmatched pairs. 34896 records in RAM.
INFO	2016-05-16 06:10:04	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:03:52s.  Time for last 1,000,000:    5s.  Last read position: chrM:12,657
INFO	2016-05-16 06:10:04	MarkDuplicates	Tracking 60992 as yet unmatched pairs. 60992 records in RAM.
INFO	2016-05-16 06:10:07	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:03:55s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,285
INFO	2016-05-16 06:10:07	MarkDuplicates	Tracking 37076 as yet unmatched pairs. 37076 records in RAM.
INFO	2016-05-16 06:10:10	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:03:58s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,872
INFO	2016-05-16 06:10:10	MarkDuplicates	Tracking 46814 as yet unmatched pairs. 46814 records in RAM.
INFO	2016-05-16 06:10:13	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:04:01s.  Time for last 1,000,000:    3s.  Last read position: chrM:14,799
INFO	2016-05-16 06:10:13	MarkDuplicates	Tracking 9138 as yet unmatched pairs. 9138 records in RAM.
INFO	2016-05-16 06:10:16	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:04:04s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,268
INFO	2016-05-16 06:10:16	MarkDuplicates	Tracking 48378 as yet unmatched pairs. 48378 records in RAM.
INFO	2016-05-16 06:10:19	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:04:07s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,690
INFO	2016-05-16 06:10:19	MarkDuplicates	Tracking 62450 as yet unmatched pairs. 62450 records in RAM.
INFO	2016-05-16 06:10:23	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:04:11s.  Time for last 1,000,000:    3s.  Last read position: chrM:16,300
INFO	2016-05-16 06:10:23	MarkDuplicates	Tracking 50600 as yet unmatched pairs. 50600 records in RAM.
INFO	2016-05-16 06:10:42	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:04:31s.  Time for last 1,000,000:   19s.  Last read position: chrX:42,602,871
INFO	2016-05-16 06:10:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 06:10:48	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:04:36s.  Time for last 1,000,000:    5s.  Last read position: chrX:144,542,281
INFO	2016-05-16 06:10:48	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 06:10:48	MarkDuplicates	Read 60132266 records. 0 pairs never matched.
INFO	2016-05-16 06:10:49	MarkDuplicates	After buildSortedReadEndLists freeMemory: 4039121616; totalMemory: 4066377728; maxMemory: 4066377728
INFO	2016-05-16 06:10:49	MarkDuplicates	Will retain up to 127074304 duplicate indices before spilling to disk.
INFO	2016-05-16 06:10:49	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-05-16 06:11:02	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-05-16 06:11:16	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-05-16 06:11:18	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2938880320; totalMemory: 3981967360; maxMemory: 3981967360
INFO	2016-05-16 06:11:18	MarkDuplicates	Marking 36491126 records as duplicates.
INFO	2016-05-16 06:11:18	MarkDuplicates	Found 6655038 optical duplicate clusters.
INFO	2016-05-16 06:12:44	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:25s.  Time for last 10,000,000:   85s.  Last read position: chr17:15,135,692
INFO	2016-05-16 06:14:13	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:02:55s.  Time for last 10,000,000:   89s.  Last read position: chr2:151,761,396
INFO	2016-05-16 06:15:43	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:04:24s.  Time for last 10,000,000:   89s.  Last read position: chr6:157,010,060
INFO	2016-05-16 06:17:06	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:05:48s.  Time for last 10,000,000:   83s.  Last read position: chrM:3,235
INFO	2016-05-16 06:18:21	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:07:03s.  Time for last 10,000,000:   74s.  Last read position: chrM:11,316
INFO	2016-05-16 06:19:39	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:08:21s.  Time for last 10,000,000:   77s.  Last read position: chrX:144,542,281
INFO	2016-05-16 06:19:40	MarkDuplicates	Before output close freeMemory: 4118728688; totalMemory: 4149215232; maxMemory: 4149215232
INFO	2016-05-16 06:19:40	MarkDuplicates	After output close freeMemory: 4118727632; totalMemory: 4149215232; maxMemory: 4149215232
[Mon May 16 06:19:40 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 13.48 minutes.
Runtime.totalMemory()=4149215232
[bam_sort_core] merging from 25 files...

 

 
# 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/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-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 15 files...

 

 
# 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/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-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

 

 
# 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/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | grep -v "chrM" | shuf -n 17500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-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

 

 
# 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/ATAC3+4/align/rep2/ATAC4-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/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz

# SYS command. line 472

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz | grep -P -v 'chrM' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz; mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-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

 

 
# 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/ATAC3+4/align/rep2/ATAC4-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/ATAC3+4/align/rep2/ATAC4-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

 

 
# 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/ATAC3+4/align/rep2/ATAC4-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/ATAC3+4/align/rep2/ATAC4-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

 

 
# 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/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz -p=1 \
			-filtchr=chrM -savp=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf -out=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2/ATAC4-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/ATAC3+4/qc/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp

# SYS command. line 175

 mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc
 

   
--------------------Stdout--------------------
################
ChIP data: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-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/ATAC3+4/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/ATAC3+4/qc/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf 
result filename: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2/ATAC4-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/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz 
opened /tmp/RtmplMtP1Q/ATAC4-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign1812f251ce2db
done. read 17871057 fragments
ChIP data read length 76 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1943348 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.201234881423893 
Top 3 estimates for fragment length 0 
Window half size 590 
Phantom peak location 70 
Phantom peak Correlation 0.2019764 
Normalized Strand cross-correlation coefficient (NSC) 1.035506 
Relative Strand Cross correlation Coefficient (RSC) 0.9029606 
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

 

 
# 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/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/signal/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/signal/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg
 

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
INFO  @ Mon, 16 May 2016 06:05:49: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-01
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is on
 
INFO  @ Mon, 16 May 2016 06:05:49: #1 read tag files... 
INFO  @ Mon, 16 May 2016 06:05:49: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 06:05:51:  1000000 
INFO  @ Mon, 16 May 2016 06:05:52:  2000000 
INFO  @ Mon, 16 May 2016 06:05:54:  3000000 
INFO  @ Mon, 16 May 2016 06:05:56:  4000000 
INFO  @ Mon, 16 May 2016 06:05:57:  5000000 
INFO  @ Mon, 16 May 2016 06:05:59:  6000000 
INFO  @ Mon, 16 May 2016 06:06:01:  7000000 
INFO  @ Mon, 16 May 2016 06:06:03:  8000000 
INFO  @ Mon, 16 May 2016 06:06:05:  9000000 
INFO  @ Mon, 16 May 2016 06:06:07:  10000000 
INFO  @ Mon, 16 May 2016 06:06:09:  11000000 
INFO  @ Mon, 16 May 2016 06:06:10:  12000000 
INFO  @ Mon, 16 May 2016 06:06:12:  13000000 
INFO  @ Mon, 16 May 2016 06:06:14:  14000000 
INFO  @ Mon, 16 May 2016 06:06:15:  15000000 
INFO  @ Mon, 16 May 2016 06:06:17:  16000000 
INFO  @ Mon, 16 May 2016 06:06:19:  17000000 
INFO  @ Mon, 16 May 2016 06:06:20:  18000000 
INFO  @ Mon, 16 May 2016 06:06:22:  19000000 
INFO  @ Mon, 16 May 2016 06:06:24:  20000000 
INFO  @ Mon, 16 May 2016 06:06:25:  21000000 
INFO  @ Mon, 16 May 2016 06:06:27:  22000000 
INFO  @ Mon, 16 May 2016 06:06:29:  23000000 
INFO  @ Mon, 16 May 2016 06:06:31:  24000000 
INFO  @ Mon, 16 May 2016 06:06:33:  25000000 
INFO  @ Mon, 16 May 2016 06:06:34:  26000000 
INFO  @ Mon, 16 May 2016 06:06:36:  27000000 
INFO  @ Mon, 16 May 2016 06:06:37:  28000000 
INFO  @ Mon, 16 May 2016 06:06:39:  29000000 
INFO  @ Mon, 16 May 2016 06:06:41:  30000000 
INFO  @ Mon, 16 May 2016 06:06:42:  31000000 
INFO  @ Mon, 16 May 2016 06:06:44:  32000000 
INFO  @ Mon, 16 May 2016 06:06:46:  33000000 
INFO  @ Mon, 16 May 2016 06:06:48:  34000000 
INFO  @ Mon, 16 May 2016 06:06:50:  35000000 
INFO  @ Mon, 16 May 2016 06:06:52: #1 tag size is determined as 68 bps 
INFO  @ Mon, 16 May 2016 06:06:52: #1 tag size = 68 
INFO  @ Mon, 16 May 2016 06:06:52: #1  total tags in treatment: 35000000 
INFO  @ Mon, 16 May 2016 06:06:52: #1 finished! 
INFO  @ Mon, 16 May 2016 06:06:52: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 06:06:52: #2 Skipped... 
INFO  @ Mon, 16 May 2016 06:06:52: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 06:06:52: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 06:06:52: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 06:06:52: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Mon, 16 May 2016 06:06:52: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 06:08:04: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 06:10:24: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls 
INFO  @ Mon, 16 May 2016 06:10:28: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Mon, 16 May 2016 06:10:31: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Mon, 16 May 2016 06:10:34: Done! 
INFO  @ Mon, 16 May 2016 06:10:47: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Mon, 16 May 2016 06:10:47: #1 read tag files... 
INFO  @ Mon, 16 May 2016 06:10:47: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 06:10:48:  1000000 
INFO  @ Mon, 16 May 2016 06:10:50:  2000000 
INFO  @ Mon, 16 May 2016 06:10:52:  3000000 
INFO  @ Mon, 16 May 2016 06:10:54:  4000000 
INFO  @ Mon, 16 May 2016 06:10:56:  5000000 
INFO  @ Mon, 16 May 2016 06:10:59:  6000000 
INFO  @ Mon, 16 May 2016 06:11:01:  7000000 
INFO  @ Mon, 16 May 2016 06:11:03:  8000000 
INFO  @ Mon, 16 May 2016 06:11:05:  9000000 
INFO  @ Mon, 16 May 2016 06:11:07:  10000000 
INFO  @ Mon, 16 May 2016 06:11:08:  11000000 
INFO  @ Mon, 16 May 2016 06:11:10:  12000000 
INFO  @ Mon, 16 May 2016 06:11:13:  13000000 
INFO  @ Mon, 16 May 2016 06:11:15:  14000000 
INFO  @ Mon, 16 May 2016 06:11:16:  15000000 
INFO  @ Mon, 16 May 2016 06:11:18:  16000000 
INFO  @ Mon, 16 May 2016 06:11:20:  17000000 
INFO  @ Mon, 16 May 2016 06:11:22:  18000000 
INFO  @ Mon, 16 May 2016 06:11:24:  19000000 
INFO  @ Mon, 16 May 2016 06:11:25:  20000000 
INFO  @ Mon, 16 May 2016 06:11:27:  21000000 
INFO  @ Mon, 16 May 2016 06:11:29:  22000000 
INFO  @ Mon, 16 May 2016 06:11:31:  23000000 
INFO  @ Mon, 16 May 2016 06:11:33:  24000000 
INFO  @ Mon, 16 May 2016 06:11:35:  25000000 
INFO  @ Mon, 16 May 2016 06:11:36:  26000000 
INFO  @ Mon, 16 May 2016 06:11:38:  27000000 
INFO  @ Mon, 16 May 2016 06:11:40:  28000000 
INFO  @ Mon, 16 May 2016 06:11:42:  29000000 
INFO  @ Mon, 16 May 2016 06:11:44:  30000000 
INFO  @ Mon, 16 May 2016 06:11:46:  31000000 
INFO  @ Mon, 16 May 2016 06:11:48:  32000000 
INFO  @ Mon, 16 May 2016 06:11:50:  33000000 
INFO  @ Mon, 16 May 2016 06:11:52:  34000000 
INFO  @ Mon, 16 May 2016 06:11:54:  35000000 
INFO  @ Mon, 16 May 2016 06:11:56: #1 tag size is determined as 68 bps 
INFO  @ Mon, 16 May 2016 06:11:56: #1 tag size = 68 
INFO  @ Mon, 16 May 2016 06:11:56: #1  total tags in treatment: 35000000 
INFO  @ Mon, 16 May 2016 06:11:56: #1 finished! 
INFO  @ Mon, 16 May 2016 06:11:56: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 06:11:56: #2 Skipped... 
INFO  @ Mon, 16 May 2016 06:11:56: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 06:11:56: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 06:11:56: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 06:11:56: #3 Going to call summits inside each peak ... 
INFO  @ Mon, 16 May 2016 06:11:56: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Mon, 16 May 2016 06:11:56: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 06:13:20: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Mon, 16 May 2016 06:13:20: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Mon, 16 May 2016 06:13:20: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Mon, 16 May 2016 06:13:20: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Mon, 16 May 2016 06:13:20: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 06:23:47: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls 
INFO  @ Mon, 16 May 2016 06:23:55: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Mon, 16 May 2016 06:24:00: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_summits.bed 
INFO  @ Mon, 16 May 2016 06:24:04: Done! 

 

 
# 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/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/signal/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/signal/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg
 

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
INFO  @ Mon, 16 May 2016 06:05:48: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is on
 
INFO  @ Mon, 16 May 2016 06:05:48: #1 read tag files... 
INFO  @ Mon, 16 May 2016 06:05:48: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 06:05:50:  1000000 
INFO  @ Mon, 16 May 2016 06:05:52:  2000000 
INFO  @ Mon, 16 May 2016 06:05:54:  3000000 
INFO  @ Mon, 16 May 2016 06:05:56:  4000000 
INFO  @ Mon, 16 May 2016 06:05:58:  5000000 
INFO  @ Mon, 16 May 2016 06:06:00:  6000000 
INFO  @ Mon, 16 May 2016 06:06:02:  7000000 
INFO  @ Mon, 16 May 2016 06:06:04:  8000000 
INFO  @ Mon, 16 May 2016 06:06:06:  9000000 
INFO  @ Mon, 16 May 2016 06:06:08:  10000000 
INFO  @ Mon, 16 May 2016 06:06:10:  11000000 
INFO  @ Mon, 16 May 2016 06:06:12:  12000000 
INFO  @ Mon, 16 May 2016 06:06:15:  13000000 
INFO  @ Mon, 16 May 2016 06:06:17:  14000000 
INFO  @ Mon, 16 May 2016 06:06:19:  15000000 
INFO  @ Mon, 16 May 2016 06:06:21:  16000000 
INFO  @ Mon, 16 May 2016 06:06:23:  17000000 
INFO  @ Mon, 16 May 2016 06:06:25:  18000000 
INFO  @ Mon, 16 May 2016 06:06:27:  19000000 
INFO  @ Mon, 16 May 2016 06:06:29:  20000000 
INFO  @ Mon, 16 May 2016 06:06:31:  21000000 
INFO  @ Mon, 16 May 2016 06:06:33:  22000000 
INFO  @ Mon, 16 May 2016 06:06:35:  23000000 
INFO  @ Mon, 16 May 2016 06:06:37:  24000000 
INFO  @ Mon, 16 May 2016 06:06:39:  25000000 
INFO  @ Mon, 16 May 2016 06:06:40:  26000000 
INFO  @ Mon, 16 May 2016 06:06:42:  27000000 
INFO  @ Mon, 16 May 2016 06:06:44:  28000000 
INFO  @ Mon, 16 May 2016 06:06:46:  29000000 
INFO  @ Mon, 16 May 2016 06:06:47:  30000000 
INFO  @ Mon, 16 May 2016 06:06:49:  31000000 
INFO  @ Mon, 16 May 2016 06:06:51:  32000000 
INFO  @ Mon, 16 May 2016 06:06:53:  33000000 
INFO  @ Mon, 16 May 2016 06:06:56:  34000000 
INFO  @ Mon, 16 May 2016 06:06:58:  35000000 
INFO  @ Mon, 16 May 2016 06:07:01: #1 tag size is determined as 68 bps 
INFO  @ Mon, 16 May 2016 06:07:01: #1 tag size = 68 
INFO  @ Mon, 16 May 2016 06:07:01: #1  total tags in treatment: 35000000 
INFO  @ Mon, 16 May 2016 06:07:01: #1 finished! 
INFO  @ Mon, 16 May 2016 06:07:01: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 06:07:01: #2 Skipped... 
INFO  @ Mon, 16 May 2016 06:07:01: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 06:07:01: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 06:07:01: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 06:07:01: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Mon, 16 May 2016 06:07:01: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 06:08:16: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 06:09:53: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls 
INFO  @ Mon, 16 May 2016 06:09:57: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.broadPeak 
INFO  @ Mon, 16 May 2016 06:10:00: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.gappedPeak 
INFO  @ Mon, 16 May 2016 06:10:02: Done! 
INFO  @ Mon, 16 May 2016 06:10:14: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Mon, 16 May 2016 06:10:14: #1 read tag files... 
INFO  @ Mon, 16 May 2016 06:10:14: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 06:10:16:  1000000 
INFO  @ Mon, 16 May 2016 06:10:18:  2000000 
INFO  @ Mon, 16 May 2016 06:10:19:  3000000 
INFO  @ Mon, 16 May 2016 06:10:21:  4000000 
INFO  @ Mon, 16 May 2016 06:10:23:  5000000 
INFO  @ Mon, 16 May 2016 06:10:24:  6000000 
INFO  @ Mon, 16 May 2016 06:10:26:  7000000 
INFO  @ Mon, 16 May 2016 06:10:27:  8000000 
INFO  @ Mon, 16 May 2016 06:10:29:  9000000 
INFO  @ Mon, 16 May 2016 06:10:31:  10000000 
INFO  @ Mon, 16 May 2016 06:10:33:  11000000 
INFO  @ Mon, 16 May 2016 06:10:34:  12000000 
INFO  @ Mon, 16 May 2016 06:10:36:  13000000 
INFO  @ Mon, 16 May 2016 06:10:37:  14000000 
INFO  @ Mon, 16 May 2016 06:10:39:  15000000 
INFO  @ Mon, 16 May 2016 06:10:41:  16000000 
INFO  @ Mon, 16 May 2016 06:10:42:  17000000 
INFO  @ Mon, 16 May 2016 06:10:44:  18000000 
INFO  @ Mon, 16 May 2016 06:10:45:  19000000 
INFO  @ Mon, 16 May 2016 06:10:47:  20000000 
INFO  @ Mon, 16 May 2016 06:10:49:  21000000 
INFO  @ Mon, 16 May 2016 06:10:50:  22000000 
INFO  @ Mon, 16 May 2016 06:10:52:  23000000 
INFO  @ Mon, 16 May 2016 06:10:53:  24000000 
INFO  @ Mon, 16 May 2016 06:10:55:  25000000 
INFO  @ Mon, 16 May 2016 06:10:57:  26000000 
INFO  @ Mon, 16 May 2016 06:10:58:  27000000 
INFO  @ Mon, 16 May 2016 06:11:00:  28000000 
INFO  @ Mon, 16 May 2016 06:11:01:  29000000 
INFO  @ Mon, 16 May 2016 06:11:03:  30000000 
INFO  @ Mon, 16 May 2016 06:11:05:  31000000 
INFO  @ Mon, 16 May 2016 06:11:07:  32000000 
INFO  @ Mon, 16 May 2016 06:11:08:  33000000 
INFO  @ Mon, 16 May 2016 06:11:10:  34000000 
INFO  @ Mon, 16 May 2016 06:11:12:  35000000 
INFO  @ Mon, 16 May 2016 06:11:15: #1 tag size is determined as 68 bps 
INFO  @ Mon, 16 May 2016 06:11:15: #1 tag size = 68 
INFO  @ Mon, 16 May 2016 06:11:15: #1  total tags in treatment: 35000000 
INFO  @ Mon, 16 May 2016 06:11:15: #1 finished! 
INFO  @ Mon, 16 May 2016 06:11:15: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 06:11:15: #2 Skipped... 
INFO  @ Mon, 16 May 2016 06:11:15: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 06:11:15: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 06:11:15: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 06:11:15: #3 Going to call summits inside each peak ... 
INFO  @ Mon, 16 May 2016 06:11:15: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Mon, 16 May 2016 06:11:15: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 06:12:31: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Mon, 16 May 2016 06:12:31: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_treat_pileup.bdg 
INFO  @ Mon, 16 May 2016 06:12:31: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_control_lambda.bdg 
INFO  @ Mon, 16 May 2016 06:12:31: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Mon, 16 May 2016 06:12:31: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 06:18:08: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls 
INFO  @ Mon, 16 May 2016 06:18:09: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.narrowPeak 
INFO  @ Mon, 16 May 2016 06:18:11: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_summits.bed 
INFO  @ Mon, 16 May 2016 06:18:11: Done! 
INFO  @ Mon, 16 May 2016 06:18:15: Read and build treatment bedGraph... 
INFO  @ Mon, 16 May 2016 06:19:28: Read and build control bedGraph... 
INFO  @ Mon, 16 May 2016 06:20:01: Build scoreTrackII... 
INFO  @ Mon, 16 May 2016 06:20:33: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Mon, 16 May 2016 06:24:23: Write bedGraph of scores... 
INFO  @ Mon, 16 May 2016 06:27:02: Finished 'FE'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_FE.bdg'! 
INFO  @ Mon, 16 May 2016 06:32:49: Read and build treatment bedGraph... 
INFO  @ Mon, 16 May 2016 06:33:57: Read and build control bedGraph... 
INFO  @ Mon, 16 May 2016 06:34:30: Build scoreTrackII... 
INFO  @ Mon, 16 May 2016 06:34:57: Values in your input bedGraph files will be multiplied by 35.000000 ... 
INFO  @ Mon, 16 May 2016 06:39:08: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Mon, 16 May 2016 06:39:35: Write bedGraph of scores... 
INFO  @ Mon, 16 May 2016 06:42:05: Finished 'ppois'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_ppois.bdg'! 

 

 
# 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/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-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 10 files...

 

 
# 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/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-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

 

 
# 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/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | grep -v "chrM" | shuf -n 17500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-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

 

 
# 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/ATAC3+4/align/rep1/ATAC3-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/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz

# SYS command. line 472

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz | grep -P -v 'chrM' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz; mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-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

 

 
# 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/ATAC3+4/align/rep1/ATAC3-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/ATAC3+4/align/rep1/ATAC3-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

 

 
# 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/ATAC3+4/align/rep1/ATAC3-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/ATAC3+4/align/rep1/ATAC3-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

 

 
# 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/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz -p=1 \
			-filtchr=chrM -savp=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf -out=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1/ATAC3-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/ATAC3+4/qc/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp

# SYS command. line 175

 mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc
 

   
--------------------Stdout--------------------
################
ChIP data: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-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/ATAC3+4/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/ATAC3+4/qc/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf 
result filename: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1/ATAC3-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/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz 
opened /tmp/Rtmpq6KHax/ATAC3-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign1895ff3c69a0
done. read 10919292 fragments
ChIP data read length 76 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1287568 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.137745304527071 
Top 3 estimates for fragment length 0 
Window half size 560 
Phantom peak location 70 
Phantom peak Correlation 0.1384792 
Normalized Strand cross-correlation coefficient (NSC) 1.06981 
Relative Strand Cross correlation Coefficient (RSC) 0.9245154 
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

 

 
# 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/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/signal/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/signal/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg
 

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
INFO  @ Mon, 16 May 2016 07:09:01: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-01
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is on
 
INFO  @ Mon, 16 May 2016 07:09:01: #1 read tag files... 
INFO  @ Mon, 16 May 2016 07:09:01: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 07:09:03:  1000000 
INFO  @ Mon, 16 May 2016 07:09:05:  2000000 
INFO  @ Mon, 16 May 2016 07:09:06:  3000000 
INFO  @ Mon, 16 May 2016 07:09:08:  4000000 
INFO  @ Mon, 16 May 2016 07:09:09:  5000000 
INFO  @ Mon, 16 May 2016 07:09:11:  6000000 
INFO  @ Mon, 16 May 2016 07:09:14:  7000000 
INFO  @ Mon, 16 May 2016 07:09:15:  8000000 
INFO  @ Mon, 16 May 2016 07:09:17:  9000000 
INFO  @ Mon, 16 May 2016 07:09:18:  10000000 
INFO  @ Mon, 16 May 2016 07:09:20:  11000000 
INFO  @ Mon, 16 May 2016 07:09:22:  12000000 
INFO  @ Mon, 16 May 2016 07:09:24:  13000000 
INFO  @ Mon, 16 May 2016 07:09:25:  14000000 
INFO  @ Mon, 16 May 2016 07:09:27:  15000000 
INFO  @ Mon, 16 May 2016 07:09:29:  16000000 
INFO  @ Mon, 16 May 2016 07:09:31:  17000000 
INFO  @ Mon, 16 May 2016 07:09:33:  18000000 
INFO  @ Mon, 16 May 2016 07:09:35:  19000000 
INFO  @ Mon, 16 May 2016 07:09:36:  20000000 
INFO  @ Mon, 16 May 2016 07:09:38:  21000000 
INFO  @ Mon, 16 May 2016 07:09:41: #1 tag size is determined as 60 bps 
INFO  @ Mon, 16 May 2016 07:09:41: #1 tag size = 60 
INFO  @ Mon, 16 May 2016 07:09:41: #1  total tags in treatment: 21838584 
INFO  @ Mon, 16 May 2016 07:09:41: #1 finished! 
INFO  @ Mon, 16 May 2016 07:09:41: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 07:09:41: #2 Skipped... 
INFO  @ Mon, 16 May 2016 07:09:41: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 07:09:41: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 07:09:41: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 07:09:41: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Mon, 16 May 2016 07:09:41: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 07:10:25: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 07:12:09: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls 
INFO  @ Mon, 16 May 2016 07:12:13: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Mon, 16 May 2016 07:12:16: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Mon, 16 May 2016 07:12:19: Done! 
INFO  @ Mon, 16 May 2016 07:12:31: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Mon, 16 May 2016 07:12:31: #1 read tag files... 
INFO  @ Mon, 16 May 2016 07:12:31: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 07:12:33:  1000000 
INFO  @ Mon, 16 May 2016 07:12:34:  2000000 
INFO  @ Mon, 16 May 2016 07:12:36:  3000000 
INFO  @ Mon, 16 May 2016 07:12:38:  4000000 
INFO  @ Mon, 16 May 2016 07:12:40:  5000000 
INFO  @ Mon, 16 May 2016 07:12:41:  6000000 
INFO  @ Mon, 16 May 2016 07:12:43:  7000000 
INFO  @ Mon, 16 May 2016 07:12:45:  8000000 
INFO  @ Mon, 16 May 2016 07:12:47:  9000000 
INFO  @ Mon, 16 May 2016 07:12:48:  10000000 
INFO  @ Mon, 16 May 2016 07:12:50:  11000000 
INFO  @ Mon, 16 May 2016 07:12:52:  12000000 
INFO  @ Mon, 16 May 2016 07:12:54:  13000000 
INFO  @ Mon, 16 May 2016 07:12:56:  14000000 
INFO  @ Mon, 16 May 2016 07:12:58:  15000000 
INFO  @ Mon, 16 May 2016 07:13:00:  16000000 
INFO  @ Mon, 16 May 2016 07:13:01:  17000000 
INFO  @ Mon, 16 May 2016 07:13:03:  18000000 
INFO  @ Mon, 16 May 2016 07:13:05:  19000000 
INFO  @ Mon, 16 May 2016 07:13:07:  20000000 
INFO  @ Mon, 16 May 2016 07:13:09:  21000000 
INFO  @ Mon, 16 May 2016 07:13:12: #1 tag size is determined as 60 bps 
INFO  @ Mon, 16 May 2016 07:13:12: #1 tag size = 60 
INFO  @ Mon, 16 May 2016 07:13:12: #1  total tags in treatment: 21838584 
INFO  @ Mon, 16 May 2016 07:13:12: #1 finished! 
INFO  @ Mon, 16 May 2016 07:13:12: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 07:13:12: #2 Skipped... 
INFO  @ Mon, 16 May 2016 07:13:12: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 07:13:12: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 07:13:12: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 07:13:12: #3 Going to call summits inside each peak ... 
INFO  @ Mon, 16 May 2016 07:13:12: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Mon, 16 May 2016 07:13:12: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 07:13:56: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Mon, 16 May 2016 07:13:56: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Mon, 16 May 2016 07:13:56: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Mon, 16 May 2016 07:13:56: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Mon, 16 May 2016 07:13:56: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 07:22:22: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls 
INFO  @ Mon, 16 May 2016 07:22:29: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Mon, 16 May 2016 07:22:34: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_summits.bed 
INFO  @ Mon, 16 May 2016 07:22:38: Done! 

 

 
# 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/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/signal/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/signal/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg
 

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
INFO  @ Mon, 16 May 2016 07:09:01: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is on
 
INFO  @ Mon, 16 May 2016 07:09:01: #1 read tag files... 
INFO  @ Mon, 16 May 2016 07:09:01: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 07:09:03:  1000000 
INFO  @ Mon, 16 May 2016 07:09:05:  2000000 
INFO  @ Mon, 16 May 2016 07:09:06:  3000000 
INFO  @ Mon, 16 May 2016 07:09:08:  4000000 
INFO  @ Mon, 16 May 2016 07:09:09:  5000000 
INFO  @ Mon, 16 May 2016 07:09:11:  6000000 
INFO  @ Mon, 16 May 2016 07:09:13:  7000000 
INFO  @ Mon, 16 May 2016 07:09:14:  8000000 
INFO  @ Mon, 16 May 2016 07:09:16:  9000000 
INFO  @ Mon, 16 May 2016 07:09:17:  10000000 
INFO  @ Mon, 16 May 2016 07:09:19:  11000000 
INFO  @ Mon, 16 May 2016 07:09:21:  12000000 
INFO  @ Mon, 16 May 2016 07:09:22:  13000000 
INFO  @ Mon, 16 May 2016 07:09:24:  14000000 
INFO  @ Mon, 16 May 2016 07:09:25:  15000000 
INFO  @ Mon, 16 May 2016 07:09:27:  16000000 
INFO  @ Mon, 16 May 2016 07:09:28:  17000000 
INFO  @ Mon, 16 May 2016 07:09:30:  18000000 
INFO  @ Mon, 16 May 2016 07:09:32:  19000000 
INFO  @ Mon, 16 May 2016 07:09:33:  20000000 
INFO  @ Mon, 16 May 2016 07:09:35:  21000000 
INFO  @ Mon, 16 May 2016 07:09:38: #1 tag size is determined as 60 bps 
INFO  @ Mon, 16 May 2016 07:09:38: #1 tag size = 60 
INFO  @ Mon, 16 May 2016 07:09:38: #1  total tags in treatment: 21838584 
INFO  @ Mon, 16 May 2016 07:09:38: #1 finished! 
INFO  @ Mon, 16 May 2016 07:09:38: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 07:09:38: #2 Skipped... 
INFO  @ Mon, 16 May 2016 07:09:38: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 07:09:38: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 07:09:38: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 07:09:38: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Mon, 16 May 2016 07:09:38: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 07:10:19: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 07:11:30: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls 
INFO  @ Mon, 16 May 2016 07:11:34: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.broadPeak 
INFO  @ Mon, 16 May 2016 07:11:37: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.gappedPeak 
INFO  @ Mon, 16 May 2016 07:11:40: Done! 
INFO  @ Mon, 16 May 2016 07:11:53: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Mon, 16 May 2016 07:11:53: #1 read tag files... 
INFO  @ Mon, 16 May 2016 07:11:53: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 07:11:55:  1000000 
INFO  @ Mon, 16 May 2016 07:11:56:  2000000 
INFO  @ Mon, 16 May 2016 07:11:58:  3000000 
INFO  @ Mon, 16 May 2016 07:12:00:  4000000 
INFO  @ Mon, 16 May 2016 07:12:01:  5000000 
INFO  @ Mon, 16 May 2016 07:12:03:  6000000 
INFO  @ Mon, 16 May 2016 07:12:05:  7000000 
INFO  @ Mon, 16 May 2016 07:12:06:  8000000 
INFO  @ Mon, 16 May 2016 07:12:08:  9000000 
INFO  @ Mon, 16 May 2016 07:12:10:  10000000 
INFO  @ Mon, 16 May 2016 07:12:11:  11000000 
INFO  @ Mon, 16 May 2016 07:12:13:  12000000 
INFO  @ Mon, 16 May 2016 07:12:14:  13000000 
INFO  @ Mon, 16 May 2016 07:12:16:  14000000 
INFO  @ Mon, 16 May 2016 07:12:18:  15000000 
INFO  @ Mon, 16 May 2016 07:12:19:  16000000 
INFO  @ Mon, 16 May 2016 07:12:21:  17000000 
INFO  @ Mon, 16 May 2016 07:12:23:  18000000 
INFO  @ Mon, 16 May 2016 07:12:24:  19000000 
INFO  @ Mon, 16 May 2016 07:12:26:  20000000 
INFO  @ Mon, 16 May 2016 07:12:28:  21000000 
INFO  @ Mon, 16 May 2016 07:12:30: #1 tag size is determined as 60 bps 
INFO  @ Mon, 16 May 2016 07:12:30: #1 tag size = 60 
INFO  @ Mon, 16 May 2016 07:12:30: #1  total tags in treatment: 21838584 
INFO  @ Mon, 16 May 2016 07:12:30: #1 finished! 
INFO  @ Mon, 16 May 2016 07:12:30: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 07:12:30: #2 Skipped... 
INFO  @ Mon, 16 May 2016 07:12:30: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 07:12:30: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 07:12:30: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 07:12:30: #3 Going to call summits inside each peak ... 
INFO  @ Mon, 16 May 2016 07:12:30: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Mon, 16 May 2016 07:12:30: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 07:13:11: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Mon, 16 May 2016 07:13:11: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_treat_pileup.bdg 
INFO  @ Mon, 16 May 2016 07:13:11: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_control_lambda.bdg 
INFO  @ Mon, 16 May 2016 07:13:11: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Mon, 16 May 2016 07:13:11: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 07:17:12: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls 
INFO  @ Mon, 16 May 2016 07:17:15: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.narrowPeak 
INFO  @ Mon, 16 May 2016 07:17:16: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_summits.bed 
INFO  @ Mon, 16 May 2016 07:17:17: Done! 
INFO  @ Mon, 16 May 2016 07:17:21: Read and build treatment bedGraph... 
INFO  @ Mon, 16 May 2016 07:18:06: Read and build control bedGraph... 
INFO  @ Mon, 16 May 2016 07:18:27: Build scoreTrackII... 
INFO  @ Mon, 16 May 2016 07:18:45: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Mon, 16 May 2016 07:21:13: Write bedGraph of scores... 
INFO  @ Mon, 16 May 2016 07:22:44: Finished 'FE'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_FE.bdg'! 
INFO  @ Mon, 16 May 2016 07:26:17: Read and build treatment bedGraph... 
INFO  @ Mon, 16 May 2016 07:27:00: Read and build control bedGraph... 
INFO  @ Mon, 16 May 2016 07:27:22: Build scoreTrackII... 
INFO  @ Mon, 16 May 2016 07:27:39: Values in your input bedGraph files will be multiplied by 21.838584 ... 
INFO  @ Mon, 16 May 2016 07:30:01: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Mon, 16 May 2016 07:30:18: Write bedGraph of scores... 
INFO  @ Mon, 16 May 2016 07:31:39: Finished 'ppois'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_ppois.bdg'! 

 

 
# 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/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz  | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/pooled_rep/ATAC3-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

 

 
# 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/ATAC3+4/align/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/align/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/signal/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/align/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/signal/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_control_lambda.bdg
 

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
INFO  @ Mon, 16 May 2016 07:36:46: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/align/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-01
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is on
 
INFO  @ Mon, 16 May 2016 07:36:46: #1 read tag files... 
INFO  @ Mon, 16 May 2016 07:36:46: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 07:36:47:  1000000 
INFO  @ Mon, 16 May 2016 07:36:49:  2000000 
INFO  @ Mon, 16 May 2016 07:36:51:  3000000 
INFO  @ Mon, 16 May 2016 07:36:52:  4000000 
INFO  @ Mon, 16 May 2016 07:36:54:  5000000 
INFO  @ Mon, 16 May 2016 07:36:56:  6000000 
INFO  @ Mon, 16 May 2016 07:36:58:  7000000 
INFO  @ Mon, 16 May 2016 07:36:59:  8000000 
INFO  @ Mon, 16 May 2016 07:37:01:  9000000 
INFO  @ Mon, 16 May 2016 07:37:02:  10000000 
INFO  @ Mon, 16 May 2016 07:37:04:  11000000 
INFO  @ Mon, 16 May 2016 07:37:06:  12000000 
INFO  @ Mon, 16 May 2016 07:37:07:  13000000 
INFO  @ Mon, 16 May 2016 07:37:09:  14000000 
INFO  @ Mon, 16 May 2016 07:37:10:  15000000 
INFO  @ Mon, 16 May 2016 07:37:12:  16000000 
INFO  @ Mon, 16 May 2016 07:37:14:  17000000 
INFO  @ Mon, 16 May 2016 07:37:15:  18000000 
INFO  @ Mon, 16 May 2016 07:37:17:  19000000 
INFO  @ Mon, 16 May 2016 07:37:19:  20000000 
INFO  @ Mon, 16 May 2016 07:37:20:  21000000 
INFO  @ Mon, 16 May 2016 07:37:22:  22000000 
INFO  @ Mon, 16 May 2016 07:37:24:  23000000 
INFO  @ Mon, 16 May 2016 07:37:25:  24000000 
INFO  @ Mon, 16 May 2016 07:37:27:  25000000 
INFO  @ Mon, 16 May 2016 07:37:29:  26000000 
INFO  @ Mon, 16 May 2016 07:37:30:  27000000 
INFO  @ Mon, 16 May 2016 07:37:32:  28000000 
INFO  @ Mon, 16 May 2016 07:37:33:  29000000 
INFO  @ Mon, 16 May 2016 07:37:35:  30000000 
INFO  @ Mon, 16 May 2016 07:37:37:  31000000 
INFO  @ Mon, 16 May 2016 07:37:39:  32000000 
INFO  @ Mon, 16 May 2016 07:37:40:  33000000 
INFO  @ Mon, 16 May 2016 07:37:42:  34000000 
INFO  @ Mon, 16 May 2016 07:37:43:  35000000 
INFO  @ Mon, 16 May 2016 07:37:45:  36000000 
INFO  @ Mon, 16 May 2016 07:37:47:  37000000 
INFO  @ Mon, 16 May 2016 07:37:48:  38000000 
INFO  @ Mon, 16 May 2016 07:37:50:  39000000 
INFO  @ Mon, 16 May 2016 07:37:52:  40000000 
INFO  @ Mon, 16 May 2016 07:37:53:  41000000 
INFO  @ Mon, 16 May 2016 07:37:55:  42000000 
INFO  @ Mon, 16 May 2016 07:37:57:  43000000 
INFO  @ Mon, 16 May 2016 07:37:58:  44000000 
INFO  @ Mon, 16 May 2016 07:38:00:  45000000 
INFO  @ Mon, 16 May 2016 07:38:01:  46000000 
INFO  @ Mon, 16 May 2016 07:38:03:  47000000 
INFO  @ Mon, 16 May 2016 07:38:05:  48000000 
INFO  @ Mon, 16 May 2016 07:38:06:  49000000 
INFO  @ Mon, 16 May 2016 07:38:08:  50000000 
INFO  @ Mon, 16 May 2016 07:38:09:  51000000 
INFO  @ Mon, 16 May 2016 07:38:11:  52000000 
INFO  @ Mon, 16 May 2016 07:38:13:  53000000 
INFO  @ Mon, 16 May 2016 07:38:14:  54000000 
INFO  @ Mon, 16 May 2016 07:38:16:  55000000 
INFO  @ Mon, 16 May 2016 07:38:17:  56000000 
INFO  @ Mon, 16 May 2016 07:38:23: #1 tag size is determined as 60 bps 
INFO  @ Mon, 16 May 2016 07:38:23: #1 tag size = 60 
INFO  @ Mon, 16 May 2016 07:38:23: #1  total tags in treatment: 56838584 
INFO  @ Mon, 16 May 2016 07:38:23: #1 finished! 
INFO  @ Mon, 16 May 2016 07:38:23: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 07:38:23: #2 Skipped... 
INFO  @ Mon, 16 May 2016 07:38:23: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 07:38:23: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 07:38:23: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 07:38:23: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Mon, 16 May 2016 07:38:23: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 07:40:15: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 07:43:54: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.xls 
INFO  @ Mon, 16 May 2016 07:43:57: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.broadPeak 
INFO  @ Mon, 16 May 2016 07:43:59: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.gappedPeak 
INFO  @ Mon, 16 May 2016 07:44:01: Done! 
INFO  @ Mon, 16 May 2016 07:44:16: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/align/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Mon, 16 May 2016 07:44:16: #1 read tag files... 
INFO  @ Mon, 16 May 2016 07:44:16: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 07:44:18:  1000000 
INFO  @ Mon, 16 May 2016 07:44:19:  2000000 
INFO  @ Mon, 16 May 2016 07:44:21:  3000000 
INFO  @ Mon, 16 May 2016 07:44:23:  4000000 
INFO  @ Mon, 16 May 2016 07:44:24:  5000000 
INFO  @ Mon, 16 May 2016 07:44:26:  6000000 
INFO  @ Mon, 16 May 2016 07:44:27:  7000000 
INFO  @ Mon, 16 May 2016 07:44:29:  8000000 
INFO  @ Mon, 16 May 2016 07:44:31:  9000000 
INFO  @ Mon, 16 May 2016 07:44:32:  10000000 
INFO  @ Mon, 16 May 2016 07:44:34:  11000000 
INFO  @ Mon, 16 May 2016 07:44:35:  12000000 
INFO  @ Mon, 16 May 2016 07:44:37:  13000000 
INFO  @ Mon, 16 May 2016 07:44:39:  14000000 
INFO  @ Mon, 16 May 2016 07:44:40:  15000000 
INFO  @ Mon, 16 May 2016 07:44:42:  16000000 
INFO  @ Mon, 16 May 2016 07:44:43:  17000000 
INFO  @ Mon, 16 May 2016 07:44:45:  18000000 
INFO  @ Mon, 16 May 2016 07:44:47:  19000000 
INFO  @ Mon, 16 May 2016 07:44:48:  20000000 
INFO  @ Mon, 16 May 2016 07:44:50:  21000000 
INFO  @ Mon, 16 May 2016 07:44:51:  22000000 
INFO  @ Mon, 16 May 2016 07:44:53:  23000000 
INFO  @ Mon, 16 May 2016 07:44:55:  24000000 
INFO  @ Mon, 16 May 2016 07:44:56:  25000000 
INFO  @ Mon, 16 May 2016 07:44:58:  26000000 
INFO  @ Mon, 16 May 2016 07:44:59:  27000000 
INFO  @ Mon, 16 May 2016 07:45:01:  28000000 
INFO  @ Mon, 16 May 2016 07:45:03:  29000000 
INFO  @ Mon, 16 May 2016 07:45:04:  30000000 
INFO  @ Mon, 16 May 2016 07:45:06:  31000000 
INFO  @ Mon, 16 May 2016 07:45:07:  32000000 
INFO  @ Mon, 16 May 2016 07:45:09:  33000000 
INFO  @ Mon, 16 May 2016 07:45:11:  34000000 
INFO  @ Mon, 16 May 2016 07:45:12:  35000000 
INFO  @ Mon, 16 May 2016 07:45:14:  36000000 
INFO  @ Mon, 16 May 2016 07:45:15:  37000000 
INFO  @ Mon, 16 May 2016 07:45:17:  38000000 
INFO  @ Mon, 16 May 2016 07:45:19:  39000000 
INFO  @ Mon, 16 May 2016 07:45:20:  40000000 
INFO  @ Mon, 16 May 2016 07:45:22:  41000000 
INFO  @ Mon, 16 May 2016 07:45:23:  42000000 
INFO  @ Mon, 16 May 2016 07:45:25:  43000000 
INFO  @ Mon, 16 May 2016 07:45:27:  44000000 
INFO  @ Mon, 16 May 2016 07:45:28:  45000000 
INFO  @ Mon, 16 May 2016 07:45:30:  46000000 
INFO  @ Mon, 16 May 2016 07:45:32:  47000000 
INFO  @ Mon, 16 May 2016 07:45:33:  48000000 
INFO  @ Mon, 16 May 2016 07:45:35:  49000000 
INFO  @ Mon, 16 May 2016 07:45:36:  50000000 
INFO  @ Mon, 16 May 2016 07:45:38:  51000000 
INFO  @ Mon, 16 May 2016 07:45:40:  52000000 
INFO  @ Mon, 16 May 2016 07:45:41:  53000000 
INFO  @ Mon, 16 May 2016 07:45:43:  54000000 
INFO  @ Mon, 16 May 2016 07:45:44:  55000000 
INFO  @ Mon, 16 May 2016 07:45:46:  56000000 
INFO  @ Mon, 16 May 2016 07:45:51: #1 tag size is determined as 60 bps 
INFO  @ Mon, 16 May 2016 07:45:51: #1 tag size = 60 
INFO  @ Mon, 16 May 2016 07:45:51: #1  total tags in treatment: 56838584 
INFO  @ Mon, 16 May 2016 07:45:51: #1 finished! 
INFO  @ Mon, 16 May 2016 07:45:51: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 07:45:51: #2 Skipped... 
INFO  @ Mon, 16 May 2016 07:45:51: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 07:45:51: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 07:45:51: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 07:45:51: #3 Going to call summits inside each peak ... 
INFO  @ Mon, 16 May 2016 07:45:51: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Mon, 16 May 2016 07:45:51: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 07:48:18: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Mon, 16 May 2016 07:48:18: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_treat_pileup.bdg 
INFO  @ Mon, 16 May 2016 07:48:18: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_control_lambda.bdg 
INFO  @ Mon, 16 May 2016 07:48:18: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Mon, 16 May 2016 07:48:18: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 07:59:44: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.xls 
INFO  @ Mon, 16 May 2016 07:59:51: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.narrowPeak 
INFO  @ Mon, 16 May 2016 07:59:55: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_summits.bed 
INFO  @ Mon, 16 May 2016 07:59:58: Done! 

 

 
# 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/ATAC3+4/align/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/align/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/signal/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/align/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/signal/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_control_lambda.bdg
 

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
INFO  @ Mon, 16 May 2016 07:36:46: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is on
 
INFO  @ Mon, 16 May 2016 07:36:46: #1 read tag files... 
INFO  @ Mon, 16 May 2016 07:36:46: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 07:36:48:  1000000 
INFO  @ Mon, 16 May 2016 07:36:49:  2000000 
INFO  @ Mon, 16 May 2016 07:36:51:  3000000 
INFO  @ Mon, 16 May 2016 07:36:52:  4000000 
INFO  @ Mon, 16 May 2016 07:36:54:  5000000 
INFO  @ Mon, 16 May 2016 07:36:56:  6000000 
INFO  @ Mon, 16 May 2016 07:36:57:  7000000 
INFO  @ Mon, 16 May 2016 07:36:59:  8000000 
INFO  @ Mon, 16 May 2016 07:37:01:  9000000 
INFO  @ Mon, 16 May 2016 07:37:03:  10000000 
INFO  @ Mon, 16 May 2016 07:37:05:  11000000 
INFO  @ Mon, 16 May 2016 07:37:07:  12000000 
INFO  @ Mon, 16 May 2016 07:37:09:  13000000 
INFO  @ Mon, 16 May 2016 07:37:10:  14000000 
INFO  @ Mon, 16 May 2016 07:37:12:  15000000 
INFO  @ Mon, 16 May 2016 07:37:14:  16000000 
INFO  @ Mon, 16 May 2016 07:37:16:  17000000 
INFO  @ Mon, 16 May 2016 07:37:18:  18000000 
INFO  @ Mon, 16 May 2016 07:37:20:  19000000 
INFO  @ Mon, 16 May 2016 07:37:21:  20000000 
INFO  @ Mon, 16 May 2016 07:37:23:  21000000 
INFO  @ Mon, 16 May 2016 07:37:26:  22000000 
INFO  @ Mon, 16 May 2016 07:37:27:  23000000 
INFO  @ Mon, 16 May 2016 07:37:29:  24000000 
INFO  @ Mon, 16 May 2016 07:37:31:  25000000 
INFO  @ Mon, 16 May 2016 07:37:33:  26000000 
INFO  @ Mon, 16 May 2016 07:37:35:  27000000 
INFO  @ Mon, 16 May 2016 07:37:36:  28000000 
INFO  @ Mon, 16 May 2016 07:37:38:  29000000 
INFO  @ Mon, 16 May 2016 07:37:40:  30000000 
INFO  @ Mon, 16 May 2016 07:37:41:  31000000 
INFO  @ Mon, 16 May 2016 07:37:43:  32000000 
INFO  @ Mon, 16 May 2016 07:37:45:  33000000 
INFO  @ Mon, 16 May 2016 07:37:47:  34000000 
INFO  @ Mon, 16 May 2016 07:37:48:  35000000 
INFO  @ Mon, 16 May 2016 07:37:50:  36000000 
INFO  @ Mon, 16 May 2016 07:37:52:  37000000 
INFO  @ Mon, 16 May 2016 07:37:53:  38000000 
INFO  @ Mon, 16 May 2016 07:37:55:  39000000 
INFO  @ Mon, 16 May 2016 07:37:56:  40000000 
INFO  @ Mon, 16 May 2016 07:37:58:  41000000 
INFO  @ Mon, 16 May 2016 07:38:00:  42000000 
INFO  @ Mon, 16 May 2016 07:38:01:  43000000 
INFO  @ Mon, 16 May 2016 07:38:03:  44000000 
INFO  @ Mon, 16 May 2016 07:38:04:  45000000 
INFO  @ Mon, 16 May 2016 07:38:06:  46000000 
INFO  @ Mon, 16 May 2016 07:38:08:  47000000 
INFO  @ Mon, 16 May 2016 07:38:09:  48000000 
INFO  @ Mon, 16 May 2016 07:38:11:  49000000 
INFO  @ Mon, 16 May 2016 07:38:12:  50000000 
INFO  @ Mon, 16 May 2016 07:38:14:  51000000 
INFO  @ Mon, 16 May 2016 07:38:16:  52000000 
INFO  @ Mon, 16 May 2016 07:38:17:  53000000 
INFO  @ Mon, 16 May 2016 07:38:19:  54000000 
INFO  @ Mon, 16 May 2016 07:38:20:  55000000 
INFO  @ Mon, 16 May 2016 07:38:22:  56000000 
INFO  @ Mon, 16 May 2016 07:38:27: #1 tag size is determined as 60 bps 
INFO  @ Mon, 16 May 2016 07:38:27: #1 tag size = 60 
INFO  @ Mon, 16 May 2016 07:38:27: #1  total tags in treatment: 56838584 
INFO  @ Mon, 16 May 2016 07:38:27: #1 finished! 
INFO  @ Mon, 16 May 2016 07:38:27: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 07:38:27: #2 Skipped... 
INFO  @ Mon, 16 May 2016 07:38:27: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 07:38:27: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 07:38:27: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 07:38:27: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Mon, 16 May 2016 07:38:27: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 07:40:28: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 07:43:19: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.xls 
INFO  @ Mon, 16 May 2016 07:43:23: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.broadPeak 
INFO  @ Mon, 16 May 2016 07:43:25: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.gappedPeak 
INFO  @ Mon, 16 May 2016 07:43:27: Done! 
INFO  @ Mon, 16 May 2016 07:43:38: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Mon, 16 May 2016 07:43:38: #1 read tag files... 
INFO  @ Mon, 16 May 2016 07:43:38: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 07:43:40:  1000000 
INFO  @ Mon, 16 May 2016 07:43:41:  2000000 
INFO  @ Mon, 16 May 2016 07:43:43:  3000000 
INFO  @ Mon, 16 May 2016 07:43:45:  4000000 
INFO  @ Mon, 16 May 2016 07:43:46:  5000000 
INFO  @ Mon, 16 May 2016 07:43:48:  6000000 
INFO  @ Mon, 16 May 2016 07:43:50:  7000000 
INFO  @ Mon, 16 May 2016 07:43:51:  8000000 
INFO  @ Mon, 16 May 2016 07:43:53:  9000000 
INFO  @ Mon, 16 May 2016 07:43:55:  10000000 
INFO  @ Mon, 16 May 2016 07:43:56:  11000000 
INFO  @ Mon, 16 May 2016 07:43:58:  12000000 
INFO  @ Mon, 16 May 2016 07:44:00:  13000000 
INFO  @ Mon, 16 May 2016 07:44:01:  14000000 
INFO  @ Mon, 16 May 2016 07:44:03:  15000000 
INFO  @ Mon, 16 May 2016 07:44:05:  16000000 
INFO  @ Mon, 16 May 2016 07:44:06:  17000000 
INFO  @ Mon, 16 May 2016 07:44:08:  18000000 
INFO  @ Mon, 16 May 2016 07:44:10:  19000000 
INFO  @ Mon, 16 May 2016 07:44:11:  20000000 
INFO  @ Mon, 16 May 2016 07:44:13:  21000000 
INFO  @ Mon, 16 May 2016 07:44:15:  22000000 
INFO  @ Mon, 16 May 2016 07:44:16:  23000000 
INFO  @ Mon, 16 May 2016 07:44:18:  24000000 
INFO  @ Mon, 16 May 2016 07:44:20:  25000000 
INFO  @ Mon, 16 May 2016 07:44:21:  26000000 
INFO  @ Mon, 16 May 2016 07:44:23:  27000000 
INFO  @ Mon, 16 May 2016 07:44:25:  28000000 
INFO  @ Mon, 16 May 2016 07:44:26:  29000000 
INFO  @ Mon, 16 May 2016 07:44:28:  30000000 
INFO  @ Mon, 16 May 2016 07:44:30:  31000000 
INFO  @ Mon, 16 May 2016 07:44:32:  32000000 
INFO  @ Mon, 16 May 2016 07:44:33:  33000000 
INFO  @ Mon, 16 May 2016 07:44:35:  34000000 
INFO  @ Mon, 16 May 2016 07:44:37:  35000000 
INFO  @ Mon, 16 May 2016 07:44:38:  36000000 
INFO  @ Mon, 16 May 2016 07:44:40:  37000000 
INFO  @ Mon, 16 May 2016 07:44:41:  38000000 
INFO  @ Mon, 16 May 2016 07:44:43:  39000000 
INFO  @ Mon, 16 May 2016 07:44:45:  40000000 
INFO  @ Mon, 16 May 2016 07:44:46:  41000000 
INFO  @ Mon, 16 May 2016 07:44:48:  42000000 
INFO  @ Mon, 16 May 2016 07:44:50:  43000000 
INFO  @ Mon, 16 May 2016 07:44:51:  44000000 
INFO  @ Mon, 16 May 2016 07:44:53:  45000000 
INFO  @ Mon, 16 May 2016 07:44:55:  46000000 
INFO  @ Mon, 16 May 2016 07:44:56:  47000000 
INFO  @ Mon, 16 May 2016 07:44:58:  48000000 
INFO  @ Mon, 16 May 2016 07:45:00:  49000000 
INFO  @ Mon, 16 May 2016 07:45:01:  50000000 
INFO  @ Mon, 16 May 2016 07:45:03:  51000000 
INFO  @ Mon, 16 May 2016 07:45:05:  52000000 
INFO  @ Mon, 16 May 2016 07:45:06:  53000000 
INFO  @ Mon, 16 May 2016 07:45:08:  54000000 
INFO  @ Mon, 16 May 2016 07:45:10:  55000000 
INFO  @ Mon, 16 May 2016 07:45:11:  56000000 
INFO  @ Mon, 16 May 2016 07:45:17: #1 tag size is determined as 60 bps 
INFO  @ Mon, 16 May 2016 07:45:17: #1 tag size = 60 
INFO  @ Mon, 16 May 2016 07:45:17: #1  total tags in treatment: 56838584 
INFO  @ Mon, 16 May 2016 07:45:17: #1 finished! 
INFO  @ Mon, 16 May 2016 07:45:17: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 07:45:17: #2 Skipped... 
INFO  @ Mon, 16 May 2016 07:45:17: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 07:45:17: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 07:45:17: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 07:45:17: #3 Going to call summits inside each peak ... 
INFO  @ Mon, 16 May 2016 07:45:17: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Mon, 16 May 2016 07:45:17: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 07:47:53: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Mon, 16 May 2016 07:47:53: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_treat_pileup.bdg 
INFO  @ Mon, 16 May 2016 07:47:53: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_control_lambda.bdg 
INFO  @ Mon, 16 May 2016 07:47:53: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Mon, 16 May 2016 07:47:53: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 07:55:30: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.xls 
INFO  @ Mon, 16 May 2016 07:55:32: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.narrowPeak 
INFO  @ Mon, 16 May 2016 07:55:33: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_summits.bed 
INFO  @ Mon, 16 May 2016 07:55:34: Done! 
INFO  @ Mon, 16 May 2016 07:55:39: Read and build treatment bedGraph... 
INFO  @ Mon, 16 May 2016 07:57:42: Read and build control bedGraph... 
INFO  @ Mon, 16 May 2016 07:58:33: Build scoreTrackII... 
INFO  @ Mon, 16 May 2016 07:59:39: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Mon, 16 May 2016 08:05:31: Write bedGraph of scores... 
INFO  @ Mon, 16 May 2016 08:09:30: Finished 'FE'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_FE.bdg'! 
INFO  @ Mon, 16 May 2016 08:21:18: Read and build treatment bedGraph... 
INFO  @ Mon, 16 May 2016 08:23:12: Read and build control bedGraph... 
INFO  @ Mon, 16 May 2016 08:24:05: Build scoreTrackII... 
INFO  @ Mon, 16 May 2016 08:24:59: Values in your input bedGraph files will be multiplied by 56.838584 ... 
INFO  @ Mon, 16 May 2016 08:30:52: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Mon, 16 May 2016 08:31:42: Write bedGraph of scores... 
INFO  @ Mon, 16 May 2016 08:34:40: Finished 'ppois'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_ppois.bdg'! 

 

 
# 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/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-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

 

 
# 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/ATAC3+4/peak/macs2/rep1/ATAC3-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/ATAC3+4/peak/macs2/rep1/ATAC3-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

 

 
# 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/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-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

 

 
# 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/ATAC3+4/peak/macs2/rep2/ATAC4-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/ATAC3+4/peak/macs2/rep2/ATAC4-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

 

 
# 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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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

 

 
# 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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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

 

 
# 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/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz --peak-list /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-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/ATAC3+4/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/ATAC3+4/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/ATAC3+4/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/ATAC3+4/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/ATAC3+4/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/ATAC3+4/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/ATAC3+4/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/ATAC3+4/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/ATAC3+4/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/ATAC3+4/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt
 

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