Script file	/users/pangwei/bds_atac/atac.bds
Program ID	atac.bds.20160516_201635_170
Start time	2016-05-16 20:16:35
Run time	02:23:01.007
Tasks executed	16
Tasks failed	0
Tasks failed names
Arguments*	[-out_dir, /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4, -num_rep, 2, -fastq1_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC3/ATAC3-trimmed-pair1.fastq.gz, -fastq1_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC3/ATAC3-trimmed-pair2.fastq.gz, -fastq2_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC4/ATAC4-trimmed-pair1.fastq.gz, -fastq2_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC4/ATAC4-trimmed-pair2.fastq.gz, -subsample, 17500000, -true_rep, -species, hg19]
System*	local
Cpus*	1
Exit value	0

Thread ID	Parent	Tasks
thread_Root	None	atac.bds.20160516_201635_170/task.idr.idr2_rep1_rep2.line_61.id_6 atac.bds.20160516_201635_170/task.base.line_414.id_9 atac.bds.20160516_201635_170/task.base.line_414.id_10 atac.bds.20160516_201635_170/task.base.line_414.id_11 atac.bds.20160516_201635_170/task.base.line_414.id_12 atac.bds.20160516_201635_170/task.idr.idr_final_qc.line_196.id_13 atac.bds.20160516_201635_170/task.report.line_418.id_18 atac.bds.20160516_201635_170/task.report.line_418.id_19 atac.bds.20160516_201635_170/task.report.line_418.id_20 atac.bds.20160516_201635_170/task.report_graphviz.line_93.id_21 atac.bds.20160516_201635_170/task.report.line_383.id_26 atac.bds.20160516_201635_170/task.report.line_383.id_27
thread_20	thread_Root
thread_35	thread_Root	atac.bds.20160516_201635_170_parallel_35/task.postalign_bam.srt_bam_rep1.line_345.id_14 atac.bds.20160516_201635_170_parallel_35/task.atac.ataqc_rep1.line_815.id_17
thread_21	thread_Root
thread_36	thread_Root	atac.bds.20160516_201635_170_parallel_36/task.postalign_bam.srt_bam_rep2.line_345.id_15 atac.bds.20160516_201635_170_parallel_36/task.atac.ataqc_rep2.line_815.id_16

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.idr.idr2_rep1_rep2.line_61.id_6
Name	idr2 rep1-rep2
Thread	thread_Root
PID	130136

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

Start	2016-05-16 20:16:36
End	2016-05-16 20:21:16
Elapsed	00:04:39
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt.png /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz
Dependencies

 
# SYS command. line 63

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

# SYS command. line 65

 idr --samples /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz --peak-list /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/pooled_rep/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt --rank p.value --soft-idr-threshold 0.1 \
			--plot --use-best-multisummit-IDR

# SYS command. line 69

 idr_thresh_transformed=$(awk -v p=0.1 'BEGIN{print -log(p)/log(10)}')

# SYS command. line 72

 awk 'BEGIN{OFS="\t"} $12>='"${idr_thresh_transformed}"' {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.narrowPeak.gz

# SYS command. line 75

 awk 'BEGIN{OFS="\t"} $12>='"${idr_thresh_transformed}"' {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,"0"}' /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.13-col.bed.gz

# SYS command. line 78

 bedtools intersect -v -a /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.narrowPeak.gz -b /mnt/data/ENCODE/blacklists/wgEncodeDacMapabilityConsensusExcludable.bed.gz | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz; bedtools intersect -v -a /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.13-col.bed.gz -b /mnt/data/ENCODE/blacklists/wgEncodeDacMapabilityConsensusExcludable.bed.gz | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz

# SYS command. line 80

 gzip -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt

    
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac_py3/bin to PATH
Initial parameter values: [0.10 1.00 0.20 0.50]
Final parameter values: [1.45 0.88 0.59 0.31]
Number of reported peaks - 183962/183962 (100.0%)

Number of peaks passing IDR cutoff of 0.1 - 59094/183962 (32.1%)

Num	2
ID	task.base.line_414.id_9
Name	task.base.line_414.id_9
Thread	thread_Root
PID	131463

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

Start	2016-05-16 20:21:16
End	2016-05-16 20:21:17
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 416

 cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz

Num	3
ID	task.base.line_414.id_10
Name	task.base.line_414.id_10
Thread	thread_Root
PID	131473

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

Start	2016-05-16 20:21:16
End	2016-05-16 20:21:17
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 416

 cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz

Num	4
ID	task.base.line_414.id_11
Name	task.base.line_414.id_11
Thread	thread_Root
PID	131480

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

Start	2016-05-16 20:21:17
End	2016-05-16 20:21:17
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.gz
Dependencies

 
# SYS command. line 416

 cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.gz

Num	5
ID	task.base.line_414.id_12
Name	task.base.line_414.id_12
Thread	thread_Root
PID	131491

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

Start	2016-05-16 20:21:17
End	2016-05-16 20:21:17
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.13-col.bed.gz
Dependencies

 
# SYS command. line 416

 cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.13-col.bed.gz

Num	6
ID	task.idr.idr_final_qc.line_196.id_13
Name	idr final qc
Thread	thread_Root
PID	131511

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

Start	2016-05-16 20:21:17
End	2016-05-16 20:21:18
Elapsed	00:00:01
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/IDR_final.qc
Dependencies

 
# SYS command. line 198

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

# SYS command. line 200

 echo -e "Nt\t""Np\tconservative_set\toptimal_set\trescue_ratio\tself_consistency_ratio\treproducibility" > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/IDR_final.qc

# SYS command. line 201

 echo -e "59125\t""0\trep1-rep2\trep1-rep2\tInfinity\tNaN\t0" >> /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/IDR_final.qc

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

Num	7
ID	task.postalign_bam.srt_bam_rep1.line_345.id_14
Name	srt_bam rep1
Thread	thread_35
PID	131517

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

Start	2016-05-16 20:21:17
End	2016-05-16 20:46:29
Elapsed	00:25:11
Timeout	00:00:-1
Wall Timeout	100 days

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

 
# SYS command. line 347

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

# SYS command. line 353

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

# SYS command. line 354

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

# SYS command. line 356

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

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

Num	8
ID	task.postalign_bam.srt_bam_rep2.line_345.id_15
Name	srt_bam rep2
Thread	thread_36
PID	131525

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

Start	2016-05-16 20:21:18
End	2016-05-16 20:41:46
Elapsed	00:20:28
Timeout	00:00:-1
Wall Timeout	100 days

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

 
# SYS command. line 347

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

# SYS command. line 353

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

# SYS command. line 354

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

# SYS command. line 356

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

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

Num	9
ID	task.atac.ataqc_rep2.line_815.id_16
Name	ataqc rep2
Thread	thread_36
PID	132401

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

Start	2016-05-16 20:41:47
End	2016-05-16 22:32:49
Elapsed	01:51:01
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC4/ATAC4-trimmed-pair1.fastq.gz /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC4/ATAC4-trimmed-pair2.fastq.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2/ATAC4-trimmed-pair1.trim.PE2SE.align.log /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.pbc.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2/ATAC4-trimmed-pair1.trim.PE2SE.dup.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/signal/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2/ATAC4-trimmed-pair1.PE2SE_qc.html /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2/ATAC4-trimmed-pair1.PE2SE_qc.txt
Dependencies

 
# SYS command. line 817

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

# SYS command. line 821

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

# SYS command. line 823

 cd /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2

# SYS command. line 825

 /users/pangwei/bds_atac/ataqc/run_ataqc.py \
			    --workdir /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2 \
			    --outdir /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2 \
			    --outprefix ATAC4-trimmed-pair1.PE2SE \
			    --genome hg19 \
			    --ref /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/encodeHg19Male.fa \
			    --tss /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/hg19_RefSeq_stranded.bed.gz \
			    --dnase /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_all_p10_ucsc.bed.gz \
			    --blacklist /mnt/data/ENCODE/blacklists/wgEncodeDacMapabilityConsensusExcludable.bed.gz \
			    --prom /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_prom_p2.bed.gz \
			    --enh /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_enh_p2.bed.gz \
			    --reg2map /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/dnase_avgs_reg2map_p10_merged_named.pvals.gz \
			    --meta /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/eid_to_mnemonic.txt \
			    --pbc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.pbc.qc\
			    --fastq1 /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC4/ATAC4-trimmed-pair1.fastq.gz --fastq2 /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC4/ATAC4-trimmed-pair2.fastq.gz \
			    --alignedbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.bam \
			    --alignmentlog /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2/ATAC4-trimmed-pair1.trim.PE2SE.align.log \
			    --coordsortbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.srt.bam \
			    --duplog /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2/ATAC4-trimmed-pair1.trim.PE2SE.dup.qc \
			    --finalbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.bam \
			    --finalbed /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz \
			    --bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/signal/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig \
			    --peaks /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz \
			     \
			    --idr_peaks /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz

   
--------------------Stdout--------------------
Run time: 1:50:51

 
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
ERROR	2016-05-16 20:46:23	ProcessExecutor	Warning messages:
ERROR	2016-05-16 20:46:23	ProcessExecutor	1: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
ERROR	2016-05-16 20:46:23	ProcessExecutor	  zero-length arrow is of indeterminate angle and so skipped
ERROR	2016-05-16 20:46:23	ProcessExecutor	2: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
ERROR	2016-05-16 20:46:23	ProcessExecutor	  zero-length arrow is of indeterminate angle and so skipped
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
[bam_sort_core] merging from 28 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
processing chromosomes
/users/pangwei/bds_atac/ataqc/run_ataqc.py:851: FutureWarning: sort(columns=....) is deprecated, use sort_values(by=.....)
  sorted_results = merged.sort('corr', ascending=True)

Num	10
ID	task.atac.ataqc_rep1.line_815.id_17
Name	ataqc rep1
Thread	thread_35
PID	132603

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

Start	2016-05-16 20:46:30
End	2016-05-16 22:39:15
Elapsed	01:52:44
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC3/ATAC3-trimmed-pair1.fastq.gz /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC3/ATAC3-trimmed-pair2.fastq.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1/ATAC3-trimmed-pair1.trim.PE2SE.align.log /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.pbc.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1/ATAC3-trimmed-pair1.trim.PE2SE.dup.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/signal/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1/ATAC3-trimmed-pair1.PE2SE_qc.html /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1/ATAC3-trimmed-pair1.PE2SE_qc.txt
Dependencies

 
# SYS command. line 817

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

# SYS command. line 821

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

# SYS command. line 823

 cd /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1

# SYS command. line 825

 /users/pangwei/bds_atac/ataqc/run_ataqc.py \
			    --workdir /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1 \
			    --outdir /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1 \
			    --outprefix ATAC3-trimmed-pair1.PE2SE \
			    --genome hg19 \
			    --ref /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/encodeHg19Male.fa \
			    --tss /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/hg19_RefSeq_stranded.bed.gz \
			    --dnase /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_all_p10_ucsc.bed.gz \
			    --blacklist /mnt/data/ENCODE/blacklists/wgEncodeDacMapabilityConsensusExcludable.bed.gz \
			    --prom /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_prom_p2.bed.gz \
			    --enh /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_enh_p2.bed.gz \
			    --reg2map /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/dnase_avgs_reg2map_p10_merged_named.pvals.gz \
			    --meta /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/eid_to_mnemonic.txt \
			    --pbc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.pbc.qc\
			    --fastq1 /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC3/ATAC3-trimmed-pair1.fastq.gz --fastq2 /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC3/ATAC3-trimmed-pair2.fastq.gz \
			    --alignedbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.bam \
			    --alignmentlog /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1/ATAC3-trimmed-pair1.trim.PE2SE.align.log \
			    --coordsortbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.srt.bam \
			    --duplog /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1/ATAC3-trimmed-pair1.trim.PE2SE.dup.qc \
			    --finalbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.bam \
			    --finalbed /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/align/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz \
			    --bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/signal/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig \
			    --peaks /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz \
			     \
			    --idr_peaks /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz

   
--------------------Stdout--------------------
Run time: 1:52:42

 
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
ERROR	2016-05-16 20:50:10	ProcessExecutor	Warning messages:
ERROR	2016-05-16 20:50:10	ProcessExecutor	1: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
ERROR	2016-05-16 20:50:10	ProcessExecutor	  zero-length arrow is of indeterminate angle and so skipped
ERROR	2016-05-16 20:50:10	ProcessExecutor	2: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
ERROR	2016-05-16 20:50:10	ProcessExecutor	  zero-length arrow is of indeterminate angle and so skipped
ERROR	2016-05-16 20:50:10	ProcessExecutor	3: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
ERROR	2016-05-16 20:50:10	ProcessExecutor	  zero-length arrow is of indeterminate angle and so skipped
ERROR	2016-05-16 20:50:10	ProcessExecutor	4: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
ERROR	2016-05-16 20:50:10	ProcessExecutor	  zero-length arrow is of indeterminate angle and so skipped
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
[bam_sort_core] merging from 38 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
processing chromosomes
/users/pangwei/bds_atac/ataqc/run_ataqc.py:851: FutureWarning: sort(columns=....) is deprecated, use sort_values(by=.....)
  sorted_results = merged.sort('corr', ascending=True)

Num	11
ID	task.report.line_418.id_18
Name	task.report.line_418.id_18
Thread	thread_Root
PID	135874

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

Start	2016-05-16 22:39:17
End	2016-05-16 22:39:18
Elapsed	00:00:01
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.hammock.gz
Dependencies

 
# SYS command. line 420

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

# SYS command. line 421

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.tmp

# SYS command. line 423

 /users/pangwei/bds_atac/utils/narrowpeak_idr.py /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.hammock

# SYS command. line 424

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.tmp

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

Num	12
ID	task.report.line_418.id_19
Name	task.report.line_418.id_19
Thread	thread_Root
PID	135942

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

Start	2016-05-16 22:39:19
End	2016-05-16 22:39:26
Elapsed	00:00:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.hammock.gz
Dependencies

 
# SYS command. line 420

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

# SYS command. line 421

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.tmp

# SYS command. line 423

 /users/pangwei/bds_atac/utils/narrowpeak.py /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.hammock

# SYS command. line 424

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.tmp

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

Num	13
ID	task.report.line_418.id_20
Name	task.report.line_418.id_20
Thread	thread_Root
PID	136014

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

Start	2016-05-16 22:39:27
End	2016-05-16 22:39:31
Elapsed	00:00:04
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz
Output files	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.hammock.gz
Dependencies

 
# SYS command. line 420

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

# SYS command. line 421

 zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.tmp

# SYS command. line 423

 /users/pangwei/bds_atac/utils/narrowpeak.py /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/peak/macs2/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.hammock

# SYS command. line 424

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

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

Num	14
ID	task.report_graphviz.line_93.id_21
Name	task.report_graphviz.line_93.id_21
Thread	thread_Root
PID	136102

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

Start	2016-05-16 22:39:32
End	2016-05-16 22:39:35
Elapsed	00:00:03
Timeout	00:00:-1
Wall Timeout	100 days

Input files
Output files
Dependencies

 
# SYS command. line 94

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

# SYS command. line 95

 dot -Tsvg /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/report/workflow.dot > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/report/workflow.svg

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

Num	15
ID	task.report.line_383.id_26
Name	task.report.line_383.id_26
Thread	thread_Root
PID	136109

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

Start	2016-05-16 22:39:32
End	2016-05-16 22:39:33
Elapsed	00:00:01
Timeout	00:00:-1
Wall Timeout	100 days

Input files
Output files
Dependencies

 
# SYS command. line 384

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

# SYS command. line 385

 gs -dFirstPage=1 -dLastPage=1 -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -r110x110 \
			-dUseCropBox -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -sDEVICE=png16m \
			-sOutputFile=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.png \
			-r144 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep1/ATAC3-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf

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

Num	16
ID	task.report.line_383.id_27
Name	task.report.line_383.id_27
Thread	thread_Root
PID	136122

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

Start	2016-05-16 22:39:32
End	2016-05-16 22:39:33
Elapsed	00:00:01
Timeout	00:00:-1
Wall Timeout	100 days

Input files
Output files
Dependencies

 
# SYS command. line 384

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

# SYS command. line 385

 gs -dFirstPage=1 -dLastPage=1 -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -r110x110 \
			-dUseCropBox -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -sDEVICE=png16m \
			-sOutputFile=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.png \
			-r144 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4/qc/rep2/ATAC4-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf

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

Type	Name	Value
string	_	/usr/bin/bds
string	_LMFILES_	/software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/samtools/1.2:/software/modulefiles/bedtools/2.23.0:/software/modulefiles/rsem/1.2.21
string	_ZSH_TMUX_FIXED_CONFIG	/users/pangwei/.oh-my-zsh/plugins/tmux/tmux.extra.conf
bool	allowEmpty	false
string[]	args	[-out_dir, /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC3+4, -num_rep, 2, -fastq1_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC3/ATAC3-trimmed-pair1.fastq.gz, -fastq1_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC3/ATAC3-trimmed-pair2.fastq.gz, -fastq2_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC4/ATAC4-trimmed-pair1.fastq.gz, -fastq2_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC4/ATAC4-trimmed-pair2.fastq.gz, -subsample, 17500000, -true_rep, -species, hg19]
string	C_INCLUDE_PATH	/software/samtools/samtools-1.2/include/htslib
bool	canFail	false
int	cpus	1
int	cpusLocal	48
int	day	86400
real	E	2.718281828459045
int	G	1073741824
string	HOME	/users/pangwei/
int	hour	3600
int	K	1024
string	LANG	en_US.UTF-8
string	LC_CTYPE	en_US.UTF-8
string	LD_LIBRARY_PATH	/software/samtools/samtools-1.2/lib:/usr/local/cudnn-3/lib64/:/usr/local/cudnn-3/lib64/
string	LESS	-R
string	LOADEDMODULES	modsappsdir/modsappsdir:samtools/1.2:bedtools/2.23.0:rsem/1.2.21
string	LOGNAME	pangwei
string	LSCOLORS	Gxfxcxdxbxegedabagacad
int	M	1048576
string	MAIL	/var/mail/pangwei
string	MANPATH	/software/samtools/samtools-1.2/share/man:/usr/share/man
int	mem	-1
int	minute	60
string	MODULE_VERSION	3.2.10
string	MODULE_VERSION_STACK	3.2.10
string	MODULEPATH	/usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles
string	MODULESAPPSDIR	/software
string	MODULESHOME	/software/env_module/3.2.10
string	node
int	P	1125899906842624
string	PAGER	less
string	PATH	/software/RSEM/rsem-1.2.21/:/software/bedtools/2.23.0/bin:/software/samtools/samtools-1.2/bin:/users/pangwei/anaconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
real	PI	3.141592653589793
string	ppwd	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata
string	programName	atac.bds
string	programPath	/users/pangwei/bds_atac/atac.bds
string	PWD	/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata
string	PYTHONPATH	/home/jisraeli/src/caffe_atac/python/:/users/pangwei/stemcells:/home/jisraeli/src/caffe_atac/python/:/users/pangwei/stemcells:
string	queue
int	retry	0
string	SAMTOOLS_HOME	/software/samtools/samtools-1.2/bin
string	SHELL	/usr/bin/zsh
string	SHLVL	3
string	SSH_AUTH_SOCK	/tmp/ssh-5gr8qSU2WF/agent.74700
string	SSH_CLIENT	171.65.76.244 36245 22
string	SSH_CONNECTION	171.65.76.244 49273 171.65.76.236 22
string	SSH_TTY	/dev/pts/0
string	system	local
int	T	1099511627776
string	TERM	screen
string	THEANO_FLAGS	device=gpu6,floatX=float32,warn_float64=warn,optimizer_excluding=cudnn
int	timeout	-1
string	TMUX	/tmp/tmux-1077/default,106699,3
string	TMUX_PANE	%3
string	USER	pangwei
string	UTIL_SCRIPTS_DIR	/users/pangwei/av_scripts
int	walltimeout	8640000
int	week	604800
string	WWW	/srv/www/kundaje/pangwei
string	XDG_RUNTIME_DIR	/run/user/1077
string	XDG_SESSION_ID	1907
string	ZSH	/users/pangwei//.oh-my-zsh
string	ZSH_TMUX_TERM	screen

BigDataScript report: atac.bds

Timeline

Task Graph

Parallel (threads) details

Task details

Global scope