Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20161221_141407_680
Start time	2016-12-21 14:14:07
Run time	11:56:13.327
Tasks executed	3
Tasks failed	1
Tasks failed names	macs2 rep1
Arguments*	[-title, ZNF189, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF189/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/align/rep1/SRR1370880_1.bam, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz, -final_stage, idr, $]
System*	sge
Cpus*	-1
Exit value	1

Thread ID	Parent	Tasks
thread_Root	None	chipseq.bds.20161221_141407_680/task.callpeak_macs2.macs2_rep1.line_67.id_10 chipseq.bds.20161221_141407_680/task.callpeak_macs2.macs2_rep1_pr1.line_67.id_11 chipseq.bds.20161221_141407_680/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	19482

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

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

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/align/rep1/SRR1370880_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/ZNF189/out/peak/macs2/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/signal/macs2/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/signal/macs2/rep1/SRR1370880_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/ZNF189/out/align/rep1/SRR1370880_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/ZNF189/out/peak/macs2/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 155 --keep-dup all -B --SPMR

# SYS command. line 78

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/rep1/SRR1370880_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/ZNF189/out/peak/macs2/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 81

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/rep1/SRR1370880_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/ZNF189/out/align/rep1/SRR1370880_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/ZNF189/out/peak/macs2/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 155 --keep-dup all

# SYS command. line 91

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/rep1/SRR1370880_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/ZNF189/out/peak/macs2/rep1/SRR1370880_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/ZNF189/out/peak/macs2/rep1/SRR1370880_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/ZNF189/out/peak/macs2/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 95

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/rep1/SRR1370880_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/ZNF189/out/peak/macs2/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/rep1/SRR1370880_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/ZNF189/out/peak/macs2/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/rep1 -o "SRR1370880_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/ZNF189/out/peak/macs2/rep1/SRR1370880_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/ZNF189/out/peak/macs2/rep1/SRR1370880_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/ZNF189/out/peak/macs2/rep1/SRR1370880_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/ZNF189/out/peak/macs2/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/rep1/SRR1370880_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/ZNF189/out/peak/macs2/rep1/SRR1370880_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/ZNF189/out/signal/macs2/rep1/SRR1370880_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/ZNF189/out/peak/macs2/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/rep1/SRR1370880_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/ZNF189/out/align/rep1/SRR1370880_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/ZNF189/out/peak/macs2/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/rep1 -o "SRR1370880_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/ZNF189/out/peak/macs2/rep1/SRR1370880_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/ZNF189/out/peak/macs2/rep1/SRR1370880_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/ZNF189/out/peak/macs2/rep1/SRR1370880_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/ZNF189/out/peak/macs2/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/rep1/SRR1370880_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/ZNF189/out/peak/macs2/rep1/SRR1370880_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/ZNF189/out/signal/macs2/rep1/SRR1370880_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/ZNF189/out/peak/macs2/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/rep1/SRR1370880_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/ZNF189/out/peak/macs2/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/rep1/SRR1370880_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--------------------
61049 (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 00:12:21: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/align/rep1/SRR1370880_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/ZNF189/out/peak/macs2/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 155 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/align/rep1/SRR1370880_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 00:12:21: #1 read tag files... 
INFO  @ Thu, 22 Dec 2016 00:12:21: #1 read treatment tags... 
INFO  @ Thu, 22 Dec 2016 00:12:28:  1000000 
INFO  @ Thu, 22 Dec 2016 00:12:36:  2000000 
INFO  @ Thu, 22 Dec 2016 00:12:43:  3000000 
INFO  @ Thu, 22 Dec 2016 00:12:51:  4000000 
INFO  @ Thu, 22 Dec 2016 00:12:58:  5000000 
INFO  @ Thu, 22 Dec 2016 00:13:06:  6000000 
INFO  @ Thu, 22 Dec 2016 00:13:13:  7000000 
INFO  @ Thu, 22 Dec 2016 00:13:20:  8000000 
INFO  @ Thu, 22 Dec 2016 00:13:28:  9000000 
INFO  @ Thu, 22 Dec 2016 00:13:35:  10000000 
INFO  @ Thu, 22 Dec 2016 00:13:43:  11000000 
INFO  @ Thu, 22 Dec 2016 00:13:50:  12000000 
INFO  @ Thu, 22 Dec 2016 00:13:58:  13000000 
INFO  @ Thu, 22 Dec 2016 00:14:05:  14000000 
INFO  @ Thu, 22 Dec 2016 00:14:13:  15000000 
INFO  @ Thu, 22 Dec 2016 00:14:20:  16000000 
INFO  @ Thu, 22 Dec 2016 00:14:28:  17000000 
INFO  @ Thu, 22 Dec 2016 00:14:36:  18000000 
INFO  @ Thu, 22 Dec 2016 00:14:43:  19000000 
INFO  @ Thu, 22 Dec 2016 00:14:51:  20000000 
INFO  @ Thu, 22 Dec 2016 00:14:57: #1.2 read input tags... 
INFO  @ Thu, 22 Dec 2016 00:15:05:  1000000 
INFO  @ Thu, 22 Dec 2016 00:15:12:  2000000 
INFO  @ Thu, 22 Dec 2016 00:15:20:  3000000 
INFO  @ Thu, 22 Dec 2016 00:15:27:  4000000 
INFO  @ Thu, 22 Dec 2016 00:15:35:  5000000 
INFO  @ Thu, 22 Dec 2016 00:15:43:  6000000 
INFO  @ Thu, 22 Dec 2016 00:15:50:  7000000 
INFO  @ Thu, 22 Dec 2016 00:15:58:  8000000 
INFO  @ Thu, 22 Dec 2016 00:16:05:  9000000 
INFO  @ Thu, 22 Dec 2016 00:16:13:  10000000 
INFO  @ Thu, 22 Dec 2016 00:16:20:  11000000 
INFO  @ Thu, 22 Dec 2016 00:16:28:  12000000 
INFO  @ Thu, 22 Dec 2016 00:16:35:  13000000 
INFO  @ Thu, 22 Dec 2016 00:16:43:  14000000 
INFO  @ Thu, 22 Dec 2016 00:16:50:  15000000 
INFO  @ Thu, 22 Dec 2016 00:16:58:  16000000 
INFO  @ Thu, 22 Dec 2016 00:17:05:  17000000 
INFO  @ Thu, 22 Dec 2016 00:17:13:  18000000 
INFO  @ Thu, 22 Dec 2016 00:17:21:  19000000 
INFO  @ Thu, 22 Dec 2016 00:17:28:  20000000 
INFO  @ Thu, 22 Dec 2016 00:17:36:  21000000 
INFO  @ Thu, 22 Dec 2016 00:17:43:  22000000 
INFO  @ Thu, 22 Dec 2016 00:17:51:  23000000 
INFO  @ Thu, 22 Dec 2016 00:17:58:  24000000 
INFO  @ Thu, 22 Dec 2016 00:18:06:  25000000 
INFO  @ Thu, 22 Dec 2016 00:18:13:  26000000 
INFO  @ Thu, 22 Dec 2016 00:18:21:  27000000 
INFO  @ Thu, 22 Dec 2016 00:18:28:  28000000 
INFO  @ Thu, 22 Dec 2016 00:18:36:  29000000 
INFO  @ Thu, 22 Dec 2016 00:18:43:  30000000 
INFO  @ Thu, 22 Dec 2016 00:18:51:  31000000 
INFO  @ Thu, 22 Dec 2016 00:18:58:  32000000 
INFO  @ Thu, 22 Dec 2016 00:19:06:  33000000 
INFO  @ Thu, 22 Dec 2016 00:19:13:  34000000 
INFO  @ Thu, 22 Dec 2016 00:19:21:  35000000 
INFO  @ Thu, 22 Dec 2016 00:19:28:  36000000 
INFO  @ Thu, 22 Dec 2016 00:19:36:  37000000 
INFO  @ Thu, 22 Dec 2016 00:19:44:  38000000 
INFO  @ Thu, 22 Dec 2016 00:19:51:  39000000 
INFO  @ Thu, 22 Dec 2016 00:19:59:  40000000 
INFO  @ Thu, 22 Dec 2016 00:20:06:  41000000 
INFO  @ Thu, 22 Dec 2016 00:20:14:  42000000 
INFO  @ Thu, 22 Dec 2016 00:20:21:  43000000 
INFO  @ Thu, 22 Dec 2016 00:20:29:  44000000 
INFO  @ Thu, 22 Dec 2016 00:20:36:  45000000 
INFO  @ Thu, 22 Dec 2016 00:20:44:  46000000 
INFO  @ Thu, 22 Dec 2016 00:20:51:  47000000 
INFO  @ Thu, 22 Dec 2016 00:20:59:  48000000 
INFO  @ Thu, 22 Dec 2016 00:21:06:  49000000 
INFO  @ Thu, 22 Dec 2016 00:21:14:  50000000 
INFO  @ Thu, 22 Dec 2016 00:21:18: #1 tag size is determined as 50 bps 
INFO  @ Thu, 22 Dec 2016 00:21:18: #1 tag size = 50 
INFO  @ Thu, 22 Dec 2016 00:21:18: #1  total tags in treatment: 20777944 
INFO  @ Thu, 22 Dec 2016 00:21:18: #1  total tags in control: 50000000 
INFO  @ Thu, 22 Dec 2016 00:21:18: #1 finished! 
INFO  @ Thu, 22 Dec 2016 00:21:18: #2 Build Peak Model... 
INFO  @ Thu, 22 Dec 2016 00:21:18: #2 Skipped... 
INFO  @ Thu, 22 Dec 2016 00:21:18: #2 Use 155 as fragment length 
INFO  @ Thu, 22 Dec 2016 00:21:18: #3 Call peaks... 
INFO  @ Thu, 22 Dec 2016 00:21:18: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 22 Dec 2016 00:21:18: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 22 Dec 2016 00:29:54: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 22 Dec 2016 00:29:54: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 22 Dec 2016 00:29:54: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Thu, 22 Dec 2016 00:29:54: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 22 Dec 2016 00:29:54: #3 Call peaks for each chromosome... 
INFO  @ Thu, 22 Dec 2016 00:50:38: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 22 Dec 2016 00:50:42: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 22 Dec 2016 00:50:45: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Thu, 22 Dec 2016 00:50:47: Done! 
INFO  @ Thu, 22 Dec 2016 00:50:55: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/align/rep1/SRR1370880_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/ZNF189/out/peak/macs2/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 155 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/align/rep1/SRR1370880_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 00:50:55: #1 read tag files... 
INFO  @ Thu, 22 Dec 2016 00:50:55: #1 read treatment tags... 
INFO  @ Thu, 22 Dec 2016 00:51:02:  1000000 
INFO  @ Thu, 22 Dec 2016 00:51:10:  2000000 
INFO  @ Thu, 22 Dec 2016 00:51:18:  3000000 
INFO  @ Thu, 22 Dec 2016 00:51:26:  4000000 
INFO  @ Thu, 22 Dec 2016 00:51:33:  5000000 
INFO  @ Thu, 22 Dec 2016 00:51:41:  6000000 
INFO  @ Thu, 22 Dec 2016 00:51:48:  7000000 
INFO  @ Thu, 22 Dec 2016 00:51:56:  8000000 
INFO  @ Thu, 22 Dec 2016 00:52:03:  9000000 
INFO  @ Thu, 22 Dec 2016 00:52:11:  10000000 
INFO  @ Thu, 22 Dec 2016 00:52:19:  11000000 
INFO  @ Thu, 22 Dec 2016 00:52:26:  12000000 
INFO  @ Thu, 22 Dec 2016 00:52:34:  13000000 
INFO  @ Thu, 22 Dec 2016 00:52:42:  14000000 
INFO  @ Thu, 22 Dec 2016 00:52:49:  15000000 
INFO  @ Thu, 22 Dec 2016 00:52:57:  16000000 
INFO  @ Thu, 22 Dec 2016 00:53:05:  17000000 
INFO  @ Thu, 22 Dec 2016 00:53:13:  18000000 
INFO  @ Thu, 22 Dec 2016 00:53:20:  19000000 
INFO  @ Thu, 22 Dec 2016 00:53:28:  20000000 
INFO  @ Thu, 22 Dec 2016 00:53:35: #1.2 read input tags... 
INFO  @ Thu, 22 Dec 2016 00:53:42:  1000000 
INFO  @ Thu, 22 Dec 2016 00:53:50:  2000000 
INFO  @ Thu, 22 Dec 2016 00:53:58:  3000000 
INFO  @ Thu, 22 Dec 2016 00:54:05:  4000000 
INFO  @ Thu, 22 Dec 2016 00:54:13:  5000000 
INFO  @ Thu, 22 Dec 2016 00:54:21:  6000000 
INFO  @ Thu, 22 Dec 2016 00:54:29:  7000000 
INFO  @ Thu, 22 Dec 2016 00:54:36:  8000000 
INFO  @ Thu, 22 Dec 2016 00:54:44:  9000000 
INFO  @ Thu, 22 Dec 2016 00:54:52:  10000000 
INFO  @ Thu, 22 Dec 2016 00:55:00:  11000000 
INFO  @ Thu, 22 Dec 2016 00:55:07:  12000000 
INFO  @ Thu, 22 Dec 2016 00:55:15:  13000000 
INFO  @ Thu, 22 Dec 2016 00:55:23:  14000000 
INFO  @ Thu, 22 Dec 2016 00:55:30:  15000000 
INFO  @ Thu, 22 Dec 2016 00:55:38:  16000000 
INFO  @ Thu, 22 Dec 2016 00:55:46:  17000000 
INFO  @ Thu, 22 Dec 2016 00:55:54:  18000000 
INFO  @ Thu, 22 Dec 2016 00:56:02:  19000000 
INFO  @ Thu, 22 Dec 2016 00:56:09:  20000000 
INFO  @ Thu, 22 Dec 2016 00:56:17:  21000000 
INFO  @ Thu, 22 Dec 2016 00:56:25:  22000000 
INFO  @ Thu, 22 Dec 2016 00:56:33:  23000000 
INFO  @ Thu, 22 Dec 2016 00:56:41:  24000000 
INFO  @ Thu, 22 Dec 2016 00:56:49:  25000000 
INFO  @ Thu, 22 Dec 2016 00:56:56:  26000000 
INFO  @ Thu, 22 Dec 2016 00:57:04:  27000000 
INFO  @ Thu, 22 Dec 2016 00:57:12:  28000000 
INFO  @ Thu, 22 Dec 2016 00:57:20:  29000000 
INFO  @ Thu, 22 Dec 2016 00:57:28:  30000000 
INFO  @ Thu, 22 Dec 2016 00:57:36:  31000000 
INFO  @ Thu, 22 Dec 2016 00:57:44:  32000000 
INFO  @ Thu, 22 Dec 2016 00:57:52:  33000000 
INFO  @ Thu, 22 Dec 2016 00:57:59:  34000000 
INFO  @ Thu, 22 Dec 2016 00:58:07:  35000000 
INFO  @ Thu, 22 Dec 2016 00:58:15:  36000000 
INFO  @ Thu, 22 Dec 2016 00:58:23:  37000000 
INFO  @ Thu, 22 Dec 2016 00:58:31:  38000000 
INFO  @ Thu, 22 Dec 2016 00:58:38:  39000000 
INFO  @ Thu, 22 Dec 2016 00:58:46:  40000000 
INFO  @ Thu, 22 Dec 2016 00:58:54:  41000000 
INFO  @ Thu, 22 Dec 2016 00:59:02:  42000000 
INFO  @ Thu, 22 Dec 2016 00:59:09:  43000000 
INFO  @ Thu, 22 Dec 2016 00:59:17:  44000000 
INFO  @ Thu, 22 Dec 2016 00:59:25:  45000000 
INFO  @ Thu, 22 Dec 2016 00:59:32:  46000000 
INFO  @ Thu, 22 Dec 2016 00:59:40:  47000000 
INFO  @ Thu, 22 Dec 2016 00:59:48:  48000000 
INFO  @ Thu, 22 Dec 2016 00:59:55:  49000000 
INFO  @ Thu, 22 Dec 2016 01:00:03:  50000000 
INFO  @ Thu, 22 Dec 2016 01:00:08: #1 tag size is determined as 50 bps 
INFO  @ Thu, 22 Dec 2016 01:00:08: #1 tag size = 50 
INFO  @ Thu, 22 Dec 2016 01:00:08: #1  total tags in treatment: 20777944 
INFO  @ Thu, 22 Dec 2016 01:00:08: #1  total tags in control: 50000000 
INFO  @ Thu, 22 Dec 2016 01:00:08: #1 finished! 
INFO  @ Thu, 22 Dec 2016 01:00:08: #2 Build Peak Model... 
INFO  @ Thu, 22 Dec 2016 01:00:08: #2 Skipped... 
INFO  @ Thu, 22 Dec 2016 01:00:08: #2 Use 155 as fragment length 
INFO  @ Thu, 22 Dec 2016 01:00:08: #3 Call peaks... 
INFO  @ Thu, 22 Dec 2016 01:00:08: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 22 Dec 2016 01:00:08: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 22 Dec 2016 01:09:02: #3 Call peaks for each chromosome... 
INFO  @ Thu, 22 Dec 2016 01:17:27: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 22 Dec 2016 01:17:42: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Thu, 22 Dec 2016 01:17:53: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/rep1/SRR1370880_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 22 Dec 2016 01:18:02: Done! 
INFO  @ Thu, 22 Dec 2016 01:18:30: Read and build treatment bedGraph... 
INFO  @ Thu, 22 Dec 2016 01:21:40: Read and build control bedGraph... 
INFO  @ Thu, 22 Dec 2016 01:29:32: Build scoreTrackII... 
INFO  @ Thu, 22 Dec 2016 01:32:26: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Thu, 22 Dec 2016 01:57:51: Write bedGraph of scores... 
INFO  @ Thu, 22 Dec 2016 02:10:18: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/rep1/SRR1370880_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:                 19482
submission_time:            Wed Dec 21 14:14:14 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/ZNF189
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/chipseq.bds.20161221_141407_680/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/ZNF189/chipseq.bds.20161221_141407_680/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=48010.ZNF189.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/ZNF189,JAVA_HOME=/usr/lib/jvm/java-8-oracle,LOADEDMODULES=modsappsdir/modsappsdir:samtools/1.2,SSH_CONNECTION=171.65.77.8 32898 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,MANPATH=/software/samtools/samtools-1.2/share/man:/usr/share/man,MODULEPATH=/usr/local/Modules/versions				:/usr/local/Modules/$MODULE_VERSION/modulefiles	:/modules/				:/software/modulefiles,MODULESAPPSDIR=/software,MODULESHOME=/software/env_module/3.2.10
scheduling info:            queue instance "q@kali" dropped because it is temporarily not available
                            queue instance "q@surya" dropped because it is disabled
                            queue instance "amd.q@wotan" dropped because it is full
                            queue instance "q@nandi" dropped because it is full
                            queue instance "q@kadru" dropped because it is full
                            All queues dropped because of overload or full

Num	2
ID	task.callpeak_macs2.macs2_rep1_pr1.line_67.id_11
Name	macs2 rep1-pr1
Thread	thread_Root
PID	19483

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

Start	2016-12-21 14:14:16
End	2016-12-22 01:08:21
Elapsed	10:54:04
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/align/pseudo_reps/rep1/pr1/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_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/ZNF189/out/align/pseudo_reps/rep1/pr1/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 155 --keep-dup all -B --SPMR

# SYS command. line 78

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_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/ZNF189/out/align/pseudo_reps/rep1/pr1/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 155 --keep-dup all

# SYS command. line 91

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_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/ZNF189/out/align/pseudo_reps/rep1/pr1/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_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--------------------
10035 (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 00:33:30: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/align/pseudo_reps/rep1/pr1/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 155 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/align/pseudo_reps/rep1/pr1/SRR1370880_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 00:33:30: #1 read tag files... 
INFO  @ Thu, 22 Dec 2016 00:33:30: #1 read treatment tags... 
INFO  @ Thu, 22 Dec 2016 00:33:31:  1000000 
INFO  @ Thu, 22 Dec 2016 00:33:33:  2000000 
INFO  @ Thu, 22 Dec 2016 00:33:35:  3000000 
INFO  @ Thu, 22 Dec 2016 00:33:37:  4000000 
INFO  @ Thu, 22 Dec 2016 00:33:38:  5000000 
INFO  @ Thu, 22 Dec 2016 00:33:40:  6000000 
INFO  @ Thu, 22 Dec 2016 00:33:42:  7000000 
INFO  @ Thu, 22 Dec 2016 00:33:43:  8000000 
INFO  @ Thu, 22 Dec 2016 00:33:45:  9000000 
INFO  @ Thu, 22 Dec 2016 00:33:47:  10000000 
INFO  @ Thu, 22 Dec 2016 00:33:48: #1.2 read input tags... 
INFO  @ Thu, 22 Dec 2016 00:33:50:  1000000 
INFO  @ Thu, 22 Dec 2016 00:33:51:  2000000 
INFO  @ Thu, 22 Dec 2016 00:33:53:  3000000 
INFO  @ Thu, 22 Dec 2016 00:33:54:  4000000 
INFO  @ Thu, 22 Dec 2016 00:33:56:  5000000 
INFO  @ Thu, 22 Dec 2016 00:33:58:  6000000 
INFO  @ Thu, 22 Dec 2016 00:33:59:  7000000 
INFO  @ Thu, 22 Dec 2016 00:34:01:  8000000 
INFO  @ Thu, 22 Dec 2016 00:34:02:  9000000 
INFO  @ Thu, 22 Dec 2016 00:34:04:  10000000 
INFO  @ Thu, 22 Dec 2016 00:34:06:  11000000 
INFO  @ Thu, 22 Dec 2016 00:34:07:  12000000 
INFO  @ Thu, 22 Dec 2016 00:34:09:  13000000 
INFO  @ Thu, 22 Dec 2016 00:34:11:  14000000 
INFO  @ Thu, 22 Dec 2016 00:34:12:  15000000 
INFO  @ Thu, 22 Dec 2016 00:34:14:  16000000 
INFO  @ Thu, 22 Dec 2016 00:34:16:  17000000 
INFO  @ Thu, 22 Dec 2016 00:34:17:  18000000 
INFO  @ Thu, 22 Dec 2016 00:34:19:  19000000 
INFO  @ Thu, 22 Dec 2016 00:34:21:  20000000 
INFO  @ Thu, 22 Dec 2016 00:34:22:  21000000 
INFO  @ Thu, 22 Dec 2016 00:34:24:  22000000 
INFO  @ Thu, 22 Dec 2016 00:34:25:  23000000 
INFO  @ Thu, 22 Dec 2016 00:34:27:  24000000 
INFO  @ Thu, 22 Dec 2016 00:34:29:  25000000 
INFO  @ Thu, 22 Dec 2016 00:34:30:  26000000 
INFO  @ Thu, 22 Dec 2016 00:34:32:  27000000 
INFO  @ Thu, 22 Dec 2016 00:34:33:  28000000 
INFO  @ Thu, 22 Dec 2016 00:34:35:  29000000 
INFO  @ Thu, 22 Dec 2016 00:34:36:  30000000 
INFO  @ Thu, 22 Dec 2016 00:34:38:  31000000 
INFO  @ Thu, 22 Dec 2016 00:34:39:  32000000 
INFO  @ Thu, 22 Dec 2016 00:34:41:  33000000 
INFO  @ Thu, 22 Dec 2016 00:34:43:  34000000 
INFO  @ Thu, 22 Dec 2016 00:34:44:  35000000 
INFO  @ Thu, 22 Dec 2016 00:34:46:  36000000 
INFO  @ Thu, 22 Dec 2016 00:34:47:  37000000 
INFO  @ Thu, 22 Dec 2016 00:34:49:  38000000 
INFO  @ Thu, 22 Dec 2016 00:34:50:  39000000 
INFO  @ Thu, 22 Dec 2016 00:34:52:  40000000 
INFO  @ Thu, 22 Dec 2016 00:34:54:  41000000 
INFO  @ Thu, 22 Dec 2016 00:34:55:  42000000 
INFO  @ Thu, 22 Dec 2016 00:34:57:  43000000 
INFO  @ Thu, 22 Dec 2016 00:34:59:  44000000 
INFO  @ Thu, 22 Dec 2016 00:35:00:  45000000 
INFO  @ Thu, 22 Dec 2016 00:35:02:  46000000 
INFO  @ Thu, 22 Dec 2016 00:35:03:  47000000 
INFO  @ Thu, 22 Dec 2016 00:35:05:  48000000 
INFO  @ Thu, 22 Dec 2016 00:35:06:  49000000 
INFO  @ Thu, 22 Dec 2016 00:35:08:  50000000 
INFO  @ Thu, 22 Dec 2016 00:35:10: #1 tag size is determined as 49 bps 
INFO  @ Thu, 22 Dec 2016 00:35:10: #1 tag size = 49 
INFO  @ Thu, 22 Dec 2016 00:35:10: #1  total tags in treatment: 10388972 
INFO  @ Thu, 22 Dec 2016 00:35:10: #1  total tags in control: 50000000 
INFO  @ Thu, 22 Dec 2016 00:35:10: #1 finished! 
INFO  @ Thu, 22 Dec 2016 00:35:10: #2 Build Peak Model... 
INFO  @ Thu, 22 Dec 2016 00:35:10: #2 Skipped... 
INFO  @ Thu, 22 Dec 2016 00:35:10: #2 Use 155 as fragment length 
INFO  @ Thu, 22 Dec 2016 00:35:10: #3 Call peaks... 
INFO  @ Thu, 22 Dec 2016 00:35:10: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 22 Dec 2016 00:35:10: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 22 Dec 2016 00:42:57: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 22 Dec 2016 00:42:57: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 22 Dec 2016 00:42:57: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Thu, 22 Dec 2016 00:42:57: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 22 Dec 2016 00:42:57: #3 Call peaks for each chromosome... 
INFO  @ Thu, 22 Dec 2016 00:50:58: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 22 Dec 2016 00:50:58: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 22 Dec 2016 00:50:59: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Thu, 22 Dec 2016 00:51:00: Done! 
INFO  @ Thu, 22 Dec 2016 00:51:06: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/align/pseudo_reps/rep1/pr1/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 155 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/align/pseudo_reps/rep1/pr1/SRR1370880_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 00:51:06: #1 read tag files... 
INFO  @ Thu, 22 Dec 2016 00:51:06: #1 read treatment tags... 
INFO  @ Thu, 22 Dec 2016 00:51:07:  1000000 
INFO  @ Thu, 22 Dec 2016 00:51:09:  2000000 
INFO  @ Thu, 22 Dec 2016 00:51:11:  3000000 
INFO  @ Thu, 22 Dec 2016 00:51:12:  4000000 
INFO  @ Thu, 22 Dec 2016 00:51:14:  5000000 
INFO  @ Thu, 22 Dec 2016 00:51:16:  6000000 
INFO  @ Thu, 22 Dec 2016 00:51:17:  7000000 
INFO  @ Thu, 22 Dec 2016 00:51:19:  8000000 
INFO  @ Thu, 22 Dec 2016 00:51:21:  9000000 
INFO  @ Thu, 22 Dec 2016 00:51:22:  10000000 
INFO  @ Thu, 22 Dec 2016 00:51:23: #1.2 read input tags... 
INFO  @ Thu, 22 Dec 2016 00:51:25:  1000000 
INFO  @ Thu, 22 Dec 2016 00:51:27:  2000000 
INFO  @ Thu, 22 Dec 2016 00:51:28:  3000000 
INFO  @ Thu, 22 Dec 2016 00:51:30:  4000000 
INFO  @ Thu, 22 Dec 2016 00:51:31:  5000000 
INFO  @ Thu, 22 Dec 2016 00:51:33:  6000000 
INFO  @ Thu, 22 Dec 2016 00:51:34:  7000000 
INFO  @ Thu, 22 Dec 2016 00:51:36:  8000000 
INFO  @ Thu, 22 Dec 2016 00:51:38:  9000000 
INFO  @ Thu, 22 Dec 2016 00:51:39:  10000000 
INFO  @ Thu, 22 Dec 2016 00:51:41:  11000000 
INFO  @ Thu, 22 Dec 2016 00:51:42:  12000000 
INFO  @ Thu, 22 Dec 2016 00:51:44:  13000000 
INFO  @ Thu, 22 Dec 2016 00:51:45:  14000000 
INFO  @ Thu, 22 Dec 2016 00:51:47:  15000000 
INFO  @ Thu, 22 Dec 2016 00:51:49:  16000000 
INFO  @ Thu, 22 Dec 2016 00:51:50:  17000000 
INFO  @ Thu, 22 Dec 2016 00:51:52:  18000000 
INFO  @ Thu, 22 Dec 2016 00:51:54:  19000000 
INFO  @ Thu, 22 Dec 2016 00:51:56:  20000000 
INFO  @ Thu, 22 Dec 2016 00:51:57:  21000000 
INFO  @ Thu, 22 Dec 2016 00:51:59:  22000000 
INFO  @ Thu, 22 Dec 2016 00:52:00:  23000000 
INFO  @ Thu, 22 Dec 2016 00:52:02:  24000000 
INFO  @ Thu, 22 Dec 2016 00:52:03:  25000000 
INFO  @ Thu, 22 Dec 2016 00:52:05:  26000000 
INFO  @ Thu, 22 Dec 2016 00:52:07:  27000000 
INFO  @ Thu, 22 Dec 2016 00:52:08:  28000000 
INFO  @ Thu, 22 Dec 2016 00:52:10:  29000000 
INFO  @ Thu, 22 Dec 2016 00:52:11:  30000000 
INFO  @ Thu, 22 Dec 2016 00:52:13:  31000000 
INFO  @ Thu, 22 Dec 2016 00:52:15:  32000000 
INFO  @ Thu, 22 Dec 2016 00:52:16:  33000000 
INFO  @ Thu, 22 Dec 2016 00:52:18:  34000000 
INFO  @ Thu, 22 Dec 2016 00:52:20:  35000000 
INFO  @ Thu, 22 Dec 2016 00:52:21:  36000000 
INFO  @ Thu, 22 Dec 2016 00:52:23:  37000000 
INFO  @ Thu, 22 Dec 2016 00:52:25:  38000000 
INFO  @ Thu, 22 Dec 2016 00:52:26:  39000000 
INFO  @ Thu, 22 Dec 2016 00:52:28:  40000000 
INFO  @ Thu, 22 Dec 2016 00:52:29:  41000000 
INFO  @ Thu, 22 Dec 2016 00:52:31:  42000000 
INFO  @ Thu, 22 Dec 2016 00:52:32:  43000000 
INFO  @ Thu, 22 Dec 2016 00:52:34:  44000000 
INFO  @ Thu, 22 Dec 2016 00:52:35:  45000000 
INFO  @ Thu, 22 Dec 2016 00:52:37:  46000000 
INFO  @ Thu, 22 Dec 2016 00:52:38:  47000000 
INFO  @ Thu, 22 Dec 2016 00:52:40:  48000000 
INFO  @ Thu, 22 Dec 2016 00:52:42:  49000000 
INFO  @ Thu, 22 Dec 2016 00:52:43:  50000000 
INFO  @ Thu, 22 Dec 2016 00:52:45: #1 tag size is determined as 49 bps 
INFO  @ Thu, 22 Dec 2016 00:52:45: #1 tag size = 49 
INFO  @ Thu, 22 Dec 2016 00:52:45: #1  total tags in treatment: 10388972 
INFO  @ Thu, 22 Dec 2016 00:52:45: #1  total tags in control: 50000000 
INFO  @ Thu, 22 Dec 2016 00:52:45: #1 finished! 
INFO  @ Thu, 22 Dec 2016 00:52:45: #2 Build Peak Model... 
INFO  @ Thu, 22 Dec 2016 00:52:45: #2 Skipped... 
INFO  @ Thu, 22 Dec 2016 00:52:45: #2 Use 155 as fragment length 
INFO  @ Thu, 22 Dec 2016 00:52:45: #3 Call peaks... 
INFO  @ Thu, 22 Dec 2016 00:52:45: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 22 Dec 2016 00:52:45: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 22 Dec 2016 01:00:30: #3 Call peaks for each chromosome... 
INFO  @ Thu, 22 Dec 2016 01:07:45: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 22 Dec 2016 01:07:50: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Thu, 22 Dec 2016 01:07:54: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 22 Dec 2016 01:07:58: Done!

Num	3
ID	task.callpeak_macs2.macs2_rep1_pr2.line_67.id_12
Name	macs2 rep1-pr2
Thread	thread_Root
PID	19484

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

Start	2016-12-21 14:14:17
End	2016-12-22 01:28:08
Elapsed	11:13:50
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/align/pseudo_reps/rep1/pr2/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_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/ZNF189/out/align/pseudo_reps/rep1/pr2/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 155 --keep-dup all -B --SPMR

# SYS command. line 78

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_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/ZNF189/out/align/pseudo_reps/rep1/pr2/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 155 --keep-dup all

# SYS command. line 91

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_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/ZNF189/out/align/pseudo_reps/rep1/pr2/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_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--------------------
10336 (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 01:08:29: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/align/pseudo_reps/rep1/pr2/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 155 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/align/pseudo_reps/rep1/pr2/SRR1370880_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 01:08:29: #1 read tag files... 
INFO  @ Thu, 22 Dec 2016 01:08:29: #1 read treatment tags... 
INFO  @ Thu, 22 Dec 2016 01:08:31:  1000000 
INFO  @ Thu, 22 Dec 2016 01:08:33:  2000000 
INFO  @ Thu, 22 Dec 2016 01:08:35:  3000000 
INFO  @ Thu, 22 Dec 2016 01:08:37:  4000000 
INFO  @ Thu, 22 Dec 2016 01:08:39:  5000000 
INFO  @ Thu, 22 Dec 2016 01:08:41:  6000000 
INFO  @ Thu, 22 Dec 2016 01:08:43:  7000000 
INFO  @ Thu, 22 Dec 2016 01:08:45:  8000000 
INFO  @ Thu, 22 Dec 2016 01:08:47:  9000000 
INFO  @ Thu, 22 Dec 2016 01:08:48:  10000000 
INFO  @ Thu, 22 Dec 2016 01:08:50: #1.2 read input tags... 
INFO  @ Thu, 22 Dec 2016 01:08:52:  1000000 
INFO  @ Thu, 22 Dec 2016 01:08:54:  2000000 
INFO  @ Thu, 22 Dec 2016 01:08:55:  3000000 
INFO  @ Thu, 22 Dec 2016 01:08:57:  4000000 
INFO  @ Thu, 22 Dec 2016 01:08:59:  5000000 
INFO  @ Thu, 22 Dec 2016 01:09:01:  6000000 
INFO  @ Thu, 22 Dec 2016 01:09:03:  7000000 
INFO  @ Thu, 22 Dec 2016 01:09:05:  8000000 
INFO  @ Thu, 22 Dec 2016 01:09:06:  9000000 
INFO  @ Thu, 22 Dec 2016 01:09:08:  10000000 
INFO  @ Thu, 22 Dec 2016 01:09:10:  11000000 
INFO  @ Thu, 22 Dec 2016 01:09:12:  12000000 
INFO  @ Thu, 22 Dec 2016 01:09:14:  13000000 
INFO  @ Thu, 22 Dec 2016 01:09:16:  14000000 
INFO  @ Thu, 22 Dec 2016 01:09:17:  15000000 
INFO  @ Thu, 22 Dec 2016 01:09:19:  16000000 
INFO  @ Thu, 22 Dec 2016 01:09:21:  17000000 
INFO  @ Thu, 22 Dec 2016 01:09:23:  18000000 
INFO  @ Thu, 22 Dec 2016 01:09:25:  19000000 
INFO  @ Thu, 22 Dec 2016 01:09:27:  20000000 
INFO  @ Thu, 22 Dec 2016 01:09:28:  21000000 
INFO  @ Thu, 22 Dec 2016 01:09:30:  22000000 
INFO  @ Thu, 22 Dec 2016 01:09:32:  23000000 
INFO  @ Thu, 22 Dec 2016 01:09:34:  24000000 
INFO  @ Thu, 22 Dec 2016 01:09:36:  25000000 
INFO  @ Thu, 22 Dec 2016 01:09:37:  26000000 
INFO  @ Thu, 22 Dec 2016 01:09:39:  27000000 
INFO  @ Thu, 22 Dec 2016 01:09:41:  28000000 
INFO  @ Thu, 22 Dec 2016 01:09:43:  29000000 
INFO  @ Thu, 22 Dec 2016 01:09:45:  30000000 
INFO  @ Thu, 22 Dec 2016 01:09:46:  31000000 
INFO  @ Thu, 22 Dec 2016 01:09:48:  32000000 
INFO  @ Thu, 22 Dec 2016 01:09:50:  33000000 
INFO  @ Thu, 22 Dec 2016 01:09:52:  34000000 
INFO  @ Thu, 22 Dec 2016 01:09:54:  35000000 
INFO  @ Thu, 22 Dec 2016 01:09:56:  36000000 
INFO  @ Thu, 22 Dec 2016 01:09:57:  37000000 
INFO  @ Thu, 22 Dec 2016 01:09:59:  38000000 
INFO  @ Thu, 22 Dec 2016 01:10:01:  39000000 
INFO  @ Thu, 22 Dec 2016 01:10:03:  40000000 
INFO  @ Thu, 22 Dec 2016 01:10:05:  41000000 
INFO  @ Thu, 22 Dec 2016 01:10:07:  42000000 
INFO  @ Thu, 22 Dec 2016 01:10:08:  43000000 
INFO  @ Thu, 22 Dec 2016 01:10:10:  44000000 
INFO  @ Thu, 22 Dec 2016 01:10:12:  45000000 
INFO  @ Thu, 22 Dec 2016 01:10:14:  46000000 
INFO  @ Thu, 22 Dec 2016 01:10:16:  47000000 
INFO  @ Thu, 22 Dec 2016 01:10:17:  48000000 
INFO  @ Thu, 22 Dec 2016 01:10:19:  49000000 
INFO  @ Thu, 22 Dec 2016 01:10:21:  50000000 
INFO  @ Thu, 22 Dec 2016 01:10:23: #1 tag size is determined as 50 bps 
INFO  @ Thu, 22 Dec 2016 01:10:23: #1 tag size = 50 
INFO  @ Thu, 22 Dec 2016 01:10:23: #1  total tags in treatment: 10388972 
INFO  @ Thu, 22 Dec 2016 01:10:23: #1  total tags in control: 50000000 
INFO  @ Thu, 22 Dec 2016 01:10:23: #1 finished! 
INFO  @ Thu, 22 Dec 2016 01:10:23: #2 Build Peak Model... 
INFO  @ Thu, 22 Dec 2016 01:10:23: #2 Skipped... 
INFO  @ Thu, 22 Dec 2016 01:10:23: #2 Use 155 as fragment length 
INFO  @ Thu, 22 Dec 2016 01:10:23: #3 Call peaks... 
INFO  @ Thu, 22 Dec 2016 01:10:23: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 22 Dec 2016 01:10:23: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 22 Dec 2016 01:13:57: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 22 Dec 2016 01:13:57: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 22 Dec 2016 01:13:57: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Thu, 22 Dec 2016 01:13:57: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 22 Dec 2016 01:13:57: #3 Call peaks for each chromosome... 
INFO  @ Thu, 22 Dec 2016 01:19:10: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 22 Dec 2016 01:19:11: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 22 Dec 2016 01:19:12: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Thu, 22 Dec 2016 01:19:12: Done! 
INFO  @ Thu, 22 Dec 2016 01:19:17: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/align/pseudo_reps/rep1/pr2/SRR1370880_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/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 155 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/align/pseudo_reps/rep1/pr2/SRR1370880_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 01:19:17: #1 read tag files... 
INFO  @ Thu, 22 Dec 2016 01:19:17: #1 read treatment tags... 
INFO  @ Thu, 22 Dec 2016 01:19:19:  1000000 
INFO  @ Thu, 22 Dec 2016 01:19:21:  2000000 
INFO  @ Thu, 22 Dec 2016 01:19:22:  3000000 
INFO  @ Thu, 22 Dec 2016 01:19:24:  4000000 
INFO  @ Thu, 22 Dec 2016 01:19:26:  5000000 
INFO  @ Thu, 22 Dec 2016 01:19:27:  6000000 
INFO  @ Thu, 22 Dec 2016 01:19:29:  7000000 
INFO  @ Thu, 22 Dec 2016 01:19:31:  8000000 
INFO  @ Thu, 22 Dec 2016 01:19:32:  9000000 
INFO  @ Thu, 22 Dec 2016 01:19:34:  10000000 
INFO  @ Thu, 22 Dec 2016 01:19:35: #1.2 read input tags... 
INFO  @ Thu, 22 Dec 2016 01:19:37:  1000000 
INFO  @ Thu, 22 Dec 2016 01:19:39:  2000000 
INFO  @ Thu, 22 Dec 2016 01:19:40:  3000000 
INFO  @ Thu, 22 Dec 2016 01:19:42:  4000000 
INFO  @ Thu, 22 Dec 2016 01:19:43:  5000000 
INFO  @ Thu, 22 Dec 2016 01:19:45:  6000000 
INFO  @ Thu, 22 Dec 2016 01:19:47:  7000000 
INFO  @ Thu, 22 Dec 2016 01:19:49:  8000000 
INFO  @ Thu, 22 Dec 2016 01:19:51:  9000000 
INFO  @ Thu, 22 Dec 2016 01:19:53:  10000000 
INFO  @ Thu, 22 Dec 2016 01:19:54:  11000000 
INFO  @ Thu, 22 Dec 2016 01:19:56:  12000000 
INFO  @ Thu, 22 Dec 2016 01:19:58:  13000000 
INFO  @ Thu, 22 Dec 2016 01:19:59:  14000000 
INFO  @ Thu, 22 Dec 2016 01:20:01:  15000000 
INFO  @ Thu, 22 Dec 2016 01:20:03:  16000000 
INFO  @ Thu, 22 Dec 2016 01:20:04:  17000000 
INFO  @ Thu, 22 Dec 2016 01:20:06:  18000000 
INFO  @ Thu, 22 Dec 2016 01:20:08:  19000000 
INFO  @ Thu, 22 Dec 2016 01:20:09:  20000000 
INFO  @ Thu, 22 Dec 2016 01:20:11:  21000000 
INFO  @ Thu, 22 Dec 2016 01:20:12:  22000000 
INFO  @ Thu, 22 Dec 2016 01:20:14:  23000000 
INFO  @ Thu, 22 Dec 2016 01:20:16:  24000000 
INFO  @ Thu, 22 Dec 2016 01:20:17:  25000000 
INFO  @ Thu, 22 Dec 2016 01:20:19:  26000000 
INFO  @ Thu, 22 Dec 2016 01:20:21:  27000000 
INFO  @ Thu, 22 Dec 2016 01:20:22:  28000000 
INFO  @ Thu, 22 Dec 2016 01:20:24:  29000000 
INFO  @ Thu, 22 Dec 2016 01:20:25:  30000000 
INFO  @ Thu, 22 Dec 2016 01:20:27:  31000000 
INFO  @ Thu, 22 Dec 2016 01:20:29:  32000000 
INFO  @ Thu, 22 Dec 2016 01:20:30:  33000000 
INFO  @ Thu, 22 Dec 2016 01:20:32:  34000000 
INFO  @ Thu, 22 Dec 2016 01:20:34:  35000000 
INFO  @ Thu, 22 Dec 2016 01:20:35:  36000000 
INFO  @ Thu, 22 Dec 2016 01:20:37:  37000000 
INFO  @ Thu, 22 Dec 2016 01:20:39:  38000000 
INFO  @ Thu, 22 Dec 2016 01:20:40:  39000000 
INFO  @ Thu, 22 Dec 2016 01:20:42:  40000000 
INFO  @ Thu, 22 Dec 2016 01:20:43:  41000000 
INFO  @ Thu, 22 Dec 2016 01:20:45:  42000000 
INFO  @ Thu, 22 Dec 2016 01:20:47:  43000000 
INFO  @ Thu, 22 Dec 2016 01:20:48:  44000000 
INFO  @ Thu, 22 Dec 2016 01:20:50:  45000000 
INFO  @ Thu, 22 Dec 2016 01:20:52:  46000000 
INFO  @ Thu, 22 Dec 2016 01:20:53:  47000000 
INFO  @ Thu, 22 Dec 2016 01:20:55:  48000000 
INFO  @ Thu, 22 Dec 2016 01:20:56:  49000000 
INFO  @ Thu, 22 Dec 2016 01:20:58:  50000000 
INFO  @ Thu, 22 Dec 2016 01:21:00: #1 tag size is determined as 50 bps 
INFO  @ Thu, 22 Dec 2016 01:21:00: #1 tag size = 50 
INFO  @ Thu, 22 Dec 2016 01:21:00: #1  total tags in treatment: 10388972 
INFO  @ Thu, 22 Dec 2016 01:21:00: #1  total tags in control: 50000000 
INFO  @ Thu, 22 Dec 2016 01:21:00: #1 finished! 
INFO  @ Thu, 22 Dec 2016 01:21:00: #2 Build Peak Model... 
INFO  @ Thu, 22 Dec 2016 01:21:00: #2 Skipped... 
INFO  @ Thu, 22 Dec 2016 01:21:00: #2 Use 155 as fragment length 
INFO  @ Thu, 22 Dec 2016 01:21:00: #3 Call peaks... 
INFO  @ Thu, 22 Dec 2016 01:21:00: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 22 Dec 2016 01:21:00: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 22 Dec 2016 01:24:31: #3 Call peaks for each chromosome... 
INFO  @ Thu, 22 Dec 2016 01:27:39: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 22 Dec 2016 01:27:44: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Thu, 22 Dec 2016 01:27:48: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370880_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 22 Dec 2016 01:27:52: Done!

BigDataScript report: chipseq.bds

Timeline

Task Graph

Parallel (threads) details

Task details

Global scope

Type	Name	Value
string	_	/usr/bin/bds
string	_LMFILES_	/software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/samtools/1.2
bool	allowEmpty	false
string[]	args	[-title, ZNF189, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF189/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF189/out/align/rep1/SRR1370880_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/ZNF189
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/ZNF189
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	48010.ZNF189.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