Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20161221_152636_769
Start time	2016-12-21 15:26:36
Run time	14:42:36.677
Tasks executed	3
Tasks failed	1
Tasks failed names	macs2 rep1
Arguments*	[-title, CTCF, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/CTCF/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/align/rep1/SRR1370879_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.20161221_152636_769/task.callpeak_macs2.macs2_rep1.line_71.id_10 chipseq.bds.20161221_152636_769/task.callpeak_macs2.macs2_rep1_pr1.line_71.id_11 chipseq.bds.20161221_152636_769/task.callpeak_macs2.macs2_rep1_pr2.line_71.id_12
thread_42	thread_Root
thread_41	thread_Root

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.callpeak_macs2.macs2_rep1.line_71.id_10
Name	macs2 rep1
Thread	thread_Root
PID	19551

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

Start	2016-12-21 15:26:44
End	2016-12-21 15:26:44
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/align/rep1/SRR1370879_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/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/signal/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/signal/macs2/rep1/SRR1370879_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/CTCF/out/align/rep1/SRR1370879_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/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 65 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_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/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_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/CTCF/out/align/rep1/SRR1370879_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/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 65 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_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/CTCF/out/peak/macs2/rep1/SRR1370879_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/CTCF/out/peak/macs2/rep1/SRR1370879_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/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_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/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_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/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1 -o "SRR1370879_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/CTCF/out/peak/macs2/rep1/SRR1370879_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/CTCF/out/peak/macs2/rep1/SRR1370879_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/CTCF/out/peak/macs2/rep1/SRR1370879_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/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_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/CTCF/out/peak/macs2/rep1/SRR1370879_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/CTCF/out/signal/macs2/rep1/SRR1370879_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/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_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/CTCF/out/align/rep1/SRR1370879_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/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1 -o "SRR1370879_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/CTCF/out/peak/macs2/rep1/SRR1370879_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/CTCF/out/peak/macs2/rep1/SRR1370879_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/CTCF/out/peak/macs2/rep1/SRR1370879_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/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_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/CTCF/out/peak/macs2/rep1/SRR1370879_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/CTCF/out/signal/macs2/rep1/SRR1370879_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/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_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/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_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--------------------
18196 (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  @ Thu, 22 Dec 2016 05:38:44: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/align/rep1/SRR1370879_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/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 65 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/align/rep1/SRR1370879_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  @ Thu, 22 Dec 2016 05:38:44: #1 read tag files... 
INFO  @ Thu, 22 Dec 2016 05:38:44: #1 read treatment tags... 
INFO  @ Thu, 22 Dec 2016 05:38:46:  1000000 
INFO  @ Thu, 22 Dec 2016 05:38:48:  2000000 
INFO  @ Thu, 22 Dec 2016 05:38:50:  3000000 
INFO  @ Thu, 22 Dec 2016 05:38:52:  4000000 
INFO  @ Thu, 22 Dec 2016 05:38:54:  5000000 
INFO  @ Thu, 22 Dec 2016 05:38:54: #1.2 read input tags... 
INFO  @ Thu, 22 Dec 2016 05:38:57:  1000000 
INFO  @ Thu, 22 Dec 2016 05:38:58:  2000000 
INFO  @ Thu, 22 Dec 2016 05:39:00:  3000000 
INFO  @ Thu, 22 Dec 2016 05:39:02:  4000000 
INFO  @ Thu, 22 Dec 2016 05:39:03:  5000000 
INFO  @ Thu, 22 Dec 2016 05:39:05:  6000000 
INFO  @ Thu, 22 Dec 2016 05:39:07:  7000000 
INFO  @ Thu, 22 Dec 2016 05:39:08:  8000000 
INFO  @ Thu, 22 Dec 2016 05:39:10:  9000000 
INFO  @ Thu, 22 Dec 2016 05:39:12:  10000000 
INFO  @ Thu, 22 Dec 2016 05:39:13:  11000000 
INFO  @ Thu, 22 Dec 2016 05:39:15:  12000000 
INFO  @ Thu, 22 Dec 2016 05:39:17:  13000000 
INFO  @ Thu, 22 Dec 2016 05:39:18:  14000000 
INFO  @ Thu, 22 Dec 2016 05:39:20:  15000000 
INFO  @ Thu, 22 Dec 2016 05:39:22:  16000000 
INFO  @ Thu, 22 Dec 2016 05:39:24:  17000000 
INFO  @ Thu, 22 Dec 2016 05:39:25:  18000000 
INFO  @ Thu, 22 Dec 2016 05:39:27:  19000000 
INFO  @ Thu, 22 Dec 2016 05:39:29:  20000000 
INFO  @ Thu, 22 Dec 2016 05:39:30:  21000000 
INFO  @ Thu, 22 Dec 2016 05:39:32:  22000000 
INFO  @ Thu, 22 Dec 2016 05:39:34:  23000000 
INFO  @ Thu, 22 Dec 2016 05:39:35:  24000000 
INFO  @ Thu, 22 Dec 2016 05:39:37:  25000000 
INFO  @ Thu, 22 Dec 2016 05:39:39:  26000000 
INFO  @ Thu, 22 Dec 2016 05:39:40:  27000000 
INFO  @ Thu, 22 Dec 2016 05:39:42:  28000000 
INFO  @ Thu, 22 Dec 2016 05:39:44:  29000000 
INFO  @ Thu, 22 Dec 2016 05:39:45:  30000000 
INFO  @ Thu, 22 Dec 2016 05:39:48:  31000000 
INFO  @ Thu, 22 Dec 2016 05:39:50:  32000000 
INFO  @ Thu, 22 Dec 2016 05:39:52:  33000000 
INFO  @ Thu, 22 Dec 2016 05:39:53:  34000000 
INFO  @ Thu, 22 Dec 2016 05:39:55:  35000000 
INFO  @ Thu, 22 Dec 2016 05:39:57:  36000000 
INFO  @ Thu, 22 Dec 2016 05:39:58:  37000000 
INFO  @ Thu, 22 Dec 2016 05:40:00:  38000000 
INFO  @ Thu, 22 Dec 2016 05:40:02:  39000000 
INFO  @ Thu, 22 Dec 2016 05:40:03:  40000000 
INFO  @ Thu, 22 Dec 2016 05:40:05:  41000000 
INFO  @ Thu, 22 Dec 2016 05:40:07:  42000000 
INFO  @ Thu, 22 Dec 2016 05:40:09:  43000000 
INFO  @ Thu, 22 Dec 2016 05:40:10:  44000000 
INFO  @ Thu, 22 Dec 2016 05:40:12:  45000000 
INFO  @ Thu, 22 Dec 2016 05:40:14:  46000000 
INFO  @ Thu, 22 Dec 2016 05:40:15:  47000000 
INFO  @ Thu, 22 Dec 2016 05:40:17:  48000000 
INFO  @ Thu, 22 Dec 2016 05:40:19:  49000000 
INFO  @ Thu, 22 Dec 2016 05:40:20:  50000000 
INFO  @ Thu, 22 Dec 2016 05:40:22: #1 tag size is determined as 51 bps 
INFO  @ Thu, 22 Dec 2016 05:40:22: #1 tag size = 51 
INFO  @ Thu, 22 Dec 2016 05:40:22: #1  total tags in treatment: 5392519 
INFO  @ Thu, 22 Dec 2016 05:40:22: #1  total tags in control: 50000000 
INFO  @ Thu, 22 Dec 2016 05:40:22: #1 finished! 
INFO  @ Thu, 22 Dec 2016 05:40:22: #2 Build Peak Model... 
INFO  @ Thu, 22 Dec 2016 05:40:22: #2 Skipped... 
INFO  @ Thu, 22 Dec 2016 05:40:22: #2 Use 65 as fragment length 
INFO  @ Thu, 22 Dec 2016 05:40:22: #3 Call peaks... 
INFO  @ Thu, 22 Dec 2016 05:40:22: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 22 Dec 2016 05:40:22: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 22 Dec 2016 05:43:28: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 22 Dec 2016 05:43:28: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 22 Dec 2016 05:43:28: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Thu, 22 Dec 2016 05:43:28: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 22 Dec 2016 05:43:28: #3 Call peaks for each chromosome... 
INFO  @ Thu, 22 Dec 2016 05:48:27: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 22 Dec 2016 05:48:38: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 22 Dec 2016 05:48:45: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Thu, 22 Dec 2016 05:48:50: Done! 
INFO  @ Thu, 22 Dec 2016 05:49:01: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/align/rep1/SRR1370879_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/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 65 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/align/rep1/SRR1370879_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  @ Thu, 22 Dec 2016 05:49:01: #1 read tag files... 
INFO  @ Thu, 22 Dec 2016 05:49:01: #1 read treatment tags... 
INFO  @ Thu, 22 Dec 2016 05:49:03:  1000000 
INFO  @ Thu, 22 Dec 2016 05:49:04:  2000000 
INFO  @ Thu, 22 Dec 2016 05:49:06:  3000000 
INFO  @ Thu, 22 Dec 2016 05:49:07:  4000000 
INFO  @ Thu, 22 Dec 2016 05:49:09:  5000000 
INFO  @ Thu, 22 Dec 2016 05:49:10: #1.2 read input tags... 
INFO  @ Thu, 22 Dec 2016 05:49:11:  1000000 
INFO  @ Thu, 22 Dec 2016 05:49:13:  2000000 
INFO  @ Thu, 22 Dec 2016 05:49:14:  3000000 
INFO  @ Thu, 22 Dec 2016 05:49:16:  4000000 
INFO  @ Thu, 22 Dec 2016 05:49:18:  5000000 
INFO  @ Thu, 22 Dec 2016 05:49:19:  6000000 
INFO  @ Thu, 22 Dec 2016 05:49:21:  7000000 
INFO  @ Thu, 22 Dec 2016 05:49:22:  8000000 
INFO  @ Thu, 22 Dec 2016 05:49:24:  9000000 
INFO  @ Thu, 22 Dec 2016 05:49:25:  10000000 
INFO  @ Thu, 22 Dec 2016 05:49:27:  11000000 
INFO  @ Thu, 22 Dec 2016 05:49:29:  12000000 
INFO  @ Thu, 22 Dec 2016 05:49:30:  13000000 
INFO  @ Thu, 22 Dec 2016 05:49:32:  14000000 
INFO  @ Thu, 22 Dec 2016 05:49:33:  15000000 
INFO  @ Thu, 22 Dec 2016 05:49:35:  16000000 
INFO  @ Thu, 22 Dec 2016 05:49:36:  17000000 
INFO  @ Thu, 22 Dec 2016 05:49:38:  18000000 
INFO  @ Thu, 22 Dec 2016 05:49:40:  19000000 
INFO  @ Thu, 22 Dec 2016 05:49:41:  20000000 
INFO  @ Thu, 22 Dec 2016 05:49:43:  21000000 
INFO  @ Thu, 22 Dec 2016 05:49:44:  22000000 
INFO  @ Thu, 22 Dec 2016 05:49:46:  23000000 
INFO  @ Thu, 22 Dec 2016 05:49:47:  24000000 
INFO  @ Thu, 22 Dec 2016 05:49:49:  25000000 
INFO  @ Thu, 22 Dec 2016 05:49:51:  26000000 
INFO  @ Thu, 22 Dec 2016 05:49:53:  27000000 
INFO  @ Thu, 22 Dec 2016 05:49:54:  28000000 
INFO  @ Thu, 22 Dec 2016 05:49:56:  29000000 
INFO  @ Thu, 22 Dec 2016 05:49:57:  30000000 
INFO  @ Thu, 22 Dec 2016 05:49:59:  31000000 
INFO  @ Thu, 22 Dec 2016 05:50:00:  32000000 
INFO  @ Thu, 22 Dec 2016 05:50:02:  33000000 
INFO  @ Thu, 22 Dec 2016 05:50:04:  34000000 
INFO  @ Thu, 22 Dec 2016 05:50:05:  35000000 
INFO  @ Thu, 22 Dec 2016 05:50:07:  36000000 
INFO  @ Thu, 22 Dec 2016 05:50:08:  37000000 
INFO  @ Thu, 22 Dec 2016 05:50:10:  38000000 
INFO  @ Thu, 22 Dec 2016 05:50:11:  39000000 
INFO  @ Thu, 22 Dec 2016 05:50:13:  40000000 
INFO  @ Thu, 22 Dec 2016 05:50:14:  41000000 
INFO  @ Thu, 22 Dec 2016 05:50:16:  42000000 
INFO  @ Thu, 22 Dec 2016 05:50:18:  43000000 
INFO  @ Thu, 22 Dec 2016 05:50:19:  44000000 
INFO  @ Thu, 22 Dec 2016 05:50:21:  45000000 
INFO  @ Thu, 22 Dec 2016 05:50:22:  46000000 
INFO  @ Thu, 22 Dec 2016 05:50:24:  47000000 
INFO  @ Thu, 22 Dec 2016 05:50:26:  48000000 
INFO  @ Thu, 22 Dec 2016 05:50:27:  49000000 
INFO  @ Thu, 22 Dec 2016 05:50:29:  50000000 
INFO  @ Thu, 22 Dec 2016 05:50:30: #1 tag size is determined as 51 bps 
INFO  @ Thu, 22 Dec 2016 05:50:30: #1 tag size = 51 
INFO  @ Thu, 22 Dec 2016 05:50:30: #1  total tags in treatment: 5392519 
INFO  @ Thu, 22 Dec 2016 05:50:30: #1  total tags in control: 50000000 
INFO  @ Thu, 22 Dec 2016 05:50:30: #1 finished! 
INFO  @ Thu, 22 Dec 2016 05:50:30: #2 Build Peak Model... 
INFO  @ Thu, 22 Dec 2016 05:50:30: #2 Skipped... 
INFO  @ Thu, 22 Dec 2016 05:50:30: #2 Use 65 as fragment length 
INFO  @ Thu, 22 Dec 2016 05:50:30: #3 Call peaks... 
INFO  @ Thu, 22 Dec 2016 05:50:30: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 22 Dec 2016 05:50:30: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 22 Dec 2016 05:54:17: #3 Call peaks for each chromosome... 
INFO  @ Thu, 22 Dec 2016 05:58:41: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 22 Dec 2016 05:58:59: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Thu, 22 Dec 2016 05:59:11: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 22 Dec 2016 05:59:23: Done! 
INFO  @ Thu, 22 Dec 2016 06:00:21: Read and build treatment bedGraph... 
INFO  @ Thu, 22 Dec 2016 06:00:33: Read and build control bedGraph... 
INFO  @ Thu, 22 Dec 2016 06:02:34: Build scoreTrackII... 
INFO  @ Thu, 22 Dec 2016 06:03:20: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Thu, 22 Dec 2016 06:08:03: Write bedGraph of scores... 
INFO  @ Thu, 22 Dec 2016 06:09:11: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_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:                 19551
exec_file:                  job_scripts/19551
submission_time:            Wed Dec 21 15:26:44 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/CTCF
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/chipseq.bds.20161221_152636_769/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/CTCF/chipseq.bds.20161221_152636_769/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=51961.CTCF_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=CTCF_2015,PWD=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF,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
script_file:                STDIN
usage    1:                 cpu=00:31:27, mem=4832.02005 GBs, io=57.48615, vmem=3.999G, maxvmem=4.007G
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@nandi" dropped because it is full
                            queue instance "q@kadru" 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	19552

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

Start	2016-12-21 15:26:47
End	2016-12-22 06:04:39
Elapsed	14:37:51
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/align/pseudo_reps/rep1/pr1/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_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/CTCF/out/align/pseudo_reps/rep1/pr1/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 65 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_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/CTCF/out/align/pseudo_reps/rep1/pr1/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 65 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_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/CTCF/out/align/pseudo_reps/rep1/pr1/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_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--------------------
18306 (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  @ Thu, 22 Dec 2016 05:39:00: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/align/pseudo_reps/rep1/pr1/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 65 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/align/pseudo_reps/rep1/pr1/SRR1370879_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  @ Thu, 22 Dec 2016 05:39:00: #1 read tag files... 
INFO  @ Thu, 22 Dec 2016 05:39:00: #1 read treatment tags... 
INFO  @ Thu, 22 Dec 2016 05:39:02:  1000000 
INFO  @ Thu, 22 Dec 2016 05:39:04:  2000000 
INFO  @ Thu, 22 Dec 2016 05:39:05: #1.2 read input tags... 
INFO  @ Thu, 22 Dec 2016 05:39:07:  1000000 
INFO  @ Thu, 22 Dec 2016 05:39:09:  2000000 
INFO  @ Thu, 22 Dec 2016 05:39:10:  3000000 
INFO  @ Thu, 22 Dec 2016 05:39:12:  4000000 
INFO  @ Thu, 22 Dec 2016 05:39:13:  5000000 
INFO  @ Thu, 22 Dec 2016 05:39:15:  6000000 
INFO  @ Thu, 22 Dec 2016 05:39:17:  7000000 
INFO  @ Thu, 22 Dec 2016 05:39:18:  8000000 
INFO  @ Thu, 22 Dec 2016 05:39:20:  9000000 
INFO  @ Thu, 22 Dec 2016 05:39:22:  10000000 
INFO  @ Thu, 22 Dec 2016 05:39:23:  11000000 
INFO  @ Thu, 22 Dec 2016 05:39:25:  12000000 
INFO  @ Thu, 22 Dec 2016 05:39:27:  13000000 
INFO  @ Thu, 22 Dec 2016 05:39:28:  14000000 
INFO  @ Thu, 22 Dec 2016 05:39:30:  15000000 
INFO  @ Thu, 22 Dec 2016 05:39:32:  16000000 
INFO  @ Thu, 22 Dec 2016 05:39:33:  17000000 
INFO  @ Thu, 22 Dec 2016 05:39:35:  18000000 
INFO  @ Thu, 22 Dec 2016 05:39:37:  19000000 
INFO  @ Thu, 22 Dec 2016 05:39:39:  20000000 
INFO  @ Thu, 22 Dec 2016 05:39:40:  21000000 
INFO  @ Thu, 22 Dec 2016 05:39:42:  22000000 
INFO  @ Thu, 22 Dec 2016 05:39:44:  23000000 
INFO  @ Thu, 22 Dec 2016 05:39:45:  24000000 
INFO  @ Thu, 22 Dec 2016 05:39:47:  25000000 
INFO  @ Thu, 22 Dec 2016 05:39:49:  26000000 
INFO  @ Thu, 22 Dec 2016 05:39:50:  27000000 
INFO  @ Thu, 22 Dec 2016 05:39:52:  28000000 
INFO  @ Thu, 22 Dec 2016 05:39:53:  29000000 
INFO  @ Thu, 22 Dec 2016 05:39:55:  30000000 
INFO  @ Thu, 22 Dec 2016 05:39:57:  31000000 
INFO  @ Thu, 22 Dec 2016 05:39:58:  32000000 
INFO  @ Thu, 22 Dec 2016 05:40:00:  33000000 
INFO  @ Thu, 22 Dec 2016 05:40:02:  34000000 
INFO  @ Thu, 22 Dec 2016 05:40:03:  35000000 
INFO  @ Thu, 22 Dec 2016 05:40:05:  36000000 
INFO  @ Thu, 22 Dec 2016 05:40:06:  37000000 
INFO  @ Thu, 22 Dec 2016 05:40:08:  38000000 
INFO  @ Thu, 22 Dec 2016 05:40:10:  39000000 
INFO  @ Thu, 22 Dec 2016 05:40:11:  40000000 
INFO  @ Thu, 22 Dec 2016 05:40:13:  41000000 
INFO  @ Thu, 22 Dec 2016 05:40:15:  42000000 
INFO  @ Thu, 22 Dec 2016 05:40:16:  43000000 
INFO  @ Thu, 22 Dec 2016 05:40:18:  44000000 
INFO  @ Thu, 22 Dec 2016 05:40:19:  45000000 
INFO  @ Thu, 22 Dec 2016 05:40:21:  46000000 
INFO  @ Thu, 22 Dec 2016 05:40:23:  47000000 
INFO  @ Thu, 22 Dec 2016 05:40:24:  48000000 
INFO  @ Thu, 22 Dec 2016 05:40:26:  49000000 
INFO  @ Thu, 22 Dec 2016 05:40:27:  50000000 
INFO  @ Thu, 22 Dec 2016 05:40:29: #1 tag size is determined as 51 bps 
INFO  @ Thu, 22 Dec 2016 05:40:29: #1 tag size = 51 
INFO  @ Thu, 22 Dec 2016 05:40:29: #1  total tags in treatment: 2696260 
INFO  @ Thu, 22 Dec 2016 05:40:29: #1  total tags in control: 50000000 
INFO  @ Thu, 22 Dec 2016 05:40:29: #1 finished! 
INFO  @ Thu, 22 Dec 2016 05:40:29: #2 Build Peak Model... 
INFO  @ Thu, 22 Dec 2016 05:40:29: #2 Skipped... 
INFO  @ Thu, 22 Dec 2016 05:40:29: #2 Use 65 as fragment length 
INFO  @ Thu, 22 Dec 2016 05:40:29: #3 Call peaks... 
INFO  @ Thu, 22 Dec 2016 05:40:29: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 22 Dec 2016 05:40:29: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 22 Dec 2016 05:45:25: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 22 Dec 2016 05:45:25: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 22 Dec 2016 05:45:25: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Thu, 22 Dec 2016 05:45:25: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 22 Dec 2016 05:45:25: #3 Call peaks for each chromosome... 
INFO  @ Thu, 22 Dec 2016 05:50:48: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 22 Dec 2016 05:51:00: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 22 Dec 2016 05:51:11: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Thu, 22 Dec 2016 05:51:17: Done! 
INFO  @ Thu, 22 Dec 2016 05:51:30: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/align/pseudo_reps/rep1/pr1/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 65 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/align/pseudo_reps/rep1/pr1/SRR1370879_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  @ Thu, 22 Dec 2016 05:51:30: #1 read tag files... 
INFO  @ Thu, 22 Dec 2016 05:51:30: #1 read treatment tags... 
INFO  @ Thu, 22 Dec 2016 05:51:32:  1000000 
INFO  @ Thu, 22 Dec 2016 05:51:34:  2000000 
INFO  @ Thu, 22 Dec 2016 05:51:35: #1.2 read input tags... 
INFO  @ Thu, 22 Dec 2016 05:51:37:  1000000 
INFO  @ Thu, 22 Dec 2016 05:51:39:  2000000 
INFO  @ Thu, 22 Dec 2016 05:51:40:  3000000 
INFO  @ Thu, 22 Dec 2016 05:51:42:  4000000 
INFO  @ Thu, 22 Dec 2016 05:51:44:  5000000 
INFO  @ Thu, 22 Dec 2016 05:51:45:  6000000 
INFO  @ Thu, 22 Dec 2016 05:51:47:  7000000 
INFO  @ Thu, 22 Dec 2016 05:51:48:  8000000 
INFO  @ Thu, 22 Dec 2016 05:51:50:  9000000 
INFO  @ Thu, 22 Dec 2016 05:51:52:  10000000 
INFO  @ Thu, 22 Dec 2016 05:51:53:  11000000 
INFO  @ Thu, 22 Dec 2016 05:51:55:  12000000 
INFO  @ Thu, 22 Dec 2016 05:51:57:  13000000 
INFO  @ Thu, 22 Dec 2016 05:51:58:  14000000 
INFO  @ Thu, 22 Dec 2016 05:52:00:  15000000 
INFO  @ Thu, 22 Dec 2016 05:52:02:  16000000 
INFO  @ Thu, 22 Dec 2016 05:52:03:  17000000 
INFO  @ Thu, 22 Dec 2016 05:52:05:  18000000 
INFO  @ Thu, 22 Dec 2016 05:52:07:  19000000 
INFO  @ Thu, 22 Dec 2016 05:52:08:  20000000 
INFO  @ Thu, 22 Dec 2016 05:52:10:  21000000 
INFO  @ Thu, 22 Dec 2016 05:52:12:  22000000 
INFO  @ Thu, 22 Dec 2016 05:52:13:  23000000 
INFO  @ Thu, 22 Dec 2016 05:52:15:  24000000 
INFO  @ Thu, 22 Dec 2016 05:52:16:  25000000 
INFO  @ Thu, 22 Dec 2016 05:52:18:  26000000 
INFO  @ Thu, 22 Dec 2016 05:52:20:  27000000 
INFO  @ Thu, 22 Dec 2016 05:52:21:  28000000 
INFO  @ Thu, 22 Dec 2016 05:52:23:  29000000 
INFO  @ Thu, 22 Dec 2016 05:52:24:  30000000 
INFO  @ Thu, 22 Dec 2016 05:52:26:  31000000 
INFO  @ Thu, 22 Dec 2016 05:52:28:  32000000 
INFO  @ Thu, 22 Dec 2016 05:52:29:  33000000 
INFO  @ Thu, 22 Dec 2016 05:52:31:  34000000 
INFO  @ Thu, 22 Dec 2016 05:52:32:  35000000 
INFO  @ Thu, 22 Dec 2016 05:52:34:  36000000 
INFO  @ Thu, 22 Dec 2016 05:52:36:  37000000 
INFO  @ Thu, 22 Dec 2016 05:52:38:  38000000 
INFO  @ Thu, 22 Dec 2016 05:52:39:  39000000 
INFO  @ Thu, 22 Dec 2016 05:52:41:  40000000 
INFO  @ Thu, 22 Dec 2016 05:52:42:  41000000 
INFO  @ Thu, 22 Dec 2016 05:52:44:  42000000 
INFO  @ Thu, 22 Dec 2016 05:52:46:  43000000 
INFO  @ Thu, 22 Dec 2016 05:52:47:  44000000 
INFO  @ Thu, 22 Dec 2016 05:52:49:  45000000 
INFO  @ Thu, 22 Dec 2016 05:52:51:  46000000 
INFO  @ Thu, 22 Dec 2016 05:52:52:  47000000 
INFO  @ Thu, 22 Dec 2016 05:52:54:  48000000 
INFO  @ Thu, 22 Dec 2016 05:52:56:  49000000 
INFO  @ Thu, 22 Dec 2016 05:52:58:  50000000 
INFO  @ Thu, 22 Dec 2016 05:52:59: #1 tag size is determined as 51 bps 
INFO  @ Thu, 22 Dec 2016 05:52:59: #1 tag size = 51 
INFO  @ Thu, 22 Dec 2016 05:52:59: #1  total tags in treatment: 2696260 
INFO  @ Thu, 22 Dec 2016 05:52:59: #1  total tags in control: 50000000 
INFO  @ Thu, 22 Dec 2016 05:52:59: #1 finished! 
INFO  @ Thu, 22 Dec 2016 05:52:59: #2 Build Peak Model... 
INFO  @ Thu, 22 Dec 2016 05:52:59: #2 Skipped... 
INFO  @ Thu, 22 Dec 2016 05:52:59: #2 Use 65 as fragment length 
INFO  @ Thu, 22 Dec 2016 05:52:59: #3 Call peaks... 
INFO  @ Thu, 22 Dec 2016 05:52:59: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 22 Dec 2016 05:52:59: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 22 Dec 2016 05:56:32: #3 Call peaks for each chromosome... 
INFO  @ Thu, 22 Dec 2016 06:04:33: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 22 Dec 2016 06:04:34: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Thu, 22 Dec 2016 06:04:34: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370879_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 22 Dec 2016 06:04:35: Done!

Num	3
ID	task.callpeak_macs2.macs2_rep1_pr2.line_71.id_12
Name	macs2 rep1-pr2
Thread	thread_Root
PID	19553

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

Start	2016-12-21 15:26:49
End	2016-12-22 06:05:37
Elapsed	14:38:47
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/align/pseudo_reps/rep1/pr2/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_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/CTCF/out/align/pseudo_reps/rep1/pr2/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 65 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_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/CTCF/out/align/pseudo_reps/rep1/pr2/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 65 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_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/CTCF/out/align/pseudo_reps/rep1/pr2/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_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--------------------
18421 (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  @ Thu, 22 Dec 2016 05:41:16: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/align/pseudo_reps/rep1/pr2/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 65 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/align/pseudo_reps/rep1/pr2/SRR1370879_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  @ Thu, 22 Dec 2016 05:41:16: #1 read tag files... 
INFO  @ Thu, 22 Dec 2016 05:41:16: #1 read treatment tags... 
INFO  @ Thu, 22 Dec 2016 05:41:18:  1000000 
INFO  @ Thu, 22 Dec 2016 05:41:19:  2000000 
INFO  @ Thu, 22 Dec 2016 05:41:21: #1.2 read input tags... 
INFO  @ Thu, 22 Dec 2016 05:41:23:  1000000 
INFO  @ Thu, 22 Dec 2016 05:41:24:  2000000 
INFO  @ Thu, 22 Dec 2016 05:41:26:  3000000 
INFO  @ Thu, 22 Dec 2016 05:41:28:  4000000 
INFO  @ Thu, 22 Dec 2016 05:41:29:  5000000 
INFO  @ Thu, 22 Dec 2016 05:41:31:  6000000 
INFO  @ Thu, 22 Dec 2016 05:41:32:  7000000 
INFO  @ Thu, 22 Dec 2016 05:41:34:  8000000 
INFO  @ Thu, 22 Dec 2016 05:41:36:  9000000 
INFO  @ Thu, 22 Dec 2016 05:41:37:  10000000 
INFO  @ Thu, 22 Dec 2016 05:41:39:  11000000 
INFO  @ Thu, 22 Dec 2016 05:41:41:  12000000 
INFO  @ Thu, 22 Dec 2016 05:41:42:  13000000 
INFO  @ Thu, 22 Dec 2016 05:41:44:  14000000 
INFO  @ Thu, 22 Dec 2016 05:41:46:  15000000 
INFO  @ Thu, 22 Dec 2016 05:41:47:  16000000 
INFO  @ Thu, 22 Dec 2016 05:41:49:  17000000 
INFO  @ Thu, 22 Dec 2016 05:41:51:  18000000 
INFO  @ Thu, 22 Dec 2016 05:41:53:  19000000 
INFO  @ Thu, 22 Dec 2016 05:41:54:  20000000 
INFO  @ Thu, 22 Dec 2016 05:41:56:  21000000 
INFO  @ Thu, 22 Dec 2016 05:41:58:  22000000 
INFO  @ Thu, 22 Dec 2016 05:41:59:  23000000 
INFO  @ Thu, 22 Dec 2016 05:42:01:  24000000 
INFO  @ Thu, 22 Dec 2016 05:42:03:  25000000 
INFO  @ Thu, 22 Dec 2016 05:42:04:  26000000 
INFO  @ Thu, 22 Dec 2016 05:42:06:  27000000 
INFO  @ Thu, 22 Dec 2016 05:42:08:  28000000 
INFO  @ Thu, 22 Dec 2016 05:42:09:  29000000 
INFO  @ Thu, 22 Dec 2016 05:42:11:  30000000 
INFO  @ Thu, 22 Dec 2016 05:42:13:  31000000 
INFO  @ Thu, 22 Dec 2016 05:42:14:  32000000 
INFO  @ Thu, 22 Dec 2016 05:42:16:  33000000 
INFO  @ Thu, 22 Dec 2016 05:42:18:  34000000 
INFO  @ Thu, 22 Dec 2016 05:42:19:  35000000 
INFO  @ Thu, 22 Dec 2016 05:42:21:  36000000 
INFO  @ Thu, 22 Dec 2016 05:42:23:  37000000 
INFO  @ Thu, 22 Dec 2016 05:42:24:  38000000 
INFO  @ Thu, 22 Dec 2016 05:42:26:  39000000 
INFO  @ Thu, 22 Dec 2016 05:42:28:  40000000 
INFO  @ Thu, 22 Dec 2016 05:42:29:  41000000 
INFO  @ Thu, 22 Dec 2016 05:42:31:  42000000 
INFO  @ Thu, 22 Dec 2016 05:42:33:  43000000 
INFO  @ Thu, 22 Dec 2016 05:42:34:  44000000 
INFO  @ Thu, 22 Dec 2016 05:42:36:  45000000 
INFO  @ Thu, 22 Dec 2016 05:42:38:  46000000 
INFO  @ Thu, 22 Dec 2016 05:42:39:  47000000 
INFO  @ Thu, 22 Dec 2016 05:42:41:  48000000 
INFO  @ Thu, 22 Dec 2016 05:42:43:  49000000 
INFO  @ Thu, 22 Dec 2016 05:42:44:  50000000 
INFO  @ Thu, 22 Dec 2016 05:42:46: #1 tag size is determined as 50 bps 
INFO  @ Thu, 22 Dec 2016 05:42:46: #1 tag size = 50 
INFO  @ Thu, 22 Dec 2016 05:42:46: #1  total tags in treatment: 2696259 
INFO  @ Thu, 22 Dec 2016 05:42:46: #1  total tags in control: 50000000 
INFO  @ Thu, 22 Dec 2016 05:42:46: #1 finished! 
INFO  @ Thu, 22 Dec 2016 05:42:46: #2 Build Peak Model... 
INFO  @ Thu, 22 Dec 2016 05:42:46: #2 Skipped... 
INFO  @ Thu, 22 Dec 2016 05:42:46: #2 Use 65 as fragment length 
INFO  @ Thu, 22 Dec 2016 05:42:46: #3 Call peaks... 
INFO  @ Thu, 22 Dec 2016 05:42:46: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 22 Dec 2016 05:42:46: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 22 Dec 2016 05:46:32: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 22 Dec 2016 05:46:32: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 22 Dec 2016 05:46:32: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Thu, 22 Dec 2016 05:46:32: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 22 Dec 2016 05:46:32: #3 Call peaks for each chromosome... 
INFO  @ Thu, 22 Dec 2016 05:51:34: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 22 Dec 2016 05:51:46: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 22 Dec 2016 05:51:56: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Thu, 22 Dec 2016 05:52:02: Done! 
INFO  @ Thu, 22 Dec 2016 05:52:17: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/align/pseudo_reps/rep1/pr2/SRR1370879_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/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 65 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/align/pseudo_reps/rep1/pr2/SRR1370879_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  @ Thu, 22 Dec 2016 05:52:17: #1 read tag files... 
INFO  @ Thu, 22 Dec 2016 05:52:17: #1 read treatment tags... 
INFO  @ Thu, 22 Dec 2016 05:52:19:  1000000 
INFO  @ Thu, 22 Dec 2016 05:52:21:  2000000 
INFO  @ Thu, 22 Dec 2016 05:52:22: #1.2 read input tags... 
INFO  @ Thu, 22 Dec 2016 05:52:24:  1000000 
INFO  @ Thu, 22 Dec 2016 05:52:25:  2000000 
INFO  @ Thu, 22 Dec 2016 05:52:27:  3000000 
INFO  @ Thu, 22 Dec 2016 05:52:29:  4000000 
INFO  @ Thu, 22 Dec 2016 05:52:30:  5000000 
INFO  @ Thu, 22 Dec 2016 05:52:32:  6000000 
INFO  @ Thu, 22 Dec 2016 05:52:34:  7000000 
INFO  @ Thu, 22 Dec 2016 05:52:35:  8000000 
INFO  @ Thu, 22 Dec 2016 05:52:37:  9000000 
INFO  @ Thu, 22 Dec 2016 05:52:39:  10000000 
INFO  @ Thu, 22 Dec 2016 05:52:40:  11000000 
INFO  @ Thu, 22 Dec 2016 05:52:42:  12000000 
INFO  @ Thu, 22 Dec 2016 05:52:44:  13000000 
INFO  @ Thu, 22 Dec 2016 05:52:45:  14000000 
INFO  @ Thu, 22 Dec 2016 05:52:47:  15000000 
INFO  @ Thu, 22 Dec 2016 05:52:49:  16000000 
INFO  @ Thu, 22 Dec 2016 05:52:50:  17000000 
INFO  @ Thu, 22 Dec 2016 05:52:52:  18000000 
INFO  @ Thu, 22 Dec 2016 05:52:54:  19000000 
INFO  @ Thu, 22 Dec 2016 05:52:55:  20000000 
INFO  @ Thu, 22 Dec 2016 05:52:57:  21000000 
INFO  @ Thu, 22 Dec 2016 05:52:59:  22000000 
INFO  @ Thu, 22 Dec 2016 05:53:00:  23000000 
INFO  @ Thu, 22 Dec 2016 05:53:02:  24000000 
INFO  @ Thu, 22 Dec 2016 05:53:04:  25000000 
INFO  @ Thu, 22 Dec 2016 05:53:05:  26000000 
INFO  @ Thu, 22 Dec 2016 05:53:07:  27000000 
INFO  @ Thu, 22 Dec 2016 05:53:09:  28000000 
INFO  @ Thu, 22 Dec 2016 05:53:10:  29000000 
INFO  @ Thu, 22 Dec 2016 05:53:12:  30000000 
INFO  @ Thu, 22 Dec 2016 05:53:14:  31000000 
INFO  @ Thu, 22 Dec 2016 05:53:15:  32000000 
INFO  @ Thu, 22 Dec 2016 05:53:17:  33000000 
INFO  @ Thu, 22 Dec 2016 05:53:18:  34000000 
INFO  @ Thu, 22 Dec 2016 05:53:20:  35000000 
INFO  @ Thu, 22 Dec 2016 05:53:22:  36000000 
INFO  @ Thu, 22 Dec 2016 05:53:24:  37000000 
INFO  @ Thu, 22 Dec 2016 05:53:25:  38000000 
INFO  @ Thu, 22 Dec 2016 05:53:27:  39000000 
INFO  @ Thu, 22 Dec 2016 05:53:29:  40000000 
INFO  @ Thu, 22 Dec 2016 05:53:30:  41000000 
INFO  @ Thu, 22 Dec 2016 05:53:32:  42000000 
INFO  @ Thu, 22 Dec 2016 05:53:34:  43000000 
INFO  @ Thu, 22 Dec 2016 05:53:35:  44000000 
INFO  @ Thu, 22 Dec 2016 05:53:37:  45000000 
INFO  @ Thu, 22 Dec 2016 05:53:39:  46000000 
INFO  @ Thu, 22 Dec 2016 05:53:40:  47000000 
INFO  @ Thu, 22 Dec 2016 05:53:42:  48000000 
INFO  @ Thu, 22 Dec 2016 05:53:44:  49000000 
INFO  @ Thu, 22 Dec 2016 05:53:45:  50000000 
INFO  @ Thu, 22 Dec 2016 05:53:47: #1 tag size is determined as 50 bps 
INFO  @ Thu, 22 Dec 2016 05:53:47: #1 tag size = 50 
INFO  @ Thu, 22 Dec 2016 05:53:47: #1  total tags in treatment: 2696259 
INFO  @ Thu, 22 Dec 2016 05:53:47: #1  total tags in control: 50000000 
INFO  @ Thu, 22 Dec 2016 05:53:47: #1 finished! 
INFO  @ Thu, 22 Dec 2016 05:53:47: #2 Build Peak Model... 
INFO  @ Thu, 22 Dec 2016 05:53:47: #2 Skipped... 
INFO  @ Thu, 22 Dec 2016 05:53:47: #2 Use 65 as fragment length 
INFO  @ Thu, 22 Dec 2016 05:53:47: #3 Call peaks... 
INFO  @ Thu, 22 Dec 2016 05:53:47: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 22 Dec 2016 05:53:47: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 22 Dec 2016 05:57:45: #3 Call peaks for each chromosome... 
INFO  @ Thu, 22 Dec 2016 06:05:30: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 22 Dec 2016 06:05:31: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Thu, 22 Dec 2016 06:05:31: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370879_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 22 Dec 2016 06:05:32: 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, CTCF, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/CTCF/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/align/rep1/SRR1370879_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/CTCF
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/CTCF
string	queue
int	retry	0
string	SAMTOOLS_HOME	/software/samtools/samtools-1.2/bin
string	SCREEN_Name	CTCF_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	51961.CTCF_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