Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20161221_141400_070
Start time	2016-12-21 14:14:00
Run time	10:19:07.765
Tasks executed	3
Tasks failed	1
Tasks failed names	macs2 rep1
Arguments*	[-title, ZFP3, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZFP3/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/align/rep1/SRR1370876_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_141400_070/task.callpeak_macs2.macs2_rep1.line_67.id_10 chipseq.bds.20161221_141400_070/task.callpeak_macs2.macs2_rep1_pr1.line_67.id_11 chipseq.bds.20161221_141400_070/task.callpeak_macs2.macs2_rep1_pr2.line_67.id_12
thread_42	thread_Root
thread_41	thread_Root

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.callpeak_macs2.macs2_rep1.line_67.id_10
Name	macs2 rep1
Thread	thread_Root
PID	19479

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

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

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/align/rep1/SRR1370876_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/ZFP3/out/peak/macs2/rep1/SRR1370876_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/rep1/SRR1370876_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/rep1/SRR1370876_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/signal/macs2/rep1/SRR1370876_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/signal/macs2/rep1/SRR1370876_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/ZFP3/out/align/rep1/SRR1370876_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/ZFP3/out/peak/macs2/rep1/SRR1370876_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 135 --keep-dup all -B --SPMR

# SYS command. line 78

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/rep1/SRR1370876_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/ZFP3/out/peak/macs2/rep1/SRR1370876_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 81

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/rep1/SRR1370876_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/rep1/SRR1370876_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/rep1/SRR1370876_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/ZFP3/out/align/rep1/SRR1370876_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/ZFP3/out/peak/macs2/rep1/SRR1370876_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 135 --keep-dup all

# SYS command. line 91

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/rep1/SRR1370876_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/ZFP3/out/peak/macs2/rep1/SRR1370876_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/ZFP3/out/peak/macs2/rep1/SRR1370876_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/ZFP3/out/peak/macs2/rep1/SRR1370876_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 95

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/rep1/SRR1370876_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/rep1/SRR1370876_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/rep1/SRR1370876_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/rep1/SRR1370876_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/ZFP3/out/peak/macs2/rep1/SRR1370876_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/rep1/SRR1370876_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/ZFP3/out/peak/macs2/rep1/SRR1370876_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/rep1/SRR1370876_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/rep1 -o "SRR1370876_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/ZFP3/out/peak/macs2/rep1/SRR1370876_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/ZFP3/out/peak/macs2/rep1/SRR1370876_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/ZFP3/out/peak/macs2/rep1/SRR1370876_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/ZFP3/out/peak/macs2/rep1/SRR1370876_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/rep1/SRR1370876_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/ZFP3/out/peak/macs2/rep1/SRR1370876_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/ZFP3/out/signal/macs2/rep1/SRR1370876_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/ZFP3/out/peak/macs2/rep1/SRR1370876_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/rep1/SRR1370876_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/ZFP3/out/align/rep1/SRR1370876_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/ZFP3/out/peak/macs2/rep1/SRR1370876_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/rep1/SRR1370876_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/rep1 -o "SRR1370876_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/ZFP3/out/peak/macs2/rep1/SRR1370876_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/ZFP3/out/peak/macs2/rep1/SRR1370876_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/ZFP3/out/peak/macs2/rep1/SRR1370876_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/ZFP3/out/peak/macs2/rep1/SRR1370876_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/rep1/SRR1370876_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/ZFP3/out/peak/macs2/rep1/SRR1370876_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/ZFP3/out/signal/macs2/rep1/SRR1370876_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/ZFP3/out/peak/macs2/rep1/SRR1370876_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/rep1/SRR1370876_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/ZFP3/out/peak/macs2/rep1/SRR1370876_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/rep1/SRR1370876_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--------------------
9035 (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  @ Wed, 21 Dec 2016 23:01:29: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/align/rep1/SRR1370876_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/ZFP3/out/peak/macs2/rep1/SRR1370876_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 135 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/rep1/SRR1370876_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/align/rep1/SRR1370876_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  @ Wed, 21 Dec 2016 23:01:29: #1 read tag files... 
INFO  @ Wed, 21 Dec 2016 23:01:29: #1 read treatment tags... 
INFO  @ Wed, 21 Dec 2016 23:01:31:  1000000 
INFO  @ Wed, 21 Dec 2016 23:01:33:  2000000 
INFO  @ Wed, 21 Dec 2016 23:01:34:  3000000 
INFO  @ Wed, 21 Dec 2016 23:01:36:  4000000 
INFO  @ Wed, 21 Dec 2016 23:01:37:  5000000 
INFO  @ Wed, 21 Dec 2016 23:01:39:  6000000 
INFO  @ Wed, 21 Dec 2016 23:01:41:  7000000 
INFO  @ Wed, 21 Dec 2016 23:01:42:  8000000 
INFO  @ Wed, 21 Dec 2016 23:01:44:  9000000 
INFO  @ Wed, 21 Dec 2016 23:01:45:  10000000 
INFO  @ Wed, 21 Dec 2016 23:01:47:  11000000 
INFO  @ Wed, 21 Dec 2016 23:01:48: #1.2 read input tags... 
INFO  @ Wed, 21 Dec 2016 23:01:50:  1000000 
INFO  @ Wed, 21 Dec 2016 23:01:52:  2000000 
INFO  @ Wed, 21 Dec 2016 23:01:53:  3000000 
INFO  @ Wed, 21 Dec 2016 23:01:55:  4000000 
INFO  @ Wed, 21 Dec 2016 23:01:57:  5000000 
INFO  @ Wed, 21 Dec 2016 23:01:58:  6000000 
INFO  @ Wed, 21 Dec 2016 23:02:00:  7000000 
INFO  @ Wed, 21 Dec 2016 23:02:01:  8000000 
INFO  @ Wed, 21 Dec 2016 23:02:03:  9000000 
INFO  @ Wed, 21 Dec 2016 23:02:05:  10000000 
INFO  @ Wed, 21 Dec 2016 23:02:06:  11000000 
INFO  @ Wed, 21 Dec 2016 23:02:08:  12000000 
INFO  @ Wed, 21 Dec 2016 23:02:10:  13000000 
INFO  @ Wed, 21 Dec 2016 23:02:11:  14000000 
INFO  @ Wed, 21 Dec 2016 23:02:13:  15000000 
INFO  @ Wed, 21 Dec 2016 23:02:14:  16000000 
INFO  @ Wed, 21 Dec 2016 23:02:16:  17000000 
INFO  @ Wed, 21 Dec 2016 23:02:17:  18000000 
INFO  @ Wed, 21 Dec 2016 23:02:19:  19000000 
INFO  @ Wed, 21 Dec 2016 23:02:21:  20000000 
INFO  @ Wed, 21 Dec 2016 23:02:22:  21000000 
INFO  @ Wed, 21 Dec 2016 23:02:24:  22000000 
INFO  @ Wed, 21 Dec 2016 23:02:25:  23000000 
INFO  @ Wed, 21 Dec 2016 23:02:27:  24000000 
INFO  @ Wed, 21 Dec 2016 23:02:29:  25000000 
INFO  @ Wed, 21 Dec 2016 23:02:30:  26000000 
INFO  @ Wed, 21 Dec 2016 23:02:32:  27000000 
INFO  @ Wed, 21 Dec 2016 23:02:33:  28000000 
INFO  @ Wed, 21 Dec 2016 23:02:35:  29000000 
INFO  @ Wed, 21 Dec 2016 23:02:36:  30000000 
INFO  @ Wed, 21 Dec 2016 23:02:38:  31000000 
INFO  @ Wed, 21 Dec 2016 23:02:40:  32000000 
INFO  @ Wed, 21 Dec 2016 23:02:41:  33000000 
INFO  @ Wed, 21 Dec 2016 23:02:43:  34000000 
INFO  @ Wed, 21 Dec 2016 23:02:44:  35000000 
INFO  @ Wed, 21 Dec 2016 23:02:46:  36000000 
INFO  @ Wed, 21 Dec 2016 23:02:48:  37000000 
INFO  @ Wed, 21 Dec 2016 23:02:49:  38000000 
INFO  @ Wed, 21 Dec 2016 23:02:51:  39000000 
INFO  @ Wed, 21 Dec 2016 23:02:53:  40000000 
INFO  @ Wed, 21 Dec 2016 23:02:54:  41000000 
INFO  @ Wed, 21 Dec 2016 23:02:56:  42000000 
INFO  @ Wed, 21 Dec 2016 23:02:57:  43000000 
INFO  @ Wed, 21 Dec 2016 23:02:59:  44000000 
INFO  @ Wed, 21 Dec 2016 23:03:01:  45000000 
INFO  @ Wed, 21 Dec 2016 23:03:02:  46000000 
INFO  @ Wed, 21 Dec 2016 23:03:04:  47000000 
INFO  @ Wed, 21 Dec 2016 23:03:05:  48000000 
INFO  @ Wed, 21 Dec 2016 23:03:07:  49000000 
INFO  @ Wed, 21 Dec 2016 23:03:09:  50000000 
INFO  @ Wed, 21 Dec 2016 23:03:10: #1 tag size is determined as 49 bps 
INFO  @ Wed, 21 Dec 2016 23:03:10: #1 tag size = 49 
INFO  @ Wed, 21 Dec 2016 23:03:10: #1  total tags in treatment: 11883862 
INFO  @ Wed, 21 Dec 2016 23:03:10: #1  total tags in control: 50000000 
INFO  @ Wed, 21 Dec 2016 23:03:10: #1 finished! 
INFO  @ Wed, 21 Dec 2016 23:03:10: #2 Build Peak Model... 
INFO  @ Wed, 21 Dec 2016 23:03:10: #2 Skipped... 
INFO  @ Wed, 21 Dec 2016 23:03:10: #2 Use 135 as fragment length 
INFO  @ Wed, 21 Dec 2016 23:03:10: #3 Call peaks... 
INFO  @ Wed, 21 Dec 2016 23:03:10: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Wed, 21 Dec 2016 23:03:10: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 21 Dec 2016 23:06:49: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Wed, 21 Dec 2016 23:06:49: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/rep1/SRR1370876_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Wed, 21 Dec 2016 23:06:49: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/rep1/SRR1370876_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Wed, 21 Dec 2016 23:06:49: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Wed, 21 Dec 2016 23:06:49: #3 Call peaks for each chromosome... 
INFO  @ Wed, 21 Dec 2016 23:12:11: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/rep1/SRR1370876_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Wed, 21 Dec 2016 23:12:13: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/rep1/SRR1370876_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Wed, 21 Dec 2016 23:12:13: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/rep1/SRR1370876_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Wed, 21 Dec 2016 23:12:14: Done! 
INFO  @ Wed, 21 Dec 2016 23:12:18: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/align/rep1/SRR1370876_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/ZFP3/out/peak/macs2/rep1/SRR1370876_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 135 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/rep1/SRR1370876_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/align/rep1/SRR1370876_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  @ Wed, 21 Dec 2016 23:12:18: #1 read tag files... 
INFO  @ Wed, 21 Dec 2016 23:12:18: #1 read treatment tags... 
INFO  @ Wed, 21 Dec 2016 23:12:19:  1000000 
INFO  @ Wed, 21 Dec 2016 23:12:21:  2000000 
INFO  @ Wed, 21 Dec 2016 23:12:22:  3000000 
INFO  @ Wed, 21 Dec 2016 23:12:24:  4000000 
INFO  @ Wed, 21 Dec 2016 23:12:26:  5000000 
INFO  @ Wed, 21 Dec 2016 23:12:27:  6000000 
INFO  @ Wed, 21 Dec 2016 23:12:29:  7000000 
INFO  @ Wed, 21 Dec 2016 23:12:30:  8000000 
INFO  @ Wed, 21 Dec 2016 23:12:32:  9000000 
INFO  @ Wed, 21 Dec 2016 23:12:33:  10000000 
INFO  @ Wed, 21 Dec 2016 23:12:35:  11000000 
INFO  @ Wed, 21 Dec 2016 23:12:36: #1.2 read input tags... 
INFO  @ Wed, 21 Dec 2016 23:12:38:  1000000 
INFO  @ Wed, 21 Dec 2016 23:12:40:  2000000 
INFO  @ Wed, 21 Dec 2016 23:12:41:  3000000 
INFO  @ Wed, 21 Dec 2016 23:12:43:  4000000 
INFO  @ Wed, 21 Dec 2016 23:12:44:  5000000 
INFO  @ Wed, 21 Dec 2016 23:12:46:  6000000 
INFO  @ Wed, 21 Dec 2016 23:12:47:  7000000 
INFO  @ Wed, 21 Dec 2016 23:12:49:  8000000 
INFO  @ Wed, 21 Dec 2016 23:12:50:  9000000 
INFO  @ Wed, 21 Dec 2016 23:12:52:  10000000 
INFO  @ Wed, 21 Dec 2016 23:12:54:  11000000 
INFO  @ Wed, 21 Dec 2016 23:12:55:  12000000 
INFO  @ Wed, 21 Dec 2016 23:12:57:  13000000 
INFO  @ Wed, 21 Dec 2016 23:12:58:  14000000 
INFO  @ Wed, 21 Dec 2016 23:13:00:  15000000 
INFO  @ Wed, 21 Dec 2016 23:13:01:  16000000 
INFO  @ Wed, 21 Dec 2016 23:13:03:  17000000 
INFO  @ Wed, 21 Dec 2016 23:13:05:  18000000 
INFO  @ Wed, 21 Dec 2016 23:13:06:  19000000 
INFO  @ Wed, 21 Dec 2016 23:13:08:  20000000 
INFO  @ Wed, 21 Dec 2016 23:13:09:  21000000 
INFO  @ Wed, 21 Dec 2016 23:13:11:  22000000 
INFO  @ Wed, 21 Dec 2016 23:13:12:  23000000 
INFO  @ Wed, 21 Dec 2016 23:13:14:  24000000 
INFO  @ Wed, 21 Dec 2016 23:13:15:  25000000 
INFO  @ Wed, 21 Dec 2016 23:13:17:  26000000 
INFO  @ Wed, 21 Dec 2016 23:13:19:  27000000 
INFO  @ Wed, 21 Dec 2016 23:13:20:  28000000 
INFO  @ Wed, 21 Dec 2016 23:13:22:  29000000 
INFO  @ Wed, 21 Dec 2016 23:13:23:  30000000 
INFO  @ Wed, 21 Dec 2016 23:13:25:  31000000 
INFO  @ Wed, 21 Dec 2016 23:13:26:  32000000 
INFO  @ Wed, 21 Dec 2016 23:13:28:  33000000 
INFO  @ Wed, 21 Dec 2016 23:13:29:  34000000 
INFO  @ Wed, 21 Dec 2016 23:13:31:  35000000 
INFO  @ Wed, 21 Dec 2016 23:13:33:  36000000 
INFO  @ Wed, 21 Dec 2016 23:13:34:  37000000 
INFO  @ Wed, 21 Dec 2016 23:13:36:  38000000 
INFO  @ Wed, 21 Dec 2016 23:13:37:  39000000 
INFO  @ Wed, 21 Dec 2016 23:13:39:  40000000 
INFO  @ Wed, 21 Dec 2016 23:13:40:  41000000 
INFO  @ Wed, 21 Dec 2016 23:13:42:  42000000 
INFO  @ Wed, 21 Dec 2016 23:13:44:  43000000 
INFO  @ Wed, 21 Dec 2016 23:13:45:  44000000 
INFO  @ Wed, 21 Dec 2016 23:13:47:  45000000 
INFO  @ Wed, 21 Dec 2016 23:13:48:  46000000 
INFO  @ Wed, 21 Dec 2016 23:13:50:  47000000 
INFO  @ Wed, 21 Dec 2016 23:13:51:  48000000 
INFO  @ Wed, 21 Dec 2016 23:13:53:  49000000 
INFO  @ Wed, 21 Dec 2016 23:13:54:  50000000 
INFO  @ Wed, 21 Dec 2016 23:13:56: #1 tag size is determined as 49 bps 
INFO  @ Wed, 21 Dec 2016 23:13:56: #1 tag size = 49 
INFO  @ Wed, 21 Dec 2016 23:13:56: #1  total tags in treatment: 11883862 
INFO  @ Wed, 21 Dec 2016 23:13:56: #1  total tags in control: 50000000 
INFO  @ Wed, 21 Dec 2016 23:13:56: #1 finished! 
INFO  @ Wed, 21 Dec 2016 23:13:56: #2 Build Peak Model... 
INFO  @ Wed, 21 Dec 2016 23:13:56: #2 Skipped... 
INFO  @ Wed, 21 Dec 2016 23:13:56: #2 Use 135 as fragment length 
INFO  @ Wed, 21 Dec 2016 23:13:56: #3 Call peaks... 
INFO  @ Wed, 21 Dec 2016 23:13:56: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Wed, 21 Dec 2016 23:13:56: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 21 Dec 2016 23:17:35: #3 Call peaks for each chromosome... 
INFO  @ Wed, 21 Dec 2016 23:20:54: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/rep1/SRR1370876_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Wed, 21 Dec 2016 23:21:01: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/rep1/SRR1370876_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Wed, 21 Dec 2016 23:21:06: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/rep1/SRR1370876_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Wed, 21 Dec 2016 23:21:10: Done! 
INFO  @ Wed, 21 Dec 2016 23:21:30: Read and build treatment bedGraph... 
INFO  @ Wed, 21 Dec 2016 23:21:55: Read and build control bedGraph... 
INFO  @ Wed, 21 Dec 2016 23:23:45: Build scoreTrackII... 
INFO  @ Wed, 21 Dec 2016 23:24:44: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Wed, 21 Dec 2016 23:29:31: Write bedGraph of scores... 
INFO  @ Wed, 21 Dec 2016 23:31:48: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/rep1/SRR1370876_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:                 19479
exec_file:                  job_scripts/19479
submission_time:            Wed Dec 21 14:14:06 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/ZFP3
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/chipseq.bds.20161221_141400_070/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/ZFP3/chipseq.bds.20161221_141400_070/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=47230.ZFP3.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/ZFP3,JAVA_HOME=/usr/lib/jvm/java-8-oracle,LOADEDMODULES=modsappsdir/modsappsdir:samtools/1.2,SSH_CONNECTION=171.65.77.8 32898 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,MANPATH=/software/samtools/samtools-1.2/share/man:/usr/share/man,MODULEPATH=/usr/local/Modules/versions				:/usr/local/Modules/$MODULE_VERSION/modulefiles	:/modules/				:/software/modulefiles,MODULESAPPSDIR=/software,MODULESHOME=/software/env_module/3.2.10
script_file:                STDIN
usage    1:                 cpu=00:30:38, mem=3143.89887 GBs, io=48.60406, vmem=115.336M, maxvmem=4.031G
scheduling info:            queue instance "q@kali" dropped because it is temporarily not available
                            queue instance "q@surya" dropped because it is disabled
                            queue instance "amd.q@wotan" dropped because it is full
                            queue instance "q@nandi" dropped because it is full
                            queue instance "q@kadru" dropped because it is full
                            All queues dropped because of overload or full

Num	2
ID	task.callpeak_macs2.macs2_rep1_pr1.line_67.id_11
Name	macs2 rep1-pr1
Thread	thread_Root
PID	19480

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

Start	2016-12-21 14:14:09
End	2016-12-21 23:57:23
Elapsed	09:43:13
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/align/pseudo_reps/rep1/pr1/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_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/ZFP3/out/align/pseudo_reps/rep1/pr1/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 135 --keep-dup all -B --SPMR

# SYS command. line 78

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_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/ZFP3/out/align/pseudo_reps/rep1/pr1/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 135 --keep-dup all

# SYS command. line 91

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_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/ZFP3/out/align/pseudo_reps/rep1/pr1/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_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--------------------
9372 (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  @ Wed, 21 Dec 2016 23:32:00: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/align/pseudo_reps/rep1/pr1/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 135 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/align/pseudo_reps/rep1/pr1/SRR1370876_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  @ Wed, 21 Dec 2016 23:32:00: #1 read tag files... 
INFO  @ Wed, 21 Dec 2016 23:32:00: #1 read treatment tags... 
INFO  @ Wed, 21 Dec 2016 23:32:02:  1000000 
INFO  @ Wed, 21 Dec 2016 23:32:03:  2000000 
INFO  @ Wed, 21 Dec 2016 23:32:05:  3000000 
INFO  @ Wed, 21 Dec 2016 23:32:07:  4000000 
INFO  @ Wed, 21 Dec 2016 23:32:08:  5000000 
INFO  @ Wed, 21 Dec 2016 23:32:11: #1.2 read input tags... 
INFO  @ Wed, 21 Dec 2016 23:32:12:  1000000 
INFO  @ Wed, 21 Dec 2016 23:32:14:  2000000 
INFO  @ Wed, 21 Dec 2016 23:32:16:  3000000 
INFO  @ Wed, 21 Dec 2016 23:32:17:  4000000 
INFO  @ Wed, 21 Dec 2016 23:32:19:  5000000 
INFO  @ Wed, 21 Dec 2016 23:32:20:  6000000 
INFO  @ Wed, 21 Dec 2016 23:32:22:  7000000 
INFO  @ Wed, 21 Dec 2016 23:32:23:  8000000 
INFO  @ Wed, 21 Dec 2016 23:32:25:  9000000 
INFO  @ Wed, 21 Dec 2016 23:32:27:  10000000 
INFO  @ Wed, 21 Dec 2016 23:32:28:  11000000 
INFO  @ Wed, 21 Dec 2016 23:32:30:  12000000 
INFO  @ Wed, 21 Dec 2016 23:32:31:  13000000 
INFO  @ Wed, 21 Dec 2016 23:32:33:  14000000 
INFO  @ Wed, 21 Dec 2016 23:32:34:  15000000 
INFO  @ Wed, 21 Dec 2016 23:32:36:  16000000 
INFO  @ Wed, 21 Dec 2016 23:32:38:  17000000 
INFO  @ Wed, 21 Dec 2016 23:32:39:  18000000 
INFO  @ Wed, 21 Dec 2016 23:32:41:  19000000 
INFO  @ Wed, 21 Dec 2016 23:32:42:  20000000 
INFO  @ Wed, 21 Dec 2016 23:32:44:  21000000 
INFO  @ Wed, 21 Dec 2016 23:32:46:  22000000 
INFO  @ Wed, 21 Dec 2016 23:32:47:  23000000 
INFO  @ Wed, 21 Dec 2016 23:32:49:  24000000 
INFO  @ Wed, 21 Dec 2016 23:32:50:  25000000 
INFO  @ Wed, 21 Dec 2016 23:32:52:  26000000 
INFO  @ Wed, 21 Dec 2016 23:32:53:  27000000 
INFO  @ Wed, 21 Dec 2016 23:32:55:  28000000 
INFO  @ Wed, 21 Dec 2016 23:32:57:  29000000 
INFO  @ Wed, 21 Dec 2016 23:32:58:  30000000 
INFO  @ Wed, 21 Dec 2016 23:33:00:  31000000 
INFO  @ Wed, 21 Dec 2016 23:33:01:  32000000 
INFO  @ Wed, 21 Dec 2016 23:33:03:  33000000 
INFO  @ Wed, 21 Dec 2016 23:33:05:  34000000 
INFO  @ Wed, 21 Dec 2016 23:33:06:  35000000 
INFO  @ Wed, 21 Dec 2016 23:33:08:  36000000 
INFO  @ Wed, 21 Dec 2016 23:33:09:  37000000 
INFO  @ Wed, 21 Dec 2016 23:33:11:  38000000 
INFO  @ Wed, 21 Dec 2016 23:33:13:  39000000 
INFO  @ Wed, 21 Dec 2016 23:33:15:  40000000 
INFO  @ Wed, 21 Dec 2016 23:33:16:  41000000 
INFO  @ Wed, 21 Dec 2016 23:33:18:  42000000 
INFO  @ Wed, 21 Dec 2016 23:33:19:  43000000 
INFO  @ Wed, 21 Dec 2016 23:33:21:  44000000 
INFO  @ Wed, 21 Dec 2016 23:33:22:  45000000 
INFO  @ Wed, 21 Dec 2016 23:33:24:  46000000 
INFO  @ Wed, 21 Dec 2016 23:33:26:  47000000 
INFO  @ Wed, 21 Dec 2016 23:33:27:  48000000 
INFO  @ Wed, 21 Dec 2016 23:33:29:  49000000 
INFO  @ Wed, 21 Dec 2016 23:33:30:  50000000 
INFO  @ Wed, 21 Dec 2016 23:33:32: #1 tag size is determined as 50 bps 
INFO  @ Wed, 21 Dec 2016 23:33:32: #1 tag size = 50 
INFO  @ Wed, 21 Dec 2016 23:33:32: #1  total tags in treatment: 5941931 
INFO  @ Wed, 21 Dec 2016 23:33:32: #1  total tags in control: 50000000 
INFO  @ Wed, 21 Dec 2016 23:33:32: #1 finished! 
INFO  @ Wed, 21 Dec 2016 23:33:32: #2 Build Peak Model... 
INFO  @ Wed, 21 Dec 2016 23:33:32: #2 Skipped... 
INFO  @ Wed, 21 Dec 2016 23:33:32: #2 Use 135 as fragment length 
INFO  @ Wed, 21 Dec 2016 23:33:32: #3 Call peaks... 
INFO  @ Wed, 21 Dec 2016 23:33:32: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Wed, 21 Dec 2016 23:33:32: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 21 Dec 2016 23:37:33: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Wed, 21 Dec 2016 23:37:33: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Wed, 21 Dec 2016 23:37:33: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Wed, 21 Dec 2016 23:37:33: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Wed, 21 Dec 2016 23:37:33: #3 Call peaks for each chromosome... 
INFO  @ Wed, 21 Dec 2016 23:42:34: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Wed, 21 Dec 2016 23:42:36: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Wed, 21 Dec 2016 23:42:37: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Wed, 21 Dec 2016 23:42:38: Done! 
INFO  @ Wed, 21 Dec 2016 23:42:42: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/align/pseudo_reps/rep1/pr1/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 135 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/align/pseudo_reps/rep1/pr1/SRR1370876_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  @ Wed, 21 Dec 2016 23:42:42: #1 read tag files... 
INFO  @ Wed, 21 Dec 2016 23:42:42: #1 read treatment tags... 
INFO  @ Wed, 21 Dec 2016 23:42:44:  1000000 
INFO  @ Wed, 21 Dec 2016 23:42:46:  2000000 
INFO  @ Wed, 21 Dec 2016 23:42:47:  3000000 
INFO  @ Wed, 21 Dec 2016 23:42:49:  4000000 
INFO  @ Wed, 21 Dec 2016 23:42:50:  5000000 
INFO  @ Wed, 21 Dec 2016 23:42:52: #1.2 read input tags... 
INFO  @ Wed, 21 Dec 2016 23:42:54:  1000000 
INFO  @ Wed, 21 Dec 2016 23:42:55:  2000000 
INFO  @ Wed, 21 Dec 2016 23:42:57:  3000000 
INFO  @ Wed, 21 Dec 2016 23:42:59:  4000000 
INFO  @ Wed, 21 Dec 2016 23:43:00:  5000000 
INFO  @ Wed, 21 Dec 2016 23:43:02:  6000000 
INFO  @ Wed, 21 Dec 2016 23:43:03:  7000000 
INFO  @ Wed, 21 Dec 2016 23:43:05:  8000000 
INFO  @ Wed, 21 Dec 2016 23:43:06:  9000000 
INFO  @ Wed, 21 Dec 2016 23:43:08:  10000000 
INFO  @ Wed, 21 Dec 2016 23:43:09:  11000000 
INFO  @ Wed, 21 Dec 2016 23:43:11:  12000000 
INFO  @ Wed, 21 Dec 2016 23:43:12:  13000000 
INFO  @ Wed, 21 Dec 2016 23:43:14:  14000000 
INFO  @ Wed, 21 Dec 2016 23:43:16:  15000000 
INFO  @ Wed, 21 Dec 2016 23:43:17:  16000000 
INFO  @ Wed, 21 Dec 2016 23:43:19:  17000000 
INFO  @ Wed, 21 Dec 2016 23:43:20:  18000000 
INFO  @ Wed, 21 Dec 2016 23:43:22:  19000000 
INFO  @ Wed, 21 Dec 2016 23:43:23:  20000000 
INFO  @ Wed, 21 Dec 2016 23:43:25:  21000000 
INFO  @ Wed, 21 Dec 2016 23:43:27:  22000000 
INFO  @ Wed, 21 Dec 2016 23:43:28:  23000000 
INFO  @ Wed, 21 Dec 2016 23:43:30:  24000000 
INFO  @ Wed, 21 Dec 2016 23:43:31:  25000000 
INFO  @ Wed, 21 Dec 2016 23:43:33:  26000000 
INFO  @ Wed, 21 Dec 2016 23:43:35:  27000000 
INFO  @ Wed, 21 Dec 2016 23:43:36:  28000000 
INFO  @ Wed, 21 Dec 2016 23:43:38:  29000000 
INFO  @ Wed, 21 Dec 2016 23:43:39:  30000000 
INFO  @ Wed, 21 Dec 2016 23:43:41:  31000000 
INFO  @ Wed, 21 Dec 2016 23:43:43:  32000000 
INFO  @ Wed, 21 Dec 2016 23:43:44:  33000000 
INFO  @ Wed, 21 Dec 2016 23:43:46:  34000000 
INFO  @ Wed, 21 Dec 2016 23:43:47:  35000000 
INFO  @ Wed, 21 Dec 2016 23:43:49:  36000000 
INFO  @ Wed, 21 Dec 2016 23:43:51:  37000000 
INFO  @ Wed, 21 Dec 2016 23:43:52:  38000000 
INFO  @ Wed, 21 Dec 2016 23:43:54:  39000000 
INFO  @ Wed, 21 Dec 2016 23:43:55:  40000000 
INFO  @ Wed, 21 Dec 2016 23:43:57:  41000000 
INFO  @ Wed, 21 Dec 2016 23:43:59:  42000000 
INFO  @ Wed, 21 Dec 2016 23:44:00:  43000000 
INFO  @ Wed, 21 Dec 2016 23:44:02:  44000000 
INFO  @ Wed, 21 Dec 2016 23:44:03:  45000000 
INFO  @ Wed, 21 Dec 2016 23:44:05:  46000000 
INFO  @ Wed, 21 Dec 2016 23:44:07:  47000000 
INFO  @ Wed, 21 Dec 2016 23:44:08:  48000000 
INFO  @ Wed, 21 Dec 2016 23:44:10:  49000000 
INFO  @ Wed, 21 Dec 2016 23:44:11:  50000000 
INFO  @ Wed, 21 Dec 2016 23:44:13: #1 tag size is determined as 50 bps 
INFO  @ Wed, 21 Dec 2016 23:44:13: #1 tag size = 50 
INFO  @ Wed, 21 Dec 2016 23:44:13: #1  total tags in treatment: 5941931 
INFO  @ Wed, 21 Dec 2016 23:44:13: #1  total tags in control: 50000000 
INFO  @ Wed, 21 Dec 2016 23:44:13: #1 finished! 
INFO  @ Wed, 21 Dec 2016 23:44:13: #2 Build Peak Model... 
INFO  @ Wed, 21 Dec 2016 23:44:13: #2 Skipped... 
INFO  @ Wed, 21 Dec 2016 23:44:13: #2 Use 135 as fragment length 
INFO  @ Wed, 21 Dec 2016 23:44:13: #3 Call peaks... 
INFO  @ Wed, 21 Dec 2016 23:44:13: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Wed, 21 Dec 2016 23:44:13: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 21 Dec 2016 23:48:19: #3 Call peaks for each chromosome... 
INFO  @ Wed, 21 Dec 2016 23:56:22: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Wed, 21 Dec 2016 23:56:32: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Wed, 21 Dec 2016 23:56:38: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370876_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Wed, 21 Dec 2016 23:56:44: Done!

Num	3
ID	task.callpeak_macs2.macs2_rep1_pr2.line_67.id_12
Name	macs2 rep1-pr2
Thread	thread_Root
PID	19481

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

Start	2016-12-21 14:14:10
End	2016-12-22 00:33:07
Elapsed	10:18:56
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/align/pseudo_reps/rep1/pr2/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_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/ZFP3/out/align/pseudo_reps/rep1/pr2/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 135 --keep-dup all -B --SPMR

# SYS command. line 78

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_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/ZFP3/out/align/pseudo_reps/rep1/pr2/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 135 --keep-dup all

# SYS command. line 91

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_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/ZFP3/out/align/pseudo_reps/rep1/pr2/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_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--------------------
9716 (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  @ Wed, 21 Dec 2016 23:57:45: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/align/pseudo_reps/rep1/pr2/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 135 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/align/pseudo_reps/rep1/pr2/SRR1370876_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  @ Wed, 21 Dec 2016 23:57:45: #1 read tag files... 
INFO  @ Wed, 21 Dec 2016 23:57:45: #1 read treatment tags... 
INFO  @ Wed, 21 Dec 2016 23:57:47:  1000000 
INFO  @ Wed, 21 Dec 2016 23:57:49:  2000000 
INFO  @ Wed, 21 Dec 2016 23:57:50:  3000000 
INFO  @ Wed, 21 Dec 2016 23:57:52:  4000000 
INFO  @ Wed, 21 Dec 2016 23:57:54:  5000000 
INFO  @ Wed, 21 Dec 2016 23:57:56: #1.2 read input tags... 
INFO  @ Wed, 21 Dec 2016 23:57:57:  1000000 
INFO  @ Wed, 21 Dec 2016 23:57:59:  2000000 
INFO  @ Wed, 21 Dec 2016 23:58:01:  3000000 
INFO  @ Wed, 21 Dec 2016 23:58:02:  4000000 
INFO  @ Wed, 21 Dec 2016 23:58:04:  5000000 
INFO  @ Wed, 21 Dec 2016 23:58:05:  6000000 
INFO  @ Wed, 21 Dec 2016 23:58:07:  7000000 
INFO  @ Wed, 21 Dec 2016 23:58:09:  8000000 
INFO  @ Wed, 21 Dec 2016 23:58:10:  9000000 
INFO  @ Wed, 21 Dec 2016 23:58:12:  10000000 
INFO  @ Wed, 21 Dec 2016 23:58:14:  11000000 
INFO  @ Wed, 21 Dec 2016 23:58:15:  12000000 
INFO  @ Wed, 21 Dec 2016 23:58:17:  13000000 
INFO  @ Wed, 21 Dec 2016 23:58:19:  14000000 
INFO  @ Wed, 21 Dec 2016 23:58:20:  15000000 
INFO  @ Wed, 21 Dec 2016 23:58:22:  16000000 
INFO  @ Wed, 21 Dec 2016 23:58:23:  17000000 
INFO  @ Wed, 21 Dec 2016 23:58:25:  18000000 
INFO  @ Wed, 21 Dec 2016 23:58:27:  19000000 
INFO  @ Wed, 21 Dec 2016 23:58:28:  20000000 
INFO  @ Wed, 21 Dec 2016 23:58:30:  21000000 
INFO  @ Wed, 21 Dec 2016 23:58:31:  22000000 
INFO  @ Wed, 21 Dec 2016 23:58:33:  23000000 
INFO  @ Wed, 21 Dec 2016 23:58:35:  24000000 
INFO  @ Wed, 21 Dec 2016 23:58:36:  25000000 
INFO  @ Wed, 21 Dec 2016 23:58:38:  26000000 
INFO  @ Wed, 21 Dec 2016 23:58:39:  27000000 
INFO  @ Wed, 21 Dec 2016 23:58:41:  28000000 
INFO  @ Wed, 21 Dec 2016 23:58:42:  29000000 
INFO  @ Wed, 21 Dec 2016 23:58:44:  30000000 
INFO  @ Wed, 21 Dec 2016 23:58:46:  31000000 
INFO  @ Wed, 21 Dec 2016 23:58:47:  32000000 
INFO  @ Wed, 21 Dec 2016 23:58:49:  33000000 
INFO  @ Wed, 21 Dec 2016 23:58:50:  34000000 
INFO  @ Wed, 21 Dec 2016 23:58:52:  35000000 
INFO  @ Wed, 21 Dec 2016 23:58:53:  36000000 
INFO  @ Wed, 21 Dec 2016 23:58:55:  37000000 
INFO  @ Wed, 21 Dec 2016 23:58:57:  38000000 
INFO  @ Wed, 21 Dec 2016 23:58:58:  39000000 
INFO  @ Wed, 21 Dec 2016 23:59:00:  40000000 
INFO  @ Wed, 21 Dec 2016 23:59:01:  41000000 
INFO  @ Wed, 21 Dec 2016 23:59:03:  42000000 
INFO  @ Wed, 21 Dec 2016 23:59:04:  43000000 
INFO  @ Wed, 21 Dec 2016 23:59:06:  44000000 
INFO  @ Wed, 21 Dec 2016 23:59:08:  45000000 
INFO  @ Wed, 21 Dec 2016 23:59:09:  46000000 
INFO  @ Wed, 21 Dec 2016 23:59:11:  47000000 
INFO  @ Wed, 21 Dec 2016 23:59:12:  48000000 
INFO  @ Wed, 21 Dec 2016 23:59:14:  49000000 
INFO  @ Wed, 21 Dec 2016 23:59:15:  50000000 
INFO  @ Wed, 21 Dec 2016 23:59:17: #1 tag size is determined as 51 bps 
INFO  @ Wed, 21 Dec 2016 23:59:17: #1 tag size = 51 
INFO  @ Wed, 21 Dec 2016 23:59:17: #1  total tags in treatment: 5941931 
INFO  @ Wed, 21 Dec 2016 23:59:17: #1  total tags in control: 50000000 
INFO  @ Wed, 21 Dec 2016 23:59:17: #1 finished! 
INFO  @ Wed, 21 Dec 2016 23:59:17: #2 Build Peak Model... 
INFO  @ Wed, 21 Dec 2016 23:59:17: #2 Skipped... 
INFO  @ Wed, 21 Dec 2016 23:59:17: #2 Use 135 as fragment length 
INFO  @ Wed, 21 Dec 2016 23:59:17: #3 Call peaks... 
INFO  @ Wed, 21 Dec 2016 23:59:17: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Wed, 21 Dec 2016 23:59:17: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 22 Dec 2016 00:06:53: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 22 Dec 2016 00:06:53: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 22 Dec 2016 00:06:53: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Thu, 22 Dec 2016 00:06:53: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 22 Dec 2016 00:06:53: #3 Call peaks for each chromosome... 
INFO  @ Thu, 22 Dec 2016 00:14:13: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 22 Dec 2016 00:14:15: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 22 Dec 2016 00:14:16: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Thu, 22 Dec 2016 00:14:17: Done! 
INFO  @ Thu, 22 Dec 2016 00:14:23: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/align/pseudo_reps/rep1/pr2/SRR1370876_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/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 135 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/align/pseudo_reps/rep1/pr2/SRR1370876_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 00:14:23: #1 read tag files... 
INFO  @ Thu, 22 Dec 2016 00:14:23: #1 read treatment tags... 
INFO  @ Thu, 22 Dec 2016 00:14:25:  1000000 
INFO  @ Thu, 22 Dec 2016 00:14:27:  2000000 
INFO  @ Thu, 22 Dec 2016 00:14:28:  3000000 
INFO  @ Thu, 22 Dec 2016 00:14:30:  4000000 
INFO  @ Thu, 22 Dec 2016 00:14:32:  5000000 
INFO  @ Thu, 22 Dec 2016 00:14:34: #1.2 read input tags... 
INFO  @ Thu, 22 Dec 2016 00:14:35:  1000000 
INFO  @ Thu, 22 Dec 2016 00:14:37:  2000000 
INFO  @ Thu, 22 Dec 2016 00:14:38:  3000000 
INFO  @ Thu, 22 Dec 2016 00:14:40:  4000000 
INFO  @ Thu, 22 Dec 2016 00:14:42:  5000000 
INFO  @ Thu, 22 Dec 2016 00:14:43:  6000000 
INFO  @ Thu, 22 Dec 2016 00:14:45:  7000000 
INFO  @ Thu, 22 Dec 2016 00:14:46:  8000000 
INFO  @ Thu, 22 Dec 2016 00:14:48:  9000000 
INFO  @ Thu, 22 Dec 2016 00:14:50:  10000000 
INFO  @ Thu, 22 Dec 2016 00:14:51:  11000000 
INFO  @ Thu, 22 Dec 2016 00:14:53:  12000000 
INFO  @ Thu, 22 Dec 2016 00:14:54:  13000000 
INFO  @ Thu, 22 Dec 2016 00:14:56:  14000000 
INFO  @ Thu, 22 Dec 2016 00:14:57:  15000000 
INFO  @ Thu, 22 Dec 2016 00:14:59:  16000000 
INFO  @ Thu, 22 Dec 2016 00:15:01:  17000000 
INFO  @ Thu, 22 Dec 2016 00:15:02:  18000000 
INFO  @ Thu, 22 Dec 2016 00:15:04:  19000000 
INFO  @ Thu, 22 Dec 2016 00:15:05:  20000000 
INFO  @ Thu, 22 Dec 2016 00:15:07:  21000000 
INFO  @ Thu, 22 Dec 2016 00:15:09:  22000000 
INFO  @ Thu, 22 Dec 2016 00:15:10:  23000000 
INFO  @ Thu, 22 Dec 2016 00:15:12:  24000000 
INFO  @ Thu, 22 Dec 2016 00:15:13:  25000000 
INFO  @ Thu, 22 Dec 2016 00:15:15:  26000000 
INFO  @ Thu, 22 Dec 2016 00:15:17:  27000000 
INFO  @ Thu, 22 Dec 2016 00:15:18:  28000000 
INFO  @ Thu, 22 Dec 2016 00:15:20:  29000000 
INFO  @ Thu, 22 Dec 2016 00:15:21:  30000000 
INFO  @ Thu, 22 Dec 2016 00:15:23:  31000000 
INFO  @ Thu, 22 Dec 2016 00:15:25:  32000000 
INFO  @ Thu, 22 Dec 2016 00:15:26:  33000000 
INFO  @ Thu, 22 Dec 2016 00:15:28:  34000000 
INFO  @ Thu, 22 Dec 2016 00:15:29:  35000000 
INFO  @ Thu, 22 Dec 2016 00:15:31:  36000000 
INFO  @ Thu, 22 Dec 2016 00:15:33:  37000000 
INFO  @ Thu, 22 Dec 2016 00:15:34:  38000000 
INFO  @ Thu, 22 Dec 2016 00:15:36:  39000000 
INFO  @ Thu, 22 Dec 2016 00:15:37:  40000000 
INFO  @ Thu, 22 Dec 2016 00:15:39:  41000000 
INFO  @ Thu, 22 Dec 2016 00:15:41:  42000000 
INFO  @ Thu, 22 Dec 2016 00:15:42:  43000000 
INFO  @ Thu, 22 Dec 2016 00:15:44:  44000000 
INFO  @ Thu, 22 Dec 2016 00:15:45:  45000000 
INFO  @ Thu, 22 Dec 2016 00:15:47:  46000000 
INFO  @ Thu, 22 Dec 2016 00:15:49:  47000000 
INFO  @ Thu, 22 Dec 2016 00:15:50:  48000000 
INFO  @ Thu, 22 Dec 2016 00:15:52:  49000000 
INFO  @ Thu, 22 Dec 2016 00:15:53:  50000000 
INFO  @ Thu, 22 Dec 2016 00:15:55: #1 tag size is determined as 51 bps 
INFO  @ Thu, 22 Dec 2016 00:15:55: #1 tag size = 51 
INFO  @ Thu, 22 Dec 2016 00:15:55: #1  total tags in treatment: 5941931 
INFO  @ Thu, 22 Dec 2016 00:15:55: #1  total tags in control: 50000000 
INFO  @ Thu, 22 Dec 2016 00:15:55: #1 finished! 
INFO  @ Thu, 22 Dec 2016 00:15:55: #2 Build Peak Model... 
INFO  @ Thu, 22 Dec 2016 00:15:55: #2 Skipped... 
INFO  @ Thu, 22 Dec 2016 00:15:55: #2 Use 135 as fragment length 
INFO  @ Thu, 22 Dec 2016 00:15:55: #3 Call peaks... 
INFO  @ Thu, 22 Dec 2016 00:15:55: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 22 Dec 2016 00:15:55: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 22 Dec 2016 00:23:51: #3 Call peaks for each chromosome... 
INFO  @ Thu, 22 Dec 2016 00:32:08: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 22 Dec 2016 00:32:16: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Thu, 22 Dec 2016 00:32:23: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370876_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 22 Dec 2016 00:32:29: 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, ZFP3, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZFP3/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZFP3/out/align/rep1/SRR1370876_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/ZFP3
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/ZFP3
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	47230.ZFP3.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