Script file	/users/pangwei/bds_atac/atac.bds
Program ID	atac.bds.20160513_182610_353
Start time	2016-05-13 18:26:10
Run time	10:04:33.931
Tasks executed	20
Tasks failed	2
Tasks failed names	macs2_atac rep2.pval0.1 macs2_atac rep2
Arguments*	[-out_dir, /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4, -num_rep, 2, -fastq1_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC3/ATAC3-trimmed-pair1.fastq.gz, -fastq1_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC3/ATAC3-trimmed-pair2.fastq.gz, -fastq2_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC4/ATAC4-trimmed-pair1.fastq.gz, -fastq2_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC4/ATAC4-trimmed-pair2.fastq.gz, -subsample, 17500000, -true_rep, -species, hg19]
System*	local
Cpus*	1
Exit value	1

Thread ID	Parent	Tasks
thread_Root	None
thread_21	thread_Root	atac.bds.20160513_182610_353_parallel_21/task.align_bowtie2.bowtie2_PE_rep2.line_133.id_6 atac.bds.20160513_182610_353_parallel_21/task.postalign_bam.dedup_bam_PE_rep2.line_215.id_8 atac.bds.20160513_182610_353_parallel_21/task.postalign_bam.nmsrt_bam_rep2.line_321.id_10 atac.bds.20160513_182610_353_parallel_21/task.postalign_bam.bam_to_bedpe_rep2.line_425.id_11 atac.bds.20160513_182610_353_parallel_21/task.postalign_bed.subsample_bedpe_rep2.line_116.id_12 atac.bds.20160513_182610_353_parallel_21/task.postalign_bam.bedpe_to_tag_rep2.line_465.id_13 atac.bds.20160513_182610_353_parallel_21/task.postalign_bed.shift_tag_rep2.line_140.id_14 atac.bds.20160513_182610_353_parallel_21/task.postalign_bed.subsample_bedpe2tagrep2.line_89.id_15 atac.bds.20160513_182610_353_parallel_21/task.postalign_bed.xcor_rep2.line_165.id_16 atac.bds.20160513_182610_353_parallel_21/task.callpeak_macs2.macs2_atac_rep2.pval0.1.line_192.id_17 atac.bds.20160513_182610_353_parallel_21/task.callpeak_macs2.macs2_atac_rep2.line_192.id_18
thread_20	thread_Root	atac.bds.20160513_182610_353_parallel_20/task.align_bowtie2.bowtie2_PE_rep1.line_133.id_7 atac.bds.20160513_182610_353_parallel_20/task.postalign_bam.dedup_bam_PE_rep1.line_215.id_9 atac.bds.20160513_182610_353_parallel_20/task.postalign_bam.nmsrt_bam_rep1.line_321.id_19 atac.bds.20160513_182610_353_parallel_20/task.postalign_bam.bam_to_bedpe_rep1.line_425.id_20 atac.bds.20160513_182610_353_parallel_20/task.postalign_bed.subsample_bedpe_rep1.line_116.id_21 atac.bds.20160513_182610_353_parallel_20/task.postalign_bam.bedpe_to_tag_rep1.line_465.id_22 atac.bds.20160513_182610_353_parallel_20/task.postalign_bed.shift_tag_rep1.line_140.id_23 atac.bds.20160513_182610_353_parallel_20/task.postalign_bed.subsample_bedpe2tagrep1.line_89.id_24 atac.bds.20160513_182610_353_parallel_20/task.postalign_bed.xcor_rep1.line_165.id_25

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.align_bowtie2.bowtie2_PE_rep2.line_133.id_6
Name	bowtie2_PE rep2
Thread	thread_21
PID	103517

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

Start	2016-05-13 18:26:11
End	2016-05-14 00:45:58
Elapsed	06:19:46
Timeout	00:00:-1
Wall Timeout	100 days

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

# SYS command. line 142

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

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 28 files...

Num	2
ID	task.align_bowtie2.bowtie2_PE_rep1.line_133.id_7
Name	bowtie2_PE rep1
Thread	thread_20
PID	103521

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

Start	2016-05-13 18:26:11
End	2016-05-14 02:16:42
Elapsed	07:50:30
Timeout	00:00:-1
Wall Timeout	100 days

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

# SYS command. line 142

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

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 37 files...

Num	3
ID	task.postalign_bam.dedup_bam_PE_rep2.line_215.id_8
Name	dedup_bam_PE rep2
Thread	thread_21
PID	1097

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

Start	2016-05-14 00:45:59
End	2016-05-14 02:51:58
Elapsed	02:05:59
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2/ATAC4-trimmed-pair1.trim.PE2SE.dup.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2/ATAC4-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/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.dupmark

# SYS command. line 230

 echo

# SYS command. line 237

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

# SYS command. line 238

 samtools view -F 1804 -f 2 -u /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.filt

# SYS command. line 239

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

# SYS command. line 243

 export _JAVA_OPTIONS="-Xms256M -Xmx4G -XX:ParallelGCThreads=1"

# SYS command. line 244

 export MAX_JAVA_MEM="12G"

# SYS command. line 247

 if [ -f ${PICARDROOT}/MarkDuplicates.jar ]; then \
			java -Xmx4G -jar ${PICARDROOT}/MarkDuplicates.jar \
				INPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2/ATAC4-trimmed-pair1.trim.PE2SE.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
			else \
			java -Xmx4G -jar ${PICARDROOT}/picard.jar MarkDuplicates \
				INPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2/ATAC4-trimmed-pair1.trim.PE2SE.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
			fi

# SYS command. line 265

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

# SYS command. line 267

 samtools view -F 1804 -f 2 -b /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.filt.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 269

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

# SYS command. line 271

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

# SYS command. line 275

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

# SYS command. line 286

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

# SYS command. line 287

 bedtools bamtobed -bedpe -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam | \
			awk 'BEGIN{OFS="\t"}{print $1,$2,$4,$6,$9,$10}' | \
			grep -v 'chrM' | sort | uniq -c | \
			awk 'BEGIN{mt=0;m0=0;m1=0;m2=0} ($1==1){m1=m1+1} ($1==2){m2=m2+1} {m0=m0+1} {mt=mt+$1} END{printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1/m2}' > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.pbc.qc

# SYS command. line 291

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

# SYS command. line 293

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

# SYS command. line 294

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

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



 
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 21 files...
[bam_sort_core] merging from 21 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Sat May 14 01:49:48 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2/ATAC4-trimmed-pair1.trim.PE2SE.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Sat May 14 01:49:48 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	2016-05-14 01:49:48	MarkDuplicates	Start of doWork freeMemory: 254890432; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-14 01:49:48	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-05-14 01:49:48	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-05-14 01:50:07	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:17s.  Time for last 1,000,000:   17s.  Last read position: chr10:74,124,139
INFO	2016-05-14 01:50:07	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-14 01:50:16	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:27s.  Time for last 1,000,000:    9s.  Last read position: chr10:132,107,667
INFO	2016-05-14 01:50:16	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 01:50:28	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:39s.  Time for last 1,000,000:   12s.  Last read position: chr11:60,823,574
INFO	2016-05-14 01:50:28	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 01:50:36	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:46s.  Time for last 1,000,000:    7s.  Last read position: chr11:117,293,957
INFO	2016-05-14 01:50:36	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 01:50:43	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:54s.  Time for last 1,000,000:    7s.  Last read position: chr12:47,193,361
INFO	2016-05-14 01:50:43	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 01:50:50	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:01:01s.  Time for last 1,000,000:    6s.  Last read position: chr12:110,185,504
INFO	2016-05-14 01:50:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 01:50:57	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:01:08s.  Time for last 1,000,000:    7s.  Last read position: chr13:53,245,407
INFO	2016-05-14 01:50:57	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 01:51:06	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:01:16s.  Time for last 1,000,000:    8s.  Last read position: chr14:32,548,618
INFO	2016-05-14 01:51:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 01:51:15	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:01:25s.  Time for last 1,000,000:    8s.  Last read position: chr14:96,525,271
INFO	2016-05-14 01:51:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 01:51:18	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:01:29s.  Time for last 1,000,000:    3s.  Last read position: chr15:70,478,482
INFO	2016-05-14 01:51:18	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 01:51:28	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:39s.  Time for last 1,000,000:    9s.  Last read position: chr16:21,584,966
INFO	2016-05-14 01:51:28	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-14 01:51:34	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:44s.  Time for last 1,000,000:    5s.  Last read position: chr16:87,904,667
INFO	2016-05-14 01:51:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 01:51:40	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:51s.  Time for last 1,000,000:    6s.  Last read position: chr17:47,979,114
INFO	2016-05-14 01:51:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 01:51:49	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:59s.  Time for last 1,000,000:    8s.  Last read position: chr18:24,183,934
INFO	2016-05-14 01:51:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 01:52:10	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:02:20s.  Time for last 1,000,000:   21s.  Last read position: chr19:7,973,961
INFO	2016-05-14 01:52:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 01:52:16	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:02:26s.  Time for last 1,000,000:    6s.  Last read position: chr19:56,834,594
INFO	2016-05-14 01:52:16	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 01:52:25	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:02:35s.  Time for last 1,000,000:    8s.  Last read position: chr1:39,296,860
INFO	2016-05-14 01:52:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 01:52:30	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:02:41s.  Time for last 1,000,000:    5s.  Last read position: chr1:100,970,703
INFO	2016-05-14 01:52:30	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 01:52:36	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:02:46s.  Time for last 1,000,000:    5s.  Last read position: chr1:185,283,547
INFO	2016-05-14 01:52:36	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 01:52:44	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:02:55s.  Time for last 1,000,000:    8s.  Last read position: chr1:247,443,074
INFO	2016-05-14 01:52:44	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 01:52:50	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:03:01s.  Time for last 1,000,000:    5s.  Last read position: chr20:54,327,904
INFO	2016-05-14 01:52:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 01:52:57	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:03:08s.  Time for last 1,000,000:    7s.  Last read position: chr22:29,402,968
INFO	2016-05-14 01:52:57	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-14 01:53:07	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:03:17s.  Time for last 1,000,000:    9s.  Last read position: chr2:27,876,314
INFO	2016-05-14 01:53:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 01:53:14	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:03:25s.  Time for last 1,000,000:    7s.  Last read position: chr2:96,976,623
INFO	2016-05-14 01:53:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 01:53:22	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:03:33s.  Time for last 1,000,000:    8s.  Last read position: chr2:166,679,206
INFO	2016-05-14 01:53:22	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 01:53:34	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:03:45s.  Time for last 1,000,000:   12s.  Last read position: chr2:233,323,025
INFO	2016-05-14 01:53:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 01:53:41	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:03:52s.  Time for last 1,000,000:    6s.  Last read position: chr3:47,474,263
INFO	2016-05-14 01:53:41	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 01:53:49	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:04:00s.  Time for last 1,000,000:    7s.  Last read position: chr3:119,087,487
INFO	2016-05-14 01:53:49	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-14 01:53:55	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:04:05s.  Time for last 1,000,000:    5s.  Last read position: chr3:184,245,820
INFO	2016-05-14 01:53:55	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 01:54:19	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:04:29s.  Time for last 1,000,000:   24s.  Last read position: chr4:53,171,418
INFO	2016-05-14 01:54:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 01:54:26	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:04:37s.  Time for last 1,000,000:    7s.  Last read position: chr4:131,567,992
INFO	2016-05-14 01:54:26	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 01:54:33	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:04:44s.  Time for last 1,000,000:    7s.  Last read position: chr5:14,553,706
INFO	2016-05-14 01:54:33	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 01:54:39	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:04:50s.  Time for last 1,000,000:    6s.  Last read position: chr5:93,791,390
INFO	2016-05-14 01:54:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 01:54:47	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:04:58s.  Time for last 1,000,000:    7s.  Last read position: chr5:156,679,778
INFO	2016-05-14 01:54:47	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 01:54:52	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:05:03s.  Time for last 1,000,000:    5s.  Last read position: chr6:33,247,358
INFO	2016-05-14 01:54:52	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 01:54:58	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:05:08s.  Time for last 1,000,000:    5s.  Last read position: chr6:105,502,535
INFO	2016-05-14 01:54:58	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 01:55:05	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:05:16s.  Time for last 1,000,000:    7s.  Last read position: chr7:598,814
INFO	2016-05-14 01:55:05	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 01:55:10	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:05:21s.  Time for last 1,000,000:    5s.  Last read position: chr7:70,486,662
INFO	2016-05-14 01:55:10	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 01:55:18	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:05:29s.  Time for last 1,000,000:    7s.  Last read position: chr7:137,650,210
INFO	2016-05-14 01:55:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 01:55:26	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:05:37s.  Time for last 1,000,000:    7s.  Last read position: chr8:40,706,520
INFO	2016-05-14 01:55:26	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 01:55:37	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:05:48s.  Time for last 1,000,000:   11s.  Last read position: chr8:117,247,323
INFO	2016-05-14 01:55:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 01:55:43	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:05:54s.  Time for last 1,000,000:    5s.  Last read position: chr9:35,662,360
INFO	2016-05-14 01:55:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 01:55:51	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:06:02s.  Time for last 1,000,000:    7s.  Last read position: chr9:127,962,882
INFO	2016-05-14 01:55:51	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-14 01:55:56	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:06:07s.  Time for last 1,000,000:    5s.  Last read position: chrM:1,857
INFO	2016-05-14 01:55:56	MarkDuplicates	Tracking 6770 as yet unmatched pairs. 6770 records in RAM.
INFO	2016-05-14 01:56:06	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:06:17s.  Time for last 1,000,000:    9s.  Last read position: chrM:4,023
INFO	2016-05-14 01:56:06	MarkDuplicates	Tracking 4528 as yet unmatched pairs. 4528 records in RAM.
INFO	2016-05-14 01:56:13	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:06:24s.  Time for last 1,000,000:    6s.  Last read position: chrM:7,802
INFO	2016-05-14 01:56:13	MarkDuplicates	Tracking 7300 as yet unmatched pairs. 7300 records in RAM.
INFO	2016-05-14 01:56:16	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:06:27s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,063
INFO	2016-05-14 01:56:16	MarkDuplicates	Tracking 9242 as yet unmatched pairs. 9242 records in RAM.
INFO	2016-05-14 01:56:20	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:06:31s.  Time for last 1,000,000:    4s.  Last read position: chrM:13,559
INFO	2016-05-14 01:56:20	MarkDuplicates	Tracking 4852 as yet unmatched pairs. 4852 records in RAM.
INFO	2016-05-14 01:56:25	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:06:35s.  Time for last 1,000,000:    4s.  Last read position: chrM:15,838
INFO	2016-05-14 01:56:25	MarkDuplicates	Tracking 13874 as yet unmatched pairs. 13874 records in RAM.
INFO	2016-05-14 01:56:29	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:06:39s.  Time for last 1,000,000:    4s.  Last read position: chrX:48,553,495
INFO	2016-05-14 01:56:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 01:56:35	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:06:46s.  Time for last 1,000,000:    6s.  Last read position: chrX:133,871,633
INFO	2016-05-14 01:56:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 01:56:38	MarkDuplicates	Read 51292280 records. 0 pairs never matched.
INFO	2016-05-14 01:56:46	MarkDuplicates	After buildSortedReadEndLists freeMemory: 2975166640; totalMemory: 3003121664; maxMemory: 3817865216
INFO	2016-05-14 01:56:46	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-05-14 01:56:46	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-05-14 01:57:01	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-05-14 01:57:26	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-05-14 01:57:27	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2011622112; totalMemory: 2993160192; maxMemory: 3817865216
INFO	2016-05-14 01:57:27	MarkDuplicates	Marking 14581496 records as duplicates.
INFO	2016-05-14 01:57:27	MarkDuplicates	Found 1420693 optical duplicate clusters.
INFO	2016-05-14 01:59:51	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:02:23s.  Time for last 10,000,000:  143s.  Last read position: chr15:70,478,482
INFO	2016-05-14 02:02:13	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:04:45s.  Time for last 10,000,000:  141s.  Last read position: chr1:247,443,074
INFO	2016-05-14 02:04:39	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:07:11s.  Time for last 10,000,000:  146s.  Last read position: chr4:53,171,418
INFO	2016-05-14 02:07:06	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:09:38s.  Time for last 10,000,000:  147s.  Last read position: chr8:40,706,520
INFO	2016-05-14 02:09:12	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:11:44s.  Time for last 10,000,000:  125s.  Last read position: chrX:48,553,495
INFO	2016-05-14 02:09:30	MarkDuplicates	Before output close freeMemory: 3043175216; totalMemory: 3073376256; maxMemory: 3817865216
INFO	2016-05-14 02:09:30	MarkDuplicates	After output close freeMemory: 3043174160; totalMemory: 3073376256; maxMemory: 3817865216
[Sat May 14 02:09:30 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 19.71 minutes.
Runtime.totalMemory()=3073376256
[bam_sort_core] merging from 21 files...

Num	4
ID	task.postalign_bam.dedup_bam_PE_rep1.line_215.id_9
Name	dedup_bam_PE rep1
Thread	thread_20
PID	10102

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

Start	2016-05-14 02:16:43
End	2016-05-14 04:15:50
Elapsed	01:59:06
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1/ATAC3-trimmed-pair1.trim.PE2SE.dup.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1/ATAC3-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/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.dupmark

# SYS command. line 230

 echo

# SYS command. line 237

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

# SYS command. line 238

 samtools view -F 1804 -f 2 -u /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.filt

# SYS command. line 239

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

# SYS command. line 243

 export _JAVA_OPTIONS="-Xms256M -Xmx4G -XX:ParallelGCThreads=1"

# SYS command. line 244

 export MAX_JAVA_MEM="12G"

# SYS command. line 247

 if [ -f ${PICARDROOT}/MarkDuplicates.jar ]; then \
			java -Xmx4G -jar ${PICARDROOT}/MarkDuplicates.jar \
				INPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1/ATAC3-trimmed-pair1.trim.PE2SE.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
			else \
			java -Xmx4G -jar ${PICARDROOT}/picard.jar MarkDuplicates \
				INPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1/ATAC3-trimmed-pair1.trim.PE2SE.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
			fi

# SYS command. line 265

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

# SYS command. line 267

 samtools view -F 1804 -f 2 -b /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.filt.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 269

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

# SYS command. line 271

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

# SYS command. line 275

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

# SYS command. line 286

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

# SYS command. line 287

 bedtools bamtobed -bedpe -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam | \
			awk 'BEGIN{OFS="\t"}{print $1,$2,$4,$6,$9,$10}' | \
			grep -v 'chrM' | sort | uniq -c | \
			awk 'BEGIN{mt=0;m0=0;m1=0;m2=0} ($1==1){m1=m1+1} ($1==2){m2=m2+1} {m0=m0+1} {mt=mt+$1} END{printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1/m2}' > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.pbc.qc

# SYS command. line 291

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

# SYS command. line 293

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

# SYS command. line 294

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

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



 
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 25 files...
[bam_sort_core] merging from 25 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Sat May 14 03:21:56 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1/ATAC3-trimmed-pair1.trim.PE2SE.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Sat May 14 03:21:56 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	2016-05-14 03:21:56	MarkDuplicates	Start of doWork freeMemory: 254889872; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-14 03:21:56	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-05-14 03:21:56	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-05-14 03:22:10	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:13s.  Time for last 1,000,000:   13s.  Last read position: chr10:86,549,094
INFO	2016-05-14 03:22:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 03:22:21	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:25s.  Time for last 1,000,000:   11s.  Last read position: chr11:17,193,753
INFO	2016-05-14 03:22:21	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 03:22:25	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:29s.  Time for last 1,000,000:    3s.  Last read position: chr11:93,861,804
INFO	2016-05-14 03:22:25	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-05-14 03:22:31	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:35s.  Time for last 1,000,000:    6s.  Last read position: chr12:33,262,622
INFO	2016-05-14 03:22:31	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 03:22:40	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:44s.  Time for last 1,000,000:    8s.  Last read position: chr12:114,193,095
INFO	2016-05-14 03:22:40	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 03:22:47	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:50s.  Time for last 1,000,000:    6s.  Last read position: chr13:81,871,720
INFO	2016-05-14 03:22:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 03:22:52	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:56s.  Time for last 1,000,000:    5s.  Last read position: chr14:71,352,686
INFO	2016-05-14 03:22:52	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 03:22:58	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:01:02s.  Time for last 1,000,000:    5s.  Last read position: chr15:62,773,208
INFO	2016-05-14 03:22:58	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 03:23:03	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:01:07s.  Time for last 1,000,000:    4s.  Last read position: chr16:27,298,244
INFO	2016-05-14 03:23:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 03:23:09	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:01:12s.  Time for last 1,000,000:    5s.  Last read position: chr17:15,135,692
INFO	2016-05-14 03:23:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 03:23:14	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:17s.  Time for last 1,000,000:    5s.  Last read position: chr17:80,281,273
INFO	2016-05-14 03:23:14	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 03:23:22	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:26s.  Time for last 1,000,000:    8s.  Last read position: chr19:3,586,853
INFO	2016-05-14 03:23:22	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-14 03:23:28	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:32s.  Time for last 1,000,000:    6s.  Last read position: chr1:1,398,031
INFO	2016-05-14 03:23:28	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 03:23:34	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:37s.  Time for last 1,000,000:    5s.  Last read position: chr1:57,728,395
INFO	2016-05-14 03:23:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 03:23:50	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:54s.  Time for last 1,000,000:   16s.  Last read position: chr1:160,772,328
INFO	2016-05-14 03:23:50	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 03:23:53	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:57s.  Time for last 1,000,000:    3s.  Last read position: chr1:234,436,520
INFO	2016-05-14 03:23:53	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 03:23:57	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:02:00s.  Time for last 1,000,000:    3s.  Last read position: chr20:57,267,687
INFO	2016-05-14 03:23:57	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-14 03:24:00	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:02:04s.  Time for last 1,000,000:    3s.  Last read position: chr22:43,628,911
INFO	2016-05-14 03:24:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 03:24:05	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:02:09s.  Time for last 1,000,000:    5s.  Last read position: chr2:63,277,263
INFO	2016-05-14 03:24:05	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-14 03:24:09	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:02:13s.  Time for last 1,000,000:    3s.  Last read position: chr2:151,761,396
INFO	2016-05-14 03:24:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 03:24:14	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:02:18s.  Time for last 1,000,000:    5s.  Last read position: chr2:232,610,604
INFO	2016-05-14 03:24:14	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-14 03:24:19	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:02:23s.  Time for last 1,000,000:    5s.  Last read position: chr3:55,670,831
INFO	2016-05-14 03:24:19	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 03:24:27	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:02:31s.  Time for last 1,000,000:    8s.  Last read position: chr3:142,297,945
INFO	2016-05-14 03:24:27	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 03:24:31	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:02:35s.  Time for last 1,000,000:    4s.  Last read position: chr4:20,868,619
INFO	2016-05-14 03:24:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 03:24:37	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:02:40s.  Time for last 1,000,000:    5s.  Last read position: chr4:115,779,520
INFO	2016-05-14 03:24:37	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 03:24:42	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:02:45s.  Time for last 1,000,000:    5s.  Last read position: chr5:13,575,179
INFO	2016-05-14 03:24:42	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 03:24:49	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:02:52s.  Time for last 1,000,000:    6s.  Last read position: chr5:109,374,820
INFO	2016-05-14 03:24:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 03:24:53	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:02:56s.  Time for last 1,000,000:    4s.  Last read position: chr5:176,925,430
INFO	2016-05-14 03:24:53	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-14 03:24:58	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:03:02s.  Time for last 1,000,000:    5s.  Last read position: chr6:72,198,121
INFO	2016-05-14 03:24:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 03:25:21	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:03:25s.  Time for last 1,000,000:   23s.  Last read position: chr6:157,010,060
INFO	2016-05-14 03:25:21	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 03:25:27	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:03:31s.  Time for last 1,000,000:    5s.  Last read position: chr7:68,837,457
INFO	2016-05-14 03:25:27	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 03:25:33	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:03:37s.  Time for last 1,000,000:    5s.  Last read position: chr7:150,422,796
INFO	2016-05-14 03:25:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 03:25:38	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:03:42s.  Time for last 1,000,000:    5s.  Last read position: chr8:74,842,120
INFO	2016-05-14 03:25:38	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 03:25:42	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:03:45s.  Time for last 1,000,000:    3s.  Last read position: chr9:8,650,915
INFO	2016-05-14 03:25:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 03:25:45	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:03:49s.  Time for last 1,000,000:    3s.  Last read position: chr9:119,134,365
INFO	2016-05-14 03:25:45	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 03:25:48	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:03:52s.  Time for last 1,000,000:    3s.  Last read position: chrM:518
INFO	2016-05-14 03:25:48	MarkDuplicates	Tracking 9690 as yet unmatched pairs. 9690 records in RAM.
INFO	2016-05-14 03:25:53	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:03:57s.  Time for last 1,000,000:    4s.  Last read position: chrM:1,316
INFO	2016-05-14 03:25:53	MarkDuplicates	Tracking 53188 as yet unmatched pairs. 53188 records in RAM.
INFO	2016-05-14 03:25:56	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:04:00s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,010
INFO	2016-05-14 03:25:56	MarkDuplicates	Tracking 40586 as yet unmatched pairs. 40586 records in RAM.
INFO	2016-05-14 03:25:59	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:04:03s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,766
INFO	2016-05-14 03:25:59	MarkDuplicates	Tracking 102666 as yet unmatched pairs. 102666 records in RAM.
INFO	2016-05-14 03:26:04	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:04:07s.  Time for last 1,000,000:    4s.  Last read position: chrM:3,235
INFO	2016-05-14 03:26:04	MarkDuplicates	Tracking 90636 as yet unmatched pairs. 90636 records in RAM.
INFO	2016-05-14 03:26:09	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:04:12s.  Time for last 1,000,000:    4s.  Last read position: chrM:3,582
INFO	2016-05-14 03:26:09	MarkDuplicates	Tracking 31062 as yet unmatched pairs. 31062 records in RAM.
INFO	2016-05-14 03:26:17	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:04:21s.  Time for last 1,000,000:    8s.  Last read position: chrM:4,015
INFO	2016-05-14 03:26:17	MarkDuplicates	Tracking 26592 as yet unmatched pairs. 26592 records in RAM.
INFO	2016-05-14 03:26:21	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:04:25s.  Time for last 1,000,000:    4s.  Last read position: chrM:5,311
INFO	2016-05-14 03:26:21	MarkDuplicates	Tracking 21132 as yet unmatched pairs. 21132 records in RAM.
INFO	2016-05-14 03:26:27	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:04:31s.  Time for last 1,000,000:    5s.  Last read position: chrM:6,286
INFO	2016-05-14 03:26:27	MarkDuplicates	Tracking 51006 as yet unmatched pairs. 51006 records in RAM.
INFO	2016-05-14 03:26:40	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:04:43s.  Time for last 1,000,000:   12s.  Last read position: chrM:6,679
INFO	2016-05-14 03:26:40	MarkDuplicates	Tracking 25158 as yet unmatched pairs. 25158 records in RAM.
INFO	2016-05-14 03:26:46	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:04:50s.  Time for last 1,000,000:    6s.  Last read position: chrM:7,785
INFO	2016-05-14 03:26:46	MarkDuplicates	Tracking 33782 as yet unmatched pairs. 33782 records in RAM.
INFO	2016-05-14 03:26:52	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:04:56s.  Time for last 1,000,000:    5s.  Last read position: chrM:8,479
INFO	2016-05-14 03:26:52	MarkDuplicates	Tracking 54136 as yet unmatched pairs. 54136 records in RAM.
INFO	2016-05-14 03:26:58	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:05:02s.  Time for last 1,000,000:    6s.  Last read position: chrM:9,710
INFO	2016-05-14 03:26:58	MarkDuplicates	Tracking 48660 as yet unmatched pairs. 48660 records in RAM.
INFO	2016-05-14 03:27:02	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:05:05s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,429
INFO	2016-05-14 03:27:02	MarkDuplicates	Tracking 33750 as yet unmatched pairs. 33750 records in RAM.
INFO	2016-05-14 03:27:05	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:05:08s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,316
INFO	2016-05-14 03:27:05	MarkDuplicates	Tracking 29254 as yet unmatched pairs. 29254 records in RAM.
INFO	2016-05-14 03:27:08	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:05:12s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,023
INFO	2016-05-14 03:27:08	MarkDuplicates	Tracking 34896 as yet unmatched pairs. 34896 records in RAM.
INFO	2016-05-14 03:27:11	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:05:15s.  Time for last 1,000,000:    3s.  Last read position: chrM:12,657
INFO	2016-05-14 03:27:11	MarkDuplicates	Tracking 60992 as yet unmatched pairs. 60992 records in RAM.
INFO	2016-05-14 03:27:18	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:05:22s.  Time for last 1,000,000:    6s.  Last read position: chrM:13,285
INFO	2016-05-14 03:27:18	MarkDuplicates	Tracking 37076 as yet unmatched pairs. 37076 records in RAM.
INFO	2016-05-14 03:27:24	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:05:28s.  Time for last 1,000,000:    6s.  Last read position: chrM:13,872
INFO	2016-05-14 03:27:24	MarkDuplicates	Tracking 46814 as yet unmatched pairs. 46814 records in RAM.
INFO	2016-05-14 03:27:30	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:05:33s.  Time for last 1,000,000:    5s.  Last read position: chrM:14,799
INFO	2016-05-14 03:27:30	MarkDuplicates	Tracking 9138 as yet unmatched pairs. 9138 records in RAM.
INFO	2016-05-14 03:27:35	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:05:39s.  Time for last 1,000,000:    5s.  Last read position: chrM:15,268
INFO	2016-05-14 03:27:35	MarkDuplicates	Tracking 48378 as yet unmatched pairs. 48378 records in RAM.
INFO	2016-05-14 03:27:40	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:05:44s.  Time for last 1,000,000:    4s.  Last read position: chrM:15,690
INFO	2016-05-14 03:27:40	MarkDuplicates	Tracking 62450 as yet unmatched pairs. 62450 records in RAM.
INFO	2016-05-14 03:27:47	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:05:50s.  Time for last 1,000,000:    6s.  Last read position: chrM:16,300
INFO	2016-05-14 03:27:47	MarkDuplicates	Tracking 50600 as yet unmatched pairs. 50600 records in RAM.
INFO	2016-05-14 03:28:13	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:06:16s.  Time for last 1,000,000:   26s.  Last read position: chrX:42,602,871
INFO	2016-05-14 03:28:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 03:28:17	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:06:21s.  Time for last 1,000,000:    4s.  Last read position: chrX:144,542,281
INFO	2016-05-14 03:28:17	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-14 03:28:18	MarkDuplicates	Read 60132266 records. 0 pairs never matched.
INFO	2016-05-14 03:28:19	MarkDuplicates	After buildSortedReadEndLists freeMemory: 3904790856; totalMemory: 3932160000; maxMemory: 3932160000
INFO	2016-05-14 03:28:19	MarkDuplicates	Will retain up to 122880000 duplicate indices before spilling to disk.
INFO	2016-05-14 03:28:19	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-05-14 03:28:31	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-05-14 03:28:46	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-05-14 03:28:48	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2835623664; totalMemory: 3845128192; maxMemory: 3845128192
INFO	2016-05-14 03:28:48	MarkDuplicates	Marking 36491126 records as duplicates.
INFO	2016-05-14 03:28:48	MarkDuplicates	Found 6655038 optical duplicate clusters.
INFO	2016-05-14 03:30:26	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:37s.  Time for last 10,000,000:   97s.  Last read position: chr17:15,135,692
INFO	2016-05-14 03:32:12	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:03:23s.  Time for last 10,000,000:  105s.  Last read position: chr2:151,761,396
INFO	2016-05-14 03:34:14	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:05:25s.  Time for last 10,000,000:  122s.  Last read position: chr6:157,010,060
INFO	2016-05-14 03:35:56	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:07:06s.  Time for last 10,000,000:  101s.  Last read position: chrM:3,235
INFO	2016-05-14 03:37:27	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:08:38s.  Time for last 10,000,000:   91s.  Last read position: chrM:11,316
INFO	2016-05-14 03:38:57	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:10:08s.  Time for last 10,000,000:   90s.  Last read position: chrX:144,542,281
INFO	2016-05-14 03:38:58	MarkDuplicates	Before output close freeMemory: 3981889232; totalMemory: 4012376064; maxMemory: 4012376064
INFO	2016-05-14 03:38:58	MarkDuplicates	After output close freeMemory: 3981888176; totalMemory: 4012376064; maxMemory: 4012376064
[Sat May 14 03:38:58 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 17.04 minutes.
Runtime.totalMemory()=4012376064
[bam_sort_core] merging from 25 files...

Num	5
ID	task.postalign_bam.nmsrt_bam_rep2.line_321.id_10
Name	nmsrt_bam rep2
Thread	thread_21
PID	11441

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

Start	2016-05-14 02:51:58
End	2016-05-14 03:09:33
Elapsed	00:17:34
Timeout	00:00:-1
Wall Timeout	100 days

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

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 15 files...

Num	6
ID	task.postalign_bam.bam_to_bedpe_rep2.line_425.id_11
Name	bam_to_bedpe rep2
Thread	thread_21
PID	13930

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

Start	2016-05-14 03:09:33
End	2016-05-14 03:12:05
Elapsed	00:02:32
Timeout	00:00:-1
Wall Timeout	100 days

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

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

Num	7
ID	task.postalign_bed.subsample_bedpe_rep2.line_116.id_12
Name	subsample_bedpe rep2
Thread	thread_21
PID	14004

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

Start	2016-05-14 03:12:07
End	2016-05-14 03:13:58
Elapsed	00:01:51
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-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/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | grep -v "chrM" | shuf -n 17500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz

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

Num	8
ID	task.postalign_bam.bedpe_to_tag_rep2.line_465.id_13
Name	bedpe_to_tag rep2
Thread	thread_21
PID	14544

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

Start	2016-05-14 03:13:59
End	2016-05-14 03:15:48
Elapsed	00:01:49
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-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/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz | awk 'BEGIN{OFS="\t"}{printf "%s\t%s\t%s\tN\t1000\t%s\n%s\t%s\t%s\tN\t1000\t%s\n",$1,$2,$3,$9,$4,$5,$6,$10}' | \
			gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz

# SYS command. line 472

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

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

Num	9
ID	task.postalign_bed.shift_tag_rep2.line_140.id_14
Name	shift_tag rep2
Thread	thread_21
PID	14616

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

Start	2016-05-14 03:15:49
End	2016-05-14 03:17:15
Elapsed	00:01:25
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-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/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz | awk -F $'\t' 'BEGIN {OFS = FS}{ if ($6 == "+") {$2 = $2 + 4} else if ($6 == "-") {$3 = $3 - 5} print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz

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

Num	10
ID	task.postalign_bed.subsample_bedpe2tagrep2.line_89.id_15
Name	subsample_bedpe2tagrep2
Thread	thread_21
PID	14685

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

Start	2016-05-14 03:17:16
End	2016-05-14 03:18:41
Elapsed	00:01:25
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-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/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | \
			grep -v "chrM" | shuf -n 25000000 | \
			awk 'BEGIN{OFS="\t"}{print $1,$2,$3,"N","1000",$9}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz

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

Num	11
ID	task.postalign_bed.xcor_rep2.line_165.id_16
Name	xcor rep2
Thread	thread_21
PID	14754

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

Start	2016-05-14 03:18:42
End	2016-05-14 03:49:34
Elapsed	00:30:52
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.25.cc.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/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz -p=1 \
			-filtchr=chrM -savp=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf -out=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc -speak=0

# SYS command. line 174

 sed -r 's/,[^\t]+//g' /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp

# SYS command. line 175

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

   
--------------------Stdout--------------------
################
ChIP data: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz 
Control data: NA 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 0 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: NA 
Output Directory: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2 
narrowPeak output file name: NA 
regionPeak output file name: NA 
Rdata filename: NA 
plot pdf filename: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf 
result filename: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz 
opened /tmp/Rtmpffv4EE/ATAC4-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign3a377d754413
done. read 17871057 fragments
ChIP data read length 75 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1943348 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.201234881423893 
Top 3 estimates for fragment length 0 
Window half size 590 
Phantom peak location 65 
Phantom peak Correlation 0.2020369 
Normalized Strand cross-correlation coefficient (NSC) 1.035506 
Relative Strand Cross correlation Coefficient (RSC) 0.8958713 
Phantom Peak Quality Tag 0 
null device 
          1 

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

Num	12
ID	task.callpeak_macs2.macs2_atac_rep2.pval0.1.line_192.id_17
Name	macs2_atac rep2.pval0.1
Thread	thread_21
PID	14756

OK	false
Exit Code	1
Retries
State	ERROR
Dep.	ERROR
Cpus	2
Mem

Start	2016-05-14 03:18:42
End	2016-05-14 03:18:42
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz
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/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 --broad --keep-dup all

# SYS command. line 202

 sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.broadPeak.gz

# SYS command. line 203

 sort -k 14gr,14gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz

# SYS command. line 204

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.broadPeak

# SYS command. line 205

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.gappedPeak

# SYS command. line 207

 macs2 callpeak \
			-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits

# SYS command. line 212

 sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz

# SYS command. line 213

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.narrowPeak

# SYS command. line 214

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.xls

# SYS command. line 215

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_summits.bed

# SYS command. line 217

 if [[ false == "true" ]]; then \
			\
			macs2 bdgcmp -t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_FE.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/signal/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			\
			# sval counts the number of tags per million in the (compressed) BED file; \
			sval=$(wc -l <(zcat -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_ppois.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/signal/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			\
			fi

# SYS command. line 243

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
Traceback (most recent call last):
  File "/users/pangwei/anaconda3/envs/bds_atac/bin/macs2", line 4, in 
    __import__('pkg_resources').run_script('MACS2==2.1.0.20150731', 'macs2')
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/setuptools-20.7.0-py2.7.egg/pkg_resources/__init__.py", line 719, in run_script
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/setuptools-20.7.0-py2.7.egg/pkg_resources/__init__.py", line 1511, in run_script
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 614, in 
    
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 55, in main
    
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/callpeak_cmd.py", line 30, in 
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/OptValidator.py", line 27, in 
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/IO/Parser.py", line 7, in 
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/IO/Parser.py", line 6, in __bootstrap__
  File "__init__.pxd", line 155, in init MACS2.IO.Parser (MACS2/IO/Parser.c:24419)
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/numpy/__init__.py", line 180, in 
    from . import add_newdocs
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/numpy/add_newdocs.py", line 13, in 
    from numpy.lib import add_newdoc
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/numpy/lib/__init__.py", line 8, in 
    from .type_check import *
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/numpy/lib/type_check.py", line 11, in 
    import numpy.core.numeric as _nx
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/numpy/core/__init__.py", line 14, in 
    from . import multiarray
ImportError: libopenblasp-r0-39a31c03.2.18.so: cannot open shared object file: No such file or directory

Num	13
ID	task.callpeak_macs2.macs2_atac_rep2.line_192.id_18
Name	macs2_atac rep2
Thread	thread_21
PID	14770

OK	false
Exit Code	1
Retries
State	ERROR
Dep.	ERROR
Cpus	2
Mem

Start	2016-05-14 03:18:42
End	2016-05-14 03:18:42
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.gappedPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/signal/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/signal/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig
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/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -g "hs" -p 0.01 \
			--nomodel --shift -75 --extsize 150 --broad --keep-dup all

# SYS command. line 202

 sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.broadPeak.gz

# SYS command. line 203

 sort -k 14gr,14gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.gappedPeak.gz

# SYS command. line 204

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.broadPeak

# SYS command. line 205

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.gappedPeak

# SYS command. line 207

 macs2 callpeak \
			-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -g "hs" -p 0.01 \
			--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits

# SYS command. line 212

 sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz

# SYS command. line 213

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.narrowPeak

# SYS command. line 214

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.xls

# SYS command. line 215

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_summits.bed

# SYS command. line 217

 if [[ true == "true" ]]; then \
			\
			macs2 bdgcmp -t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_FE.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/signal/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph; \
			\
			# sval counts the number of tags per million in the (compressed) BED file; \
			sval=$(wc -l <(zcat -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_ppois.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/signal/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph; \
			\
			fi

# SYS command. line 243

 rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
Traceback (most recent call last):
  File "/users/pangwei/anaconda3/envs/bds_atac/bin/macs2", line 4, in 
    __import__('pkg_resources').run_script('MACS2==2.1.0.20150731', 'macs2')
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/setuptools-20.7.0-py2.7.egg/pkg_resources/__init__.py", line 719, in run_script
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/setuptools-20.7.0-py2.7.egg/pkg_resources/__init__.py", line 1511, in run_script
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 614, in 
    
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 55, in main
    
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/callpeak_cmd.py", line 30, in 
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/OptValidator.py", line 27, in 
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/IO/Parser.py", line 7, in 
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/IO/Parser.py", line 6, in __bootstrap__
  File "__init__.pxd", line 155, in init MACS2.IO.Parser (MACS2/IO/Parser.c:24419)
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/numpy/__init__.py", line 180, in 
    from . import add_newdocs
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/numpy/add_newdocs.py", line 13, in 
    from numpy.lib import add_newdoc
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/numpy/lib/__init__.py", line 8, in 
    from .type_check import *
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/numpy/lib/type_check.py", line 11, in 
    import numpy.core.numeric as _nx
  File "/users/pangwei/anaconda3/envs/bds_atac/lib/python2.7/site-packages/numpy/core/__init__.py", line 14, in 
    from . import multiarray
ImportError: libopenblasp-r0-39a31c03.2.18.so: cannot open shared object file: No such file or directory

Num	14
ID	task.postalign_bam.nmsrt_bam_rep1.line_321.id_19
Name	nmsrt_bam rep1
Thread	thread_20
PID	15952

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

Start	2016-05-14 04:15:50
End	2016-05-14 04:25:47
Elapsed	00:09:57
Timeout	00:00:-1
Wall Timeout	100 days

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

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 10 files...

Num	15
ID	task.postalign_bam.bam_to_bedpe_rep1.line_425.id_20
Name	bam_to_bedpe rep1
Thread	thread_20
PID	16100

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

Start	2016-05-14 04:25:48
End	2016-05-14 04:27:04
Elapsed	00:01:16
Timeout	00:00:-1
Wall Timeout	100 days

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

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

Num	16
ID	task.postalign_bed.subsample_bedpe_rep1.line_116.id_21
Name	subsample_bedpe rep1
Thread	thread_20
PID	16163

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

Start	2016-05-14 04:27:05
End	2016-05-14 04:28:09
Elapsed	00:01:04
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-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/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | grep -v "chrM" | shuf -n 17500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz

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

Num	17
ID	task.postalign_bam.bedpe_to_tag_rep1.line_465.id_22
Name	bedpe_to_tag rep1
Thread	thread_20
PID	16226

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

Start	2016-05-14 04:28:10
End	2016-05-14 04:29:16
Elapsed	00:01:06
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-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/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz | awk 'BEGIN{OFS="\t"}{printf "%s\t%s\t%s\tN\t1000\t%s\n%s\t%s\t%s\tN\t1000\t%s\n",$1,$2,$3,$9,$4,$5,$6,$10}' | \
			gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz

# SYS command. line 472

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

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

Num	18
ID	task.postalign_bed.shift_tag_rep1.line_140.id_23
Name	shift_tag rep1
Thread	thread_20
PID	16293

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

Start	2016-05-14 04:29:17
End	2016-05-14 04:30:10
Elapsed	00:00:53
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-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/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz | awk -F $'\t' 'BEGIN {OFS = FS}{ if ($6 == "+") {$2 = $2 + 4} else if ($6 == "-") {$3 = $3 - 5} print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz

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

Num	19
ID	task.postalign_bed.subsample_bedpe2tagrep1.line_89.id_24
Name	subsample_bedpe2tagrep1
Thread	thread_20
PID	16356

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

Start	2016-05-14 04:30:11
End	2016-05-14 04:30:43
Elapsed	00:00:32
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-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/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | \
			grep -v "chrM" | shuf -n 25000000 | \
			awk 'BEGIN{OFS="\t"}{print $1,$2,$3,"N","1000",$9}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz

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

Num	20
ID	task.postalign_bed.xcor_rep1.line_165.id_25
Name	xcor rep1
Thread	thread_20
PID

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

Start
End
Elapsed
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.25.cc.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/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz -p=1 \
			-filtchr=chrM -savp=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf -out=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc -speak=0

# SYS command. line 174

 sed -r 's/,[^\t]+//g' /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp

# SYS command. line 175

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

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/ATAC3+4, -num_rep, 2, -fastq1_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC3/ATAC3-trimmed-pair1.fastq.gz, -fastq1_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC3/ATAC3-trimmed-pair2.fastq.gz, -fastq2_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC4/ATAC4-trimmed-pair1.fastq.gz, -fastq2_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC4/ATAC4-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
string	OLDPWD	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4
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	2
string	SSH_AUTH_SOCK	/tmp/ssh-5gr8qSU2WF/agent.74700
string	SSH_CLIENT	171.65.76.244 36245 22
string	SSH_CONNECTION	171.65.76.244 49273 171.65.76.236 22
string	SSH_TTY	/dev/pts/0
string	system	local
int	T	1099511627776
string	TERM	screen
string	THEANO_FLAGS	device=gpu6,floatX=float32,warn_float64=warn,optimizer_excluding=cudnn
int	timeout	-1
string	TMUX	/tmp/tmux-1077/default,106699,3
string	TMUX_PANE	%3
string	USER	pangwei
string	UTIL_SCRIPTS_DIR	/users/pangwei/av_scripts
int	walltimeout	8640000
int	week	604800
string	WWW	/srv/www/kundaje/pangwei
string	XDG_RUNTIME_DIR	/run/user/1077
string	XDG_SESSION_ID	1907
string	ZSH	/users/pangwei//.oh-my-zsh
string	ZSH_TMUX_TERM	screen

BigDataScript report: atac.bds

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