Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20161106_180921_471
Start time	2016-11-06 18:09:21
Run time	00:22:53.288
Tasks executed	3
Tasks failed	1
Tasks failed names	macs2 rep1
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, -gensz, mm, -chrsz, /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes, $]
System*	sge
Cpus*	-1
Exit value	1

Thread ID	Parent	Tasks
thread_Root	None	chipseq.bds.20161106_180921_471/task.callpeak_macs2.macs2_rep1.line_67.id_10 chipseq.bds.20161106_180921_471/task.callpeak_macs2.macs2_rep1_pr1.line_67.id_11 chipseq.bds.20161106_180921_471/task.callpeak_macs2.macs2_rep1_pr2.line_67.id_12
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	4376

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

Start	2016-11-06 18:09:32
End	2016-11-06 18:09:32
Elapsed	00:00:00
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/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.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/annotations/by_organism/mouse/mm10/mm10.male.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/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.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/annotations/by_organism/mouse/mm10/mm10.male.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--------------------
3560 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
INFO  @ Sun, 06 Nov 2016 18:21:01: 
# 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  @ Sun, 06 Nov 2016 18:21:01: #1 read tag files... 
INFO  @ Sun, 06 Nov 2016 18:21:01: #1 read treatment tags... 
INFO  @ Sun, 06 Nov 2016 18:21:04:  1000000 
INFO  @ Sun, 06 Nov 2016 18:21:06:  2000000 
INFO  @ Sun, 06 Nov 2016 18:21:07:  3000000 
INFO  @ Sun, 06 Nov 2016 18:21:09:  4000000 
INFO  @ Sun, 06 Nov 2016 18:21:10:  5000000 
INFO  @ Sun, 06 Nov 2016 18:21:12:  6000000 
INFO  @ Sun, 06 Nov 2016 18:21:13:  7000000 
INFO  @ Sun, 06 Nov 2016 18:21:15:  8000000 
INFO  @ Sun, 06 Nov 2016 18:21:16:  9000000 
INFO  @ Sun, 06 Nov 2016 18:21:17:  10000000 
INFO  @ Sun, 06 Nov 2016 18:21:19:  11000000 
INFO  @ Sun, 06 Nov 2016 18:21:20:  12000000 
INFO  @ Sun, 06 Nov 2016 18:21:22:  13000000 
INFO  @ Sun, 06 Nov 2016 18:21:23:  14000000 
INFO  @ Sun, 06 Nov 2016 18:21:25:  15000000 
INFO  @ Sun, 06 Nov 2016 18:21:26:  16000000 
INFO  @ Sun, 06 Nov 2016 18:21:27: #1.2 read input tags... 
INFO  @ Sun, 06 Nov 2016 18:21:29:  1000000 
INFO  @ Sun, 06 Nov 2016 18:21:31:  2000000 
INFO  @ Sun, 06 Nov 2016 18:21:32:  3000000 
INFO  @ Sun, 06 Nov 2016 18:21:33: #1 tag size is determined as 35 bps 
INFO  @ Sun, 06 Nov 2016 18:21:33: #1 tag size = 35 
INFO  @ Sun, 06 Nov 2016 18:21:33: #1  total tags in treatment: 16775425 
INFO  @ Sun, 06 Nov 2016 18:21:33: #1  total tags in control: 3384182 
INFO  @ Sun, 06 Nov 2016 18:21:33: #1 finished! 
INFO  @ Sun, 06 Nov 2016 18:21:33: #2 Build Peak Model... 
INFO  @ Sun, 06 Nov 2016 18:21:33: #2 Skipped... 
INFO  @ Sun, 06 Nov 2016 18:21:33: #2 Use 110 as fragment length 
INFO  @ Sun, 06 Nov 2016 18:21:33: #3 Call peaks... 
INFO  @ Sun, 06 Nov 2016 18:21:33: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Sun, 06 Nov 2016 18:21:33: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 06 Nov 2016 18:22:02: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Sun, 06 Nov 2016 18:22:02: #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  @ Sun, 06 Nov 2016 18:22:02: #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  @ Sun, 06 Nov 2016 18:22:02: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Sun, 06 Nov 2016 18:22:02: #3 Call peaks for each chromosome... 
INFO  @ Sun, 06 Nov 2016 18:23:30: #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  @ Sun, 06 Nov 2016 18:23:31: #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  @ Sun, 06 Nov 2016 18:23:32: #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  @ Sun, 06 Nov 2016 18:23:34: Done! 
INFO  @ Sun, 06 Nov 2016 18:23:39: 
# 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  @ Sun, 06 Nov 2016 18:23:39: #1 read tag files... 
INFO  @ Sun, 06 Nov 2016 18:23:39: #1 read treatment tags... 
INFO  @ Sun, 06 Nov 2016 18:23:40:  1000000 
INFO  @ Sun, 06 Nov 2016 18:23:42:  2000000 
INFO  @ Sun, 06 Nov 2016 18:23:43:  3000000 
INFO  @ Sun, 06 Nov 2016 18:23:45:  4000000 
INFO  @ Sun, 06 Nov 2016 18:23:46:  5000000 
INFO  @ Sun, 06 Nov 2016 18:23:48:  6000000 
INFO  @ Sun, 06 Nov 2016 18:23:49:  7000000 
INFO  @ Sun, 06 Nov 2016 18:23:51:  8000000 
INFO  @ Sun, 06 Nov 2016 18:23:52:  9000000 
INFO  @ Sun, 06 Nov 2016 18:23:54:  10000000 
INFO  @ Sun, 06 Nov 2016 18:23:55:  11000000 
INFO  @ Sun, 06 Nov 2016 18:23:57:  12000000 
INFO  @ Sun, 06 Nov 2016 18:23:58:  13000000 
INFO  @ Sun, 06 Nov 2016 18:24:00:  14000000 
INFO  @ Sun, 06 Nov 2016 18:24:01:  15000000 
INFO  @ Sun, 06 Nov 2016 18:24:03:  16000000 
INFO  @ Sun, 06 Nov 2016 18:24:04: #1.2 read input tags... 
INFO  @ Sun, 06 Nov 2016 18:24:06:  1000000 
INFO  @ Sun, 06 Nov 2016 18:24:07:  2000000 
INFO  @ Sun, 06 Nov 2016 18:24:09:  3000000 
INFO  @ Sun, 06 Nov 2016 18:24:09: #1 tag size is determined as 35 bps 
INFO  @ Sun, 06 Nov 2016 18:24:09: #1 tag size = 35 
INFO  @ Sun, 06 Nov 2016 18:24:09: #1  total tags in treatment: 16775425 
INFO  @ Sun, 06 Nov 2016 18:24:09: #1  total tags in control: 3384182 
INFO  @ Sun, 06 Nov 2016 18:24:09: #1 finished! 
INFO  @ Sun, 06 Nov 2016 18:24:09: #2 Build Peak Model... 
INFO  @ Sun, 06 Nov 2016 18:24:09: #2 Skipped... 
INFO  @ Sun, 06 Nov 2016 18:24:09: #2 Use 110 as fragment length 
INFO  @ Sun, 06 Nov 2016 18:24:09: #3 Call peaks... 
INFO  @ Sun, 06 Nov 2016 18:24:09: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Sun, 06 Nov 2016 18:24:09: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 06 Nov 2016 18:24:35: #3 Call peaks for each chromosome... 
INFO  @ Sun, 06 Nov 2016 18:25:08: #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  @ Sun, 06 Nov 2016 18:25:11: #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  @ Sun, 06 Nov 2016 18:25:12: #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  @ Sun, 06 Nov 2016 18:25:13: Done! 
INFO  @ Sun, 06 Nov 2016 18:25:19: Read and build treatment bedGraph... 
INFO  @ Sun, 06 Nov 2016 18:25:53: Read and build control bedGraph... 
INFO  @ Sun, 06 Nov 2016 18:26:07: Build scoreTrackII... 
INFO  @ Sun, 06 Nov 2016 18:26:18: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Sun, 06 Nov 2016 18:27:56: Write bedGraph of scores... 
INFO  @ Sun, 06 Nov 2016 18:28:55: 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'! 
Chromosome KQ030491.1 isn't in /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes line 1 of stdin


 
--------------------Post mortem info--------------------
==============================================================
job_number:                 4376
exec_file:                  job_scripts/4376
submission_time:            Sun Nov  6 18:09:32 2016
owner:                      imk1
uid:                        1048
group:                      users
gid:                        100
sge_o_home:                 /users/imk1/
sge_o_log_name:             imk1
sge_o_path:                 /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
sge_o_shell:                /bin/bash
sge_o_workdir:              /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/chipseq.bds.20161106_180921_471/task.callpeak_macs2.macs2_rep1.line_67.id_10.stderr.cluster
mail_list:                  imk1@surya
notify:                     FALSE
job_name:                   STDIN
stdout_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/chipseq.bds.20161106_180921_471/task.callpeak_macs2.macs2_rep1.line_67.id_10.stdout.cluster
jobshare:                   0
env_list:                   MAIL=/var/mail/imk1,SSH_CLIENT=171.65.77.8 55144 22,USER=imk1,J2SDKDIR=/usr/lib/jvm/java-8-oracle,SHLVL=3,J2REDIR=/usr/lib/jvm/java-8-oracle/jre,HOME=/users/imk1/,SSH_TTY=/dev/pts/4,LOGNAME=imk1,_=/usr/bin/bds,XDG_SESSION_ID=20,TERM=screen,SGE_ROOT=/var/lib/gridengine,PATH=/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,DERBY_HOME=/usr/lib/jvm/java-8-oracle/db,XDG_RUNTIME_DIR=/run/user/1048,DISPLAY=localhost:12.0,SGE_CELL=default,STY=35661.WT.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,KRB5CCNAME=FILE:/tmp/krb5cc_1048_N5SeQf,XFILESEARCHPATH=/usr/dt/app-defaults/%L/Dt,MODULE_VERSION=3.2.10,MODULE_VERSION_STACK=3.2.10,WINDOW=0,NLSPATH=/usr/dt/lib/nls/msg/%L/%N.cat,PWD=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT,JAVA_HOME=/usr/lib/jvm/java-8-oracle,LOADEDMODULES=NONE,SSH_CONNECTION=171.65.77.8 55144 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,MODULEPATH=/usr/local/Modules/versions				:/usr/local/Modules/$MODULE_VERSION/modulefiles	:/modules/				:/software/modulefiles,MODULESHOME=/software/env_module/3.2.10
script_file:                STDIN
usage    1:                 cpu=00:07:34, mem=1004.59882 GBs, io=11.83445, vmem=2.725G, maxvmem=3.751G
scheduling info:            queue instance "q@kadru" dropped because it is full

Num	2
ID	task.callpeak_macs2.macs2_rep1_pr1.line_67.id_11
Name	macs2 rep1-pr1
Thread	thread_Root
PID	4387

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

Start	2016-11-06 18:09:36
End	2016-11-06 18:32:14
Elapsed	00:22:38
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.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/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gappedPeak.gz
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/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.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/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.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/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.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/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.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/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.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/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.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/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.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/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.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/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.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/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.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/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.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/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_summits.bed

# SYS command. line 100

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.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/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr1 -o "wt_allReps.nodup.pr1.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/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_FE.bdg -g /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.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/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.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/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.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/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.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/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.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/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.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/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr1 -o "wt_allReps.nodup.pr1.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/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_ppois.bdg -g /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.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/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.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/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.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/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.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/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.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/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.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--------------------
39916 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
INFO  @ Sun, 06 Nov 2016 18:23:08: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.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/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.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/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.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  @ Sun, 06 Nov 2016 18:23:08: #1 read tag files... 
INFO  @ Sun, 06 Nov 2016 18:23:08: #1 read treatment tags... 
INFO  @ Sun, 06 Nov 2016 18:23:17:  1000000 
INFO  @ Sun, 06 Nov 2016 18:23:23:  2000000 
INFO  @ Sun, 06 Nov 2016 18:23:30:  3000000 
INFO  @ Sun, 06 Nov 2016 18:23:36:  4000000 
INFO  @ Sun, 06 Nov 2016 18:23:42:  5000000 
INFO  @ Sun, 06 Nov 2016 18:23:48:  6000000 
INFO  @ Sun, 06 Nov 2016 18:23:54:  7000000 
INFO  @ Sun, 06 Nov 2016 18:24:01:  8000000 
INFO  @ Sun, 06 Nov 2016 18:24:05: #1.2 read input tags... 
INFO  @ Sun, 06 Nov 2016 18:24:19:  1000000 
INFO  @ Sun, 06 Nov 2016 18:24:25:  2000000 
INFO  @ Sun, 06 Nov 2016 18:24:31:  3000000 
INFO  @ Sun, 06 Nov 2016 18:24:34: #1 tag size is determined as 35 bps 
INFO  @ Sun, 06 Nov 2016 18:24:34: #1 tag size = 35 
INFO  @ Sun, 06 Nov 2016 18:24:34: #1  total tags in treatment: 8387713 
INFO  @ Sun, 06 Nov 2016 18:24:34: #1  total tags in control: 3384182 
INFO  @ Sun, 06 Nov 2016 18:24:34: #1 finished! 
INFO  @ Sun, 06 Nov 2016 18:24:34: #2 Build Peak Model... 
INFO  @ Sun, 06 Nov 2016 18:24:34: #2 Skipped... 
INFO  @ Sun, 06 Nov 2016 18:24:34: #2 Use 110 as fragment length 
INFO  @ Sun, 06 Nov 2016 18:24:34: #3 Call peaks... 
INFO  @ Sun, 06 Nov 2016 18:24:34: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Sun, 06 Nov 2016 18:24:34: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 06 Nov 2016 18:25:18: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Sun, 06 Nov 2016 18:25:18: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Sun, 06 Nov 2016 18:25:18: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_control_lambda.bdg 
INFO  @ Sun, 06 Nov 2016 18:25:18: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Sun, 06 Nov 2016 18:25:18: #3 Call peaks for each chromosome... 
INFO  @ Sun, 06 Nov 2016 18:28:23: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 06 Nov 2016 18:28:26: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Sun, 06 Nov 2016 18:28:29: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_summits.bed 
INFO  @ Sun, 06 Nov 2016 18:28:31: Done! 
INFO  @ Sun, 06 Nov 2016 18:28:37: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.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/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.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/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.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  @ Sun, 06 Nov 2016 18:28:37: #1 read tag files... 
INFO  @ Sun, 06 Nov 2016 18:28:37: #1 read treatment tags... 
INFO  @ Sun, 06 Nov 2016 18:28:45:  1000000 
INFO  @ Sun, 06 Nov 2016 18:28:51:  2000000 
INFO  @ Sun, 06 Nov 2016 18:28:58:  3000000 
INFO  @ Sun, 06 Nov 2016 18:29:04:  4000000 
INFO  @ Sun, 06 Nov 2016 18:29:11:  5000000 
INFO  @ Sun, 06 Nov 2016 18:29:17:  6000000 
INFO  @ Sun, 06 Nov 2016 18:29:23:  7000000 
INFO  @ Sun, 06 Nov 2016 18:29:30:  8000000 
INFO  @ Sun, 06 Nov 2016 18:29:33: #1.2 read input tags... 
INFO  @ Sun, 06 Nov 2016 18:29:41:  1000000 
INFO  @ Sun, 06 Nov 2016 18:29:47:  2000000 
INFO  @ Sun, 06 Nov 2016 18:29:54:  3000000 
INFO  @ Sun, 06 Nov 2016 18:29:57: #1 tag size is determined as 35 bps 
INFO  @ Sun, 06 Nov 2016 18:29:57: #1 tag size = 35 
INFO  @ Sun, 06 Nov 2016 18:29:57: #1  total tags in treatment: 8387713 
INFO  @ Sun, 06 Nov 2016 18:29:57: #1  total tags in control: 3384182 
INFO  @ Sun, 06 Nov 2016 18:29:57: #1 finished! 
INFO  @ Sun, 06 Nov 2016 18:29:57: #2 Build Peak Model... 
INFO  @ Sun, 06 Nov 2016 18:29:57: #2 Skipped... 
INFO  @ Sun, 06 Nov 2016 18:29:57: #2 Use 110 as fragment length 
INFO  @ Sun, 06 Nov 2016 18:29:57: #3 Call peaks... 
INFO  @ Sun, 06 Nov 2016 18:29:57: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Sun, 06 Nov 2016 18:29:57: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 06 Nov 2016 18:30:47: #3 Call peaks for each chromosome... 
INFO  @ Sun, 06 Nov 2016 18:31:53: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 06 Nov 2016 18:31:57: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.broadPeak 
INFO  @ Sun, 06 Nov 2016 18:31:59: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Sun, 06 Nov 2016 18:32:02: Done!

Num	3
ID	task.callpeak_macs2.macs2_rep1_pr2.line_67.id_12
Name	macs2 rep1-pr2
Thread	thread_Root
PID	4391

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

Start	2016-11-06 18:09:39
End	2016-11-06 18:27:15
Elapsed	00:17:35
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.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/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gappedPeak.gz
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/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.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/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.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/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.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/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.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/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.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/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.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/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.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/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.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/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.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/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.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/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.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/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_summits.bed

# SYS command. line 100

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.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/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr2 -o "wt_allReps.nodup.pr2.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/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_FE.bdg -g /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.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/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.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/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.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/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.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/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.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/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.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/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr2 -o "wt_allReps.nodup.pr2.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/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_ppois.bdg -g /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.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/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.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/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.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/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.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/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.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/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.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--------------------
4493 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
INFO  @ Sun, 06 Nov 2016 18:24:17: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.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/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.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/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.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  @ Sun, 06 Nov 2016 18:24:17: #1 read tag files... 
INFO  @ Sun, 06 Nov 2016 18:24:17: #1 read treatment tags... 
INFO  @ Sun, 06 Nov 2016 18:24:20:  1000000 
INFO  @ Sun, 06 Nov 2016 18:24:21:  2000000 
INFO  @ Sun, 06 Nov 2016 18:24:23:  3000000 
INFO  @ Sun, 06 Nov 2016 18:24:25:  4000000 
INFO  @ Sun, 06 Nov 2016 18:24:26:  5000000 
INFO  @ Sun, 06 Nov 2016 18:24:28:  6000000 
INFO  @ Sun, 06 Nov 2016 18:24:29:  7000000 
INFO  @ Sun, 06 Nov 2016 18:24:31:  8000000 
INFO  @ Sun, 06 Nov 2016 18:24:33: #1.2 read input tags... 
INFO  @ Sun, 06 Nov 2016 18:24:35:  1000000 
INFO  @ Sun, 06 Nov 2016 18:24:36:  2000000 
INFO  @ Sun, 06 Nov 2016 18:24:38:  3000000 
INFO  @ Sun, 06 Nov 2016 18:24:38: #1 tag size is determined as 35 bps 
INFO  @ Sun, 06 Nov 2016 18:24:38: #1 tag size = 35 
INFO  @ Sun, 06 Nov 2016 18:24:38: #1  total tags in treatment: 8387712 
INFO  @ Sun, 06 Nov 2016 18:24:38: #1  total tags in control: 3384182 
INFO  @ Sun, 06 Nov 2016 18:24:38: #1 finished! 
INFO  @ Sun, 06 Nov 2016 18:24:38: #2 Build Peak Model... 
INFO  @ Sun, 06 Nov 2016 18:24:38: #2 Skipped... 
INFO  @ Sun, 06 Nov 2016 18:24:38: #2 Use 110 as fragment length 
INFO  @ Sun, 06 Nov 2016 18:24:38: #3 Call peaks... 
INFO  @ Sun, 06 Nov 2016 18:24:38: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Sun, 06 Nov 2016 18:24:38: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 06 Nov 2016 18:24:56: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Sun, 06 Nov 2016 18:24:56: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Sun, 06 Nov 2016 18:24:56: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_control_lambda.bdg 
INFO  @ Sun, 06 Nov 2016 18:24:56: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Sun, 06 Nov 2016 18:24:56: #3 Call peaks for each chromosome... 
INFO  @ Sun, 06 Nov 2016 18:25:54: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 06 Nov 2016 18:25:55: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Sun, 06 Nov 2016 18:25:59: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_summits.bed 
INFO  @ Sun, 06 Nov 2016 18:26:00: Done! 
INFO  @ Sun, 06 Nov 2016 18:26:03: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.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/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.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/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.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  @ Sun, 06 Nov 2016 18:26:03: #1 read tag files... 
INFO  @ Sun, 06 Nov 2016 18:26:03: #1 read treatment tags... 
INFO  @ Sun, 06 Nov 2016 18:26:05:  1000000 
INFO  @ Sun, 06 Nov 2016 18:26:07:  2000000 
INFO  @ Sun, 06 Nov 2016 18:26:08:  3000000 
INFO  @ Sun, 06 Nov 2016 18:26:10:  4000000 
INFO  @ Sun, 06 Nov 2016 18:26:11:  5000000 
INFO  @ Sun, 06 Nov 2016 18:26:13:  6000000 
INFO  @ Sun, 06 Nov 2016 18:26:14:  7000000 
INFO  @ Sun, 06 Nov 2016 18:26:16:  8000000 
INFO  @ Sun, 06 Nov 2016 18:26:17: #1.2 read input tags... 
INFO  @ Sun, 06 Nov 2016 18:26:19:  1000000 
INFO  @ Sun, 06 Nov 2016 18:26:20:  2000000 
INFO  @ Sun, 06 Nov 2016 18:26:22:  3000000 
INFO  @ Sun, 06 Nov 2016 18:26:22: #1 tag size is determined as 35 bps 
INFO  @ Sun, 06 Nov 2016 18:26:22: #1 tag size = 35 
INFO  @ Sun, 06 Nov 2016 18:26:22: #1  total tags in treatment: 8387712 
INFO  @ Sun, 06 Nov 2016 18:26:22: #1  total tags in control: 3384182 
INFO  @ Sun, 06 Nov 2016 18:26:22: #1 finished! 
INFO  @ Sun, 06 Nov 2016 18:26:22: #2 Build Peak Model... 
INFO  @ Sun, 06 Nov 2016 18:26:22: #2 Skipped... 
INFO  @ Sun, 06 Nov 2016 18:26:22: #2 Use 110 as fragment length 
INFO  @ Sun, 06 Nov 2016 18:26:22: #3 Call peaks... 
INFO  @ Sun, 06 Nov 2016 18:26:22: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Sun, 06 Nov 2016 18:26:22: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 06 Nov 2016 18:26:41: #3 Call peaks for each chromosome... 
INFO  @ Sun, 06 Nov 2016 18:27:07: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 06 Nov 2016 18:27:08: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.broadPeak 
INFO  @ Sun, 06 Nov 2016 18:27:08: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/macs2/pseudo_reps/rep1/pr2/wt_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Sun, 06 Nov 2016 18:27:09: Done!

BigDataScript report: chipseq.bds

Timeline

Task Graph

Parallel (threads) details

Task details

Global scope

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, -gensz, mm, -chrsz, /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes, $]
bool	canFail	false
int	cpus	-1
int	cpusLocal	56
int	day	86400
string	DERBY_HOME	/usr/lib/jvm/java-8-oracle/db
string	DISPLAY	localhost:12.0
real	E	2.718281828459045
int	G	1073741824
string	HOME	/users/imk1/
int	hour	3600
string	J2REDIR	/usr/lib/jvm/java-8-oracle/jre
string	J2SDKDIR	/usr/lib/jvm/java-8-oracle
string	JAVA_HOME	/usr/lib/jvm/java-8-oracle
int	K	1024
string	KRB5CCNAME	FILE:/tmp/krb5cc_1048_N5SeQf
string	LANG	en_US.UTF-8
string	LOADEDMODULES
string	LOGNAME	imk1
int	M	1048576
string	MAIL	/var/mail/imk1
int	mem	-1
int	minute	60
string	MODULE_VERSION	3.2.10
string	MODULE_VERSION_STACK	3.2.10
string	MODULEPATH	/usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$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	/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
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	queue
int	retry	0
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	35661.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
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