Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20161221_141456_303
Start time	2016-12-21 14:14:56
Run time	14:25:03.150
Tasks executed	3
Tasks failed	1
Tasks failed names	macs2 rep1
Arguments*	[-title, ZNF692, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF692/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/align/rep1/SRR1370907_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_141456_303/task.callpeak_macs2.macs2_rep1.line_67.id_10 chipseq.bds.20161221_141456_303/task.callpeak_macs2.macs2_rep1_pr1.line_67.id_11 chipseq.bds.20161221_141456_303/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	19500

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

Start	2016-12-21 14:15:02
End	2016-12-21 14:15:02
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/align/rep1/SRR1370907_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/ZNF692/out/peak/macs2/rep1/SRR1370907_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/rep1/SRR1370907_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/rep1/SRR1370907_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/signal/macs2/rep1/SRR1370907_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/signal/macs2/rep1/SRR1370907_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/ZNF692/out/align/rep1/SRR1370907_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/ZNF692/out/peak/macs2/rep1/SRR1370907_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR

# SYS command. line 78

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/rep1/SRR1370907_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/ZNF692/out/peak/macs2/rep1/SRR1370907_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 81

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/rep1/SRR1370907_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/rep1/SRR1370907_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/rep1/SRR1370907_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/ZNF692/out/align/rep1/SRR1370907_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/ZNF692/out/peak/macs2/rep1/SRR1370907_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all

# SYS command. line 91

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/rep1/SRR1370907_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/ZNF692/out/peak/macs2/rep1/SRR1370907_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/ZNF692/out/peak/macs2/rep1/SRR1370907_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/ZNF692/out/peak/macs2/rep1/SRR1370907_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 95

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/rep1/SRR1370907_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/rep1/SRR1370907_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/rep1/SRR1370907_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/rep1/SRR1370907_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/ZNF692/out/peak/macs2/rep1/SRR1370907_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/rep1/SRR1370907_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/ZNF692/out/peak/macs2/rep1/SRR1370907_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/rep1/SRR1370907_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/rep1 -o "SRR1370907_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/ZNF692/out/peak/macs2/rep1/SRR1370907_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/ZNF692/out/peak/macs2/rep1/SRR1370907_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/ZNF692/out/peak/macs2/rep1/SRR1370907_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/ZNF692/out/peak/macs2/rep1/SRR1370907_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/rep1/SRR1370907_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/ZNF692/out/peak/macs2/rep1/SRR1370907_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/ZNF692/out/signal/macs2/rep1/SRR1370907_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/ZNF692/out/peak/macs2/rep1/SRR1370907_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/rep1/SRR1370907_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/ZNF692/out/align/rep1/SRR1370907_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/ZNF692/out/peak/macs2/rep1/SRR1370907_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/rep1/SRR1370907_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/rep1 -o "SRR1370907_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/ZNF692/out/peak/macs2/rep1/SRR1370907_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/ZNF692/out/peak/macs2/rep1/SRR1370907_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/ZNF692/out/peak/macs2/rep1/SRR1370907_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/ZNF692/out/peak/macs2/rep1/SRR1370907_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/rep1/SRR1370907_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/ZNF692/out/peak/macs2/rep1/SRR1370907_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/ZNF692/out/signal/macs2/rep1/SRR1370907_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/ZNF692/out/peak/macs2/rep1/SRR1370907_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/rep1/SRR1370907_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/ZNF692/out/peak/macs2/rep1/SRR1370907_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/rep1/SRR1370907_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--------------------
14158 (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 03:57:59: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/align/rep1/SRR1370907_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/ZNF692/out/peak/macs2/rep1/SRR1370907_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/rep1/SRR1370907_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/align/rep1/SRR1370907_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 03:57:59: #1 read tag files... 
INFO  @ Thu, 22 Dec 2016 03:57:59: #1 read treatment tags... 
INFO  @ Thu, 22 Dec 2016 03:58:01:  1000000 
INFO  @ Thu, 22 Dec 2016 03:58:03:  2000000 
INFO  @ Thu, 22 Dec 2016 03:58:04:  3000000 
INFO  @ Thu, 22 Dec 2016 03:58:06:  4000000 
INFO  @ Thu, 22 Dec 2016 03:58:07:  5000000 
INFO  @ Thu, 22 Dec 2016 03:58:09:  6000000 
INFO  @ Thu, 22 Dec 2016 03:58:10:  7000000 
INFO  @ Thu, 22 Dec 2016 03:58:12:  8000000 
INFO  @ Thu, 22 Dec 2016 03:58:14:  9000000 
INFO  @ Thu, 22 Dec 2016 03:58:15:  10000000 
INFO  @ Thu, 22 Dec 2016 03:58:17:  11000000 
INFO  @ Thu, 22 Dec 2016 03:58:18:  12000000 
INFO  @ Thu, 22 Dec 2016 03:58:20:  13000000 
INFO  @ Thu, 22 Dec 2016 03:58:21:  14000000 
INFO  @ Thu, 22 Dec 2016 03:58:23:  15000000 
INFO  @ Thu, 22 Dec 2016 03:58:24:  16000000 
INFO  @ Thu, 22 Dec 2016 03:58:26:  17000000 
INFO  @ Thu, 22 Dec 2016 03:58:27:  18000000 
INFO  @ Thu, 22 Dec 2016 03:58:29: #1.2 read input tags... 
INFO  @ Thu, 22 Dec 2016 03:58:31:  1000000 
INFO  @ Thu, 22 Dec 2016 03:58:32:  2000000 
INFO  @ Thu, 22 Dec 2016 03:58:34:  3000000 
INFO  @ Thu, 22 Dec 2016 03:58:35:  4000000 
INFO  @ Thu, 22 Dec 2016 03:58:37:  5000000 
INFO  @ Thu, 22 Dec 2016 03:58:39:  6000000 
INFO  @ Thu, 22 Dec 2016 03:58:40:  7000000 
INFO  @ Thu, 22 Dec 2016 03:58:42:  8000000 
INFO  @ Thu, 22 Dec 2016 03:58:43:  9000000 
INFO  @ Thu, 22 Dec 2016 03:58:45:  10000000 
INFO  @ Thu, 22 Dec 2016 03:58:46:  11000000 
INFO  @ Thu, 22 Dec 2016 03:58:48:  12000000 
INFO  @ Thu, 22 Dec 2016 03:58:50:  13000000 
INFO  @ Thu, 22 Dec 2016 03:58:51:  14000000 
INFO  @ Thu, 22 Dec 2016 03:58:53:  15000000 
INFO  @ Thu, 22 Dec 2016 03:58:54:  16000000 
INFO  @ Thu, 22 Dec 2016 03:58:56:  17000000 
INFO  @ Thu, 22 Dec 2016 03:58:58:  18000000 
INFO  @ Thu, 22 Dec 2016 03:58:59:  19000000 
INFO  @ Thu, 22 Dec 2016 03:59:01:  20000000 
INFO  @ Thu, 22 Dec 2016 03:59:02:  21000000 
INFO  @ Thu, 22 Dec 2016 03:59:04:  22000000 
INFO  @ Thu, 22 Dec 2016 03:59:05:  23000000 
INFO  @ Thu, 22 Dec 2016 03:59:07:  24000000 
INFO  @ Thu, 22 Dec 2016 03:59:09:  25000000 
INFO  @ Thu, 22 Dec 2016 03:59:10:  26000000 
INFO  @ Thu, 22 Dec 2016 03:59:12:  27000000 
INFO  @ Thu, 22 Dec 2016 03:59:13:  28000000 
INFO  @ Thu, 22 Dec 2016 03:59:15:  29000000 
INFO  @ Thu, 22 Dec 2016 03:59:16:  30000000 
INFO  @ Thu, 22 Dec 2016 03:59:18:  31000000 
INFO  @ Thu, 22 Dec 2016 03:59:19:  32000000 
INFO  @ Thu, 22 Dec 2016 03:59:21:  33000000 
INFO  @ Thu, 22 Dec 2016 03:59:23:  34000000 
INFO  @ Thu, 22 Dec 2016 03:59:24:  35000000 
INFO  @ Thu, 22 Dec 2016 03:59:26:  36000000 
INFO  @ Thu, 22 Dec 2016 03:59:27:  37000000 
INFO  @ Thu, 22 Dec 2016 03:59:29:  38000000 
INFO  @ Thu, 22 Dec 2016 03:59:30:  39000000 
INFO  @ Thu, 22 Dec 2016 03:59:32:  40000000 
INFO  @ Thu, 22 Dec 2016 03:59:34:  41000000 
INFO  @ Thu, 22 Dec 2016 03:59:35:  42000000 
INFO  @ Thu, 22 Dec 2016 03:59:37:  43000000 
INFO  @ Thu, 22 Dec 2016 03:59:38:  44000000 
INFO  @ Thu, 22 Dec 2016 03:59:40:  45000000 
INFO  @ Thu, 22 Dec 2016 03:59:41:  46000000 
INFO  @ Thu, 22 Dec 2016 03:59:43:  47000000 
INFO  @ Thu, 22 Dec 2016 03:59:44:  48000000 
INFO  @ Thu, 22 Dec 2016 03:59:46:  49000000 
INFO  @ Thu, 22 Dec 2016 03:59:48:  50000000 
INFO  @ Thu, 22 Dec 2016 03:59:49: #1 tag size is determined as 48 bps 
INFO  @ Thu, 22 Dec 2016 03:59:49: #1 tag size = 48 
INFO  @ Thu, 22 Dec 2016 03:59:49: #1  total tags in treatment: 18754971 
INFO  @ Thu, 22 Dec 2016 03:59:49: #1  total tags in control: 50000000 
INFO  @ Thu, 22 Dec 2016 03:59:49: #1 finished! 
INFO  @ Thu, 22 Dec 2016 03:59:49: #2 Build Peak Model... 
INFO  @ Thu, 22 Dec 2016 03:59:49: #2 Skipped... 
INFO  @ Thu, 22 Dec 2016 03:59:49: #2 Use 145 as fragment length 
INFO  @ Thu, 22 Dec 2016 03:59:49: #3 Call peaks... 
INFO  @ Thu, 22 Dec 2016 03:59:49: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 22 Dec 2016 03:59:49: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 22 Dec 2016 04:03:40: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 22 Dec 2016 04:03:40: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/rep1/SRR1370907_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 22 Dec 2016 04:03:40: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/rep1/SRR1370907_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Thu, 22 Dec 2016 04:03:40: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 22 Dec 2016 04:03:40: #3 Call peaks for each chromosome... 
INFO  @ Thu, 22 Dec 2016 04:11:00: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/rep1/SRR1370907_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 22 Dec 2016 04:11:01: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/rep1/SRR1370907_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 22 Dec 2016 04:11:01: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/rep1/SRR1370907_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Thu, 22 Dec 2016 04:11:01: Done! 
INFO  @ Thu, 22 Dec 2016 04:11:06: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/align/rep1/SRR1370907_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/ZNF692/out/peak/macs2/rep1/SRR1370907_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/rep1/SRR1370907_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/align/rep1/SRR1370907_1.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Thu, 22 Dec 2016 04:11:06: #1 read tag files... 
INFO  @ Thu, 22 Dec 2016 04:11:06: #1 read treatment tags... 
INFO  @ Thu, 22 Dec 2016 04:11:07:  1000000 
INFO  @ Thu, 22 Dec 2016 04:11:09:  2000000 
INFO  @ Thu, 22 Dec 2016 04:11:11:  3000000 
INFO  @ Thu, 22 Dec 2016 04:11:12:  4000000 
INFO  @ Thu, 22 Dec 2016 04:11:14:  5000000 
INFO  @ Thu, 22 Dec 2016 04:11:15:  6000000 
INFO  @ Thu, 22 Dec 2016 04:11:17:  7000000 
INFO  @ Thu, 22 Dec 2016 04:11:18:  8000000 
INFO  @ Thu, 22 Dec 2016 04:11:20:  9000000 
INFO  @ Thu, 22 Dec 2016 04:11:22:  10000000 
INFO  @ Thu, 22 Dec 2016 04:11:23:  11000000 
INFO  @ Thu, 22 Dec 2016 04:11:25:  12000000 
INFO  @ Thu, 22 Dec 2016 04:11:26:  13000000 
INFO  @ Thu, 22 Dec 2016 04:11:28:  14000000 
INFO  @ Thu, 22 Dec 2016 04:11:29:  15000000 
INFO  @ Thu, 22 Dec 2016 04:11:31:  16000000 
INFO  @ Thu, 22 Dec 2016 04:11:33:  17000000 
INFO  @ Thu, 22 Dec 2016 04:11:34:  18000000 
INFO  @ Thu, 22 Dec 2016 04:11:36: #1.2 read input tags... 
INFO  @ Thu, 22 Dec 2016 04:11:37:  1000000 
INFO  @ Thu, 22 Dec 2016 04:11:39:  2000000 
INFO  @ Thu, 22 Dec 2016 04:11:41:  3000000 
INFO  @ Thu, 22 Dec 2016 04:11:42:  4000000 
INFO  @ Thu, 22 Dec 2016 04:11:44:  5000000 
INFO  @ Thu, 22 Dec 2016 04:11:46:  6000000 
INFO  @ Thu, 22 Dec 2016 04:11:47:  7000000 
INFO  @ Thu, 22 Dec 2016 04:11:49:  8000000 
INFO  @ Thu, 22 Dec 2016 04:11:50:  9000000 
INFO  @ Thu, 22 Dec 2016 04:11:52:  10000000 
INFO  @ Thu, 22 Dec 2016 04:11:54:  11000000 
INFO  @ Thu, 22 Dec 2016 04:11:55:  12000000 
INFO  @ Thu, 22 Dec 2016 04:11:57:  13000000 
INFO  @ Thu, 22 Dec 2016 04:11:59:  14000000 
INFO  @ Thu, 22 Dec 2016 04:12:00:  15000000 
INFO  @ Thu, 22 Dec 2016 04:12:02:  16000000 
INFO  @ Thu, 22 Dec 2016 04:12:03:  17000000 
INFO  @ Thu, 22 Dec 2016 04:12:05:  18000000 
INFO  @ Thu, 22 Dec 2016 04:12:07:  19000000 
INFO  @ Thu, 22 Dec 2016 04:12:08:  20000000 
INFO  @ Thu, 22 Dec 2016 04:12:10:  21000000 
INFO  @ Thu, 22 Dec 2016 04:12:11:  22000000 
INFO  @ Thu, 22 Dec 2016 04:12:13:  23000000 
INFO  @ Thu, 22 Dec 2016 04:12:15:  24000000 
INFO  @ Thu, 22 Dec 2016 04:12:16:  25000000 
INFO  @ Thu, 22 Dec 2016 04:12:18:  26000000 
INFO  @ Thu, 22 Dec 2016 04:12:19:  27000000 
INFO  @ Thu, 22 Dec 2016 04:12:21:  28000000 
INFO  @ Thu, 22 Dec 2016 04:12:22:  29000000 
INFO  @ Thu, 22 Dec 2016 04:12:24:  30000000 
INFO  @ Thu, 22 Dec 2016 04:12:26:  31000000 
INFO  @ Thu, 22 Dec 2016 04:12:27:  32000000 
INFO  @ Thu, 22 Dec 2016 04:12:29:  33000000 
INFO  @ Thu, 22 Dec 2016 04:12:31:  34000000 
INFO  @ Thu, 22 Dec 2016 04:12:32:  35000000 
INFO  @ Thu, 22 Dec 2016 04:12:34:  36000000 
INFO  @ Thu, 22 Dec 2016 04:12:35:  37000000 
INFO  @ Thu, 22 Dec 2016 04:12:37:  38000000 
INFO  @ Thu, 22 Dec 2016 04:12:39:  39000000 
INFO  @ Thu, 22 Dec 2016 04:12:41:  40000000 
INFO  @ Thu, 22 Dec 2016 04:12:42:  41000000 
INFO  @ Thu, 22 Dec 2016 04:12:44:  42000000 
INFO  @ Thu, 22 Dec 2016 04:12:45:  43000000 
INFO  @ Thu, 22 Dec 2016 04:12:47:  44000000 
INFO  @ Thu, 22 Dec 2016 04:12:49:  45000000 
INFO  @ Thu, 22 Dec 2016 04:12:50:  46000000 
INFO  @ Thu, 22 Dec 2016 04:12:52:  47000000 
INFO  @ Thu, 22 Dec 2016 04:12:54:  48000000 
INFO  @ Thu, 22 Dec 2016 04:12:55:  49000000 
INFO  @ Thu, 22 Dec 2016 04:12:57:  50000000 
INFO  @ Thu, 22 Dec 2016 04:12:59: #1 tag size is determined as 48 bps 
INFO  @ Thu, 22 Dec 2016 04:12:59: #1 tag size = 48 
INFO  @ Thu, 22 Dec 2016 04:12:59: #1  total tags in treatment: 18754971 
INFO  @ Thu, 22 Dec 2016 04:12:59: #1  total tags in control: 50000000 
INFO  @ Thu, 22 Dec 2016 04:12:59: #1 finished! 
INFO  @ Thu, 22 Dec 2016 04:12:59: #2 Build Peak Model... 
INFO  @ Thu, 22 Dec 2016 04:12:59: #2 Skipped... 
INFO  @ Thu, 22 Dec 2016 04:12:59: #2 Use 145 as fragment length 
INFO  @ Thu, 22 Dec 2016 04:12:59: #3 Call peaks... 
INFO  @ Thu, 22 Dec 2016 04:12:59: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 22 Dec 2016 04:12:59: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 22 Dec 2016 04:19:59: #3 Call peaks for each chromosome... 
INFO  @ Thu, 22 Dec 2016 04:26:25: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/rep1/SRR1370907_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 22 Dec 2016 04:26:31: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/rep1/SRR1370907_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Thu, 22 Dec 2016 04:26:35: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/rep1/SRR1370907_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 22 Dec 2016 04:26:39: Done! 
INFO  @ Thu, 22 Dec 2016 04:27:04: Read and build treatment bedGraph... 
INFO  @ Thu, 22 Dec 2016 04:27:46: Read and build control bedGraph... 
INFO  @ Thu, 22 Dec 2016 04:29:48: Build scoreTrackII... 
INFO  @ Thu, 22 Dec 2016 04:30:49: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Thu, 22 Dec 2016 04:36:35: Write bedGraph of scores... 
INFO  @ Thu, 22 Dec 2016 04:39:56: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/rep1/SRR1370907_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:                 19500
submission_time:            Wed Dec 21 14:15:02 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/ZNF692
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/chipseq.bds.20161221_141456_303/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/ZNF692/chipseq.bds.20161221_141456_303/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=52217.ZNF692.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/ZNF692,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	19501

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

Start	2016-12-21 14:15:05
End	2016-12-22 04:17:17
Elapsed	14:02:12
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/align/pseudo_reps/rep1/pr1/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_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/ZNF692/out/align/pseudo_reps/rep1/pr1/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR

# SYS command. line 78

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_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/ZNF692/out/align/pseudo_reps/rep1/pr1/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all

# SYS command. line 91

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_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/ZNF692/out/align/pseudo_reps/rep1/pr1/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_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--------------------
14271 (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 03:58:59: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/align/pseudo_reps/rep1/pr1/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/align/pseudo_reps/rep1/pr1/SRR1370907_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 03:58:59: #1 read tag files... 
INFO  @ Thu, 22 Dec 2016 03:58:59: #1 read treatment tags... 
INFO  @ Thu, 22 Dec 2016 03:59:01:  1000000 
INFO  @ Thu, 22 Dec 2016 03:59:03:  2000000 
INFO  @ Thu, 22 Dec 2016 03:59:05:  3000000 
INFO  @ Thu, 22 Dec 2016 03:59:07:  4000000 
INFO  @ Thu, 22 Dec 2016 03:59:08:  5000000 
INFO  @ Thu, 22 Dec 2016 03:59:10:  6000000 
INFO  @ Thu, 22 Dec 2016 03:59:12:  7000000 
INFO  @ Thu, 22 Dec 2016 03:59:13:  8000000 
INFO  @ Thu, 22 Dec 2016 03:59:15:  9000000 
INFO  @ Thu, 22 Dec 2016 03:59:16: #1.2 read input tags... 
INFO  @ Thu, 22 Dec 2016 03:59:18:  1000000 
INFO  @ Thu, 22 Dec 2016 03:59:20:  2000000 
INFO  @ Thu, 22 Dec 2016 03:59:21:  3000000 
INFO  @ Thu, 22 Dec 2016 03:59:23:  4000000 
INFO  @ Thu, 22 Dec 2016 03:59:25:  5000000 
INFO  @ Thu, 22 Dec 2016 03:59:26:  6000000 
INFO  @ Thu, 22 Dec 2016 03:59:28:  7000000 
INFO  @ Thu, 22 Dec 2016 03:59:29:  8000000 
INFO  @ Thu, 22 Dec 2016 03:59:31:  9000000 
INFO  @ Thu, 22 Dec 2016 03:59:33:  10000000 
INFO  @ Thu, 22 Dec 2016 03:59:34:  11000000 
INFO  @ Thu, 22 Dec 2016 03:59:36:  12000000 
INFO  @ Thu, 22 Dec 2016 03:59:38:  13000000 
INFO  @ Thu, 22 Dec 2016 03:59:39:  14000000 
INFO  @ Thu, 22 Dec 2016 03:59:41:  15000000 
INFO  @ Thu, 22 Dec 2016 03:59:43:  16000000 
INFO  @ Thu, 22 Dec 2016 03:59:44:  17000000 
INFO  @ Thu, 22 Dec 2016 03:59:46:  18000000 
INFO  @ Thu, 22 Dec 2016 03:59:48:  19000000 
INFO  @ Thu, 22 Dec 2016 03:59:51:  20000000 
INFO  @ Thu, 22 Dec 2016 03:59:52:  21000000 
INFO  @ Thu, 22 Dec 2016 03:59:54:  22000000 
INFO  @ Thu, 22 Dec 2016 03:59:55:  23000000 
INFO  @ Thu, 22 Dec 2016 03:59:57:  24000000 
INFO  @ Thu, 22 Dec 2016 03:59:59:  25000000 
INFO  @ Thu, 22 Dec 2016 04:00:00:  26000000 
INFO  @ Thu, 22 Dec 2016 04:00:02:  27000000 
INFO  @ Thu, 22 Dec 2016 04:00:04:  28000000 
INFO  @ Thu, 22 Dec 2016 04:00:05:  29000000 
INFO  @ Thu, 22 Dec 2016 04:00:07:  30000000 
INFO  @ Thu, 22 Dec 2016 04:00:08:  31000000 
INFO  @ Thu, 22 Dec 2016 04:00:10:  32000000 
INFO  @ Thu, 22 Dec 2016 04:00:12:  33000000 
INFO  @ Thu, 22 Dec 2016 04:00:13:  34000000 
INFO  @ Thu, 22 Dec 2016 04:00:15:  35000000 
INFO  @ Thu, 22 Dec 2016 04:00:17:  36000000 
INFO  @ Thu, 22 Dec 2016 04:00:18:  37000000 
INFO  @ Thu, 22 Dec 2016 04:00:20:  38000000 
INFO  @ Thu, 22 Dec 2016 04:00:21:  39000000 
INFO  @ Thu, 22 Dec 2016 04:00:23:  40000000 
INFO  @ Thu, 22 Dec 2016 04:00:25:  41000000 
INFO  @ Thu, 22 Dec 2016 04:00:26:  42000000 
INFO  @ Thu, 22 Dec 2016 04:00:28:  43000000 
INFO  @ Thu, 22 Dec 2016 04:00:30:  44000000 
INFO  @ Thu, 22 Dec 2016 04:00:31:  45000000 
INFO  @ Thu, 22 Dec 2016 04:00:33:  46000000 
INFO  @ Thu, 22 Dec 2016 04:00:34:  47000000 
INFO  @ Thu, 22 Dec 2016 04:00:36:  48000000 
INFO  @ Thu, 22 Dec 2016 04:00:38:  49000000 
INFO  @ Thu, 22 Dec 2016 04:00:39:  50000000 
INFO  @ Thu, 22 Dec 2016 04:00:41: #1 tag size is determined as 51 bps 
INFO  @ Thu, 22 Dec 2016 04:00:41: #1 tag size = 51 
INFO  @ Thu, 22 Dec 2016 04:00:41: #1  total tags in treatment: 9377486 
INFO  @ Thu, 22 Dec 2016 04:00:41: #1  total tags in control: 50000000 
INFO  @ Thu, 22 Dec 2016 04:00:41: #1 finished! 
INFO  @ Thu, 22 Dec 2016 04:00:41: #2 Build Peak Model... 
INFO  @ Thu, 22 Dec 2016 04:00:41: #2 Skipped... 
INFO  @ Thu, 22 Dec 2016 04:00:41: #2 Use 145 as fragment length 
INFO  @ Thu, 22 Dec 2016 04:00:41: #3 Call peaks... 
INFO  @ Thu, 22 Dec 2016 04:00:41: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 22 Dec 2016 04:00:41: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 22 Dec 2016 04:03:38: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 22 Dec 2016 04:03:38: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 22 Dec 2016 04:03:38: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Thu, 22 Dec 2016 04:03:38: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 22 Dec 2016 04:03:38: #3 Call peaks for each chromosome... 
INFO  @ Thu, 22 Dec 2016 04:08:21: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 22 Dec 2016 04:08:21: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 22 Dec 2016 04:08:22: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Thu, 22 Dec 2016 04:08:22: Done! 
INFO  @ Thu, 22 Dec 2016 04:08:25: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/align/pseudo_reps/rep1/pr1/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/align/pseudo_reps/rep1/pr1/SRR1370907_1.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Thu, 22 Dec 2016 04:08:25: #1 read tag files... 
INFO  @ Thu, 22 Dec 2016 04:08:25: #1 read treatment tags... 
INFO  @ Thu, 22 Dec 2016 04:08:27:  1000000 
INFO  @ Thu, 22 Dec 2016 04:08:29:  2000000 
INFO  @ Thu, 22 Dec 2016 04:08:31:  3000000 
INFO  @ Thu, 22 Dec 2016 04:08:32:  4000000 
INFO  @ Thu, 22 Dec 2016 04:08:34:  5000000 
INFO  @ Thu, 22 Dec 2016 04:08:36:  6000000 
INFO  @ Thu, 22 Dec 2016 04:08:37:  7000000 
INFO  @ Thu, 22 Dec 2016 04:08:39:  8000000 
INFO  @ Thu, 22 Dec 2016 04:08:41:  9000000 
INFO  @ Thu, 22 Dec 2016 04:08:42: #1.2 read input tags... 
INFO  @ Thu, 22 Dec 2016 04:08:44:  1000000 
INFO  @ Thu, 22 Dec 2016 04:08:46:  2000000 
INFO  @ Thu, 22 Dec 2016 04:08:47:  3000000 
INFO  @ Thu, 22 Dec 2016 04:08:49:  4000000 
INFO  @ Thu, 22 Dec 2016 04:08:51:  5000000 
INFO  @ Thu, 22 Dec 2016 04:08:52:  6000000 
INFO  @ Thu, 22 Dec 2016 04:08:54:  7000000 
INFO  @ Thu, 22 Dec 2016 04:08:55:  8000000 
INFO  @ Thu, 22 Dec 2016 04:08:57:  9000000 
INFO  @ Thu, 22 Dec 2016 04:08:59:  10000000 
INFO  @ Thu, 22 Dec 2016 04:09:00:  11000000 
INFO  @ Thu, 22 Dec 2016 04:09:02:  12000000 
INFO  @ Thu, 22 Dec 2016 04:09:04:  13000000 
INFO  @ Thu, 22 Dec 2016 04:09:05:  14000000 
INFO  @ Thu, 22 Dec 2016 04:09:07:  15000000 
INFO  @ Thu, 22 Dec 2016 04:09:09:  16000000 
INFO  @ Thu, 22 Dec 2016 04:09:10:  17000000 
INFO  @ Thu, 22 Dec 2016 04:09:12:  18000000 
INFO  @ Thu, 22 Dec 2016 04:09:14:  19000000 
INFO  @ Thu, 22 Dec 2016 04:09:15:  20000000 
INFO  @ Thu, 22 Dec 2016 04:09:17:  21000000 
INFO  @ Thu, 22 Dec 2016 04:09:19:  22000000 
INFO  @ Thu, 22 Dec 2016 04:09:20:  23000000 
INFO  @ Thu, 22 Dec 2016 04:09:22:  24000000 
INFO  @ Thu, 22 Dec 2016 04:09:23:  25000000 
INFO  @ Thu, 22 Dec 2016 04:09:25:  26000000 
INFO  @ Thu, 22 Dec 2016 04:09:27:  27000000 
INFO  @ Thu, 22 Dec 2016 04:09:28:  28000000 
INFO  @ Thu, 22 Dec 2016 04:09:30:  29000000 
INFO  @ Thu, 22 Dec 2016 04:09:32:  30000000 
INFO  @ Thu, 22 Dec 2016 04:09:33:  31000000 
INFO  @ Thu, 22 Dec 2016 04:09:35:  32000000 
INFO  @ Thu, 22 Dec 2016 04:09:37:  33000000 
INFO  @ Thu, 22 Dec 2016 04:09:38:  34000000 
INFO  @ Thu, 22 Dec 2016 04:09:40:  35000000 
INFO  @ Thu, 22 Dec 2016 04:09:42:  36000000 
INFO  @ Thu, 22 Dec 2016 04:09:43:  37000000 
INFO  @ Thu, 22 Dec 2016 04:09:45:  38000000 
INFO  @ Thu, 22 Dec 2016 04:09:47:  39000000 
INFO  @ Thu, 22 Dec 2016 04:09:48:  40000000 
INFO  @ Thu, 22 Dec 2016 04:09:50:  41000000 
INFO  @ Thu, 22 Dec 2016 04:09:51:  42000000 
INFO  @ Thu, 22 Dec 2016 04:09:53:  43000000 
INFO  @ Thu, 22 Dec 2016 04:09:55:  44000000 
INFO  @ Thu, 22 Dec 2016 04:09:56:  45000000 
INFO  @ Thu, 22 Dec 2016 04:09:58:  46000000 
INFO  @ Thu, 22 Dec 2016 04:10:00:  47000000 
INFO  @ Thu, 22 Dec 2016 04:10:01:  48000000 
INFO  @ Thu, 22 Dec 2016 04:10:03:  49000000 
INFO  @ Thu, 22 Dec 2016 04:10:05:  50000000 
INFO  @ Thu, 22 Dec 2016 04:10:06: #1 tag size is determined as 51 bps 
INFO  @ Thu, 22 Dec 2016 04:10:06: #1 tag size = 51 
INFO  @ Thu, 22 Dec 2016 04:10:06: #1  total tags in treatment: 9377486 
INFO  @ Thu, 22 Dec 2016 04:10:06: #1  total tags in control: 50000000 
INFO  @ Thu, 22 Dec 2016 04:10:06: #1 finished! 
INFO  @ Thu, 22 Dec 2016 04:10:06: #2 Build Peak Model... 
INFO  @ Thu, 22 Dec 2016 04:10:06: #2 Skipped... 
INFO  @ Thu, 22 Dec 2016 04:10:06: #2 Use 145 as fragment length 
INFO  @ Thu, 22 Dec 2016 04:10:06: #3 Call peaks... 
INFO  @ Thu, 22 Dec 2016 04:10:06: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 22 Dec 2016 04:10:06: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 22 Dec 2016 04:13:31: #3 Call peaks for each chromosome... 
INFO  @ Thu, 22 Dec 2016 04:16:43: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 22 Dec 2016 04:16:49: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Thu, 22 Dec 2016 04:16:54: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370907_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 22 Dec 2016 04:16:58: Done!

Num	3
ID	task.callpeak_macs2.macs2_rep1_pr2.line_67.id_12
Name	macs2 rep1-pr2
Thread	thread_Root
PID	19503

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

Start	2016-12-21 14:15:06
End	2016-12-22 04:36:02
Elapsed	14:20:55
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/align/pseudo_reps/rep1/pr2/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_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/ZNF692/out/align/pseudo_reps/rep1/pr2/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR

# SYS command. line 78

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_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/ZNF692/out/align/pseudo_reps/rep1/pr2/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all

# SYS command. line 91

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_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/ZNF692/out/align/pseudo_reps/rep1/pr2/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_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--------------------
14736 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
INFO  @ Thu, 22 Dec 2016 04:17:29: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/align/pseudo_reps/rep1/pr2/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/align/pseudo_reps/rep1/pr2/SRR1370907_1.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Thu, 22 Dec 2016 04:17:29: #1 read tag files... 
INFO  @ Thu, 22 Dec 2016 04:17:29: #1 read treatment tags... 
INFO  @ Thu, 22 Dec 2016 04:17:31:  1000000 
INFO  @ Thu, 22 Dec 2016 04:17:33:  2000000 
INFO  @ Thu, 22 Dec 2016 04:17:35:  3000000 
INFO  @ Thu, 22 Dec 2016 04:17:36:  4000000 
INFO  @ Thu, 22 Dec 2016 04:17:38:  5000000 
INFO  @ Thu, 22 Dec 2016 04:17:40:  6000000 
INFO  @ Thu, 22 Dec 2016 04:17:41:  7000000 
INFO  @ Thu, 22 Dec 2016 04:17:43:  8000000 
INFO  @ Thu, 22 Dec 2016 04:17:45:  9000000 
INFO  @ Thu, 22 Dec 2016 04:17:46: #1.2 read input tags... 
INFO  @ Thu, 22 Dec 2016 04:17:48:  1000000 
INFO  @ Thu, 22 Dec 2016 04:17:49:  2000000 
INFO  @ Thu, 22 Dec 2016 04:17:51:  3000000 
INFO  @ Thu, 22 Dec 2016 04:17:52:  4000000 
INFO  @ Thu, 22 Dec 2016 04:17:54:  5000000 
INFO  @ Thu, 22 Dec 2016 04:17:55:  6000000 
INFO  @ Thu, 22 Dec 2016 04:17:57:  7000000 
INFO  @ Thu, 22 Dec 2016 04:17:59:  8000000 
INFO  @ Thu, 22 Dec 2016 04:18:00:  9000000 
INFO  @ Thu, 22 Dec 2016 04:18:02:  10000000 
INFO  @ Thu, 22 Dec 2016 04:18:03:  11000000 
INFO  @ Thu, 22 Dec 2016 04:18:05:  12000000 
INFO  @ Thu, 22 Dec 2016 04:18:06:  13000000 
INFO  @ Thu, 22 Dec 2016 04:18:08:  14000000 
INFO  @ Thu, 22 Dec 2016 04:18:09:  15000000 
INFO  @ Thu, 22 Dec 2016 04:18:11:  16000000 
INFO  @ Thu, 22 Dec 2016 04:18:13:  17000000 
INFO  @ Thu, 22 Dec 2016 04:18:14:  18000000 
INFO  @ Thu, 22 Dec 2016 04:18:16:  19000000 
INFO  @ Thu, 22 Dec 2016 04:18:17:  20000000 
INFO  @ Thu, 22 Dec 2016 04:18:19:  21000000 
INFO  @ Thu, 22 Dec 2016 04:18:20:  22000000 
INFO  @ Thu, 22 Dec 2016 04:18:22:  23000000 
INFO  @ Thu, 22 Dec 2016 04:18:23:  24000000 
INFO  @ Thu, 22 Dec 2016 04:18:25:  25000000 
INFO  @ Thu, 22 Dec 2016 04:18:27:  26000000 
INFO  @ Thu, 22 Dec 2016 04:18:28:  27000000 
INFO  @ Thu, 22 Dec 2016 04:18:30:  28000000 
INFO  @ Thu, 22 Dec 2016 04:18:31:  29000000 
INFO  @ Thu, 22 Dec 2016 04:18:33:  30000000 
INFO  @ Thu, 22 Dec 2016 04:18:34:  31000000 
INFO  @ Thu, 22 Dec 2016 04:18:36:  32000000 
INFO  @ Thu, 22 Dec 2016 04:18:38:  33000000 
INFO  @ Thu, 22 Dec 2016 04:18:39:  34000000 
INFO  @ Thu, 22 Dec 2016 04:18:41:  35000000 
INFO  @ Thu, 22 Dec 2016 04:18:42:  36000000 
INFO  @ Thu, 22 Dec 2016 04:18:44:  37000000 
INFO  @ Thu, 22 Dec 2016 04:18:45:  38000000 
INFO  @ Thu, 22 Dec 2016 04:18:47:  39000000 
INFO  @ Thu, 22 Dec 2016 04:18:49:  40000000 
INFO  @ Thu, 22 Dec 2016 04:18:50:  41000000 
INFO  @ Thu, 22 Dec 2016 04:18:52:  42000000 
INFO  @ Thu, 22 Dec 2016 04:18:53:  43000000 
INFO  @ Thu, 22 Dec 2016 04:18:55:  44000000 
INFO  @ Thu, 22 Dec 2016 04:18:57:  45000000 
INFO  @ Thu, 22 Dec 2016 04:18:58:  46000000 
INFO  @ Thu, 22 Dec 2016 04:19:00:  47000000 
INFO  @ Thu, 22 Dec 2016 04:19:01:  48000000 
INFO  @ Thu, 22 Dec 2016 04:19:03:  49000000 
INFO  @ Thu, 22 Dec 2016 04:19:05:  50000000 
INFO  @ Thu, 22 Dec 2016 04:19:06: #1 tag size is determined as 51 bps 
INFO  @ Thu, 22 Dec 2016 04:19:06: #1 tag size = 51 
INFO  @ Thu, 22 Dec 2016 04:19:06: #1  total tags in treatment: 9377485 
INFO  @ Thu, 22 Dec 2016 04:19:06: #1  total tags in control: 50000000 
INFO  @ Thu, 22 Dec 2016 04:19:06: #1 finished! 
INFO  @ Thu, 22 Dec 2016 04:19:06: #2 Build Peak Model... 
INFO  @ Thu, 22 Dec 2016 04:19:06: #2 Skipped... 
INFO  @ Thu, 22 Dec 2016 04:19:06: #2 Use 145 as fragment length 
INFO  @ Thu, 22 Dec 2016 04:19:06: #3 Call peaks... 
INFO  @ Thu, 22 Dec 2016 04:19:06: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Thu, 22 Dec 2016 04:19:06: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 22 Dec 2016 04:22:26: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 22 Dec 2016 04:22:26: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Thu, 22 Dec 2016 04:22:26: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Thu, 22 Dec 2016 04:22:26: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Thu, 22 Dec 2016 04:22:26: #3 Call peaks for each chromosome... 
INFO  @ Thu, 22 Dec 2016 04:27:19: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 22 Dec 2016 04:27:19: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Thu, 22 Dec 2016 04:27:19: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Thu, 22 Dec 2016 04:27:20: Done! 
INFO  @ Thu, 22 Dec 2016 04:27:23: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/align/pseudo_reps/rep1/pr2/SRR1370907_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/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/align/pseudo_reps/rep1/pr2/SRR1370907_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 04:27:23: #1 read tag files... 
INFO  @ Thu, 22 Dec 2016 04:27:23: #1 read treatment tags... 
INFO  @ Thu, 22 Dec 2016 04:27:25:  1000000 
INFO  @ Thu, 22 Dec 2016 04:27:27:  2000000 
INFO  @ Thu, 22 Dec 2016 04:27:28:  3000000 
INFO  @ Thu, 22 Dec 2016 04:27:30:  4000000 
INFO  @ Thu, 22 Dec 2016 04:27:32:  5000000 
INFO  @ Thu, 22 Dec 2016 04:27:33:  6000000 
INFO  @ Thu, 22 Dec 2016 04:27:35:  7000000 
INFO  @ Thu, 22 Dec 2016 04:27:37:  8000000 
INFO  @ Thu, 22 Dec 2016 04:27:38:  9000000 
INFO  @ Thu, 22 Dec 2016 04:27:39: #1.2 read input tags... 
INFO  @ Thu, 22 Dec 2016 04:27:41:  1000000 
INFO  @ Thu, 22 Dec 2016 04:27:43:  2000000 
INFO  @ Thu, 22 Dec 2016 04:27:44:  3000000 
INFO  @ Thu, 22 Dec 2016 04:27:46:  4000000 
INFO  @ Thu, 22 Dec 2016 04:27:47:  5000000 
INFO  @ Thu, 22 Dec 2016 04:27:49:  6000000 
INFO  @ Thu, 22 Dec 2016 04:27:50:  7000000 
INFO  @ Thu, 22 Dec 2016 04:27:52:  8000000 
INFO  @ Thu, 22 Dec 2016 04:27:54:  9000000 
INFO  @ Thu, 22 Dec 2016 04:27:55:  10000000 
INFO  @ Thu, 22 Dec 2016 04:27:57:  11000000 
INFO  @ Thu, 22 Dec 2016 04:27:58:  12000000 
INFO  @ Thu, 22 Dec 2016 04:28:00:  13000000 
INFO  @ Thu, 22 Dec 2016 04:28:01:  14000000 
INFO  @ Thu, 22 Dec 2016 04:28:03:  15000000 
INFO  @ Thu, 22 Dec 2016 04:28:04:  16000000 
INFO  @ Thu, 22 Dec 2016 04:28:06:  17000000 
INFO  @ Thu, 22 Dec 2016 04:28:07:  18000000 
INFO  @ Thu, 22 Dec 2016 04:28:09:  19000000 
INFO  @ Thu, 22 Dec 2016 04:28:11:  20000000 
INFO  @ Thu, 22 Dec 2016 04:28:12:  21000000 
INFO  @ Thu, 22 Dec 2016 04:28:14:  22000000 
INFO  @ Thu, 22 Dec 2016 04:28:15:  23000000 
INFO  @ Thu, 22 Dec 2016 04:28:17:  24000000 
INFO  @ Thu, 22 Dec 2016 04:28:18:  25000000 
INFO  @ Thu, 22 Dec 2016 04:28:20:  26000000 
INFO  @ Thu, 22 Dec 2016 04:28:21:  27000000 
INFO  @ Thu, 22 Dec 2016 04:28:23:  28000000 
INFO  @ Thu, 22 Dec 2016 04:28:25:  29000000 
INFO  @ Thu, 22 Dec 2016 04:28:26:  30000000 
INFO  @ Thu, 22 Dec 2016 04:28:28:  31000000 
INFO  @ Thu, 22 Dec 2016 04:28:29:  32000000 
INFO  @ Thu, 22 Dec 2016 04:28:31:  33000000 
INFO  @ Thu, 22 Dec 2016 04:28:32:  34000000 
INFO  @ Thu, 22 Dec 2016 04:28:34:  35000000 
INFO  @ Thu, 22 Dec 2016 04:28:35:  36000000 
INFO  @ Thu, 22 Dec 2016 04:28:37:  37000000 
INFO  @ Thu, 22 Dec 2016 04:28:38:  38000000 
INFO  @ Thu, 22 Dec 2016 04:28:40:  39000000 
INFO  @ Thu, 22 Dec 2016 04:28:42:  40000000 
INFO  @ Thu, 22 Dec 2016 04:28:43:  41000000 
INFO  @ Thu, 22 Dec 2016 04:28:45:  42000000 
INFO  @ Thu, 22 Dec 2016 04:28:46:  43000000 
INFO  @ Thu, 22 Dec 2016 04:28:48:  44000000 
INFO  @ Thu, 22 Dec 2016 04:28:49:  45000000 
INFO  @ Thu, 22 Dec 2016 04:28:51:  46000000 
INFO  @ Thu, 22 Dec 2016 04:28:52:  47000000 
INFO  @ Thu, 22 Dec 2016 04:28:54:  48000000 
INFO  @ Thu, 22 Dec 2016 04:28:55:  49000000 
INFO  @ Thu, 22 Dec 2016 04:28:57:  50000000 
INFO  @ Thu, 22 Dec 2016 04:28:59: #1 tag size is determined as 51 bps 
INFO  @ Thu, 22 Dec 2016 04:28:59: #1 tag size = 51 
INFO  @ Thu, 22 Dec 2016 04:28:59: #1  total tags in treatment: 9377485 
INFO  @ Thu, 22 Dec 2016 04:28:59: #1  total tags in control: 50000000 
INFO  @ Thu, 22 Dec 2016 04:28:59: #1 finished! 
INFO  @ Thu, 22 Dec 2016 04:28:59: #2 Build Peak Model... 
INFO  @ Thu, 22 Dec 2016 04:28:59: #2 Skipped... 
INFO  @ Thu, 22 Dec 2016 04:28:59: #2 Use 145 as fragment length 
INFO  @ Thu, 22 Dec 2016 04:28:59: #3 Call peaks... 
INFO  @ Thu, 22 Dec 2016 04:28:59: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 22 Dec 2016 04:28:59: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 22 Dec 2016 04:32:13: #3 Call peaks for each chromosome... 
INFO  @ Thu, 22 Dec 2016 04:35:29: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Thu, 22 Dec 2016 04:35:36: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Thu, 22 Dec 2016 04:35:41: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370907_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 22 Dec 2016 04:35:45: 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, ZNF692, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF692/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF692/out/align/rep1/SRR1370907_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/ZNF692
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/ZNF692
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	52217.ZNF692.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