Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20161107_130605_519
Start time	2016-11-07 13:06:05
Run time	00:14:36.325
Tasks executed	2
Tasks failed	0
Tasks failed names
Arguments*	[-title, WT, -nth, 5, -species, mm10, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/MouseMutantData/WT/out, -tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.nodup.tagAlign.gz, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz, $]
System*	sge
Cpus*	-1
Exit value	0

Thread ID	Parent	Tasks
thread_Root	None	chipseq.bds.20161107_130605_519/task.callpeak_macs2.macs2_rep1.line_67.id_10 chipseq.bds.20161107_130605_519/task.graphviz.report.line_97.id_13
thread_42	thread_Root
thread_41	thread_Root

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.callpeak_macs2.macs2_rep1.line_67.id_10
Name	macs2 rep1
Thread	thread_Root
PID	4554

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

Start	2016-11-07 13:06:11
End	2016-11-07 13:20:34
Elapsed	00:14:22
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.nodup.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/signal/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/signal/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bw
Dependencies

 
# SYS command. line 69

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 70

 export LC_COLLATE=C

# SYS command. line 75

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --nomodel --shift 0 --extsize 110 --keep-dup all -B --SPMR

# SYS command. line 78

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.narrowPeak.gz

# SYS command. line 81

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_summits.bed

# SYS command. line 88

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --broad --nomodel --shift 0 --extsize 110 --keep-dup all

# SYS command. line 91

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.broadPeak.gz

# SYS command. line 92

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gappedPeak.gz

# SYS command. line 95

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_summits.bed

# SYS command. line 100

 if [[ true == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 111

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1 -o "wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 114

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/mm10/mm10.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/mm10/mm10.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 115

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_FE.bdg

# SYS command. line 118

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 119

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/mm10/mm10.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/signal/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bw

# SYS command. line 120

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 126

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 128

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

# SYS command. line 130

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1 -o "wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 133

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/mm10/mm10.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/mm10/mm10.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 134

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_ppois.bdg

# SYS command. line 137

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 138

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/mm10/mm10.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/signal/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bw

# SYS command. line 139

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 141

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 143

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
24051 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Mon, 07 Nov 2016 13:06:31: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --nomodel --shift 0 --extsize 110 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz']
# effective genome size = 1.87e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Mon, 07 Nov 2016 13:06:31: #1 read tag files... 
INFO  @ Mon, 07 Nov 2016 13:06:31: #1 read treatment tags... 
INFO  @ Mon, 07 Nov 2016 13:06:33:  1000000 
INFO  @ Mon, 07 Nov 2016 13:06:35:  2000000 
INFO  @ Mon, 07 Nov 2016 13:06:36:  3000000 
INFO  @ Mon, 07 Nov 2016 13:06:37:  4000000 
INFO  @ Mon, 07 Nov 2016 13:06:39:  5000000 
INFO  @ Mon, 07 Nov 2016 13:06:40:  6000000 
INFO  @ Mon, 07 Nov 2016 13:06:42:  7000000 
INFO  @ Mon, 07 Nov 2016 13:06:43:  8000000 
INFO  @ Mon, 07 Nov 2016 13:06:44:  9000000 
INFO  @ Mon, 07 Nov 2016 13:06:46:  10000000 
INFO  @ Mon, 07 Nov 2016 13:06:47:  11000000 
INFO  @ Mon, 07 Nov 2016 13:06:49:  12000000 
INFO  @ Mon, 07 Nov 2016 13:06:50:  13000000 
INFO  @ Mon, 07 Nov 2016 13:06:51:  14000000 
INFO  @ Mon, 07 Nov 2016 13:06:53:  15000000 
INFO  @ Mon, 07 Nov 2016 13:06:54:  16000000 
INFO  @ Mon, 07 Nov 2016 13:06:55: #1.2 read input tags... 
INFO  @ Mon, 07 Nov 2016 13:06:57:  1000000 
INFO  @ Mon, 07 Nov 2016 13:06:58:  2000000 
INFO  @ Mon, 07 Nov 2016 13:07:00:  3000000 
INFO  @ Mon, 07 Nov 2016 13:07:00: #1 tag size is determined as 35 bps 
INFO  @ Mon, 07 Nov 2016 13:07:00: #1 tag size = 35 
INFO  @ Mon, 07 Nov 2016 13:07:00: #1  total tags in treatment: 16775425 
INFO  @ Mon, 07 Nov 2016 13:07:00: #1  total tags in control: 3384182 
INFO  @ Mon, 07 Nov 2016 13:07:00: #1 finished! 
INFO  @ Mon, 07 Nov 2016 13:07:00: #2 Build Peak Model... 
INFO  @ Mon, 07 Nov 2016 13:07:00: #2 Skipped... 
INFO  @ Mon, 07 Nov 2016 13:07:00: #2 Use 110 as fragment length 
INFO  @ Mon, 07 Nov 2016 13:07:00: #3 Call peaks... 
INFO  @ Mon, 07 Nov 2016 13:07:00: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Mon, 07 Nov 2016 13:07:00: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 07 Nov 2016 13:07:30: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Mon, 07 Nov 2016 13:07:30: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Mon, 07 Nov 2016 13:07:30: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_control_lambda.bdg 
INFO  @ Mon, 07 Nov 2016 13:07:30: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Mon, 07 Nov 2016 13:07:30: #3 Call peaks for each chromosome... 
INFO  @ Mon, 07 Nov 2016 13:08:48: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.xls 
INFO  @ Mon, 07 Nov 2016 13:08:48: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Mon, 07 Nov 2016 13:08:49: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_summits.bed 
INFO  @ Mon, 07 Nov 2016 13:08:49: Done! 
INFO  @ Mon, 07 Nov 2016 13:08:52: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --broad --nomodel --shift 0 --extsize 110 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz']
# effective genome size = 1.87e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Mon, 07 Nov 2016 13:08:52: #1 read tag files... 
INFO  @ Mon, 07 Nov 2016 13:08:52: #1 read treatment tags... 
INFO  @ Mon, 07 Nov 2016 13:08:54:  1000000 
INFO  @ Mon, 07 Nov 2016 13:08:55:  2000000 
INFO  @ Mon, 07 Nov 2016 13:08:57:  3000000 
INFO  @ Mon, 07 Nov 2016 13:08:58:  4000000 
INFO  @ Mon, 07 Nov 2016 13:08:59:  5000000 
INFO  @ Mon, 07 Nov 2016 13:09:01:  6000000 
INFO  @ Mon, 07 Nov 2016 13:09:02:  7000000 
INFO  @ Mon, 07 Nov 2016 13:09:04:  8000000 
INFO  @ Mon, 07 Nov 2016 13:09:05:  9000000 
INFO  @ Mon, 07 Nov 2016 13:09:06:  10000000 
INFO  @ Mon, 07 Nov 2016 13:09:08:  11000000 
INFO  @ Mon, 07 Nov 2016 13:09:09:  12000000 
INFO  @ Mon, 07 Nov 2016 13:09:10:  13000000 
INFO  @ Mon, 07 Nov 2016 13:09:12:  14000000 
INFO  @ Mon, 07 Nov 2016 13:09:13:  15000000 
INFO  @ Mon, 07 Nov 2016 13:09:15:  16000000 
INFO  @ Mon, 07 Nov 2016 13:09:16: #1.2 read input tags... 
INFO  @ Mon, 07 Nov 2016 13:09:17:  1000000 
INFO  @ Mon, 07 Nov 2016 13:09:19:  2000000 
INFO  @ Mon, 07 Nov 2016 13:09:20:  3000000 
INFO  @ Mon, 07 Nov 2016 13:09:21: #1 tag size is determined as 35 bps 
INFO  @ Mon, 07 Nov 2016 13:09:21: #1 tag size = 35 
INFO  @ Mon, 07 Nov 2016 13:09:21: #1  total tags in treatment: 16775425 
INFO  @ Mon, 07 Nov 2016 13:09:21: #1  total tags in control: 3384182 
INFO  @ Mon, 07 Nov 2016 13:09:21: #1 finished! 
INFO  @ Mon, 07 Nov 2016 13:09:21: #2 Build Peak Model... 
INFO  @ Mon, 07 Nov 2016 13:09:21: #2 Skipped... 
INFO  @ Mon, 07 Nov 2016 13:09:21: #2 Use 110 as fragment length 
INFO  @ Mon, 07 Nov 2016 13:09:21: #3 Call peaks... 
INFO  @ Mon, 07 Nov 2016 13:09:21: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Mon, 07 Nov 2016 13:09:21: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Mon, 07 Nov 2016 13:09:53: #3 Call peaks for each chromosome... 
INFO  @ Mon, 07 Nov 2016 13:10:27: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.xls 
INFO  @ Mon, 07 Nov 2016 13:10:28: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.broadPeak 
INFO  @ Mon, 07 Nov 2016 13:10:29: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Mon, 07 Nov 2016 13:10:29: Done! 
INFO  @ Mon, 07 Nov 2016 13:10:34: Read and build treatment bedGraph... 
INFO  @ Mon, 07 Nov 2016 13:11:03: Read and build control bedGraph... 
INFO  @ Mon, 07 Nov 2016 13:11:14: Build scoreTrackII... 
INFO  @ Mon, 07 Nov 2016 13:11:31: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Mon, 07 Nov 2016 13:13:06: Write bedGraph of scores... 
INFO  @ Mon, 07 Nov 2016 13:14:06: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_FE.bdg'! 
INFO  @ Mon, 07 Nov 2016 13:16:31: Read and build treatment bedGraph... 
INFO  @ Mon, 07 Nov 2016 13:17:00: Read and build control bedGraph... 
INFO  @ Mon, 07 Nov 2016 13:17:11: Build scoreTrackII... 
INFO  @ Mon, 07 Nov 2016 13:17:30: Values in your input bedGraph files will be multiplied by 3.384182 ... 
INFO  @ Mon, 07 Nov 2016 13:18:55: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Mon, 07 Nov 2016 13:19:07: Write bedGraph of scores... 
INFO  @ Mon, 07 Nov 2016 13:19:30: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/rep1/wt_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_ppois.bdg'!

Num	2
ID	task.graphviz.report.line_97.id_13
Name	report
Thread	thread_Root
PID	27257

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

Start	2016-11-07 13:20:39
End	2016-11-07 13:20:41
Elapsed	00:00:02
Timeout	00:00:-1
Wall Timeout	100 days

Input files
Output files
Dependencies

 
# SYS command. line 98

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 99

 dot -Tsvg /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/report/WT_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/report/WT_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/report/WT_workflow.svg" # to suppress dot font error (exit code=1)

   
--------------------Stdout--------------------
27261 (process ID) old priority 0, new priority 10

Type	Name	Value
string	_	/usr/bin/bds
bool	allowEmpty	false
string[]	args	[-title, WT, -nth, 5, -species, mm10, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/MouseMutantData/WT/out, -tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.nodup.tagAlign.gz, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz, $]
bool	canFail	false
int	cpus	-1
int	cpusLocal	56
int	day	86400
string	DEEPLIFT_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift
string	DERBY_HOME	/usr/lib/jvm/java-8-oracle/db
string	DISPLAY	localhost:12.0
real	E	2.718281828459045
string	ENHANCER_SCRIPTS_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/
int	G	1073741824
string	HOME	/users/imk1/
int	hour	3600
string	J2REDIR	/usr/lib/jvm/java-8-oracle/jre
string	J2SDKDIR	/usr/lib/jvm/java-8-oracle
string	JAVA_HOME	/usr/lib/jvm/java-8-oracle
int	K	1024
string	KERAS_DIR	/users/imk1/.local/lib/python2.7/site-packages/keras/
string	KRB5CCNAME	FILE:/tmp/krb5cc_1048_N5SeQf
string	LANG	en_US.UTF-8
string	LOADEDMODULES
string	LOGNAME	imk1
int	M	1048576
string	MAIL	/var/mail/imk1
int	mem	-1
int	minute	60
string	MODULE_VERSION	3.2.10
string	MODULE_VERSION_STACK	3.2.10
string	MODULEPATH	/usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles
string	MODULESHOME	/software/env_module/3.2.10
string	NLSPATH	/usr/dt/lib/nls/msg/%L/%N.cat
string	node
int	P	1125899906842624
string	PATH	/users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/srv/scratch/imk1/TFBindingPredictionProject/src/R-3.2.3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/users/imk1/edirect:/users/imk1/edirect
string	PERL5LIB	/users/imk1/perl5/lib/perl5
string	PERL_LOCAL_LIB_ROOT	/users/imk1/perl5
string	PERL_MB_OPT	--install_base \"/users/imk1/perl5\"
string	PERL_MM_OPT	INSTALL_BASE=/users/imk1/perl5
real	PI	3.141592653589793
string	ppwd	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT
string	programName	chipseq.bds
string	programPath	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/chipseq.bds
string	PWD	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT
string	PYTHONPATH	/users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/
string	queue
int	retry	0
string	RULEFITBASE	/srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/
string	SHELL	/bin/bash
string	SHLVL	3
string	SSH_CLIENT	171.65.77.8 55144 22
string	SSH_CONNECTION	171.65.77.8 55144 171.65.76.63 22
string	SSH_TTY	/dev/pts/4
string	STY	22858.WT.BDS
string	system	sge
int	T	1099511627776
string	TERM	screen
string	TERMCAP	SC\|screen\|VT 100/ANSI X3.64 virtual terminal:\\\n\t:DO=\\E[%dB:LE=\\E[%dD:RI=\\E[%dC:UP=\\E[%dA:bs:bt=\\E[Z:\\\n\t:cd=\\E[J:ce=\\E[K:cl=\\E[H\\E[J:cm=\\E[%i%d;%dH:ct=\\E[3g:\\\n\t:do=^J:nd=\\E[C:pt:rc=\\E8:rs=\\Ec:sc=\\E7:st=\\EH:up=\\EM:\\\n\t:le=^H:bl=^G:cr=^M:it#8:ho=\\E[H:nw=\\EE:ta=^I:is=\\E)0:\\\n\t:li#24:co#80:am:xn:xv:LP:sr=\\EM:al=\\E[L:AL=\\E[%dL:\\\n\t:cs=\\E[%i%d;%dr:dl=\\E[M:DL=\\E[%dM:dc=\\E[P:DC=\\E[%dP:\\\n\t:im=\\E[4h:ei=\\E[4l:mi:IC=\\E[%d@:ks=\\E[?1h\\E=:\\\n\t:ke=\\E[?1l\\E>:vi=\\E[?25l:ve=\\E[34h\\E[?25h:vs=\\E[34l:\\\n\t:ti=\\E[?1049h:te=\\E[?1049l:Km=\\E[M:k0=\\E[10~:k1=\\EOP:\\\n\t:k2=\\EOQ:k3=\\EOR:k4=\\EOS:k5=\\E[15~:k6=\\E[17~:k7=\\E[18~:\\\n\t:k8=\\E[19~:k9=\\E[20~:k;=\\E[21~:F1=\\E[23~:F2=\\E[24~:\\\n\t:kh=\\E[1~:@1=\\E[1~:kH=\\E[4~:@7=\\E[4~:kN=\\E[6~:kP=\\E[5~:\\\n\t:kI=\\E[2~:kD=\\E[3~:ku=\\EOA:kd=\\EOB:kr=\\EOC:kl=\\EOD:
int	timeout	-1
string	USER	imk1
string	UTIL_SCRIPTS_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/av_scripts/
int	walltimeout	8640000
int	week	604800
string	WINDOW	0
string	XDG_RUNTIME_DIR	/run/user/1048
string	XDG_SESSION_ID	20
string	XFILESEARCHPATH	/usr/dt/app-defaults/%L/Dt

BigDataScript report: chipseq.bds

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Parallel (threads) details

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Global scope