Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20161221_141459_791
Start time	2016-12-21 14:14:59
Run time	15:27:52.610
Tasks executed	3
Tasks failed	1
Tasks failed names	macs2 rep1
Arguments*	[-title, ZNF684, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF684/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/align/rep1/SRR1370904_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_141459_791/task.callpeak_macs2.macs2_rep1.line_67.id_10 chipseq.bds.20161221_141459_791/task.callpeak_macs2.macs2_rep1_pr1.line_67.id_11 chipseq.bds.20161221_141459_791/task.callpeak_macs2.macs2_rep1_pr2.line_67.id_12
thread_41	thread_Root
thread_42	thread_Root

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.callpeak_macs2.macs2_rep1.line_67.id_10
Name	macs2 rep1
Thread	thread_Root
PID	19502

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

Start	2016-12-21 14:15:06
End	2016-12-21 14:15:06
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/align/rep1/SRR1370904_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/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/signal/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/signal/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw
Dependencies

 
# SYS command. line 69

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

# SYS command. line 70

 export LC_COLLATE=C

# SYS command. line 75

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/align/rep1/SRR1370904_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/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 170 --keep-dup all -B --SPMR

# SYS command. line 78

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_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/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 81

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 88

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/align/rep1/SRR1370904_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/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 170 --keep-dup all

# SYS command. line 91

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_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/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz

# SYS command. line 92

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_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/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 95

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 100

 if [[ true == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_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 111

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1 -o "SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -m FE

# SYS command. line 114

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_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/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph

# SYS command. line 115

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg

# SYS command. line 118

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 119

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_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/ZNF684/out/signal/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw

# SYS command. line 120

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 126

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/align/rep1/SRR1370904_1.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 128

 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 130

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1 -o "SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 133

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_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/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph

# SYS command. line 134

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg

# SYS command. line 137

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 138

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_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/ZNF684/out/signal/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw

# SYS command. line 139

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 141

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg

# SYS command. line 143

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

   
--------------------Stdout--------------------
14422 (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 04:03:14: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/align/rep1/SRR1370904_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/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 170 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/align/rep1/SRR1370904_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 04:03:14: #1 read tag files... 
INFO  @ Thu, 22 Dec 2016 04:03:14: #1 read treatment tags... 
INFO  @ Thu, 22 Dec 2016 04:03:16:  1000000 
INFO  @ Thu, 22 Dec 2016 04:03:18:  2000000 
INFO  @ Thu, 22 Dec 2016 04:03:19:  3000000 
INFO  @ Thu, 22 Dec 2016 04:03:21:  4000000 
INFO  @ Thu, 22 Dec 2016 04:03:22:  5000000 
INFO  @ Thu, 22 Dec 2016 04:03:24:  6000000 
INFO  @ Thu, 22 Dec 2016 04:03:26:  7000000 
INFO  @ Thu, 22 Dec 2016 04:03:27:  8000000 
INFO  @ Thu, 22 Dec 2016 04:03:29:  9000000 
INFO  @ Thu, 22 Dec 2016 04:03:30:  10000000 
INFO  @ Thu, 22 Dec 2016 04:03:32:  11000000 
INFO  @ Thu, 22 Dec 2016 04:03:34:  12000000 
INFO  @ Thu, 22 Dec 2016 04:03:35:  13000000 
INFO  @ Thu, 22 Dec 2016 04:03:37:  14000000 
INFO  @ Thu, 22 Dec 2016 04:03:38:  15000000 
INFO  @ Thu, 22 Dec 2016 04:03:40:  16000000 
INFO  @ Thu, 22 Dec 2016 04:03:42:  17000000 
INFO  @ Thu, 22 Dec 2016 04:03:43:  18000000 
INFO  @ Thu, 22 Dec 2016 04:03:45:  19000000 
INFO  @ Thu, 22 Dec 2016 04:03:47:  20000000 
INFO  @ Thu, 22 Dec 2016 04:03:48: #1.2 read input tags... 
INFO  @ Thu, 22 Dec 2016 04:03:50:  1000000 
INFO  @ Thu, 22 Dec 2016 04:03:51:  2000000 
INFO  @ Thu, 22 Dec 2016 04:03:53:  3000000 
INFO  @ Thu, 22 Dec 2016 04:03:55:  4000000 
INFO  @ Thu, 22 Dec 2016 04:03:56:  5000000 
INFO  @ Thu, 22 Dec 2016 04:03:58:  6000000 
INFO  @ Thu, 22 Dec 2016 04:03:59:  7000000 
INFO  @ Thu, 22 Dec 2016 04:04:01:  8000000 
INFO  @ Thu, 22 Dec 2016 04:04:03:  9000000 
INFO  @ Thu, 22 Dec 2016 04:04:04:  10000000 
INFO  @ Thu, 22 Dec 2016 04:04:06:  11000000 
INFO  @ Thu, 22 Dec 2016 04:04:08:  12000000 
INFO  @ Thu, 22 Dec 2016 04:04:09:  13000000 
INFO  @ Thu, 22 Dec 2016 04:04:11:  14000000 
INFO  @ Thu, 22 Dec 2016 04:04:12:  15000000 
INFO  @ Thu, 22 Dec 2016 04:04:14:  16000000 
INFO  @ Thu, 22 Dec 2016 04:04:16:  17000000 
INFO  @ Thu, 22 Dec 2016 04:04:17:  18000000 
INFO  @ Thu, 22 Dec 2016 04:04:19:  19000000 
INFO  @ Thu, 22 Dec 2016 04:04:21:  20000000 
INFO  @ Thu, 22 Dec 2016 04:04:22:  21000000 
INFO  @ Thu, 22 Dec 2016 04:04:24:  22000000 
INFO  @ Thu, 22 Dec 2016 04:04:25:  23000000 
INFO  @ Thu, 22 Dec 2016 04:04:27:  24000000 
INFO  @ Thu, 22 Dec 2016 04:04:29:  25000000 
INFO  @ Thu, 22 Dec 2016 04:04:30:  26000000 
INFO  @ Thu, 22 Dec 2016 04:04:32:  27000000 
INFO  @ Thu, 22 Dec 2016 04:04:33:  28000000 
INFO  @ Thu, 22 Dec 2016 04:04:35:  29000000 
INFO  @ Thu, 22 Dec 2016 04:04:37:  30000000 
INFO  @ Thu, 22 Dec 2016 04:04:38:  31000000 
INFO  @ Thu, 22 Dec 2016 04:04:40:  32000000 
INFO  @ Thu, 22 Dec 2016 04:04:42:  33000000 
INFO  @ Thu, 22 Dec 2016 04:04:43:  34000000 
INFO  @ Thu, 22 Dec 2016 04:04:45:  35000000 
INFO  @ Thu, 22 Dec 2016 04:04:46:  36000000 
INFO  @ Thu, 22 Dec 2016 04:04:48:  37000000 
INFO  @ Thu, 22 Dec 2016 04:04:50:  38000000 
INFO  @ Thu, 22 Dec 2016 04:04:51:  39000000 
INFO  @ Thu, 22 Dec 2016 04:04:53:  40000000 
INFO  @ Thu, 22 Dec 2016 04:04:54:  41000000 
INFO  @ Thu, 22 Dec 2016 04:04:56:  42000000 
INFO  @ Thu, 22 Dec 2016 04:04:58:  43000000 
INFO  @ Thu, 22 Dec 2016 04:04:59:  44000000 
INFO  @ Thu, 22 Dec 2016 04:05:01:  45000000 
INFO  @ Thu, 22 Dec 2016 04:05:02:  46000000 
INFO  @ Thu, 22 Dec 2016 04:05:04:  47000000 
INFO  @ Thu, 22 Dec 2016 04:05:06:  48000000 
INFO  @ Thu, 22 Dec 2016 04:05:07:  49000000 
INFO  @ Thu, 22 Dec 2016 04:05:09:  50000000 
INFO  @ Thu, 22 Dec 2016 04:05:10: #1 tag size is determined as 51 bps 
INFO  @ Thu, 22 Dec 2016 04:05:10: #1 tag size = 51 
INFO  @ Thu, 22 Dec 2016 04:05:10: #1  total tags in treatment: 20752479 
INFO  @ Thu, 22 Dec 2016 04:05:10: #1  total tags in control: 50000000 
INFO  @ Thu, 22 Dec 2016 04:05:10: #1 finished! 
INFO  @ Thu, 22 Dec 2016 04:05:10: #2 Build Peak Model... 
INFO  @ Thu, 22 Dec 2016 04:05:10: #2 Skipped... 
INFO  @ Thu, 22 Dec 2016 04:05:10: #2 Use 170 as fragment length 
INFO  @ Thu, 22 Dec 2016 04:05:10: #3 Call peaks... 
INFO  @ Thu, 22 Dec 2016 04:05:10: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 22 Dec 2016 04:05:10: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 22 Dec 2016 04:11:23: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 22 Dec 2016 04:11:23: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 22 Dec 2016 04:11:23: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Thu, 22 Dec 2016 04:11:23: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 22 Dec 2016 04:11:23: #3 Call peaks for each chromosome... 
INFO  @ Thu, 22 Dec 2016 04:19:57: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 22 Dec 2016 04:19:57: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 22 Dec 2016 04:19:57: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Thu, 22 Dec 2016 04:19:58: Done! 
INFO  @ Thu, 22 Dec 2016 04:20:02: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/align/rep1/SRR1370904_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/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 170 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/align/rep1/SRR1370904_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 04:20:02: #1 read tag files... 
INFO  @ Thu, 22 Dec 2016 04:20:02: #1 read treatment tags... 
INFO  @ Thu, 22 Dec 2016 04:20:04:  1000000 
INFO  @ Thu, 22 Dec 2016 04:20:05:  2000000 
INFO  @ Thu, 22 Dec 2016 04:20:07:  3000000 
INFO  @ Thu, 22 Dec 2016 04:20:08:  4000000 
INFO  @ Thu, 22 Dec 2016 04:20:10:  5000000 
INFO  @ Thu, 22 Dec 2016 04:20:11:  6000000 
INFO  @ Thu, 22 Dec 2016 04:20:13:  7000000 
INFO  @ Thu, 22 Dec 2016 04:20:15:  8000000 
INFO  @ Thu, 22 Dec 2016 04:20:16:  9000000 
INFO  @ Thu, 22 Dec 2016 04:20:18:  10000000 
INFO  @ Thu, 22 Dec 2016 04:20:19:  11000000 
INFO  @ Thu, 22 Dec 2016 04:20:21:  12000000 
INFO  @ Thu, 22 Dec 2016 04:20:23:  13000000 
INFO  @ Thu, 22 Dec 2016 04:20:24:  14000000 
INFO  @ Thu, 22 Dec 2016 04:20:26:  15000000 
INFO  @ Thu, 22 Dec 2016 04:20:27:  16000000 
INFO  @ Thu, 22 Dec 2016 04:20:29:  17000000 
INFO  @ Thu, 22 Dec 2016 04:20:30:  18000000 
INFO  @ Thu, 22 Dec 2016 04:20:32:  19000000 
INFO  @ Thu, 22 Dec 2016 04:20:33:  20000000 
INFO  @ Thu, 22 Dec 2016 04:20:35: #1.2 read input tags... 
INFO  @ Thu, 22 Dec 2016 04:20:36:  1000000 
INFO  @ Thu, 22 Dec 2016 04:20:38:  2000000 
INFO  @ Thu, 22 Dec 2016 04:20:40:  3000000 
INFO  @ Thu, 22 Dec 2016 04:20:41:  4000000 
INFO  @ Thu, 22 Dec 2016 04:20:43:  5000000 
INFO  @ Thu, 22 Dec 2016 04:20:44:  6000000 
INFO  @ Thu, 22 Dec 2016 04:20:46:  7000000 
INFO  @ Thu, 22 Dec 2016 04:20:47:  8000000 
INFO  @ Thu, 22 Dec 2016 04:20:49:  9000000 
INFO  @ Thu, 22 Dec 2016 04:20:51:  10000000 
INFO  @ Thu, 22 Dec 2016 04:20:52:  11000000 
INFO  @ Thu, 22 Dec 2016 04:20:54:  12000000 
INFO  @ Thu, 22 Dec 2016 04:20:56:  13000000 
INFO  @ Thu, 22 Dec 2016 04:20:57:  14000000 
INFO  @ Thu, 22 Dec 2016 04:20:59:  15000000 
INFO  @ Thu, 22 Dec 2016 04:21:00:  16000000 
INFO  @ Thu, 22 Dec 2016 04:21:02:  17000000 
INFO  @ Thu, 22 Dec 2016 04:21:04:  18000000 
INFO  @ Thu, 22 Dec 2016 04:21:05:  19000000 
INFO  @ Thu, 22 Dec 2016 04:21:07:  20000000 
INFO  @ Thu, 22 Dec 2016 04:21:09:  21000000 
INFO  @ Thu, 22 Dec 2016 04:21:10:  22000000 
INFO  @ Thu, 22 Dec 2016 04:21:12:  23000000 
INFO  @ Thu, 22 Dec 2016 04:21:13:  24000000 
INFO  @ Thu, 22 Dec 2016 04:21:15:  25000000 
INFO  @ Thu, 22 Dec 2016 04:21:17:  26000000 
INFO  @ Thu, 22 Dec 2016 04:21:18:  27000000 
INFO  @ Thu, 22 Dec 2016 04:21:20:  28000000 
INFO  @ Thu, 22 Dec 2016 04:21:22:  29000000 
INFO  @ Thu, 22 Dec 2016 04:21:23:  30000000 
INFO  @ Thu, 22 Dec 2016 04:21:25:  31000000 
INFO  @ Thu, 22 Dec 2016 04:21:26:  32000000 
INFO  @ Thu, 22 Dec 2016 04:21:28:  33000000 
INFO  @ Thu, 22 Dec 2016 04:21:30:  34000000 
INFO  @ Thu, 22 Dec 2016 04:21:31:  35000000 
INFO  @ Thu, 22 Dec 2016 04:21:33:  36000000 
INFO  @ Thu, 22 Dec 2016 04:21:34:  37000000 
INFO  @ Thu, 22 Dec 2016 04:21:36:  38000000 
INFO  @ Thu, 22 Dec 2016 04:21:38:  39000000 
INFO  @ Thu, 22 Dec 2016 04:21:39:  40000000 
INFO  @ Thu, 22 Dec 2016 04:21:41:  41000000 
INFO  @ Thu, 22 Dec 2016 04:21:42:  42000000 
INFO  @ Thu, 22 Dec 2016 04:21:44:  43000000 
INFO  @ Thu, 22 Dec 2016 04:21:46:  44000000 
INFO  @ Thu, 22 Dec 2016 04:21:48:  45000000 
INFO  @ Thu, 22 Dec 2016 04:21:49:  46000000 
INFO  @ Thu, 22 Dec 2016 04:21:51:  47000000 
INFO  @ Thu, 22 Dec 2016 04:21:52:  48000000 
INFO  @ Thu, 22 Dec 2016 04:21:54:  49000000 
INFO  @ Thu, 22 Dec 2016 04:21:56:  50000000 
INFO  @ Thu, 22 Dec 2016 04:21:57: #1 tag size is determined as 51 bps 
INFO  @ Thu, 22 Dec 2016 04:21:57: #1 tag size = 51 
INFO  @ Thu, 22 Dec 2016 04:21:57: #1  total tags in treatment: 20752479 
INFO  @ Thu, 22 Dec 2016 04:21:57: #1  total tags in control: 50000000 
INFO  @ Thu, 22 Dec 2016 04:21:57: #1 finished! 
INFO  @ Thu, 22 Dec 2016 04:21:57: #2 Build Peak Model... 
INFO  @ Thu, 22 Dec 2016 04:21:57: #2 Skipped... 
INFO  @ Thu, 22 Dec 2016 04:21:57: #2 Use 170 as fragment length 
INFO  @ Thu, 22 Dec 2016 04:21:57: #3 Call peaks... 
INFO  @ Thu, 22 Dec 2016 04:21:57: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 22 Dec 2016 04:21:57: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 22 Dec 2016 04:29:08: #3 Call peaks for each chromosome... 
INFO  @ Thu, 22 Dec 2016 04:34:44: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 22 Dec 2016 04:34:49: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Thu, 22 Dec 2016 04:34:52: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 22 Dec 2016 04:34:55: Done! 
INFO  @ Thu, 22 Dec 2016 04:35:11: Read and build treatment bedGraph... 
INFO  @ Thu, 22 Dec 2016 04:36:01: Read and build control bedGraph... 
INFO  @ Thu, 22 Dec 2016 04:37:50: Build scoreTrackII... 
INFO  @ Thu, 22 Dec 2016 04:39:30: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Thu, 22 Dec 2016 04:44:56: Write bedGraph of scores... 
INFO  @ Thu, 22 Dec 2016 04:48:33: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/rep1/SRR1370904_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:                 19502
submission_time:            Wed Dec 21 14:15:06 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/ZNF684
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/chipseq.bds.20161221_141459_791/task.callpeak_macs2.macs2_rep1.line_67.id_10.stderr.cluster
mail_list:                  imk1@surya
notify:                     FALSE
job_name:                   STDIN
stdout_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/chipseq.bds.20161221_141459_791/task.callpeak_macs2.macs2_rep1.line_67.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=52014.ZNF684.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,PWD=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684,JAVA_HOME=/usr/lib/jvm/java-8-oracle,LOADEDMODULES=modsappsdir/modsappsdir:samtools/1.2,SSH_CONNECTION=171.65.77.8 32898 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,MANPATH=/software/samtools/samtools-1.2/share/man:/usr/share/man,MODULEPATH=/usr/local/Modules/versions				:/usr/local/Modules/$MODULE_VERSION/modulefiles	:/modules/				:/software/modulefiles,MODULESAPPSDIR=/software,MODULESHOME=/software/env_module/3.2.10
scheduling info:            queue instance "q@kali" dropped because it is temporarily not available
                            queue instance "q@surya" dropped because it is disabled
                            queue instance "amd.q@wotan" dropped because it is full
                            queue instance "q@kadru" dropped because it is full
                            queue instance "q@nandi" dropped because it is full
                            All queues dropped because of overload or full

Num	2
ID	task.callpeak_macs2.macs2_rep1_pr1.line_67.id_11
Name	macs2 rep1-pr1
Thread	thread_Root
PID	19505

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

Start	2016-12-21 14:15:09
End	2016-12-22 04:58:25
Elapsed	14:43:16
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/align/pseudo_reps/rep1/pr1/SRR1370904_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/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
Dependencies

 
# SYS command. line 69

 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 70

 export LC_COLLATE=C

# SYS command. line 75

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/align/pseudo_reps/rep1/pr1/SRR1370904_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/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 170 --keep-dup all -B --SPMR

# SYS command. line 78

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_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/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 81

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 88

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/align/pseudo_reps/rep1/pr1/SRR1370904_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/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 170 --keep-dup all

# SYS command. line 91

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_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/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz

# SYS command. line 92

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_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/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 95

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 100

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_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 111

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -m FE

# SYS command. line 114

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_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/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph

# SYS command. line 115

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg

# SYS command. line 118

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 119

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_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/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw

# SYS command. line 120

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 126

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/align/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 128

 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 130

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 133

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_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/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph

# SYS command. line 134

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg

# SYS command. line 137

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 138

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_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/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw

# SYS command. line 139

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 141

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg

# SYS command. line 143

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

   
--------------------Stdout--------------------
15282 (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 04:36:16: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/align/pseudo_reps/rep1/pr1/SRR1370904_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/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 170 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/align/pseudo_reps/rep1/pr1/SRR1370904_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 04:36:16: #1 read tag files... 
INFO  @ Thu, 22 Dec 2016 04:36:16: #1 read treatment tags... 
INFO  @ Thu, 22 Dec 2016 04:36:18:  1000000 
INFO  @ Thu, 22 Dec 2016 04:36:20:  2000000 
INFO  @ Thu, 22 Dec 2016 04:36:21:  3000000 
INFO  @ Thu, 22 Dec 2016 04:36:23:  4000000 
INFO  @ Thu, 22 Dec 2016 04:36:25:  5000000 
INFO  @ Thu, 22 Dec 2016 04:36:27:  6000000 
INFO  @ Thu, 22 Dec 2016 04:36:29:  7000000 
INFO  @ Thu, 22 Dec 2016 04:36:30:  8000000 
INFO  @ Thu, 22 Dec 2016 04:36:32:  9000000 
INFO  @ Thu, 22 Dec 2016 04:36:34:  10000000 
INFO  @ Thu, 22 Dec 2016 04:36:35: #1.2 read input tags... 
INFO  @ Thu, 22 Dec 2016 04:36:37:  1000000 
INFO  @ Thu, 22 Dec 2016 04:36:38:  2000000 
INFO  @ Thu, 22 Dec 2016 04:36:40:  3000000 
INFO  @ Thu, 22 Dec 2016 04:36:42:  4000000 
INFO  @ Thu, 22 Dec 2016 04:36:43:  5000000 
INFO  @ Thu, 22 Dec 2016 04:36:45:  6000000 
INFO  @ Thu, 22 Dec 2016 04:36:47:  7000000 
INFO  @ Thu, 22 Dec 2016 04:36:48:  8000000 
INFO  @ Thu, 22 Dec 2016 04:36:50:  9000000 
INFO  @ Thu, 22 Dec 2016 04:36:51:  10000000 
INFO  @ Thu, 22 Dec 2016 04:36:53:  11000000 
INFO  @ Thu, 22 Dec 2016 04:36:55:  12000000 
INFO  @ Thu, 22 Dec 2016 04:36:56:  13000000 
INFO  @ Thu, 22 Dec 2016 04:36:58:  14000000 
INFO  @ Thu, 22 Dec 2016 04:37:00:  15000000 
INFO  @ Thu, 22 Dec 2016 04:37:01:  16000000 
INFO  @ Thu, 22 Dec 2016 04:37:03:  17000000 
INFO  @ Thu, 22 Dec 2016 04:37:05:  18000000 
INFO  @ Thu, 22 Dec 2016 04:37:06:  19000000 
INFO  @ Thu, 22 Dec 2016 04:37:08:  20000000 
INFO  @ Thu, 22 Dec 2016 04:37:10:  21000000 
INFO  @ Thu, 22 Dec 2016 04:37:11:  22000000 
INFO  @ Thu, 22 Dec 2016 04:37:13:  23000000 
INFO  @ Thu, 22 Dec 2016 04:37:15:  24000000 
INFO  @ Thu, 22 Dec 2016 04:37:16:  25000000 
INFO  @ Thu, 22 Dec 2016 04:37:18:  26000000 
INFO  @ Thu, 22 Dec 2016 04:37:20:  27000000 
INFO  @ Thu, 22 Dec 2016 04:37:21:  28000000 
INFO  @ Thu, 22 Dec 2016 04:37:23:  29000000 
INFO  @ Thu, 22 Dec 2016 04:37:24:  30000000 
INFO  @ Thu, 22 Dec 2016 04:37:26:  31000000 
INFO  @ Thu, 22 Dec 2016 04:37:27:  32000000 
INFO  @ Thu, 22 Dec 2016 04:37:29:  33000000 
INFO  @ Thu, 22 Dec 2016 04:37:31:  34000000 
INFO  @ Thu, 22 Dec 2016 04:37:32:  35000000 
INFO  @ Thu, 22 Dec 2016 04:37:34:  36000000 
INFO  @ Thu, 22 Dec 2016 04:37:35:  37000000 
INFO  @ Thu, 22 Dec 2016 04:37:37:  38000000 
INFO  @ Thu, 22 Dec 2016 04:37:39:  39000000 
INFO  @ Thu, 22 Dec 2016 04:37:40:  40000000 
INFO  @ Thu, 22 Dec 2016 04:37:42:  41000000 
INFO  @ Thu, 22 Dec 2016 04:37:43:  42000000 
INFO  @ Thu, 22 Dec 2016 04:37:45:  43000000 
INFO  @ Thu, 22 Dec 2016 04:37:47:  44000000 
INFO  @ Thu, 22 Dec 2016 04:37:48:  45000000 
INFO  @ Thu, 22 Dec 2016 04:37:50:  46000000 
INFO  @ Thu, 22 Dec 2016 04:37:51:  47000000 
INFO  @ Thu, 22 Dec 2016 04:37:53:  48000000 
INFO  @ Thu, 22 Dec 2016 04:37:55:  49000000 
INFO  @ Thu, 22 Dec 2016 04:37:56:  50000000 
INFO  @ Thu, 22 Dec 2016 04:37:58: #1 tag size is determined as 51 bps 
INFO  @ Thu, 22 Dec 2016 04:37:58: #1 tag size = 51 
INFO  @ Thu, 22 Dec 2016 04:37:58: #1  total tags in treatment: 10376240 
INFO  @ Thu, 22 Dec 2016 04:37:58: #1  total tags in control: 50000000 
INFO  @ Thu, 22 Dec 2016 04:37:58: #1 finished! 
INFO  @ Thu, 22 Dec 2016 04:37:58: #2 Build Peak Model... 
INFO  @ Thu, 22 Dec 2016 04:37:58: #2 Skipped... 
INFO  @ Thu, 22 Dec 2016 04:37:58: #2 Use 170 as fragment length 
INFO  @ Thu, 22 Dec 2016 04:37:58: #3 Call peaks... 
INFO  @ Thu, 22 Dec 2016 04:37:58: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 22 Dec 2016 04:37:58: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 22 Dec 2016 04:43:19: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 22 Dec 2016 04:43:19: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 22 Dec 2016 04:43:19: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Thu, 22 Dec 2016 04:43:19: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 22 Dec 2016 04:43:19: #3 Call peaks for each chromosome... 
INFO  @ Thu, 22 Dec 2016 04:49:50: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 22 Dec 2016 04:49:50: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 22 Dec 2016 04:49:51: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Thu, 22 Dec 2016 04:49:51: Done! 
INFO  @ Thu, 22 Dec 2016 04:49:54: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/align/pseudo_reps/rep1/pr1/SRR1370904_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/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 170 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/align/pseudo_reps/rep1/pr1/SRR1370904_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 04:49:54: #1 read tag files... 
INFO  @ Thu, 22 Dec 2016 04:49:54: #1 read treatment tags... 
INFO  @ Thu, 22 Dec 2016 04:49:56:  1000000 
INFO  @ Thu, 22 Dec 2016 04:49:58:  2000000 
INFO  @ Thu, 22 Dec 2016 04:50:00:  3000000 
INFO  @ Thu, 22 Dec 2016 04:50:01:  4000000 
INFO  @ Thu, 22 Dec 2016 04:50:03:  5000000 
INFO  @ Thu, 22 Dec 2016 04:50:05:  6000000 
INFO  @ Thu, 22 Dec 2016 04:50:06:  7000000 
INFO  @ Thu, 22 Dec 2016 04:50:08:  8000000 
INFO  @ Thu, 22 Dec 2016 04:50:10:  9000000 
INFO  @ Thu, 22 Dec 2016 04:50:11:  10000000 
INFO  @ Thu, 22 Dec 2016 04:50:13: #1.2 read input tags... 
INFO  @ Thu, 22 Dec 2016 04:50:14:  1000000 
INFO  @ Thu, 22 Dec 2016 04:50:16:  2000000 
INFO  @ Thu, 22 Dec 2016 04:50:18:  3000000 
INFO  @ Thu, 22 Dec 2016 04:50:19:  4000000 
INFO  @ Thu, 22 Dec 2016 04:50:21:  5000000 
INFO  @ Thu, 22 Dec 2016 04:50:22:  6000000 
INFO  @ Thu, 22 Dec 2016 04:50:24:  7000000 
INFO  @ Thu, 22 Dec 2016 04:50:25:  8000000 
INFO  @ Thu, 22 Dec 2016 04:50:27:  9000000 
INFO  @ Thu, 22 Dec 2016 04:50:29:  10000000 
INFO  @ Thu, 22 Dec 2016 04:50:30:  11000000 
INFO  @ Thu, 22 Dec 2016 04:50:32:  12000000 
INFO  @ Thu, 22 Dec 2016 04:50:33:  13000000 
INFO  @ Thu, 22 Dec 2016 04:50:35:  14000000 
INFO  @ Thu, 22 Dec 2016 04:50:37:  15000000 
INFO  @ Thu, 22 Dec 2016 04:50:38:  16000000 
INFO  @ Thu, 22 Dec 2016 04:50:40:  17000000 
INFO  @ Thu, 22 Dec 2016 04:50:41:  18000000 
INFO  @ Thu, 22 Dec 2016 04:50:43:  19000000 
INFO  @ Thu, 22 Dec 2016 04:50:44:  20000000 
INFO  @ Thu, 22 Dec 2016 04:50:46:  21000000 
INFO  @ Thu, 22 Dec 2016 04:50:48:  22000000 
INFO  @ Thu, 22 Dec 2016 04:50:49:  23000000 
INFO  @ Thu, 22 Dec 2016 04:50:51:  24000000 
INFO  @ Thu, 22 Dec 2016 04:50:52:  25000000 
INFO  @ Thu, 22 Dec 2016 04:50:54:  26000000 
INFO  @ Thu, 22 Dec 2016 04:50:55:  27000000 
INFO  @ Thu, 22 Dec 2016 04:50:57:  28000000 
INFO  @ Thu, 22 Dec 2016 04:50:59:  29000000 
INFO  @ Thu, 22 Dec 2016 04:51:00:  30000000 
INFO  @ Thu, 22 Dec 2016 04:51:02:  31000000 
INFO  @ Thu, 22 Dec 2016 04:51:03:  32000000 
INFO  @ Thu, 22 Dec 2016 04:51:05:  33000000 
INFO  @ Thu, 22 Dec 2016 04:51:07:  34000000 
INFO  @ Thu, 22 Dec 2016 04:51:08:  35000000 
INFO  @ Thu, 22 Dec 2016 04:51:10:  36000000 
INFO  @ Thu, 22 Dec 2016 04:51:11:  37000000 
INFO  @ Thu, 22 Dec 2016 04:51:13:  38000000 
INFO  @ Thu, 22 Dec 2016 04:51:14:  39000000 
INFO  @ Thu, 22 Dec 2016 04:51:16:  40000000 
INFO  @ Thu, 22 Dec 2016 04:51:18:  41000000 
INFO  @ Thu, 22 Dec 2016 04:51:19:  42000000 
INFO  @ Thu, 22 Dec 2016 04:51:21:  43000000 
INFO  @ Thu, 22 Dec 2016 04:51:22:  44000000 
INFO  @ Thu, 22 Dec 2016 04:51:24:  45000000 
INFO  @ Thu, 22 Dec 2016 04:51:26:  46000000 
INFO  @ Thu, 22 Dec 2016 04:51:27:  47000000 
INFO  @ Thu, 22 Dec 2016 04:51:29:  48000000 
INFO  @ Thu, 22 Dec 2016 04:51:30:  49000000 
INFO  @ Thu, 22 Dec 2016 04:51:32:  50000000 
INFO  @ Thu, 22 Dec 2016 04:51:34: #1 tag size is determined as 51 bps 
INFO  @ Thu, 22 Dec 2016 04:51:34: #1 tag size = 51 
INFO  @ Thu, 22 Dec 2016 04:51:34: #1  total tags in treatment: 10376240 
INFO  @ Thu, 22 Dec 2016 04:51:34: #1  total tags in control: 50000000 
INFO  @ Thu, 22 Dec 2016 04:51:34: #1 finished! 
INFO  @ Thu, 22 Dec 2016 04:51:34: #2 Build Peak Model... 
INFO  @ Thu, 22 Dec 2016 04:51:34: #2 Skipped... 
INFO  @ Thu, 22 Dec 2016 04:51:34: #2 Use 170 as fragment length 
INFO  @ Thu, 22 Dec 2016 04:51:34: #3 Call peaks... 
INFO  @ Thu, 22 Dec 2016 04:51:34: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 22 Dec 2016 04:51:34: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 22 Dec 2016 04:54:54: #3 Call peaks for each chromosome... 
INFO  @ Thu, 22 Dec 2016 04:57:55: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 22 Dec 2016 04:58:00: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Thu, 22 Dec 2016 04:58:05: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370904_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 22 Dec 2016 04:58:09: Done!

Num	3
ID	task.callpeak_macs2.macs2_rep1_pr2.line_67.id_12
Name	macs2 rep1-pr2
Thread	thread_Root
PID	19507

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

Start	2016-12-21 14:15:10
End	2016-12-22 05:42:52
Elapsed	15:27:41
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/align/pseudo_reps/rep1/pr2/SRR1370904_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/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
Dependencies

 
# SYS command. line 69

 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 70

 export LC_COLLATE=C

# SYS command. line 75

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/align/pseudo_reps/rep1/pr2/SRR1370904_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/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 170 --keep-dup all -B --SPMR

# SYS command. line 78

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_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/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 81

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 88

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/align/pseudo_reps/rep1/pr2/SRR1370904_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/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 170 --keep-dup all

# SYS command. line 91

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_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/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz

# SYS command. line 92

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_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/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 95

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 100

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_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 111

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -m FE

# SYS command. line 114

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_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/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph

# SYS command. line 115

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg

# SYS command. line 118

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 119

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_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/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw

# SYS command. line 120

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 126

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/align/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 128

 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 130

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 133

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_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/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph

# SYS command. line 134

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg

# SYS command. line 137

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 138

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_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/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw

# SYS command. line 139

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 141

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg

# SYS command. line 143

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

   
--------------------Stdout--------------------
62504 (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 04:44:48: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/align/pseudo_reps/rep1/pr2/SRR1370904_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/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 170 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/align/pseudo_reps/rep1/pr2/SRR1370904_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 04:44:48: #1 read tag files... 
INFO  @ Thu, 22 Dec 2016 04:44:48: #1 read treatment tags... 
INFO  @ Thu, 22 Dec 2016 04:44:56:  1000000 
INFO  @ Thu, 22 Dec 2016 04:45:04:  2000000 
INFO  @ Thu, 22 Dec 2016 04:45:11:  3000000 
INFO  @ Thu, 22 Dec 2016 04:45:19:  4000000 
INFO  @ Thu, 22 Dec 2016 04:45:27:  5000000 
INFO  @ Thu, 22 Dec 2016 04:45:34:  6000000 
INFO  @ Thu, 22 Dec 2016 04:45:42:  7000000 
INFO  @ Thu, 22 Dec 2016 04:45:50:  8000000 
INFO  @ Thu, 22 Dec 2016 04:45:57:  9000000 
INFO  @ Thu, 22 Dec 2016 04:46:05:  10000000 
INFO  @ Thu, 22 Dec 2016 04:46:09: #1.2 read input tags... 
INFO  @ Thu, 22 Dec 2016 04:46:17:  1000000 
INFO  @ Thu, 22 Dec 2016 04:46:24:  2000000 
INFO  @ Thu, 22 Dec 2016 04:46:32:  3000000 
INFO  @ Thu, 22 Dec 2016 04:46:39:  4000000 
INFO  @ Thu, 22 Dec 2016 04:46:47:  5000000 
INFO  @ Thu, 22 Dec 2016 04:46:55:  6000000 
INFO  @ Thu, 22 Dec 2016 04:47:02:  7000000 
INFO  @ Thu, 22 Dec 2016 04:47:10:  8000000 
INFO  @ Thu, 22 Dec 2016 04:47:17:  9000000 
INFO  @ Thu, 22 Dec 2016 04:47:25:  10000000 
INFO  @ Thu, 22 Dec 2016 04:47:32:  11000000 
INFO  @ Thu, 22 Dec 2016 04:47:40:  12000000 
INFO  @ Thu, 22 Dec 2016 04:47:48:  13000000 
INFO  @ Thu, 22 Dec 2016 04:47:55:  14000000 
INFO  @ Thu, 22 Dec 2016 04:48:03:  15000000 
INFO  @ Thu, 22 Dec 2016 04:48:11:  16000000 
INFO  @ Thu, 22 Dec 2016 04:48:18:  17000000 
INFO  @ Thu, 22 Dec 2016 04:48:26:  18000000 
INFO  @ Thu, 22 Dec 2016 04:48:34:  19000000 
INFO  @ Thu, 22 Dec 2016 04:48:42:  20000000 
INFO  @ Thu, 22 Dec 2016 04:48:49:  21000000 
INFO  @ Thu, 22 Dec 2016 04:48:57:  22000000 
INFO  @ Thu, 22 Dec 2016 04:49:05:  23000000 
INFO  @ Thu, 22 Dec 2016 04:49:12:  24000000 
INFO  @ Thu, 22 Dec 2016 04:49:20:  25000000 
INFO  @ Thu, 22 Dec 2016 04:49:28:  26000000 
INFO  @ Thu, 22 Dec 2016 04:49:35:  27000000 
INFO  @ Thu, 22 Dec 2016 04:49:43:  28000000 
INFO  @ Thu, 22 Dec 2016 04:49:51:  29000000 
INFO  @ Thu, 22 Dec 2016 04:49:59:  30000000 
INFO  @ Thu, 22 Dec 2016 04:50:06:  31000000 
INFO  @ Thu, 22 Dec 2016 04:50:14:  32000000 
INFO  @ Thu, 22 Dec 2016 04:50:22:  33000000 
INFO  @ Thu, 22 Dec 2016 04:50:31:  34000000 
INFO  @ Thu, 22 Dec 2016 04:50:39:  35000000 
INFO  @ Thu, 22 Dec 2016 04:50:47:  36000000 
INFO  @ Thu, 22 Dec 2016 04:50:54:  37000000 
INFO  @ Thu, 22 Dec 2016 04:51:02:  38000000 
INFO  @ Thu, 22 Dec 2016 04:51:10:  39000000 
INFO  @ Thu, 22 Dec 2016 04:51:17:  40000000 
INFO  @ Thu, 22 Dec 2016 04:51:25:  41000000 
INFO  @ Thu, 22 Dec 2016 04:51:33:  42000000 
INFO  @ Thu, 22 Dec 2016 04:51:40:  43000000 
INFO  @ Thu, 22 Dec 2016 04:51:48:  44000000 
INFO  @ Thu, 22 Dec 2016 04:51:55:  45000000 
INFO  @ Thu, 22 Dec 2016 04:52:03:  46000000 
INFO  @ Thu, 22 Dec 2016 04:52:11:  47000000 
INFO  @ Thu, 22 Dec 2016 04:52:18:  48000000 
INFO  @ Thu, 22 Dec 2016 04:52:26:  49000000 
INFO  @ Thu, 22 Dec 2016 04:52:33:  50000000 
INFO  @ Thu, 22 Dec 2016 04:52:38: #1 tag size is determined as 51 bps 
INFO  @ Thu, 22 Dec 2016 04:52:38: #1 tag size = 51 
INFO  @ Thu, 22 Dec 2016 04:52:38: #1  total tags in treatment: 10376239 
INFO  @ Thu, 22 Dec 2016 04:52:38: #1  total tags in control: 50000000 
INFO  @ Thu, 22 Dec 2016 04:52:38: #1 finished! 
INFO  @ Thu, 22 Dec 2016 04:52:38: #2 Build Peak Model... 
INFO  @ Thu, 22 Dec 2016 04:52:38: #2 Skipped... 
INFO  @ Thu, 22 Dec 2016 04:52:38: #2 Use 170 as fragment length 
INFO  @ Thu, 22 Dec 2016 04:52:38: #3 Call peaks... 
INFO  @ Thu, 22 Dec 2016 04:52:38: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 22 Dec 2016 04:52:38: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 22 Dec 2016 05:00:42: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 22 Dec 2016 05:00:42: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 22 Dec 2016 05:00:42: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Thu, 22 Dec 2016 05:00:42: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 22 Dec 2016 05:00:42: #3 Call peaks for each chromosome... 
INFO  @ Thu, 22 Dec 2016 05:17:30: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 22 Dec 2016 05:17:31: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 22 Dec 2016 05:17:32: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Thu, 22 Dec 2016 05:17:33: Done! 
INFO  @ Thu, 22 Dec 2016 05:17:40: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/align/pseudo_reps/rep1/pr2/SRR1370904_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/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 170 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/align/pseudo_reps/rep1/pr2/SRR1370904_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 05:17:40: #1 read tag files... 
INFO  @ Thu, 22 Dec 2016 05:17:40: #1 read treatment tags... 
INFO  @ Thu, 22 Dec 2016 05:17:47:  1000000 
INFO  @ Thu, 22 Dec 2016 05:17:55:  2000000 
INFO  @ Thu, 22 Dec 2016 05:18:03:  3000000 
INFO  @ Thu, 22 Dec 2016 05:18:11:  4000000 
INFO  @ Thu, 22 Dec 2016 05:18:19:  5000000 
INFO  @ Thu, 22 Dec 2016 05:18:26:  6000000 
INFO  @ Thu, 22 Dec 2016 05:18:34:  7000000 
INFO  @ Thu, 22 Dec 2016 05:18:42:  8000000 
INFO  @ Thu, 22 Dec 2016 05:18:50:  9000000 
INFO  @ Thu, 22 Dec 2016 05:18:57:  10000000 
INFO  @ Thu, 22 Dec 2016 05:19:02: #1.2 read input tags... 
INFO  @ Thu, 22 Dec 2016 05:19:09:  1000000 
INFO  @ Thu, 22 Dec 2016 05:19:17:  2000000 
INFO  @ Thu, 22 Dec 2016 05:19:25:  3000000 
INFO  @ Thu, 22 Dec 2016 05:19:32:  4000000 
INFO  @ Thu, 22 Dec 2016 05:19:40:  5000000 
INFO  @ Thu, 22 Dec 2016 05:19:48:  6000000 
INFO  @ Thu, 22 Dec 2016 05:19:55:  7000000 
INFO  @ Thu, 22 Dec 2016 05:20:03:  8000000 
INFO  @ Thu, 22 Dec 2016 05:20:11:  9000000 
INFO  @ Thu, 22 Dec 2016 05:20:19:  10000000 
INFO  @ Thu, 22 Dec 2016 05:20:26:  11000000 
INFO  @ Thu, 22 Dec 2016 05:20:34:  12000000 
INFO  @ Thu, 22 Dec 2016 05:20:42:  13000000 
INFO  @ Thu, 22 Dec 2016 05:20:49:  14000000 
INFO  @ Thu, 22 Dec 2016 05:20:57:  15000000 
INFO  @ Thu, 22 Dec 2016 05:21:05:  16000000 
INFO  @ Thu, 22 Dec 2016 05:21:14:  17000000 
INFO  @ Thu, 22 Dec 2016 05:21:24:  18000000 
INFO  @ Thu, 22 Dec 2016 05:21:33:  19000000 
INFO  @ Thu, 22 Dec 2016 05:21:43:  20000000 
INFO  @ Thu, 22 Dec 2016 05:21:52:  21000000 
INFO  @ Thu, 22 Dec 2016 05:22:01:  22000000 
INFO  @ Thu, 22 Dec 2016 05:22:10:  23000000 
INFO  @ Thu, 22 Dec 2016 05:22:17:  24000000 
INFO  @ Thu, 22 Dec 2016 05:22:25:  25000000 
INFO  @ Thu, 22 Dec 2016 05:22:33:  26000000 
INFO  @ Thu, 22 Dec 2016 05:22:41:  27000000 
INFO  @ Thu, 22 Dec 2016 05:22:48:  28000000 
INFO  @ Thu, 22 Dec 2016 05:22:56:  29000000 
INFO  @ Thu, 22 Dec 2016 05:23:04:  30000000 
INFO  @ Thu, 22 Dec 2016 05:23:11:  31000000 
INFO  @ Thu, 22 Dec 2016 05:23:19:  32000000 
INFO  @ Thu, 22 Dec 2016 05:23:27:  33000000 
INFO  @ Thu, 22 Dec 2016 05:23:35:  34000000 
INFO  @ Thu, 22 Dec 2016 05:23:42:  35000000 
INFO  @ Thu, 22 Dec 2016 05:23:50:  36000000 
INFO  @ Thu, 22 Dec 2016 05:23:58:  37000000 
INFO  @ Thu, 22 Dec 2016 05:24:06:  38000000 
INFO  @ Thu, 22 Dec 2016 05:24:13:  39000000 
INFO  @ Thu, 22 Dec 2016 05:24:21:  40000000 
INFO  @ Thu, 22 Dec 2016 05:24:29:  41000000 
INFO  @ Thu, 22 Dec 2016 05:24:36:  42000000 
INFO  @ Thu, 22 Dec 2016 05:24:44:  43000000 
INFO  @ Thu, 22 Dec 2016 05:24:52:  44000000 
INFO  @ Thu, 22 Dec 2016 05:24:59:  45000000 
INFO  @ Thu, 22 Dec 2016 05:25:07:  46000000 
INFO  @ Thu, 22 Dec 2016 05:25:14:  47000000 
INFO  @ Thu, 22 Dec 2016 05:25:22:  48000000 
INFO  @ Thu, 22 Dec 2016 05:25:30:  49000000 
INFO  @ Thu, 22 Dec 2016 05:25:37:  50000000 
INFO  @ Thu, 22 Dec 2016 05:25:41: #1 tag size is determined as 51 bps 
INFO  @ Thu, 22 Dec 2016 05:25:41: #1 tag size = 51 
INFO  @ Thu, 22 Dec 2016 05:25:41: #1  total tags in treatment: 10376239 
INFO  @ Thu, 22 Dec 2016 05:25:41: #1  total tags in control: 50000000 
INFO  @ Thu, 22 Dec 2016 05:25:41: #1 finished! 
INFO  @ Thu, 22 Dec 2016 05:25:41: #2 Build Peak Model... 
INFO  @ Thu, 22 Dec 2016 05:25:41: #2 Skipped... 
INFO  @ Thu, 22 Dec 2016 05:25:41: #2 Use 170 as fragment length 
INFO  @ Thu, 22 Dec 2016 05:25:41: #3 Call peaks... 
INFO  @ Thu, 22 Dec 2016 05:25:41: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 22 Dec 2016 05:25:41: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 22 Dec 2016 05:33:54: #3 Call peaks for each chromosome... 
INFO  @ Thu, 22 Dec 2016 05:41:32: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 22 Dec 2016 05:41:53: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Thu, 22 Dec 2016 05:42:08: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370904_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 22 Dec 2016 05:42:20: 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, ZNF684, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF684/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF684/out/align/rep1/SRR1370904_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/ZNF684
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/ZNF684
string	queue
int	retry	0
string	SAMTOOLS_HOME	/software/samtools/samtools-1.2/bin
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	52014.ZNF684.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