Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20161222_171808_579
Start time	2016-12-22 17:18:08
Run time	1 day 10:09:02.730
Tasks executed	3
Tasks failed	1
Tasks failed names	macs2 rep1
Arguments*	[-title, ZBTB12, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZBTB12/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/align/rep1/SRR1370883_1.bam, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz, -final_stage, idr, $]
System*	sge
Cpus*	-1
Exit value	1

Thread ID	Parent	Tasks
thread_Root	None	chipseq.bds.20161222_171808_579/task.callpeak_macs2.macs2_rep1.line_71.id_10 chipseq.bds.20161222_171808_579/task.callpeak_macs2.macs2_rep1_pr1.line_71.id_11 chipseq.bds.20161222_171808_579/task.callpeak_macs2.macs2_rep1_pr2.line_71.id_12
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_71.id_10
Name	macs2 rep1
Thread	thread_Root
PID	19997

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

Start	2016-12-22 17:18:16
End	2016-12-22 17:18:16
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/align/rep1/SRR1370883_1.nodup.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/signal/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/signal/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw
Dependencies

 
# SYS command. line 73

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 74

 export LC_COLLATE=C

# SYS command. line 79

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/align/rep1/SRR1370883_1.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 160 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/align/rep1/SRR1370883_1.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 160 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 110

 if [[ true == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.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 121

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1 -o "SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/signal/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/align/rep1/SRR1370883_1.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.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 140

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1 -o "SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 143

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/signal/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg

# SYS command. line 153

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

   
--------------------Stdout--------------------
22731 (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  @ Sat, 24 Dec 2016 01:47:49: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/align/rep1/SRR1370883_1.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 160 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/align/rep1/SRR1370883_1.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+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  @ Sat, 24 Dec 2016 01:47:49: #1 read tag files... 
INFO  @ Sat, 24 Dec 2016 01:47:49: #1 read treatment tags... 
INFO  @ Sat, 24 Dec 2016 01:47:57:  1000000 
INFO  @ Sat, 24 Dec 2016 01:48:05:  2000000 
INFO  @ Sat, 24 Dec 2016 01:48:12:  3000000 
INFO  @ Sat, 24 Dec 2016 01:48:20:  4000000 
INFO  @ Sat, 24 Dec 2016 01:48:27:  5000000 
INFO  @ Sat, 24 Dec 2016 01:48:35:  6000000 
INFO  @ Sat, 24 Dec 2016 01:48:43:  7000000 
INFO  @ Sat, 24 Dec 2016 01:48:51: #1.2 read input tags... 
INFO  @ Sat, 24 Dec 2016 01:48:59:  1000000 
INFO  @ Sat, 24 Dec 2016 01:49:06:  2000000 
INFO  @ Sat, 24 Dec 2016 01:49:14:  3000000 
INFO  @ Sat, 24 Dec 2016 01:49:22:  4000000 
INFO  @ Sat, 24 Dec 2016 01:49:30:  5000000 
INFO  @ Sat, 24 Dec 2016 01:49:38:  6000000 
INFO  @ Sat, 24 Dec 2016 01:49:46:  7000000 
INFO  @ Sat, 24 Dec 2016 01:49:53:  8000000 
INFO  @ Sat, 24 Dec 2016 01:50:01:  9000000 
INFO  @ Sat, 24 Dec 2016 01:50:09:  10000000 
INFO  @ Sat, 24 Dec 2016 01:50:17:  11000000 
INFO  @ Sat, 24 Dec 2016 01:50:24:  12000000 
INFO  @ Sat, 24 Dec 2016 01:50:32:  13000000 
INFO  @ Sat, 24 Dec 2016 01:50:40:  14000000 
INFO  @ Sat, 24 Dec 2016 01:50:48:  15000000 
INFO  @ Sat, 24 Dec 2016 01:50:56:  16000000 
INFO  @ Sat, 24 Dec 2016 01:51:04:  17000000 
INFO  @ Sat, 24 Dec 2016 01:51:12:  18000000 
INFO  @ Sat, 24 Dec 2016 01:51:19:  19000000 
INFO  @ Sat, 24 Dec 2016 01:51:27:  20000000 
INFO  @ Sat, 24 Dec 2016 01:51:35:  21000000 
INFO  @ Sat, 24 Dec 2016 01:51:43:  22000000 
INFO  @ Sat, 24 Dec 2016 01:51:51:  23000000 
INFO  @ Sat, 24 Dec 2016 01:51:59:  24000000 
INFO  @ Sat, 24 Dec 2016 01:52:06:  25000000 
INFO  @ Sat, 24 Dec 2016 01:52:14:  26000000 
INFO  @ Sat, 24 Dec 2016 01:52:22:  27000000 
INFO  @ Sat, 24 Dec 2016 01:52:30:  28000000 
INFO  @ Sat, 24 Dec 2016 01:52:38:  29000000 
INFO  @ Sat, 24 Dec 2016 01:52:46:  30000000 
INFO  @ Sat, 24 Dec 2016 01:52:54:  31000000 
INFO  @ Sat, 24 Dec 2016 01:53:02:  32000000 
INFO  @ Sat, 24 Dec 2016 01:53:10:  33000000 
INFO  @ Sat, 24 Dec 2016 01:53:18:  34000000 
INFO  @ Sat, 24 Dec 2016 01:53:26:  35000000 
INFO  @ Sat, 24 Dec 2016 01:53:34:  36000000 
INFO  @ Sat, 24 Dec 2016 01:53:41:  37000000 
INFO  @ Sat, 24 Dec 2016 01:53:49:  38000000 
INFO  @ Sat, 24 Dec 2016 01:53:57:  39000000 
INFO  @ Sat, 24 Dec 2016 01:54:05:  40000000 
INFO  @ Sat, 24 Dec 2016 01:54:13:  41000000 
INFO  @ Sat, 24 Dec 2016 01:54:20:  42000000 
INFO  @ Sat, 24 Dec 2016 01:54:28:  43000000 
INFO  @ Sat, 24 Dec 2016 01:54:36:  44000000 
INFO  @ Sat, 24 Dec 2016 01:54:44:  45000000 
INFO  @ Sat, 24 Dec 2016 01:54:51:  46000000 
INFO  @ Sat, 24 Dec 2016 01:54:59:  47000000 
INFO  @ Sat, 24 Dec 2016 01:55:07:  48000000 
INFO  @ Sat, 24 Dec 2016 01:55:15:  49000000 
INFO  @ Sat, 24 Dec 2016 01:55:23:  50000000 
INFO  @ Sat, 24 Dec 2016 01:55:27: #1 tag size is determined as 51 bps 
INFO  @ Sat, 24 Dec 2016 01:55:27: #1 tag size = 51 
INFO  @ Sat, 24 Dec 2016 01:55:27: #1  total tags in treatment: 7894407 
INFO  @ Sat, 24 Dec 2016 01:55:27: #1  total tags in control: 50000000 
INFO  @ Sat, 24 Dec 2016 01:55:27: #1 finished! 
INFO  @ Sat, 24 Dec 2016 01:55:27: #2 Build Peak Model... 
INFO  @ Sat, 24 Dec 2016 01:55:27: #2 Skipped... 
INFO  @ Sat, 24 Dec 2016 01:55:27: #2 Use 160 as fragment length 
INFO  @ Sat, 24 Dec 2016 01:55:27: #3 Call peaks... 
INFO  @ Sat, 24 Dec 2016 01:55:27: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Sat, 24 Dec 2016 01:55:27: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sat, 24 Dec 2016 02:03:27: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Sat, 24 Dec 2016 02:03:27: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Sat, 24 Dec 2016 02:03:27: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Sat, 24 Dec 2016 02:03:27: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Sat, 24 Dec 2016 02:03:27: #3 Call peaks for each chromosome... 
INFO  @ Sat, 24 Dec 2016 02:21:32: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Sat, 24 Dec 2016 02:21:35: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Sat, 24 Dec 2016 02:21:38: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Sat, 24 Dec 2016 02:21:40: Done! 
INFO  @ Sat, 24 Dec 2016 02:21:47: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/align/rep1/SRR1370883_1.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 160 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/align/rep1/SRR1370883_1.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+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  @ Sat, 24 Dec 2016 02:21:47: #1 read tag files... 
INFO  @ Sat, 24 Dec 2016 02:21:47: #1 read treatment tags... 
INFO  @ Sat, 24 Dec 2016 02:21:55:  1000000 
INFO  @ Sat, 24 Dec 2016 02:22:02:  2000000 
INFO  @ Sat, 24 Dec 2016 02:22:10:  3000000 
INFO  @ Sat, 24 Dec 2016 02:22:18:  4000000 
INFO  @ Sat, 24 Dec 2016 02:22:25:  5000000 
INFO  @ Sat, 24 Dec 2016 02:22:33:  6000000 
INFO  @ Sat, 24 Dec 2016 02:22:40:  7000000 
INFO  @ Sat, 24 Dec 2016 02:22:47: #1.2 read input tags... 
INFO  @ Sat, 24 Dec 2016 02:22:55:  1000000 
INFO  @ Sat, 24 Dec 2016 02:23:02:  2000000 
INFO  @ Sat, 24 Dec 2016 02:23:10:  3000000 
INFO  @ Sat, 24 Dec 2016 02:23:18:  4000000 
INFO  @ Sat, 24 Dec 2016 02:23:25:  5000000 
INFO  @ Sat, 24 Dec 2016 02:23:33:  6000000 
INFO  @ Sat, 24 Dec 2016 02:23:41:  7000000 
INFO  @ Sat, 24 Dec 2016 02:23:48:  8000000 
INFO  @ Sat, 24 Dec 2016 02:23:56:  9000000 
INFO  @ Sat, 24 Dec 2016 02:24:04:  10000000 
INFO  @ Sat, 24 Dec 2016 02:24:11:  11000000 
INFO  @ Sat, 24 Dec 2016 02:24:19:  12000000 
INFO  @ Sat, 24 Dec 2016 02:24:26:  13000000 
INFO  @ Sat, 24 Dec 2016 02:24:34:  14000000 
INFO  @ Sat, 24 Dec 2016 02:24:42:  15000000 
INFO  @ Sat, 24 Dec 2016 02:24:49:  16000000 
INFO  @ Sat, 24 Dec 2016 02:24:57:  17000000 
INFO  @ Sat, 24 Dec 2016 02:25:05:  18000000 
INFO  @ Sat, 24 Dec 2016 02:25:12:  19000000 
INFO  @ Sat, 24 Dec 2016 02:25:20:  20000000 
INFO  @ Sat, 24 Dec 2016 02:25:28:  21000000 
INFO  @ Sat, 24 Dec 2016 02:25:35:  22000000 
INFO  @ Sat, 24 Dec 2016 02:25:43:  23000000 
INFO  @ Sat, 24 Dec 2016 02:25:51:  24000000 
INFO  @ Sat, 24 Dec 2016 02:25:58:  25000000 
INFO  @ Sat, 24 Dec 2016 02:26:06:  26000000 
INFO  @ Sat, 24 Dec 2016 02:26:14:  27000000 
INFO  @ Sat, 24 Dec 2016 02:26:22:  28000000 
INFO  @ Sat, 24 Dec 2016 02:26:29:  29000000 
INFO  @ Sat, 24 Dec 2016 02:26:37:  30000000 
INFO  @ Sat, 24 Dec 2016 02:26:45:  31000000 
INFO  @ Sat, 24 Dec 2016 02:26:52:  32000000 
INFO  @ Sat, 24 Dec 2016 02:27:00:  33000000 
INFO  @ Sat, 24 Dec 2016 02:27:08:  34000000 
INFO  @ Sat, 24 Dec 2016 02:27:16:  35000000 
INFO  @ Sat, 24 Dec 2016 02:27:24:  36000000 
INFO  @ Sat, 24 Dec 2016 02:27:31:  37000000 
INFO  @ Sat, 24 Dec 2016 02:27:39:  38000000 
INFO  @ Sat, 24 Dec 2016 02:27:47:  39000000 
INFO  @ Sat, 24 Dec 2016 02:27:55:  40000000 
INFO  @ Sat, 24 Dec 2016 02:28:03:  41000000 
INFO  @ Sat, 24 Dec 2016 02:28:10:  42000000 
INFO  @ Sat, 24 Dec 2016 02:28:18:  43000000 
INFO  @ Sat, 24 Dec 2016 02:28:26:  44000000 
INFO  @ Sat, 24 Dec 2016 02:28:33:  45000000 
INFO  @ Sat, 24 Dec 2016 02:28:41:  46000000 
INFO  @ Sat, 24 Dec 2016 02:28:49:  47000000 
INFO  @ Sat, 24 Dec 2016 02:28:56:  48000000 
INFO  @ Sat, 24 Dec 2016 02:29:04:  49000000 
INFO  @ Sat, 24 Dec 2016 02:29:11:  50000000 
INFO  @ Sat, 24 Dec 2016 02:29:16: #1 tag size is determined as 51 bps 
INFO  @ Sat, 24 Dec 2016 02:29:16: #1 tag size = 51 
INFO  @ Sat, 24 Dec 2016 02:29:16: #1  total tags in treatment: 7894407 
INFO  @ Sat, 24 Dec 2016 02:29:16: #1  total tags in control: 50000000 
INFO  @ Sat, 24 Dec 2016 02:29:16: #1 finished! 
INFO  @ Sat, 24 Dec 2016 02:29:16: #2 Build Peak Model... 
INFO  @ Sat, 24 Dec 2016 02:29:16: #2 Skipped... 
INFO  @ Sat, 24 Dec 2016 02:29:16: #2 Use 160 as fragment length 
INFO  @ Sat, 24 Dec 2016 02:29:16: #3 Call peaks... 
INFO  @ Sat, 24 Dec 2016 02:29:16: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Sat, 24 Dec 2016 02:29:16: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sat, 24 Dec 2016 02:37:19: #3 Call peaks for each chromosome... 
INFO  @ Sat, 24 Dec 2016 02:46:36: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Sat, 24 Dec 2016 02:47:02: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Sat, 24 Dec 2016 02:47:21: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Sat, 24 Dec 2016 02:47:35: Done! 
INFO  @ Sat, 24 Dec 2016 02:48:14: Read and build treatment bedGraph... 
INFO  @ Sat, 24 Dec 2016 02:49:26: Read and build control bedGraph... 
INFO  @ Sat, 24 Dec 2016 02:57:25: Build scoreTrackII... 
INFO  @ Sat, 24 Dec 2016 02:59:52: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Sat, 24 Dec 2016 03:21:07: Write bedGraph of scores... 
INFO  @ Sat, 24 Dec 2016 03:27:08: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/rep1/SRR1370883_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_FE.bdg'! 
Chromosome KN196487.1 isn't in /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes line 1 of stdin


 
--------------------Post mortem info--------------------
==============================================================
job_number:                 19997
submission_time:            Thu Dec 22 17:18:16 2016
owner:                      imk1
uid:                        1048
group:                      users
gid:                        100
sge_o_home:                 /users/imk1/
sge_o_log_name:             imk1
sge_o_path:                 /software/samtools/samtools-1.2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/users/imk1/edirect
sge_o_shell:                /bin/bash
sge_o_workdir:              /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/chipseq.bds.20161222_171808_579/task.callpeak_macs2.macs2_rep1.line_71.id_10.stderr.cluster
mail_list:                  imk1@surya
notify:                     FALSE
job_name:                   STDIN
stdout_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/chipseq.bds.20161222_171808_579/task.callpeak_macs2.macs2_rep1.line_71.id_10.stdout.cluster
jobshare:                   0
env_list:                   C_INCLUDE_PATH=/software/samtools/samtools-1.2/include/htslib,MAIL=/var/mail/imk1,SSH_CLIENT=171.65.77.8 32898 22,USER=imk1,J2SDKDIR=/usr/lib/jvm/java-8-oracle,SHLVL=3,J2REDIR=/usr/lib/jvm/java-8-oracle/jre,HOME=/users/imk1/,SAMTOOLS_HOME=/software/samtools/samtools-1.2/bin,SSH_TTY=/dev/pts/4,_LMFILES_=/software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/samtools/1.2,LOGNAME=imk1,_=/usr/bin/bds,XDG_SESSION_ID=9035,TERM=screen,SGE_ROOT=/var/lib/gridengine,PATH=/software/samtools/samtools-1.2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/users/imk1/edirect,DERBY_HOME=/usr/lib/jvm/java-8-oracle/db,XDG_RUNTIME_DIR=/run/user/1048,DISPLAY=localhost:12.0,SGE_CELL=default,STY=23557.ZBTB12_2015.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,KRB5CCNAME=FILE:/tmp/krb5cc_1048_cTVn8v,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,SCREEN_Name=ZBTB12_2015,PWD=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12,JAVA_HOME=/usr/lib/jvm/java-8-oracle,LOADEDMODULES=modsappsdir/modsappsdir:samtools/1.2,SSH_CONNECTION=171.65.77.8 32898 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,MANPATH=/software/samtools/samtools-1.2/share/man:/usr/share/man,MODULEPATH=/usr/local/Modules/versions				:/usr/local/Modules/$MODULE_VERSION/modulefiles	:/modules/				:/software/modulefiles,MODULESAPPSDIR=/software,MODULESHOME=/software/env_module/3.2.10
scheduling info:            queue instance "q@kali" dropped because it is temporarily not available
                            queue instance "q@surya" dropped because it is disabled
                            queue instance "amd.q@wotan" dropped because it is full
                            queue instance "q@kadru" dropped because it is full
                            queue instance "q@nandi" dropped because it is full
                            All queues dropped because of overload or full

Num	2
ID	task.callpeak_macs2.macs2_rep1_pr1.line_71.id_11
Name	macs2 rep1-pr1
Thread	thread_Root
PID	19998

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

Start	2016-12-22 17:18:18
End	2016-12-24 02:47:25
Elapsed	1 day 09:29:06
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/align/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
Dependencies

 
# SYS command. line 73

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 74

 export LC_COLLATE=C

# SYS command. line 79

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/align/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 160 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/align/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 160 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 110

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.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 121

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/align/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.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 140

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 143

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg

# SYS command. line 153

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

   
--------------------Stdout--------------------
22872 (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  @ Sat, 24 Dec 2016 01:50:33: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/align/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 160 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/align/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+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  @ Sat, 24 Dec 2016 01:50:33: #1 read tag files... 
INFO  @ Sat, 24 Dec 2016 01:50:33: #1 read treatment tags... 
INFO  @ Sat, 24 Dec 2016 01:50:41:  1000000 
INFO  @ Sat, 24 Dec 2016 01:50:49:  2000000 
INFO  @ Sat, 24 Dec 2016 01:50:57:  3000000 
INFO  @ Sat, 24 Dec 2016 01:51:05: #1.2 read input tags... 
INFO  @ Sat, 24 Dec 2016 01:51:12:  1000000 
INFO  @ Sat, 24 Dec 2016 01:51:20:  2000000 
INFO  @ Sat, 24 Dec 2016 01:51:28:  3000000 
INFO  @ Sat, 24 Dec 2016 01:51:35:  4000000 
INFO  @ Sat, 24 Dec 2016 01:51:43:  5000000 
INFO  @ Sat, 24 Dec 2016 01:51:51:  6000000 
INFO  @ Sat, 24 Dec 2016 01:51:58:  7000000 
INFO  @ Sat, 24 Dec 2016 01:52:06:  8000000 
INFO  @ Sat, 24 Dec 2016 01:52:13:  9000000 
INFO  @ Sat, 24 Dec 2016 01:52:21:  10000000 
INFO  @ Sat, 24 Dec 2016 01:52:28:  11000000 
INFO  @ Sat, 24 Dec 2016 01:52:36:  12000000 
INFO  @ Sat, 24 Dec 2016 01:52:44:  13000000 
INFO  @ Sat, 24 Dec 2016 01:52:51:  14000000 
INFO  @ Sat, 24 Dec 2016 01:52:59:  15000000 
INFO  @ Sat, 24 Dec 2016 01:53:06:  16000000 
INFO  @ Sat, 24 Dec 2016 01:53:14:  17000000 
INFO  @ Sat, 24 Dec 2016 01:53:22:  18000000 
INFO  @ Sat, 24 Dec 2016 01:53:29:  19000000 
INFO  @ Sat, 24 Dec 2016 01:53:37:  20000000 
INFO  @ Sat, 24 Dec 2016 01:53:44:  21000000 
INFO  @ Sat, 24 Dec 2016 01:53:52:  22000000 
INFO  @ Sat, 24 Dec 2016 01:53:59:  23000000 
INFO  @ Sat, 24 Dec 2016 01:54:07:  24000000 
INFO  @ Sat, 24 Dec 2016 01:54:15:  25000000 
INFO  @ Sat, 24 Dec 2016 01:54:22:  26000000 
INFO  @ Sat, 24 Dec 2016 01:54:30:  27000000 
INFO  @ Sat, 24 Dec 2016 01:54:37:  28000000 
INFO  @ Sat, 24 Dec 2016 01:54:45:  29000000 
INFO  @ Sat, 24 Dec 2016 01:54:53:  30000000 
INFO  @ Sat, 24 Dec 2016 01:55:00:  31000000 
INFO  @ Sat, 24 Dec 2016 01:55:08:  32000000 
INFO  @ Sat, 24 Dec 2016 01:55:15:  33000000 
INFO  @ Sat, 24 Dec 2016 01:55:23:  34000000 
INFO  @ Sat, 24 Dec 2016 01:55:31:  35000000 
INFO  @ Sat, 24 Dec 2016 01:55:38:  36000000 
INFO  @ Sat, 24 Dec 2016 01:55:46:  37000000 
INFO  @ Sat, 24 Dec 2016 01:55:54:  38000000 
INFO  @ Sat, 24 Dec 2016 01:56:01:  39000000 
INFO  @ Sat, 24 Dec 2016 01:56:09:  40000000 
INFO  @ Sat, 24 Dec 2016 01:56:16:  41000000 
INFO  @ Sat, 24 Dec 2016 01:56:24:  42000000 
INFO  @ Sat, 24 Dec 2016 01:56:32:  43000000 
INFO  @ Sat, 24 Dec 2016 01:56:39:  44000000 
INFO  @ Sat, 24 Dec 2016 01:56:47:  45000000 
INFO  @ Sat, 24 Dec 2016 01:56:54:  46000000 
INFO  @ Sat, 24 Dec 2016 01:57:02:  47000000 
INFO  @ Sat, 24 Dec 2016 01:57:09:  48000000 
INFO  @ Sat, 24 Dec 2016 01:57:17:  49000000 
INFO  @ Sat, 24 Dec 2016 01:57:24:  50000000 
INFO  @ Sat, 24 Dec 2016 01:57:29: #1 tag size is determined as 51 bps 
INFO  @ Sat, 24 Dec 2016 01:57:29: #1 tag size = 51 
INFO  @ Sat, 24 Dec 2016 01:57:29: #1  total tags in treatment: 3947204 
INFO  @ Sat, 24 Dec 2016 01:57:29: #1  total tags in control: 50000000 
INFO  @ Sat, 24 Dec 2016 01:57:29: #1 finished! 
INFO  @ Sat, 24 Dec 2016 01:57:29: #2 Build Peak Model... 
INFO  @ Sat, 24 Dec 2016 01:57:29: #2 Skipped... 
INFO  @ Sat, 24 Dec 2016 01:57:29: #2 Use 160 as fragment length 
INFO  @ Sat, 24 Dec 2016 01:57:29: #3 Call peaks... 
INFO  @ Sat, 24 Dec 2016 01:57:29: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Sat, 24 Dec 2016 01:57:29: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sat, 24 Dec 2016 02:04:57: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Sat, 24 Dec 2016 02:04:57: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Sat, 24 Dec 2016 02:04:57: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Sat, 24 Dec 2016 02:04:57: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Sat, 24 Dec 2016 02:04:57: #3 Call peaks for each chromosome... 
INFO  @ Sat, 24 Dec 2016 02:20:40: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Sat, 24 Dec 2016 02:20:45: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Sat, 24 Dec 2016 02:20:49: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Sat, 24 Dec 2016 02:20:52: Done! 
INFO  @ Sat, 24 Dec 2016 02:20:59: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/align/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 160 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/align/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+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  @ Sat, 24 Dec 2016 02:20:59: #1 read tag files... 
INFO  @ Sat, 24 Dec 2016 02:20:59: #1 read treatment tags... 
INFO  @ Sat, 24 Dec 2016 02:21:07:  1000000 
INFO  @ Sat, 24 Dec 2016 02:21:15:  2000000 
INFO  @ Sat, 24 Dec 2016 02:21:23:  3000000 
INFO  @ Sat, 24 Dec 2016 02:21:31: #1.2 read input tags... 
INFO  @ Sat, 24 Dec 2016 02:21:38:  1000000 
INFO  @ Sat, 24 Dec 2016 02:21:46:  2000000 
INFO  @ Sat, 24 Dec 2016 02:21:54:  3000000 
INFO  @ Sat, 24 Dec 2016 02:22:02:  4000000 
INFO  @ Sat, 24 Dec 2016 02:22:09:  5000000 
INFO  @ Sat, 24 Dec 2016 02:22:17:  6000000 
INFO  @ Sat, 24 Dec 2016 02:22:25:  7000000 
INFO  @ Sat, 24 Dec 2016 02:22:33:  8000000 
INFO  @ Sat, 24 Dec 2016 02:22:41:  9000000 
INFO  @ Sat, 24 Dec 2016 02:22:49:  10000000 
INFO  @ Sat, 24 Dec 2016 02:22:56:  11000000 
INFO  @ Sat, 24 Dec 2016 02:23:04:  12000000 
INFO  @ Sat, 24 Dec 2016 02:23:12:  13000000 
INFO  @ Sat, 24 Dec 2016 02:23:19:  14000000 
INFO  @ Sat, 24 Dec 2016 02:23:27:  15000000 
INFO  @ Sat, 24 Dec 2016 02:23:35:  16000000 
INFO  @ Sat, 24 Dec 2016 02:23:42:  17000000 
INFO  @ Sat, 24 Dec 2016 02:23:50:  18000000 
INFO  @ Sat, 24 Dec 2016 02:23:58:  19000000 
INFO  @ Sat, 24 Dec 2016 02:24:05:  20000000 
INFO  @ Sat, 24 Dec 2016 02:24:13:  21000000 
INFO  @ Sat, 24 Dec 2016 02:24:21:  22000000 
INFO  @ Sat, 24 Dec 2016 02:24:29:  23000000 
INFO  @ Sat, 24 Dec 2016 02:24:36:  24000000 
INFO  @ Sat, 24 Dec 2016 02:24:44:  25000000 
INFO  @ Sat, 24 Dec 2016 02:24:52:  26000000 
INFO  @ Sat, 24 Dec 2016 02:25:00:  27000000 
INFO  @ Sat, 24 Dec 2016 02:25:08:  28000000 
INFO  @ Sat, 24 Dec 2016 02:25:15:  29000000 
INFO  @ Sat, 24 Dec 2016 02:25:23:  30000000 
INFO  @ Sat, 24 Dec 2016 02:25:31:  31000000 
INFO  @ Sat, 24 Dec 2016 02:25:39:  32000000 
INFO  @ Sat, 24 Dec 2016 02:25:46:  33000000 
INFO  @ Sat, 24 Dec 2016 02:25:54:  34000000 
INFO  @ Sat, 24 Dec 2016 02:26:02:  35000000 
INFO  @ Sat, 24 Dec 2016 02:26:10:  36000000 
INFO  @ Sat, 24 Dec 2016 02:26:18:  37000000 
INFO  @ Sat, 24 Dec 2016 02:26:25:  38000000 
INFO  @ Sat, 24 Dec 2016 02:26:33:  39000000 
INFO  @ Sat, 24 Dec 2016 02:26:40:  40000000 
INFO  @ Sat, 24 Dec 2016 02:26:48:  41000000 
INFO  @ Sat, 24 Dec 2016 02:26:56:  42000000 
INFO  @ Sat, 24 Dec 2016 02:27:03:  43000000 
INFO  @ Sat, 24 Dec 2016 02:27:11:  44000000 
INFO  @ Sat, 24 Dec 2016 02:27:19:  45000000 
INFO  @ Sat, 24 Dec 2016 02:27:26:  46000000 
INFO  @ Sat, 24 Dec 2016 02:27:34:  47000000 
INFO  @ Sat, 24 Dec 2016 02:27:42:  48000000 
INFO  @ Sat, 24 Dec 2016 02:27:49:  49000000 
INFO  @ Sat, 24 Dec 2016 02:27:57:  50000000 
INFO  @ Sat, 24 Dec 2016 02:28:01: #1 tag size is determined as 51 bps 
INFO  @ Sat, 24 Dec 2016 02:28:01: #1 tag size = 51 
INFO  @ Sat, 24 Dec 2016 02:28:01: #1  total tags in treatment: 3947204 
INFO  @ Sat, 24 Dec 2016 02:28:01: #1  total tags in control: 50000000 
INFO  @ Sat, 24 Dec 2016 02:28:01: #1 finished! 
INFO  @ Sat, 24 Dec 2016 02:28:01: #2 Build Peak Model... 
INFO  @ Sat, 24 Dec 2016 02:28:01: #2 Skipped... 
INFO  @ Sat, 24 Dec 2016 02:28:01: #2 Use 160 as fragment length 
INFO  @ Sat, 24 Dec 2016 02:28:01: #3 Call peaks... 
INFO  @ Sat, 24 Dec 2016 02:28:01: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Sat, 24 Dec 2016 02:28:01: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sat, 24 Dec 2016 02:35:59: #3 Call peaks for each chromosome... 
INFO  @ Sat, 24 Dec 2016 02:45:30: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Sat, 24 Dec 2016 02:46:00: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Sat, 24 Dec 2016 02:46:22: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370883_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Sat, 24 Dec 2016 02:46:40: Done!

Num	3
ID	task.callpeak_macs2.macs2_rep1_pr2.line_71.id_12
Name	macs2 rep1-pr2
Thread	thread_Root
PID	19999

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

Start	2016-12-22 17:18:19
End	2016-12-24 02:12:38
Elapsed	1 day 08:54:18
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/align/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
Dependencies

 
# SYS command. line 73

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 74

 export LC_COLLATE=C

# SYS command. line 79

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/align/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 160 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/align/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 160 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 110

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.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 121

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/align/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.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 140

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 143

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg

# SYS command. line 153

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

   
--------------------Stdout--------------------
31359 (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  @ Sat, 24 Dec 2016 01:52:45: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/align/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 160 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/align/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+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  @ Sat, 24 Dec 2016 01:52:45: #1 read tag files... 
INFO  @ Sat, 24 Dec 2016 01:52:45: #1 read treatment tags... 
INFO  @ Sat, 24 Dec 2016 01:52:47:  1000000 
INFO  @ Sat, 24 Dec 2016 01:52:50:  2000000 
INFO  @ Sat, 24 Dec 2016 01:52:52:  3000000 
INFO  @ Sat, 24 Dec 2016 01:52:54: #1.2 read input tags... 
INFO  @ Sat, 24 Dec 2016 01:52:56:  1000000 
INFO  @ Sat, 24 Dec 2016 01:52:58:  2000000 
INFO  @ Sat, 24 Dec 2016 01:53:00:  3000000 
INFO  @ Sat, 24 Dec 2016 01:53:02:  4000000 
INFO  @ Sat, 24 Dec 2016 01:53:03:  5000000 
INFO  @ Sat, 24 Dec 2016 01:53:05:  6000000 
INFO  @ Sat, 24 Dec 2016 01:53:07:  7000000 
INFO  @ Sat, 24 Dec 2016 01:53:08:  8000000 
INFO  @ Sat, 24 Dec 2016 01:53:10:  9000000 
INFO  @ Sat, 24 Dec 2016 01:53:12:  10000000 
INFO  @ Sat, 24 Dec 2016 01:53:13:  11000000 
INFO  @ Sat, 24 Dec 2016 01:53:15:  12000000 
INFO  @ Sat, 24 Dec 2016 01:53:17:  13000000 
INFO  @ Sat, 24 Dec 2016 01:53:18:  14000000 
INFO  @ Sat, 24 Dec 2016 01:53:20:  15000000 
INFO  @ Sat, 24 Dec 2016 01:53:22:  16000000 
INFO  @ Sat, 24 Dec 2016 01:53:23:  17000000 
INFO  @ Sat, 24 Dec 2016 01:53:25:  18000000 
INFO  @ Sat, 24 Dec 2016 01:53:26:  19000000 
INFO  @ Sat, 24 Dec 2016 01:53:28:  20000000 
INFO  @ Sat, 24 Dec 2016 01:53:30:  21000000 
INFO  @ Sat, 24 Dec 2016 01:53:31:  22000000 
INFO  @ Sat, 24 Dec 2016 01:53:33:  23000000 
INFO  @ Sat, 24 Dec 2016 01:53:34:  24000000 
INFO  @ Sat, 24 Dec 2016 01:53:36:  25000000 
INFO  @ Sat, 24 Dec 2016 01:53:37:  26000000 
INFO  @ Sat, 24 Dec 2016 01:53:39:  27000000 
INFO  @ Sat, 24 Dec 2016 01:53:40:  28000000 
INFO  @ Sat, 24 Dec 2016 01:53:42:  29000000 
INFO  @ Sat, 24 Dec 2016 01:53:43:  30000000 
INFO  @ Sat, 24 Dec 2016 01:53:45:  31000000 
INFO  @ Sat, 24 Dec 2016 01:53:47:  32000000 
INFO  @ Sat, 24 Dec 2016 01:53:48:  33000000 
INFO  @ Sat, 24 Dec 2016 01:53:50:  34000000 
INFO  @ Sat, 24 Dec 2016 01:53:51:  35000000 
INFO  @ Sat, 24 Dec 2016 01:53:53:  36000000 
INFO  @ Sat, 24 Dec 2016 01:53:54:  37000000 
INFO  @ Sat, 24 Dec 2016 01:53:56:  38000000 
INFO  @ Sat, 24 Dec 2016 01:53:58:  39000000 
INFO  @ Sat, 24 Dec 2016 01:53:59:  40000000 
INFO  @ Sat, 24 Dec 2016 01:54:01:  41000000 
INFO  @ Sat, 24 Dec 2016 01:54:02:  42000000 
INFO  @ Sat, 24 Dec 2016 01:54:04:  43000000 
INFO  @ Sat, 24 Dec 2016 01:54:05:  44000000 
INFO  @ Sat, 24 Dec 2016 01:54:07:  45000000 
INFO  @ Sat, 24 Dec 2016 01:54:08:  46000000 
INFO  @ Sat, 24 Dec 2016 01:54:10:  47000000 
INFO  @ Sat, 24 Dec 2016 01:54:12:  48000000 
INFO  @ Sat, 24 Dec 2016 01:54:13:  49000000 
INFO  @ Sat, 24 Dec 2016 01:54:15:  50000000 
INFO  @ Sat, 24 Dec 2016 01:54:17: #1 tag size is determined as 51 bps 
INFO  @ Sat, 24 Dec 2016 01:54:17: #1 tag size = 51 
INFO  @ Sat, 24 Dec 2016 01:54:17: #1  total tags in treatment: 3947203 
INFO  @ Sat, 24 Dec 2016 01:54:17: #1  total tags in control: 50000000 
INFO  @ Sat, 24 Dec 2016 01:54:17: #1 finished! 
INFO  @ Sat, 24 Dec 2016 01:54:17: #2 Build Peak Model... 
INFO  @ Sat, 24 Dec 2016 01:54:17: #2 Skipped... 
INFO  @ Sat, 24 Dec 2016 01:54:17: #2 Use 160 as fragment length 
INFO  @ Sat, 24 Dec 2016 01:54:17: #3 Call peaks... 
INFO  @ Sat, 24 Dec 2016 01:54:17: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Sat, 24 Dec 2016 01:54:17: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sat, 24 Dec 2016 01:57:29: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Sat, 24 Dec 2016 01:57:29: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Sat, 24 Dec 2016 01:57:29: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Sat, 24 Dec 2016 01:57:29: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Sat, 24 Dec 2016 01:57:29: #3 Call peaks for each chromosome... 
INFO  @ Sat, 24 Dec 2016 02:02:33: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Sat, 24 Dec 2016 02:02:35: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Sat, 24 Dec 2016 02:02:36: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Sat, 24 Dec 2016 02:02:37: Done! 
INFO  @ Sat, 24 Dec 2016 02:02:40: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/align/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 160 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/align/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+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  @ Sat, 24 Dec 2016 02:02:40: #1 read tag files... 
INFO  @ Sat, 24 Dec 2016 02:02:40: #1 read treatment tags... 
INFO  @ Sat, 24 Dec 2016 02:02:43:  1000000 
INFO  @ Sat, 24 Dec 2016 02:02:47:  2000000 
INFO  @ Sat, 24 Dec 2016 02:02:50:  3000000 
INFO  @ Sat, 24 Dec 2016 02:02:53: #1.2 read input tags... 
INFO  @ Sat, 24 Dec 2016 02:02:56:  1000000 
INFO  @ Sat, 24 Dec 2016 02:02:59:  2000000 
INFO  @ Sat, 24 Dec 2016 02:03:02:  3000000 
INFO  @ Sat, 24 Dec 2016 02:03:04:  4000000 
INFO  @ Sat, 24 Dec 2016 02:03:06:  5000000 
INFO  @ Sat, 24 Dec 2016 02:03:08:  6000000 
INFO  @ Sat, 24 Dec 2016 02:03:11:  7000000 
INFO  @ Sat, 24 Dec 2016 02:03:13:  8000000 
INFO  @ Sat, 24 Dec 2016 02:03:15:  9000000 
INFO  @ Sat, 24 Dec 2016 02:03:17:  10000000 
INFO  @ Sat, 24 Dec 2016 02:03:19:  11000000 
INFO  @ Sat, 24 Dec 2016 02:03:21:  12000000 
INFO  @ Sat, 24 Dec 2016 02:03:23:  13000000 
INFO  @ Sat, 24 Dec 2016 02:03:25:  14000000 
INFO  @ Sat, 24 Dec 2016 02:03:27:  15000000 
INFO  @ Sat, 24 Dec 2016 02:03:29:  16000000 
INFO  @ Sat, 24 Dec 2016 02:03:30:  17000000 
INFO  @ Sat, 24 Dec 2016 02:03:32:  18000000 
INFO  @ Sat, 24 Dec 2016 02:03:34:  19000000 
INFO  @ Sat, 24 Dec 2016 02:03:36:  20000000 
INFO  @ Sat, 24 Dec 2016 02:03:37:  21000000 
INFO  @ Sat, 24 Dec 2016 02:03:39:  22000000 
INFO  @ Sat, 24 Dec 2016 02:03:41:  23000000 
INFO  @ Sat, 24 Dec 2016 02:03:43:  24000000 
INFO  @ Sat, 24 Dec 2016 02:03:45:  25000000 
INFO  @ Sat, 24 Dec 2016 02:03:46:  26000000 
INFO  @ Sat, 24 Dec 2016 02:03:48:  27000000 
INFO  @ Sat, 24 Dec 2016 02:03:50:  28000000 
INFO  @ Sat, 24 Dec 2016 02:03:52:  29000000 
INFO  @ Sat, 24 Dec 2016 02:03:54:  30000000 
INFO  @ Sat, 24 Dec 2016 02:03:57:  31000000 
INFO  @ Sat, 24 Dec 2016 02:03:59:  32000000 
INFO  @ Sat, 24 Dec 2016 02:04:01:  33000000 
INFO  @ Sat, 24 Dec 2016 02:04:03:  34000000 
INFO  @ Sat, 24 Dec 2016 02:04:05:  35000000 
INFO  @ Sat, 24 Dec 2016 02:04:07:  36000000 
INFO  @ Sat, 24 Dec 2016 02:04:09:  37000000 
INFO  @ Sat, 24 Dec 2016 02:04:11:  38000000 
INFO  @ Sat, 24 Dec 2016 02:04:13:  39000000 
INFO  @ Sat, 24 Dec 2016 02:04:15:  40000000 
INFO  @ Sat, 24 Dec 2016 02:04:17:  41000000 
INFO  @ Sat, 24 Dec 2016 02:04:19:  42000000 
INFO  @ Sat, 24 Dec 2016 02:04:21:  43000000 
INFO  @ Sat, 24 Dec 2016 02:04:23:  44000000 
INFO  @ Sat, 24 Dec 2016 02:04:25:  45000000 
INFO  @ Sat, 24 Dec 2016 02:04:27:  46000000 
INFO  @ Sat, 24 Dec 2016 02:04:29:  47000000 
INFO  @ Sat, 24 Dec 2016 02:04:31:  48000000 
INFO  @ Sat, 24 Dec 2016 02:04:33:  49000000 
INFO  @ Sat, 24 Dec 2016 02:04:36:  50000000 
INFO  @ Sat, 24 Dec 2016 02:04:38: #1 tag size is determined as 51 bps 
INFO  @ Sat, 24 Dec 2016 02:04:38: #1 tag size = 51 
INFO  @ Sat, 24 Dec 2016 02:04:38: #1  total tags in treatment: 3947203 
INFO  @ Sat, 24 Dec 2016 02:04:38: #1  total tags in control: 50000000 
INFO  @ Sat, 24 Dec 2016 02:04:38: #1 finished! 
INFO  @ Sat, 24 Dec 2016 02:04:38: #2 Build Peak Model... 
INFO  @ Sat, 24 Dec 2016 02:04:38: #2 Skipped... 
INFO  @ Sat, 24 Dec 2016 02:04:38: #2 Use 160 as fragment length 
INFO  @ Sat, 24 Dec 2016 02:04:38: #3 Call peaks... 
INFO  @ Sat, 24 Dec 2016 02:04:38: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Sat, 24 Dec 2016 02:04:38: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sat, 24 Dec 2016 02:08:18: #3 Call peaks for each chromosome... 
INFO  @ Sat, 24 Dec 2016 02:11:55: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Sat, 24 Dec 2016 02:12:04: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Sat, 24 Dec 2016 02:12:10: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370883_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Sat, 24 Dec 2016 02:12:17: Done!

BigDataScript report: chipseq.bds

Timeline

Task Graph

Parallel (threads) details

Task details

Global scope

Type	Name	Value
string	_	/usr/bin/bds
string	_LMFILES_	/software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/samtools/1.2
bool	allowEmpty	false
string[]	args	[-title, ZBTB12, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZBTB12/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12/out/align/rep1/SRR1370883_1.bam, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz, -final_stage, idr, $]
string	C_INCLUDE_PATH	/software/samtools/samtools-1.2/include/htslib
bool	canFail	false
int	cpus	-1
int	cpusLocal	56
int	day	86400
string	DERBY_HOME	/usr/lib/jvm/java-8-oracle/db
string	DISPLAY	localhost:12.0
real	E	2.718281828459045
int	G	1073741824
string	HOME	/users/imk1/
int	hour	3600
string	J2REDIR	/usr/lib/jvm/java-8-oracle/jre
string	J2SDKDIR	/usr/lib/jvm/java-8-oracle
string	JAVA_HOME	/usr/lib/jvm/java-8-oracle
int	K	1024
string	KRB5CCNAME	FILE:/tmp/krb5cc_1048_cTVn8v
string	LANG	en_US.UTF-8
string	LOADEDMODULES	modsappsdir/modsappsdir:samtools/1.2
string	LOGNAME	imk1
int	M	1048576
string	MAIL	/var/mail/imk1
string	MANPATH	/software/samtools/samtools-1.2/share/man:/usr/share/man
int	mem	-1
int	minute	60
string	MODULE_VERSION	3.2.10
string	MODULE_VERSION_STACK	3.2.10
string	MODULEPATH	/usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles
string	MODULESAPPSDIR	/software
string	MODULESHOME	/software/env_module/3.2.10
string	NLSPATH	/usr/dt/lib/nls/msg/%L/%N.cat
string	node
int	P	1125899906842624
string	PATH	/software/samtools/samtools-1.2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/users/imk1/edirect
real	PI	3.141592653589793
string	ppwd	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12
string	programName	chipseq.bds
string	programPath	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
string	PWD	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZBTB12
string	queue
int	retry	0
string	SAMTOOLS_HOME	/software/samtools/samtools-1.2/bin
string	SCREEN_Name	ZBTB12_2015
string	SHELL	/bin/bash
string	SHLVL	3
string	SSH_CLIENT	171.65.77.8 32898 22
string	SSH_CONNECTION	171.65.77.8 32898 171.65.76.63 22
string	SSH_TTY	/dev/pts/4
string	STY	23557.ZBTB12_2015.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	9035
string	XFILESEARCHPATH	/usr/dt/app-defaults/%L/Dt