BigDataScript report: chipseq.bds

Script file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20161221_141432_107
Start time 2016-12-21 14:14:32
Run time 13:30:27.456
Tasks executed 3
Tasks failed 1
Tasks failed names 
macs2 rep1
Arguments* [-title, ZNF416, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF416/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/align/rep1/SRR1370905_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
* Values in global scope when program finished execution.

Timeline

Task Graph

Parallel (threads) details

Thread ID Parent Tasks
thread_Root None 
 chipseq.bds.20161221_141432_107/task.callpeak_macs2.macs2_rep1.line_67.id_10
chipseq.bds.20161221_141432_107/task.callpeak_macs2.macs2_rep1_pr1.line_67.id_11
chipseq.bds.20161221_141432_107/task.callpeak_macs2.macs2_rep1_pr2.line_67.id_12
thread_41 thread_Root
thread_42 thread_Root

Task details

Task Execution Time Dependencies Task program, Errors, StdOut / StdErr
Num 1
ID task.callpeak_macs2.macs2_rep1.line_67.id_10
Name macs2 rep1
Thread thread_Root
PID 19488
OK false
Exit Code 1
Retries
State ERROR
Dep. ERROR
Cpus
Mem
Start 2016-12-21 14:14:39
End 2016-12-21 14:14:39
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/align/rep1/SRR1370905_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/ZNF416/out/peak/macs2/rep1/SRR1370905_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/rep1/SRR1370905_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/rep1/SRR1370905_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/signal/macs2/rep1/SRR1370905_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/signal/macs2/rep1/SRR1370905_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/ZNF416/out/align/rep1/SRR1370905_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/ZNF416/out/peak/macs2/rep1/SRR1370905_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 160 --keep-dup all -B --SPMR

# SYS command. line 78

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/rep1/SRR1370905_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/ZNF416/out/peak/macs2/rep1/SRR1370905_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 81

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/rep1/SRR1370905_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/rep1/SRR1370905_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/rep1/SRR1370905_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/ZNF416/out/align/rep1/SRR1370905_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/ZNF416/out/peak/macs2/rep1/SRR1370905_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 160 --keep-dup all

# SYS command. line 91

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/rep1/SRR1370905_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/ZNF416/out/peak/macs2/rep1/SRR1370905_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/ZNF416/out/peak/macs2/rep1/SRR1370905_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/ZNF416/out/peak/macs2/rep1/SRR1370905_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 95

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/rep1/SRR1370905_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/rep1/SRR1370905_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/rep1/SRR1370905_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/rep1/SRR1370905_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/ZNF416/out/peak/macs2/rep1/SRR1370905_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/rep1/SRR1370905_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/ZNF416/out/peak/macs2/rep1/SRR1370905_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/rep1/SRR1370905_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/rep1 -o "SRR1370905_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/ZNF416/out/peak/macs2/rep1/SRR1370905_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/ZNF416/out/peak/macs2/rep1/SRR1370905_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/ZNF416/out/peak/macs2/rep1/SRR1370905_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/ZNF416/out/peak/macs2/rep1/SRR1370905_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/rep1/SRR1370905_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/ZNF416/out/peak/macs2/rep1/SRR1370905_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/ZNF416/out/signal/macs2/rep1/SRR1370905_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/ZNF416/out/peak/macs2/rep1/SRR1370905_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/rep1/SRR1370905_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/ZNF416/out/align/rep1/SRR1370905_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/ZNF416/out/peak/macs2/rep1/SRR1370905_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/rep1/SRR1370905_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/rep1 -o "SRR1370905_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/ZNF416/out/peak/macs2/rep1/SRR1370905_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/ZNF416/out/peak/macs2/rep1/SRR1370905_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/ZNF416/out/peak/macs2/rep1/SRR1370905_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/ZNF416/out/peak/macs2/rep1/SRR1370905_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/rep1/SRR1370905_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/ZNF416/out/peak/macs2/rep1/SRR1370905_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/ZNF416/out/signal/macs2/rep1/SRR1370905_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/ZNF416/out/peak/macs2/rep1/SRR1370905_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/rep1/SRR1370905_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/ZNF416/out/peak/macs2/rep1/SRR1370905_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/rep1/SRR1370905_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--------------------
61777 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
INFO  @ Thu, 22 Dec 2016 02:10:34: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/align/rep1/SRR1370905_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/ZNF416/out/peak/macs2/rep1/SRR1370905_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 160 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/rep1/SRR1370905_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/align/rep1/SRR1370905_1.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Thu, 22 Dec 2016 02:10:34: #1 read tag files... 
INFO  @ Thu, 22 Dec 2016 02:10:34: #1 read treatment tags... 
INFO  @ Thu, 22 Dec 2016 02:10:42:  1000000 
INFO  @ Thu, 22 Dec 2016 02:10:49:  2000000 
INFO  @ Thu, 22 Dec 2016 02:10:57:  3000000 
INFO  @ Thu, 22 Dec 2016 02:11:04:  4000000 
INFO  @ Thu, 22 Dec 2016 02:11:12:  5000000 
INFO  @ Thu, 22 Dec 2016 02:11:12: #1.2 read input tags... 
INFO  @ Thu, 22 Dec 2016 02:11:20:  1000000 
INFO  @ Thu, 22 Dec 2016 02:11:27:  2000000 
INFO  @ Thu, 22 Dec 2016 02:11:35:  3000000 
INFO  @ Thu, 22 Dec 2016 02:11:43:  4000000 
INFO  @ Thu, 22 Dec 2016 02:11:50:  5000000 
INFO  @ Thu, 22 Dec 2016 02:11:58:  6000000 
INFO  @ Thu, 22 Dec 2016 02:12:06:  7000000 
INFO  @ Thu, 22 Dec 2016 02:12:13:  8000000 
INFO  @ Thu, 22 Dec 2016 02:12:21:  9000000 
INFO  @ Thu, 22 Dec 2016 02:12:28:  10000000 
INFO  @ Thu, 22 Dec 2016 02:12:36:  11000000 
INFO  @ Thu, 22 Dec 2016 02:12:43:  12000000 
INFO  @ Thu, 22 Dec 2016 02:12:51:  13000000 
INFO  @ Thu, 22 Dec 2016 02:12:58:  14000000 
INFO  @ Thu, 22 Dec 2016 02:13:06:  15000000 
INFO  @ Thu, 22 Dec 2016 02:13:13:  16000000 
INFO  @ Thu, 22 Dec 2016 02:13:21:  17000000 
INFO  @ Thu, 22 Dec 2016 02:13:29:  18000000 
INFO  @ Thu, 22 Dec 2016 02:13:36:  19000000 
INFO  @ Thu, 22 Dec 2016 02:13:44:  20000000 
INFO  @ Thu, 22 Dec 2016 02:13:51:  21000000 
INFO  @ Thu, 22 Dec 2016 02:13:59:  22000000 
INFO  @ Thu, 22 Dec 2016 02:14:06:  23000000 
INFO  @ Thu, 22 Dec 2016 02:14:14:  24000000 
INFO  @ Thu, 22 Dec 2016 02:14:22:  25000000 
INFO  @ Thu, 22 Dec 2016 02:14:29:  26000000 
INFO  @ Thu, 22 Dec 2016 02:14:37:  27000000 
INFO  @ Thu, 22 Dec 2016 02:14:44:  28000000 
INFO  @ Thu, 22 Dec 2016 02:14:52:  29000000 
INFO  @ Thu, 22 Dec 2016 02:15:00:  30000000 
INFO  @ Thu, 22 Dec 2016 02:15:07:  31000000 
INFO  @ Thu, 22 Dec 2016 02:15:15:  32000000 
INFO  @ Thu, 22 Dec 2016 02:15:22:  33000000 
INFO  @ Thu, 22 Dec 2016 02:15:30:  34000000 
INFO  @ Thu, 22 Dec 2016 02:15:37:  35000000 
INFO  @ Thu, 22 Dec 2016 02:15:45:  36000000 
INFO  @ Thu, 22 Dec 2016 02:15:53:  37000000 
INFO  @ Thu, 22 Dec 2016 02:16:00:  38000000 
INFO  @ Thu, 22 Dec 2016 02:16:08:  39000000 
INFO  @ Thu, 22 Dec 2016 02:16:15:  40000000 
INFO  @ Thu, 22 Dec 2016 02:16:23:  41000000 
INFO  @ Thu, 22 Dec 2016 02:16:30:  42000000 
INFO  @ Thu, 22 Dec 2016 02:16:38:  43000000 
INFO  @ Thu, 22 Dec 2016 02:16:45:  44000000 
INFO  @ Thu, 22 Dec 2016 02:16:53:  45000000 
INFO  @ Thu, 22 Dec 2016 02:17:00:  46000000 
INFO  @ Thu, 22 Dec 2016 02:17:08:  47000000 
INFO  @ Thu, 22 Dec 2016 02:17:15:  48000000 
INFO  @ Thu, 22 Dec 2016 02:17:23:  49000000 
INFO  @ Thu, 22 Dec 2016 02:17:30:  50000000 
INFO  @ Thu, 22 Dec 2016 02:17:34: #1 tag size is determined as 68 bps 
INFO  @ Thu, 22 Dec 2016 02:17:34: #1 tag size = 68 
INFO  @ Thu, 22 Dec 2016 02:17:34: #1  total tags in treatment: 5036018 
INFO  @ Thu, 22 Dec 2016 02:17:34: #1  total tags in control: 50000000 
INFO  @ Thu, 22 Dec 2016 02:17:34: #1 finished! 
INFO  @ Thu, 22 Dec 2016 02:17:34: #2 Build Peak Model... 
INFO  @ Thu, 22 Dec 2016 02:17:34: #2 Skipped... 
INFO  @ Thu, 22 Dec 2016 02:17:34: #2 Use 160 as fragment length 
INFO  @ Thu, 22 Dec 2016 02:17:34: #3 Call peaks... 
INFO  @ Thu, 22 Dec 2016 02:17:34: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 22 Dec 2016 02:17:34: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 22 Dec 2016 02:25:44: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 22 Dec 2016 02:25:44: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/rep1/SRR1370905_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 22 Dec 2016 02:25:44: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/rep1/SRR1370905_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Thu, 22 Dec 2016 02:25:44: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 22 Dec 2016 02:25:44: #3 Call peaks for each chromosome... 
INFO  @ Thu, 22 Dec 2016 02:42:27: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/rep1/SRR1370905_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 22 Dec 2016 02:42:37: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/rep1/SRR1370905_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 22 Dec 2016 02:42:43: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/rep1/SRR1370905_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Thu, 22 Dec 2016 02:42:47: Done! 
INFO  @ Thu, 22 Dec 2016 02:42:57: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/align/rep1/SRR1370905_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/ZNF416/out/peak/macs2/rep1/SRR1370905_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 160 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/rep1/SRR1370905_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/align/rep1/SRR1370905_1.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Thu, 22 Dec 2016 02:42:57: #1 read tag files... 
INFO  @ Thu, 22 Dec 2016 02:42:57: #1 read treatment tags... 
INFO  @ Thu, 22 Dec 2016 02:43:04:  1000000 
INFO  @ Thu, 22 Dec 2016 02:43:12:  2000000 
INFO  @ Thu, 22 Dec 2016 02:43:19:  3000000 
INFO  @ Thu, 22 Dec 2016 02:43:27:  4000000 
INFO  @ Thu, 22 Dec 2016 02:43:34:  5000000 
INFO  @ Thu, 22 Dec 2016 02:43:35: #1.2 read input tags... 
INFO  @ Thu, 22 Dec 2016 02:43:43:  1000000 
INFO  @ Thu, 22 Dec 2016 02:43:50:  2000000 
INFO  @ Thu, 22 Dec 2016 02:43:58:  3000000 
INFO  @ Thu, 22 Dec 2016 02:44:06:  4000000 
INFO  @ Thu, 22 Dec 2016 02:44:13:  5000000 
INFO  @ Thu, 22 Dec 2016 02:44:21:  6000000 
INFO  @ Thu, 22 Dec 2016 02:44:28:  7000000 
INFO  @ Thu, 22 Dec 2016 02:44:36:  8000000 
INFO  @ Thu, 22 Dec 2016 02:44:44:  9000000 
INFO  @ Thu, 22 Dec 2016 02:44:51:  10000000 
INFO  @ Thu, 22 Dec 2016 02:44:59:  11000000 
INFO  @ Thu, 22 Dec 2016 02:45:07:  12000000 
INFO  @ Thu, 22 Dec 2016 02:45:15:  13000000 
INFO  @ Thu, 22 Dec 2016 02:45:22:  14000000 
INFO  @ Thu, 22 Dec 2016 02:45:30:  15000000 
INFO  @ Thu, 22 Dec 2016 02:45:38:  16000000 
INFO  @ Thu, 22 Dec 2016 02:45:46:  17000000 
INFO  @ Thu, 22 Dec 2016 02:45:53:  18000000 
INFO  @ Thu, 22 Dec 2016 02:46:01:  19000000 
INFO  @ Thu, 22 Dec 2016 02:46:08:  20000000 
INFO  @ Thu, 22 Dec 2016 02:46:16:  21000000 
INFO  @ Thu, 22 Dec 2016 02:46:24:  22000000 
INFO  @ Thu, 22 Dec 2016 02:46:31:  23000000 
INFO  @ Thu, 22 Dec 2016 02:46:39:  24000000 
INFO  @ Thu, 22 Dec 2016 02:46:47:  25000000 
INFO  @ Thu, 22 Dec 2016 02:46:54:  26000000 
INFO  @ Thu, 22 Dec 2016 02:47:02:  27000000 
INFO  @ Thu, 22 Dec 2016 02:47:09:  28000000 
INFO  @ Thu, 22 Dec 2016 02:47:17:  29000000 
INFO  @ Thu, 22 Dec 2016 02:47:25:  30000000 
INFO  @ Thu, 22 Dec 2016 02:47:32:  31000000 
INFO  @ Thu, 22 Dec 2016 02:47:40:  32000000 
INFO  @ Thu, 22 Dec 2016 02:47:48:  33000000 
INFO  @ Thu, 22 Dec 2016 02:47:55:  34000000 
INFO  @ Thu, 22 Dec 2016 02:48:03:  35000000 
INFO  @ Thu, 22 Dec 2016 02:48:11:  36000000 
INFO  @ Thu, 22 Dec 2016 02:48:18:  37000000 
INFO  @ Thu, 22 Dec 2016 02:48:26:  38000000 
INFO  @ Thu, 22 Dec 2016 02:48:34:  39000000 
INFO  @ Thu, 22 Dec 2016 02:48:41:  40000000 
INFO  @ Thu, 22 Dec 2016 02:48:49:  41000000 
INFO  @ Thu, 22 Dec 2016 02:48:57:  42000000 
INFO  @ Thu, 22 Dec 2016 02:49:04:  43000000 
INFO  @ Thu, 22 Dec 2016 02:49:12:  44000000 
INFO  @ Thu, 22 Dec 2016 02:49:19:  45000000 
INFO  @ Thu, 22 Dec 2016 02:49:27:  46000000 
INFO  @ Thu, 22 Dec 2016 02:49:35:  47000000 
INFO  @ Thu, 22 Dec 2016 02:49:42:  48000000 
INFO  @ Thu, 22 Dec 2016 02:49:50:  49000000 
INFO  @ Thu, 22 Dec 2016 02:49:58:  50000000 
INFO  @ Thu, 22 Dec 2016 02:50:02: #1 tag size is determined as 68 bps 
INFO  @ Thu, 22 Dec 2016 02:50:02: #1 tag size = 68 
INFO  @ Thu, 22 Dec 2016 02:50:02: #1  total tags in treatment: 5036018 
INFO  @ Thu, 22 Dec 2016 02:50:02: #1  total tags in control: 50000000 
INFO  @ Thu, 22 Dec 2016 02:50:02: #1 finished! 
INFO  @ Thu, 22 Dec 2016 02:50:02: #2 Build Peak Model... 
INFO  @ Thu, 22 Dec 2016 02:50:02: #2 Skipped... 
INFO  @ Thu, 22 Dec 2016 02:50:02: #2 Use 160 as fragment length 
INFO  @ Thu, 22 Dec 2016 02:50:02: #3 Call peaks... 
INFO  @ Thu, 22 Dec 2016 02:50:02: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 22 Dec 2016 02:50:02: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 22 Dec 2016 02:57:51: #3 Call peaks for each chromosome... 
INFO  @ Thu, 22 Dec 2016 03:07:56: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/rep1/SRR1370905_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 22 Dec 2016 03:08:26: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/rep1/SRR1370905_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Thu, 22 Dec 2016 03:08:47: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/rep1/SRR1370905_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 22 Dec 2016 03:09:04: Done! 
INFO  @ Thu, 22 Dec 2016 03:09:49: Read and build treatment bedGraph... 
INFO  @ Thu, 22 Dec 2016 03:10:36: Read and build control bedGraph... 
INFO  @ Thu, 22 Dec 2016 03:18:37: Build scoreTrackII... 
INFO  @ Thu, 22 Dec 2016 03:20:49: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Thu, 22 Dec 2016 03:40:56: Write bedGraph of scores... 
INFO  @ Thu, 22 Dec 2016 03:44:57: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/rep1/SRR1370905_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:                 19488
exec_file:                  job_scripts/19488
submission_time:            Wed Dec 21 14:14:39 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/ZNF416
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/chipseq.bds.20161221_141432_107/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/ZNF416/chipseq.bds.20161221_141432_107/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=49923.ZNF416.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/ZNF416,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=01:34:21, mem=14380.11983 GBs, io=46.76695, vmem=911.531M, maxvmem=3.973G
scheduling info:            queue instance "q@kali" dropped because it is temporarily not available
                            queue instance "q@surya" dropped because it is disabled
                            queue instance "amd.q@wotan" dropped because it is full
                            queue instance "q@kadru" dropped because it is full
                            queue instance "q@nandi" dropped because it is full
                            All queues dropped because of overload or full
Num 2
ID task.callpeak_macs2.macs2_rep1_pr1.line_67.id_11
Name macs2 rep1-pr1
Thread thread_Root
PID 19489
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2016-12-21 14:14:42
End 2016-12-22 02:38:53
Elapsed 12:24:11
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/align/pseudo_reps/rep1/pr1/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_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/ZNF416/out/align/pseudo_reps/rep1/pr1/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 160 --keep-dup all -B --SPMR

# SYS command. line 78

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_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/ZNF416/out/align/pseudo_reps/rep1/pr1/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 160 --keep-dup all

# SYS command. line 91

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_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/ZNF416/out/align/pseudo_reps/rep1/pr1/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_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--------------------
11548 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
INFO  @ Thu, 22 Dec 2016 02:20:29: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/align/pseudo_reps/rep1/pr1/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 160 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/align/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Thu, 22 Dec 2016 02:20:29: #1 read tag files... 
INFO  @ Thu, 22 Dec 2016 02:20:29: #1 read treatment tags... 
INFO  @ Thu, 22 Dec 2016 02:20:31:  1000000 
INFO  @ Thu, 22 Dec 2016 02:20:33:  2000000 
INFO  @ Thu, 22 Dec 2016 02:20:34: #1.2 read input tags... 
INFO  @ Thu, 22 Dec 2016 02:20:36:  1000000 
INFO  @ Thu, 22 Dec 2016 02:20:38:  2000000 
INFO  @ Thu, 22 Dec 2016 02:20:39:  3000000 
INFO  @ Thu, 22 Dec 2016 02:20:41:  4000000 
INFO  @ Thu, 22 Dec 2016 02:20:42:  5000000 
INFO  @ Thu, 22 Dec 2016 02:20:44:  6000000 
INFO  @ Thu, 22 Dec 2016 02:20:45:  7000000 
INFO  @ Thu, 22 Dec 2016 02:20:47:  8000000 
INFO  @ Thu, 22 Dec 2016 02:20:49:  9000000 
INFO  @ Thu, 22 Dec 2016 02:20:50:  10000000 
INFO  @ Thu, 22 Dec 2016 02:20:52:  11000000 
INFO  @ Thu, 22 Dec 2016 02:20:53:  12000000 
INFO  @ Thu, 22 Dec 2016 02:20:55:  13000000 
INFO  @ Thu, 22 Dec 2016 02:20:57:  14000000 
INFO  @ Thu, 22 Dec 2016 02:20:58:  15000000 
INFO  @ Thu, 22 Dec 2016 02:21:00:  16000000 
INFO  @ Thu, 22 Dec 2016 02:21:01:  17000000 
INFO  @ Thu, 22 Dec 2016 02:21:03:  18000000 
INFO  @ Thu, 22 Dec 2016 02:21:05:  19000000 
INFO  @ Thu, 22 Dec 2016 02:21:06:  20000000 
INFO  @ Thu, 22 Dec 2016 02:21:08:  21000000 
INFO  @ Thu, 22 Dec 2016 02:21:09:  22000000 
INFO  @ Thu, 22 Dec 2016 02:21:11:  23000000 
INFO  @ Thu, 22 Dec 2016 02:21:12:  24000000 
INFO  @ Thu, 22 Dec 2016 02:21:14:  25000000 
INFO  @ Thu, 22 Dec 2016 02:21:16:  26000000 
INFO  @ Thu, 22 Dec 2016 02:21:17:  27000000 
INFO  @ Thu, 22 Dec 2016 02:21:19:  28000000 
INFO  @ Thu, 22 Dec 2016 02:21:20:  29000000 
INFO  @ Thu, 22 Dec 2016 02:21:22:  30000000 
INFO  @ Thu, 22 Dec 2016 02:21:24:  31000000 
INFO  @ Thu, 22 Dec 2016 02:21:25:  32000000 
INFO  @ Thu, 22 Dec 2016 02:21:27:  33000000 
INFO  @ Thu, 22 Dec 2016 02:21:28:  34000000 
INFO  @ Thu, 22 Dec 2016 02:21:30:  35000000 
INFO  @ Thu, 22 Dec 2016 02:21:31:  36000000 
INFO  @ Thu, 22 Dec 2016 02:21:33:  37000000 
INFO  @ Thu, 22 Dec 2016 02:21:34:  38000000 
INFO  @ Thu, 22 Dec 2016 02:21:36:  39000000 
INFO  @ Thu, 22 Dec 2016 02:21:38:  40000000 
INFO  @ Thu, 22 Dec 2016 02:21:39:  41000000 
INFO  @ Thu, 22 Dec 2016 02:21:41:  42000000 
INFO  @ Thu, 22 Dec 2016 02:21:42:  43000000 
INFO  @ Thu, 22 Dec 2016 02:21:44:  44000000 
INFO  @ Thu, 22 Dec 2016 02:21:45:  45000000 
INFO  @ Thu, 22 Dec 2016 02:21:47:  46000000 
INFO  @ Thu, 22 Dec 2016 02:21:49:  47000000 
INFO  @ Thu, 22 Dec 2016 02:21:50:  48000000 
INFO  @ Thu, 22 Dec 2016 02:21:52:  49000000 
INFO  @ Thu, 22 Dec 2016 02:21:53:  50000000 
INFO  @ Thu, 22 Dec 2016 02:21:55: #1 tag size is determined as 69 bps 
INFO  @ Thu, 22 Dec 2016 02:21:55: #1 tag size = 69 
INFO  @ Thu, 22 Dec 2016 02:21:55: #1  total tags in treatment: 2518009 
INFO  @ Thu, 22 Dec 2016 02:21:55: #1  total tags in control: 50000000 
INFO  @ Thu, 22 Dec 2016 02:21:55: #1 finished! 
INFO  @ Thu, 22 Dec 2016 02:21:55: #2 Build Peak Model... 
INFO  @ Thu, 22 Dec 2016 02:21:55: #2 Skipped... 
INFO  @ Thu, 22 Dec 2016 02:21:55: #2 Use 160 as fragment length 
INFO  @ Thu, 22 Dec 2016 02:21:55: #3 Call peaks... 
INFO  @ Thu, 22 Dec 2016 02:21:55: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 22 Dec 2016 02:21:55: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 22 Dec 2016 02:26:05: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 22 Dec 2016 02:26:05: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 22 Dec 2016 02:26:05: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Thu, 22 Dec 2016 02:26:05: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 22 Dec 2016 02:26:05: #3 Call peaks for each chromosome... 
INFO  @ Thu, 22 Dec 2016 02:30:50: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 22 Dec 2016 02:30:51: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 22 Dec 2016 02:30:52: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Thu, 22 Dec 2016 02:30:53: Done! 
INFO  @ Thu, 22 Dec 2016 02:30:57: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/align/pseudo_reps/rep1/pr1/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 160 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/align/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Thu, 22 Dec 2016 02:30:57: #1 read tag files... 
INFO  @ Thu, 22 Dec 2016 02:30:57: #1 read treatment tags... 
INFO  @ Thu, 22 Dec 2016 02:30:59:  1000000 
INFO  @ Thu, 22 Dec 2016 02:31:01:  2000000 
INFO  @ Thu, 22 Dec 2016 02:31:02: #1.2 read input tags... 
INFO  @ Thu, 22 Dec 2016 02:31:03:  1000000 
INFO  @ Thu, 22 Dec 2016 02:31:05:  2000000 
INFO  @ Thu, 22 Dec 2016 02:31:06:  3000000 
INFO  @ Thu, 22 Dec 2016 02:31:08:  4000000 
INFO  @ Thu, 22 Dec 2016 02:31:10:  5000000 
INFO  @ Thu, 22 Dec 2016 02:31:11:  6000000 
INFO  @ Thu, 22 Dec 2016 02:31:13:  7000000 
INFO  @ Thu, 22 Dec 2016 02:31:14:  8000000 
INFO  @ Thu, 22 Dec 2016 02:31:16:  9000000 
INFO  @ Thu, 22 Dec 2016 02:31:17:  10000000 
INFO  @ Thu, 22 Dec 2016 02:31:19:  11000000 
INFO  @ Thu, 22 Dec 2016 02:31:21:  12000000 
INFO  @ Thu, 22 Dec 2016 02:31:22:  13000000 
INFO  @ Thu, 22 Dec 2016 02:31:24:  14000000 
INFO  @ Thu, 22 Dec 2016 02:31:25:  15000000 
INFO  @ Thu, 22 Dec 2016 02:31:27:  16000000 
INFO  @ Thu, 22 Dec 2016 02:31:28:  17000000 
INFO  @ Thu, 22 Dec 2016 02:31:30:  18000000 
INFO  @ Thu, 22 Dec 2016 02:31:32:  19000000 
INFO  @ Thu, 22 Dec 2016 02:31:33:  20000000 
INFO  @ Thu, 22 Dec 2016 02:31:35:  21000000 
INFO  @ Thu, 22 Dec 2016 02:31:37:  22000000 
INFO  @ Thu, 22 Dec 2016 02:31:38:  23000000 
INFO  @ Thu, 22 Dec 2016 02:31:40:  24000000 
INFO  @ Thu, 22 Dec 2016 02:31:42:  25000000 
INFO  @ Thu, 22 Dec 2016 02:31:43:  26000000 
INFO  @ Thu, 22 Dec 2016 02:31:45:  27000000 
INFO  @ Thu, 22 Dec 2016 02:31:47:  28000000 
INFO  @ Thu, 22 Dec 2016 02:31:48:  29000000 
INFO  @ Thu, 22 Dec 2016 02:31:50:  30000000 
INFO  @ Thu, 22 Dec 2016 02:31:52:  31000000 
INFO  @ Thu, 22 Dec 2016 02:31:53:  32000000 
INFO  @ Thu, 22 Dec 2016 02:31:55:  33000000 
INFO  @ Thu, 22 Dec 2016 02:31:57:  34000000 
INFO  @ Thu, 22 Dec 2016 02:31:58:  35000000 
INFO  @ Thu, 22 Dec 2016 02:32:00:  36000000 
INFO  @ Thu, 22 Dec 2016 02:32:02:  37000000 
INFO  @ Thu, 22 Dec 2016 02:32:03:  38000000 
INFO  @ Thu, 22 Dec 2016 02:32:05:  39000000 
INFO  @ Thu, 22 Dec 2016 02:32:07:  40000000 
INFO  @ Thu, 22 Dec 2016 02:32:08:  41000000 
INFO  @ Thu, 22 Dec 2016 02:32:10:  42000000 
INFO  @ Thu, 22 Dec 2016 02:32:12:  43000000 
INFO  @ Thu, 22 Dec 2016 02:32:13:  44000000 
INFO  @ Thu, 22 Dec 2016 02:32:15:  45000000 
INFO  @ Thu, 22 Dec 2016 02:32:17:  46000000 
INFO  @ Thu, 22 Dec 2016 02:32:18:  47000000 
INFO  @ Thu, 22 Dec 2016 02:32:20:  48000000 
INFO  @ Thu, 22 Dec 2016 02:32:22:  49000000 
INFO  @ Thu, 22 Dec 2016 02:32:23:  50000000 
INFO  @ Thu, 22 Dec 2016 02:32:25: #1 tag size is determined as 69 bps 
INFO  @ Thu, 22 Dec 2016 02:32:25: #1 tag size = 69 
INFO  @ Thu, 22 Dec 2016 02:32:25: #1  total tags in treatment: 2518009 
INFO  @ Thu, 22 Dec 2016 02:32:25: #1  total tags in control: 50000000 
INFO  @ Thu, 22 Dec 2016 02:32:25: #1 finished! 
INFO  @ Thu, 22 Dec 2016 02:32:25: #2 Build Peak Model... 
INFO  @ Thu, 22 Dec 2016 02:32:25: #2 Skipped... 
INFO  @ Thu, 22 Dec 2016 02:32:25: #2 Use 160 as fragment length 
INFO  @ Thu, 22 Dec 2016 02:32:25: #3 Call peaks... 
INFO  @ Thu, 22 Dec 2016 02:32:25: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 22 Dec 2016 02:32:25: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 22 Dec 2016 02:35:36: #3 Call peaks for each chromosome... 
INFO  @ Thu, 22 Dec 2016 02:38:13: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 22 Dec 2016 02:38:21: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Thu, 22 Dec 2016 02:38:26: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370905_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 22 Dec 2016 02:38:31: Done!
Num 3
ID task.callpeak_macs2.macs2_rep1_pr2.line_67.id_12
Name macs2 rep1-pr2
Thread thread_Root
PID 19490
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2016-12-21 14:14:44
End 2016-12-22 02:48:53
Elapsed 12:34:08
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/align/pseudo_reps/rep1/pr2/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_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/ZNF416/out/align/pseudo_reps/rep1/pr2/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 160 --keep-dup all -B --SPMR

# SYS command. line 78

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_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/ZNF416/out/align/pseudo_reps/rep1/pr2/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 160 --keep-dup all

# SYS command. line 91

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_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/ZNF416/out/align/pseudo_reps/rep1/pr2/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_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--------------------
12115 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
INFO  @ Thu, 22 Dec 2016 02:29:00: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/align/pseudo_reps/rep1/pr2/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 160 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/align/pseudo_reps/rep1/pr2/SRR1370905_1.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Thu, 22 Dec 2016 02:29:00: #1 read tag files... 
INFO  @ Thu, 22 Dec 2016 02:29:00: #1 read treatment tags... 
INFO  @ Thu, 22 Dec 2016 02:29:02:  1000000 
INFO  @ Thu, 22 Dec 2016 02:29:04:  2000000 
INFO  @ Thu, 22 Dec 2016 02:29:05: #1.2 read input tags... 
INFO  @ Thu, 22 Dec 2016 02:29:07:  1000000 
INFO  @ Thu, 22 Dec 2016 02:29:08:  2000000 
INFO  @ Thu, 22 Dec 2016 02:29:10:  3000000 
INFO  @ Thu, 22 Dec 2016 02:29:11:  4000000 
INFO  @ Thu, 22 Dec 2016 02:29:13:  5000000 
INFO  @ Thu, 22 Dec 2016 02:29:14:  6000000 
INFO  @ Thu, 22 Dec 2016 02:29:16:  7000000 
INFO  @ Thu, 22 Dec 2016 02:29:18:  8000000 
INFO  @ Thu, 22 Dec 2016 02:29:19:  9000000 
INFO  @ Thu, 22 Dec 2016 02:29:21:  10000000 
INFO  @ Thu, 22 Dec 2016 02:29:22:  11000000 
INFO  @ Thu, 22 Dec 2016 02:29:24:  12000000 
INFO  @ Thu, 22 Dec 2016 02:29:25:  13000000 
INFO  @ Thu, 22 Dec 2016 02:29:27:  14000000 
INFO  @ Thu, 22 Dec 2016 02:29:28:  15000000 
INFO  @ Thu, 22 Dec 2016 02:29:30:  16000000 
INFO  @ Thu, 22 Dec 2016 02:29:32:  17000000 
INFO  @ Thu, 22 Dec 2016 02:29:33:  18000000 
INFO  @ Thu, 22 Dec 2016 02:29:35:  19000000 
INFO  @ Thu, 22 Dec 2016 02:29:36:  20000000 
INFO  @ Thu, 22 Dec 2016 02:29:38:  21000000 
INFO  @ Thu, 22 Dec 2016 02:29:39:  22000000 
INFO  @ Thu, 22 Dec 2016 02:29:41:  23000000 
INFO  @ Thu, 22 Dec 2016 02:29:43:  24000000 
INFO  @ Thu, 22 Dec 2016 02:29:44:  25000000 
INFO  @ Thu, 22 Dec 2016 02:29:46:  26000000 
INFO  @ Thu, 22 Dec 2016 02:29:47:  27000000 
INFO  @ Thu, 22 Dec 2016 02:29:49:  28000000 
INFO  @ Thu, 22 Dec 2016 02:29:50:  29000000 
INFO  @ Thu, 22 Dec 2016 02:29:52:  30000000 
INFO  @ Thu, 22 Dec 2016 02:29:54:  31000000 
INFO  @ Thu, 22 Dec 2016 02:29:55:  32000000 
INFO  @ Thu, 22 Dec 2016 02:29:57:  33000000 
INFO  @ Thu, 22 Dec 2016 02:29:58:  34000000 
INFO  @ Thu, 22 Dec 2016 02:30:00:  35000000 
INFO  @ Thu, 22 Dec 2016 02:30:01:  36000000 
INFO  @ Thu, 22 Dec 2016 02:30:03:  37000000 
INFO  @ Thu, 22 Dec 2016 02:30:05:  38000000 
INFO  @ Thu, 22 Dec 2016 02:30:06:  39000000 
INFO  @ Thu, 22 Dec 2016 02:30:08:  40000000 
INFO  @ Thu, 22 Dec 2016 02:30:09:  41000000 
INFO  @ Thu, 22 Dec 2016 02:30:11:  42000000 
INFO  @ Thu, 22 Dec 2016 02:30:12:  43000000 
INFO  @ Thu, 22 Dec 2016 02:30:14:  44000000 
INFO  @ Thu, 22 Dec 2016 02:30:15:  45000000 
INFO  @ Thu, 22 Dec 2016 02:30:17:  46000000 
INFO  @ Thu, 22 Dec 2016 02:30:19:  47000000 
INFO  @ Thu, 22 Dec 2016 02:30:20:  48000000 
INFO  @ Thu, 22 Dec 2016 02:30:22:  49000000 
INFO  @ Thu, 22 Dec 2016 02:30:23:  50000000 
INFO  @ Thu, 22 Dec 2016 02:30:25: #1 tag size is determined as 69 bps 
INFO  @ Thu, 22 Dec 2016 02:30:25: #1 tag size = 69 
INFO  @ Thu, 22 Dec 2016 02:30:25: #1  total tags in treatment: 2518009 
INFO  @ Thu, 22 Dec 2016 02:30:25: #1  total tags in control: 50000000 
INFO  @ Thu, 22 Dec 2016 02:30:25: #1 finished! 
INFO  @ Thu, 22 Dec 2016 02:30:25: #2 Build Peak Model... 
INFO  @ Thu, 22 Dec 2016 02:30:25: #2 Skipped... 
INFO  @ Thu, 22 Dec 2016 02:30:25: #2 Use 160 as fragment length 
INFO  @ Thu, 22 Dec 2016 02:30:25: #3 Call peaks... 
INFO  @ Thu, 22 Dec 2016 02:30:25: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 22 Dec 2016 02:30:25: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 22 Dec 2016 02:34:36: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 22 Dec 2016 02:34:36: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 22 Dec 2016 02:34:36: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Thu, 22 Dec 2016 02:34:36: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 22 Dec 2016 02:34:36: #3 Call peaks for each chromosome... 
INFO  @ Thu, 22 Dec 2016 02:40:20: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 22 Dec 2016 02:40:21: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 22 Dec 2016 02:40:22: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Thu, 22 Dec 2016 02:40:23: Done! 
INFO  @ Thu, 22 Dec 2016 02:40:26: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/align/pseudo_reps/rep1/pr2/SRR1370905_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/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 160 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/align/pseudo_reps/rep1/pr2/SRR1370905_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 02:40:26: #1 read tag files... 
INFO  @ Thu, 22 Dec 2016 02:40:26: #1 read treatment tags... 
INFO  @ Thu, 22 Dec 2016 02:40:28:  1000000 
INFO  @ Thu, 22 Dec 2016 02:40:30:  2000000 
INFO  @ Thu, 22 Dec 2016 02:40:31: #1.2 read input tags... 
INFO  @ Thu, 22 Dec 2016 02:40:33:  1000000 
INFO  @ Thu, 22 Dec 2016 02:40:34:  2000000 
INFO  @ Thu, 22 Dec 2016 02:40:36:  3000000 
INFO  @ Thu, 22 Dec 2016 02:40:38:  4000000 
INFO  @ Thu, 22 Dec 2016 02:40:39:  5000000 
INFO  @ Thu, 22 Dec 2016 02:40:41:  6000000 
INFO  @ Thu, 22 Dec 2016 02:40:43:  7000000 
INFO  @ Thu, 22 Dec 2016 02:40:44:  8000000 
INFO  @ Thu, 22 Dec 2016 02:40:46:  9000000 
INFO  @ Thu, 22 Dec 2016 02:40:47:  10000000 
INFO  @ Thu, 22 Dec 2016 02:40:49:  11000000 
INFO  @ Thu, 22 Dec 2016 02:40:51:  12000000 
INFO  @ Thu, 22 Dec 2016 02:40:52:  13000000 
INFO  @ Thu, 22 Dec 2016 02:40:54:  14000000 
INFO  @ Thu, 22 Dec 2016 02:40:56:  15000000 
INFO  @ Thu, 22 Dec 2016 02:40:57:  16000000 
INFO  @ Thu, 22 Dec 2016 02:40:59:  17000000 
INFO  @ Thu, 22 Dec 2016 02:41:01:  18000000 
INFO  @ Thu, 22 Dec 2016 02:41:02:  19000000 
INFO  @ Thu, 22 Dec 2016 02:41:04:  20000000 
INFO  @ Thu, 22 Dec 2016 02:41:06:  21000000 
INFO  @ Thu, 22 Dec 2016 02:41:07:  22000000 
INFO  @ Thu, 22 Dec 2016 02:41:09:  23000000 
INFO  @ Thu, 22 Dec 2016 02:41:10:  24000000 
INFO  @ Thu, 22 Dec 2016 02:41:12:  25000000 
INFO  @ Thu, 22 Dec 2016 02:41:14:  26000000 
INFO  @ Thu, 22 Dec 2016 02:41:15:  27000000 
INFO  @ Thu, 22 Dec 2016 02:41:17:  28000000 
INFO  @ Thu, 22 Dec 2016 02:41:19:  29000000 
INFO  @ Thu, 22 Dec 2016 02:41:20:  30000000 
INFO  @ Thu, 22 Dec 2016 02:41:22:  31000000 
INFO  @ Thu, 22 Dec 2016 02:41:23:  32000000 
INFO  @ Thu, 22 Dec 2016 02:41:25:  33000000 
INFO  @ Thu, 22 Dec 2016 02:41:27:  34000000 
INFO  @ Thu, 22 Dec 2016 02:41:28:  35000000 
INFO  @ Thu, 22 Dec 2016 02:41:30:  36000000 
INFO  @ Thu, 22 Dec 2016 02:41:32:  37000000 
INFO  @ Thu, 22 Dec 2016 02:41:34:  38000000 
INFO  @ Thu, 22 Dec 2016 02:41:35:  39000000 
INFO  @ Thu, 22 Dec 2016 02:41:37:  40000000 
INFO  @ Thu, 22 Dec 2016 02:41:39:  41000000 
INFO  @ Thu, 22 Dec 2016 02:41:40:  42000000 
INFO  @ Thu, 22 Dec 2016 02:41:42:  43000000 
INFO  @ Thu, 22 Dec 2016 02:41:43:  44000000 
INFO  @ Thu, 22 Dec 2016 02:41:45:  45000000 
INFO  @ Thu, 22 Dec 2016 02:41:47:  46000000 
INFO  @ Thu, 22 Dec 2016 02:41:48:  47000000 
INFO  @ Thu, 22 Dec 2016 02:41:50:  48000000 
INFO  @ Thu, 22 Dec 2016 02:41:52:  49000000 
INFO  @ Thu, 22 Dec 2016 02:41:53:  50000000 
INFO  @ Thu, 22 Dec 2016 02:41:55: #1 tag size is determined as 69 bps 
INFO  @ Thu, 22 Dec 2016 02:41:55: #1 tag size = 69 
INFO  @ Thu, 22 Dec 2016 02:41:55: #1  total tags in treatment: 2518009 
INFO  @ Thu, 22 Dec 2016 02:41:55: #1  total tags in control: 50000000 
INFO  @ Thu, 22 Dec 2016 02:41:55: #1 finished! 
INFO  @ Thu, 22 Dec 2016 02:41:55: #2 Build Peak Model... 
INFO  @ Thu, 22 Dec 2016 02:41:55: #2 Skipped... 
INFO  @ Thu, 22 Dec 2016 02:41:55: #2 Use 160 as fragment length 
INFO  @ Thu, 22 Dec 2016 02:41:55: #3 Call peaks... 
INFO  @ Thu, 22 Dec 2016 02:41:55: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 22 Dec 2016 02:41:55: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 22 Dec 2016 02:45:06: #3 Call peaks for each chromosome... 
INFO  @ Thu, 22 Dec 2016 02:48:13: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 22 Dec 2016 02:48:21: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Thu, 22 Dec 2016 02:48:26: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370905_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 22 Dec 2016 02:48:32: Done!

Global scope

Note: Global scope when program finished execution.
Type Name Value
string _ /usr/bin/bds
string _LMFILES_ /software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/samtools/1.2
bool allowEmpty false
string[] args [-title, ZNF416, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF416/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF416/out/align/rep1/SRR1370905_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/ZNF416
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/ZNF416
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 49923.ZNF416.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