BigDataScript report: chipseq.bds

Script file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20161222_184633_146
Start time 2016-12-22 18:46:33
Run time 1 day 08:09:38.828
Tasks executed 1
Tasks failed 1
Tasks failed names 
macs2 rep1
Arguments* [-title, CTCF, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/CTCF/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/align/rep1/SRR1370879_1.bam, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz, -final_stage, idr, -chrsz, /mnt/data/bds_pipeline_genome_data/hg38/hg38_1-21MXY.chrom.sizes, $]
System* sge
Cpus* -1
Exit value 1
* Values in global scope when program finished execution.

Timeline

Task Graph

Parallel (threads) details

Thread ID Parent Tasks
thread_Root None 
 chipseq.bds.20161222_184633_146/task.callpeak_macs2.macs2_rep1.line_71.id_10
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_71.id_10
Name macs2 rep1
Thread thread_Root
PID 20026
OK false
Exit Code 1
Retries
State ERROR
Dep. ERROR
Cpus
Mem
Start 2016-12-22 18:46:39
End 2016-12-22 18:46:39
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/align/rep1/SRR1370879_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/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/signal/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/signal/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw
Dependencies 
 
# SYS command. line 73

 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 74

 export LC_COLLATE=C

# SYS command. line 79

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/align/rep1/SRR1370879_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/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 65 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_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/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/align/rep1/SRR1370879_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/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 65 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_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/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_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/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 110

 if [[ true == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_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 121

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1 -o "SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38_1-21MXY.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38_1-21MXY.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38_1-21MXY.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/signal/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/align/rep1/SRR1370879_1.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 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 140

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1 -o "SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 143

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38_1-21MXY.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38_1-21MXY.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38_1-21MXY.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/signal/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg

# SYS command. line 153

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
   
--------------------Stdout--------------------
33696 (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  @ Sat, 24 Dec 2016 02:22:00: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/align/rep1/SRR1370879_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/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 65 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/align/rep1/SRR1370879_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  @ Sat, 24 Dec 2016 02:22:00: #1 read tag files... 
INFO  @ Sat, 24 Dec 2016 02:22:00: #1 read treatment tags... 
INFO  @ Sat, 24 Dec 2016 02:22:02:  1000000 
INFO  @ Sat, 24 Dec 2016 02:22:04:  2000000 
INFO  @ Sat, 24 Dec 2016 02:22:06:  3000000 
INFO  @ Sat, 24 Dec 2016 02:22:08:  4000000 
INFO  @ Sat, 24 Dec 2016 02:22:10:  5000000 
INFO  @ Sat, 24 Dec 2016 02:22:11: #1.2 read input tags... 
INFO  @ Sat, 24 Dec 2016 02:22:13:  1000000 
INFO  @ Sat, 24 Dec 2016 02:22:15:  2000000 
INFO  @ Sat, 24 Dec 2016 02:22:17:  3000000 
INFO  @ Sat, 24 Dec 2016 02:22:19:  4000000 
INFO  @ Sat, 24 Dec 2016 02:22:21:  5000000 
INFO  @ Sat, 24 Dec 2016 02:22:23:  6000000 
INFO  @ Sat, 24 Dec 2016 02:22:25:  7000000 
INFO  @ Sat, 24 Dec 2016 02:22:27:  8000000 
INFO  @ Sat, 24 Dec 2016 02:22:29:  9000000 
INFO  @ Sat, 24 Dec 2016 02:22:31:  10000000 
INFO  @ Sat, 24 Dec 2016 02:22:32:  11000000 
INFO  @ Sat, 24 Dec 2016 02:22:34:  12000000 
INFO  @ Sat, 24 Dec 2016 02:22:36:  13000000 
INFO  @ Sat, 24 Dec 2016 02:22:37:  14000000 
INFO  @ Sat, 24 Dec 2016 02:22:39:  15000000 
INFO  @ Sat, 24 Dec 2016 02:22:41:  16000000 
INFO  @ Sat, 24 Dec 2016 02:22:42:  17000000 
INFO  @ Sat, 24 Dec 2016 02:22:44:  18000000 
INFO  @ Sat, 24 Dec 2016 02:22:45:  19000000 
INFO  @ Sat, 24 Dec 2016 02:22:47:  20000000 
INFO  @ Sat, 24 Dec 2016 02:22:49:  21000000 
INFO  @ Sat, 24 Dec 2016 02:22:50:  22000000 
INFO  @ Sat, 24 Dec 2016 02:22:52:  23000000 
INFO  @ Sat, 24 Dec 2016 02:22:53:  24000000 
INFO  @ Sat, 24 Dec 2016 02:22:55:  25000000 
INFO  @ Sat, 24 Dec 2016 02:22:57:  26000000 
INFO  @ Sat, 24 Dec 2016 02:22:58:  27000000 
INFO  @ Sat, 24 Dec 2016 02:23:00:  28000000 
INFO  @ Sat, 24 Dec 2016 02:23:01:  29000000 
INFO  @ Sat, 24 Dec 2016 02:23:03:  30000000 
INFO  @ Sat, 24 Dec 2016 02:23:04:  31000000 
INFO  @ Sat, 24 Dec 2016 02:23:06:  32000000 
INFO  @ Sat, 24 Dec 2016 02:23:07:  33000000 
INFO  @ Sat, 24 Dec 2016 02:23:09:  34000000 
INFO  @ Sat, 24 Dec 2016 02:23:11:  35000000 
INFO  @ Sat, 24 Dec 2016 02:23:12:  36000000 
INFO  @ Sat, 24 Dec 2016 02:23:14:  37000000 
INFO  @ Sat, 24 Dec 2016 02:23:15:  38000000 
INFO  @ Sat, 24 Dec 2016 02:23:17:  39000000 
INFO  @ Sat, 24 Dec 2016 02:23:18:  40000000 
INFO  @ Sat, 24 Dec 2016 02:23:20:  41000000 
INFO  @ Sat, 24 Dec 2016 02:23:22:  42000000 
INFO  @ Sat, 24 Dec 2016 02:23:23:  43000000 
INFO  @ Sat, 24 Dec 2016 02:23:25:  44000000 
INFO  @ Sat, 24 Dec 2016 02:23:27:  45000000 
INFO  @ Sat, 24 Dec 2016 02:23:28:  46000000 
INFO  @ Sat, 24 Dec 2016 02:23:30:  47000000 
INFO  @ Sat, 24 Dec 2016 02:23:31:  48000000 
INFO  @ Sat, 24 Dec 2016 02:23:33:  49000000 
INFO  @ Sat, 24 Dec 2016 02:23:34:  50000000 
INFO  @ Sat, 24 Dec 2016 02:23:36: #1 tag size is determined as 51 bps 
INFO  @ Sat, 24 Dec 2016 02:23:36: #1 tag size = 51 
INFO  @ Sat, 24 Dec 2016 02:23:36: #1  total tags in treatment: 5392519 
INFO  @ Sat, 24 Dec 2016 02:23:36: #1  total tags in control: 50000000 
INFO  @ Sat, 24 Dec 2016 02:23:36: #1 finished! 
INFO  @ Sat, 24 Dec 2016 02:23:36: #2 Build Peak Model... 
INFO  @ Sat, 24 Dec 2016 02:23:36: #2 Skipped... 
INFO  @ Sat, 24 Dec 2016 02:23:36: #2 Use 65 as fragment length 
INFO  @ Sat, 24 Dec 2016 02:23:36: #3 Call peaks... 
INFO  @ Sat, 24 Dec 2016 02:23:36: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Sat, 24 Dec 2016 02:23:36: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sat, 24 Dec 2016 02:26:49: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Sat, 24 Dec 2016 02:26:49: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Sat, 24 Dec 2016 02:26:49: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Sat, 24 Dec 2016 02:26:49: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Sat, 24 Dec 2016 02:26:49: #3 Call peaks for each chromosome... 
INFO  @ Sat, 24 Dec 2016 02:31:58: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Sat, 24 Dec 2016 02:32:09: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Sat, 24 Dec 2016 02:32:16: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Sat, 24 Dec 2016 02:32:21: Done! 
INFO  @ Sat, 24 Dec 2016 02:32:32: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/align/rep1/SRR1370879_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/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 65 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/align/rep1/SRR1370879_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  @ Sat, 24 Dec 2016 02:32:32: #1 read tag files... 
INFO  @ Sat, 24 Dec 2016 02:32:32: #1 read treatment tags... 
INFO  @ Sat, 24 Dec 2016 02:32:35:  1000000 
INFO  @ Sat, 24 Dec 2016 02:32:38:  2000000 
INFO  @ Sat, 24 Dec 2016 02:32:40:  3000000 
INFO  @ Sat, 24 Dec 2016 02:32:42:  4000000 
INFO  @ Sat, 24 Dec 2016 02:32:44:  5000000 
INFO  @ Sat, 24 Dec 2016 02:32:45: #1.2 read input tags... 
INFO  @ Sat, 24 Dec 2016 02:32:46:  1000000 
INFO  @ Sat, 24 Dec 2016 02:32:48:  2000000 
INFO  @ Sat, 24 Dec 2016 02:32:50:  3000000 
INFO  @ Sat, 24 Dec 2016 02:32:52:  4000000 
INFO  @ Sat, 24 Dec 2016 02:32:53:  5000000 
INFO  @ Sat, 24 Dec 2016 02:32:55:  6000000 
INFO  @ Sat, 24 Dec 2016 02:32:57:  7000000 
INFO  @ Sat, 24 Dec 2016 02:32:59:  8000000 
INFO  @ Sat, 24 Dec 2016 02:33:00:  9000000 
INFO  @ Sat, 24 Dec 2016 02:33:02:  10000000 
INFO  @ Sat, 24 Dec 2016 02:33:04:  11000000 
INFO  @ Sat, 24 Dec 2016 02:33:05:  12000000 
INFO  @ Sat, 24 Dec 2016 02:33:07:  13000000 
INFO  @ Sat, 24 Dec 2016 02:33:09:  14000000 
INFO  @ Sat, 24 Dec 2016 02:33:11:  15000000 
INFO  @ Sat, 24 Dec 2016 02:33:12:  16000000 
INFO  @ Sat, 24 Dec 2016 02:33:14:  17000000 
INFO  @ Sat, 24 Dec 2016 02:33:16:  18000000 
INFO  @ Sat, 24 Dec 2016 02:33:17:  19000000 
INFO  @ Sat, 24 Dec 2016 02:33:19:  20000000 
INFO  @ Sat, 24 Dec 2016 02:33:21:  21000000 
INFO  @ Sat, 24 Dec 2016 02:33:22:  22000000 
INFO  @ Sat, 24 Dec 2016 02:33:24:  23000000 
INFO  @ Sat, 24 Dec 2016 02:33:26:  24000000 
INFO  @ Sat, 24 Dec 2016 02:33:28:  25000000 
INFO  @ Sat, 24 Dec 2016 02:33:29:  26000000 
INFO  @ Sat, 24 Dec 2016 02:33:31:  27000000 
INFO  @ Sat, 24 Dec 2016 02:33:33:  28000000 
INFO  @ Sat, 24 Dec 2016 02:33:34:  29000000 
INFO  @ Sat, 24 Dec 2016 02:33:36:  30000000 
INFO  @ Sat, 24 Dec 2016 02:33:38:  31000000 
INFO  @ Sat, 24 Dec 2016 02:33:40:  32000000 
INFO  @ Sat, 24 Dec 2016 02:33:41:  33000000 
INFO  @ Sat, 24 Dec 2016 02:33:43:  34000000 
INFO  @ Sat, 24 Dec 2016 02:33:45:  35000000 
INFO  @ Sat, 24 Dec 2016 02:33:47:  36000000 
INFO  @ Sat, 24 Dec 2016 02:33:48:  37000000 
INFO  @ Sat, 24 Dec 2016 02:33:50:  38000000 
INFO  @ Sat, 24 Dec 2016 02:33:52:  39000000 
INFO  @ Sat, 24 Dec 2016 02:33:53:  40000000 
INFO  @ Sat, 24 Dec 2016 02:33:55:  41000000 
INFO  @ Sat, 24 Dec 2016 02:33:57:  42000000 
INFO  @ Sat, 24 Dec 2016 02:33:58:  43000000 
INFO  @ Sat, 24 Dec 2016 02:34:00:  44000000 
INFO  @ Sat, 24 Dec 2016 02:34:02:  45000000 
INFO  @ Sat, 24 Dec 2016 02:34:04:  46000000 
INFO  @ Sat, 24 Dec 2016 02:34:05:  47000000 
INFO  @ Sat, 24 Dec 2016 02:34:07:  48000000 
INFO  @ Sat, 24 Dec 2016 02:34:09:  49000000 
INFO  @ Sat, 24 Dec 2016 02:34:11:  50000000 
INFO  @ Sat, 24 Dec 2016 02:34:13: #1 tag size is determined as 51 bps 
INFO  @ Sat, 24 Dec 2016 02:34:13: #1 tag size = 51 
INFO  @ Sat, 24 Dec 2016 02:34:13: #1  total tags in treatment: 5392519 
INFO  @ Sat, 24 Dec 2016 02:34:13: #1  total tags in control: 50000000 
INFO  @ Sat, 24 Dec 2016 02:34:13: #1 finished! 
INFO  @ Sat, 24 Dec 2016 02:34:13: #2 Build Peak Model... 
INFO  @ Sat, 24 Dec 2016 02:34:13: #2 Skipped... 
INFO  @ Sat, 24 Dec 2016 02:34:13: #2 Use 65 as fragment length 
INFO  @ Sat, 24 Dec 2016 02:34:13: #3 Call peaks... 
INFO  @ Sat, 24 Dec 2016 02:34:13: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Sat, 24 Dec 2016 02:34:13: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sat, 24 Dec 2016 02:39:01: #3 Call peaks for each chromosome... 
INFO  @ Sat, 24 Dec 2016 02:43:36: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Sat, 24 Dec 2016 02:44:01: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Sat, 24 Dec 2016 02:44:20: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Sat, 24 Dec 2016 02:44:38: Done! 
INFO  @ Sat, 24 Dec 2016 02:45:21: Read and build treatment bedGraph... 
INFO  @ Sat, 24 Dec 2016 02:45:38: Read and build control bedGraph... 
INFO  @ Sat, 24 Dec 2016 02:48:00: Build scoreTrackII... 
INFO  @ Sat, 24 Dec 2016 02:48:49: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Sat, 24 Dec 2016 02:54:42: Write bedGraph of scores... 
INFO  @ Sat, 24 Dec 2016 02:56:09: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/peak/macs2/rep1/SRR1370879_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_FE.bdg'! 
Chromosome KN196487.1 isn't in /mnt/data/bds_pipeline_genome_data/hg38/hg38_1-21MXY.chrom.sizes line 1 of stdin


 
--------------------Post mortem info--------------------
==============================================================
job_number:                 20026
exec_file:                  job_scripts/20026
submission_time:            Thu Dec 22 18:46:39 2016
owner:                      imk1
uid:                        1048
group:                      users
gid:                        100
sge_o_home:                 /users/imk1/
sge_o_log_name:             imk1
sge_o_path:                 /software/samtools/samtools-1.2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/users/imk1/edirect
sge_o_shell:                /bin/bash
sge_o_workdir:              /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/chipseq.bds.20161222_184633_146/task.callpeak_macs2.macs2_rep1.line_71.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/CTCF/chipseq.bds.20161222_184633_146/task.callpeak_macs2.macs2_rep1.line_71.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=3092.CTCF_2015.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,SCREEN_Name=CTCF_2015,PWD=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF,JAVA_HOME=/usr/lib/jvm/java-8-oracle,LOADEDMODULES=modsappsdir/modsappsdir:samtools/1.2,SSH_CONNECTION=171.65.77.8 32898 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,MANPATH=/software/samtools/samtools-1.2/share/man:/usr/share/man,MODULEPATH=/usr/local/Modules/versions				:/usr/local/Modules/$MODULE_VERSION/modulefiles	:/modules/				:/software/modulefiles,MODULESAPPSDIR=/software,MODULESHOME=/software/env_module/3.2.10
script_file:                STDIN
usage    1:                 cpu=00:35:06, mem=4654.61623 GBs, io=57.45192, vmem=1.891G, maxvmem=4.005G
scheduling info:            queue instance "q@kali" dropped because it is temporarily not available
                            queue instance "q@surya" dropped because it is disabled
                            queue instance "amd.q@wotan" dropped because it is full
                            queue instance "q@kadru" dropped because it is full
                            queue instance "q@nandi" dropped because it is full
                            All queues dropped because of overload or full

Global scope

Note: Global scope when program finished execution.
Type Name Value
string _ /usr/bin/bds
string _LMFILES_ /software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/samtools/1.2
bool allowEmpty false
string[] args [-title, CTCF, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/CTCF/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/CTCF/out/align/rep1/SRR1370879_1.bam, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz, -final_stage, idr, -chrsz, /mnt/data/bds_pipeline_genome_data/hg38/hg38_1-21MXY.chrom.sizes, $]
string C_INCLUDE_PATH /software/samtools/samtools-1.2/include/htslib
bool canFail false
int cpus -1
int cpusLocal 56
int day 86400
string DERBY_HOME /usr/lib/jvm/java-8-oracle/db
string DISPLAY localhost:12.0
real E 2.718281828459045
int G 1073741824
string HOME /users/imk1/
int hour 3600
string J2REDIR /usr/lib/jvm/java-8-oracle/jre
string J2SDKDIR /usr/lib/jvm/java-8-oracle
string JAVA_HOME /usr/lib/jvm/java-8-oracle
int K 1024
string KRB5CCNAME FILE:/tmp/krb5cc_1048_cTVn8v
string LANG en_US.UTF-8
string LOADEDMODULES modsappsdir/modsappsdir:samtools/1.2
string LOGNAME imk1
int M 1048576
string MAIL /var/mail/imk1
string MANPATH /software/samtools/samtools-1.2/share/man:/usr/share/man
int mem -1
int minute 60
string MODULE_VERSION 3.2.10
string MODULE_VERSION_STACK 3.2.10
string MODULEPATH /usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$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/CTCF
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/CTCF
string queue
int retry 0
string SAMTOOLS_HOME /software/samtools/samtools-1.2/bin
string SCREEN_Name CTCF_2015
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 3092.CTCF_2015.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