Script file	/users/pangwei/bds_atac/atac.bds
Program ID	atac.bds.20160513_182614_603
Start time	2016-05-13 18:26:14
Run time	16:53:53.644
Tasks executed	20
Tasks failed	2
Tasks failed names	macs2_atac rep1.pval0.1 macs2_atac rep1
Arguments*	[-out_dir, /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10, -num_rep, 2, -fastq1_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC9/ATAC9-trimmed-pair1.fastq.gz, -fastq1_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC9/ATAC9-trimmed-pair2.fastq.gz, -fastq2_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC10/ATAC10-trimmed-pair1.fastq.gz, -fastq2_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC10/ATAC10-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_182614_603_parallel_21/task.align_bowtie2.bowtie2_PE_rep2.line_133.id_7 atac.bds.20160513_182614_603_parallel_21/task.postalign_bam.dedup_bam_PE_rep2.line_215.id_18 atac.bds.20160513_182614_603_parallel_21/task.postalign_bam.nmsrt_bam_rep2.line_321.id_19 atac.bds.20160513_182614_603_parallel_21/task.postalign_bam.bam_to_bedpe_rep2.line_425.id_20 atac.bds.20160513_182614_603_parallel_21/task.postalign_bed.subsample_bedpe_rep2.line_116.id_21 atac.bds.20160513_182614_603_parallel_21/task.postalign_bam.bedpe_to_tag_rep2.line_465.id_22 atac.bds.20160513_182614_603_parallel_21/task.postalign_bed.shift_tag_rep2.line_140.id_23 atac.bds.20160513_182614_603_parallel_21/task.postalign_bed.subsample_bedpe2tagrep2.line_89.id_24 atac.bds.20160513_182614_603_parallel_21/task.postalign_bed.xcor_rep2.line_165.id_25
thread_20	thread_Root	atac.bds.20160513_182614_603_parallel_20/task.align_bowtie2.bowtie2_PE_rep1.line_133.id_6 atac.bds.20160513_182614_603_parallel_20/task.postalign_bam.dedup_bam_PE_rep1.line_215.id_8 atac.bds.20160513_182614_603_parallel_20/task.postalign_bam.nmsrt_bam_rep1.line_321.id_9 atac.bds.20160513_182614_603_parallel_20/task.postalign_bam.bam_to_bedpe_rep1.line_425.id_10 atac.bds.20160513_182614_603_parallel_20/task.postalign_bed.subsample_bedpe_rep1.line_116.id_11 atac.bds.20160513_182614_603_parallel_20/task.postalign_bam.bedpe_to_tag_rep1.line_465.id_12 atac.bds.20160513_182614_603_parallel_20/task.postalign_bed.shift_tag_rep1.line_140.id_13 atac.bds.20160513_182614_603_parallel_20/task.postalign_bed.subsample_bedpe2tagrep1.line_89.id_14 atac.bds.20160513_182614_603_parallel_20/task.postalign_bed.xcor_rep1.line_165.id_15 atac.bds.20160513_182614_603_parallel_20/task.callpeak_macs2.macs2_atac_rep1.pval0.1.line_192.id_16 atac.bds.20160513_182614_603_parallel_20/task.callpeak_macs2.macs2_atac_rep1.line_192.id_17

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.align_bowtie2.bowtie2_PE_rep2.line_133.id_7
Name	bowtie2_PE rep2
Thread	thread_21
PID	103873

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

Start	2016-05-13 18:26:15
End	2016-05-14 07:42:45
Elapsed	13:16:29
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.fastq.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair2.trim.fastq.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-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/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.fastq.gz -2 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair2.trim.fastq.gz 2>/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.align.log | samtools view -bS - | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE

# SYS command. line 142

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-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 79 files...

Num	2
ID	task.align_bowtie2.bowtie2_PE_rep1.line_133.id_6
Name	bowtie2_PE rep1
Thread	thread_20
PID	103867

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

Start	2016-05-13 18:26:14
End	2016-05-14 01:49:22
Elapsed	07:23:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.fastq.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair2.trim.fastq.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-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/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.fastq.gz -2 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair2.trim.fastq.gz 2>/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.align.log | samtools view -bS - | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE

# SYS command. line 142

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-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 39 files...

Num	3
ID	task.postalign_bam.dedup_bam_PE_rep1.line_215.id_8
Name	dedup_bam_PE rep1
Thread	thread_20
PID	8661

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

Start	2016-05-14 01:49:23
End	2016-05-14 03:50:44
Elapsed	02:01:21
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.dup.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-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/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-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/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-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/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.filt

# SYS command. line 239

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-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/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-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/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-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/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-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/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.filt.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 269

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 271

 if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.bai" ]; then \
			cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.bai; \
			fi

# SYS command. line 275

 samtools flagstat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc

# SYS command. line 286

 samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.filt.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.filt.bam.tmp

# SYS command. line 287

 bedtools bamtobed -bedpe -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-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/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.pbc.qc

# SYS command. line 291

 rm /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam

# SYS command. line 293

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.filt.bam

# SYS command. line 294

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-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 23 files...
[bam_sort_core] merging from 23 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Sat May 14 02:55:42 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-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 02:55:42 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 02:55:42	MarkDuplicates	Start of doWork freeMemory: 254889840; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-14 02:55:42	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-05-14 02:55:42	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-05-14 02:55:56	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:13s.  Time for last 1,000,000:   13s.  Last read position: chr10:128,004,598
INFO	2016-05-14 02:55:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 02:56:10	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:27s.  Time for last 1,000,000:   14s.  Last read position: chr11:107,713,464
INFO	2016-05-14 02:56:10	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 02:56:26	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:43s.  Time for last 1,000,000:   15s.  Last read position: chr12:99,101,091
INFO	2016-05-14 02:56:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 02:56:34	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:51s.  Time for last 1,000,000:    8s.  Last read position: chr14:23,499,403
INFO	2016-05-14 02:56:34	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 02:56:44	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:01:01s.  Time for last 1,000,000:    9s.  Last read position: chr15:63,648,805
INFO	2016-05-14 02:56:44	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 02:56:49	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:01:06s.  Time for last 1,000,000:    5s.  Last read position: chr16:73,776,412
INFO	2016-05-14 02:56:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 02:57:00	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:01:16s.  Time for last 1,000,000:   10s.  Last read position: chr17:75,051,408
INFO	2016-05-14 02:57:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 02:57:06	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:01:23s.  Time for last 1,000,000:    6s.  Last read position: chr19:30,017,055
INFO	2016-05-14 02:57:06	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-14 02:57:17	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:01:34s.  Time for last 1,000,000:   11s.  Last read position: chr1:36,897,460
INFO	2016-05-14 02:57:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 02:57:24	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:01:41s.  Time for last 1,000,000:    6s.  Last read position: chr1:181,224,755
INFO	2016-05-14 02:57:24	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 02:57:35	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:52s.  Time for last 1,000,000:   11s.  Last read position: chr20:48,402,858
INFO	2016-05-14 02:57:35	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 02:57:42	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:58s.  Time for last 1,000,000:    6s.  Last read position: chr2:16,341,525
INFO	2016-05-14 02:57:42	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 02:57:49	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:02:06s.  Time for last 1,000,000:    7s.  Last read position: chr2:154,152,526
INFO	2016-05-14 02:57:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 02:57:59	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:02:16s.  Time for last 1,000,000:   10s.  Last read position: chr3:38,760,092
INFO	2016-05-14 02:57:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 02:58:18	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:02:35s.  Time for last 1,000,000:   18s.  Last read position: chr3:178,162,831
INFO	2016-05-14 02:58:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 02:58:25	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:02:42s.  Time for last 1,000,000:    6s.  Last read position: chr4:127,557,362
INFO	2016-05-14 02:58:25	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 02:58:34	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:02:51s.  Time for last 1,000,000:    9s.  Last read position: chr5:97,098,452
INFO	2016-05-14 02:58:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 02:58:40	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:02:57s.  Time for last 1,000,000:    5s.  Last read position: chr6:16,217,184
INFO	2016-05-14 02:58:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 02:58:45	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:03:02s.  Time for last 1,000,000:    5s.  Last read position: chr6:159,419,780
INFO	2016-05-14 02:58:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 02:58:52	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:03:09s.  Time for last 1,000,000:    6s.  Last read position: chr7:127,032,700
INFO	2016-05-14 02:58:52	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-14 02:58:58	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:03:15s.  Time for last 1,000,000:    5s.  Last read position: chr8:102,130,910
INFO	2016-05-14 02:58:58	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 02:59:06	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:03:23s.  Time for last 1,000,000:    7s.  Last read position: chr9:117,755,846
INFO	2016-05-14 02:59:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 02:59:16	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:03:33s.  Time for last 1,000,000:   10s.  Last read position: chrM:475
INFO	2016-05-14 02:59:16	MarkDuplicates	Tracking 9146 as yet unmatched pairs. 9146 records in RAM.
INFO	2016-05-14 02:59:23	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:03:40s.  Time for last 1,000,000:    7s.  Last read position: chrM:911
INFO	2016-05-14 02:59:23	MarkDuplicates	Tracking 22912 as yet unmatched pairs. 22912 records in RAM.
INFO	2016-05-14 02:59:30	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:03:47s.  Time for last 1,000,000:    6s.  Last read position: chrM:1,541
INFO	2016-05-14 02:59:30	MarkDuplicates	Tracking 28486 as yet unmatched pairs. 28486 records in RAM.
INFO	2016-05-14 02:59:38	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:03:55s.  Time for last 1,000,000:    7s.  Last read position: chrM:2,234
INFO	2016-05-14 02:59:38	MarkDuplicates	Tracking 20536 as yet unmatched pairs. 20536 records in RAM.
INFO	2016-05-14 02:59:44	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:04:00s.  Time for last 1,000,000:    5s.  Last read position: chrM:2,727
INFO	2016-05-14 02:59:44	MarkDuplicates	Tracking 83304 as yet unmatched pairs. 83304 records in RAM.
INFO	2016-05-14 02:59:52	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:04:08s.  Time for last 1,000,000:    8s.  Last read position: chrM:3,019
INFO	2016-05-14 02:59:52	MarkDuplicates	Tracking 48106 as yet unmatched pairs. 48106 records in RAM.
INFO	2016-05-14 03:00:03	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:04:20s.  Time for last 1,000,000:   11s.  Last read position: chrM:3,335
INFO	2016-05-14 03:00:03	MarkDuplicates	Tracking 76624 as yet unmatched pairs. 76624 records in RAM.
INFO	2016-05-14 03:00:24	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:04:41s.  Time for last 1,000,000:   20s.  Last read position: chrM:3,553
INFO	2016-05-14 03:00:24	MarkDuplicates	Tracking 3532 as yet unmatched pairs. 3532 records in RAM.
INFO	2016-05-14 03:00:29	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:04:46s.  Time for last 1,000,000:    5s.  Last read position: chrM:3,769
INFO	2016-05-14 03:00:29	MarkDuplicates	Tracking 53064 as yet unmatched pairs. 53064 records in RAM.
INFO	2016-05-14 03:00:33	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:04:49s.  Time for last 1,000,000:    3s.  Last read position: chrM:4,300
INFO	2016-05-14 03:00:33	MarkDuplicates	Tracking 14968 as yet unmatched pairs. 14968 records in RAM.
INFO	2016-05-14 03:00:37	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:04:54s.  Time for last 1,000,000:    4s.  Last read position: chrM:5,311
INFO	2016-05-14 03:00:37	MarkDuplicates	Tracking 17522 as yet unmatched pairs. 17522 records in RAM.
INFO	2016-05-14 03:00:41	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:04:58s.  Time for last 1,000,000:    4s.  Last read position: chrM:6,227
INFO	2016-05-14 03:00:41	MarkDuplicates	Tracking 32156 as yet unmatched pairs. 32156 records in RAM.
INFO	2016-05-14 03:00:45	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:05:02s.  Time for last 1,000,000:    4s.  Last read position: chrM:6,472
INFO	2016-05-14 03:00:45	MarkDuplicates	Tracking 24088 as yet unmatched pairs. 24088 records in RAM.
INFO	2016-05-14 03:00:52	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:05:09s.  Time for last 1,000,000:    6s.  Last read position: chrM:7,006
INFO	2016-05-14 03:00:52	MarkDuplicates	Tracking 14878 as yet unmatched pairs. 14878 records in RAM.
INFO	2016-05-14 03:00:57	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:05:14s.  Time for last 1,000,000:    5s.  Last read position: chrM:7,862
INFO	2016-05-14 03:00:57	MarkDuplicates	Tracking 31530 as yet unmatched pairs. 31530 records in RAM.
INFO	2016-05-14 03:01:06	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:05:23s.  Time for last 1,000,000:    9s.  Last read position: chrM:8,625
INFO	2016-05-14 03:01:06	MarkDuplicates	Tracking 5936 as yet unmatched pairs. 5936 records in RAM.
INFO	2016-05-14 03:01:12	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:05:29s.  Time for last 1,000,000:    6s.  Last read position: chrM:9,401
INFO	2016-05-14 03:01:12	MarkDuplicates	Tracking 5168 as yet unmatched pairs. 5168 records in RAM.
INFO	2016-05-14 03:01:20	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:05:37s.  Time for last 1,000,000:    8s.  Last read position: chrM:10,093
INFO	2016-05-14 03:01:20	MarkDuplicates	Tracking 31954 as yet unmatched pairs. 31954 records in RAM.
INFO	2016-05-14 03:01:27	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:05:43s.  Time for last 1,000,000:    6s.  Last read position: chrM:10,652
INFO	2016-05-14 03:01:27	MarkDuplicates	Tracking 30780 as yet unmatched pairs. 30780 records in RAM.
INFO	2016-05-14 03:01:33	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:05:50s.  Time for last 1,000,000:    6s.  Last read position: chrM:11,236
INFO	2016-05-14 03:01:33	MarkDuplicates	Tracking 36586 as yet unmatched pairs. 36586 records in RAM.
INFO	2016-05-14 03:01:40	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:05:57s.  Time for last 1,000,000:    7s.  Last read position: chrM:11,771
INFO	2016-05-14 03:01:40	MarkDuplicates	Tracking 20536 as yet unmatched pairs. 20536 records in RAM.
INFO	2016-05-14 03:01:47	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:06:04s.  Time for last 1,000,000:    7s.  Last read position: chrM:12,187
INFO	2016-05-14 03:01:47	MarkDuplicates	Tracking 23264 as yet unmatched pairs. 23264 records in RAM.
INFO	2016-05-14 03:02:00	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:06:17s.  Time for last 1,000,000:   12s.  Last read position: chrM:12,619
INFO	2016-05-14 03:02:00	MarkDuplicates	Tracking 52114 as yet unmatched pairs. 52114 records in RAM.
INFO	2016-05-14 03:02:07	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:06:23s.  Time for last 1,000,000:    6s.  Last read position: chrM:13,089
INFO	2016-05-14 03:02:07	MarkDuplicates	Tracking 35568 as yet unmatched pairs. 35568 records in RAM.
INFO	2016-05-14 03:02:12	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:06:29s.  Time for last 1,000,000:    5s.  Last read position: chrM:13,429
INFO	2016-05-14 03:02:12	MarkDuplicates	Tracking 34346 as yet unmatched pairs. 34346 records in RAM.
INFO	2016-05-14 03:02:19	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:06:36s.  Time for last 1,000,000:    7s.  Last read position: chrM:13,917
INFO	2016-05-14 03:02:19	MarkDuplicates	Tracking 18834 as yet unmatched pairs. 18834 records in RAM.
INFO	2016-05-14 03:02:28	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:06:45s.  Time for last 1,000,000:    8s.  Last read position: chrM:14,419
INFO	2016-05-14 03:02:28	MarkDuplicates	Tracking 9978 as yet unmatched pairs. 9978 records in RAM.
INFO	2016-05-14 03:02:33	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:06:50s.  Time for last 1,000,000:    5s.  Last read position: chrM:15,048
INFO	2016-05-14 03:02:33	MarkDuplicates	Tracking 93278 as yet unmatched pairs. 93278 records in RAM.
INFO	2016-05-14 03:02:37	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:06:54s.  Time for last 1,000,000:    4s.  Last read position: chrM:15,279
INFO	2016-05-14 03:02:37	MarkDuplicates	Tracking 27942 as yet unmatched pairs. 27942 records in RAM.
INFO	2016-05-14 03:02:40	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:06:57s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,575
INFO	2016-05-14 03:02:40	MarkDuplicates	Tracking 21932 as yet unmatched pairs. 21932 records in RAM.
INFO	2016-05-14 03:02:47	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:07:04s.  Time for last 1,000,000:    7s.  Last read position: chrM:15,821
INFO	2016-05-14 03:02:47	MarkDuplicates	Tracking 81784 as yet unmatched pairs. 81784 records in RAM.
INFO	2016-05-14 03:02:54	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:07:10s.  Time for last 1,000,000:    6s.  Last read position: chrM:16,322
INFO	2016-05-14 03:02:54	MarkDuplicates	Tracking 49494 as yet unmatched pairs. 49494 records in RAM.
INFO	2016-05-14 03:03:01	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:07:18s.  Time for last 1,000,000:    7s.  Last read position: chrX:29,595,230
INFO	2016-05-14 03:03:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 03:03:05	MarkDuplicates	Read 55728728 records. 0 pairs never matched.
INFO	2016-05-14 03:03:21	MarkDuplicates	After buildSortedReadEndLists freeMemory: 3138022384; totalMemory: 3165650944; maxMemory: 3817865216
INFO	2016-05-14 03:03:21	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-05-14 03:03:21	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-05-14 03:03:49	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-05-14 03:04:12	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-05-14 03:04:14	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2230138432; totalMemory: 3211264000; maxMemory: 3817865216
INFO	2016-05-14 03:04:14	MarkDuplicates	Marking 35262490 records as duplicates.
INFO	2016-05-14 03:04:14	MarkDuplicates	Found 10938300 optical duplicate clusters.
INFO	2016-05-14 03:06:34	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:02:19s.  Time for last 10,000,000:  139s.  Last read position: chr1:181,224,755
INFO	2016-05-14 03:08:27	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:04:11s.  Time for last 10,000,000:  112s.  Last read position: chr7:127,032,700
INFO	2016-05-14 03:10:10	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:05:54s.  Time for last 10,000,000:  103s.  Last read position: chrM:3,553
INFO	2016-05-14 03:11:42	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:07:26s.  Time for last 10,000,000:   92s.  Last read position: chrM:10,093
INFO	2016-05-14 03:13:20	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:09:04s.  Time for last 10,000,000:   98s.  Last read position: chrM:15,048
INFO	2016-05-14 03:14:10	MarkDuplicates	Before output close freeMemory: 3276466920; totalMemory: 3306684416; maxMemory: 3817865216
INFO	2016-05-14 03:14:10	MarkDuplicates	After output close freeMemory: 3276465800; totalMemory: 3306684416; maxMemory: 3817865216
[Sat May 14 03:14:10 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 18.46 minutes.
Runtime.totalMemory()=3306684416
[bam_sort_core] merging from 23 files...

Num	4
ID	task.postalign_bam.nmsrt_bam_rep1.line_321.id_9
Name	nmsrt_bam rep1
Thread	thread_20
PID	15187

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

Start	2016-05-14 03:50:45
End	2016-05-14 03:59:33
Elapsed	00:08:48
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-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/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-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 9 files...

Num	5
ID	task.postalign_bam.bam_to_bedpe_rep1.line_425.id_10
Name	bam_to_bedpe rep1
Thread	thread_20
PID	15309

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

Start	2016-05-14 03:59:34
End	2016-05-14 04:00:38
Elapsed	00:01:04
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-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/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz

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

Num	6
ID	task.postalign_bed.subsample_bedpe_rep1.line_116.id_11
Name	subsample_bedpe rep1
Thread	thread_20
PID	15372

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

Start	2016-05-14 04:00:40
End	2016-05-14 04:01:34
Elapsed	00:00:54
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-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/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | grep -v "chrM" | shuf -n 17500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz

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

Num	7
ID	task.postalign_bam.bedpe_to_tag_rep1.line_465.id_12
Name	bedpe_to_tag rep1
Thread	thread_20
PID	15436

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

Start	2016-05-14 04:01:35
End	2016-05-14 04:02:35
Elapsed	00:01:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-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/ATAC9+10/align/rep1/ATAC9-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/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz

# SYS command. line 472

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz | grep -P -v 'chrM' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz; mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz

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

Num	8
ID	task.postalign_bed.shift_tag_rep1.line_140.id_13
Name	shift_tag rep1
Thread	thread_20
PID	15504

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

Start	2016-05-14 04:02:36
End	2016-05-14 04:03:16
Elapsed	00:00:40
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-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/ATAC9+10/align/rep1/ATAC9-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/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz

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

Num	9
ID	task.postalign_bed.subsample_bedpe2tagrep1.line_89.id_14
Name	subsample_bedpe2tagrep1
Thread	thread_20
PID	15565

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

Start	2016-05-14 04:03:17
End	2016-05-14 04:03:45
Elapsed	00:00:27
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-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/ATAC9+10/align/rep1/ATAC9-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/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz

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

Num	10
ID	task.postalign_bed.xcor_rep1.line_165.id_15
Name	xcor rep1
Thread	thread_20
PID	15627

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

Start	2016-05-14 04:03:45
End	2016-05-14 04:18:19
Elapsed	00:14:33
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-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/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz -p=1 \
			-filtchr=chrM -savp=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf -out=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-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/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp

# SYS command. line 175

 mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc

   
--------------------Stdout--------------------
################
ChIP data: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-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/ATAC9+10/align/rep1 
narrowPeak output file name: NA 
regionPeak output file name: NA 
Rdata filename: NA 
plot pdf filename: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf 
result filename: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep1/ATAC9-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/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz 
opened /tmp/RtmpqFFbyx/ATAC9-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign3da03ca152af
done. read 9408184 fragments
ChIP data read length 75 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1125057 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.13267687246943 
Top 3 estimates for fragment length 0 
Window half size 405 
Phantom peak location 65 
Phantom peak Correlation 0.1360169 
Normalized Strand cross-correlation coefficient (NSC) 1.17929 
Relative Strand Cross correlation Coefficient (RSC) 0.8579389 
Phantom Peak Quality Tag 0 
null device 
          1 

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

Num	11
ID	task.callpeak_macs2.macs2_atac_rep1.pval0.1.line_192.id_16
Name	macs2_atac rep1.pval0.1
Thread	thread_20
PID	15632

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

Start	2016-05-14 04:03:45
End	2016-05-14 04:03:45
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/signal/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/signal/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-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	12
ID	task.callpeak_macs2.macs2_atac_rep1.line_192.id_17
Name	macs2_atac rep1
Thread	thread_20
PID	15644

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

Start	2016-05-14 04:03:46
End	2016-05-14 04:03:46
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.gappedPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/signal/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/signal/macs2/rep1/ATAC9-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/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m FE;\
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/signal/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/align/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph; \
			rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/signal/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig"; \
			rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-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/ATAC9+10/peak/macs2/rep1/ATAC9-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/peak/macs2/rep1/ATAC9-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	13
ID	task.postalign_bam.dedup_bam_PE_rep2.line_215.id_18
Name	dedup_bam_PE rep2
Thread	thread_21
PID	18563

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

Start	2016-05-14 07:42:46
End	2016-05-14 10:58:07
Elapsed	03:15:21
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.dup.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-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/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-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/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-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/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.filt

# SYS command. line 239

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-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/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-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/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-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/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-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/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.filt.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 269

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 271

 if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.bai" ]; then \
			cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.bai; \
			fi

# SYS command. line 275

 samtools flagstat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc

# SYS command. line 286

 samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.filt.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.filt.bam.tmp

# SYS command. line 287

 bedtools bamtobed -bedpe -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-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/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.pbc.qc

# SYS command. line 291

 rm /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam

# SYS command. line 293

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.filt.bam

# SYS command. line 294

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-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 46 files...
[bam_sort_core] merging from 46 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Sat May 14 09:29:23 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-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 09:29:23 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 09:29:24	MarkDuplicates	Start of doWork freeMemory: 254889832; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-14 09:29:24	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-05-14 09:29:24	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-05-14 09:29:32	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:07s.  Time for last 1,000,000:    7s.  Last read position: chr10:72,319,294
INFO	2016-05-14 09:29:32	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:29:40	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:15s.  Time for last 1,000,000:    8s.  Last read position: chr10:125,579,807
INFO	2016-05-14 09:29:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:29:44	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:20s.  Time for last 1,000,000:    4s.  Last read position: chr11:45,743,014
INFO	2016-05-14 09:29:44	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:29:49	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:24s.  Time for last 1,000,000:    4s.  Last read position: chr11:103,975,525
INFO	2016-05-14 09:29:49	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:29:53	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:28s.  Time for last 1,000,000:    3s.  Last read position: chr12:23,057,129
INFO	2016-05-14 09:29:53	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:29:57	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:33s.  Time for last 1,000,000:    4s.  Last read position: chr12:90,357,714
INFO	2016-05-14 09:29:57	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:30:01	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:36s.  Time for last 1,000,000:    3s.  Last read position: chr13:31,102,261
INFO	2016-05-14 09:30:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:30:06	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:41s.  Time for last 1,000,000:    4s.  Last read position: chr13:104,210,461
INFO	2016-05-14 09:30:06	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:30:10	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:45s.  Time for last 1,000,000:    3s.  Last read position: chr14:73,565,939
INFO	2016-05-14 09:30:10	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:30:15	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:50s.  Time for last 1,000,000:    5s.  Last read position: chr15:46,551,348
INFO	2016-05-14 09:30:15	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:30:18	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:53s.  Time for last 1,000,000:    3s.  Last read position: chr15:100,524,426
INFO	2016-05-14 09:30:18	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:30:22	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:00:57s.  Time for last 1,000,000:    3s.  Last read position: chr16:66,711,478
INFO	2016-05-14 09:30:22	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:30:28	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:03s.  Time for last 1,000,000:    5s.  Last read position: chr17:26,526,013
INFO	2016-05-14 09:30:28	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:30:32	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:07s.  Time for last 1,000,000:    3s.  Last read position: chr17:74,976,604
INFO	2016-05-14 09:30:32	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:30:47	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:22s.  Time for last 1,000,000:   14s.  Last read position: chr18:55,620,070
INFO	2016-05-14 09:30:47	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:30:51	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:26s.  Time for last 1,000,000:    3s.  Last read position: chr19:33,608,715
INFO	2016-05-14 09:30:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:30:56	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:01:31s.  Time for last 1,000,000:    4s.  Last read position: chr1:4,116,737
INFO	2016-05-14 09:30:56	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-05-14 09:30:59	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:01:34s.  Time for last 1,000,000:    3s.  Last read position: chr1:46,490,976
INFO	2016-05-14 09:30:59	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:31:03	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:01:38s.  Time for last 1,000,000:    3s.  Last read position: chr1:109,811,510
INFO	2016-05-14 09:31:03	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:31:08	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:01:43s.  Time for last 1,000,000:    5s.  Last read position: chr1:192,491,702
INFO	2016-05-14 09:31:08	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:31:11	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:01:46s.  Time for last 1,000,000:    3s.  Last read position: chr1:248,569,105
INFO	2016-05-14 09:31:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:31:15	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:01:50s.  Time for last 1,000,000:    3s.  Last read position: chr20:54,360,873
INFO	2016-05-14 09:31:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:31:18	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:01:53s.  Time for last 1,000,000:    3s.  Last read position: chr22:30,273,924
INFO	2016-05-14 09:31:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:31:24	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:02:00s.  Time for last 1,000,000:    6s.  Last read position: chr2:27,590,658
INFO	2016-05-14 09:31:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:31:28	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:02:04s.  Time for last 1,000,000:    3s.  Last read position: chr2:91,703,389
INFO	2016-05-14 09:31:28	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:31:33	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:02:08s.  Time for last 1,000,000:    4s.  Last read position: chr2:162,410,549
INFO	2016-05-14 09:31:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:31:37	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:02:12s.  Time for last 1,000,000:    4s.  Last read position: chr2:225,873,994
INFO	2016-05-14 09:31:37	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:31:44	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:02:19s.  Time for last 1,000,000:    6s.  Last read position: chr3:38,570,221
INFO	2016-05-14 09:31:44	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:31:48	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:02:23s.  Time for last 1,000,000:    4s.  Last read position: chr3:106,199,813
INFO	2016-05-14 09:31:48	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:32:00	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:02:36s.  Time for last 1,000,000:   12s.  Last read position: chr3:169,856,976
INFO	2016-05-14 09:32:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:32:05	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:02:40s.  Time for last 1,000,000:    4s.  Last read position: chr4:29,901,313
INFO	2016-05-14 09:32:05	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:32:09	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:02:44s.  Time for last 1,000,000:    4s.  Last read position: chr4:107,891,152
INFO	2016-05-14 09:32:09	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-14 09:32:13	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:02:48s.  Time for last 1,000,000:    4s.  Last read position: chr4:181,298,258
INFO	2016-05-14 09:32:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:32:17	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:02:52s.  Time for last 1,000,000:    3s.  Last read position: chr5:63,661,351
INFO	2016-05-14 09:32:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:32:20	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:02:55s.  Time for last 1,000,000:    3s.  Last read position: chr5:133,647,309
INFO	2016-05-14 09:32:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:32:24	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:02:59s.  Time for last 1,000,000:    3s.  Last read position: chr5:172,181,872
INFO	2016-05-14 09:32:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:32:27	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:03:02s.  Time for last 1,000,000:    3s.  Last read position: chr6:42,421,022
INFO	2016-05-14 09:32:27	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-05-14 09:32:33	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:03:08s.  Time for last 1,000,000:    6s.  Last read position: chr6:116,619,586
INFO	2016-05-14 09:32:33	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-05-14 09:32:37	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:03:12s.  Time for last 1,000,000:    3s.  Last read position: chr7:5,466,360
INFO	2016-05-14 09:32:37	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-05-14 09:32:41	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:03:16s.  Time for last 1,000,000:    4s.  Last read position: chr7:77,025,097
INFO	2016-05-14 09:32:41	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:32:45	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:03:20s.  Time for last 1,000,000:    3s.  Last read position: chr7:139,979,740
INFO	2016-05-14 09:32:45	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:32:49	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:03:24s.  Time for last 1,000,000:    3s.  Last read position: chr8:41,707,447
INFO	2016-05-14 09:32:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:32:53	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:03:28s.  Time for last 1,000,000:    3s.  Last read position: chr8:111,693,131
INFO	2016-05-14 09:32:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:33:00	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:03:35s.  Time for last 1,000,000:    7s.  Last read position: chr9:27,788,952
INFO	2016-05-14 09:33:00	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:33:08	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:03:43s.  Time for last 1,000,000:    7s.  Last read position: chr9:120,709,280
INFO	2016-05-14 09:33:08	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:33:11	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:03:46s.  Time for last 1,000,000:    3s.  Last read position: chrM:113
INFO	2016-05-14 09:33:11	MarkDuplicates	Tracking 56020 as yet unmatched pairs. 56020 records in RAM.
INFO	2016-05-14 09:33:14	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:03:49s.  Time for last 1,000,000:    3s.  Last read position: chrM:468
INFO	2016-05-14 09:33:14	MarkDuplicates	Tracking 21228 as yet unmatched pairs. 21228 records in RAM.
INFO	2016-05-14 09:33:20	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:03:55s.  Time for last 1,000,000:    5s.  Last read position: chrM:683
INFO	2016-05-14 09:33:20	MarkDuplicates	Tracking 65148 as yet unmatched pairs. 65148 records in RAM.
INFO	2016-05-14 09:33:24	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:03:59s.  Time for last 1,000,000:    4s.  Last read position: chrM:869
INFO	2016-05-14 09:33:24	MarkDuplicates	Tracking 56436 as yet unmatched pairs. 56436 records in RAM.
INFO	2016-05-14 09:33:30	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:04:05s.  Time for last 1,000,000:    5s.  Last read position: chrM:1,292
INFO	2016-05-14 09:33:30	MarkDuplicates	Tracking 60896 as yet unmatched pairs. 60896 records in RAM.
INFO	2016-05-14 09:33:33	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:04:08s.  Time for last 1,000,000:    3s.  Last read position: chrM:1,506
INFO	2016-05-14 09:33:33	MarkDuplicates	Tracking 73564 as yet unmatched pairs. 73564 records in RAM.
INFO	2016-05-14 09:33:36	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:04:11s.  Time for last 1,000,000:    3s.  Last read position: chrM:1,833
INFO	2016-05-14 09:33:36	MarkDuplicates	Tracking 47920 as yet unmatched pairs. 47920 records in RAM.
INFO	2016-05-14 09:33:39	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:04:15s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,167
INFO	2016-05-14 09:33:39	MarkDuplicates	Tracking 54546 as yet unmatched pairs. 54546 records in RAM.
INFO	2016-05-14 09:33:43	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:04:18s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,562
INFO	2016-05-14 09:33:43	MarkDuplicates	Tracking 60178 as yet unmatched pairs. 60178 records in RAM.
INFO	2016-05-14 09:33:46	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:04:21s.  Time for last 1,000,000:    3s.  Last read position: chrM:2,709
INFO	2016-05-14 09:33:46	MarkDuplicates	Tracking 132600 as yet unmatched pairs. 132600 records in RAM.
INFO	2016-05-14 09:33:52	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:04:27s.  Time for last 1,000,000:    6s.  Last read position: chrM:2,852
INFO	2016-05-14 09:33:52	MarkDuplicates	Tracking 184308 as yet unmatched pairs. 184308 records in RAM.
INFO	2016-05-14 09:33:57	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:04:32s.  Time for last 1,000,000:    4s.  Last read position: chrM:3,016
INFO	2016-05-14 09:33:57	MarkDuplicates	Tracking 107256 as yet unmatched pairs. 107256 records in RAM.
INFO	2016-05-14 09:34:00	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:04:35s.  Time for last 1,000,000:    3s.  Last read position: chrM:3,204
INFO	2016-05-14 09:34:00	MarkDuplicates	Tracking 137464 as yet unmatched pairs. 137464 records in RAM.
INFO	2016-05-14 09:34:13	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:04:48s.  Time for last 1,000,000:   13s.  Last read position: chrM:3,334
INFO	2016-05-14 09:34:13	MarkDuplicates	Tracking 154712 as yet unmatched pairs. 154712 records in RAM.
INFO	2016-05-14 09:34:17	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:04:53s.  Time for last 1,000,000:    4s.  Last read position: chrM:3,434
INFO	2016-05-14 09:34:17	MarkDuplicates	Tracking 115654 as yet unmatched pairs. 115654 records in RAM.
INFO	2016-05-14 09:34:22	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:04:57s.  Time for last 1,000,000:    4s.  Last read position: chrM:3,578
INFO	2016-05-14 09:34:22	MarkDuplicates	Tracking 33100 as yet unmatched pairs. 33100 records in RAM.
INFO	2016-05-14 09:34:26	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:05:01s.  Time for last 1,000,000:    4s.  Last read position: chrM:3,688
INFO	2016-05-14 09:34:26	MarkDuplicates	Tracking 137678 as yet unmatched pairs. 137678 records in RAM.
INFO	2016-05-14 09:34:31	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:05:06s.  Time for last 1,000,000:    5s.  Last read position: chrM:3,810
INFO	2016-05-14 09:34:31	MarkDuplicates	Tracking 129436 as yet unmatched pairs. 129436 records in RAM.
INFO	2016-05-14 09:34:35	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:05:10s.  Time for last 1,000,000:    3s.  Last read position: chrM:4,013
INFO	2016-05-14 09:34:35	MarkDuplicates	Tracking 31286 as yet unmatched pairs. 31286 records in RAM.
INFO	2016-05-14 09:34:38	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:05:13s.  Time for last 1,000,000:    3s.  Last read position: chrM:4,698
INFO	2016-05-14 09:34:38	MarkDuplicates	Tracking 12436 as yet unmatched pairs. 12436 records in RAM.
INFO	2016-05-14 09:34:41	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:05:16s.  Time for last 1,000,000:    3s.  Last read position: chrM:4,970
INFO	2016-05-14 09:34:41	MarkDuplicates	Tracking 73120 as yet unmatched pairs. 73120 records in RAM.
INFO	2016-05-14 09:34:44	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:05:19s.  Time for last 1,000,000:    3s.  Last read position: chrM:5,357
INFO	2016-05-14 09:34:44	MarkDuplicates	Tracking 56642 as yet unmatched pairs. 56642 records in RAM.
INFO	2016-05-14 09:34:47	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:05:22s.  Time for last 1,000,000:    3s.  Last read position: chrM:5,994
INFO	2016-05-14 09:34:47	MarkDuplicates	Tracking 33428 as yet unmatched pairs. 33428 records in RAM.
INFO	2016-05-14 09:34:50	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:05:26s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,256
INFO	2016-05-14 09:34:50	MarkDuplicates	Tracking 66760 as yet unmatched pairs. 66760 records in RAM.
INFO	2016-05-14 09:34:56	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:05:31s.  Time for last 1,000,000:    5s.  Last read position: chrM:6,414
INFO	2016-05-14 09:34:56	MarkDuplicates	Tracking 55924 as yet unmatched pairs. 55924 records in RAM.
INFO	2016-05-14 09:34:59	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:05:34s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,546
INFO	2016-05-14 09:34:59	MarkDuplicates	Tracking 55240 as yet unmatched pairs. 55240 records in RAM.
INFO	2016-05-14 09:35:02	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:05:37s.  Time for last 1,000,000:    3s.  Last read position: chrM:6,913
INFO	2016-05-14 09:35:02	MarkDuplicates	Tracking 81308 as yet unmatched pairs. 81308 records in RAM.
INFO	2016-05-14 09:35:05	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:05:40s.  Time for last 1,000,000:    3s.  Last read position: chrM:7,224
INFO	2016-05-14 09:35:05	MarkDuplicates	Tracking 34696 as yet unmatched pairs. 34696 records in RAM.
INFO	2016-05-14 09:35:13	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:05:48s.  Time for last 1,000,000:    7s.  Last read position: chrM:7,794
INFO	2016-05-14 09:35:13	MarkDuplicates	Tracking 28824 as yet unmatched pairs. 28824 records in RAM.
INFO	2016-05-14 09:35:16	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:05:51s.  Time for last 1,000,000:    3s.  Last read position: chrM:8,002
INFO	2016-05-14 09:35:16	MarkDuplicates	Tracking 49930 as yet unmatched pairs. 49930 records in RAM.
INFO	2016-05-14 09:35:19	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:05:54s.  Time for last 1,000,000:    3s.  Last read position: chrM:8,404
INFO	2016-05-14 09:35:19	MarkDuplicates	Tracking 24682 as yet unmatched pairs. 24682 records in RAM.
INFO	2016-05-14 09:35:22	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:05:57s.  Time for last 1,000,000:    3s.  Last read position: chrM:8,929
INFO	2016-05-14 09:35:22	MarkDuplicates	Tracking 20154 as yet unmatched pairs. 20154 records in RAM.
INFO	2016-05-14 09:35:27	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:06:02s.  Time for last 1,000,000:    5s.  Last read position: chrM:9,268
INFO	2016-05-14 09:35:27	MarkDuplicates	Tracking 43146 as yet unmatched pairs. 43146 records in RAM.
INFO	2016-05-14 09:35:30	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:06:05s.  Time for last 1,000,000:    2s.  Last read position: chrM:9,619
INFO	2016-05-14 09:35:30	MarkDuplicates	Tracking 32900 as yet unmatched pairs. 32900 records in RAM.
INFO	2016-05-14 09:35:34	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:06:09s.  Time for last 1,000,000:    3s.  Last read position: chrM:9,874
INFO	2016-05-14 09:35:34	MarkDuplicates	Tracking 109046 as yet unmatched pairs. 109046 records in RAM.
INFO	2016-05-14 09:35:37	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:06:12s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,169
INFO	2016-05-14 09:35:37	MarkDuplicates	Tracking 51130 as yet unmatched pairs. 51130 records in RAM.
INFO	2016-05-14 09:35:40	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:06:15s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,407
INFO	2016-05-14 09:35:40	MarkDuplicates	Tracking 79384 as yet unmatched pairs. 79384 records in RAM.
INFO	2016-05-14 09:35:43	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:06:18s.  Time for last 1,000,000:    3s.  Last read position: chrM:10,660
INFO	2016-05-14 09:35:43	MarkDuplicates	Tracking 45668 as yet unmatched pairs. 45668 records in RAM.
INFO	2016-05-14 09:35:46	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:06:21s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,138
INFO	2016-05-14 09:35:46	MarkDuplicates	Tracking 60534 as yet unmatched pairs. 60534 records in RAM.
INFO	2016-05-14 09:35:49	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:06:24s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,305
INFO	2016-05-14 09:35:49	MarkDuplicates	Tracking 46364 as yet unmatched pairs. 46364 records in RAM.
INFO	2016-05-14 09:35:55	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:06:30s.  Time for last 1,000,000:    6s.  Last read position: chrM:11,543
INFO	2016-05-14 09:35:55	MarkDuplicates	Tracking 90836 as yet unmatched pairs. 90836 records in RAM.
INFO	2016-05-14 09:35:59	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:06:34s.  Time for last 1,000,000:    3s.  Last read position: chrM:11,829
INFO	2016-05-14 09:35:59	MarkDuplicates	Tracking 19306 as yet unmatched pairs. 19306 records in RAM.
INFO	2016-05-14 09:36:03	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:06:38s.  Time for last 1,000,000:    4s.  Last read position: chrM:12,066
INFO	2016-05-14 09:36:03	MarkDuplicates	Tracking 34962 as yet unmatched pairs. 34962 records in RAM.
INFO	2016-05-14 09:36:18	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:06:53s.  Time for last 1,000,000:   14s.  Last read position: chrM:12,351
INFO	2016-05-14 09:36:18	MarkDuplicates	Tracking 43520 as yet unmatched pairs. 43520 records in RAM.
INFO	2016-05-14 09:36:23	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:06:58s.  Time for last 1,000,000:    5s.  Last read position: chrM:12,547
INFO	2016-05-14 09:36:23	MarkDuplicates	Tracking 83988 as yet unmatched pairs. 83988 records in RAM.
INFO	2016-05-14 09:36:28	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:07:03s.  Time for last 1,000,000:    5s.  Last read position: chrM:12,680
INFO	2016-05-14 09:36:28	MarkDuplicates	Tracking 124124 as yet unmatched pairs. 124124 records in RAM.
INFO	2016-05-14 09:36:33	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:07:08s.  Time for last 1,000,000:    5s.  Last read position: chrM:12,985
INFO	2016-05-14 09:36:33	MarkDuplicates	Tracking 15576 as yet unmatched pairs. 15576 records in RAM.
INFO	2016-05-14 09:36:38	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:07:13s.  Time for last 1,000,000:    4s.  Last read position: chrM:13,161
INFO	2016-05-14 09:36:38	MarkDuplicates	Tracking 57878 as yet unmatched pairs. 57878 records in RAM.
INFO	2016-05-14 09:36:43	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:07:18s.  Time for last 1,000,000:    5s.  Last read position: chrM:13,334
INFO	2016-05-14 09:36:43	MarkDuplicates	Tracking 64850 as yet unmatched pairs. 64850 records in RAM.
INFO	2016-05-14 09:36:49	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:07:24s.  Time for last 1,000,000:    5s.  Last read position: chrM:13,506
INFO	2016-05-14 09:36:49	MarkDuplicates	Tracking 53046 as yet unmatched pairs. 53046 records in RAM.
INFO	2016-05-14 09:36:52	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:07:27s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,769
INFO	2016-05-14 09:36:52	MarkDuplicates	Tracking 26514 as yet unmatched pairs. 26514 records in RAM.
INFO	2016-05-14 09:36:55	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:07:30s.  Time for last 1,000,000:    3s.  Last read position: chrM:13,953
INFO	2016-05-14 09:36:55	MarkDuplicates	Tracking 55162 as yet unmatched pairs. 55162 records in RAM.
INFO	2016-05-14 09:36:58	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:07:33s.  Time for last 1,000,000:    3s.  Last read position: chrM:14,270
INFO	2016-05-14 09:36:58	MarkDuplicates	Tracking 43710 as yet unmatched pairs. 43710 records in RAM.
INFO	2016-05-14 09:37:01	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:07:36s.  Time for last 1,000,000:    3s.  Last read position: chrM:14,465
INFO	2016-05-14 09:37:01	MarkDuplicates	Tracking 37396 as yet unmatched pairs. 37396 records in RAM.
INFO	2016-05-14 09:37:04	MarkDuplicates	Read   100,000,000 records.  Elapsed time: 00:07:40s.  Time for last 1,000,000:    3s.  Last read position: chrM:14,916
INFO	2016-05-14 09:37:04	MarkDuplicates	Tracking 62252 as yet unmatched pairs. 62252 records in RAM.
INFO	2016-05-14 09:37:08	MarkDuplicates	Read   101,000,000 records.  Elapsed time: 00:07:43s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,067
INFO	2016-05-14 09:37:08	MarkDuplicates	Tracking 164752 as yet unmatched pairs. 164752 records in RAM.
INFO	2016-05-14 09:37:11	MarkDuplicates	Read   102,000,000 records.  Elapsed time: 00:07:46s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,192
INFO	2016-05-14 09:37:11	MarkDuplicates	Tracking 50078 as yet unmatched pairs. 50078 records in RAM.
INFO	2016-05-14 09:37:18	MarkDuplicates	Read   103,000,000 records.  Elapsed time: 00:07:54s.  Time for last 1,000,000:    7s.  Last read position: chrM:15,337
INFO	2016-05-14 09:37:18	MarkDuplicates	Tracking 93888 as yet unmatched pairs. 93888 records in RAM.
INFO	2016-05-14 09:37:23	MarkDuplicates	Read   104,000,000 records.  Elapsed time: 00:07:58s.  Time for last 1,000,000:    4s.  Last read position: chrM:15,466
INFO	2016-05-14 09:37:23	MarkDuplicates	Tracking 35498 as yet unmatched pairs. 35498 records in RAM.
INFO	2016-05-14 09:37:26	MarkDuplicates	Read   105,000,000 records.  Elapsed time: 00:08:01s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,603
INFO	2016-05-14 09:37:26	MarkDuplicates	Tracking 51536 as yet unmatched pairs. 51536 records in RAM.
INFO	2016-05-14 09:37:29	MarkDuplicates	Read   106,000,000 records.  Elapsed time: 00:08:05s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,729
INFO	2016-05-14 09:37:29	MarkDuplicates	Tracking 100152 as yet unmatched pairs. 100152 records in RAM.
INFO	2016-05-14 09:37:33	MarkDuplicates	Read   107,000,000 records.  Elapsed time: 00:08:08s.  Time for last 1,000,000:    3s.  Last read position: chrM:15,839
INFO	2016-05-14 09:37:33	MarkDuplicates	Tracking 137504 as yet unmatched pairs. 137504 records in RAM.
INFO	2016-05-14 09:37:36	MarkDuplicates	Read   108,000,000 records.  Elapsed time: 00:08:11s.  Time for last 1,000,000:    3s.  Last read position: chrM:16,059
INFO	2016-05-14 09:37:36	MarkDuplicates	Tracking 64102 as yet unmatched pairs. 64102 records in RAM.
INFO	2016-05-14 09:37:39	MarkDuplicates	Read   109,000,000 records.  Elapsed time: 00:08:14s.  Time for last 1,000,000:    3s.  Last read position: chrM:16,328
INFO	2016-05-14 09:37:39	MarkDuplicates	Tracking 97556 as yet unmatched pairs. 97556 records in RAM.
INFO	2016-05-14 09:37:42	MarkDuplicates	Read   110,000,000 records.  Elapsed time: 00:08:17s.  Time for last 1,000,000:    3s.  Last read position: chrM:16,438
INFO	2016-05-14 09:37:42	MarkDuplicates	Tracking 58590 as yet unmatched pairs. 58590 records in RAM.
INFO	2016-05-14 09:37:46	MarkDuplicates	Read   111,000,000 records.  Elapsed time: 00:08:21s.  Time for last 1,000,000:    3s.  Last read position: chrX:34,826,939
INFO	2016-05-14 09:37:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-05-14 09:37:49	MarkDuplicates	Read   112,000,000 records.  Elapsed time: 00:08:24s.  Time for last 1,000,000:    3s.  Last read position: chrX:120,451,384
INFO	2016-05-14 09:37:49	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-05-14 09:37:54	MarkDuplicates	Read 112486288 records. 0 pairs never matched.
INFO	2016-05-14 09:38:03	MarkDuplicates	After buildSortedReadEndLists freeMemory: 3800139576; totalMemory: 3827302400; maxMemory: 3827302400
INFO	2016-05-14 09:38:03	MarkDuplicates	Will retain up to 119603200 duplicate indices before spilling to disk.
INFO	2016-05-14 09:38:03	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-05-14 09:38:50	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-05-14 09:39:17	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-05-14 09:39:21	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2856574648; totalMemory: 3840933888; maxMemory: 3840933888
INFO	2016-05-14 09:39:21	MarkDuplicates	Marking 75201558 records as duplicates.
INFO	2016-05-14 09:39:21	MarkDuplicates	Found 24625117 optical duplicate clusters.
INFO	2016-05-14 09:41:02	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:39s.  Time for last 10,000,000:   99s.  Last read position: chr15:46,551,348
INFO	2016-05-14 09:42:38	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:03:15s.  Time for last 10,000,000:   96s.  Last read position: chr1:192,491,702
INFO	2016-05-14 09:44:17	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:04:54s.  Time for last 10,000,000:   99s.  Last read position: chr3:169,856,976
INFO	2016-05-14 09:45:54	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:06:31s.  Time for last 10,000,000:   97s.  Last read position: chr7:77,025,097
INFO	2016-05-14 09:47:26	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:08:03s.  Time for last 10,000,000:   91s.  Last read position: chrM:1,292
INFO	2016-05-14 09:48:48	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:09:25s.  Time for last 10,000,000:   82s.  Last read position: chrM:3,434
INFO	2016-05-14 09:50:07	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:10:44s.  Time for last 10,000,000:   78s.  Last read position: chrM:6,414
INFO	2016-05-14 09:51:26	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:12:03s.  Time for last 10,000,000:   79s.  Last read position: chrM:9,874
INFO	2016-05-14 09:52:47	MarkDuplicates	Written    90,000,000 records.  Elapsed time: 00:13:24s.  Time for last 10,000,000:   81s.  Last read position: chrM:12,547
INFO	2016-05-14 09:54:07	MarkDuplicates	Written   100,000,000 records.  Elapsed time: 00:14:44s.  Time for last 10,000,000:   80s.  Last read position: chrM:14,916
INFO	2016-05-14 09:55:30	MarkDuplicates	Written   110,000,000 records.  Elapsed time: 00:16:06s.  Time for last 10,000,000:   82s.  Last read position: chrM:16,438
INFO	2016-05-14 09:55:53	MarkDuplicates	Before output close freeMemory: 3886155864; totalMemory: 3916431360; maxMemory: 3916431360
INFO	2016-05-14 09:55:53	MarkDuplicates	After output close freeMemory: 3886154808; totalMemory: 3916431360; maxMemory: 3916431360
[Sat May 14 09:55:53 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 26.49 minutes.
Runtime.totalMemory()=3916431360
[bam_sort_core] merging from 46 files...

Num	14
ID	task.postalign_bam.nmsrt_bam_rep2.line_321.id_19
Name	nmsrt_bam rep2
Thread	thread_21
PID	20850

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

Start	2016-05-14 10:58:08
End	2016-05-14 11:13:21
Elapsed	00:15:13
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-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/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.nmsrt

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 16 files...

Num	15
ID	task.postalign_bam.bam_to_bedpe_rep2.line_425.id_20
Name	bam_to_bedpe rep2
Thread	thread_21
PID	20991

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

Start	2016-05-14 11:13:22
End	2016-05-14 11:15:05
Elapsed	00:01:43
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-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/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz

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

Num	16
ID	task.postalign_bed.subsample_bedpe_rep2.line_116.id_21
Name	subsample_bedpe rep2
Thread	thread_21
PID	21057

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

Start	2016-05-14 11:15:07
End	2016-05-14 11:16:45
Elapsed	00:01:38
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-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/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | grep -v "chrM" | shuf -n 17500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz

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

Num	17
ID	task.postalign_bam.bedpe_to_tag_rep2.line_465.id_22
Name	bedpe_to_tag rep2
Thread	thread_21
PID	21124

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

Start	2016-05-14 11:16:46
End	2016-05-14 11:18:20
Elapsed	00:01:34
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-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/ATAC9+10/align/rep2/ATAC10-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/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz

# SYS command. line 472

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz | grep -P -v 'chrM' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz; mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz

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

Num	18
ID	task.postalign_bed.shift_tag_rep2.line_140.id_23
Name	shift_tag rep2
Thread	thread_21
PID	21196

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

Start	2016-05-14 11:18:21
End	2016-05-14 11:19:16
Elapsed	00:00:55
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-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/ATAC9+10/align/rep2/ATAC10-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/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz

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

Num	19
ID	task.postalign_bed.subsample_bedpe2tagrep2.line_89.id_24
Name	subsample_bedpe2tagrep2
Thread	thread_21
PID	21258

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

Start	2016-05-14 11:19:17
End	2016-05-14 11:20:07
Elapsed	00:00:50
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/align/rep2/ATAC10-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/ATAC9+10/align/rep2/ATAC10-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/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz

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

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

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/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-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/ATAC9+10/align/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz -p=1 \
			-filtchr=chrM -savp=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf -out=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-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/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp

# SYS command. line 175

 mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC9+10/qc/rep2/ATAC10-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/ATAC9+10, -num_rep, 2, -fastq1_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC9/ATAC9-trimmed-pair1.fastq.gz, -fastq1_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC9/ATAC9-trimmed-pair2.fastq.gz, -fastq2_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC10/ATAC10-trimmed-pair1.fastq.gz, -fastq2_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC10/ATAC10-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

Timeline

Task Graph

Parallel (threads) details

Task details

Global scope