BigDataScript report: chipseq.bds

Script file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20161106_180922_372
Start time 2016-11-06 18:09:22
Run time 00:33:24.282
Tasks executed 3
Tasks failed 1
Tasks failed names 
macs2 rep1
Arguments* [-title, WT_NOBEADS, -nth, 5, -species, mm10, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out, -tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/rep1/wt_noBeads_allReps.nodup.tagAlign.gz, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz, -gensz, mm, -chrsz, /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.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.20161106_180922_372/task.callpeak_macs2.macs2_rep1.line_67.id_10
chipseq.bds.20161106_180922_372/task.callpeak_macs2.macs2_rep1_pr1.line_67.id_11
chipseq.bds.20161106_180922_372/task.callpeak_macs2.macs2_rep1_pr2.line_67.id_12
thread_42 thread_Root
thread_41 thread_Root

Task details

Task Execution Time Dependencies Task program, Errors, StdOut / StdErr
Num 1
ID task.callpeak_macs2.macs2_rep1.line_67.id_10
Name macs2 rep1
Thread thread_Root
PID 4365
OK false
Exit Code 1
Retries
State ERROR
Dep. ERROR
Cpus
Mem
Start 2016-11-06 18:09:30
End 2016-11-06 18:09:30
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/rep1/wt_noBeads_allReps.nodup.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/signal/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/signal/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bw
Dependencies 
 
# SYS command. line 69

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${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/MouseMutantData/WT_NOBEADS/out/align/rep1/wt_noBeads_allReps.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --nomodel --shift 0 --extsize 110 --keep-dup all -B --SPMR

# SYS command. line 78

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.narrowPeak.gz

# SYS command. line 81

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_summits.bed

# SYS command. line 88

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/rep1/wt_noBeads_allReps.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --broad --nomodel --shift 0 --extsize 110 --keep-dup all

# SYS command. line 91

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.broadPeak.gz

# SYS command. line 92

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gappedPeak.gz

# SYS command. line 95

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_summits.bed

# SYS command. line 100

 if [[ true == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.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/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1 -o "wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 114

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_FE.bdg -g /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 115

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_FE.bdg

# SYS command. line 118

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 119

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/signal/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bw

# SYS command. line 120

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 126

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

# SYS command. line 128

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.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/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1 -o "wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 133

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_ppois.bdg -g /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 134

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_ppois.bdg

# SYS command. line 137

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 138

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/signal/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bw

# SYS command. line 139

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 141

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.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--------------------
2637 (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  @ Sun, 06 Nov 2016 18:19:33: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/rep1/wt_noBeads_allReps.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --nomodel --shift 0 --extsize 110 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/rep1/wt_noBeads_allReps.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz']
# effective genome size = 1.87e+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  @ Sun, 06 Nov 2016 18:19:33: #1 read tag files... 
INFO  @ Sun, 06 Nov 2016 18:19:33: #1 read treatment tags... 
INFO  @ Sun, 06 Nov 2016 18:19:35:  1000000 
INFO  @ Sun, 06 Nov 2016 18:19:37:  2000000 
INFO  @ Sun, 06 Nov 2016 18:19:38:  3000000 
INFO  @ Sun, 06 Nov 2016 18:19:40:  4000000 
INFO  @ Sun, 06 Nov 2016 18:19:42:  5000000 
INFO  @ Sun, 06 Nov 2016 18:19:43:  6000000 
INFO  @ Sun, 06 Nov 2016 18:19:45:  7000000 
INFO  @ Sun, 06 Nov 2016 18:19:46:  8000000 
INFO  @ Sun, 06 Nov 2016 18:19:48:  9000000 
INFO  @ Sun, 06 Nov 2016 18:19:49:  10000000 
INFO  @ Sun, 06 Nov 2016 18:19:51:  11000000 
INFO  @ Sun, 06 Nov 2016 18:19:52:  12000000 
INFO  @ Sun, 06 Nov 2016 18:19:54:  13000000 
INFO  @ Sun, 06 Nov 2016 18:19:56:  14000000 
INFO  @ Sun, 06 Nov 2016 18:19:57:  15000000 
INFO  @ Sun, 06 Nov 2016 18:19:59:  16000000 
INFO  @ Sun, 06 Nov 2016 18:20:01:  17000000 
INFO  @ Sun, 06 Nov 2016 18:20:02:  18000000 
INFO  @ Sun, 06 Nov 2016 18:20:04:  19000000 
INFO  @ Sun, 06 Nov 2016 18:20:05:  20000000 
INFO  @ Sun, 06 Nov 2016 18:20:07:  21000000 
INFO  @ Sun, 06 Nov 2016 18:20:08:  22000000 
INFO  @ Sun, 06 Nov 2016 18:20:10:  23000000 
INFO  @ Sun, 06 Nov 2016 18:20:12:  24000000 
INFO  @ Sun, 06 Nov 2016 18:20:13:  25000000 
INFO  @ Sun, 06 Nov 2016 18:20:15:  26000000 
INFO  @ Sun, 06 Nov 2016 18:20:17:  27000000 
INFO  @ Sun, 06 Nov 2016 18:20:18:  28000000 
INFO  @ Sun, 06 Nov 2016 18:20:20:  29000000 
INFO  @ Sun, 06 Nov 2016 18:20:21:  30000000 
INFO  @ Sun, 06 Nov 2016 18:20:23:  31000000 
INFO  @ Sun, 06 Nov 2016 18:20:24:  32000000 
INFO  @ Sun, 06 Nov 2016 18:20:26:  33000000 
INFO  @ Sun, 06 Nov 2016 18:20:27:  34000000 
INFO  @ Sun, 06 Nov 2016 18:20:29:  35000000 
INFO  @ Sun, 06 Nov 2016 18:20:31:  36000000 
INFO  @ Sun, 06 Nov 2016 18:20:32:  37000000 
INFO  @ Sun, 06 Nov 2016 18:20:34:  38000000 
INFO  @ Sun, 06 Nov 2016 18:20:36:  39000000 
INFO  @ Sun, 06 Nov 2016 18:20:37:  40000000 
INFO  @ Sun, 06 Nov 2016 18:20:39:  41000000 
INFO  @ Sun, 06 Nov 2016 18:20:40:  42000000 
INFO  @ Sun, 06 Nov 2016 18:20:42:  43000000 
INFO  @ Sun, 06 Nov 2016 18:20:43:  44000000 
INFO  @ Sun, 06 Nov 2016 18:20:45:  45000000 
INFO  @ Sun, 06 Nov 2016 18:20:47:  46000000 
INFO  @ Sun, 06 Nov 2016 18:20:49:  47000000 
INFO  @ Sun, 06 Nov 2016 18:20:50:  48000000 
INFO  @ Sun, 06 Nov 2016 18:20:52:  49000000 
INFO  @ Sun, 06 Nov 2016 18:20:54:  50000000 
INFO  @ Sun, 06 Nov 2016 18:20:56:  51000000 
INFO  @ Sun, 06 Nov 2016 18:20:57:  52000000 
INFO  @ Sun, 06 Nov 2016 18:20:59:  53000000 
INFO  @ Sun, 06 Nov 2016 18:21:00:  54000000 
INFO  @ Sun, 06 Nov 2016 18:21:02:  55000000 
INFO  @ Sun, 06 Nov 2016 18:21:04:  56000000 
INFO  @ Sun, 06 Nov 2016 18:21:06:  57000000 
INFO  @ Sun, 06 Nov 2016 18:21:07:  58000000 
INFO  @ Sun, 06 Nov 2016 18:21:09:  59000000 
INFO  @ Sun, 06 Nov 2016 18:21:10:  60000000 
INFO  @ Sun, 06 Nov 2016 18:21:12:  61000000 
INFO  @ Sun, 06 Nov 2016 18:21:13:  62000000 
INFO  @ Sun, 06 Nov 2016 18:21:15:  63000000 
INFO  @ Sun, 06 Nov 2016 18:21:16:  64000000 
INFO  @ Sun, 06 Nov 2016 18:21:18:  65000000 
INFO  @ Sun, 06 Nov 2016 18:21:19:  66000000 
INFO  @ Sun, 06 Nov 2016 18:21:21:  67000000 
INFO  @ Sun, 06 Nov 2016 18:21:23: #1.2 read input tags... 
INFO  @ Sun, 06 Nov 2016 18:21:25:  1000000 
INFO  @ Sun, 06 Nov 2016 18:21:26:  2000000 
INFO  @ Sun, 06 Nov 2016 18:21:28:  3000000 
INFO  @ Sun, 06 Nov 2016 18:21:28: #1 tag size is determined as 49 bps 
INFO  @ Sun, 06 Nov 2016 18:21:28: #1 tag size = 49 
INFO  @ Sun, 06 Nov 2016 18:21:28: #1  total tags in treatment: 67841614 
INFO  @ Sun, 06 Nov 2016 18:21:28: #1  total tags in control: 3384182 
INFO  @ Sun, 06 Nov 2016 18:21:28: #1 finished! 
INFO  @ Sun, 06 Nov 2016 18:21:28: #2 Build Peak Model... 
INFO  @ Sun, 06 Nov 2016 18:21:28: #2 Skipped... 
INFO  @ Sun, 06 Nov 2016 18:21:28: #2 Use 110 as fragment length 
INFO  @ Sun, 06 Nov 2016 18:21:28: #3 Call peaks... 
INFO  @ Sun, 06 Nov 2016 18:21:28: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Sun, 06 Nov 2016 18:21:28: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 06 Nov 2016 18:22:39: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Sun, 06 Nov 2016 18:22:39: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Sun, 06 Nov 2016 18:22:39: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_control_lambda.bdg 
INFO  @ Sun, 06 Nov 2016 18:22:39: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Sun, 06 Nov 2016 18:22:39: #3 Call peaks for each chromosome... 
INFO  @ Sun, 06 Nov 2016 18:27:01: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 06 Nov 2016 18:27:01: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Sun, 06 Nov 2016 18:27:02: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_summits.bed 
INFO  @ Sun, 06 Nov 2016 18:27:02: Done! 
INFO  @ Sun, 06 Nov 2016 18:27:04: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/rep1/wt_noBeads_allReps.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --broad --nomodel --shift 0 --extsize 110 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/rep1/wt_noBeads_allReps.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz']
# effective genome size = 1.87e+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  @ Sun, 06 Nov 2016 18:27:04: #1 read tag files... 
INFO  @ Sun, 06 Nov 2016 18:27:04: #1 read treatment tags... 
INFO  @ Sun, 06 Nov 2016 18:27:06:  1000000 
INFO  @ Sun, 06 Nov 2016 18:27:08:  2000000 
INFO  @ Sun, 06 Nov 2016 18:27:09:  3000000 
INFO  @ Sun, 06 Nov 2016 18:27:11:  4000000 
INFO  @ Sun, 06 Nov 2016 18:27:13:  5000000 
INFO  @ Sun, 06 Nov 2016 18:27:14:  6000000 
INFO  @ Sun, 06 Nov 2016 18:27:16:  7000000 
INFO  @ Sun, 06 Nov 2016 18:27:17:  8000000 
INFO  @ Sun, 06 Nov 2016 18:27:19:  9000000 
INFO  @ Sun, 06 Nov 2016 18:27:20:  10000000 
INFO  @ Sun, 06 Nov 2016 18:27:22:  11000000 
INFO  @ Sun, 06 Nov 2016 18:27:23:  12000000 
INFO  @ Sun, 06 Nov 2016 18:27:25:  13000000 
INFO  @ Sun, 06 Nov 2016 18:27:26:  14000000 
INFO  @ Sun, 06 Nov 2016 18:27:28:  15000000 
INFO  @ Sun, 06 Nov 2016 18:27:29:  16000000 
INFO  @ Sun, 06 Nov 2016 18:27:31:  17000000 
INFO  @ Sun, 06 Nov 2016 18:27:33:  18000000 
INFO  @ Sun, 06 Nov 2016 18:27:34:  19000000 
INFO  @ Sun, 06 Nov 2016 18:27:36:  20000000 
INFO  @ Sun, 06 Nov 2016 18:27:37:  21000000 
INFO  @ Sun, 06 Nov 2016 18:27:39:  22000000 
INFO  @ Sun, 06 Nov 2016 18:27:40:  23000000 
INFO  @ Sun, 06 Nov 2016 18:27:42:  24000000 
INFO  @ Sun, 06 Nov 2016 18:27:43:  25000000 
INFO  @ Sun, 06 Nov 2016 18:27:45:  26000000 
INFO  @ Sun, 06 Nov 2016 18:27:46:  27000000 
INFO  @ Sun, 06 Nov 2016 18:27:48:  28000000 
INFO  @ Sun, 06 Nov 2016 18:27:49:  29000000 
INFO  @ Sun, 06 Nov 2016 18:27:51:  30000000 
INFO  @ Sun, 06 Nov 2016 18:27:52:  31000000 
INFO  @ Sun, 06 Nov 2016 18:27:54:  32000000 
INFO  @ Sun, 06 Nov 2016 18:27:55:  33000000 
INFO  @ Sun, 06 Nov 2016 18:27:57:  34000000 
INFO  @ Sun, 06 Nov 2016 18:27:58:  35000000 
INFO  @ Sun, 06 Nov 2016 18:28:00:  36000000 
INFO  @ Sun, 06 Nov 2016 18:28:01:  37000000 
INFO  @ Sun, 06 Nov 2016 18:28:03:  38000000 
INFO  @ Sun, 06 Nov 2016 18:28:05:  39000000 
INFO  @ Sun, 06 Nov 2016 18:28:06:  40000000 
INFO  @ Sun, 06 Nov 2016 18:28:08:  41000000 
INFO  @ Sun, 06 Nov 2016 18:28:09:  42000000 
INFO  @ Sun, 06 Nov 2016 18:28:11:  43000000 
INFO  @ Sun, 06 Nov 2016 18:28:12:  44000000 
INFO  @ Sun, 06 Nov 2016 18:28:14:  45000000 
INFO  @ Sun, 06 Nov 2016 18:28:15:  46000000 
INFO  @ Sun, 06 Nov 2016 18:28:17:  47000000 
INFO  @ Sun, 06 Nov 2016 18:28:18:  48000000 
INFO  @ Sun, 06 Nov 2016 18:28:20:  49000000 
INFO  @ Sun, 06 Nov 2016 18:28:21:  50000000 
INFO  @ Sun, 06 Nov 2016 18:28:23:  51000000 
INFO  @ Sun, 06 Nov 2016 18:28:24:  52000000 
INFO  @ Sun, 06 Nov 2016 18:28:26:  53000000 
INFO  @ Sun, 06 Nov 2016 18:28:27:  54000000 
INFO  @ Sun, 06 Nov 2016 18:28:29:  55000000 
INFO  @ Sun, 06 Nov 2016 18:28:30:  56000000 
INFO  @ Sun, 06 Nov 2016 18:28:32:  57000000 
INFO  @ Sun, 06 Nov 2016 18:28:34:  58000000 
INFO  @ Sun, 06 Nov 2016 18:28:35:  59000000 
INFO  @ Sun, 06 Nov 2016 18:28:37:  60000000 
INFO  @ Sun, 06 Nov 2016 18:28:38:  61000000 
INFO  @ Sun, 06 Nov 2016 18:28:40:  62000000 
INFO  @ Sun, 06 Nov 2016 18:28:41:  63000000 
INFO  @ Sun, 06 Nov 2016 18:28:43:  64000000 
INFO  @ Sun, 06 Nov 2016 18:28:44:  65000000 
INFO  @ Sun, 06 Nov 2016 18:28:46:  66000000 
INFO  @ Sun, 06 Nov 2016 18:28:47:  67000000 
INFO  @ Sun, 06 Nov 2016 18:28:49: #1.2 read input tags... 
INFO  @ Sun, 06 Nov 2016 18:28:51:  1000000 
INFO  @ Sun, 06 Nov 2016 18:28:53:  2000000 
INFO  @ Sun, 06 Nov 2016 18:28:54:  3000000 
INFO  @ Sun, 06 Nov 2016 18:28:55: #1 tag size is determined as 49 bps 
INFO  @ Sun, 06 Nov 2016 18:28:55: #1 tag size = 49 
INFO  @ Sun, 06 Nov 2016 18:28:55: #1  total tags in treatment: 67841614 
INFO  @ Sun, 06 Nov 2016 18:28:55: #1  total tags in control: 3384182 
INFO  @ Sun, 06 Nov 2016 18:28:55: #1 finished! 
INFO  @ Sun, 06 Nov 2016 18:28:55: #2 Build Peak Model... 
INFO  @ Sun, 06 Nov 2016 18:28:55: #2 Skipped... 
INFO  @ Sun, 06 Nov 2016 18:28:55: #2 Use 110 as fragment length 
INFO  @ Sun, 06 Nov 2016 18:28:55: #3 Call peaks... 
INFO  @ Sun, 06 Nov 2016 18:28:55: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Sun, 06 Nov 2016 18:28:55: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 06 Nov 2016 18:30:12: #3 Call peaks for each chromosome... 
INFO  @ Sun, 06 Nov 2016 18:30:58: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 06 Nov 2016 18:30:58: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.broadPeak 
INFO  @ Sun, 06 Nov 2016 18:30:59: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Sun, 06 Nov 2016 18:30:59: Done! 
INFO  @ Sun, 06 Nov 2016 18:31:02: Read and build treatment bedGraph... 
INFO  @ Sun, 06 Nov 2016 18:33:20: Read and build control bedGraph... 
INFO  @ Sun, 06 Nov 2016 18:33:32: Build scoreTrackII... 
INFO  @ Sun, 06 Nov 2016 18:34:14: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Sun, 06 Nov 2016 18:38:46: Write bedGraph of scores... 
INFO  @ Sun, 06 Nov 2016 18:42:24: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_FE.bdg'! 
Chromosome KQ030491.1 isn't in /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes line 1 of stdin


 
--------------------Post mortem info--------------------
==============================================================
job_number:                 4365
exec_file:                  job_scripts/4365
submission_time:            Sun Nov  6 18:09:30 2016
owner:                      imk1
uid:                        1048
group:                      users
gid:                        100
sge_o_home:                 /users/imk1/
sge_o_log_name:             imk1
sge_o_path:                 /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/MouseMutantData/WT_NOBEADS
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/chipseq.bds.20161106_180922_372/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/MouseMutantData/WT_NOBEADS/chipseq.bds.20161106_180922_372/task.callpeak_macs2.macs2_rep1.line_67.id_10.stdout.cluster
jobshare:                   0
env_list:                   MAIL=/var/mail/imk1,SSH_CLIENT=171.65.77.8 55144 22,USER=imk1,J2SDKDIR=/usr/lib/jvm/java-8-oracle,SHLVL=3,J2REDIR=/usr/lib/jvm/java-8-oracle/jre,HOME=/users/imk1/,SSH_TTY=/dev/pts/4,LOGNAME=imk1,_=/usr/bin/bds,XDG_SESSION_ID=20,TERM=screen,SGE_ROOT=/var/lib/gridengine,PATH=/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=35766.WT_NOBEADS.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,KRB5CCNAME=FILE:/tmp/krb5cc_1048_N5SeQf,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/MouseMutantData/WT_NOBEADS,JAVA_HOME=/usr/lib/jvm/java-8-oracle,LOADEDMODULES=NONE,SSH_CONNECTION=171.65.77.8 55144 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,MODULEPATH=/usr/local/Modules/versions				:/usr/local/Modules/$MODULE_VERSION/modulefiles	:/modules/				:/software/modulefiles,MODULESHOME=/software/env_module/3.2.10
script_file:                STDIN
usage    1:                 cpu=00:22:38, mem=2363.56029 GBs, io=32.66097, vmem=921.414M, maxvmem=3.974G
scheduling info:            queue instance "q@kadru" dropped because it is full
Num 2
ID task.callpeak_macs2.macs2_rep1_pr1.line_67.id_11
Name macs2 rep1-pr1
Thread thread_Root
PID 4380
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2016-11-06 18:09:34
End 2016-11-06 18:42:46
Elapsed 00:33:12
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gappedPeak.gz
Dependencies 
 
# SYS command. line 69

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${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/MouseMutantData/WT_NOBEADS/out/align/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --nomodel --shift 0 --extsize 110 --keep-dup all -B --SPMR

# SYS command. line 78

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.narrowPeak.gz

# SYS command. line 81

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_summits.bed

# SYS command. line 88

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --broad --nomodel --shift 0 --extsize 110 --keep-dup all

# SYS command. line 91

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.broadPeak.gz

# SYS command. line 92

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gappedPeak.gz

# SYS command. line 95

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_summits.bed

# SYS command. line 100

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.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/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1 -o "wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 114

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_FE.bdg -g /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 115

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_FE.bdg

# SYS command. line 118

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 119

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bw

# SYS command. line 120

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 126

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 128

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.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/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1 -o "wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 133

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_ppois.bdg -g /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 134

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_ppois.bdg

# SYS command. line 137

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 138

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bw

# SYS command. line 139

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 141

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.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--------------------
39088 (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  @ Sun, 06 Nov 2016 18:21:21: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --nomodel --shift 0 --extsize 110 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz']
# effective genome size = 1.87e+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  @ Sun, 06 Nov 2016 18:21:21: #1 read tag files... 
INFO  @ Sun, 06 Nov 2016 18:21:21: #1 read treatment tags... 
INFO  @ Sun, 06 Nov 2016 18:21:29:  1000000 
INFO  @ Sun, 06 Nov 2016 18:21:35:  2000000 
INFO  @ Sun, 06 Nov 2016 18:21:41:  3000000 
INFO  @ Sun, 06 Nov 2016 18:21:48:  4000000 
INFO  @ Sun, 06 Nov 2016 18:21:54:  5000000 
INFO  @ Sun, 06 Nov 2016 18:22:00:  6000000 
INFO  @ Sun, 06 Nov 2016 18:22:07:  7000000 
INFO  @ Sun, 06 Nov 2016 18:22:13:  8000000 
INFO  @ Sun, 06 Nov 2016 18:22:19:  9000000 
INFO  @ Sun, 06 Nov 2016 18:22:25:  10000000 
INFO  @ Sun, 06 Nov 2016 18:22:32:  11000000 
INFO  @ Sun, 06 Nov 2016 18:22:38:  12000000 
INFO  @ Sun, 06 Nov 2016 18:22:44:  13000000 
INFO  @ Sun, 06 Nov 2016 18:22:50:  14000000 
INFO  @ Sun, 06 Nov 2016 18:22:57:  15000000 
INFO  @ Sun, 06 Nov 2016 18:23:03:  16000000 
INFO  @ Sun, 06 Nov 2016 18:23:09:  17000000 
INFO  @ Sun, 06 Nov 2016 18:23:15:  18000000 
INFO  @ Sun, 06 Nov 2016 18:23:22:  19000000 
INFO  @ Sun, 06 Nov 2016 18:23:28:  20000000 
INFO  @ Sun, 06 Nov 2016 18:23:34:  21000000 
INFO  @ Sun, 06 Nov 2016 18:23:40:  22000000 
INFO  @ Sun, 06 Nov 2016 18:23:47:  23000000 
INFO  @ Sun, 06 Nov 2016 18:23:53:  24000000 
INFO  @ Sun, 06 Nov 2016 18:23:59:  25000000 
INFO  @ Sun, 06 Nov 2016 18:24:05:  26000000 
INFO  @ Sun, 06 Nov 2016 18:24:12:  27000000 
INFO  @ Sun, 06 Nov 2016 18:24:18:  28000000 
INFO  @ Sun, 06 Nov 2016 18:24:24:  29000000 
INFO  @ Sun, 06 Nov 2016 18:24:31:  30000000 
INFO  @ Sun, 06 Nov 2016 18:24:37:  31000000 
INFO  @ Sun, 06 Nov 2016 18:24:43:  32000000 
INFO  @ Sun, 06 Nov 2016 18:24:49:  33000000 
INFO  @ Sun, 06 Nov 2016 18:24:59: #1.2 read input tags... 
INFO  @ Sun, 06 Nov 2016 18:25:06:  1000000 
INFO  @ Sun, 06 Nov 2016 18:25:12:  2000000 
INFO  @ Sun, 06 Nov 2016 18:25:18:  3000000 
INFO  @ Sun, 06 Nov 2016 18:25:21: #1 tag size is determined as 48 bps 
INFO  @ Sun, 06 Nov 2016 18:25:21: #1 tag size = 48 
INFO  @ Sun, 06 Nov 2016 18:25:21: #1  total tags in treatment: 33920807 
INFO  @ Sun, 06 Nov 2016 18:25:21: #1  total tags in control: 3384182 
INFO  @ Sun, 06 Nov 2016 18:25:21: #1 finished! 
INFO  @ Sun, 06 Nov 2016 18:25:21: #2 Build Peak Model... 
INFO  @ Sun, 06 Nov 2016 18:25:21: #2 Skipped... 
INFO  @ Sun, 06 Nov 2016 18:25:21: #2 Use 110 as fragment length 
INFO  @ Sun, 06 Nov 2016 18:25:21: #3 Call peaks... 
INFO  @ Sun, 06 Nov 2016 18:25:21: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Sun, 06 Nov 2016 18:25:21: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 06 Nov 2016 18:27:22: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Sun, 06 Nov 2016 18:27:22: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Sun, 06 Nov 2016 18:27:22: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_control_lambda.bdg 
INFO  @ Sun, 06 Nov 2016 18:27:22: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Sun, 06 Nov 2016 18:27:22: #3 Call peaks for each chromosome... 
INFO  @ Sun, 06 Nov 2016 18:35:39: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 06 Nov 2016 18:35:39: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Sun, 06 Nov 2016 18:35:40: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_summits.bed 
INFO  @ Sun, 06 Nov 2016 18:35:40: Done! 
INFO  @ Sun, 06 Nov 2016 18:35:45: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --broad --nomodel --shift 0 --extsize 110 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/pseudo_reps/rep1/pr1/wt_noBeads_allReps.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz']
# effective genome size = 1.87e+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  @ Sun, 06 Nov 2016 18:35:45: #1 read tag files... 
INFO  @ Sun, 06 Nov 2016 18:35:45: #1 read treatment tags... 
INFO  @ Sun, 06 Nov 2016 18:35:53:  1000000 
INFO  @ Sun, 06 Nov 2016 18:36:00:  2000000 
INFO  @ Sun, 06 Nov 2016 18:36:06:  3000000 
INFO  @ Sun, 06 Nov 2016 18:36:12:  4000000 
INFO  @ Sun, 06 Nov 2016 18:36:19:  5000000 
INFO  @ Sun, 06 Nov 2016 18:36:25:  6000000 
INFO  @ Sun, 06 Nov 2016 18:36:32:  7000000 
INFO  @ Sun, 06 Nov 2016 18:36:38:  8000000 
INFO  @ Sun, 06 Nov 2016 18:36:44:  9000000 
INFO  @ Sun, 06 Nov 2016 18:36:50:  10000000 
INFO  @ Sun, 06 Nov 2016 18:36:56:  11000000 
INFO  @ Sun, 06 Nov 2016 18:37:03:  12000000 
INFO  @ Sun, 06 Nov 2016 18:37:09:  13000000 
INFO  @ Sun, 06 Nov 2016 18:37:16:  14000000 
INFO  @ Sun, 06 Nov 2016 18:37:22:  15000000 
INFO  @ Sun, 06 Nov 2016 18:37:28:  16000000 
INFO  @ Sun, 06 Nov 2016 18:37:35:  17000000 
INFO  @ Sun, 06 Nov 2016 18:37:41:  18000000 
INFO  @ Sun, 06 Nov 2016 18:37:47:  19000000 
INFO  @ Sun, 06 Nov 2016 18:37:53:  20000000 
INFO  @ Sun, 06 Nov 2016 18:38:00:  21000000 
INFO  @ Sun, 06 Nov 2016 18:38:06:  22000000 
INFO  @ Sun, 06 Nov 2016 18:38:12:  23000000 
INFO  @ Sun, 06 Nov 2016 18:38:18:  24000000 
INFO  @ Sun, 06 Nov 2016 18:38:25:  25000000 
INFO  @ Sun, 06 Nov 2016 18:38:31:  26000000 
INFO  @ Sun, 06 Nov 2016 18:38:37:  27000000 
INFO  @ Sun, 06 Nov 2016 18:38:43:  28000000 
INFO  @ Sun, 06 Nov 2016 18:38:49:  29000000 
INFO  @ Sun, 06 Nov 2016 18:38:55:  30000000 
INFO  @ Sun, 06 Nov 2016 18:39:02:  31000000 
INFO  @ Sun, 06 Nov 2016 18:39:08:  32000000 
INFO  @ Sun, 06 Nov 2016 18:39:14:  33000000 
INFO  @ Sun, 06 Nov 2016 18:39:23: #1.2 read input tags... 
INFO  @ Sun, 06 Nov 2016 18:39:29:  1000000 
INFO  @ Sun, 06 Nov 2016 18:39:35:  2000000 
INFO  @ Sun, 06 Nov 2016 18:39:41:  3000000 
INFO  @ Sun, 06 Nov 2016 18:39:44: #1 tag size is determined as 48 bps 
INFO  @ Sun, 06 Nov 2016 18:39:44: #1 tag size = 48 
INFO  @ Sun, 06 Nov 2016 18:39:44: #1  total tags in treatment: 33920807 
INFO  @ Sun, 06 Nov 2016 18:39:44: #1  total tags in control: 3384182 
INFO  @ Sun, 06 Nov 2016 18:39:44: #1 finished! 
INFO  @ Sun, 06 Nov 2016 18:39:44: #2 Build Peak Model... 
INFO  @ Sun, 06 Nov 2016 18:39:44: #2 Skipped... 
INFO  @ Sun, 06 Nov 2016 18:39:44: #2 Use 110 as fragment length 
INFO  @ Sun, 06 Nov 2016 18:39:44: #3 Call peaks... 
INFO  @ Sun, 06 Nov 2016 18:39:44: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Sun, 06 Nov 2016 18:39:44: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 06 Nov 2016 18:41:23: #3 Call peaks for each chromosome...
Num 3
ID task.callpeak_macs2.macs2_rep1_pr2.line_67.id_12
Name macs2 rep1-pr2
Thread thread_Root
PID 4383
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus
Mem
Start 2016-11-06 18:09:34
End 2016-11-06 18:29:02
Elapsed 00:19:27
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gappedPeak.gz
Dependencies 
 
# SYS command. line 69

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${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/MouseMutantData/WT_NOBEADS/out/align/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --nomodel --shift 0 --extsize 110 --keep-dup all -B --SPMR

# SYS command. line 78

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.narrowPeak.gz

# SYS command. line 81

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_summits.bed

# SYS command. line 88

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --broad --nomodel --shift 0 --extsize 110 --keep-dup all

# SYS command. line 91

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.broadPeak.gz

# SYS command. line 92

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gappedPeak.gz

# SYS command. line 95

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_summits.bed

# SYS command. line 100

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.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/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2 -o "wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 114

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_FE.bdg -g /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 115

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_FE.bdg

# SYS command. line 118

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 119

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bw

# SYS command. line 120

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 126

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 128

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.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/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2 -o "wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 133

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_ppois.bdg -g /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 134

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_ppois.bdg

# SYS command. line 137

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 138

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bw

# SYS command. line 139

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 141

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.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--------------------
46690 (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  @ Sun, 06 Nov 2016 18:22:17: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --nomodel --shift 0 --extsize 110 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz']
# effective genome size = 1.87e+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  @ Sun, 06 Nov 2016 18:22:17: #1 read tag files... 
INFO  @ Sun, 06 Nov 2016 18:22:17: #1 read treatment tags... 
INFO  @ Sun, 06 Nov 2016 18:22:20:  1000000 
INFO  @ Sun, 06 Nov 2016 18:22:21:  2000000 
INFO  @ Sun, 06 Nov 2016 18:22:23:  3000000 
INFO  @ Sun, 06 Nov 2016 18:22:25:  4000000 
INFO  @ Sun, 06 Nov 2016 18:22:27:  5000000 
INFO  @ Sun, 06 Nov 2016 18:22:29:  6000000 
INFO  @ Sun, 06 Nov 2016 18:22:30:  7000000 
INFO  @ Sun, 06 Nov 2016 18:22:32:  8000000 
INFO  @ Sun, 06 Nov 2016 18:22:34:  9000000 
INFO  @ Sun, 06 Nov 2016 18:22:36:  10000000 
INFO  @ Sun, 06 Nov 2016 18:22:38:  11000000 
INFO  @ Sun, 06 Nov 2016 18:22:39:  12000000 
INFO  @ Sun, 06 Nov 2016 18:22:41:  13000000 
INFO  @ Sun, 06 Nov 2016 18:22:42:  14000000 
INFO  @ Sun, 06 Nov 2016 18:22:44:  15000000 
INFO  @ Sun, 06 Nov 2016 18:22:46:  16000000 
INFO  @ Sun, 06 Nov 2016 18:22:48:  17000000 
INFO  @ Sun, 06 Nov 2016 18:22:50:  18000000 
INFO  @ Sun, 06 Nov 2016 18:22:52:  19000000 
INFO  @ Sun, 06 Nov 2016 18:22:54:  20000000 
INFO  @ Sun, 06 Nov 2016 18:22:55:  21000000 
INFO  @ Sun, 06 Nov 2016 18:22:57:  22000000 
INFO  @ Sun, 06 Nov 2016 18:22:59:  23000000 
INFO  @ Sun, 06 Nov 2016 18:23:00:  24000000 
INFO  @ Sun, 06 Nov 2016 18:23:02:  25000000 
INFO  @ Sun, 06 Nov 2016 18:23:04:  26000000 
INFO  @ Sun, 06 Nov 2016 18:23:06:  27000000 
INFO  @ Sun, 06 Nov 2016 18:23:08:  28000000 
INFO  @ Sun, 06 Nov 2016 18:23:10:  29000000 
INFO  @ Sun, 06 Nov 2016 18:23:12:  30000000 
INFO  @ Sun, 06 Nov 2016 18:23:13:  31000000 
INFO  @ Sun, 06 Nov 2016 18:23:15:  32000000 
INFO  @ Sun, 06 Nov 2016 18:23:17:  33000000 
INFO  @ Sun, 06 Nov 2016 18:23:20: #1.2 read input tags... 
INFO  @ Sun, 06 Nov 2016 18:23:22:  1000000 
INFO  @ Sun, 06 Nov 2016 18:23:23:  2000000 
INFO  @ Sun, 06 Nov 2016 18:23:25:  3000000 
INFO  @ Sun, 06 Nov 2016 18:23:25: #1 tag size is determined as 50 bps 
INFO  @ Sun, 06 Nov 2016 18:23:25: #1 tag size = 50 
INFO  @ Sun, 06 Nov 2016 18:23:25: #1  total tags in treatment: 33920807 
INFO  @ Sun, 06 Nov 2016 18:23:25: #1  total tags in control: 3384182 
INFO  @ Sun, 06 Nov 2016 18:23:25: #1 finished! 
INFO  @ Sun, 06 Nov 2016 18:23:25: #2 Build Peak Model... 
INFO  @ Sun, 06 Nov 2016 18:23:25: #2 Skipped... 
INFO  @ Sun, 06 Nov 2016 18:23:25: #2 Use 110 as fragment length 
INFO  @ Sun, 06 Nov 2016 18:23:25: #3 Call peaks... 
INFO  @ Sun, 06 Nov 2016 18:23:25: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Sun, 06 Nov 2016 18:23:25: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 06 Nov 2016 18:24:14: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Sun, 06 Nov 2016 18:24:14: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Sun, 06 Nov 2016 18:24:14: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_control_lambda.bdg 
INFO  @ Sun, 06 Nov 2016 18:24:14: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Sun, 06 Nov 2016 18:24:14: #3 Call peaks for each chromosome... 
INFO  @ Sun, 06 Nov 2016 18:26:53: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 06 Nov 2016 18:26:53: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Sun, 06 Nov 2016 18:26:54: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_summits.bed 
INFO  @ Sun, 06 Nov 2016 18:26:54: Done! 
INFO  @ Sun, 06 Nov 2016 18:26:56: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign -g mm -p 0.01 --broad --nomodel --shift 0 --extsize 110 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz']
# effective genome size = 1.87e+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  @ Sun, 06 Nov 2016 18:26:56: #1 read tag files... 
INFO  @ Sun, 06 Nov 2016 18:26:56: #1 read treatment tags... 
INFO  @ Sun, 06 Nov 2016 18:26:58:  1000000 
INFO  @ Sun, 06 Nov 2016 18:27:00:  2000000 
INFO  @ Sun, 06 Nov 2016 18:27:01:  3000000 
INFO  @ Sun, 06 Nov 2016 18:27:03:  4000000 
INFO  @ Sun, 06 Nov 2016 18:27:04:  5000000 
INFO  @ Sun, 06 Nov 2016 18:27:06:  6000000 
INFO  @ Sun, 06 Nov 2016 18:27:07:  7000000 
INFO  @ Sun, 06 Nov 2016 18:27:09:  8000000 
INFO  @ Sun, 06 Nov 2016 18:27:10:  9000000 
INFO  @ Sun, 06 Nov 2016 18:27:12:  10000000 
INFO  @ Sun, 06 Nov 2016 18:27:14:  11000000 
INFO  @ Sun, 06 Nov 2016 18:27:15:  12000000 
INFO  @ Sun, 06 Nov 2016 18:27:17:  13000000 
INFO  @ Sun, 06 Nov 2016 18:27:18:  14000000 
INFO  @ Sun, 06 Nov 2016 18:27:20:  15000000 
INFO  @ Sun, 06 Nov 2016 18:27:21:  16000000 
INFO  @ Sun, 06 Nov 2016 18:27:23:  17000000 
INFO  @ Sun, 06 Nov 2016 18:27:24:  18000000 
INFO  @ Sun, 06 Nov 2016 18:27:26:  19000000 
INFO  @ Sun, 06 Nov 2016 18:27:27:  20000000 
INFO  @ Sun, 06 Nov 2016 18:27:29:  21000000 
INFO  @ Sun, 06 Nov 2016 18:27:30:  22000000 
INFO  @ Sun, 06 Nov 2016 18:27:32:  23000000 
INFO  @ Sun, 06 Nov 2016 18:27:33:  24000000 
INFO  @ Sun, 06 Nov 2016 18:27:35:  25000000 
INFO  @ Sun, 06 Nov 2016 18:27:36:  26000000 
INFO  @ Sun, 06 Nov 2016 18:27:38:  27000000 
INFO  @ Sun, 06 Nov 2016 18:27:39:  28000000 
INFO  @ Sun, 06 Nov 2016 18:27:41:  29000000 
INFO  @ Sun, 06 Nov 2016 18:27:43:  30000000 
INFO  @ Sun, 06 Nov 2016 18:27:44:  31000000 
INFO  @ Sun, 06 Nov 2016 18:27:46:  32000000 
INFO  @ Sun, 06 Nov 2016 18:27:47:  33000000 
INFO  @ Sun, 06 Nov 2016 18:27:51: #1.2 read input tags... 
INFO  @ Sun, 06 Nov 2016 18:27:52:  1000000 
INFO  @ Sun, 06 Nov 2016 18:27:54:  2000000 
INFO  @ Sun, 06 Nov 2016 18:27:55:  3000000 
INFO  @ Sun, 06 Nov 2016 18:27:56: #1 tag size is determined as 50 bps 
INFO  @ Sun, 06 Nov 2016 18:27:56: #1 tag size = 50 
INFO  @ Sun, 06 Nov 2016 18:27:56: #1  total tags in treatment: 33920807 
INFO  @ Sun, 06 Nov 2016 18:27:56: #1  total tags in control: 3384182 
INFO  @ Sun, 06 Nov 2016 18:27:56: #1 finished! 
INFO  @ Sun, 06 Nov 2016 18:27:56: #2 Build Peak Model... 
INFO  @ Sun, 06 Nov 2016 18:27:56: #2 Skipped... 
INFO  @ Sun, 06 Nov 2016 18:27:56: #2 Use 110 as fragment length 
INFO  @ Sun, 06 Nov 2016 18:27:56: #3 Call peaks... 
INFO  @ Sun, 06 Nov 2016 18:27:56: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Sun, 06 Nov 2016 18:27:56: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 06 Nov 2016 18:28:38: #3 Call peaks for each chromosome... 
INFO  @ Sun, 06 Nov 2016 18:28:59: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 06 Nov 2016 18:28:59: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.broadPeak 
INFO  @ Sun, 06 Nov 2016 18:28:59: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/macs2/pseudo_reps/rep1/pr2/wt_noBeads_allReps.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Sun, 06 Nov 2016 18:29:00: Done!

Global scope

Note: Global scope when program finished execution.
Type Name Value
string _ /usr/bin/bds
bool allowEmpty false
string[] args [-title, WT_NOBEADS, -nth, 5, -species, mm10, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out, -tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/rep1/wt_noBeads_allReps.nodup.tagAlign.gz, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz, -gensz, mm, -chrsz, /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes, $]
bool canFail false
int cpus -1
int cpusLocal 56
int day 86400
string DERBY_HOME /usr/lib/jvm/java-8-oracle/db
string DISPLAY localhost:12.0
real E 2.718281828459045
int G 1073741824
string HOME /users/imk1/
int hour 3600
string J2REDIR /usr/lib/jvm/java-8-oracle/jre
string J2SDKDIR /usr/lib/jvm/java-8-oracle
string JAVA_HOME /usr/lib/jvm/java-8-oracle
int K 1024
string KRB5CCNAME FILE:/tmp/krb5cc_1048_N5SeQf
string LANG en_US.UTF-8
string LOADEDMODULES
string LOGNAME imk1
int M 1048576
string MAIL /var/mail/imk1
int mem -1
int minute 60
string MODULE_VERSION 3.2.10
string MODULE_VERSION_STACK 3.2.10
string MODULEPATH /usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles
string MODULESHOME /software/env_module/3.2.10
string NLSPATH /usr/dt/lib/nls/msg/%L/%N.cat
string node
int P 1125899906842624
string PATH /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/MouseMutantData/WT_NOBEADS
string programName chipseq.bds
string programPath /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/chipseq.bds
string PWD /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS
string queue
int retry 0
string SHELL /bin/bash
string SHLVL 3
string SSH_CLIENT 171.65.77.8 55144 22
string SSH_CONNECTION 171.65.77.8 55144 171.65.76.63 22
string SSH_TTY /dev/pts/4
string STY 35766.WT_NOBEADS.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 20
string XFILESEARCHPATH /usr/dt/app-defaults/%L/Dt