Script file	/users/pangwei/bds_atac/atac.bds
Program ID	atac.bds.20160516_201635_160
Start time	2016-05-16 20:16:35
Run time	13:44:46.976
Tasks executed	46
Tasks failed	0
Tasks failed names
Arguments*	[-out_dir, /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14, -num_rep, 2, -fastq1_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC13/ATAC13-trimmed-pair1.fastq.gz, -fastq1_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC13/ATAC13-trimmed-pair2.fastq.gz, -fastq2_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC14/ATAC14-trimmed-pair1.fastq.gz, -fastq2_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC14/ATAC14-trimmed-pair2.fastq.gz, -subsample, 17500000, -true_rep, -species, hg19]
System*	local
Cpus*	1
Exit value	0

Thread ID	Parent	Tasks
thread_Root	None	atac.bds.20160516_201635_160/task.postalign_bed.pool_tag_reps.line_405.id_27 atac.bds.20160516_201635_160/task.callpeak_macs2.macs2_atac_pooled.pval0.1.line_192.id_28 atac.bds.20160516_201635_160/task.callpeak_macs2.macs2_atac_pooled.line_192.id_29 atac.bds.20160516_201635_160/task.callpeak_etc.filt_top_peaks_rep1.line_25.id_30 atac.bds.20160516_201635_160/task.callpeak_etc.filt_top_peaks_rep1.line_25.id_31 atac.bds.20160516_201635_160/task.callpeak_etc.filt_top_peaks_rep2.line_25.id_32 atac.bds.20160516_201635_160/task.callpeak_etc.filt_top_peaks_rep2.line_25.id_33 atac.bds.20160516_201635_160/task.callpeak_etc.filt_top_peaks_pooled.line_25.id_34 atac.bds.20160516_201635_160/task.callpeak_etc.filt_top_peaks_pooled.line_25.id_35 atac.bds.20160516_201635_160/task.idr.idr2_rep1_rep2.line_61.id_36 atac.bds.20160516_201635_160/task.base.line_414.id_39 atac.bds.20160516_201635_160/task.base.line_414.id_40 atac.bds.20160516_201635_160/task.base.line_414.id_41 atac.bds.20160516_201635_160/task.base.line_414.id_42 atac.bds.20160516_201635_160/task.idr.idr_final_qc.line_196.id_43 atac.bds.20160516_201635_160/task.report.line_418.id_48 atac.bds.20160516_201635_160/task.report.line_418.id_49 atac.bds.20160516_201635_160/task.report.line_418.id_50 atac.bds.20160516_201635_160/task.report_graphviz.line_93.id_51 atac.bds.20160516_201635_160/task.report.line_383.id_56 atac.bds.20160516_201635_160/task.report.line_383.id_57
thread_21	thread_Root	atac.bds.20160516_201635_160_parallel_21/task.postalign_bam.dedup_bam_PE_rep2.line_215.id_7 atac.bds.20160516_201635_160_parallel_21/task.postalign_bam.nmsrt_bam_rep2.line_321.id_8 atac.bds.20160516_201635_160_parallel_21/task.postalign_bam.bam_to_bedpe_rep2.line_425.id_9 atac.bds.20160516_201635_160_parallel_21/task.postalign_bed.subsample_bedpe_rep2.line_116.id_10 atac.bds.20160516_201635_160_parallel_21/task.postalign_bam.bedpe_to_tag_rep2.line_465.id_11 atac.bds.20160516_201635_160_parallel_21/task.postalign_bed.shift_tag_rep2.line_140.id_12 atac.bds.20160516_201635_160_parallel_21/task.postalign_bed.subsample_bedpe2tagrep2.line_89.id_13 atac.bds.20160516_201635_160_parallel_21/task.postalign_bed.xcor_rep2.line_165.id_14 atac.bds.20160516_201635_160_parallel_21/task.callpeak_macs2.macs2_atac_rep2.pval0.1.line_192.id_15 atac.bds.20160516_201635_160_parallel_21/task.callpeak_macs2.macs2_atac_rep2.line_192.id_16
thread_20	thread_Root	atac.bds.20160516_201635_160_parallel_20/task.align_bowtie2.bowtie2_PE_rep1.line_133.id_6 atac.bds.20160516_201635_160_parallel_20/task.postalign_bam.dedup_bam_PE_rep1.line_215.id_17 atac.bds.20160516_201635_160_parallel_20/task.postalign_bam.nmsrt_bam_rep1.line_321.id_18 atac.bds.20160516_201635_160_parallel_20/task.postalign_bam.bam_to_bedpe_rep1.line_425.id_19 atac.bds.20160516_201635_160_parallel_20/task.postalign_bed.subsample_bedpe_rep1.line_116.id_20 atac.bds.20160516_201635_160_parallel_20/task.postalign_bam.bedpe_to_tag_rep1.line_465.id_21 atac.bds.20160516_201635_160_parallel_20/task.postalign_bed.shift_tag_rep1.line_140.id_22 atac.bds.20160516_201635_160_parallel_20/task.postalign_bed.subsample_bedpe2tagrep1.line_89.id_23 atac.bds.20160516_201635_160_parallel_20/task.postalign_bed.xcor_rep1.line_165.id_24 atac.bds.20160516_201635_160_parallel_20/task.callpeak_macs2.macs2_atac_rep1.pval0.1.line_192.id_25 atac.bds.20160516_201635_160_parallel_20/task.callpeak_macs2.macs2_atac_rep1.line_192.id_26
thread_77	thread_Root	atac.bds.20160516_201635_160_parallel_77/task.postalign_bam.srt_bam_rep1.line_345.id_44 atac.bds.20160516_201635_160_parallel_77/task.atac.ataqc_rep1.line_815.id_47
thread_78	thread_Root	atac.bds.20160516_201635_160_parallel_78/task.postalign_bam.srt_bam_rep2.line_345.id_45 atac.bds.20160516_201635_160_parallel_78/task.atac.ataqc_rep2.line_815.id_46

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.postalign_bam.dedup_bam_PE_rep2.line_215.id_7
Name	dedup_bam_PE rep2
Thread	thread_21
PID	129946

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

Start	2016-05-16 20:16:35
End	2016-05-16 22:21:20
Elapsed	02:04:44
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep2/ATAC14-trimmed-pair1.trim.PE2SE.dup.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.pbc.qc
Dependencies

 
# SYS command. line 217

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

# SYS command. line 228

 echo

# SYS command. line 229

 samtools view -F 1804 -f 2 -q 30 -u /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-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/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-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/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.filt

# SYS command. line 239

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-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/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep2/ATAC14-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/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep2/ATAC14-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/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-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/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.filt.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 269

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 271

 if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.bai" ]; then \
			cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.bai; \
			fi

# SYS command. line 275

 samtools flagstat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc

# SYS command. line 286

 samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.filt.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.filt.bam.tmp

# SYS command. line 287

 bedtools bamtobed -bedpe -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-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/ATAC13+14/qc/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.pbc.qc

# SYS command. line 291

 rm /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam

# SYS command. line 293

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.filt.bam

# SYS command. line 294

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-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 24 files...
[bam_sort_core] merging from 24 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Mon May 16 21:20:13 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep2/ATAC14-trimmed-pair1.trim.PE2SE.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Mon May 16 21:20:13 PDT 2016] Executing as pangwei@mitra on Linux 3.16.0-70-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_45-b14; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-05-16 21:20:13	MarkDuplicates	Start of doWork freeMemory: 254889800; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-16 21:20:13	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-05-16 21:20:13	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-05-16 21:20:29	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:14s.  Time for last 1,000,000:   14s.  Last read position: chr10:85,988,706
INFO	2016-05-16 21:20:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:20:39	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:25s.  Time for last 1,000,000:   10s.  Last read position: chr11:15,947,788
INFO	2016-05-16 21:20:39	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 21:20:52	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:37s.  Time for last 1,000,000:   12s.  Last read position: chr11:90,240,527
INFO	2016-05-16 21:20:52	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 21:20:57	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:43s.  Time for last 1,000,000:    5s.  Last read position: chr12:31,169,996
INFO	2016-05-16 21:20:57	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 21:21:05	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:50s.  Time for last 1,000,000:    7s.  Last read position: chr12:113,984,862
INFO	2016-05-16 21:21:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:21:11	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:56s.  Time for last 1,000,000:    5s.  Last read position: chr13:81,689,167
INFO	2016-05-16 21:21:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:21:19	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:01:05s.  Time for last 1,000,000:    8s.  Last read position: chr14:71,792,475
INFO	2016-05-16 21:21:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:21:26	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:01:12s.  Time for last 1,000,000:    6s.  Last read position: chr15:61,735,698
INFO	2016-05-16 21:21:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:21:35	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:01:20s.  Time for last 1,000,000:    8s.  Last read position: chr16:24,616,652
INFO	2016-05-16 21:21:35	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 21:21:42	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:01:27s.  Time for last 1,000,000:    6s.  Last read position: chr17:8,635,937
INFO	2016-05-16 21:21:42	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 21:21:52	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:37s.  Time for last 1,000,000:   10s.  Last read position: chr17:74,403,488
INFO	2016-05-16 21:21:52	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 21:21:56	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:42s.  Time for last 1,000,000:    4s.  Last read position: chr18:74,035,403
INFO	2016-05-16 21:21:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:22:03	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:48s.  Time for last 1,000,000:    6s.  Last read position: chr19:51,321,559
INFO	2016-05-16 21:22:03	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-16 21:22:13	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:58s.  Time for last 1,000,000:   10s.  Last read position: chr1:39,564,522
INFO	2016-05-16 21:22:13	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 21:22:31	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:02:16s.  Time for last 1,000,000:   17s.  Last read position: chr1:116,769,706
INFO	2016-05-16 21:22:31	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 21:22:37	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:02:22s.  Time for last 1,000,000:    6s.  Last read position: chr1:213,725,294
INFO	2016-05-16 21:22:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:22:45	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:02:31s.  Time for last 1,000,000:    8s.  Last read position: chr20:38,482,542
INFO	2016-05-16 21:22:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:22:50	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:02:36s.  Time for last 1,000,000:    4s.  Last read position: chr22:20,124,659
INFO	2016-05-16 21:22:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:22:55	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:02:41s.  Time for last 1,000,000:    5s.  Last read position: chr2:28,975,154
INFO	2016-05-16 21:22:55	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 21:23:02	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:02:47s.  Time for last 1,000,000:    6s.  Last read position: chr2:115,049,371
INFO	2016-05-16 21:23:02	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 21:23:08	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:02:54s.  Time for last 1,000,000:    6s.  Last read position: chr2:203,060,786
INFO	2016-05-16 21:23:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:23:15	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:03:00s.  Time for last 1,000,000:    6s.  Last read position: chr3:34,405,929
INFO	2016-05-16 21:23:15	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 21:23:24	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:03:09s.  Time for last 1,000,000:    9s.  Last read position: chr3:120,745,632
INFO	2016-05-16 21:23:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:23:30	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:03:16s.  Time for last 1,000,000:    6s.  Last read position: chr4:1,858,446
INFO	2016-05-16 21:23:30	MarkDuplicates	Tracking 14 as yet unmatched pairs. 14 records in RAM.
INFO	2016-05-16 21:23:36	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:03:22s.  Time for last 1,000,000:    5s.  Last read position: chr4:95,290,757
INFO	2016-05-16 21:23:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:23:46	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:03:31s.  Time for last 1,000,000:    9s.  Last read position: chr5:594,610
INFO	2016-05-16 21:23:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:23:52	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:03:37s.  Time for last 1,000,000:    6s.  Last read position: chr5:95,817,566
INFO	2016-05-16 21:23:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:23:57	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:03:42s.  Time for last 1,000,000:    5s.  Last read position: chr5:167,126,689
INFO	2016-05-16 21:23:57	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:24:03	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:03:49s.  Time for last 1,000,000:    6s.  Last read position: chr6:52,408,146
INFO	2016-05-16 21:24:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:24:25	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:04:11s.  Time for last 1,000,000:   21s.  Last read position: chr6:149,291,357
INFO	2016-05-16 21:24:25	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 21:24:30	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:04:15s.  Time for last 1,000,000:    4s.  Last read position: chr7:55,482,369
INFO	2016-05-16 21:24:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:24:35	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:04:21s.  Time for last 1,000,000:    5s.  Last read position: chr7:146,159,338
INFO	2016-05-16 21:24:35	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 21:24:40	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:04:25s.  Time for last 1,000,000:    4s.  Last read position: chr8:70,178,649
INFO	2016-05-16 21:24:40	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-16 21:24:46	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:04:31s.  Time for last 1,000,000:    6s.  Last read position: chr9:4,153,069
INFO	2016-05-16 21:24:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:24:51	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:04:36s.  Time for last 1,000,000:    4s.  Last read position: chr9:117,063,973
INFO	2016-05-16 21:24:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-16 21:24:55	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:04:41s.  Time for last 1,000,000:    4s.  Last read position: chrM:501
INFO	2016-05-16 21:24:55	MarkDuplicates	Tracking 4238 as yet unmatched pairs. 4238 records in RAM.
INFO	2016-05-16 21:25:00	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:04:45s.  Time for last 1,000,000:    4s.  Last read position: chrM:1,391
INFO	2016-05-16 21:25:00	MarkDuplicates	Tracking 20594 as yet unmatched pairs. 20594 records in RAM.
INFO	2016-05-16 21:25:06	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:04:52s.  Time for last 1,000,000:    6s.  Last read position: chrM:2,410
INFO	2016-05-16 21:25:06	MarkDuplicates	Tracking 4126 as yet unmatched pairs. 4126 records in RAM.
INFO	2016-05-16 21:25:11	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:04:56s.  Time for last 1,000,000:    4s.  Last read position: chrM:2,953
INFO	2016-05-16 21:25:11	MarkDuplicates	Tracking 24454 as yet unmatched pairs. 24454 records in RAM.
INFO	2016-05-16 21:25:17	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:05:02s.  Time for last 1,000,000:    5s.  Last read position: chrM:3,397
INFO	2016-05-16 21:25:17	MarkDuplicates	Tracking 30228 as yet unmatched pairs. 30228 records in RAM.
INFO	2016-05-16 21:25:23	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:05:08s.  Time for last 1,000,000:    5s.  Last read position: chrM:3,755
INFO	2016-05-16 21:25:23	MarkDuplicates	Tracking 26820 as yet unmatched pairs. 26820 records in RAM.
INFO	2016-05-16 21:25:32	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:05:17s.  Time for last 1,000,000:    9s.  Last read position: chrM:4,925
INFO	2016-05-16 21:25:32	MarkDuplicates	Tracking 14376 as yet unmatched pairs. 14376 records in RAM.
INFO	2016-05-16 21:25:37	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:05:23s.  Time for last 1,000,000:    5s.  Last read position: chrM:6,229
INFO	2016-05-16 21:25:37	MarkDuplicates	Tracking 20426 as yet unmatched pairs. 20426 records in RAM.
INFO	2016-05-16 21:25:43	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:05:29s.  Time for last 1,000,000:    5s.  Last read position: chrM:6,680
INFO	2016-05-16 21:25:43	MarkDuplicates	Tracking 10164 as yet unmatched pairs. 10164 records in RAM.
INFO	2016-05-16 21:25:53	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:05:39s.  Time for last 1,000,000:   10s.  Last read position: chrM:7,919
INFO	2016-05-16 21:25:53	MarkDuplicates	Tracking 7706 as yet unmatched pairs. 7706 records in RAM.
INFO	2016-05-16 21:26:00	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:05:45s.  Time for last 1,000,000:    6s.  Last read position: chrM:9,271
INFO	2016-05-16 21:26:00	MarkDuplicates	Tracking 12732 as yet unmatched pairs. 12732 records in RAM.
INFO	2016-05-16 21:26:08	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:05:53s.  Time for last 1,000,000:    7s.  Last read position: chrM:10,245
INFO	2016-05-16 21:26:08	MarkDuplicates	Tracking 10094 as yet unmatched pairs. 10094 records in RAM.
INFO	2016-05-16 21:26:12	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:05:57s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,185
INFO	2016-05-16 21:26:12	MarkDuplicates	Tracking 9000 as yet unmatched pairs. 9000 records in RAM.
INFO	2016-05-16 21:26:16	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:06:01s.  Time for last 1,000,000:    4s.  Last read position: chrM:11,875
INFO	2016-05-16 21:26:16	MarkDuplicates	Tracking 3462 as yet unmatched pairs. 3462 records in RAM.
INFO	2016-05-16 21:26:20	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:06:06s.  Time for last 1,000,000:    4s.  Last read position: chrM:12,568
INFO	2016-05-16 21:26:20	MarkDuplicates	Tracking 24230 as yet unmatched pairs. 24230 records in RAM.
INFO	2016-05-16 21:26:25	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:06:10s.  Time for last 1,000,000:    4s.  Last read position: chrM:13,194
INFO	2016-05-16 21:26:25	MarkDuplicates	Tracking 29094 as yet unmatched pairs. 29094 records in RAM.
INFO	2016-05-16 21:26:31	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:06:17s.  Time for last 1,000,000:    6s.  Last read position: chrM:13,849
INFO	2016-05-16 21:26:31	MarkDuplicates	Tracking 32570 as yet unmatched pairs. 32570 records in RAM.
INFO	2016-05-16 21:26:37	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:06:22s.  Time for last 1,000,000:    5s.  Last read position: chrM:14,734
INFO	2016-05-16 21:26:37	MarkDuplicates	Tracking 2450 as yet unmatched pairs. 2450 records in RAM.
INFO	2016-05-16 21:26:42	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:06:28s.  Time for last 1,000,000:    5s.  Last read position: chrM:15,261
INFO	2016-05-16 21:26:42	MarkDuplicates	Tracking 17746 as yet unmatched pairs. 17746 records in RAM.
INFO	2016-05-16 21:26:48	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:06:34s.  Time for last 1,000,000:    5s.  Last read position: chrM:15,697
INFO	2016-05-16 21:26:48	MarkDuplicates	Tracking 25692 as yet unmatched pairs. 25692 records in RAM.
INFO	2016-05-16 21:26:54	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:06:40s.  Time for last 1,000,000:    5s.  Last read position: chrM:16,330
INFO	2016-05-16 21:26:54	MarkDuplicates	Tracking 23714 as yet unmatched pairs. 23714 records in RAM.
INFO	2016-05-16 21:27:04	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:06:49s.  Time for last 1,000,000:    9s.  Last read position: chrX:47,404,547
INFO	2016-05-16 21:27:04	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 21:27:11	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:06:56s.  Time for last 1,000,000:    6s.  Last read position: chrX:150,944,827
INFO	2016-05-16 21:27:11	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-16 21:27:11	MarkDuplicates	Read 58059292 records. 0 pairs never matched.
INFO	2016-05-16 21:27:27	MarkDuplicates	After buildSortedReadEndLists freeMemory: 3586933552; totalMemory: 3614441472; maxMemory: 3817865216
INFO	2016-05-16 21:27:27	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-05-16 21:27:27	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-05-16 21:27:44	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-05-16 21:28:02	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-05-16 21:28:03	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2624644048; totalMemory: 3606052864; maxMemory: 3817865216
INFO	2016-05-16 21:28:03	MarkDuplicates	Marking 23140244 records as duplicates.
INFO	2016-05-16 21:28:03	MarkDuplicates	Found 6471478 optical duplicate clusters.
INFO	2016-05-16 21:30:06	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:02:02s.  Time for last 10,000,000:  122s.  Last read position: chr17:8,635,937
INFO	2016-05-16 21:32:00	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:03:55s.  Time for last 10,000,000:  113s.  Last read position: chr2:115,049,371
INFO	2016-05-16 21:33:49	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:05:44s.  Time for last 10,000,000:  108s.  Last read position: chr6:149,291,357
INFO	2016-05-16 21:35:27	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:07:22s.  Time for last 10,000,000:   98s.  Last read position: chrM:3,397
INFO	2016-05-16 21:37:00	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:08:55s.  Time for last 10,000,000:   93s.  Last read position: chrM:12,568
INFO	2016-05-16 21:38:15	MarkDuplicates	Before output close freeMemory: 3657879752; totalMemory: 3688366080; maxMemory: 3817865216
INFO	2016-05-16 21:38:15	MarkDuplicates	After output close freeMemory: 3657878696; totalMemory: 3688366080; maxMemory: 3817865216
[Mon May 16 21:38:15 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 18.04 minutes.
Runtime.totalMemory()=3688366080
[bam_sort_core] merging from 24 files...

Num	2
ID	task.align_bowtie2.bowtie2_PE_rep1.line_133.id_6
Name	bowtie2_PE rep1
Thread	thread_20
PID	129960

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

Start	2016-05-16 20:16:36
End	2016-05-17 02:29:55
Elapsed	06:13:19
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.fastq.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair2.trim.fastq.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep1/ATAC13-trimmed-pair1.trim.PE2SE.align.log
Dependencies

 
# SYS command. line 135

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

# SYS command. line 139

 bowtie2  -X2000 --mm --threads 2 -x /mnt/data/annotations/indexes/bowtie2_indexes/bowtie2/ENCODEHg19_male \
			-1 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.fastq.gz -2 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair2.trim.fastq.gz 2>/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep1/ATAC13-trimmed-pair1.trim.PE2SE.align.log | samtools view -bS - | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE

# SYS command. line 142

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-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 40 files...

Num	3
ID	task.postalign_bam.nmsrt_bam_rep2.line_321.id_8
Name	nmsrt_bam rep2
Thread	thread_21
PID	134834

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

Start	2016-05-16 22:21:20
End	2016-05-16 22:38:20
Elapsed	00:16:59
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam
Dependencies

 
# SYS command. line 323

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

# SYS command. line 325

 samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-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...

Num	4
ID	task.postalign_bam.bam_to_bedpe_rep2.line_425.id_9
Name	bam_to_bedpe rep2
Thread	thread_21
PID	135784

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

Start	2016-05-16 22:38:20
End	2016-05-16 22:40:27
Elapsed	00:02:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Dependencies	nmsrt_bam rep2 nmsrt_bam rep2

 
# SYS command. line 427

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

# SYS command. line 430

 bedtools bamtobed -bedpe -mate1 -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz

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

Num	5
ID	task.postalign_bed.subsample_bedpe_rep2.line_116.id_10
Name	subsample_bedpe rep2
Thread	thread_21
PID	136282

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

Start	2016-05-16 22:40:29
End	2016-05-16 22:42:34
Elapsed	00:02:04
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz
Dependencies

 
# SYS command. line 118

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

# SYS command. line 120

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | grep -v "chrM" | shuf -n 17500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz

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

Num	6
ID	task.postalign_bam.bedpe_to_tag_rep2.line_465.id_11
Name	bedpe_to_tag rep2
Thread	thread_21
PID	136363

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

Start	2016-05-16 22:42:35
End	2016-05-16 22:44:19
Elapsed	00:01:44
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
Dependencies

 
# SYS command. line 467

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

# SYS command. line 469

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-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/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz

# SYS command. line 472

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz | grep -P -v 'chrM' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz; mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz

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

Num	7
ID	task.postalign_bed.shift_tag_rep2.line_140.id_12
Name	shift_tag rep2
Thread	thread_21
PID	136449

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

Start	2016-05-16 22:44:20
End	2016-05-16 22:45:47
Elapsed	00:01:27
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Dependencies

 
# SYS command. line 142

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

# SYS command. line 144

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-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/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz

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

Num	8
ID	task.postalign_bed.subsample_bedpe2tagrep2.line_89.id_13
Name	subsample_bedpe2tagrep2
Thread	thread_21
PID	136525

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

Start	2016-05-16 22:45:48
End	2016-05-16 22:47:01
Elapsed	00:01:13
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
Dependencies

 
# SYS command. line 91

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

# SYS command. line 95

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-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/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz

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

Num	9
ID	task.postalign_bed.xcor_rep2.line_165.id_14
Name	xcor rep2
Thread	thread_21
PID	136598

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

Start	2016-05-16 22:47:02
End	2016-05-16 23:20:33
Elapsed	00:33:31
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf
Dependencies

 
# SYS command. line 167

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

# SYS command. line 171

 Rscript $(which run_spp_nodups.R) -rf \
			-c=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz -p=1 \
			-filtchr=chrM -savp=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf -out=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep2/ATAC14-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/ATAC13+14/qc/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp

# SYS command. line 175

 mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc

   
--------------------Stdout--------------------
################
ChIP data: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-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/ATAC13+14/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/ATAC13+14/qc/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf 
result filename: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep2/ATAC14-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/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz 
opened /tmp/Rtmpc1y8Vg/ATAC14-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign2163f2068d039
done. read 16761251 fragments
ChIP data read length 73 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1766845 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.208967806844454 
Top 3 estimates for fragment length 0 
Window half size 490 
Phantom peak location 65 
Phantom peak Correlation 0.2136727 
Normalized Strand cross-correlation coefficient (NSC) 1.182718 
Relative Strand Cross correlation Coefficient (RSC) 0.8728015 
Phantom Peak Quality Tag 0 
null device 
          1 

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

Num	10
ID	task.callpeak_macs2.macs2_atac_rep2.pval0.1.line_192.id_15
Name	macs2_atac rep2.pval0.1
Thread	thread_21
PID	136604

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

Start	2016-05-16 22:47:02
End	2016-05-16 23:05:58
Elapsed	00:18:55
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz
Dependencies

 
# SYS command. line 194

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

# SYS command. line 195

 LC_COLLATE=C

# SYS command. line 197

 macs2 callpeak \
			-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/signal/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/signal/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
INFO  @ Mon, 16 May 2016 22:47:04: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-01
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is on
 
INFO  @ Mon, 16 May 2016 22:47:04: #1 read tag files... 
INFO  @ Mon, 16 May 2016 22:47:04: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 22:47:06:  1000000 
INFO  @ Mon, 16 May 2016 22:47:08:  2000000 
INFO  @ Mon, 16 May 2016 22:47:10:  3000000 
INFO  @ Mon, 16 May 2016 22:47:13:  4000000 
INFO  @ Mon, 16 May 2016 22:47:15:  5000000 
INFO  @ Mon, 16 May 2016 22:47:17:  6000000 
INFO  @ Mon, 16 May 2016 22:47:19:  7000000 
INFO  @ Mon, 16 May 2016 22:47:20:  8000000 
INFO  @ Mon, 16 May 2016 22:47:22:  9000000 
INFO  @ Mon, 16 May 2016 22:47:24:  10000000 
INFO  @ Mon, 16 May 2016 22:47:27:  11000000 
INFO  @ Mon, 16 May 2016 22:47:29:  12000000 
INFO  @ Mon, 16 May 2016 22:47:31:  13000000 
INFO  @ Mon, 16 May 2016 22:47:33:  14000000 
INFO  @ Mon, 16 May 2016 22:47:35:  15000000 
INFO  @ Mon, 16 May 2016 22:47:37:  16000000 
INFO  @ Mon, 16 May 2016 22:47:39:  17000000 
INFO  @ Mon, 16 May 2016 22:47:41:  18000000 
INFO  @ Mon, 16 May 2016 22:47:42:  19000000 
INFO  @ Mon, 16 May 2016 22:47:44:  20000000 
INFO  @ Mon, 16 May 2016 22:47:46:  21000000 
INFO  @ Mon, 16 May 2016 22:47:48:  22000000 
INFO  @ Mon, 16 May 2016 22:47:50:  23000000 
INFO  @ Mon, 16 May 2016 22:47:52:  24000000 
INFO  @ Mon, 16 May 2016 22:47:54:  25000000 
INFO  @ Mon, 16 May 2016 22:47:56:  26000000 
INFO  @ Mon, 16 May 2016 22:47:58:  27000000 
INFO  @ Mon, 16 May 2016 22:48:01:  28000000 
INFO  @ Mon, 16 May 2016 22:48:02:  29000000 
INFO  @ Mon, 16 May 2016 22:48:04:  30000000 
INFO  @ Mon, 16 May 2016 22:48:07:  31000000 
INFO  @ Mon, 16 May 2016 22:48:08:  32000000 
INFO  @ Mon, 16 May 2016 22:48:10:  33000000 
INFO  @ Mon, 16 May 2016 22:48:14: #1 tag size is determined as 56 bps 
INFO  @ Mon, 16 May 2016 22:48:14: #1 tag size = 56 
INFO  @ Mon, 16 May 2016 22:48:14: #1  total tags in treatment: 33522502 
INFO  @ Mon, 16 May 2016 22:48:14: #1 finished! 
INFO  @ Mon, 16 May 2016 22:48:14: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 22:48:14: #2 Skipped... 
INFO  @ Mon, 16 May 2016 22:48:14: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 22:48:14: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 22:48:14: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 22:48:14: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Mon, 16 May 2016 22:48:14: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 22:49:59: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 22:52:45: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls 
INFO  @ Mon, 16 May 2016 22:52:50: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Mon, 16 May 2016 22:52:53: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Mon, 16 May 2016 22:52:56: Done! 
INFO  @ Mon, 16 May 2016 22:53:08: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Mon, 16 May 2016 22:53:08: #1 read tag files... 
INFO  @ Mon, 16 May 2016 22:53:08: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 22:53:10:  1000000 
INFO  @ Mon, 16 May 2016 22:53:12:  2000000 
INFO  @ Mon, 16 May 2016 22:53:14:  3000000 
INFO  @ Mon, 16 May 2016 22:53:16:  4000000 
INFO  @ Mon, 16 May 2016 22:53:18:  5000000 
INFO  @ Mon, 16 May 2016 22:53:20:  6000000 
INFO  @ Mon, 16 May 2016 22:53:22:  7000000 
INFO  @ Mon, 16 May 2016 22:53:25:  8000000 
INFO  @ Mon, 16 May 2016 22:53:27:  9000000 
INFO  @ Mon, 16 May 2016 22:53:28:  10000000 
INFO  @ Mon, 16 May 2016 22:53:30:  11000000 
INFO  @ Mon, 16 May 2016 22:53:32:  12000000 
INFO  @ Mon, 16 May 2016 22:53:33:  13000000 
INFO  @ Mon, 16 May 2016 22:53:35:  14000000 
INFO  @ Mon, 16 May 2016 22:53:37:  15000000 
INFO  @ Mon, 16 May 2016 22:53:38:  16000000 
INFO  @ Mon, 16 May 2016 22:53:40:  17000000 
INFO  @ Mon, 16 May 2016 22:53:42:  18000000 
INFO  @ Mon, 16 May 2016 22:53:43:  19000000 
INFO  @ Mon, 16 May 2016 22:53:45:  20000000 
INFO  @ Mon, 16 May 2016 22:53:47:  21000000 
INFO  @ Mon, 16 May 2016 22:53:49:  22000000 
INFO  @ Mon, 16 May 2016 22:53:51:  23000000 
INFO  @ Mon, 16 May 2016 22:53:53:  24000000 
INFO  @ Mon, 16 May 2016 22:53:55:  25000000 
INFO  @ Mon, 16 May 2016 22:53:56:  26000000 
INFO  @ Mon, 16 May 2016 22:53:58:  27000000 
INFO  @ Mon, 16 May 2016 22:54:00:  28000000 
INFO  @ Mon, 16 May 2016 22:54:02:  29000000 
INFO  @ Mon, 16 May 2016 22:54:04:  30000000 
INFO  @ Mon, 16 May 2016 22:54:06:  31000000 
INFO  @ Mon, 16 May 2016 22:54:09:  32000000 
INFO  @ Mon, 16 May 2016 22:54:12:  33000000 
INFO  @ Mon, 16 May 2016 22:54:16: #1 tag size is determined as 56 bps 
INFO  @ Mon, 16 May 2016 22:54:16: #1 tag size = 56 
INFO  @ Mon, 16 May 2016 22:54:16: #1  total tags in treatment: 33522502 
INFO  @ Mon, 16 May 2016 22:54:16: #1 finished! 
INFO  @ Mon, 16 May 2016 22:54:16: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 22:54:16: #2 Skipped... 
INFO  @ Mon, 16 May 2016 22:54:16: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 22:54:16: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 22:54:16: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 22:54:16: #3 Going to call summits inside each peak ... 
INFO  @ Mon, 16 May 2016 22:54:16: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Mon, 16 May 2016 22:54:16: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 22:55:49: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Mon, 16 May 2016 22:55:49: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Mon, 16 May 2016 22:55:49: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Mon, 16 May 2016 22:55:49: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Mon, 16 May 2016 22:55:49: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 23:05:36: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls 
INFO  @ Mon, 16 May 2016 23:05:42: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Mon, 16 May 2016 23:05:46: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_summits.bed 
INFO  @ Mon, 16 May 2016 23:05:50: Done!

Num	11
ID	task.callpeak_macs2.macs2_atac_rep2.line_192.id_16
Name	macs2_atac rep2
Thread	thread_21
PID	136614

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

Start	2016-05-16 22:47:02
End	2016-05-16 23:34:20
Elapsed	00:47:17
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.gappedPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/signal/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/signal/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig
Dependencies

 
# SYS command. line 194

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

# SYS command. line 195

 LC_COLLATE=C

# SYS command. line 197

 macs2 callpeak \
			-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/signal/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/signal/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
INFO  @ Mon, 16 May 2016 22:47:04: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is on
 
INFO  @ Mon, 16 May 2016 22:47:04: #1 read tag files... 
INFO  @ Mon, 16 May 2016 22:47:04: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 22:47:07:  1000000 
INFO  @ Mon, 16 May 2016 22:47:09:  2000000 
INFO  @ Mon, 16 May 2016 22:47:11:  3000000 
INFO  @ Mon, 16 May 2016 22:47:13:  4000000 
INFO  @ Mon, 16 May 2016 22:47:15:  5000000 
INFO  @ Mon, 16 May 2016 22:47:17:  6000000 
INFO  @ Mon, 16 May 2016 22:47:19:  7000000 
INFO  @ Mon, 16 May 2016 22:47:21:  8000000 
INFO  @ Mon, 16 May 2016 22:47:23:  9000000 
INFO  @ Mon, 16 May 2016 22:47:25:  10000000 
INFO  @ Mon, 16 May 2016 22:47:27:  11000000 
INFO  @ Mon, 16 May 2016 22:47:29:  12000000 
INFO  @ Mon, 16 May 2016 22:47:31:  13000000 
INFO  @ Mon, 16 May 2016 22:47:33:  14000000 
INFO  @ Mon, 16 May 2016 22:47:35:  15000000 
INFO  @ Mon, 16 May 2016 22:47:37:  16000000 
INFO  @ Mon, 16 May 2016 22:47:39:  17000000 
INFO  @ Mon, 16 May 2016 22:47:41:  18000000 
INFO  @ Mon, 16 May 2016 22:47:43:  19000000 
INFO  @ Mon, 16 May 2016 22:47:45:  20000000 
INFO  @ Mon, 16 May 2016 22:47:46:  21000000 
INFO  @ Mon, 16 May 2016 22:47:48:  22000000 
INFO  @ Mon, 16 May 2016 22:47:50:  23000000 
INFO  @ Mon, 16 May 2016 22:47:52:  24000000 
INFO  @ Mon, 16 May 2016 22:47:54:  25000000 
INFO  @ Mon, 16 May 2016 22:47:56:  26000000 
INFO  @ Mon, 16 May 2016 22:47:58:  27000000 
INFO  @ Mon, 16 May 2016 22:48:01:  28000000 
INFO  @ Mon, 16 May 2016 22:48:03:  29000000 
INFO  @ Mon, 16 May 2016 22:48:05:  30000000 
INFO  @ Mon, 16 May 2016 22:48:07:  31000000 
INFO  @ Mon, 16 May 2016 22:48:08:  32000000 
INFO  @ Mon, 16 May 2016 22:48:10:  33000000 
INFO  @ Mon, 16 May 2016 22:48:14: #1 tag size is determined as 56 bps 
INFO  @ Mon, 16 May 2016 22:48:14: #1 tag size = 56 
INFO  @ Mon, 16 May 2016 22:48:14: #1  total tags in treatment: 33522502 
INFO  @ Mon, 16 May 2016 22:48:14: #1 finished! 
INFO  @ Mon, 16 May 2016 22:48:14: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 22:48:14: #2 Skipped... 
INFO  @ Mon, 16 May 2016 22:48:14: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 22:48:14: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 22:48:14: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 22:48:14: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Mon, 16 May 2016 22:48:14: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 22:49:59: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 22:52:29: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls 
INFO  @ Mon, 16 May 2016 22:52:34: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.broadPeak 
INFO  @ Mon, 16 May 2016 22:52:37: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.gappedPeak 
INFO  @ Mon, 16 May 2016 22:52:40: Done! 
INFO  @ Mon, 16 May 2016 22:52:54: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Mon, 16 May 2016 22:52:54: #1 read tag files... 
INFO  @ Mon, 16 May 2016 22:52:54: #1 read treatment tags... 
INFO  @ Mon, 16 May 2016 22:52:56:  1000000 
INFO  @ Mon, 16 May 2016 22:52:58:  2000000 
INFO  @ Mon, 16 May 2016 22:53:00:  3000000 
INFO  @ Mon, 16 May 2016 22:53:02:  4000000 
INFO  @ Mon, 16 May 2016 22:53:04:  5000000 
INFO  @ Mon, 16 May 2016 22:53:06:  6000000 
INFO  @ Mon, 16 May 2016 22:53:08:  7000000 
INFO  @ Mon, 16 May 2016 22:53:10:  8000000 
INFO  @ Mon, 16 May 2016 22:53:12:  9000000 
INFO  @ Mon, 16 May 2016 22:53:14:  10000000 
INFO  @ Mon, 16 May 2016 22:53:16:  11000000 
INFO  @ Mon, 16 May 2016 22:53:18:  12000000 
INFO  @ Mon, 16 May 2016 22:53:20:  13000000 
INFO  @ Mon, 16 May 2016 22:53:22:  14000000 
INFO  @ Mon, 16 May 2016 22:53:24:  15000000 
INFO  @ Mon, 16 May 2016 22:53:26:  16000000 
INFO  @ Mon, 16 May 2016 22:53:28:  17000000 
INFO  @ Mon, 16 May 2016 22:53:30:  18000000 
INFO  @ Mon, 16 May 2016 22:53:32:  19000000 
INFO  @ Mon, 16 May 2016 22:53:33:  20000000 
INFO  @ Mon, 16 May 2016 22:53:35:  21000000 
INFO  @ Mon, 16 May 2016 22:53:36:  22000000 
INFO  @ Mon, 16 May 2016 22:53:38:  23000000 
INFO  @ Mon, 16 May 2016 22:53:40:  24000000 
INFO  @ Mon, 16 May 2016 22:53:42:  25000000 
INFO  @ Mon, 16 May 2016 22:53:44:  26000000 
INFO  @ Mon, 16 May 2016 22:53:45:  27000000 
INFO  @ Mon, 16 May 2016 22:53:47:  28000000 
INFO  @ Mon, 16 May 2016 22:53:48:  29000000 
INFO  @ Mon, 16 May 2016 22:53:50:  30000000 
INFO  @ Mon, 16 May 2016 22:53:52:  31000000 
INFO  @ Mon, 16 May 2016 22:53:54:  32000000 
INFO  @ Mon, 16 May 2016 22:53:56:  33000000 
INFO  @ Mon, 16 May 2016 22:54:00: #1 tag size is determined as 56 bps 
INFO  @ Mon, 16 May 2016 22:54:00: #1 tag size = 56 
INFO  @ Mon, 16 May 2016 22:54:00: #1  total tags in treatment: 33522502 
INFO  @ Mon, 16 May 2016 22:54:00: #1 finished! 
INFO  @ Mon, 16 May 2016 22:54:00: #2 Build Peak Model... 
INFO  @ Mon, 16 May 2016 22:54:00: #2 Skipped... 
INFO  @ Mon, 16 May 2016 22:54:00: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Mon, 16 May 2016 22:54:00: #2 Use 150 as fragment length 
INFO  @ Mon, 16 May 2016 22:54:00: #3 Call peaks... 
INFO  @ Mon, 16 May 2016 22:54:00: #3 Going to call summits inside each peak ... 
INFO  @ Mon, 16 May 2016 22:54:00: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Mon, 16 May 2016 22:54:00: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 16 May 2016 22:55:28: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Mon, 16 May 2016 22:55:28: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_treat_pileup.bdg 
INFO  @ Mon, 16 May 2016 22:55:28: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_control_lambda.bdg 
INFO  @ Mon, 16 May 2016 22:55:28: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Mon, 16 May 2016 22:55:28: #3 Call peaks for each chromosome... 
INFO  @ Mon, 16 May 2016 23:01:01: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls 
INFO  @ Mon, 16 May 2016 23:01:03: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.narrowPeak 
INFO  @ Mon, 16 May 2016 23:01:04: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_summits.bed 
INFO  @ Mon, 16 May 2016 23:01:05: Done! 
INFO  @ Mon, 16 May 2016 23:01:08: Read and build treatment bedGraph... 
INFO  @ Mon, 16 May 2016 23:02:24: Read and build control bedGraph... 
INFO  @ Mon, 16 May 2016 23:02:55: Build scoreTrackII... 
INFO  @ Mon, 16 May 2016 23:03:37: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Mon, 16 May 2016 23:07:33: Write bedGraph of scores... 
INFO  @ Mon, 16 May 2016 23:09:47: Finished 'FE'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_FE.bdg'! 
INFO  @ Mon, 16 May 2016 23:17:32: Read and build treatment bedGraph... 
INFO  @ Mon, 16 May 2016 23:18:54: Read and build control bedGraph... 
INFO  @ Mon, 16 May 2016 23:19:31: Build scoreTrackII... 
INFO  @ Mon, 16 May 2016 23:20:13: Values in your input bedGraph files will be multiplied by 33.522502 ... 
INFO  @ Mon, 16 May 2016 23:24:20: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Mon, 16 May 2016 23:25:00: Write bedGraph of scores... 
INFO  @ Mon, 16 May 2016 23:27:13: Finished 'ppois'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_ppois.bdg'!

Num	12
ID	task.postalign_bam.dedup_bam_PE_rep1.line_215.id_17
Name	dedup_bam_PE rep1
Thread	thread_20
PID	1341

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

Start	2016-05-17 02:29:56
End	2016-05-17 04:43:15
Elapsed	02:13:18
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep1/ATAC13-trimmed-pair1.trim.PE2SE.dup.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.pbc.qc
Dependencies

 
# SYS command. line 217

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

# SYS command. line 228

 echo

# SYS command. line 229

 samtools view -F 1804 -f 2 -q 30 -u /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-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/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-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/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.filt

# SYS command. line 239

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-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/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep1/ATAC13-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/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep1/ATAC13-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/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-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/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.filt.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 269

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 271

 if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.bai" ]; then \
			cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.bai; \
			fi

# SYS command. line 275

 samtools flagstat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc

# SYS command. line 286

 samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.filt.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.filt.bam.tmp

# SYS command. line 287

 bedtools bamtobed -bedpe -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-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/ATAC13+14/qc/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.pbc.qc

# SYS command. line 291

 rm /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam

# SYS command. line 293

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.filt.bam

# SYS command. line 294

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.dupmark.bam

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



 
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 26 files...
[bam_sort_core] merging from 26 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Tue May 17 03:39:25 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep1/ATAC13-trimmed-pair1.trim.PE2SE.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Tue May 17 03:39:25 PDT 2016] Executing as pangwei@mitra on Linux 3.16.0-70-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_45-b14; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-05-17 03:39:25	MarkDuplicates	Start of doWork freeMemory: 254889800; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-17 03:39:25	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-05-17 03:39:25	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-05-17 03:39:40	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:15s.  Time for last 1,000,000:   15s.  Last read position: chr10:80,968,814
INFO	2016-05-17 03:39:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:39:57	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:31s.  Time for last 1,000,000:   16s.  Last read position: chr11:7,362,052
INFO	2016-05-17 03:39:57	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:40:07	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:41s.  Time for last 1,000,000:   10s.  Last read position: chr11:74,154,277
INFO	2016-05-17 03:40:07	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 03:40:18	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:53s.  Time for last 1,000,000:   11s.  Last read position: chr12:6,389,470
INFO	2016-05-17 03:40:18	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 03:40:30	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:01:04s.  Time for last 1,000,000:   11s.  Last read position: chr12:85,921,751
INFO	2016-05-17 03:40:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:40:36	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:01:11s.  Time for last 1,000,000:    6s.  Last read position: chr13:39,341,968
INFO	2016-05-17 03:40:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:40:46	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:01:20s.  Time for last 1,000,000:    9s.  Last read position: chr14:26,660,625
INFO	2016-05-17 03:40:46	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 03:40:51	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:01:26s.  Time for last 1,000,000:    5s.  Last read position: chr14:100,358,981
INFO	2016-05-17 03:40:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:41:00	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:01:34s.  Time for last 1,000,000:    8s.  Last read position: chr15:79,612,290
INFO	2016-05-17 03:41:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:41:06	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:01:40s.  Time for last 1,000,000:    5s.  Last read position: chr16:52,758,578
INFO	2016-05-17 03:41:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:41:11	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:46s.  Time for last 1,000,000:    5s.  Last read position: chr17:19,620,636
INFO	2016-05-17 03:41:11	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 03:41:20	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:55s.  Time for last 1,000,000:    9s.  Last read position: chr17:78,009,440
INFO	2016-05-17 03:41:20	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 03:41:25	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:59s.  Time for last 1,000,000:    4s.  Last read position: chr18:74,704,480
INFO	2016-05-17 03:41:25	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 03:41:31	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:02:05s.  Time for last 1,000,000:    5s.  Last read position: chr19:48,996,295
INFO	2016-05-17 03:41:31	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-17 03:41:48	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:02:22s.  Time for last 1,000,000:   17s.  Last read position: chr1:32,248,097
INFO	2016-05-17 03:41:48	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 03:41:55	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:02:30s.  Time for last 1,000,000:    7s.  Last read position: chr1:99,334,803
INFO	2016-05-17 03:41:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:42:01	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:02:35s.  Time for last 1,000,000:    5s.  Last read position: chr1:193,663,502
INFO	2016-05-17 03:42:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:42:04	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:02:39s.  Time for last 1,000,000:    3s.  Last read position: chr20:12,453,533
INFO	2016-05-17 03:42:04	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:42:08	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:02:42s.  Time for last 1,000,000:    3s.  Last read position: chr21:17,756,805
INFO	2016-05-17 03:42:08	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 03:42:13	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:02:48s.  Time for last 1,000,000:    5s.  Last read position: chr22:46,397,185
INFO	2016-05-17 03:42:13	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 03:42:17	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:02:52s.  Time for last 1,000,000:    4s.  Last read position: chr2:62,948,277
INFO	2016-05-17 03:42:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:42:24	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:02:58s.  Time for last 1,000,000:    6s.  Last read position: chr2:143,249,593
INFO	2016-05-17 03:42:24	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 03:42:32	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:03:06s.  Time for last 1,000,000:    8s.  Last read position: chr2:224,846,662
INFO	2016-05-17 03:42:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:42:41	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:03:16s.  Time for last 1,000,000:    9s.  Last read position: chr3:48,868,492
INFO	2016-05-17 03:42:41	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 03:42:46	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:03:21s.  Time for last 1,000,000:    4s.  Last read position: chr3:129,003,328
INFO	2016-05-17 03:42:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:42:52	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:03:27s.  Time for last 1,000,000:    6s.  Last read position: chr4:4,861,395
INFO	2016-05-17 03:42:52	MarkDuplicates	Tracking 20 as yet unmatched pairs. 20 records in RAM.
INFO	2016-05-17 03:42:59	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:03:33s.  Time for last 1,000,000:    6s.  Last read position: chr4:93,102,928
INFO	2016-05-17 03:42:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:43:11	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:03:45s.  Time for last 1,000,000:   11s.  Last read position: chr4:183,838,259
INFO	2016-05-17 03:43:11	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-05-17 03:43:16	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:03:51s.  Time for last 1,000,000:    5s.  Last read position: chr5:79,047,278
INFO	2016-05-17 03:43:16	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 03:43:29	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:04:03s.  Time for last 1,000,000:   12s.  Last read position: chr5:148,318,403
INFO	2016-05-17 03:43:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:43:35	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:04:10s.  Time for last 1,000,000:    6s.  Last read position: chr6:33,050,238
INFO	2016-05-17 03:43:35	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-17 03:43:40	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:04:15s.  Time for last 1,000,000:    5s.  Last read position: chr6:113,899,418
INFO	2016-05-17 03:43:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:43:47	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:04:21s.  Time for last 1,000,000:    6s.  Last read position: chr7:18,272,034
INFO	2016-05-17 03:43:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:43:53	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:04:28s.  Time for last 1,000,000:    6s.  Last read position: chr7:100,807,772
INFO	2016-05-17 03:43:53	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-17 03:43:57	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:04:32s.  Time for last 1,000,000:    4s.  Last read position: chr8:17,659,060
INFO	2016-05-17 03:43:57	MarkDuplicates	Tracking 18 as yet unmatched pairs. 18 records in RAM.
INFO	2016-05-17 03:44:02	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:04:36s.  Time for last 1,000,000:    4s.  Last read position: chr8:98,083,502
INFO	2016-05-17 03:44:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:44:06	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:04:41s.  Time for last 1,000,000:    4s.  Last read position: chr9:25,528,635
INFO	2016-05-17 03:44:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:44:12	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:04:46s.  Time for last 1,000,000:    5s.  Last read position: chr9:128,014,743
INFO	2016-05-17 03:44:12	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-17 03:44:15	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:04:50s.  Time for last 1,000,000:    3s.  Last read position: chrM:526
INFO	2016-05-17 03:44:15	MarkDuplicates	Tracking 4836 as yet unmatched pairs. 4836 records in RAM.
INFO	2016-05-17 03:44:21	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:04:56s.  Time for last 1,000,000:    5s.  Last read position: chrM:1,364
INFO	2016-05-17 03:44:21	MarkDuplicates	Tracking 39884 as yet unmatched pairs. 39884 records in RAM.
INFO	2016-05-17 03:44:26	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:05:01s.  Time for last 1,000,000:    5s.  Last read position: chrM:2,234
INFO	2016-05-17 03:44:26	MarkDuplicates	Tracking 13050 as yet unmatched pairs. 13050 records in RAM.
INFO	2016-05-17 03:44:32	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:05:06s.  Time for last 1,000,000:    5s.  Last read position: chrM:2,852
INFO	2016-05-17 03:44:32	MarkDuplicates	Tracking 52080 as yet unmatched pairs. 52080 records in RAM.
INFO	2016-05-17 03:44:40	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:05:15s.  Time for last 1,000,000:    8s.  Last read position: chrM:3,329
INFO	2016-05-17 03:44:40	MarkDuplicates	Tracking 51892 as yet unmatched pairs. 51892 records in RAM.
INFO	2016-05-17 03:44:44	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:05:19s.  Time for last 1,000,000:    4s.  Last read position: chrM:3,635
INFO	2016-05-17 03:44:44	MarkDuplicates	Tracking 38918 as yet unmatched pairs. 38918 records in RAM.
INFO	2016-05-17 03:44:52	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:05:27s.  Time for last 1,000,000:    8s.  Last read position: chrM:4,101
INFO	2016-05-17 03:44:52	MarkDuplicates	Tracking 3178 as yet unmatched pairs. 3178 records in RAM.
INFO	2016-05-17 03:44:58	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:05:33s.  Time for last 1,000,000:    5s.  Last read position: chrM:5,389
INFO	2016-05-17 03:44:58	MarkDuplicates	Tracking 13692 as yet unmatched pairs. 13692 records in RAM.
INFO	2016-05-17 03:45:04	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:05:39s.  Time for last 1,000,000:    5s.  Last read position: chrM:6,371
INFO	2016-05-17 03:45:04	MarkDuplicates	Tracking 32398 as yet unmatched pairs. 32398 records in RAM.
INFO	2016-05-17 03:45:09	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:05:43s.  Time for last 1,000,000:    4s.  Last read position: chrM:7,108
INFO	2016-05-17 03:45:09	MarkDuplicates	Tracking 14492 as yet unmatched pairs. 14492 records in RAM.
INFO	2016-05-17 03:45:18	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:05:53s.  Time for last 1,000,000:    9s.  Last read position: chrM:8,137
INFO	2016-05-17 03:45:18	MarkDuplicates	Tracking 11036 as yet unmatched pairs. 11036 records in RAM.
INFO	2016-05-17 03:45:24	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:05:58s.  Time for last 1,000,000:    5s.  Last read position: chrM:9,306
INFO	2016-05-17 03:45:24	MarkDuplicates	Tracking 1794 as yet unmatched pairs. 1794 records in RAM.
INFO	2016-05-17 03:45:29	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:06:04s.  Time for last 1,000,000:    5s.  Last read position: chrM:10,272
INFO	2016-05-17 03:45:29	MarkDuplicates	Tracking 11920 as yet unmatched pairs. 11920 records in RAM.
INFO	2016-05-17 03:45:35	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:06:09s.  Time for last 1,000,000:    5s.  Last read position: chrM:11,161
INFO	2016-05-17 03:45:35	MarkDuplicates	Tracking 13680 as yet unmatched pairs. 13680 records in RAM.
INFO	2016-05-17 03:45:40	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:06:15s.  Time for last 1,000,000:    5s.  Last read position: chrM:11,795
INFO	2016-05-17 03:45:40	MarkDuplicates	Tracking 16174 as yet unmatched pairs. 16174 records in RAM.
INFO	2016-05-17 03:45:49	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:06:24s.  Time for last 1,000,000:    9s.  Last read position: chrM:12,491
INFO	2016-05-17 03:45:49	MarkDuplicates	Tracking 22070 as yet unmatched pairs. 22070 records in RAM.
INFO	2016-05-17 03:45:54	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:06:29s.  Time for last 1,000,000:    4s.  Last read position: chrM:13,071
INFO	2016-05-17 03:45:54	MarkDuplicates	Tracking 20364 as yet unmatched pairs. 20364 records in RAM.
INFO	2016-05-17 03:46:00	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:06:34s.  Time for last 1,000,000:    5s.  Last read position: chrM:13,567
INFO	2016-05-17 03:46:00	MarkDuplicates	Tracking 17760 as yet unmatched pairs. 17760 records in RAM.
INFO	2016-05-17 03:46:05	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:06:39s.  Time for last 1,000,000:    5s.  Last read position: chrM:14,291
INFO	2016-05-17 03:46:05	MarkDuplicates	Tracking 10800 as yet unmatched pairs. 10800 records in RAM.
INFO	2016-05-17 03:46:10	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:06:45s.  Time for last 1,000,000:    5s.  Last read position: chrM:15,066
INFO	2016-05-17 03:46:10	MarkDuplicates	Tracking 51198 as yet unmatched pairs. 51198 records in RAM.
INFO	2016-05-17 03:46:27	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:07:02s.  Time for last 1,000,000:   17s.  Last read position: chrM:15,442
INFO	2016-05-17 03:46:27	MarkDuplicates	Tracking 28976 as yet unmatched pairs. 28976 records in RAM.
INFO	2016-05-17 03:46:31	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:07:06s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,812
INFO	2016-05-17 03:46:31	MarkDuplicates	Tracking 45532 as yet unmatched pairs. 45532 records in RAM.
INFO	2016-05-17 03:46:35	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:07:10s.  Time for last 1,000,000:    3s.  Last read position: chrM:16,402
INFO	2016-05-17 03:46:35	MarkDuplicates	Tracking 28164 as yet unmatched pairs. 28164 records in RAM.
INFO	2016-05-17 03:46:39	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:07:14s.  Time for last 1,000,000:    4s.  Last read position: chrX:66,078,144
INFO	2016-05-17 03:46:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-17 03:46:43	MarkDuplicates	Read 62980862 records. 0 pairs never matched.
INFO	2016-05-17 03:46:45	MarkDuplicates	After buildSortedReadEndLists freeMemory: 2143568960; totalMemory: 2171600896; maxMemory: 3817865216
INFO	2016-05-17 03:46:45	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-05-17 03:46:45	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-05-17 03:47:03	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-05-17 03:47:19	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-05-17 03:47:21	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2179253424; totalMemory: 3160408064; maxMemory: 3817865216
INFO	2016-05-17 03:47:21	MarkDuplicates	Marking 25441512 records as duplicates.
INFO	2016-05-17 03:47:21	MarkDuplicates	Found 7054617 optical duplicate clusters.
INFO	2016-05-17 03:49:06	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:43s.  Time for last 10,000,000:  103s.  Last read position: chr16:52,758,578
INFO	2016-05-17 03:50:48	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:03:25s.  Time for last 10,000,000:  101s.  Last read position: chr22:46,397,185
INFO	2016-05-17 03:52:29	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:05:07s.  Time for last 10,000,000:  101s.  Last read position: chr5:148,318,403
INFO	2016-05-17 03:54:18	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:06:55s.  Time for last 10,000,000:  108s.  Last read position: chrM:1,364
INFO	2016-05-17 03:55:37	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:08:15s.  Time for last 10,000,000:   79s.  Last read position: chrM:9,306
INFO	2016-05-17 03:56:57	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:09:34s.  Time for last 10,000,000:   79s.  Last read position: chrM:15,812
INFO	2016-05-17 03:57:25	MarkDuplicates	Before output close freeMemory: 3216953816; totalMemory: 3247439872; maxMemory: 3817865216
INFO	2016-05-17 03:57:25	MarkDuplicates	After output close freeMemory: 3216952760; totalMemory: 3247439872; maxMemory: 3817865216
[Tue May 17 03:57:25 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 18.01 minutes.
Runtime.totalMemory()=3247439872
[bam_sort_core] merging from 26 files...

Num	13
ID	task.postalign_bam.nmsrt_bam_rep1.line_321.id_18
Name	nmsrt_bam rep1
Thread	thread_20
PID	7085

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

Start	2016-05-17 04:43:15
End	2016-05-17 05:00:15
Elapsed	00:16:59
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam
Dependencies

 
# SYS command. line 323

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

# SYS command. line 325

 samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-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 16 files...

Num	14
ID	task.postalign_bam.bam_to_bedpe_rep1.line_425.id_19
Name	bam_to_bedpe rep1
Thread	thread_20
PID	7839

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

Start	2016-05-17 05:00:15
End	2016-05-17 05:02:26
Elapsed	00:02:10
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Dependencies	nmsrt_bam rep1 nmsrt_bam rep1

 
# SYS command. line 427

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

# SYS command. line 430

 bedtools bamtobed -bedpe -mate1 -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz

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

Num	15
ID	task.postalign_bed.subsample_bedpe_rep1.line_116.id_20
Name	subsample_bedpe rep1
Thread	thread_20
PID	7917

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

Start	2016-05-17 05:02:27
End	2016-05-17 05:04:36
Elapsed	00:02:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz
Dependencies

 
# SYS command. line 118

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

# SYS command. line 120

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | grep -v "chrM" | shuf -n 17500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz

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

Num	16
ID	task.postalign_bam.bedpe_to_tag_rep1.line_465.id_21
Name	bedpe_to_tag rep1
Thread	thread_20
PID	8041

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

Start	2016-05-17 05:04:37
End	2016-05-17 05:06:23
Elapsed	00:01:46
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
Dependencies

 
# SYS command. line 467

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

# SYS command. line 469

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-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/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz

# SYS command. line 472

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz | grep -P -v 'chrM' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz; mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz

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

Num	17
ID	task.postalign_bed.shift_tag_rep1.line_140.id_22
Name	shift_tag rep1
Thread	thread_20
PID	8118

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

Start	2016-05-17 05:06:24
End	2016-05-17 05:07:43
Elapsed	00:01:19
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Dependencies

 
# SYS command. line 142

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

# SYS command. line 144

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-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/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz

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

Num	18
ID	task.postalign_bed.subsample_bedpe2tagrep1.line_89.id_23
Name	subsample_bedpe2tagrep1
Thread	thread_20
PID	8295

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

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

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
Dependencies

 
# SYS command. line 91

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

# SYS command. line 95

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-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/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz

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

Num	19
ID	task.postalign_bed.xcor_rep1.line_165.id_24
Name	xcor rep1
Thread	thread_20
PID	8365

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

Start	2016-05-17 05:09:06
End	2016-05-17 05:47:04
Elapsed	00:37:57
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf
Dependencies

 
# SYS command. line 167

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

# SYS command. line 171

 Rscript $(which run_spp_nodups.R) -rf \
			-c=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz -p=1 \
			-filtchr=chrM -savp=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf -out=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep1/ATAC13-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/ATAC13+14/qc/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp

# SYS command. line 175

 mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc

   
--------------------Stdout--------------------
################
ChIP data: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-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/ATAC13+14/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/ATAC13+14/qc/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf 
result filename: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep1/ATAC13-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/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz 
opened /tmp/Rtmpv0WmnA/ATAC13-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign214c47bc6d89
done. read 18000883 fragments
ChIP data read length 75 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1852198 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.222849954004333 
Top 3 estimates for fragment length 0 
Window half size 505 
Phantom peak location 65 
Phantom peak Correlation 0.2276399 
Normalized Strand cross-correlation coefficient (NSC) 1.203165 
Relative Strand Cross correlation Coefficient (RSC) 0.8870829 
Phantom Peak Quality Tag 0 
null device 
          1 

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

Num	20
ID	task.callpeak_macs2.macs2_atac_rep1.pval0.1.line_192.id_25
Name	macs2_atac rep1.pval0.1
Thread	thread_20
PID	8367

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

Start	2016-05-17 05:09:06
End	2016-05-17 05:30:51
Elapsed	00:21:45
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz
Dependencies

 
# SYS command. line 194

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

# SYS command. line 195

 LC_COLLATE=C

# SYS command. line 197

 macs2 callpeak \
			-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/signal/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/signal/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
INFO  @ Tue, 17 May 2016 05:09:09: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-01
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is on
 
INFO  @ Tue, 17 May 2016 05:09:09: #1 read tag files... 
INFO  @ Tue, 17 May 2016 05:09:09: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 05:09:12:  1000000 
INFO  @ Tue, 17 May 2016 05:09:15:  2000000 
INFO  @ Tue, 17 May 2016 05:09:18:  3000000 
INFO  @ Tue, 17 May 2016 05:09:21:  4000000 
INFO  @ Tue, 17 May 2016 05:09:23:  5000000 
INFO  @ Tue, 17 May 2016 05:09:25:  6000000 
INFO  @ Tue, 17 May 2016 05:09:27:  7000000 
INFO  @ Tue, 17 May 2016 05:09:30:  8000000 
INFO  @ Tue, 17 May 2016 05:09:33:  9000000 
INFO  @ Tue, 17 May 2016 05:09:36:  10000000 
INFO  @ Tue, 17 May 2016 05:09:39:  11000000 
INFO  @ Tue, 17 May 2016 05:09:42:  12000000 
INFO  @ Tue, 17 May 2016 05:09:45:  13000000 
INFO  @ Tue, 17 May 2016 05:09:48:  14000000 
INFO  @ Tue, 17 May 2016 05:09:49:  15000000 
INFO  @ Tue, 17 May 2016 05:09:51:  16000000 
INFO  @ Tue, 17 May 2016 05:09:52:  17000000 
INFO  @ Tue, 17 May 2016 05:09:54:  18000000 
INFO  @ Tue, 17 May 2016 05:09:56:  19000000 
INFO  @ Tue, 17 May 2016 05:09:57:  20000000 
INFO  @ Tue, 17 May 2016 05:09:59:  21000000 
INFO  @ Tue, 17 May 2016 05:10:01:  22000000 
INFO  @ Tue, 17 May 2016 05:10:02:  23000000 
INFO  @ Tue, 17 May 2016 05:10:05:  24000000 
INFO  @ Tue, 17 May 2016 05:10:07:  25000000 
INFO  @ Tue, 17 May 2016 05:10:10:  26000000 
INFO  @ Tue, 17 May 2016 05:10:13:  27000000 
INFO  @ Tue, 17 May 2016 05:10:16:  28000000 
INFO  @ Tue, 17 May 2016 05:10:19:  29000000 
INFO  @ Tue, 17 May 2016 05:10:21:  30000000 
INFO  @ Tue, 17 May 2016 05:10:23:  31000000 
INFO  @ Tue, 17 May 2016 05:10:24:  32000000 
INFO  @ Tue, 17 May 2016 05:10:26:  33000000 
INFO  @ Tue, 17 May 2016 05:10:29:  34000000 
INFO  @ Tue, 17 May 2016 05:10:32:  35000000 
INFO  @ Tue, 17 May 2016 05:10:35: #1 tag size is determined as 59 bps 
INFO  @ Tue, 17 May 2016 05:10:35: #1 tag size = 59 
INFO  @ Tue, 17 May 2016 05:10:35: #1  total tags in treatment: 35000000 
INFO  @ Tue, 17 May 2016 05:10:35: #1 finished! 
INFO  @ Tue, 17 May 2016 05:10:35: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 05:10:35: #2 Skipped... 
INFO  @ Tue, 17 May 2016 05:10:35: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 05:10:35: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 05:10:35: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 05:10:35: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 05:10:35: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 05:12:19: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 05:15:10: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 05:15:14: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 05:15:17: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 05:15:19: Done! 
INFO  @ Tue, 17 May 2016 05:15:31: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Tue, 17 May 2016 05:15:31: #1 read tag files... 
INFO  @ Tue, 17 May 2016 05:15:31: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 05:15:33:  1000000 
INFO  @ Tue, 17 May 2016 05:15:35:  2000000 
INFO  @ Tue, 17 May 2016 05:15:37:  3000000 
INFO  @ Tue, 17 May 2016 05:15:39:  4000000 
INFO  @ Tue, 17 May 2016 05:15:41:  5000000 
INFO  @ Tue, 17 May 2016 05:15:43:  6000000 
INFO  @ Tue, 17 May 2016 05:15:45:  7000000 
INFO  @ Tue, 17 May 2016 05:15:47:  8000000 
INFO  @ Tue, 17 May 2016 05:15:48:  9000000 
INFO  @ Tue, 17 May 2016 05:15:50:  10000000 
INFO  @ Tue, 17 May 2016 05:15:52:  11000000 
INFO  @ Tue, 17 May 2016 05:15:54:  12000000 
INFO  @ Tue, 17 May 2016 05:15:56:  13000000 
INFO  @ Tue, 17 May 2016 05:15:57:  14000000 
INFO  @ Tue, 17 May 2016 05:15:59:  15000000 
INFO  @ Tue, 17 May 2016 05:16:01:  16000000 
INFO  @ Tue, 17 May 2016 05:16:03:  17000000 
INFO  @ Tue, 17 May 2016 05:16:04:  18000000 
INFO  @ Tue, 17 May 2016 05:16:06:  19000000 
INFO  @ Tue, 17 May 2016 05:16:08:  20000000 
INFO  @ Tue, 17 May 2016 05:16:10:  21000000 
INFO  @ Tue, 17 May 2016 05:16:12:  22000000 
INFO  @ Tue, 17 May 2016 05:16:13:  23000000 
INFO  @ Tue, 17 May 2016 05:16:15:  24000000 
INFO  @ Tue, 17 May 2016 05:16:17:  25000000 
INFO  @ Tue, 17 May 2016 05:16:19:  26000000 
INFO  @ Tue, 17 May 2016 05:16:21:  27000000 
INFO  @ Tue, 17 May 2016 05:16:23:  28000000 
INFO  @ Tue, 17 May 2016 05:16:25:  29000000 
INFO  @ Tue, 17 May 2016 05:16:27:  30000000 
INFO  @ Tue, 17 May 2016 05:16:29:  31000000 
INFO  @ Tue, 17 May 2016 05:16:30:  32000000 
INFO  @ Tue, 17 May 2016 05:16:32:  33000000 
INFO  @ Tue, 17 May 2016 05:16:34:  34000000 
INFO  @ Tue, 17 May 2016 05:16:36:  35000000 
INFO  @ Tue, 17 May 2016 05:16:39: #1 tag size is determined as 59 bps 
INFO  @ Tue, 17 May 2016 05:16:39: #1 tag size = 59 
INFO  @ Tue, 17 May 2016 05:16:39: #1  total tags in treatment: 35000000 
INFO  @ Tue, 17 May 2016 05:16:39: #1 finished! 
INFO  @ Tue, 17 May 2016 05:16:39: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 05:16:39: #2 Skipped... 
INFO  @ Tue, 17 May 2016 05:16:39: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 05:16:39: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 05:16:39: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 05:16:39: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 05:16:39: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Tue, 17 May 2016 05:16:39: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 05:18:31: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 05:18:31: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 05:18:31: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 05:18:31: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 05:18:31: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 05:30:20: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 05:30:32: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 05:30:39: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_summits.bed 
INFO  @ Tue, 17 May 2016 05:30:43: Done!

Num	21
ID	task.callpeak_macs2.macs2_atac_rep1.line_192.id_26
Name	macs2_atac rep1
Thread	thread_20
PID	8378

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

Start	2016-05-17 05:09:06
End	2016-05-17 06:01:39
Elapsed	00:52:32
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.gappedPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/signal/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/signal/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig
Dependencies

 
# SYS command. line 194

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

# SYS command. line 195

 LC_COLLATE=C

# SYS command. line 197

 macs2 callpeak \
			-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/signal/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/signal/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
INFO  @ Tue, 17 May 2016 05:09:09: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is on
 
INFO  @ Tue, 17 May 2016 05:09:09: #1 read tag files... 
INFO  @ Tue, 17 May 2016 05:09:09: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 05:09:12:  1000000 
INFO  @ Tue, 17 May 2016 05:09:15:  2000000 
INFO  @ Tue, 17 May 2016 05:09:17:  3000000 
INFO  @ Tue, 17 May 2016 05:09:19:  4000000 
INFO  @ Tue, 17 May 2016 05:09:20:  5000000 
INFO  @ Tue, 17 May 2016 05:09:22:  6000000 
INFO  @ Tue, 17 May 2016 05:09:23:  7000000 
INFO  @ Tue, 17 May 2016 05:09:25:  8000000 
INFO  @ Tue, 17 May 2016 05:09:27:  9000000 
INFO  @ Tue, 17 May 2016 05:09:28:  10000000 
INFO  @ Tue, 17 May 2016 05:09:30:  11000000 
INFO  @ Tue, 17 May 2016 05:09:32:  12000000 
INFO  @ Tue, 17 May 2016 05:09:33:  13000000 
INFO  @ Tue, 17 May 2016 05:09:35:  14000000 
INFO  @ Tue, 17 May 2016 05:09:37:  15000000 
INFO  @ Tue, 17 May 2016 05:09:38:  16000000 
INFO  @ Tue, 17 May 2016 05:09:40:  17000000 
INFO  @ Tue, 17 May 2016 05:09:42:  18000000 
INFO  @ Tue, 17 May 2016 05:09:44:  19000000 
INFO  @ Tue, 17 May 2016 05:09:47:  20000000 
INFO  @ Tue, 17 May 2016 05:09:50:  21000000 
INFO  @ Tue, 17 May 2016 05:09:53:  22000000 
INFO  @ Tue, 17 May 2016 05:09:56:  23000000 
INFO  @ Tue, 17 May 2016 05:09:58:  24000000 
INFO  @ Tue, 17 May 2016 05:09:59:  25000000 
INFO  @ Tue, 17 May 2016 05:10:01:  26000000 
INFO  @ Tue, 17 May 2016 05:10:04:  27000000 
INFO  @ Tue, 17 May 2016 05:10:07:  28000000 
INFO  @ Tue, 17 May 2016 05:10:10:  29000000 
INFO  @ Tue, 17 May 2016 05:10:13:  30000000 
INFO  @ Tue, 17 May 2016 05:10:16:  31000000 
INFO  @ Tue, 17 May 2016 05:10:19:  32000000 
INFO  @ Tue, 17 May 2016 05:10:22:  33000000 
INFO  @ Tue, 17 May 2016 05:10:25:  34000000 
INFO  @ Tue, 17 May 2016 05:10:27:  35000000 
INFO  @ Tue, 17 May 2016 05:10:30: #1 tag size is determined as 59 bps 
INFO  @ Tue, 17 May 2016 05:10:30: #1 tag size = 59 
INFO  @ Tue, 17 May 2016 05:10:30: #1  total tags in treatment: 35000000 
INFO  @ Tue, 17 May 2016 05:10:30: #1 finished! 
INFO  @ Tue, 17 May 2016 05:10:30: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 05:10:30: #2 Skipped... 
INFO  @ Tue, 17 May 2016 05:10:30: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 05:10:30: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 05:10:30: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 05:10:30: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 05:10:30: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 05:12:11: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 05:14:40: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls 
INFO  @ Tue, 17 May 2016 05:14:44: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 05:14:47: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 05:14:49: Done! 
INFO  @ Tue, 17 May 2016 05:15:03: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Tue, 17 May 2016 05:15:03: #1 read tag files... 
INFO  @ Tue, 17 May 2016 05:15:03: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 05:15:05:  1000000 
INFO  @ Tue, 17 May 2016 05:15:07:  2000000 
INFO  @ Tue, 17 May 2016 05:15:09:  3000000 
INFO  @ Tue, 17 May 2016 05:15:11:  4000000 
INFO  @ Tue, 17 May 2016 05:15:12:  5000000 
INFO  @ Tue, 17 May 2016 05:15:14:  6000000 
INFO  @ Tue, 17 May 2016 05:15:15:  7000000 
INFO  @ Tue, 17 May 2016 05:15:17:  8000000 
INFO  @ Tue, 17 May 2016 05:15:19:  9000000 
INFO  @ Tue, 17 May 2016 05:15:20:  10000000 
INFO  @ Tue, 17 May 2016 05:15:22:  11000000 
INFO  @ Tue, 17 May 2016 05:15:24:  12000000 
INFO  @ Tue, 17 May 2016 05:15:25:  13000000 
INFO  @ Tue, 17 May 2016 05:15:27:  14000000 
INFO  @ Tue, 17 May 2016 05:15:29:  15000000 
INFO  @ Tue, 17 May 2016 05:15:30:  16000000 
INFO  @ Tue, 17 May 2016 05:15:32:  17000000 
INFO  @ Tue, 17 May 2016 05:15:34:  18000000 
INFO  @ Tue, 17 May 2016 05:15:36:  19000000 
INFO  @ Tue, 17 May 2016 05:15:38:  20000000 
INFO  @ Tue, 17 May 2016 05:15:40:  21000000 
INFO  @ Tue, 17 May 2016 05:15:42:  22000000 
INFO  @ Tue, 17 May 2016 05:15:43:  23000000 
INFO  @ Tue, 17 May 2016 05:15:45:  24000000 
INFO  @ Tue, 17 May 2016 05:15:47:  25000000 
INFO  @ Tue, 17 May 2016 05:15:48:  26000000 
INFO  @ Tue, 17 May 2016 05:15:50:  27000000 
INFO  @ Tue, 17 May 2016 05:15:52:  28000000 
INFO  @ Tue, 17 May 2016 05:15:53:  29000000 
INFO  @ Tue, 17 May 2016 05:15:55:  30000000 
INFO  @ Tue, 17 May 2016 05:15:57:  31000000 
INFO  @ Tue, 17 May 2016 05:15:58:  32000000 
INFO  @ Tue, 17 May 2016 05:16:00:  33000000 
INFO  @ Tue, 17 May 2016 05:16:02:  34000000 
INFO  @ Tue, 17 May 2016 05:16:03:  35000000 
INFO  @ Tue, 17 May 2016 05:16:06: #1 tag size is determined as 59 bps 
INFO  @ Tue, 17 May 2016 05:16:06: #1 tag size = 59 
INFO  @ Tue, 17 May 2016 05:16:06: #1  total tags in treatment: 35000000 
INFO  @ Tue, 17 May 2016 05:16:06: #1 finished! 
INFO  @ Tue, 17 May 2016 05:16:06: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 05:16:06: #2 Skipped... 
INFO  @ Tue, 17 May 2016 05:16:06: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 05:16:06: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 05:16:06: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 05:16:06: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 05:16:06: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Tue, 17 May 2016 05:16:06: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 05:17:32: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 05:17:32: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 05:17:32: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 05:17:32: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 05:17:32: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 05:25:16: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls 
INFO  @ Tue, 17 May 2016 05:25:19: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 05:25:21: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_summits.bed 
INFO  @ Tue, 17 May 2016 05:25:23: Done! 
INFO  @ Tue, 17 May 2016 05:25:29: Read and build treatment bedGraph... 
INFO  @ Tue, 17 May 2016 05:27:13: Read and build control bedGraph... 
INFO  @ Tue, 17 May 2016 05:27:53: Build scoreTrackII... 
INFO  @ Tue, 17 May 2016 05:28:30: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Tue, 17 May 2016 05:33:38: Write bedGraph of scores... 
INFO  @ Tue, 17 May 2016 05:36:38: Finished 'FE'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_FE.bdg'! 
INFO  @ Tue, 17 May 2016 05:46:29: Read and build treatment bedGraph... 
INFO  @ Tue, 17 May 2016 05:47:42: Read and build control bedGraph... 
INFO  @ Tue, 17 May 2016 05:48:11: Build scoreTrackII... 
INFO  @ Tue, 17 May 2016 05:48:46: Values in your input bedGraph files will be multiplied by 35.000000 ... 
INFO  @ Tue, 17 May 2016 05:52:49: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Tue, 17 May 2016 05:53:21: Write bedGraph of scores... 
INFO  @ Tue, 17 May 2016 05:55:26: Finished 'ppois'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_ppois.bdg'!

Num	22
ID	task.postalign_bed.pool_tag_reps.line_405.id_27
Name	pool_tag reps
Thread	thread_Root
PID	12092

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

Start	2016-05-17 06:01:40
End	2016-05-17 06:03:20
Elapsed	00:01:39
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz
Dependencies

 
# SYS command. line 407

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

# SYS command. line 408

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz  | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz

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

Num	23
ID	task.callpeak_macs2.macs2_atac_pooled.pval0.1.line_192.id_28
Name	macs2_atac pooled.pval0.1
Thread	thread_Root
PID	12178

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

Start	2016-05-17 06:03:21
End	2016-05-17 06:36:04
Elapsed	00:32:42
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.gappedPeak.gz
Dependencies

 
# SYS command. line 194

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

# SYS command. line 195

 LC_COLLATE=C

# SYS command. line 197

 macs2 callpeak \
			-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/align/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/signal/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/align/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/signal/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_control_lambda.bdg

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
INFO  @ Tue, 17 May 2016 06:03:25: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/align/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-01
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is on
 
INFO  @ Tue, 17 May 2016 06:03:25: #1 read tag files... 
INFO  @ Tue, 17 May 2016 06:03:25: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 06:03:26:  1000000 
INFO  @ Tue, 17 May 2016 06:03:28:  2000000 
INFO  @ Tue, 17 May 2016 06:03:30:  3000000 
INFO  @ Tue, 17 May 2016 06:03:31:  4000000 
INFO  @ Tue, 17 May 2016 06:03:33:  5000000 
INFO  @ Tue, 17 May 2016 06:03:34:  6000000 
INFO  @ Tue, 17 May 2016 06:03:36:  7000000 
INFO  @ Tue, 17 May 2016 06:03:38:  8000000 
INFO  @ Tue, 17 May 2016 06:03:39:  9000000 
INFO  @ Tue, 17 May 2016 06:03:41:  10000000 
INFO  @ Tue, 17 May 2016 06:03:42:  11000000 
INFO  @ Tue, 17 May 2016 06:03:44:  12000000 
INFO  @ Tue, 17 May 2016 06:03:46:  13000000 
INFO  @ Tue, 17 May 2016 06:03:47:  14000000 
INFO  @ Tue, 17 May 2016 06:03:49:  15000000 
INFO  @ Tue, 17 May 2016 06:03:50:  16000000 
INFO  @ Tue, 17 May 2016 06:03:52:  17000000 
INFO  @ Tue, 17 May 2016 06:03:54:  18000000 
INFO  @ Tue, 17 May 2016 06:03:55:  19000000 
INFO  @ Tue, 17 May 2016 06:03:57:  20000000 
INFO  @ Tue, 17 May 2016 06:03:58:  21000000 
INFO  @ Tue, 17 May 2016 06:04:00:  22000000 
INFO  @ Tue, 17 May 2016 06:04:02:  23000000 
INFO  @ Tue, 17 May 2016 06:04:03:  24000000 
INFO  @ Tue, 17 May 2016 06:04:05:  25000000 
INFO  @ Tue, 17 May 2016 06:04:06:  26000000 
INFO  @ Tue, 17 May 2016 06:04:08:  27000000 
INFO  @ Tue, 17 May 2016 06:04:10:  28000000 
INFO  @ Tue, 17 May 2016 06:04:11:  29000000 
INFO  @ Tue, 17 May 2016 06:04:13:  30000000 
INFO  @ Tue, 17 May 2016 06:04:14:  31000000 
INFO  @ Tue, 17 May 2016 06:04:16:  32000000 
INFO  @ Tue, 17 May 2016 06:04:18:  33000000 
INFO  @ Tue, 17 May 2016 06:04:19:  34000000 
INFO  @ Tue, 17 May 2016 06:04:21:  35000000 
INFO  @ Tue, 17 May 2016 06:04:22:  36000000 
INFO  @ Tue, 17 May 2016 06:04:24:  37000000 
INFO  @ Tue, 17 May 2016 06:04:26:  38000000 
INFO  @ Tue, 17 May 2016 06:04:27:  39000000 
INFO  @ Tue, 17 May 2016 06:04:29:  40000000 
INFO  @ Tue, 17 May 2016 06:04:30:  41000000 
INFO  @ Tue, 17 May 2016 06:04:32:  42000000 
INFO  @ Tue, 17 May 2016 06:04:34:  43000000 
INFO  @ Tue, 17 May 2016 06:04:35:  44000000 
INFO  @ Tue, 17 May 2016 06:04:37:  45000000 
INFO  @ Tue, 17 May 2016 06:04:38:  46000000 
INFO  @ Tue, 17 May 2016 06:04:40:  47000000 
INFO  @ Tue, 17 May 2016 06:04:42:  48000000 
INFO  @ Tue, 17 May 2016 06:04:43:  49000000 
INFO  @ Tue, 17 May 2016 06:04:45:  50000000 
INFO  @ Tue, 17 May 2016 06:04:46:  51000000 
INFO  @ Tue, 17 May 2016 06:04:48:  52000000 
INFO  @ Tue, 17 May 2016 06:04:50:  53000000 
INFO  @ Tue, 17 May 2016 06:04:51:  54000000 
INFO  @ Tue, 17 May 2016 06:04:53:  55000000 
INFO  @ Tue, 17 May 2016 06:04:55:  56000000 
INFO  @ Tue, 17 May 2016 06:04:56:  57000000 
INFO  @ Tue, 17 May 2016 06:04:58:  58000000 
INFO  @ Tue, 17 May 2016 06:04:59:  59000000 
INFO  @ Tue, 17 May 2016 06:05:01:  60000000 
INFO  @ Tue, 17 May 2016 06:05:03:  61000000 
INFO  @ Tue, 17 May 2016 06:05:04:  62000000 
INFO  @ Tue, 17 May 2016 06:05:06:  63000000 
INFO  @ Tue, 17 May 2016 06:05:07:  64000000 
INFO  @ Tue, 17 May 2016 06:05:09:  65000000 
INFO  @ Tue, 17 May 2016 06:05:11:  66000000 
INFO  @ Tue, 17 May 2016 06:05:12:  67000000 
INFO  @ Tue, 17 May 2016 06:05:14:  68000000 
INFO  @ Tue, 17 May 2016 06:05:19: #1 tag size is determined as 59 bps 
INFO  @ Tue, 17 May 2016 06:05:19: #1 tag size = 59 
INFO  @ Tue, 17 May 2016 06:05:19: #1  total tags in treatment: 68522502 
INFO  @ Tue, 17 May 2016 06:05:19: #1 finished! 
INFO  @ Tue, 17 May 2016 06:05:19: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 06:05:19: #2 Skipped... 
INFO  @ Tue, 17 May 2016 06:05:19: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 06:05:19: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 06:05:19: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 06:05:19: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 06:05:19: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 06:08:30: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 06:13:48: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 06:13:51: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 06:13:53: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 06:13:55: Done! 
INFO  @ Tue, 17 May 2016 06:14:07: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/align/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Tue, 17 May 2016 06:14:07: #1 read tag files... 
INFO  @ Tue, 17 May 2016 06:14:07: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 06:14:09:  1000000 
INFO  @ Tue, 17 May 2016 06:14:11:  2000000 
INFO  @ Tue, 17 May 2016 06:14:13:  3000000 
INFO  @ Tue, 17 May 2016 06:14:14:  4000000 
INFO  @ Tue, 17 May 2016 06:14:16:  5000000 
INFO  @ Tue, 17 May 2016 06:14:18:  6000000 
INFO  @ Tue, 17 May 2016 06:14:21:  7000000 
INFO  @ Tue, 17 May 2016 06:14:24:  8000000 
INFO  @ Tue, 17 May 2016 06:14:27:  9000000 
INFO  @ Tue, 17 May 2016 06:14:30:  10000000 
INFO  @ Tue, 17 May 2016 06:14:33:  11000000 
INFO  @ Tue, 17 May 2016 06:14:36:  12000000 
INFO  @ Tue, 17 May 2016 06:14:39:  13000000 
INFO  @ Tue, 17 May 2016 06:14:42:  14000000 
INFO  @ Tue, 17 May 2016 06:14:45:  15000000 
INFO  @ Tue, 17 May 2016 06:14:48:  16000000 
INFO  @ Tue, 17 May 2016 06:14:51:  17000000 
INFO  @ Tue, 17 May 2016 06:14:54:  18000000 
INFO  @ Tue, 17 May 2016 06:14:57:  19000000 
INFO  @ Tue, 17 May 2016 06:15:00:  20000000 
INFO  @ Tue, 17 May 2016 06:15:03:  21000000 
INFO  @ Tue, 17 May 2016 06:15:06:  22000000 
INFO  @ Tue, 17 May 2016 06:15:09:  23000000 
INFO  @ Tue, 17 May 2016 06:15:12:  24000000 
INFO  @ Tue, 17 May 2016 06:15:15:  25000000 
INFO  @ Tue, 17 May 2016 06:15:18:  26000000 
INFO  @ Tue, 17 May 2016 06:15:21:  27000000 
INFO  @ Tue, 17 May 2016 06:15:24:  28000000 
INFO  @ Tue, 17 May 2016 06:15:27:  29000000 
INFO  @ Tue, 17 May 2016 06:15:30:  30000000 
INFO  @ Tue, 17 May 2016 06:15:33:  31000000 
INFO  @ Tue, 17 May 2016 06:15:36:  32000000 
INFO  @ Tue, 17 May 2016 06:15:39:  33000000 
INFO  @ Tue, 17 May 2016 06:15:42:  34000000 
INFO  @ Tue, 17 May 2016 06:15:45:  35000000 
INFO  @ Tue, 17 May 2016 06:15:48:  36000000 
INFO  @ Tue, 17 May 2016 06:15:51:  37000000 
INFO  @ Tue, 17 May 2016 06:15:54:  38000000 
INFO  @ Tue, 17 May 2016 06:15:57:  39000000 
INFO  @ Tue, 17 May 2016 06:16:00:  40000000 
INFO  @ Tue, 17 May 2016 06:16:03:  41000000 
INFO  @ Tue, 17 May 2016 06:16:06:  42000000 
INFO  @ Tue, 17 May 2016 06:16:09:  43000000 
INFO  @ Tue, 17 May 2016 06:16:12:  44000000 
INFO  @ Tue, 17 May 2016 06:16:15:  45000000 
INFO  @ Tue, 17 May 2016 06:16:18:  46000000 
INFO  @ Tue, 17 May 2016 06:16:21:  47000000 
INFO  @ Tue, 17 May 2016 06:16:24:  48000000 
INFO  @ Tue, 17 May 2016 06:16:27:  49000000 
INFO  @ Tue, 17 May 2016 06:16:30:  50000000 
INFO  @ Tue, 17 May 2016 06:16:33:  51000000 
INFO  @ Tue, 17 May 2016 06:16:36:  52000000 
INFO  @ Tue, 17 May 2016 06:16:39:  53000000 
INFO  @ Tue, 17 May 2016 06:16:42:  54000000 
INFO  @ Tue, 17 May 2016 06:16:45:  55000000 
INFO  @ Tue, 17 May 2016 06:16:48:  56000000 
INFO  @ Tue, 17 May 2016 06:16:51:  57000000 
INFO  @ Tue, 17 May 2016 06:16:54:  58000000 
INFO  @ Tue, 17 May 2016 06:16:57:  59000000 
INFO  @ Tue, 17 May 2016 06:17:00:  60000000 
INFO  @ Tue, 17 May 2016 06:17:03:  61000000 
INFO  @ Tue, 17 May 2016 06:17:06:  62000000 
INFO  @ Tue, 17 May 2016 06:17:09:  63000000 
INFO  @ Tue, 17 May 2016 06:17:12:  64000000 
INFO  @ Tue, 17 May 2016 06:17:14:  65000000 
INFO  @ Tue, 17 May 2016 06:17:16:  66000000 
INFO  @ Tue, 17 May 2016 06:17:18:  67000000 
INFO  @ Tue, 17 May 2016 06:17:19:  68000000 
INFO  @ Tue, 17 May 2016 06:17:25: #1 tag size is determined as 59 bps 
INFO  @ Tue, 17 May 2016 06:17:25: #1 tag size = 59 
INFO  @ Tue, 17 May 2016 06:17:25: #1  total tags in treatment: 68522502 
INFO  @ Tue, 17 May 2016 06:17:25: #1 finished! 
INFO  @ Tue, 17 May 2016 06:17:25: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 06:17:25: #2 Skipped... 
INFO  @ Tue, 17 May 2016 06:17:25: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 06:17:25: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 06:17:25: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 06:17:25: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 06:17:25: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Tue, 17 May 2016 06:17:25: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 06:21:08: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 06:21:08: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 06:21:08: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 06:21:08: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 06:21:08: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 06:35:34: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.xls 
INFO  @ Tue, 17 May 2016 06:35:41: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 06:35:46: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_summits.bed 
INFO  @ Tue, 17 May 2016 06:35:49: Done!

Num	24
ID	task.callpeak_macs2.macs2_atac_pooled.line_192.id_29
Name	macs2_atac pooled
Thread	thread_Root
PID	12181

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

Start	2016-05-17 06:03:21
End	2016-05-17 07:23:52
Elapsed	01:20:30
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.gappedPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/signal/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/signal/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bigwig
Dependencies

 
# SYS command. line 194

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

# SYS command. line 195

 LC_COLLATE=C

# SYS command. line 197

 macs2 callpeak \
			-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/align/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/signal/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/align/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/signal/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_control_lambda.bdg

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
INFO  @ Tue, 17 May 2016 06:03:25: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is on
 
INFO  @ Tue, 17 May 2016 06:03:25: #1 read tag files... 
INFO  @ Tue, 17 May 2016 06:03:25: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 06:03:26:  1000000 
INFO  @ Tue, 17 May 2016 06:03:28:  2000000 
INFO  @ Tue, 17 May 2016 06:03:29:  3000000 
INFO  @ Tue, 17 May 2016 06:03:31:  4000000 
INFO  @ Tue, 17 May 2016 06:03:33:  5000000 
INFO  @ Tue, 17 May 2016 06:03:34:  6000000 
INFO  @ Tue, 17 May 2016 06:03:36:  7000000 
INFO  @ Tue, 17 May 2016 06:03:37:  8000000 
INFO  @ Tue, 17 May 2016 06:03:39:  9000000 
INFO  @ Tue, 17 May 2016 06:03:41:  10000000 
INFO  @ Tue, 17 May 2016 06:03:42:  11000000 
INFO  @ Tue, 17 May 2016 06:03:44:  12000000 
INFO  @ Tue, 17 May 2016 06:03:45:  13000000 
INFO  @ Tue, 17 May 2016 06:03:47:  14000000 
INFO  @ Tue, 17 May 2016 06:03:49:  15000000 
INFO  @ Tue, 17 May 2016 06:03:50:  16000000 
INFO  @ Tue, 17 May 2016 06:03:52:  17000000 
INFO  @ Tue, 17 May 2016 06:03:53:  18000000 
INFO  @ Tue, 17 May 2016 06:03:55:  19000000 
INFO  @ Tue, 17 May 2016 06:03:57:  20000000 
INFO  @ Tue, 17 May 2016 06:03:58:  21000000 
INFO  @ Tue, 17 May 2016 06:04:00:  22000000 
INFO  @ Tue, 17 May 2016 06:04:01:  23000000 
INFO  @ Tue, 17 May 2016 06:04:03:  24000000 
INFO  @ Tue, 17 May 2016 06:04:05:  25000000 
INFO  @ Tue, 17 May 2016 06:04:06:  26000000 
INFO  @ Tue, 17 May 2016 06:04:08:  27000000 
INFO  @ Tue, 17 May 2016 06:04:10:  28000000 
INFO  @ Tue, 17 May 2016 06:04:11:  29000000 
INFO  @ Tue, 17 May 2016 06:04:13:  30000000 
INFO  @ Tue, 17 May 2016 06:04:14:  31000000 
INFO  @ Tue, 17 May 2016 06:04:16:  32000000 
INFO  @ Tue, 17 May 2016 06:04:18:  33000000 
INFO  @ Tue, 17 May 2016 06:04:19:  34000000 
INFO  @ Tue, 17 May 2016 06:04:21:  35000000 
INFO  @ Tue, 17 May 2016 06:04:22:  36000000 
INFO  @ Tue, 17 May 2016 06:04:24:  37000000 
INFO  @ Tue, 17 May 2016 06:04:26:  38000000 
INFO  @ Tue, 17 May 2016 06:04:27:  39000000 
INFO  @ Tue, 17 May 2016 06:04:29:  40000000 
INFO  @ Tue, 17 May 2016 06:04:31:  41000000 
INFO  @ Tue, 17 May 2016 06:04:32:  42000000 
INFO  @ Tue, 17 May 2016 06:04:34:  43000000 
INFO  @ Tue, 17 May 2016 06:04:35:  44000000 
INFO  @ Tue, 17 May 2016 06:04:37:  45000000 
INFO  @ Tue, 17 May 2016 06:04:39:  46000000 
INFO  @ Tue, 17 May 2016 06:04:40:  47000000 
INFO  @ Tue, 17 May 2016 06:04:42:  48000000 
INFO  @ Tue, 17 May 2016 06:04:43:  49000000 
INFO  @ Tue, 17 May 2016 06:04:45:  50000000 
INFO  @ Tue, 17 May 2016 06:04:47:  51000000 
INFO  @ Tue, 17 May 2016 06:04:48:  52000000 
INFO  @ Tue, 17 May 2016 06:04:50:  53000000 
INFO  @ Tue, 17 May 2016 06:04:52:  54000000 
INFO  @ Tue, 17 May 2016 06:04:53:  55000000 
INFO  @ Tue, 17 May 2016 06:04:55:  56000000 
INFO  @ Tue, 17 May 2016 06:04:57:  57000000 
INFO  @ Tue, 17 May 2016 06:04:58:  58000000 
INFO  @ Tue, 17 May 2016 06:05:00:  59000000 
INFO  @ Tue, 17 May 2016 06:05:01:  60000000 
INFO  @ Tue, 17 May 2016 06:05:03:  61000000 
INFO  @ Tue, 17 May 2016 06:05:04:  62000000 
INFO  @ Tue, 17 May 2016 06:05:06:  63000000 
INFO  @ Tue, 17 May 2016 06:05:08:  64000000 
INFO  @ Tue, 17 May 2016 06:05:09:  65000000 
INFO  @ Tue, 17 May 2016 06:05:11:  66000000 
INFO  @ Tue, 17 May 2016 06:05:12:  67000000 
INFO  @ Tue, 17 May 2016 06:05:14:  68000000 
INFO  @ Tue, 17 May 2016 06:05:20: #1 tag size is determined as 59 bps 
INFO  @ Tue, 17 May 2016 06:05:20: #1 tag size = 59 
INFO  @ Tue, 17 May 2016 06:05:20: #1  total tags in treatment: 68522502 
INFO  @ Tue, 17 May 2016 06:05:20: #1 finished! 
INFO  @ Tue, 17 May 2016 06:05:20: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 06:05:20: #2 Skipped... 
INFO  @ Tue, 17 May 2016 06:05:20: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 06:05:20: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 06:05:20: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 06:05:20: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Tue, 17 May 2016 06:05:20: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 06:08:54: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 06:13:20: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.xls 
INFO  @ Tue, 17 May 2016 06:13:23: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.broadPeak 
INFO  @ Tue, 17 May 2016 06:13:25: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.gappedPeak 
INFO  @ Tue, 17 May 2016 06:13:27: Done! 
INFO  @ Tue, 17 May 2016 06:13:41: 
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Tue, 17 May 2016 06:13:41: #1 read tag files... 
INFO  @ Tue, 17 May 2016 06:13:41: #1 read treatment tags... 
INFO  @ Tue, 17 May 2016 06:13:43:  1000000 
INFO  @ Tue, 17 May 2016 06:13:45:  2000000 
INFO  @ Tue, 17 May 2016 06:13:46:  3000000 
INFO  @ Tue, 17 May 2016 06:13:48:  4000000 
INFO  @ Tue, 17 May 2016 06:13:49:  5000000 
INFO  @ Tue, 17 May 2016 06:13:51:  6000000 
INFO  @ Tue, 17 May 2016 06:13:53:  7000000 
INFO  @ Tue, 17 May 2016 06:13:55:  8000000 
INFO  @ Tue, 17 May 2016 06:13:56:  9000000 
INFO  @ Tue, 17 May 2016 06:13:58:  10000000 
INFO  @ Tue, 17 May 2016 06:14:00:  11000000 
INFO  @ Tue, 17 May 2016 06:14:01:  12000000 
INFO  @ Tue, 17 May 2016 06:14:03:  13000000 
INFO  @ Tue, 17 May 2016 06:14:04:  14000000 
INFO  @ Tue, 17 May 2016 06:14:06:  15000000 
INFO  @ Tue, 17 May 2016 06:14:08:  16000000 
INFO  @ Tue, 17 May 2016 06:14:09:  17000000 
INFO  @ Tue, 17 May 2016 06:14:11:  18000000 
INFO  @ Tue, 17 May 2016 06:14:12:  19000000 
INFO  @ Tue, 17 May 2016 06:14:14:  20000000 
INFO  @ Tue, 17 May 2016 06:14:16:  21000000 
INFO  @ Tue, 17 May 2016 06:14:17:  22000000 
INFO  @ Tue, 17 May 2016 06:14:19:  23000000 
INFO  @ Tue, 17 May 2016 06:14:20:  24000000 
INFO  @ Tue, 17 May 2016 06:14:22:  25000000 
INFO  @ Tue, 17 May 2016 06:14:24:  26000000 
INFO  @ Tue, 17 May 2016 06:14:25:  27000000 
INFO  @ Tue, 17 May 2016 06:14:27:  28000000 
INFO  @ Tue, 17 May 2016 06:14:29:  29000000 
INFO  @ Tue, 17 May 2016 06:14:30:  30000000 
INFO  @ Tue, 17 May 2016 06:14:32:  31000000 
INFO  @ Tue, 17 May 2016 06:14:34:  32000000 
INFO  @ Tue, 17 May 2016 06:14:35:  33000000 
INFO  @ Tue, 17 May 2016 06:14:37:  34000000 
INFO  @ Tue, 17 May 2016 06:14:38:  35000000 
INFO  @ Tue, 17 May 2016 06:14:40:  36000000 
INFO  @ Tue, 17 May 2016 06:14:41:  37000000 
INFO  @ Tue, 17 May 2016 06:14:43:  38000000 
INFO  @ Tue, 17 May 2016 06:14:45:  39000000 
INFO  @ Tue, 17 May 2016 06:14:46:  40000000 
INFO  @ Tue, 17 May 2016 06:14:48:  41000000 
INFO  @ Tue, 17 May 2016 06:14:50:  42000000 
INFO  @ Tue, 17 May 2016 06:14:51:  43000000 
INFO  @ Tue, 17 May 2016 06:14:53:  44000000 
INFO  @ Tue, 17 May 2016 06:14:54:  45000000 
INFO  @ Tue, 17 May 2016 06:14:56:  46000000 
INFO  @ Tue, 17 May 2016 06:14:58:  47000000 
INFO  @ Tue, 17 May 2016 06:14:59:  48000000 
INFO  @ Tue, 17 May 2016 06:15:01:  49000000 
INFO  @ Tue, 17 May 2016 06:15:03:  50000000 
INFO  @ Tue, 17 May 2016 06:15:04:  51000000 
INFO  @ Tue, 17 May 2016 06:15:06:  52000000 
INFO  @ Tue, 17 May 2016 06:15:07:  53000000 
INFO  @ Tue, 17 May 2016 06:15:09:  54000000 
INFO  @ Tue, 17 May 2016 06:15:11:  55000000 
INFO  @ Tue, 17 May 2016 06:15:12:  56000000 
INFO  @ Tue, 17 May 2016 06:15:14:  57000000 
INFO  @ Tue, 17 May 2016 06:15:16:  58000000 
INFO  @ Tue, 17 May 2016 06:15:17:  59000000 
INFO  @ Tue, 17 May 2016 06:15:19:  60000000 
INFO  @ Tue, 17 May 2016 06:15:20:  61000000 
INFO  @ Tue, 17 May 2016 06:15:22:  62000000 
INFO  @ Tue, 17 May 2016 06:15:24:  63000000 
INFO  @ Tue, 17 May 2016 06:15:25:  64000000 
INFO  @ Tue, 17 May 2016 06:15:27:  65000000 
INFO  @ Tue, 17 May 2016 06:15:28:  66000000 
INFO  @ Tue, 17 May 2016 06:15:30:  67000000 
INFO  @ Tue, 17 May 2016 06:15:32:  68000000 
INFO  @ Tue, 17 May 2016 06:15:37: #1 tag size is determined as 59 bps 
INFO  @ Tue, 17 May 2016 06:15:37: #1 tag size = 59 
INFO  @ Tue, 17 May 2016 06:15:37: #1  total tags in treatment: 68522502 
INFO  @ Tue, 17 May 2016 06:15:37: #1 finished! 
INFO  @ Tue, 17 May 2016 06:15:37: #2 Build Peak Model... 
INFO  @ Tue, 17 May 2016 06:15:37: #2 Skipped... 
INFO  @ Tue, 17 May 2016 06:15:37: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Tue, 17 May 2016 06:15:37: #2 Use 150 as fragment length 
INFO  @ Tue, 17 May 2016 06:15:37: #3 Call peaks... 
INFO  @ Tue, 17 May 2016 06:15:37: #3 Going to call summits inside each peak ... 
INFO  @ Tue, 17 May 2016 06:15:37: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Tue, 17 May 2016 06:15:37: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Tue, 17 May 2016 06:19:28: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Tue, 17 May 2016 06:19:28: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_treat_pileup.bdg 
INFO  @ Tue, 17 May 2016 06:19:28: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_control_lambda.bdg 
INFO  @ Tue, 17 May 2016 06:19:28: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Tue, 17 May 2016 06:19:28: #3 Call peaks for each chromosome... 
INFO  @ Tue, 17 May 2016 06:29:14: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.xls 
INFO  @ Tue, 17 May 2016 06:29:19: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.narrowPeak 
INFO  @ Tue, 17 May 2016 06:29:22: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_summits.bed 
INFO  @ Tue, 17 May 2016 06:29:24: Done! 
INFO  @ Tue, 17 May 2016 06:29:28: Read and build treatment bedGraph... 
INFO  @ Tue, 17 May 2016 06:32:05: Read and build control bedGraph... 
INFO  @ Tue, 17 May 2016 06:32:57: Build scoreTrackII... 
INFO  @ Tue, 17 May 2016 06:34:04: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Tue, 17 May 2016 06:40:56: Write bedGraph of scores... 
INFO  @ Tue, 17 May 2016 06:45:26: Finished 'FE'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_FE.bdg'! 
INFO  @ Tue, 17 May 2016 06:59:47: Read and build treatment bedGraph... 
INFO  @ Tue, 17 May 2016 07:01:50: Read and build control bedGraph... 
INFO  @ Tue, 17 May 2016 07:02:43: Build scoreTrackII... 
INFO  @ Tue, 17 May 2016 07:03:57: Values in your input bedGraph files will be multiplied by 68.522502 ... 
INFO  @ Tue, 17 May 2016 07:10:28: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Tue, 17 May 2016 07:11:27: Write bedGraph of scores... 
INFO  @ Tue, 17 May 2016 07:14:35: Finished 'ppois'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_ppois.bdg'!

Num	25
ID	task.callpeak_etc.filt_top_peaks_rep1.line_25.id_30
Name	filt_top_peaks rep1
Thread	thread_Root
PID	38281

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

Start	2016-05-17 07:23:52
End	2016-05-17 07:24:00
Elapsed	00:00:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz
Dependencies

 
# SYS command. line 27

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

# SYS command. line 30

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz

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

Num	26
ID	task.callpeak_etc.filt_top_peaks_rep1.line_25.id_31
Name	filt_top_peaks rep1
Thread	thread_Root
PID	38283

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

Start	2016-05-17 07:23:52
End	2016-05-17 07:23:59
Elapsed	00:00:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.gappedPeak.gz
Dependencies

 
# SYS command. line 27

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

# SYS command. line 30

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-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/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.gappedPeak.gz

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

Num	27
ID	task.callpeak_etc.filt_top_peaks_rep2.line_25.id_32
Name	filt_top_peaks rep2
Thread	thread_Root
PID	38294

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

Start	2016-05-17 07:23:52
End	2016-05-17 07:24:00
Elapsed	00:00:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz
Dependencies

 
# SYS command. line 27

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

# SYS command. line 30

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz

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

Num	28
ID	task.callpeak_etc.filt_top_peaks_rep2.line_25.id_33
Name	filt_top_peaks rep2
Thread	thread_Root
PID	38309

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

Start	2016-05-17 07:23:52
End	2016-05-17 07:23:59
Elapsed	00:00:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.gappedPeak.gz
Dependencies

 
# SYS command. line 27

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

# SYS command. line 30

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-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/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.gappedPeak.gz

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

Num	29
ID	task.callpeak_etc.filt_top_peaks_pooled.line_25.id_34
Name	filt_top_peaks pooled
Thread	thread_Root
PID	38327

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

Start	2016-05-17 07:23:53
End	2016-05-17 07:24:00
Elapsed	00:00:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz
Dependencies

 
# SYS command. line 27

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

# SYS command. line 30

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz

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

Num	30
ID	task.callpeak_etc.filt_top_peaks_pooled.line_25.id_35
Name	filt_top_peaks pooled
Thread	thread_Root
PID	38340

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

Start	2016-05-17 07:23:53
End	2016-05-17 07:23:59
Elapsed	00:00:06
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.gappedPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.gappedPeak.gz
Dependencies

 
# SYS command. line 27

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

# SYS command. line 30

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.gappedPeak.gz

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

Num	31
ID	task.idr.idr2_rep1_rep2.line_61.id_36
Name	idr2 rep1-rep2
Thread	thread_Root
PID	38642

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

Start	2016-05-17 07:24:01
End	2016-05-17 07:28:16
Elapsed	00:04:14
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt.png /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz
Dependencies

 
# SYS command. line 63

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

# SYS command. line 65

 idr --samples /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz --peak-list /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/pooled_rep/ATAC13-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/ATAC13+14/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/ATAC13+14/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/ATAC13+14/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/ATAC13+14/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/ATAC13+14/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/ATAC13+14/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/ATAC13+14/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/ATAC13+14/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/ATAC13+14/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/ATAC13+14/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac_py3/bin to PATH
Initial parameter values: [0.10 1.00 0.20 0.50]
Final parameter values: [1.86 0.70 0.85 0.33]
Number of reported peaks - 255611/255611 (100.0%)

Number of peaks passing IDR cutoff of 0.1 - 116280/255611 (45.5%)

Num	32
ID	task.base.line_414.id_39
Name	task.base.line_414.id_39
Thread	thread_Root
PID	38827

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

Start	2016-05-17 07:28:16
End	2016-05-17 07:28:17
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 416

 cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz

Num	33
ID	task.base.line_414.id_40
Name	task.base.line_414.id_40
Thread	thread_Root
PID	38832

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

Start	2016-05-17 07:28:16
End	2016-05-17 07:28:17
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 416

 cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz

Num	34
ID	task.base.line_414.id_41
Name	task.base.line_414.id_41
Thread	thread_Root
PID	38842

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

Start	2016-05-17 07:28:17
End	2016-05-17 07:28:17
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.gz
Dependencies

 
# SYS command. line 416

 cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.gz

Num	35
ID	task.base.line_414.id_42
Name	task.base.line_414.id_42
Thread	thread_Root
PID	38852

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

Start	2016-05-17 07:28:17
End	2016-05-17 07:28:17
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.13-col.bed.gz
Dependencies

 
# SYS command. line 416

 cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.13-col.bed.gz

Num	36
ID	task.idr.idr_final_qc.line_196.id_43
Name	idr final qc
Thread	thread_Root
PID	38877

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

Start	2016-05-17 07:28:17
End	2016-05-17 07:28:18
Elapsed	00:00:01
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/IDR_final.qc
Dependencies

 
# SYS command. line 198

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

# SYS command. line 200

 echo -e "Nt\t""Np\tconservative_set\toptimal_set\trescue_ratio\tself_consistency_ratio\treproducibility" > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/IDR_final.qc

# SYS command. line 201

 echo -e "116312\t""0\trep1-rep2\trep1-rep2\tInfinity\tNaN\t0" >> /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/IDR_final.qc

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

Num	37
ID	task.postalign_bam.srt_bam_rep1.line_345.id_44
Name	srt_bam rep1
Thread	thread_77
PID	38882

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

Start	2016-05-17 07:28:18
End	2016-05-17 07:56:19
Elapsed	00:28:01
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.srt.bam
Dependencies

 
# SYS command. line 347

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

# SYS command. line 353

 samtools sort /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.srt

# SYS command. line 354

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.srt.bam

# SYS command. line 356

 if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.srt.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.srt.bai" ]; then \
			cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.srt.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.srt.bai; \
			fi

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 40 files...

Num	38
ID	task.postalign_bam.srt_bam_rep2.line_345.id_45
Name	srt_bam rep2
Thread	thread_78
PID	38892

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

Start	2016-05-17 07:28:18
End	2016-05-17 07:55:47
Elapsed	00:27:29
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.srt.bam
Dependencies

 
# SYS command. line 347

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

# SYS command. line 353

 samtools sort /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.srt

# SYS command. line 354

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.srt.bam

# SYS command. line 356

 if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.srt.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.srt.bai" ]; then \
			cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.srt.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.srt.bai; \
			fi

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 38 files...

Num	39
ID	task.atac.ataqc_rep2.line_815.id_46
Name	ataqc rep2
Thread	thread_78
PID	40032

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

Start	2016-05-17 07:55:48
End	2016-05-17 09:50:05
Elapsed	01:54:17
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC14/ATAC14-trimmed-pair1.fastq.gz /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC14/ATAC14-trimmed-pair2.fastq.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep2/ATAC14-trimmed-pair1.trim.PE2SE.align.log /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.pbc.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep2/ATAC14-trimmed-pair1.trim.PE2SE.dup.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/signal/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep2/ATAC14-trimmed-pair1.PE2SE_qc.html /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep2/ATAC14-trimmed-pair1.PE2SE_qc.txt
Dependencies

 
# SYS command. line 817

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

# SYS command. line 821

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

# SYS command. line 823

 cd /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep2

# SYS command. line 825

 /users/pangwei/bds_atac/ataqc/run_ataqc.py \
			    --workdir /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep2 \
			    --outdir /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep2 \
			    --outprefix ATAC14-trimmed-pair1.PE2SE \
			    --genome hg19 \
			    --ref /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/encodeHg19Male.fa \
			    --tss /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/hg19_RefSeq_stranded.bed.gz \
			    --dnase /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_all_p10_ucsc.bed.gz \
			    --blacklist /mnt/data/ENCODE/blacklists/wgEncodeDacMapabilityConsensusExcludable.bed.gz \
			    --prom /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_prom_p2.bed.gz \
			    --enh /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_enh_p2.bed.gz \
			    --reg2map /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/dnase_avgs_reg2map_p10_merged_named.pvals.gz \
			    --meta /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/eid_to_mnemonic.txt \
			    --pbc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.pbc.qc\
			    --fastq1 /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC14/ATAC14-trimmed-pair1.fastq.gz --fastq2 /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC14/ATAC14-trimmed-pair2.fastq.gz \
			    --alignedbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.bam \
			    --alignmentlog /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep2/ATAC14-trimmed-pair1.trim.PE2SE.align.log \
			    --coordsortbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.srt.bam \
			    --duplog /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep2/ATAC14-trimmed-pair1.trim.PE2SE.dup.qc \
			    --finalbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.bam \
			    --finalbed /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz \
			    --bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/signal/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig \
			    --peaks /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz \
			     \
			    --idr_peaks /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz

   
--------------------Stdout--------------------
Run time: 1:54:13

 
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
ERROR	2016-05-17 08:00:06	ProcessExecutor	Warning messages:
ERROR	2016-05-17 08:00:06	ProcessExecutor	1: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
ERROR	2016-05-17 08:00:06	ProcessExecutor	  zero-length arrow is of indeterminate angle and so skipped
ERROR	2016-05-17 08:00:06	ProcessExecutor	2: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
ERROR	2016-05-17 08:00:06	ProcessExecutor	  zero-length arrow is of indeterminate angle and so skipped
ERROR	2016-05-17 08:00:06	ProcessExecutor	3: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
ERROR	2016-05-17 08:00:06	ProcessExecutor	  zero-length arrow is of indeterminate angle and so skipped
ERROR	2016-05-17 08:00:06	ProcessExecutor	4: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
ERROR	2016-05-17 08:00:06	ProcessExecutor	  zero-length arrow is of indeterminate angle and so skipped
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
[bam_sort_core] merging from 38 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
processing chromosomes
/users/pangwei/bds_atac/ataqc/run_ataqc.py:851: FutureWarning: sort(columns=....) is deprecated, use sort_values(by=.....)
  sorted_results = merged.sort('corr', ascending=True)

Num	40
ID	task.atac.ataqc_rep1.line_815.id_47
Name	ataqc rep1
Thread	thread_77
PID	40137

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

Start	2016-05-17 07:56:20
End	2016-05-17 10:01:02
Elapsed	02:04:41
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC13/ATAC13-trimmed-pair1.fastq.gz /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC13/ATAC13-trimmed-pair2.fastq.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep1/ATAC13-trimmed-pair1.trim.PE2SE.align.log /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.pbc.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep1/ATAC13-trimmed-pair1.trim.PE2SE.dup.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/signal/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep1/ATAC13-trimmed-pair1.PE2SE_qc.html /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep1/ATAC13-trimmed-pair1.PE2SE_qc.txt
Dependencies

 
# SYS command. line 817

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

# SYS command. line 821

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

# SYS command. line 823

 cd /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep1

# SYS command. line 825

 /users/pangwei/bds_atac/ataqc/run_ataqc.py \
			    --workdir /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep1 \
			    --outdir /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep1 \
			    --outprefix ATAC13-trimmed-pair1.PE2SE \
			    --genome hg19 \
			    --ref /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/encodeHg19Male.fa \
			    --tss /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/hg19_RefSeq_stranded.bed.gz \
			    --dnase /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_all_p10_ucsc.bed.gz \
			    --blacklist /mnt/data/ENCODE/blacklists/wgEncodeDacMapabilityConsensusExcludable.bed.gz \
			    --prom /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_prom_p2.bed.gz \
			    --enh /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_enh_p2.bed.gz \
			    --reg2map /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/dnase_avgs_reg2map_p10_merged_named.pvals.gz \
			    --meta /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/eid_to_mnemonic.txt \
			    --pbc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.pbc.qc\
			    --fastq1 /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC13/ATAC13-trimmed-pair1.fastq.gz --fastq2 /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC13/ATAC13-trimmed-pair2.fastq.gz \
			    --alignedbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.bam \
			    --alignmentlog /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep1/ATAC13-trimmed-pair1.trim.PE2SE.align.log \
			    --coordsortbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.srt.bam \
			    --duplog /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep1/ATAC13-trimmed-pair1.trim.PE2SE.dup.qc \
			    --finalbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.bam \
			    --finalbed /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz \
			    --bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/signal/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig \
			    --peaks /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz \
			     \
			    --idr_peaks /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz

   
--------------------Stdout--------------------
Run time: 2:04:38

 
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
ERROR	2016-05-17 08:00:43	ProcessExecutor	Warning messages:
ERROR	2016-05-17 08:00:43	ProcessExecutor	1: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
ERROR	2016-05-17 08:00:43	ProcessExecutor	  zero-length arrow is of indeterminate angle and so skipped
ERROR	2016-05-17 08:00:43	ProcessExecutor	2: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
ERROR	2016-05-17 08:00:43	ProcessExecutor	  zero-length arrow is of indeterminate angle and so skipped
ERROR	2016-05-17 08:00:43	ProcessExecutor	3: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
ERROR	2016-05-17 08:00:43	ProcessExecutor	  zero-length arrow is of indeterminate angle and so skipped
ERROR	2016-05-17 08:00:43	ProcessExecutor	4: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
ERROR	2016-05-17 08:00:43	ProcessExecutor	  zero-length arrow is of indeterminate angle and so skipped
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
[bam_sort_core] merging from 40 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
processing chromosomes
/users/pangwei/bds_atac/ataqc/run_ataqc.py:851: FutureWarning: sort(columns=....) is deprecated, use sort_values(by=.....)
  sorted_results = merged.sort('corr', ascending=True)

Num	41
ID	task.report.line_418.id_48
Name	task.report.line_418.id_48
Thread	thread_Root
PID	46868

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

Start	2016-05-17 10:01:04
End	2016-05-17 10:01:06
Elapsed	00:00:02
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.hammock.gz
Dependencies

 
# SYS command. line 420

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

# SYS command. line 421

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.tmp

# SYS command. line 423

 /users/pangwei/bds_atac/utils/narrowpeak_idr.py /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.hammock

# SYS command. line 424

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.tmp

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

Num	42
ID	task.report.line_418.id_49
Name	task.report.line_418.id_49
Thread	thread_Root
PID	46936

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

Start	2016-05-17 10:01:07
End	2016-05-17 10:01:12
Elapsed	00:00:05
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.hammock.gz
Dependencies

 
# SYS command. line 420

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

# SYS command. line 421

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.tmp

# SYS command. line 423

 /users/pangwei/bds_atac/utils/narrowpeak.py /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.hammock

# SYS command. line 424

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.tmp

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

Num	43
ID	task.report.line_418.id_50
Name	task.report.line_418.id_50
Thread	thread_Root
PID	47009

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

Start	2016-05-17 10:01:13
End	2016-05-17 10:01:19
Elapsed	00:00:05
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.hammock.gz
Dependencies

 
# SYS command. line 420

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

# SYS command. line 421

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.tmp

# SYS command. line 423

 /users/pangwei/bds_atac/utils/narrowpeak.py /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.hammock

# SYS command. line 424

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/peak/macs2/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.tmp

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

Num	44
ID	task.report_graphviz.line_93.id_51
Name	task.report_graphviz.line_93.id_51
Thread	thread_Root
PID	47100

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

Start	2016-05-17 10:01:19
End	2016-05-17 10:01:21
Elapsed	00:00:02
Timeout	00:00:-1
Wall Timeout	100 days

Input files
Output files
Dependencies

 
# SYS command. line 94

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

# SYS command. line 95

 dot -Tsvg /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/report/workflow.dot > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/report/workflow.svg

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

Num	45
ID	task.report.line_383.id_56
Name	task.report.line_383.id_56
Thread	thread_Root
PID	47103

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

Start	2016-05-17 10:01:19
End	2016-05-17 10:01:21
Elapsed	00:00:01
Timeout	00:00:-1
Wall Timeout	100 days

Input files
Output files
Dependencies

 
# SYS command. line 384

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

# SYS command. line 385

 gs -dFirstPage=1 -dLastPage=1 -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -r110x110 \
			-dUseCropBox -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -sDEVICE=png16m \
			-sOutputFile=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.png \
			-r144 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep1/ATAC13-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf

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

Num	46
ID	task.report.line_383.id_57
Name	task.report.line_383.id_57
Thread	thread_Root
PID	47115

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

Start	2016-05-17 10:01:20
End	2016-05-17 10:01:21
Elapsed	00:00:01
Timeout	00:00:-1
Wall Timeout	100 days

Input files
Output files
Dependencies

 
# SYS command. line 384

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

# SYS command. line 385

 gs -dFirstPage=1 -dLastPage=1 -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -r110x110 \
			-dUseCropBox -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -sDEVICE=png16m \
			-sOutputFile=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.png \
			-r144 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf

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

Type	Name	Value
string	_	/usr/bin/bds
string	_LMFILES_	/software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/samtools/1.2:/software/modulefiles/bedtools/2.23.0:/software/modulefiles/rsem/1.2.21
string	_ZSH_TMUX_FIXED_CONFIG	/users/pangwei/.oh-my-zsh/plugins/tmux/tmux.extra.conf
bool	allowEmpty	false
string[]	args	[-out_dir, /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14, -num_rep, 2, -fastq1_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC13/ATAC13-trimmed-pair1.fastq.gz, -fastq1_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC13/ATAC13-trimmed-pair2.fastq.gz, -fastq2_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC14/ATAC14-trimmed-pair1.fastq.gz, -fastq2_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC14/ATAC14-trimmed-pair2.fastq.gz, -subsample, 17500000, -true_rep, -species, hg19]
string	C_INCLUDE_PATH	/software/samtools/samtools-1.2/include/htslib
bool	canFail	false
int	cpus	1
int	cpusLocal	48
int	day	86400
real	E	2.718281828459045
int	G	1073741824
string	HOME	/users/pangwei/
int	hour	3600
int	K	1024
string	LANG	en_US.UTF-8
string	LC_CTYPE	en_US.UTF-8
string	LD_LIBRARY_PATH	/software/samtools/samtools-1.2/lib:/usr/local/cudnn-3/lib64/:/usr/local/cudnn-3/lib64/
string	LESS	-R
string	LOADEDMODULES	modsappsdir/modsappsdir:samtools/1.2:bedtools/2.23.0:rsem/1.2.21
string	LOGNAME	pangwei
string	LSCOLORS	Gxfxcxdxbxegedabagacad
int	M	1048576
string	MAIL	/var/mail/pangwei
string	MANPATH	/software/samtools/samtools-1.2/share/man:/usr/share/man
int	mem	-1
int	minute	60
string	MODULE_VERSION	3.2.10
string	MODULE_VERSION_STACK	3.2.10
string	MODULEPATH	/usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles
string	MODULESAPPSDIR	/software
string	MODULESHOME	/software/env_module/3.2.10
string	node
int	P	1125899906842624
string	PAGER	less
string	PATH	/software/RSEM/rsem-1.2.21/:/software/bedtools/2.23.0/bin:/software/samtools/samtools-1.2/bin:/users/pangwei/anaconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
real	PI	3.141592653589793
string	ppwd	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata
string	programName	atac.bds
string	programPath	/users/pangwei/bds_atac/atac.bds
string	PWD	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata
string	PYTHONPATH	/home/jisraeli/src/caffe_atac/python/:/users/pangwei/stemcells:/home/jisraeli/src/caffe_atac/python/:/users/pangwei/stemcells:
string	queue
int	retry	0
string	SAMTOOLS_HOME	/software/samtools/samtools-1.2/bin
string	SHELL	/usr/bin/zsh
string	SHLVL	3
string	SSH_AUTH_SOCK	/tmp/ssh-5gr8qSU2WF/agent.74700
string	SSH_CLIENT	171.65.76.244 36245 22
string	SSH_CONNECTION	171.65.76.244 49273 171.65.76.236 22
string	SSH_TTY	/dev/pts/0
string	system	local
int	T	1099511627776
string	TERM	screen
string	THEANO_FLAGS	device=gpu6,floatX=float32,warn_float64=warn,optimizer_excluding=cudnn
int	timeout	-1
string	TMUX	/tmp/tmux-1077/default,106699,3
string	TMUX_PANE	%3
string	USER	pangwei
string	UTIL_SCRIPTS_DIR	/users/pangwei/av_scripts
int	walltimeout	8640000
int	week	604800
string	WWW	/srv/www/kundaje/pangwei
string	XDG_RUNTIME_DIR	/run/user/1077
string	XDG_SESSION_ID	1907
string	ZSH	/users/pangwei//.oh-my-zsh
string	ZSH_TMUX_TERM	screen

BigDataScript report: atac.bds

Timeline

Task Graph

Parallel (threads) details

Task details

Global scope