Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20161106_180814_984
Start time	2016-11-06 18:08:15
Run time	01:05:05.614
Tasks executed	4
Tasks failed	0
Tasks failed names
Arguments*	[-title, SRR836476, -nth, 5, -species, mm10, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/SRR836476.fastq.gz, -ctl_fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.fastq.gz, $]
System*	sge
Cpus*	-1
Exit value	0

Thread ID	Parent	Tasks
thread_Root	None	chipseq.bds.20161106_180814_984/task.callpeak_macs2.macs2_rep1.line_67.id_10 chipseq.bds.20161106_180814_984/task.callpeak_macs2.macs2_rep1_pr1.line_67.id_11 chipseq.bds.20161106_180814_984/task.callpeak_macs2.macs2_rep1_pr2.line_67.id_12 chipseq.bds.20161106_180814_984/task.graphviz.report.line_97.id_15
thread_41	thread_Root
thread_42	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	4276

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

Start	2016-11-06 18:08:23
End	2016-11-06 19:13:15
Elapsed	01:04:52
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/rep1/SRR836476.nodup.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/rep1/SRR836476.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/rep1/SRR836476.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/signal/macs2/rep1/SRR836476.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/signal/macs2/rep1/SRR836476.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/SRR836476/out/align/rep1/SRR836476.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/rep1/SRR836476.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/SRR836476/out/peak/macs2/rep1/SRR836476.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/SRR836476/out/peak/macs2/rep1/SRR836476.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/SRR836476/out/peak/macs2/rep1/SRR836476.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/rep1/SRR836476.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/rep1/SRR836476.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/SRR836476/out/align/rep1/SRR836476.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/rep1/SRR836476.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/SRR836476/out/peak/macs2/rep1/SRR836476.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/SRR836476/out/peak/macs2/rep1/SRR836476.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/SRR836476/out/peak/macs2/rep1/SRR836476.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/SRR836476/out/peak/macs2/rep1/SRR836476.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/SRR836476/out/peak/macs2/rep1/SRR836476.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/rep1/SRR836476.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/rep1/SRR836476.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/rep1/SRR836476.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/SRR836476/out/peak/macs2/rep1/SRR836476.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/rep1/SRR836476.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/SRR836476/out/peak/macs2/rep1/SRR836476.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/rep1/SRR836476.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/rep1 -o "SRR836476.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/SRR836476/out/peak/macs2/rep1/SRR836476.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/SRR836476/out/peak/macs2/rep1/SRR836476.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/SRR836476/out/peak/macs2/rep1/SRR836476.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/SRR836476/out/peak/macs2/rep1/SRR836476.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/rep1/SRR836476.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/SRR836476/out/peak/macs2/rep1/SRR836476.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/SRR836476/out/signal/macs2/rep1/SRR836476.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/SRR836476/out/peak/macs2/rep1/SRR836476.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/rep1/SRR836476.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/SRR836476/out/align/rep1/SRR836476.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 128

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/ctl1/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/SRR836476/out/peak/macs2/rep1/SRR836476.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/rep1/SRR836476.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/rep1 -o "SRR836476.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/SRR836476/out/peak/macs2/rep1/SRR836476.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/SRR836476/out/peak/macs2/rep1/SRR836476.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/SRR836476/out/peak/macs2/rep1/SRR836476.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/SRR836476/out/peak/macs2/rep1/SRR836476.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/rep1/SRR836476.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/SRR836476/out/peak/macs2/rep1/SRR836476.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/SRR836476/out/signal/macs2/rep1/SRR836476.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/SRR836476/out/peak/macs2/rep1/SRR836476.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/rep1/SRR836476.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/SRR836476/out/peak/macs2/rep1/SRR836476.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/rep1/SRR836476.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--------------------
28922 (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 18:08:52: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/rep1/SRR836476.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/rep1/SRR836476.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/SRR836476/out/peak/macs2/rep1/SRR836476.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/rep1/SRR836476.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/ctl1/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 18:08:52: #1 read tag files... 
INFO  @ Sun, 06 Nov 2016 18:08:52: #1 read treatment tags... 
INFO  @ Sun, 06 Nov 2016 18:09:00:  1000000 
INFO  @ Sun, 06 Nov 2016 18:09:08:  2000000 
INFO  @ Sun, 06 Nov 2016 18:09:16:  3000000 
INFO  @ Sun, 06 Nov 2016 18:09:24:  4000000 
INFO  @ Sun, 06 Nov 2016 18:09:31:  5000000 
INFO  @ Sun, 06 Nov 2016 18:09:39:  6000000 
INFO  @ Sun, 06 Nov 2016 18:09:46:  7000000 
INFO  @ Sun, 06 Nov 2016 18:09:54:  8000000 
INFO  @ Sun, 06 Nov 2016 18:10:02:  9000000 
INFO  @ Sun, 06 Nov 2016 18:10:10:  10000000 
INFO  @ Sun, 06 Nov 2016 18:10:17:  11000000 
INFO  @ Sun, 06 Nov 2016 18:10:25:  12000000 
INFO  @ Sun, 06 Nov 2016 18:10:33:  13000000 
INFO  @ Sun, 06 Nov 2016 18:10:40:  14000000 
INFO  @ Sun, 06 Nov 2016 18:10:49:  15000000 
INFO  @ Sun, 06 Nov 2016 18:10:57:  16000000 
INFO  @ Sun, 06 Nov 2016 18:11:05:  17000000 
INFO  @ Sun, 06 Nov 2016 18:11:13:  18000000 
INFO  @ Sun, 06 Nov 2016 18:11:21:  19000000 
INFO  @ Sun, 06 Nov 2016 18:11:30:  20000000 
INFO  @ Sun, 06 Nov 2016 18:11:38:  21000000 
INFO  @ Sun, 06 Nov 2016 18:11:46:  22000000 
INFO  @ Sun, 06 Nov 2016 18:11:55:  23000000 
INFO  @ Sun, 06 Nov 2016 18:12:03:  24000000 
INFO  @ Sun, 06 Nov 2016 18:12:09: #1.2 read input tags... 
INFO  @ Sun, 06 Nov 2016 18:12:18:  1000000 
INFO  @ Sun, 06 Nov 2016 18:12:26:  2000000 
INFO  @ Sun, 06 Nov 2016 18:12:34:  3000000 
INFO  @ Sun, 06 Nov 2016 18:12:38: #1 tag size is determined as 49 bps 
INFO  @ Sun, 06 Nov 2016 18:12:38: #1 tag size = 49 
INFO  @ Sun, 06 Nov 2016 18:12:38: #1  total tags in treatment: 24529518 
INFO  @ Sun, 06 Nov 2016 18:12:38: #1  total tags in control: 3384182 
INFO  @ Sun, 06 Nov 2016 18:12:38: #1 finished! 
INFO  @ Sun, 06 Nov 2016 18:12:38: #2 Build Peak Model... 
INFO  @ Sun, 06 Nov 2016 18:12:38: #2 Skipped... 
INFO  @ Sun, 06 Nov 2016 18:12:38: #2 Use 110 as fragment length 
INFO  @ Sun, 06 Nov 2016 18:12:38: #3 Call peaks... 
INFO  @ Sun, 06 Nov 2016 18:12:38: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Sun, 06 Nov 2016 18:12:38: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 06 Nov 2016 18:14:24: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Sun, 06 Nov 2016 18:14:24: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/rep1/SRR836476.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Sun, 06 Nov 2016 18:14:24: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/rep1/SRR836476.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_control_lambda.bdg 
INFO  @ Sun, 06 Nov 2016 18:14:24: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Sun, 06 Nov 2016 18:14:24: #3 Call peaks for each chromosome... 
INFO  @ Sun, 06 Nov 2016 18:26:06: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/rep1/SRR836476.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 06 Nov 2016 18:26:07: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/rep1/SRR836476.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Sun, 06 Nov 2016 18:26:07: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/rep1/SRR836476.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_summits.bed 
INFO  @ Sun, 06 Nov 2016 18:26:08: Done! 
INFO  @ Sun, 06 Nov 2016 18:26:12: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/rep1/SRR836476.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/rep1/SRR836476.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/SRR836476/out/peak/macs2/rep1/SRR836476.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/rep1/SRR836476.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/ctl1/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 18:26:12: #1 read tag files... 
INFO  @ Sun, 06 Nov 2016 18:26:12: #1 read treatment tags... 
INFO  @ Sun, 06 Nov 2016 18:26:19:  1000000 
INFO  @ Sun, 06 Nov 2016 18:26:26:  2000000 
INFO  @ Sun, 06 Nov 2016 18:26:32:  3000000 
INFO  @ Sun, 06 Nov 2016 18:26:39:  4000000 
INFO  @ Sun, 06 Nov 2016 18:26:45:  5000000 
INFO  @ Sun, 06 Nov 2016 18:26:51:  6000000 
INFO  @ Sun, 06 Nov 2016 18:26:58:  7000000 
INFO  @ Sun, 06 Nov 2016 18:27:04:  8000000 
INFO  @ Sun, 06 Nov 2016 18:27:11:  9000000 
INFO  @ Sun, 06 Nov 2016 18:27:17:  10000000 
INFO  @ Sun, 06 Nov 2016 18:27:24:  11000000 
INFO  @ Sun, 06 Nov 2016 18:27:31:  12000000 
INFO  @ Sun, 06 Nov 2016 18:27:37:  13000000 
INFO  @ Sun, 06 Nov 2016 18:27:44:  14000000 
INFO  @ Sun, 06 Nov 2016 18:27:50:  15000000 
INFO  @ Sun, 06 Nov 2016 18:27:56:  16000000 
INFO  @ Sun, 06 Nov 2016 18:28:03:  17000000 
INFO  @ Sun, 06 Nov 2016 18:28:10:  18000000 
INFO  @ Sun, 06 Nov 2016 18:28:16:  19000000 
INFO  @ Sun, 06 Nov 2016 18:28:23:  20000000 
INFO  @ Sun, 06 Nov 2016 18:28:29:  21000000 
INFO  @ Sun, 06 Nov 2016 18:28:36:  22000000 
INFO  @ Sun, 06 Nov 2016 18:28:43:  23000000 
INFO  @ Sun, 06 Nov 2016 18:28:50:  24000000 
INFO  @ Sun, 06 Nov 2016 18:28:54: #1.2 read input tags... 
INFO  @ Sun, 06 Nov 2016 18:29:01:  1000000 
INFO  @ Sun, 06 Nov 2016 18:29:08:  2000000 
INFO  @ Sun, 06 Nov 2016 18:29:15:  3000000 
INFO  @ Sun, 06 Nov 2016 18:29:18: #1 tag size is determined as 49 bps 
INFO  @ Sun, 06 Nov 2016 18:29:18: #1 tag size = 49 
INFO  @ Sun, 06 Nov 2016 18:29:18: #1  total tags in treatment: 24529518 
INFO  @ Sun, 06 Nov 2016 18:29:18: #1  total tags in control: 3384182 
INFO  @ Sun, 06 Nov 2016 18:29:18: #1 finished! 
INFO  @ Sun, 06 Nov 2016 18:29:18: #2 Build Peak Model... 
INFO  @ Sun, 06 Nov 2016 18:29:18: #2 Skipped... 
INFO  @ Sun, 06 Nov 2016 18:29:18: #2 Use 110 as fragment length 
INFO  @ Sun, 06 Nov 2016 18:29:18: #3 Call peaks... 
INFO  @ Sun, 06 Nov 2016 18:29:18: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Sun, 06 Nov 2016 18:29:18: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 06 Nov 2016 18:30:49: #3 Call peaks for each chromosome... 
INFO  @ Sun, 06 Nov 2016 18:31:35: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/rep1/SRR836476.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 06 Nov 2016 18:31:37: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/rep1/SRR836476.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.broadPeak 
INFO  @ Sun, 06 Nov 2016 18:31:38: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/rep1/SRR836476.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Sun, 06 Nov 2016 18:31:39: Done! 
INFO  @ Sun, 06 Nov 2016 18:31:50: Read and build treatment bedGraph... 
INFO  @ Sun, 06 Nov 2016 18:34:53: Read and build control bedGraph... 
INFO  @ Sun, 06 Nov 2016 18:35:36: Build scoreTrackII... 
INFO  @ Sun, 06 Nov 2016 18:36:34: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Sun, 06 Nov 2016 18:44:54: Write bedGraph of scores... 
INFO  @ Sun, 06 Nov 2016 18:49:31: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/rep1/SRR836476.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_FE.bdg'! 
INFO  @ Sun, 06 Nov 2016 18:57:02: Read and build treatment bedGraph... 
INFO  @ Sun, 06 Nov 2016 18:59:47: Read and build control bedGraph... 
INFO  @ Sun, 06 Nov 2016 19:00:29: Build scoreTrackII... 
INFO  @ Sun, 06 Nov 2016 19:01:20: Values in your input bedGraph files will be multiplied by 3.384182 ... 
INFO  @ Sun, 06 Nov 2016 19:09:35: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Sun, 06 Nov 2016 19:10:22: Write bedGraph of scores... 
INFO  @ Sun, 06 Nov 2016 19:11:36: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/rep1/SRR836476.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_ppois.bdg'!

Num	2
ID	task.callpeak_macs2.macs2_rep1_pr1.line_67.id_11
Name	macs2 rep1-pr1
Thread	thread_Root
PID	4309

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

Start	2016-11-06 18:08:25
End	2016-11-06 18:27:25
Elapsed	00:19:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.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/SRR836476/out/align/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.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/SRR836476/out/align/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.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/SRR836476/out/align/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 128

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/ctl1/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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.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--------------------
29168 (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 18:08:52: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/ctl1/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 18:08:52: #1 read tag files... 
INFO  @ Sun, 06 Nov 2016 18:08:52: #1 read treatment tags... 
INFO  @ Sun, 06 Nov 2016 18:09:00:  1000000 
INFO  @ Sun, 06 Nov 2016 18:09:08:  2000000 
INFO  @ Sun, 06 Nov 2016 18:09:16:  3000000 
INFO  @ Sun, 06 Nov 2016 18:09:24:  4000000 
INFO  @ Sun, 06 Nov 2016 18:09:31:  5000000 
INFO  @ Sun, 06 Nov 2016 18:09:39:  6000000 
INFO  @ Sun, 06 Nov 2016 18:09:47:  7000000 
INFO  @ Sun, 06 Nov 2016 18:09:55:  8000000 
INFO  @ Sun, 06 Nov 2016 18:10:03:  9000000 
INFO  @ Sun, 06 Nov 2016 18:10:11:  10000000 
INFO  @ Sun, 06 Nov 2016 18:10:19:  11000000 
INFO  @ Sun, 06 Nov 2016 18:10:27:  12000000 
INFO  @ Sun, 06 Nov 2016 18:10:31: #1.2 read input tags... 
INFO  @ Sun, 06 Nov 2016 18:10:42:  1000000 
INFO  @ Sun, 06 Nov 2016 18:10:50:  2000000 
INFO  @ Sun, 06 Nov 2016 18:10:58:  3000000 
INFO  @ Sun, 06 Nov 2016 18:11:01: #1 tag size is determined as 48 bps 
INFO  @ Sun, 06 Nov 2016 18:11:01: #1 tag size = 48 
INFO  @ Sun, 06 Nov 2016 18:11:01: #1  total tags in treatment: 12264759 
INFO  @ Sun, 06 Nov 2016 18:11:01: #1  total tags in control: 3384182 
INFO  @ Sun, 06 Nov 2016 18:11:01: #1 finished! 
INFO  @ Sun, 06 Nov 2016 18:11:01: #2 Build Peak Model... 
INFO  @ Sun, 06 Nov 2016 18:11:01: #2 Skipped... 
INFO  @ Sun, 06 Nov 2016 18:11:01: #2 Use 110 as fragment length 
INFO  @ Sun, 06 Nov 2016 18:11:01: #3 Call peaks... 
INFO  @ Sun, 06 Nov 2016 18:11:01: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Sun, 06 Nov 2016 18:11:01: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 06 Nov 2016 18:12:18: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Sun, 06 Nov 2016 18:12:18: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Sun, 06 Nov 2016 18:12:18: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_control_lambda.bdg 
INFO  @ Sun, 06 Nov 2016 18:12:18: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Sun, 06 Nov 2016 18:12:18: #3 Call peaks for each chromosome... 
INFO  @ Sun, 06 Nov 2016 18:23:31: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 06 Nov 2016 18:23:35: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Sun, 06 Nov 2016 18:23:37: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_summits.bed 
INFO  @ Sun, 06 Nov 2016 18:23:37: Done! 
INFO  @ Sun, 06 Nov 2016 18:23:49: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/ctl1/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 18:23:49: #1 read tag files... 
INFO  @ Sun, 06 Nov 2016 18:23:49: #1 read treatment tags... 
INFO  @ Sun, 06 Nov 2016 18:23:59:  1000000 
INFO  @ Sun, 06 Nov 2016 18:24:05:  2000000 
INFO  @ Sun, 06 Nov 2016 18:24:11:  3000000 
INFO  @ Sun, 06 Nov 2016 18:24:17:  4000000 
INFO  @ Sun, 06 Nov 2016 18:24:23:  5000000 
INFO  @ Sun, 06 Nov 2016 18:24:29:  6000000 
INFO  @ Sun, 06 Nov 2016 18:24:35:  7000000 
INFO  @ Sun, 06 Nov 2016 18:24:41:  8000000 
INFO  @ Sun, 06 Nov 2016 18:24:48:  9000000 
INFO  @ Sun, 06 Nov 2016 18:24:54:  10000000 
INFO  @ Sun, 06 Nov 2016 18:25:00:  11000000 
INFO  @ Sun, 06 Nov 2016 18:25:06:  12000000 
INFO  @ Sun, 06 Nov 2016 18:25:09: #1.2 read input tags... 
INFO  @ Sun, 06 Nov 2016 18:25:18:  1000000 
INFO  @ Sun, 06 Nov 2016 18:25:24:  2000000 
INFO  @ Sun, 06 Nov 2016 18:25:30:  3000000 
INFO  @ Sun, 06 Nov 2016 18:25:32: #1 tag size is determined as 48 bps 
INFO  @ Sun, 06 Nov 2016 18:25:32: #1 tag size = 48 
INFO  @ Sun, 06 Nov 2016 18:25:32: #1  total tags in treatment: 12264759 
INFO  @ Sun, 06 Nov 2016 18:25:32: #1  total tags in control: 3384182 
INFO  @ Sun, 06 Nov 2016 18:25:32: #1 finished! 
INFO  @ Sun, 06 Nov 2016 18:25:32: #2 Build Peak Model... 
INFO  @ Sun, 06 Nov 2016 18:25:32: #2 Skipped... 
INFO  @ Sun, 06 Nov 2016 18:25:32: #2 Use 110 as fragment length 
INFO  @ Sun, 06 Nov 2016 18:25:32: #3 Call peaks... 
INFO  @ Sun, 06 Nov 2016 18:25:32: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Sun, 06 Nov 2016 18:25:32: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 06 Nov 2016 18:26:32: #3 Call peaks for each chromosome... 
INFO  @ Sun, 06 Nov 2016 18:27:13: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 06 Nov 2016 18:27:16: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.broadPeak 
INFO  @ Sun, 06 Nov 2016 18:27:18: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr1/SRR836476.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Sun, 06 Nov 2016 18:27:19: Done!

Num	3
ID	task.callpeak_macs2.macs2_rep1_pr2.line_67.id_12
Name	macs2 rep1-pr2
Thread	thread_Root
PID	4332

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

Start	2016-11-06 18:08:26
End	2016-11-06 18:17:27
Elapsed	00:09:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.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/SRR836476/out/align/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.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/SRR836476/out/align/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.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/SRR836476/out/align/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 128

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/ctl1/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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.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--------------------
48389 (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 18:12:38: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/ctl1/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 18:12:38: #1 read tag files... 
INFO  @ Sun, 06 Nov 2016 18:12:38: #1 read treatment tags... 
INFO  @ Sun, 06 Nov 2016 18:12:41:  1000000 
INFO  @ Sun, 06 Nov 2016 18:12:43:  2000000 
INFO  @ Sun, 06 Nov 2016 18:12:45:  3000000 
INFO  @ Sun, 06 Nov 2016 18:12:48:  4000000 
INFO  @ Sun, 06 Nov 2016 18:12:50:  5000000 
INFO  @ Sun, 06 Nov 2016 18:12:53:  6000000 
INFO  @ Sun, 06 Nov 2016 18:12:55:  7000000 
INFO  @ Sun, 06 Nov 2016 18:12:57:  8000000 
INFO  @ Sun, 06 Nov 2016 18:13:01:  9000000 
INFO  @ Sun, 06 Nov 2016 18:13:03:  10000000 
INFO  @ Sun, 06 Nov 2016 18:13:09:  11000000 
INFO  @ Sun, 06 Nov 2016 18:13:12:  12000000 
INFO  @ Sun, 06 Nov 2016 18:13:14: #1.2 read input tags... 
INFO  @ Sun, 06 Nov 2016 18:13:17:  1000000 
INFO  @ Sun, 06 Nov 2016 18:13:19:  2000000 
INFO  @ Sun, 06 Nov 2016 18:13:21:  3000000 
INFO  @ Sun, 06 Nov 2016 18:13:23: #1 tag size is determined as 50 bps 
INFO  @ Sun, 06 Nov 2016 18:13:23: #1 tag size = 50 
INFO  @ Sun, 06 Nov 2016 18:13:23: #1  total tags in treatment: 12264759 
INFO  @ Sun, 06 Nov 2016 18:13:23: #1  total tags in control: 3384182 
INFO  @ Sun, 06 Nov 2016 18:13:23: #1 finished! 
INFO  @ Sun, 06 Nov 2016 18:13:23: #2 Build Peak Model... 
INFO  @ Sun, 06 Nov 2016 18:13:23: #2 Skipped... 
INFO  @ Sun, 06 Nov 2016 18:13:23: #2 Use 110 as fragment length 
INFO  @ Sun, 06 Nov 2016 18:13:23: #3 Call peaks... 
INFO  @ Sun, 06 Nov 2016 18:13:23: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Sun, 06 Nov 2016 18:13:23: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 06 Nov 2016 18:13:59: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Sun, 06 Nov 2016 18:13:59: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Sun, 06 Nov 2016 18:13:59: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_control_lambda.bdg 
INFO  @ Sun, 06 Nov 2016 18:13:59: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Sun, 06 Nov 2016 18:13:59: #3 Call peaks for each chromosome... 
INFO  @ Sun, 06 Nov 2016 18:15:35: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 06 Nov 2016 18:15:37: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Sun, 06 Nov 2016 18:15:44: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_summits.bed 
INFO  @ Sun, 06 Nov 2016 18:15:44: Done! 
INFO  @ Sun, 06 Nov 2016 18:15:49: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.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/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/align/ctl1/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 18:15:49: #1 read tag files... 
INFO  @ Sun, 06 Nov 2016 18:15:49: #1 read treatment tags... 
INFO  @ Sun, 06 Nov 2016 18:15:51:  1000000 
INFO  @ Sun, 06 Nov 2016 18:15:53:  2000000 
INFO  @ Sun, 06 Nov 2016 18:15:55:  3000000 
INFO  @ Sun, 06 Nov 2016 18:15:57:  4000000 
INFO  @ Sun, 06 Nov 2016 18:15:59:  5000000 
INFO  @ Sun, 06 Nov 2016 18:16:01:  6000000 
INFO  @ Sun, 06 Nov 2016 18:16:03:  7000000 
INFO  @ Sun, 06 Nov 2016 18:16:05:  8000000 
INFO  @ Sun, 06 Nov 2016 18:16:08:  9000000 
INFO  @ Sun, 06 Nov 2016 18:16:10:  10000000 
INFO  @ Sun, 06 Nov 2016 18:16:12:  11000000 
INFO  @ Sun, 06 Nov 2016 18:16:14:  12000000 
INFO  @ Sun, 06 Nov 2016 18:16:15: #1.2 read input tags... 
INFO  @ Sun, 06 Nov 2016 18:16:18:  1000000 
INFO  @ Sun, 06 Nov 2016 18:16:20:  2000000 
INFO  @ Sun, 06 Nov 2016 18:16:22:  3000000 
INFO  @ Sun, 06 Nov 2016 18:16:23: #1 tag size is determined as 50 bps 
INFO  @ Sun, 06 Nov 2016 18:16:23: #1 tag size = 50 
INFO  @ Sun, 06 Nov 2016 18:16:23: #1  total tags in treatment: 12264759 
INFO  @ Sun, 06 Nov 2016 18:16:23: #1  total tags in control: 3384182 
INFO  @ Sun, 06 Nov 2016 18:16:23: #1 finished! 
INFO  @ Sun, 06 Nov 2016 18:16:23: #2 Build Peak Model... 
INFO  @ Sun, 06 Nov 2016 18:16:23: #2 Skipped... 
INFO  @ Sun, 06 Nov 2016 18:16:23: #2 Use 110 as fragment length 
INFO  @ Sun, 06 Nov 2016 18:16:23: #3 Call peaks... 
INFO  @ Sun, 06 Nov 2016 18:16:23: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Sun, 06 Nov 2016 18:16:23: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 06 Nov 2016 18:16:55: #3 Call peaks for each chromosome... 
INFO  @ Sun, 06 Nov 2016 18:17:11: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 06 Nov 2016 18:17:12: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.broadPeak 
INFO  @ Sun, 06 Nov 2016 18:17:13: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/peak/macs2/pseudo_reps/rep1/pr2/SRR836476.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Sun, 06 Nov 2016 18:17:13: Done!

Num	4
ID	task.graphviz.report.line_97.id_15
Name	report
Thread	thread_Root
PID	4487

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

Start	2016-11-06 19:13:19
End	2016-11-06 19:13:20
Elapsed	00:00:01
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/SRR836476/out/report/SRR836476_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/report/SRR836476_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out/report/SRR836476_workflow.svg" # to suppress dot font error (exit code=1)

   
--------------------Stdout--------------------
4491 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH

Type	Name	Value
string	_	/usr/bin/bds
bool	allowEmpty	false
string[]	args	[-title, SRR836476, -nth, 5, -species, mm10, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/MouseMutantData/SRR836476/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/SRR836476.fastq.gz, -ctl_fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.fastq.gz, $]
bool	canFail	false
int	cpus	-1
int	cpusLocal	56
int	day	86400
string	DERBY_HOME	/usr/lib/jvm/java-8-oracle/db
string	DISPLAY	localhost:12.0
real	E	2.718281828459045
int	G	1073741824
string	HOME	/users/imk1/
int	hour	3600
string	J2REDIR	/usr/lib/jvm/java-8-oracle/jre
string	J2SDKDIR	/usr/lib/jvm/java-8-oracle
string	JAVA_HOME	/usr/lib/jvm/java-8-oracle
int	K	1024
string	KRB5CCNAME	FILE:/tmp/krb5cc_1048_N5SeQf
string	LANG	en_US.UTF-8
string	LOADEDMODULES
string	LOGNAME	imk1
int	M	1048576
string	MAIL	/var/mail/imk1
int	mem	-1
int	minute	60
string	MODULE_VERSION	3.2.10
string	MODULE_VERSION_STACK	3.2.10
string	MODULEPATH	/usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$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/SRR836476
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/SRR836476
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	29031.SRR836476.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

BigDataScript report: chipseq.bds

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